BFO 2 Reference: BFO does not claim to be a complete coverage of all entities. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning – coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation [17 BFO 2 Reference: BFO’s treatment of continuants and occurrents – as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality – earlier called the ‘SNAP’ and ‘SPAN’ perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science [30 BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. ‘Entity’ is an example of one such primitive term. Primitive terms in a highest-level ontology such as BFO are terms that are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms. Alan Ruttenberg Albert Goldfain Barry Smith Bill Duncan Bjoern Peters Chris Mungall David Osumi-Sutherland Fabian Neuhaus James A. Overton Janna Hastings Jie Zheng Jonathan Bona Larry Hunter Leonard Jacuzzo Ludger Jansen Mark Ressler Mathias Brochhausen Mauricio Almeida Melanie Courtot Pierre Grenon Randall Dipert Robert Rovetto Ron Rudnicki Stefan Schulz Thomas Bittner Werner Ceusters Yongqun "Oliver" He 2023-08-19 The Genomic Epidemiology Ontology aims to provide a comprehensive controlled vocabulary for infectious disease surveillance and outbreak investigations. It is an application ontology that draws on many other ontologies including anatomy, taxonomy, disease, symptoms, environment and food types for foodborn pathogen metadata. Genomic Epidemiology Ontology GENEPIO The http://purl.obolibary.org/obo/bfo/classes-only.owl variant of BFO ("bfo_classes_only.owl") includes only the class hierarchy and annotations from the full OWL version of BFO 2: http://purl.obolibary.org/obo/bfo.owl ("bfo.owl"). There are no object properties or logical axioms that use the object properties in bfo_classes_only.owl. As the logical axioms in the bfo_classes_only.owl variant are limited to subclass and disjoint assertions they are much weaker than the logical axioms in bfo.owl. If you plan to use the relations that define BFO 2, you should import bfo.owl instead of bfo_classes_only.owl. To the extent that the relations are used without importing bfo.owl, be mindful that they should be used in a manner consistent with their use in bfo.owl. Otherwise if your ontology is imported by a another ontology that imports bfo.owl there may be inconsistencies. See the BFO 2 release notes for further information about BFO 2. Please note that the current release of bfo.owl uses temporal relations when the subject or object is a continuant, a major change from BFO 1. This is an early version of BFO version 2 and has not yet been extensively reviewed by the project team members. Please see the project site http://code.google.com/p/bfo/ , the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel , the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx . This ontology is generated from a specification at http://bfo.googlecode.com/svn/trunk/src/ontology/owl-group/specification/ and with the code that generates the OWL version in http://bfo.googlecode.com/svn/trunk/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label metadata section term as in existing standard term source The user interface label is the label that should be placed on a datum when presented on a form or report Damion Dooley user interface label user interface definition A user interface help annotation is a textual phrase to display with an entity on a form or report that provides some detail about what the entity is or how it is being used. Damion Dooley user interface help true Damion Dooley user interface hidden true A user interface feature is a pre-set list of features and their acceptable values that a user interface rendering system should use to display an entity on a form or report Damion Dooley user interface feature This annotation can be used to select the value specification that a referenced entity or specification component has for data entry. Can be scalar value specification / categorical tree specification etc. Damion Dooley obsolete: user interface value specification true UI regex normalize Damion Dooley user interface regular epression normalize UI regex validate Damion Dooley user interface regular expression validate UI regex format Damion Dooley user interface regular expression display format editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi&gt> example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status definition definition textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi&gt> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi&gt> GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative label A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi&gt> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label alternative term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note term tracker item An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item imported from has ID digit count Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix' annotation property value concatenated with an integer in the id range (left padded with '0's to make this many digits) Person:Alan Ruttenberg has ID digit count has ID range allocated Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID range allocated has ID policy for Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for elucidation has associated axiom(nl) has associated axiom(fol) has axiom label term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg term replaced by NIAID GSCID-BRC alternative term An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC alternative term temporal interpretation An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ https://oborel.github.io/obo-relations/temporal-semantics/ relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y is direct form of http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/ namespace contributor creator created_by creation_date has_alternative_id An alternative label for a class or property which has a more general meaning than the preferred name/primary label. http://orcid.org/0000-0001-5208-3432 https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 database_cross_reference hasDbXref An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. http://orcid.org/0000-0001-5208-3432 https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. http://orcid.org/0000-0001-5208-3432 https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. http://orcid.org/0000-0001-5208-3432 https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has synonym comment is defined by label label label see also see also backward compatible with deprecated incompatible with prior version versionInfo part of realized in occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in obsolete has string specification of true obsolete: has string value specification true obsolete: has categorical specification of true obsolete: has categorical value specification true hasCountryOfOrigin relates a time stamped measurement datum to the measurement datum that was measured Alan Ruttenberg has measurement datum has_specified_input has_specified_input The inverse property of is_specified_input_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input is_specified_input_of A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of has_specified_output has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_manufactured_by c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. Alan Ruttenberg Liju Fan is_manufactured_by is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of has category label A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale. has category label has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification participates in a relation between a continuant and a process, in which the continuant is somehow involved in the process participates in has participant a relation between a process and a continuant, in which the continuant is somehow involved in the process has participant has participant derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime location_of location of location of David Osumi-Sutherland <= Primitive instance level timing relation between events before or simultaneous with David Osumi-Sutherland t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes starts during happens during A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO Chris Mungall adjacent to adjacent to starts with ends with p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input has input input of inverse of upstream of Chris Mungall causally downstream of p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints Chris Mungall transmitted by the relationship between a fraction and the number above the line Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra AGB has numerator the relationship between a fraction and the number below the line (or divisor) Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra AGB has denominator link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch. exactMatch An object relation between a LinkML SlotDefinition to a LocalName. Damion Dooley obsolete: has primitive data type true has specified value A relation between a value specification and a literal. OBI has specified value An abstract class is a high level class or slot that is typically used to group common slots together and cannot be directly instantiated. Notes and comments about an element intended for external consumption. Date/time at which the element was created. Not Applicable; Missing; Not Collected; Not Provided; Restricted Access A value (string or URI) indicating the data collection state an instance of a slot has. A description of the element's purpose and use A list of terms from different schemas or terminology systems that have identical meaning. Id of the schema that defined the element. The imports entry that this element was derived from. Empty means primary source The ncname of the source of the name. 2021-04-26T22:15:07Z local_name_source A name assigned to an element in a given ontology. For slots with ranges of type number, the value must be equal to or lowe than this For slots with ranges of type number, the value must be equal to or higher than this true means that slot can have more than one value The unique name of the element within the context of the schema. Name is combined with the default prefix to form the globally unique subject of the target class. The string value of the slot must conform to this regular expression A list of possible values for a slot range. true if this slot is not required, but is recommended. true means that the slot must be present in the loaded definition. A reference. IAO:0000122 ('ready for release') status of the element. The uri that defines the possible values for the type definition URI is typically drawn from the set of URI's defined in OWL (https://www.w3.org/TR/2012/REC-owl2-syntax-20121211/#Datatype_Maps) Description of what the value is doing. The identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot A persistent, unique identifier of a molecular sequence database entry. Damion Dooley EDAM sequence accession The name of a field in a database. database field name no definition at source animal - laboratory Animals considered to be wild or feral or not adapted for domestic use. It does not include wild animals in zoos for which ANIMALS, ZOO is available. animal - wild the relative amounts of the purines and pyrimidines in a nucleic acid. base composition base compositions base ratio base ratios gc composition gc compositions gc content gc contents gc g+c composition g+c compositions g+c content g+c contents guanine + cytosine composition guanine + cytosine content base composition Animals kept by humans for companionship and enjoyment, as opposed to DOMESTIC ANIMALS such as livestock or farm animals, which are kept for economic reasons. animal - pet Domesticated farm animals raised for home use or profit but excluding POULTRY. Typically livestock includes CATTLE; SHEEP; HORSES; SWINE; GOATS; and others. livestock APOLLO_SV:00000000 A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an "act") that is laden with determinate, uniformily structured content. MB: Right now we represent 'purely intentional entities' as siblings to 'information content entities'. Given their nature I am not entirly sure that this is correct. It seems that both 'information content entity' and 'simulation' are subclass to 'purely intentional entity'. purely intentional entity APOLLO_SV:00000016 A duration of the parts of an infection during which the host bears an infectious disposition in a population of hosts. Mathias Brochhausen MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs. infectious period duration APOLLO_SV:00000017 A duration of the time interval between the host acquiring an infection and the host bearing a contagiousness disposition during the same disease course within a population of hosts. Mathias Brochhausen MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs The duration of the period between when an organism becomes infected and when it becomes infectious. latent period duration APOLLO_SV:00000019 Mathias Brochhausen count of simulated exposed population APOLLO_SV:00000020 Mathias Brochhausen count of simulated contagious population APOLLO_SV:00000021 Mathias Brochhausen count of simulated resistant population APOLLO_SV:00000022 The count of (simulated organisms) in a simulated population. Mathias Brochhausen MW: I know this causes problems with our set-theoretic definition. Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step. Any ideas? I’ve considered and rejected allowing individual organisms to be fractional. Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’ count of simulated population APOLLO_SV:00000031 A simulation of a population or populations of organisms of a particular biological taxon that simulates a particular type of event or types of event that occur in a specified time interval. Mathias Brochhausen simulated population APOLLO_SV:00000032 A measurement datum that is the output of counting. Mathias Brochhausen count APOLLO_SV:00000033 The planned process of finding the number of elements in a finite set of objects. Mathias Brochhausen http://en.wikipedia.org/wiki/Counting counting APOLLO_SV:00000056 Mathias Brochhausen Motivating use case is to cover Synthia data, and possibly configuration/output of the MRSA simulator in the MIDAS community (CA-MRSA Repast). hospital patient population census APOLLO_SV:00000070 A purely intentional entity that simulates an entity and its properties. simulation APOLLO_SV:00000098 The count of individuals in a contagious population (empirical or virtual). count of contagious population APOLLO_SV:00000099 The count of individuals in a resistant population (empirical or virtual). count of resistant population APOLLO_SV:00000115 The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources Mathias Brochhausen Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use. The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things. The likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient. An infection is acquired from an infectious organism or a contaminated thing. Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing infection acquisition 1 1 APOLLO_SV:00000153 A census that is the outcome of a population survey. Damion Dooley population census APOLLO_SV:00000168 Motivating use case is Synthia synthetic population data. nursery school student population census APOLLO_SV:00000169 Motivating use case is Synthia synthetic population data. primary school student population census APOLLO_SV:00000170 Motivating use case is Synthia synthetic population data. secondary school student population census APOLLO_SV:00000173 A data set of a specific entity in a specified region at a specified time. Mathias Brochhausen census APOLLO_SV:00000176 Mathias Brochhausen Motivating use case is Synthia synthetic population data. school student population census APOLLO_SV:00000211 The probability of the occurence of an infection acquisition from one infected organism to another when in contact. transmission probability APOLLO_SV:00000236 asymptomatic host APOLLO_SV:00000238 An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon. host APOLLO_SV:00000240 A information content entity that specifies the date of a census. Mathias Brochhausen census reference date APOLLO_SV:00000243 A measurement datum that quantifies a temporal region that is occupied by a processual entity. Mathias Brochhausen duration APOLLO_SV:00000258 The duration between the appearance of symptoms of a disease and the start of a treatment. Mathias Brochhausen delay from symptoms to treatment APOLLO_SV:00000265 An infection acquisition whereby a susceptible host acquires an infection from an infectious host. William R. Hogan infection acquisition from infectious host APOLLO_SV:00000267 The duration from the time an organism satisfies a case definition until a process or system detects the organism as satisfying that case definition Mathias Brochhausen time delay to case detection APOLLO_SV:00000280 A duration that measures the temporal interval occupied by a treatment course. Mathias Brochhausen duration of treatment course APOLLO_SV:00000281 The count of the number of doses that are part of a treatment course. Mathias Brochhausen number of doses in a treatment course APOLLO_SV:00000291 The duration from the time an individual receives a treatment until the time a system designed to detect that the treatment occurred detects it in a population William R. Hogan time delay of treatment detection APOLLO_SV:00000470 A data item that is about a proposition and has a numeric value between 0 and 1, inclusive, that is the output of some process of inference, such that 1) logical falsehoods and logical truths are assigned a value of 0 and 1, respectively, while contingent propositions are assigned some intermediate value; and 2) the process of inference conforms with rules for the calculation of probabilities, and that any interpretation of probability must specify the extent to which probabilities might be used to constrain the degrees of belief of rational agents. Matthew Diller William R. Hogan The first criterion is derived from Kolmogorov's Probability Calculus, while the second is derived from Salmon's Admissibility and Applicability Criteria of Adequacy. Salmon's ascertainability criterion is subsumed by the definition for 'data item'. probability APOLLO_SV:00000497 A count of individuals in a population who meet the criteria of some case definition during some time interval. Matthew Diller William R. Hogan count of disease cases APOLLO_SV:00000498 A count of disease cases in an infected population that meet the case definition criteria within a particular epidemic interval. Matthew Diller William R. Hogan count of cases in an epidemic APOLLO_SV:00000501 A population census about the organisms specific to that population that were the host in some colonization acquisition. Matthew Diller William R. Hogan population colonization census APOLLO_SV:00000511 An infection acquistion from infectious host that is causally downstream of some potentially infectious sexual contacting Matthew Diller Note that infections that are acquired in this manner do not fall within the class of sexually transmitted infections (STI's), ipso facto. This type of transmission can also occur with non-STI pathogens--such as meningitis and Zika. infection acquisition through sexual activity with infectious host APOLLO_SV:00000617 A count of simulated or physical individuals in a population. Matthew Diller population count ARO:3004299 Qualitative description of a microbial response to antimicrobial agents and the expected clinical outcome. Bacteria may be susceptible or resistant to a broad range of antibiotic drugs or drug classes, with several intermediate states or phases. antimicrobial phenotype ARO:3004300 intermediate Intermediate sensitivity of a bacterial strain to a given antibiotic occurs when it is inhibited by a concentration of the drug that is associated with uncertain therapeutic effect. The elimination of intermediate phenotype bacteria may depend on the site of infection and/or the concentration of the administered drug. Definition from https://clsi.org. I intermediate antimicrobial phenotype ARO:3004301 resistant A bacterial strain is said to be resistant to a given antibiotic when it is inhibited in vitro by a concentration of this drug that is associated with a high likelihood of therapeutic failure. R resistant antimicrobial phenotype ARO:3004302 susceptible A bacterial strain is said to be susceptible to a given antibiotic when it is inhibited in vitro by a concentration of a drug that is associated with a high likelihood of therapeutic success. S sensitive susceptible antimicrobial phenotype ARO:3004303 nonsusceptible A bacterial strain is said to be nonsusceptible to a given antibiotic drug if it demonstrates either an intermediate or resistant phenotype when exposed to a concentration of a drug that is associated with a high likelihood of therapeutic failure, i.e. if the bacterial strain is not susceptible to the antibiotic drug but not necessarily totally resistant under all conditions. Definition from https://clsi.org. NS nonsensitive nonsensitive antimicrobial phenotype nonsusceptible antimicrobial phenotype ARO:3004304 susceptible - dose dependent A bacterial strain is said to be susceptible-dose dependent (SDD) to a given antibiotic when growth is inhibited with a high likelihood of therapeutic success, but when multiple approved dosing options exist. When a higher or more frequent dose is used, the predicted therapeutic result is the same as for susceptible individuals. SSD SDD Sensitive dose dependent antimicrobial phenotype sensitive - dose dependent susceptible dose dependent antimicrobial phenotype ARO:3004305 Multidrug-resistant organisms are defined as bacterial strains that have become resistant to multiple classes of antibacterial drugs or other agents. The phenotype of these organisms is defined by the spectrum of antibiotic drug classes to which that organism is resistant. Often, these organisms are susceptible to a narrow range of available drugs, making treatment difficult and urgent. MDRO multidrug resistance antimicrobial phenotype ARO:3004360 Uses breakpoints to create standards for interpreting the clinical outcome of an MIC value for a particular microbial species and antimicrobial agent. antimicrobial resistance testing reference standard ARO:3004365 BSAC is a British inter-professional organisation involved in antibiotic education, research and leadership. Baquero F. found that the BSAC system recommends lower breakpoints than the consensus standard of all systems for antimicrobial susceptibility testing used in Europe (BSAC, DIN, SFM, SIR, NCCLS and WRG). BSAC British Society for Antimicrobial Chemotherapy (BSAC) ARO:3004366 The Clinical and Laboratory Standards Institute develops and implements clinical laboratory testing standards. CLSI NCCLS National Committee on Clinical Laboratory Standards (NCCLS) On January 1, 2005 the National Committee on Clinical Laboratory Standards (NCCLS) changed its name to CLSI Clinical and Laboratory Standards Institute (CLSI) ARO:3004367 DIN is recognized by the Federal Government of Germany as the competent standards organization for Germany and as the national standards body representing Germany in non-governmental international standards organizations. Baquero F. found that the DIN system recommends lower breakpoints than the consensus standard of all systems for antimicrobial susceptibility testing used in Europe (BSAC, DIN, SFM, SIR, NCCLS and WRG). DIN Deutsches Institut für Normung (DIN) ARO:3004368 EUCAST is a standing committee jointly organized by ESCMID, ECDC and European national breakpoint committees; it deals with breakpoints and technical aspects of phenotypic in-vitro antimicrobial susceptibility testing. EUCAST European Committee on Antimicrobial Susceptibility Testing (EUCAST) ARO:3004369 The French Society of Microbiology (SFM) is a non-profit association which aims to bring together microbiologists from French-speaking countries, working in the domains of bacteria, viruses, Fungi and parasites, and related medical, industrial and environmental microbiology, physiology, genetics, taxonomy, hygiene, and antimicrobial agents. Baquero F. found that the SFM system recommends higher breakpoints than the consensus standard of all systems for antimicrobial susceptibility testing used in Europe (BSAC, DIN, SFM, SIR, NCCLS and WRG). SFM Société Française de Microbiologie (SFM) ARO:3004371 The measured or quantified MIC. MIC value ARO:3004372 Unit for measurement of minimum inhibitory concentration (MIC). MIC unit ARO:3004388 An experimental test conducted outside of a living organism, usually in a tube or plate. in-vitro microbial susceptibility test ARO:3004390 System of analysis for determining antimicrobial susceptibility. antimicrobial resistance test platform ARO:3004391 Microbial species are inoculated in a growth medium onto which antimicrobial agents are transferred by diffusion. diffusion method ARO:3004392 Components of complex mixtures such as plant extracts are separated across a TLC plate and tested for anti-microbial activity. thin-layer chromatography (TLC)-bioautography ARO:3004393 Allows for time-dependent or concentration-dependent analysis of antimicrobial effects. Several tubes of broth culture medium containing a suspension of the test microbe are treated with varying concentrations of the antimicrobial agent and the percentage of dead cells determined at various time points. time kill curve time-kill test ARO:3004394 Relies on the indirect measurement of microbe populations by quantifying microbial ATP production. ATP bioluminescence assay ARO:3004395 Microbes exposed to antimicrobial agents are then stained with the intercalating agent propidium iodide. Damaged cells emit a positive signal that is detected by flow cytometry analysis. Flow cytometry can also be used to discriminate between dead, damaged and live cells. flow cytofluorometric method ARO:3004396 Test that directly detect the presence of a particular resistance mechanism. mechanism-specific test ARO:3004397 The microbial species are inoculated in liquid growth medium containing incremental dilutions (usually 2-fold) of the antimicrobial agent. broth dilution method ARO:3004398 Automated system of analysis for determining antimicrobial susceptibility. automated testing platform ARO:3004399 Non-automated system of analysis for determining antimicrobial susceptibility. noncommercial testing platform manual testing platform ARO:3004400 Specific automated system of analysis for determining antimicrobial susceptibility developed by Omron. MicroScan ARO:3004401 Specific automated system of analysis for determining antimicrobial susceptibility developed by Becton Dickinson. Phoenix ARO:3004402 Specific automated system of analysis for determining antimicrobial susceptibility developed by Trek, Thermo Fisher Scientific. Sensitire ARO:3004403 Specific automated system of analysis for determining antimicrobial susceptibility developed by bioMérieux. Vitek System ARO:3004404 Vendor of automated system of analysis for determining antimicrobial susceptibility. automated testing platform vendor ARO:3004405 Specific vendor of automated system of analysis for determining antimicrobial susceptibility headquartered in New Jersey, USA. Becton Dickinson is the developer of the Phoenix automated testing platform. Becton Dickinson ARO:3004406 Specific vendor of automated system of analysis for determining antimicrobial susceptibility headquartered in France. bioMérieux is the developer of the Vitek automated testing platform. bioMérieux ARO:3004407 Specific vendor of automated system of analysis for determining antimicrobial susceptibility headquartered in Berlin and Munich. Siemens ARO:3004408 Specific vendor of automated system of analysis for determining antimicrobial susceptibility based in Japan. Omron is the developer of the MicroScan automated testing platform. Omron ARO:3004409 Specific vendor of automated system of analysis for determining antimicrobial susceptibility that was acquired by Thermo Fisher Scientific Inc. Thermo Fisher Scienfiic Inc. is headquartered in Massachusetts, USA. Trek is the developer of the Sensitire automated testing platform. Thermo Fisher Scientific Trek ARO:3004410 Broth dilution conducted on 96-well microtiter plates (≤200 µL per well). micro broth dilution method ARO:3004411 This test is a common method of evaluating the antimicrobial activity of plants or microbial extracts. In this method, bacteria are inoculated onto agar plates and the antimicrobial agent is injected into the plate and allowed to diffuse. agar well diffusion method ARO:3004412 This method is commonly used to study the antagonism between microorganisms. The first bacterial strain is inoculated onto agar plates in tight streaks. The bacteria will secrete molecules that diffuse in the agar medium; this medium is cut and placed on another agar plate inoculated with another microorganism. agar plug diffusion method ARO:3004413 This method is commonly used to study the antagonism between microorganisms. The microbial strain of interest is seeded by a single streak in the center of the agar plate. After incubation, the plate is seeded with the second microorganism by single streak perpendicular to the central streak. cross streak method ARO:3004414 The antimicrobial agent is transferred from a chromatogram to an agar plate previously inoculated with the test microorganism. agar diffusion bioautography ARO:3004415 A developed TLC plate is dipped into or sprayed with a microbial suspension and then incubated. Live microbial cells are visualized using tetrazolium salts. direct bioautography ARO:3004416 The TLC plate is covered with a molten agar medium seeded with the test microbe and the antimicrobial compounds are allowed to diffuse onto the agar medium. Tetrazolium dye staining allows for visualization. agar overlay bioassay agar overlay bioautography ARO:3004419 Assay for beta lactamase detection. chromogenic cephalosporinase test ARO:3004420 Commercial colorimetric assay for detection of chloramphenicol modifying enzyme chloramphenicol acetyltransferase. chloramphenicol acetyltransferase assay (CAT) ARO:3004430 depth:1 The tissue type used to select breakpoints from a particular standard, for the interpretation of MIC results. antimicrobial resistance tissue specificity ARO:3004431 Qualitative description of a microbial response to antimicrobial agents as described by EUCAST using breakpoints determined through in-vitro testing. These breakpoints are determined irrespective of tissue specificity of infection. EUCAST antimicrobial phenotype ARO:3004432 A microbe whose susceptibility to antibiotics is comparable to that of a reference susceptible microbe, meaning that the microbe is sensitive to the particular antibiotic. wild-type ARO:3004433 A microbe whose susceptibility to antibiotics differs from that of a reference susceptible microbe, meaning that the microbe is resistant to the particular antibiotic. non wild-type ARO:3004440 order: ARO:3004303 # nonsensitive ARO:3004300 # intermediate ARO:3004302 # sensitive ARO:3004304 # sensitive - dose dependant ARO:3004301 # resistant Qualitative description of a microbial response to antimicrobial agents as described by CLSI using breakpoints that take into consideration tissue specificity of infection. CLSI antimicrobial phenotype ARO:3004723 A method to determine microbial susceptibility to antibiotics in which test bacteria is inoculated onto an agar plate that contains a concentration gradient of antibiotic. The minimum inhibitory concentration of antibiotic is assessed. gradient plate method ARO:3007193 The National Committee for Clinical Laboratory Standards is an American organization responsible for developing accredited consensus clinical laboratory standards. National Committee for Clinical Laboratory Standards (NCCLS) ARO:3007397 SIR is a revised system for antibiotic sensitivity testing in Sweden that was proposed in 1977. The SIR system included two main changes: three sensitivity groups instead of the previous four and new breakpoints for the sensitivity groups. Swedish Reference Group for Antibiotics (SIR) ARO:3007398 The WRG is a standardized antimicrobial susceptibility testing methodology created by the Dutch Commissie Richtlijnen Gevoeligheidsbepalingen in 1981. Commissie Richtlijnen Gevoeligheidsbepalingen (CRG) Committee Guidelines Susceptibility Testing Working Group Guidelines Susceptibility Testing Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) BFO:0000001 entity Entity entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) BFO:0000002 continuant Continuant continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] BFO:0000003 occurrent Occurrent occurrent An entity that has temporal parts and that happens, unfolds or develops through time. An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] BFO:0000004 ic IndependentContinuant independent continuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] BFO:0000006 s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] BFO:0000008 t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] Damion Dooley's note: this BFO class is incompatible with "immaterial entity" "n-dimensional concept". temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] BFO:0000009 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] BFO:0000011 st-region SpatiotemporalRegion the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] BFO:0000015 process Process process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) James Malone (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] http://www.ifomis.org/bfo/1.1/span#ProcessualEntity NCIt:C29862 SNOMEDCT:415178003 process process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] BFO:0000016 disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis A disposition is an entity that causes a specific process or transformation in an entity in which it inheres, under specific circumstances and in conjunction with the laws of nature. For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease. BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. James Malone modified from original b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] http://www.ifomis.org/bfo/1.1/snap#Disposition NCIt:C41205 disposition disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] BFO:0000017 realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] BFO:0000018 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] BFO:0000019 quality Quality quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities. A quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. A quality is an attribute that is intrinsically associated with its bearer (or its parts), but whose presence/absence and observed/measured value may vary. a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] http://purl.obolibrary.org/obo/PATO_0000001 https://en.wikipedia.org/wiki/Quality_(philosophy) https://www.wikidata.org/wiki/Q1207505 The etymology of "quality" is fairly well elucidated coming from Middle English, from Old French qualité, from Latin qualitatem, accusative of qualitas, from qualis (“of what kind”), from Proto-Indo-European *kʷo- (“who, how”). Cicero coined qualitas as a calque to translate the Ancient Greek word ποιότης (poiótēs, “quality”), coined by Plato from ποῖος (poîos, “of what nature, of what kind”). quality (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] BFO:0000020 sdc SpecificallyDependentContinuant specifically dependent continuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. An experimental factor which is a property or characteristic of some other entity. For example, the mouse has the colour white. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. James Malone Sirarat Sarntivijai (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] http://www.ifomis.org/bfo/1.1/snap#SpecificallyDependentContinuant BFO:0000020 SpecificallyDependentContinuant specifically dependent continuant material property specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] BFO:0000023 role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. A role is an entity which is borne in a material entity in some kinds of natural, social or institutional contexts, but which is not essential to the fundamental definition of that material entity (i.e. the material entity exists with or without the role). For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. James Malone b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] http://www.ifomis.org/bfo/1.1/snap#Role MeSH:D012380 NCIt:C48835 http://purl.obolibrary.org/obo/CHEBI_50906 role role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] BFO:0000024 fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] BFO:0000026 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] BFO:0000027 object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] BFO:0000028 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] BFO:0000029 site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) A site is an entity which consists of a characteristic spatial shape in relation to some arrangement of other material entities. James Malone b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] http://www.ifomis.org/bfo/1.1/snap#Site NCIt:C37901 SNOMEDCT:10546003 Note that this can refer to a material entity like an organ or muscle, or an immaterial entity (a site or fiat boundary) like skin, stomach cavity or lung surface. site site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] BFO:0000030 object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) BFO:0000031 gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] BFO:0000034 function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] BFO:0000035 p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] BFO:0000038 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] BFO:0000040 material MaterialEntity material entity material entity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray. An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. James Malone A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] http://www.ifomis.org/bfo/1.1/snap#MaterialEntity material type material entity material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] BFO:0000140 cf-boundary ContinuantFiatBoundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] BFO:0000141 immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity BFO:0000142 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] BFO:0000144 process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] BFO:0000145 r-quality RelationalQuality John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. a marriage bond, an instance of love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] BFO:0000146 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] BFO:0000147 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] BFO:0000148 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] BFO:0000182 history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) BTO:0000003 intestinal cell line BTO:0000067 kidney cell line BTO:0000167 adenocarcinoma cell line BTO:0000188 colonic cell line BTO:0000195 Human colon adenocarcinoma cell line, established from the primary colon tumor (adenocarcinoma) of a 72-year-old Caucasian man in 1974. CACO-2 cell BTO:0000297 carcinoma cell line BTO:0000353 lung cell line BTO:0000578 Hepatoma is a cancer originating in the liver, in liver cells. More often called hepatocarcinoma or hepatocellular carcinoma. hepatoma cell line BTO:0000711 A glioma is a type of tumor that starts in the glial cells of the brain or the spine. Gliomas comprise about 30 per cent of all brain tumors and central nervous system tumors, and 80 per cent of all malignant brain tumors. glioma cell line BTO:0000762 lung cancer cell line BTO:0000797 colonic cancer cell line BTO:0000836 The MDBK cell line was derived from a kidney of an apparently normal adult steer, February 18, 1957, by S.H. Madin and N.B. Darby. MDBK cell BTO:0001120 epithelial cell line BTO:0001444 The Vero cell line was initiated from the kidney of a normal adult African green monkey on March 27, 1962, by Y. Yasumura and Y. Kawakita at the Chiba University in Chiba, Japan. Vero cell BTO:0001865 Pig kidney cell line. Original line: PK-2a; contains type C viruses. Morphology: epithelial-like. PK-15 cell BTO:0001911 lung adenocarcinoma cell line BTO:0001913 colonic adenocarcinoma cell line BTO:0001950 Human hepatoma cell line. HuH-7 cell BTO:0002022 bronchial epithelial cell line BTO:0002035 Human glioma cell line. Morphology: glial; Species: human; Tumor: glioma. U-251MG cell BTO:0002181 A highly transformed human renal epithelial line expressing two viral oncogenes, adenovirus E1a and SV40 large T antigen. HEK-293T cell BTO:0002637 respiratory epithelium cell line BTO:0002750 Human lung adenocarcinoma cell line; established from a 25-year-old caucasian male. Calu-3 cell BTO:0002886 renal epithelium cell line BTO:0002909 Rabbit renal epithelium cell line. RK-13 cell BTO:0002924 Normal human bronchial epithelial cell line. NHBE cell BTO:0004755 This line is a clone of VERO 76. VERO C1008 cell CARO:0000000 anatomical entity CARO:0000003 CARO:0030000 biological entity CHEBI:100147 A monocarboxylic acid comprising 1,8-naphthyridin-4-one substituted by carboxylic acid, ethyl and methyl groups at positions 3, 1, and 7, respectively. An orally administered antibacterial, it is used in the treatment of lower urinary-tract infections due to Gram-negative bacteria, including the majority of E. coli, Enterobacter, Klebsiella, and Proteus species. CHEBI:7456 nalidixic acid CHEBI:100241 A quinolone that is quinolin-4(1H)-one bearing cyclopropyl, carboxylic acid, fluoro and piperazin-1-yl substituents at positions 1, 3, 6 and 7, respectively. CHEBI:102718 CHEBI:3717 CHEBI:41638 ciprofloxacin CHEBI:100246 A quinolinemonocarboxylic acid with broad-spectrum antibacterial activity against most gram-negative and gram-positive bacteria. Norfloxacin is bactericidal and its mode of action depends on blocking of bacterial DNA replication by binding itself to an enzyme called DNA gyrase. CHEBI:7629 norfloxacin CHEBI:102265 A sulfonamide consisting of pyrimidine with methyl substituents at the 4- and 6-positions and a 4-aminobenzenesulfonamido group at the 2-position. sulfamethazine CHEBI:102484 A sulfonamide antibacterial with an oxazole substituent. It has antibiotic activity against a wide range of gram-negative and gram-positive organisms. CHEBI:9343 sulfisoxazole CHEBI:116278 A fluoroquinolone antibiotic, used (generally as the hydrochloride salt) to treat bacterial infections including bronchitis and urinary tract infections. It is also used to prevent urinary tract infections prior to surgery. CHEBI:6517 lomefloxacin CHEBI:124991 A semisynthetic, first-generation cephalosporin antibiotic with acetoxymethyl and (2-thienylacetyl)nitrilo moieties at positions 3 and 7, respectively, of the core structure. Administered parenterally during surgery and to treat a wide spectrum of blood infections. CHEBI:41547 CHEBI:50895 cefalotin CHEBI:131927 A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens. dicarboxylic acids and O-substituted derivatives CHEBI:13248 Any aromatic amide obtained by acylation of aniline. anilide CHEBI:134742 delamanid CHEBI:134958 thioacetazone CHEBI:135278 Trd terizidone CHEBI:138675 Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa). gas molecular entity CHEBI:139588 An alpha-oxyketone that has a hydroxy group as the alpha-oxy moiety. alpha-hydroxy ketone CHEBI:139592 An alpha-hydroxy ketone in which the carbonyl group and the hydroxy group are linked by a carbon bearing two organyl groups. tertiary alpha-hydroxy ketone CHEBI:140325 A carboxamide resulting from the formal condensation of a carboxylic acid with a primary amine; formula RC(=O)NHR(1). secondary carboxamide CHEBI:140326 A carboxamide resulting from the formal condensation of a carboxylic acid with a secondary amine; formula RC(=O)NHR(1)R(2). tertiary carboxamide CHEBI:143084 A compound having bonds between one or more metalloid atoms and one or more carbon atoms of an organyl group. organometalloidal compound CHEBI:146295 Any organic heterotricyclic compound whose core skeleton consists of a benzodioxin ring that is ortho-fused to a pyran ring. pyranobenzodioxin CHEBI:15369 A large group of antibiotics isolated from various species of Streptomyces and characterised by having a substituted phenoxazine ring linked to two cyclic heterodetic peptides. CHEBI:13723 CHEBI:22220 CHEBI:2445 actinomycin CHEBI:15379 CHEBI:10745 CHEBI:13416 CHEBI:23833 CHEBI:25366 CHEBI:30491 CHEBI:44742 CHEBI:7860 dioxygen CHEBI:157175 A 1,8-naphthyridine derivative that is 1,4-dihydro-1,8-naphthyridine with an ethyl group at the 1 position, a carboxy group at the 3-position, an oxo sustituent at the 4-position, a fluoro substituent at the 5-position and a piperazin-1-yl group at the 7 position. An antibacterial, it is used in the treatment of urinary-tract infections and gonorrhoea. CHEBI:4796 enoxacin CHEBI:15734 A primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it. CHEBI:13676 CHEBI:14887 CHEBI:26262 CHEBI:57489 CHEBI:8406 primary alcohol CHEBI:15782 A cyclic peptide antibiotic produced by the actinomycete Streptomyces puniceus, used in the treatment of tuberculosis. CHEBI:15312 CHEBI:27296 CHEBI:579539 CHEBI:9995 viomycin CHEBI:15841 A peptide containing ten or more amino acid residues. CHEBI:14860 CHEBI:8314 polypeptide CHEBI:15986 A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues. CHEBI:13672 CHEBI:14859 CHEBI:8312 polynucleotide CHEBI:161680 A synthetic monocyclic beta-lactam antibiotic (monobactam), used primarily to treat infections caused by Gram-negative bacteria. It inhibits mucopeptide synthesis in the bacterial cell wall, thereby blocking peptidoglycan crosslinking. CHEBI:2960 CHEBI:41008 aztreonam CHEBI:16247 A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides. CHEBI:14816 CHEBI:26063 CHEBI:8150 phospholipid CHEBI:16301 The nitrogen oxoanion formed by loss of a proton from nitrous acid. CHEBI:14658 CHEBI:44396 CHEBI:7585 nitrite CHEBI:16385 Compounds having the structure RSR (R =/= H). Such compounds were once called thioethers. CHEBI:13694 CHEBI:26960 CHEBI:9340 organic sulfide CHEBI:164200 An aromatic ether that is phenol which is substituted at C-5 by a chloro group and at C-2 by a 2,4-dichlorophenoxy group. It is widely used as a preservative and antimicrobial agent in personal care products such as soaps, skin creams, toothpaste and deodorants as well as in household items such as plastic chopping boards, sports equipment and shoes. CHEBI:29697 CHEBI:47700 triclosan CHEBI:16449 An alpha-amino acid that consists of propionic acid bearing an amino substituent at position 2. CHEBI:13748 CHEBI:22277 CHEBI:2539 alanine CHEBI:16541 A naturally occurring polypeptide synthesized at the ribosome. CHEBI:8526 protein polypeptide chain CHEBI:16670 peptide Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. CHEBI:14753 CHEBI:25906 CHEBI:7990 peptide CHEBI:167559 Any oligosaccharide, polysaccharide or their derivatives consisting of monosaccharides or monosaccharide derivatives linked by glycosidic bonds. See also http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_00000001. glycan CHEBI:16869 CHEBI:14682 CHEBI:25659 CHEBI:7737 oleandomycin CHEBI:16991 deoxyribonucleic acid High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. deoxyribonucleic acid deoxyribonucleic acid CHEBI:17076 A amino cyclitol glycoside that consists of streptidine having a disaccharyl moiety attached at the 4-position. The parent of the streptomycin class STR Sm Stm CHEBI:15119 CHEBI:26784 CHEBI:45745 CHEBI:9284 streptomycin CHEBI:17087 A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H). CHEBI:13427 CHEBI:13646 CHEBI:24974 CHEBI:6127 CHEBI:8742 ketone CHEBI:17154 A pyridinecarboxamide that is pyridine in which the hydrogen at position 3 is replaced by a carboxamide group. CHEBI:14645 CHEBI:25521 CHEBI:44258 CHEBI:7556 nicotinamide CHEBI:17334 Any member of the group of substituted penams containing two methyl substituents at position 2, a carboxylate substituent at position 3 and a carboxamido group at position 6. CHEBI:14742 CHEBI:25869 CHEBI:7961 penicillin CHEBI:17478 A compound RC(=O)H, in which a carbonyl group is bonded to one hydrogen atom and to one R group. CHEBI:13432 CHEBI:13753 CHEBI:13805 CHEBI:13806 CHEBI:22291 CHEBI:2554 CHEBI:8750 aldehyde CHEBI:17630 CHEBI:14487 CHEBI:24945 CHEBI:24947 CHEBI:43482 CHEBI:6106 kanamycin A CHEBI:17632 A nitrogen oxoanion formed by loss of a proton from nitric acid. Principal species present at pH 7.3. CHEBI:14654 CHEBI:44487 CHEBI:71263 nitrate CHEBI:17658 A macrolide antibiotic that is tylonolide having mono- and diglycosyl moieties attached to two of its hydroxy groups. It is found naturally as a fermentation product of Streptomyces fradiae. CHEBI:15275 CHEBI:27172 CHEBI:46150 CHEBI:9787 tylosin CHEBI:176839 Any member of a group of vitamers that belong to the chemical structural class called pyridines that exhibit biological activity against vitamin B3 deficiency. Vitamin B3 deficiency causes a condition known as pellagra whose symptoms include depression, dermatitis and diarrhea. The vitamers include nicotinic acid and nicotinamide (and their ionized and salt forms). vitamin B3 CHEBI:17698 An organochlorine compound that is dichloro-substituted acetamide containing a nitrobenzene ring, an amide bond and two alcohol functions. CHEBI:13965 CHEBI:23106 CHEBI:23108 CHEBI:3603 CHEBI:47327 chloramphenicol CHEBI:17792 A compound containing at least one carbon-halogen bond (where X is a halogen atom). CHEBI:13444 CHEBI:36684 CHEBI:8767 organohalogen compound CHEBI:17939 An aminonucleoside antibiotic, derived from the Streptomyces alboniger bacterium, that causes premature chain termination during translation taking place in the ribosome. CHEBI:14970 CHEBI:26402 CHEBI:45182 CHEBI:8641 puromycin CHEBI:18059 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. CHEBI:14517 CHEBI:25054 CHEBI:6486 lipid CHEBI:18111 RNA molecules which are essential structural and functional components of ribosomes, the subcellular units responsible for protein synthesis. CHEBI:10636 CHEBI:15010 ribosomal RNA CHEBI:18165 CHEBI:14472 CHEBI:43447 CHEBI:6036 isopenicillin N CHEBI:18203 CHEBI:14744 CHEBI:25867 CHEBI:7964 penicillin N CHEBI:18208 A penicillin in which the substituent at position 6 of the penam ring is a phenylacetamido group. CHEBI:14743 CHEBI:25866 CHEBI:45073 CHEBI:7962 benzylpenicillin CHEBI:18254 Any nucleoside where the sugar component is D-ribose. CHEBI:13014 CHEBI:13015 CHEBI:13685 CHEBI:21085 CHEBI:26560 CHEBI:4240 CHEBI:8844 ribonucleoside CHEBI:19129 11alpha-hydroxy steroid CHEBI:204928 A cephalosporin compound having acetoxymethyl and [2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino side groups. CHEBI:112504 CHEBI:3497 CHEBI:41475 cefotaxime CHEBI:209807 A semisynthetic cephamycin antibiotic which, in addition to the methoxy group at the 7alpha position, has 2-thienylacetamido and carbamoyloxymethyl side-groups. It is resistant to beta-lactamase. CHEBI:3500 CHEBI:41436 CHEBI:471714 CHEBI:658070 cefoxitin CHEBI:21731 A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a nitrogen atom, thus creating a C-N bond. N-glycosyl compound CHEBI:22160 Compounds with the general formula RNHC(=O)CH3. acetamides CHEBI:22213 acridines CHEBI:22260 Any purine ribonucleoside that is a derivative of adenosine. adenosines CHEBI:22315 Any of the naturally occurring, basic nitrogen compounds (mostly heterocyclic) occurring mostly in the plant kingdom, but also found in bacteria, fungi, and animals. By extension, certain neutral compounds biogenetically related to basic alkaloids are also classed as alkaloids. Amino acids, peptides, proteins, nucleotides, nucleic acids, amino sugars and antibiotics are not normally regarded as alkaloids. Compounds in which the nitrogen is exocyclic (dopamine, mescaline, serotonin, etc.) are usually classed as amines rather than alkaloids. alkaloid CHEBI:22390 alpha-D-glucoside CHEBI:22478 An alcohol containing an amino functional group in addition to the alcohol-defining hydroxy group. amino alcohol CHEBI:22479 amino cyclitol glycoside CHEBI:22495 aminobenzoic acid CHEBI:22507 aminoglycoside antibiotic CHEBI:22562 Any aromatic amine that is benzene carrying at least one amino substituent and its substituted derivatives. anilines CHEBI:22563 A monoatomic or polyatomic species having one or more elementary charges of the electron. anion CHEBI:22565 A class of macrocyclic lactams that consist of an aromatic (phenyl or naphthyl) or quinonoid (benzoquinone or naphthoquinone) moiety that is bridged by an aliphatic chain. ansamycin CHEBI:22582 http://purl.obolibrary.org/obo/CHEBI_33281 obsolete: antibiotic true CHEBI:22632 arsenic molecular entity CHEBI:22712 Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives. benzenes CHEBI:22723 Any aromatic carboxylic acid that consists of benzene in which at least a single hydrogen has been substituted by a carboxy group. benzoic acids CHEBI:22727 benzopyran CHEBI:22907 A glycopeptide produced by the bacterium Streptomyces verticillus. The term, 'bleomycin' refers to a family of structurally related compounds. When used as an anti-cancer agent, the chemotherapeutical forms are primarily bleomycin A2 and B2. CHEBI:584977 bleomycin CHEBI:22928 bromine molecular entity CHEBI:22985 calcium molecular entity CHEBI:23003 Any ester of carbamic acid or its N-substituted derivatives. carbamate ester CHEBI:23007 Any carbohydrate derivative that exhibits antibiotic activity. carbohydrate-containing antibiotic CHEBI:23066 A class of beta-lactam antibiotics differing from the penicillins in having a 6-membered, rather than a 5-membered, side ring. Although cephalosporins are among the most commonly used antibiotics in the treatment of routine infections, and their use is increasing over time, they can cause a range of hypersensitivity reactions, from mild, delayed-onset cutaneous reactions to life-threatening anaphylaxis in patients with immunoglobulin E (IgE)-mediated allergy. CHEBI:3538 cephalosporin CHEBI:23089 chelate-forming peptide CHEBI:23114 chloride salt CHEBI:23117 A halogen molecular entity containing one or more atoms of chlorine. chlorine molecular entity CHEBI:23132 Any organochlorine compound containing a benzene ring which is substituted by one or more chlorines. chlorobenzenes CHEBI:23232 chromenes CHEBI:23239 chromopeptide CHEBI:23367 molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity CHEBI:23403 coumarins CHEBI:23443 CHEBI:3990 cyclic amide CHEBI:23449 cyclic peptide CHEBI:23451 A polyol consisting of a cycloalkane containing at least three hydroxy groups, each attached to a different ring carbon atom. cyclitol CHEBI:23503 A member of the class of oxazolidines that is isoxazoldin-3-one which is substituted at position 4 by an amino group. 4-amino-1,2-oxazolidin-3-one CHEBI:23643 A natural or synthetic compound having a sequence of amino and hydroxy carboxylic acid residues (usually alpha-amino and alpha-hydroxy acids), commonly but not necessarily regularly alternating. depsipeptide CHEBI:23677 An azole that is either one of a pair of heterocyclic organic compounds comprising three carbon atoms and two nitrogen atoms arranged in a ring. diazole CHEBI:23697 Any member of the class of chlorobenzenes carrying two chloro groups at unspecified positions. dichlorobenzene CHEBI:23763 Any organic heteromonocyclic compound with a structure based on a dihydropyrrole. pyrroline CHEBI:23765 quinolone CHEBI:23824 A compound that contains two hydroxy groups, generally assumed to be, but not necessarily, alcoholic. Aliphatic diols are also called glycols. diol CHEBI:23953 erythromycins CHEBI:23981 ethanolamines CHEBI:24062 fluorine molecular entity CHEBI:24129 Compounds containing at least one furan ring. furans CHEBI:24278 glucoside CHEBI:24396 Any carbohydrate derivative that consists of glycan moieties covalently attached to the side chains of the amino acid residues that constitute the peptide. CHEBI:24395 CHEBI:5478 glycopeptide CHEBI:24397 Any phospholipid that contain both phosphate and carbohydrate as integral structural components. glycophospholipid CHEBI:24400 A glycosyl compound resulting from the attachment of a glycosyl group to a non-acyl group RO-, RS-, RSe-, etc. The bond between the glycosyl group and the non-acyl group is called a glycosidic bond. By extension, the terms N-glycosides and C-glycosides are used as class names for glycosylamines and for compounds having a glycosyl group attached to a hydrocarbyl group respectively. These terms are misnomers and should not be used. The preferred terms are glycosylamines and C-glycosyl compounds, respectively. glycoside CHEBI:24431 A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity CHEBI:24432 A role played by the molecular entity or part thereof within a biological context. biological role CHEBI:24471 halogen molecular entity CHEBI:24531 heterocyclic antibiotic CHEBI:24532 A cyclic compound having as ring members atoms of carbon and at least of one other element. organic heterocyclic compound CHEBI:24533 A heterodetic cyclic peptide is a peptide consisting only of amino-acid residues, but in which the linkages forming the ring are not solely peptide bonds; one or more is an isopeptide, disulfide, ester, or other bond. heterodetic cyclic peptide CHEBI:24613 A homodetic cyclic peptide is a cyclic peptide in which the ring consists solely of amino-acid residues in peptide linkages. homodetic cyclic peptide CHEBI:24628 An imidazolidinone with oxo groups at position 2 and 4. imidazolidine-2,4-dione CHEBI:24650 A compound, RkE(=O)lNHOH, derived from an oxoacid RkE(=O)l(OH) (l =/= 0) by replacing -OH with -NHOH, and derivatives thereof. Specific examples of hydroxamic acids are preferably named as N-hydroxy amides. hydroxamic acid CHEBI:24651 Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). hydroxides CHEBI:24676 Any benzoic acid carrying one or more phenolic hydroxy groups on the benzene ring. CHEBI:50778 hydroxybenzoic acid CHEBI:24780 A five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton. imidazoles CHEBI:24782 imide CHEBI:24833 A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). oxoacid CHEBI:24834 inorganic anion CHEBI:24835 A molecular entity that contains no carbon. inorganic molecular entity CHEBI:24866 A salt is an assembly of cations and anions. salt CHEBI:24868 organic salt CHEBI:24870 A molecular entity having a net electric charge. ion CHEBI:24951 kanamycins CHEBI:24983 Oximes of ketones R2C=NOH (where R =/= H). ketoxime CHEBI:24995 Cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. lactam CHEBI:25000 Any cyclic carboxylic ester containing a 1-oxacycloalkan-2-one structure, or an analogue having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. lactone CHEBI:25022 leucomycin CHEBI:25061 lipopeptide antibiotic CHEBI:25105 A macrocyclic lactone with a ring of twelve or more members which exhibits antibiotic activity. macrolide antibiotic CHEBI:25106 A macrocyclic lactone with a ring of twelve or more members derived from a polyketide. macrolide CHEBI:25362 A molecule all atoms of which have the same atomic number. elemental molecule CHEBI:25367 Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. molecule CHEBI:25384 An oxoacid containing a single carboxy group. monocarboxylic acid CHEBI:25389 Any hydroxybenzoic acid having a single phenolic hydroxy substituent on the benzene ring. monohydroxybenzoic acid CHEBI:25477 Any benzenoid aromatic compound having a skeleton composed of two ortho-fused benzene rings. naphthalenes CHEBI:25529 A member of the class of pyridines that is a substituted pyridine in which at least one of the substituents is a carboxamide or N-substituted caraboxamide group. pyridinecarboxamide CHEBI:25558 organonitrogen heterocyclic antibiotic CHEBI:25585 nonmetal atom CHEBI:25661 oleandomycins CHEBI:25693 organic heteromonocyclic compound CHEBI:25696 Any organic ion with a net negative charge. organic anion CHEBI:25698 An organooxygen compound with formula ROR, where R is not hydrogen. ether CHEBI:25699 organic ion CHEBI:25703 organic phosphate CHEBI:25710 An organophosphorus compound is formally a compound containing at least one carbon-phosphorus bond, but the term is often extended to include esters and thioesters. organophosphorus compound CHEBI:25741 An oxide is a chemical compound of oxygen with other chemical elements. oxide CHEBI:25750 Compounds of structure R2C=NOH derived from condensation of aldehydes or ketones with hydroxylamine. Oximes from aldehydes may be called aldoximes; those from ketones may be called ketoximes. oxime CHEBI:25754 Any compound that has an aldehydic or ketonic group as well as a carboxylic acid group in the same molecule. oxo carboxylic acid CHEBI:25806 oxygen molecular entity CHEBI:25807 organooxygen heterocyclic antibiotic CHEBI:25865 penicillanic acids CHEBI:25903 A chemically diverse class of peptides that exhibit antimicrobial properties. peptide antibiotic CHEBI:26004 Any organic aromatic compound with a structure based on a phenylpropane skeleton. The class includes naturally occurring phenylpropanoid esters, flavonoids, anthocyanins, coumarins and many small phenolic molecules as well as their semi-synthetic and synthetic analogues. Phenylpropanoids are also precursors of lignin. phenylpropanoid CHEBI:26020 Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom. phosphate CHEBI:26069 HP(=O)(OH)2 (phosphonic acid) and its P-substituted derivatives. phosphonic acids CHEBI:26079 phosphoric acid derivative CHEBI:26082 phosphorus molecular entity CHEBI:26144 piperazines CHEBI:26151 piperidines CHEBI:26188 Natural and synthetic compounds containing alternating carbonyl and methylene groups ('beta-polyketones'), biogenetically derived from repeated condensation of acetyl coenzyme A (via malonyl coenzyme A), and usually the compounds derived from them by further condensations, etc. Considered by many to be synonymous with the less frequently used terms acetogenins and ketides. polyketide CHEBI:26191 A compound that contains two or more hydroxy groups. polyol CHEBI:26195 Members of the class of phenols that contain 2 or more benzene rings each of which is substituted by at least one hydroxy group. polyphenol CHEBI:26273 An amino acid derivative resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of proline by a heteroatom. The definition normally excludes peptides containing proline residues. proline derivative CHEBI:2637 An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group. Am Amk amikacin CHEBI:26394 purine nucleoside CHEBI:26399 A ribonucleoside that has a purine moiety as the nucleobase (the R group in the illustration). purine ribonucleoside CHEBI:26401 A class of imidazopyrimidines that consists of purine and its substituted derivatives. CHEBI:13678 purines CHEBI:26404 puromycins CHEBI:26416 pyridine alkaloid CHEBI:26421 Any organonitrogen heterocyclic compound based on a pyridine skeleton and its substituted derivatives. pyridines CHEBI:26455 An azole that includes only one N atom and no other heteroatom as a part of the aromatic skeleton. pyrroles CHEBI:26469 A nitrogen molecular entity that is electronically neutral but which contains a quaternary nitrogen. quaternary nitrogen compound CHEBI:26512 Any aromatic carboxylic acid that contains a quinoline moiety that is substituted by one carboxy substituent. quinolinemonocarboxylic acid CHEBI:26513 A class of aromatic heterocyclic compounds each of which contains a benzene ring ortho fused to carbons 2 and 3 of a pyridine ring. quinolines CHEBI:26580 rifamycins CHEBI:26649 An amino acid derivative resulting from reaction of serine at the amino group or the carboxy group, or from the replacement of any hydrogen of serine by a heteroatom. The definition normally excludes peptides containing serine residues. serine derivative CHEBI:267413 A monohydroxybenzoic acid consisting of 5-aminosalicylic acid (mesalazine) linked to 4-aminobenzoyl-beta-alanine via an azo bond. balsalazide CHEBI:2676 A penicillin in which the substituent at position 6 of the penam ring is a 2-amino-2-(4-hydroxyphenyl)acetamido group. Amx CHEBI:133770 amoxicillin CHEBI:26761 steroid antibiotic CHEBI:26788 streptomycins CHEBI:26822 Any sulfur molecular entity that involves either covalently bonded or anionic sulfur. sulfide CHEBI:26835 sulfur molecular entity CHEBI:26878 A tertiary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has three other carbon atoms attached to it. tertiary alcohol CHEBI:26895 A subclass of polyketides having an octahydrotetracene-2-carboxamide skeleton, substituted with many hydroxy and other groups. tetracyclines CHEBI:26912 Any oxacycle having an oxolane (tetrahydrofuran) skeleton. oxolanes CHEBI:26961 Compounds containing at least one thiophene ring. thiophenes CHEBI:26979 An organic tricyclic compound in which at least one of the rings of the tricyclic skeleton contains one or more heteroatoms. organic heterotricyclic compound CHEBI:27136 A chemical compound containing three hydroxy groups. triol CHEBI:27171 organic heterobicyclic compound CHEBI:27369 A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer). zwitterion CHEBI:27565 An aminobenzoic acid that is salicylic acid substituted by an amino group at position 4. PAS CHEBI:1789 CHEBI:20320 CHEBI:41152 4-aminosalicylic acid CHEBI:27644 A member of the class of tetracyclines with formula C22H23ClN2O8 isolated from Streptomyces aureofaciens. CHEBI:23164 CHEBI:3653 chlortetracycline CHEBI:27666 CHEBI:22218 CHEBI:2446 actinomycin D CHEBI:2790 An aminoglycoside that is 2-deoxystreptamine that is substituted on the oxygen at position 4 by an (8R)-2-amino-8-O-(4-amino-4-deoxy-alpha-D-glucopyranosyl)-2,3,7-trideoxy-7-(methylamino)-D-glycero-alpha-D-allo-octodialdo-1,5:8,4-dipyranos-1-yl) group. CHEBI:40708 apramycin CHEBI:27933 An organonitrogen heterocyclic antibiotic that contains a beta-lactam ring. CHEBI:10427 CHEBI:22844 beta-lactam antibiotic CHEBI:28001 A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile. CHEBI:27276 CHEBI:49941 CHEBI:9931 vancomycin CHEBI:28077 A member of the class of rifamycins that is a a semisynthetic antibiotic derived from Amycolatopsis rifamycinica (previously known as Amycolatopsis mediterranei and Streptomyces mediterranei). Rif CHEBI:26577 CHEBI:45308 CHEBI:8858 rifampicin CHEBI:281056 The conjugate base of loracarbef. loracarbef anion CHEBI:28368 A coumarin-derived antibiotic obtained from Streptomyces niveus. CHEBI:25597 CHEBI:44505 CHEBI:7644 novobiocin CHEBI:28659 CHEBI:26080 CHEBI:8168 phosphorus atom CHEBI:28864 A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring. CHEBI:19849 CHEBI:45933 CHEBI:9610 tobramycin CHEBI:28908 A glycophospholipid antibiotic compound with the lipid portion conjugated to a pentasaccharide fraction via a phosphate linkage. CHEBI:25360 CHEBI:5075 bambermycin CHEBI:28915 A phosphonic acid having an (R,S)-1,2-epoxypropyl group attached to phosphorus. CHEBI:24100 CHEBI:42503 CHEBI:8159 fosfomycin CHEBI:28963 Any sugar having one or more alcoholic hydroxy groups replaced by substituted or unsubstituted amino groups. CHEBI:22481 CHEBI:22530 CHEBI:2662 amino sugar CHEBI:28971 A penicillin in which the substituent at position 6 of the penam ring is a 2-amino-2-phenylacetamido group. CHEBI:22536 CHEBI:2683 CHEBI:40648 CHEBI:45042 ampicillin CHEBI:29007 A third-generation cephalosporin compound having 2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetylamino and [(2-methyl-5,6-dioxo-1,2,5,6-tetrahydro-1,2,4-triazin-3-yl)sulfanyl]methyl side-groups. CHEBI:23059 CHEBI:3513 CHEBI:446214 ceftriaxone CHEBI:29013 A steroid antibiotic that is isolated from the fermentation broth of Fusidium coccineum. CHEBI:24133 CHEBI:42742 CHEBI:5201 fusidic acid CHEBI:29067 The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated. CHEBI:13626 CHEBI:13945 CHEBI:23026 CHEBI:58657 carboxylic acid anion CHEBI:29347 A carboxamide derived from a monocarboxylic acid. CHEBI:13211 CHEBI:22207 CHEBI:25383 CHEBI:6977 monocarboxylic acid amide CHEBI:2955 A macrolide antibiotic useful for the treatment of bacterial infections. CHEBI:46596 azithromycin CHEBI:29556 A complex glycopeptide antibiotic that is isolated from Amycolatopsis orientalis. chloroeremomycin CHEBI:2956 A semisynthetic penicillin having a 6beta-{(2R)-2-[(2-oxoimidazolidine-1-carbonyl)amino]-2-phenylacetyl}amino side-group. It is an antibiotic used in treating infections caused by Pseudomonas aeruginosa, Escherichia coli and Haemophilus influenzae. CHEBI:63225 azlocillin CHEBI:29584 CHEBI:42746 GE2270A CHEBI:29630 A twelve-membered macrolide antibiotic that is biosynthesised by Streptomyces venezuelae. methymycin CHEBI:29649 A macrolide antibiotic that is narbonolide having a 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl residue attached at position 6. It is biosynthesised by Streptomyces venezuelae. CHEBI:44624 narbomycin CHEBI:29665 A macrolide antibiotic that is biosynthesised by Streptomyces venezuelae. pikromycin CHEBI:29668 Pulvomycin CHEBI:29673 A member of the class of rifamycins that exhibits antibiotic and antitubercular properties. rifamycin SV CHEBI:29688 CHEBI:46029 telithromycin CHEBI:29693 A heterodetic cyclic peptide, in which the cyclisation step involves a formal lactonisation between the carboxy group of a quinaldic acid-based residue and a secondary alcohol. An antibiotic that inhibits bacterial protein synthesis. Also acts as an antitumor agent. thiostrepton CHEBI:29705 Valnemulin CHEBI:30879 A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom. CHEBI:13804 CHEBI:22288 CHEBI:2553 alcohol CHEBI:3139 CHEBI:165316 CHEBI:357107 CHEBI:41102 CHEBI:653800 bleomycin A2 CHEBI:31577 Any organic amino compound that is a derivative of ethylenediamine. ethylenediamine derivative CHEBI:31739 A macrolide antibiotic produced by certain strains of Streptomyces narbonensis var. josamyceticus. josamycin CHEBI:31753 A macrolide antibiotic produced by Streptomyces kitasatoensis, showing activity against a wide spectrum of pathogens. leucomycin V CHEBI:31810 A fluoroquinolone antibiotic that is 4-oxo-1,4-dihydroquinoline which is substituted at positions 1, 3, 6, 7 and 8 by 2-fluoroethyl, carboxy, fluoro, 4-methylpiperazin-1-yl and fluoro groups, respectively. It is active against many Gram-positive and Gram-negative bacteria. fleroxacin CHEBI:32066 Pto CHEBI:93717 Prothionamide CHEBI:32215 thiamphenicol CHEBI:32583 calcium sulfate dihydrate CHEBI:32955 Any cyclic ether in which the oxygen atom forms part of a 3-membered ring. CHEBI:13828 CHEBI:23930 CHEBI:4812 epoxide CHEBI:32988 An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. CHEBI:22473 CHEBI:2633 amide CHEBI:33241 oxoacid derivative CHEBI:33245 An organic fundamental parent is a structure used as a basis for substitutive names in organic nomenclature, containing, in addition to one or more hydrogen atoms, a single atom of an element, a number of atoms (alike or different) linked together to form an unbranched chain, a monocyclic or polycyclic ring system, or a ring assembly or ring/chain system. organic fundamental parent CHEBI:33250 A chemical entity constituting the smallest component of an element having the chemical properties of the element. CHEBI:22671 CHEBI:23907 atom CHEBI:33256 A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. primary amide CHEBI:33257 A derivative of two oxoacids RkE(=O)l(OH)m (l =/= 0) in which two acyl groups are attached to the amino or substituted amino group. secondary amide CHEBI:33259 A molecular entity all atoms of which have the same atomic number. elemental molecular entity CHEBI:33261 An organosulfur compound is a compound containing at least one carbon-sulfur bond. CHEBI:23010 CHEBI:25714 organosulfur compound CHEBI:33262 elemental oxygen CHEBI:33263 diatomic oxygen CHEBI:33273 An anion consisting of more than one atom. polyatomic anion CHEBI:33281 A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. CHEBI:22582 antimicrobial agent CHEBI:33285 A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. heteroorganic entity CHEBI:33290 food role A physiological role played by any substance of either plant, animal or artificial origin which contains essential body nutrients that can be ingested by an organism to provide energy, promote growth, and maintain the processes of life. food CHEBI:33299 An alkaline earth molecular entity is a molecular entity containing one or more atoms of an alkaline earth metal. alkaline earth molecular entity CHEBI:33300 Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth. pnictogen CHEBI:33302 A p-block molecular entity containing any pnictogen. pnictogen molecular entity CHEBI:33304 Any p-block molecular entity containing a chalcogen. chalcogen molecular entity CHEBI:33308 An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl. CHEBI:13204 CHEBI:23028 CHEBI:3408 carboxylic ester CHEBI:33318 An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. main group element atom CHEBI:33406 organoarsenic compound CHEBI:33424 sulfur oxoacid derivative CHEBI:33458 nitrogen oxoanion CHEBI:33459 pnictogen oxoanion CHEBI:33552 sulfonic acid derivative CHEBI:33560 Any main group element atom belonging to the p-block of the periodic table. p-block element atom CHEBI:33563 Any member of class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide). Some substances classified as bacterial glycolipids have the sugar part acylated by one or more fatty acids and the glycerol part may be absent. CHEBI:24393 CHEBI:5476 glycolipid CHEBI:33575 A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid. CHEBI:13428 CHEBI:13627 CHEBI:23027 carboxylic acid CHEBI:33579 A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. main group molecular entity CHEBI:33582 carbon group molecular entity CHEBI:33595 Any molecule that consists of a series of atoms joined together to form a ring. cyclic compound CHEBI:33597 A cyclic compound having as ring members atoms of the same element only. homocyclic compound CHEBI:33598 A homocyclic compound in which all of the ring members are carbon atoms. carbocyclic compound CHEBI:33608 hydrogen molecular entity CHEBI:33635 polycyclic compound CHEBI:33636 A molecule that features two fused rings. bicyclic compound CHEBI:33655 A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character. aromatic compound CHEBI:33659 organic aromatic compound CHEBI:33661 monocyclic compound CHEBI:33670 heteromonocyclic compound CHEBI:33671 A polycyclic compound in which at least one of the rings contains at least one non-carbon atom. heteropolycyclic compound CHEBI:33672 A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom. heterobicyclic compound CHEBI:33674 An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element. s-block molecular entity CHEBI:33675 A main group molecular entity that contains one or more atoms of a p-block element. p-block molecular entity CHEBI:33692 Hydrides are chemical compounds of hydrogen with other chemical elements. hydrides CHEBI:33694 A macromolecule formed by a living organism. biomacromolecule CHEBI:33695 information biomacromolecule CHEBI:33696 nucleic acid A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. nucleic acid CHEBI:33697 High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. ribonucleic acid CHEBI:33704 An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group. CHEBI:10208 CHEBI:13779 CHEBI:22442 CHEBI:2642 alpha-amino acid CHEBI:33709 A carboxylic acid containing one or more amino groups. CHEBI:13815 CHEBI:22477 amino acid CHEBI:3371 CAP Cm capreomycin CHEBI:33822 An organic compound having at least one hydroxy group attached to a carbon atom. CHEBI:64710 organic hydroxy compound CHEBI:33832 Any organic molecule that consists of atoms connected in the form of a ring. organic cyclic compound CHEBI:33833 A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2). heteroarene CHEBI:33836 benzenoid aromatic compound CHEBI:33838 An N-glycosyl compound that has both a nucleobase, normally adenine, guanine, xanthine, thymine, cytosine or uracil, and either a ribose or deoxyribose as functional parents. CHEBI:13661 CHEBI:25611 CHEBI:7647 nucleoside CHEBI:33839 macromolecule A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. macromolecule CHEBI:33853 Organic aromatic compounds having one or more hydroxy groups attached to a benzene or other arene ring. CHEBI:13664 CHEBI:13825 CHEBI:25969 CHEBI:2857 phenols CHEBI:33856 An amino acid whose structure includes an aromatic ring. CHEBI:13820 CHEBI:22623 CHEBI:2835 aromatic amino acid CHEBI:33859 Any carboxylic acid in which the carboxy group is directly bonded to an aromatic ring. CHEBI:13817 CHEBI:13821 CHEBI:2830 aromatic carboxylic acid CHEBI:33860 An amino compound in which the amino group is linked directly to an aromatic system. CHEBI:13827 CHEBI:22622 CHEBI:22646 CHEBI:2834 CHEBI:2863 aromatic amine CHEBI:3393 A penicillin antibiotic having a 6beta-2-carboxy-2-phenylacetamido side-chain. carbenicillin CHEBI:33958 halide salt CHEBI:3478 A cephalosporin bearing chloro and (R)-2-amino-2-phenylacetamido groups at positions 3 and 7, respectively, of the cephem skeleton. CHEBI:472656 cefaclor CHEBI:3479 A cephalosporin bearing methyl and (2R)-2-amino-2-(4-hydroxyphenyl)acetamido groups at positions 3 and 7, respectively, of the cephem skeleton. cefadroxil CHEBI:3480 A cephalosporin compound having (R)-mandelamido and N-methylthiotetrazole side-groups. cefamandole CHEBI:3485 A cephalosporin compound having 7beta-2-(2-amino-thiazol-4-yl)-2-[(Z)-hydroxyimino]-acetylamino- and 3-vinyl side groups. CHEBI:184624 cefdinir CHEBI:3489 A second-generation cephalosporin antibiotic having N(1)-methyltetrazol-5-ylthiomethyl, {[(cyanomethyl)sulfanyl]acetyl}amino and methoxy side-groups at positions 3, 7beta and 7alpha respectively of the parent cephem bicyclic structure. cefmetazole CHEBI:3491 A cephalosporin bearing {[1-(sulfomethyl)-1H-tetrazol-5-yl]sulfanyl}methyl and (R)-2-hydroxy-2-phenylacetamido groups at positions 3 and 7, respectively, of the cephem skeleton. cefonicid CHEBI:3493 A semi-synthetic parenteral cephalosporin with a tetrazolyl moiety that confers beta-lactamase resistance. CHEBI:258120 cefoperazone CHEBI:34994 Any of the glycopeptides whose structure consists of teicoplanin A3-1 in which the hydroxy group of the di(aryloxy)-substituted phenol moiety has been converted to the corresponding 2-acylamino-2-deoxy-beta-D-glucoside. Members of the class differ only in the nature of the acyl group. teicoplanin A2 CHEBI:34996 A teicoplanin A2 that has decanoyl as the variable N-acyl group. teicoplanin A2-3 CHEBI:3504 A third-generation cephalosporin antibiotic with methoxymethyl and (2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetamino substituents at positions 3 and 7, respectively, of the cephem skeleton. Given by mouth as its proxetil ester prodrug, it is used to treat acute otitis media, pharyngitis, and sinusitis. CHEBI:606443 cefpodoxime CHEBI:3506 A semisynthetic, second-generation cephalosporin, with prop-1-enyl and (R)-2-amino-2-(4-hydroxyphenyl)acetamido groups at positions 3 and 7, respectively, of the cephem skeleton. It is used to treat bronchitis as well as ear, skin and other bacterial infections. cefprozil CHEBI:3508 A third-generation cephalosporin antibiotic bearing pyridinium-1-ylmethyl and {[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetamido groups at positions 3 and 7, respectively, of the cephem skeleton. ceftazidime CHEBI:3510 A third-generation cephalosporin antibiotic with a [(2Z)-2-(2-amino-1,3-thiazol-4-yl)-4-carboxybut-2-enoyl]amino substituent at the 7 position of the cephem skeleton. An orally-administered agent, ceftibuten is used as the dihydrate to treat urinary-tract and respiratory-tract infections. CHEBI:554578 ceftibuten CHEBI:35156 calcium salt CHEBI:35213 A depsipeptide in which the amino and hydroxy carboxylic acid residues are connected in a ring. cyclodepsipeptide CHEBI:35275 A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and a S atom bound to a carbon atom, thus creating a C-S bond. CHEBI:22048 CHEBI:33577 S-glycosyl compound CHEBI:35281 Neutral molecules having charge-separated forms with an onium atom which bears no hydrogen atoms and that is not adjacent to the anionic atom. onium betaine CHEBI:35285 iminium betaine CHEBI:35294 A polyclic compound in which all of the ring members are carbon atoms. carbopolycyclic compound CHEBI:35295 homopolycyclic compound CHEBI:35313 hexoside CHEBI:3534 A semisynthetic first-generation cephalosporin antibiotic having methyl and beta-(2R)-2-amino-2-phenylacetamido groups at the 3- and 7- of the cephem skeleton, respectively. It is effective against both Gram-negative and Gram-positive organisms, and is used for treatment of infections of the skin, respiratory tract and urinary tract. cephalexin CHEBI:35341 Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene. CHEBI:13687 CHEBI:26768 CHEBI:9263 steroid CHEBI:35350 CHEBI:24748 CHEBI:5814 hydroxy steroid CHEBI:35352 Any heteroorganic entity containing at least one carbon-nitrogen bond. organonitrogen compound CHEBI:35358 An amide of a sulfonic acid RS(=O)2NR'2. sulfonamide CHEBI:35362 Compounds derived from oxoacids RkE(=O)l(OH)m (l =/= 0) by replacing -OH by -NRNR2 (R groups are commonly H). (IUPAC). hydrazide CHEBI:35363 A hydrazide consisting of hydrazine carrying one or more carboacyl groups. carbohydrazide CHEBI:35406 An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen. CHEBI:33274 CHEBI:33436 oxoanion CHEBI:35436 Any glucoside in which the glycoside group is derived from D-glucose. CHEBI:21009 CHEBI:4173 D-glucoside CHEBI:3547 A first-generation cephalosporin antibiotic with a methyl substituent at position 3, and a (2R)-2-amino-2-cyclohexa-1,4-dien-1-ylacetamido substituent at position 7, of the cephem skeleton. cephradine CHEBI:35496 Any fluoroarene that is a benzene or a substituted benzene carrying at least one fluoro group. fluorobenzenes CHEBI:35504 An addition compound contains two or more simpler compounds that can be packed in a definite ratio into a crystal. The term covers donor-acceptor complexes (adducts) and a variety of lattice compounds. addition compound CHEBI:35505 An addition compound that contains water in weak chemical combination with another compound. hydrate CHEBI:35507 natural product fundamental parent CHEBI:355510 A cephalosporin with ({1-[2-(dimethylamino)ethyl]-1H-tetrazol-5-yl}sulfanyl)methyl and (2-amino-1,3-thiazol-4-yl)acetamido substituents at positions 3 and 7, respectively, of the cephem skeleton. A third generation beta-lactam cephalosporin antibiotic, it is active against a broad spectrum of both Gram positive and Gram negative bacteria. cefotiam CHEBI:35552 heterocyclic organic fundamental parent CHEBI:35568 Any molecular entity that consists of a ring having (formally) the maximum number of noncumulative double bonds. mancude ring CHEBI:35571 mancude organic heterocyclic parent CHEBI:35573 organic mancude parent CHEBI:35605 carbon oxoacid CHEBI:35618 Any ether in which the oxygen is attached to at least one aryl substituent. aromatic ether CHEBI:35627 A lactam in which the amide bond is contained within a four-membered ring, which includes the amide nitrogen and the carbonyl carbon. CHEBI:10426 CHEBI:13203 CHEBI:22845 beta-lactam CHEBI:35681 A secondary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has two other carbon atoms attached to it. CHEBI:13425 CHEBI:13686 CHEBI:26617 CHEBI:58662 CHEBI:8741 CHEBI:9077 secondary alcohol CHEBI:35689 An azole in which the five-membered heterocyclic aromatic skeleton contains four N atoms and one C atom. tetrazoles CHEBI:35692 Any carboxylic acid containing two carboxy groups. CHEBI:23692 CHEBI:36172 CHEBI:4501 dicarboxylic acid CHEBI:35701 A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter. CHEBI:23960 CHEBI:4859 ester CHEBI:35715 A compound having a nitro group, -NO2 (free valence on nitrogen), which may be attached to carbon, nitrogen (as in nitramines), or oxygen (as in nitrates), among other elements (in the absence of specification, C-nitro compounds are usually implied). nitro compound CHEBI:35716 A nitro compound having the nitro group (-NO2) attached to a carbon atom. C-nitro compound CHEBI:35727 An azole in which the five-membered heterocyclic aromatic skeleton contains three N atoms and two C atoms. triazoles CHEBI:35740 liposaccharide CHEBI:35757 A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated. CHEBI:13657 CHEBI:25382 CHEBI:3407 monocarboxylic acid anion CHEBI:35790 An azole based on a five-membered heterocyclic aromatic skeleton containing one N and one O atom. oxazole CHEBI:35850 An organosulfur compound having the structure RS(=O)2R (R =/= H). sulfone CHEBI:35871 Any monocarboxylic acid having at least one additional oxo functional group. oxo monocarboxylic acid CHEBI:35875 imidazopyrimidine CHEBI:35915 A steroid ester obtained by formal condensation of the carboxy group of any carboxylic acid with the 3-hydroxy group of a sterol. CHEBI:13220 CHEBI:15115 CHEBI:26770 CHEBI:26772 CHEBI:9268 CHEBI:9269 sterol ester CHEBI:35990 A polycyclic compound in which two rings have two or more atoms in common. bridged compound CHEBI:35991 Compound comprising a beta-lactam ring fused to a saturated 5-membered ring containing one sulfur atom. penam CHEBI:35992 Natural and synthetic antibiotics containing the 4-thia-1-azabicyclo[3.2.0]heptan-7-one structure, generally assumed to have the 5R configuration unless otherwise specified. penams CHEBI:36094 organic chloride salt CHEBI:36357 Any molecular entity consisting of more than one atom. polyatomic entity CHEBI:36358 An ion consisting of more than one atom. polyatomic ion CHEBI:36359 phosphorus oxoacid derivative CHEBI:36360 phosphorus oxoacids and derivatives CHEBI:36364 alkaline earth salt CHEBI:36416 mancude organic heterotricyclic parent CHEBI:36420 A polycyclic heteroarene that is anthracene in which one of the central CH groups is replaced by a nitrogen atom. acridine CHEBI:36586 Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives. carbonyl compound CHEBI:36587 Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element. organic oxo compound CHEBI:36683 An organochlorine compound is a compound containing at least one carbon-chlorine bond. organochlorine compound CHEBI:36688 heterotricyclic compound CHEBI:36709 Any member of the class of quinolines in which the quinoline skeleton is substituted by one or more amino or substituted-amino groups. aminoquinoline CHEBI:36785 A bicyclic compound in which all the ring atoms are carbon. carbobicyclic compound CHEBI:36807 A salt formally resulting from the reaction of hydrochloric acid with an organic base. hydrochloride CHEBI:36816 O-organyl oximes R2C=NOR' (R' =/= H). oxime O-ether CHEBI:36834 Any hydroxy steroid carrying a hydroxy group at position 3. 3-hydroxy steroid CHEBI:36835 A 3-hydroxy steroid in which the 3-hydroxy substituent is in the alpha-position. CHEBI:71194 3alpha-hydroxy steroid CHEBI:36841 11-hydroxy steroid CHEBI:36914 inorganic ion CHEBI:36962 An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. organochalcogen compound CHEBI:36963 An organochalcogen compound containing at least one carbon-oxygen bond. organooxygen compound CHEBI:37141 A compound containing at least one carbon-bromine bond. organobromine compound CHEBI:37143 An organofluorine compound is a compound containing at least one carbon-fluorine bond. organofluorine compound CHEBI:3716 A member of the class of cinnolines that is 6,7-methylenedioxycinnolin-4(1H)-one bearing an ethyl group at position 1 and a carboxylic acid group at position 3. An analogue of oxolinic acid, it has similar antibacterial actions. It was formerly used for the treatment of urinary tract infections. CHEBI:314701 cinoxacin CHEBI:37175 organic hydride CHEBI:3732 The 6-O-methyl ether of erythromycin A, clarithromycin is a macrolide antibiotic used in the treatment of respiratory-tract, skin and soft-tissue infections. It is also used to eradicate Helicobacter pylori in the treatment of peptic ulcer disease. It prevents bacteria from growing by interfering with their protein synthesis. Clr CHEBI:41676 CHEBI:442148 CHEBI:670147 clarithromycin CHEBI:37407 Any ether in which the oxygen atom forms part of a ring. CHEBI:37406 cyclic ether CHEBI:3745 A carbohydrate-containing antibiotic that is the semisynthetic derivative of lincomycin, a natural antibiotic. CHEBI:47331 clindamycin CHEBI:3749 3-Isopropylimino-3,5-dihydro-phenazine in which the hydrogen at position 5 is substituted substituted by a 4-chlorophenyl group, and that at position 2 is substituted by a (4-chlorophenyl)amino group. A dark red crystalline solid, clofazimine is an antimycobacterial and is one of the main drugs used for the treatment of multi-bacillary leprosy. However, it can cause red/brown discolouration of the skin, so other treatments are often preferred in light-skinned patients. Cfz CHEBI:355347 clofazimine CHEBI:37577 A molecular entity consisting of two or more chemical elements. heteroatomic molecular entity CHEBI:37578 Any heteroatomic molecular entity that is a chemical compound of halogen with other chemical elements. halide CHEBI:37622 An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom. CHEBI:35354 CHEBI:35355 carboxamide CHEBI:37716 Any imide in which the acyl substituents are any two from carboacyl, sulfonyl and phosphoryl mixed diacylamine CHEBI:37734 CHEBI:26019 phosphoric ester CHEBI:37773 organic phosphoramidate CHEBI:37912 Any coumarin carrying at least one hydroxy substituent. CHEBI:24691 CHEBI:24692 hydroxycoumarin CHEBI:37922 A kanamycin that is kanamycin B bearing an N-(2S)-4-amino-2-hydroxybutyryl group on the aminocyclitol ring. arbekacin CHEBI:37923 An amino cyclitol glycoside that is L-chiro-inositol in which the hydroxy groups at positions 1, 4, and 6 are replaced by aminoacetyl)methylamino, amino, and methoxy groups, respectively, and in which the hydroxy group at position 3 is converted to the corresponding 2,6-diamino-2,3,4,6,7-pentadeoxy-beta-L-lyxo-heptopyranoside. The major component of fortimicin, obtained from Micromonospora olivasterospora. It is administered (as the sulfate salt) by intramuscular injection or intravenous infusion for the treatment of severe systemic infections due to sensitive Gram-negative organisms. astromicin CHEBI:37945 A kanamycin that is kanamycin B lacking the 3- and 4-hydroxy groups on the 2,6-diaminosugar ring. dibekacin CHEBI:38032 A carbopolyclic compound comprising of three carbocyclic rings. carbotricyclic compound CHEBI:38064 heteroarenecarboxylate ester CHEBI:38099 thiadiazoles CHEBI:38101 Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms. organonitrogen heterocyclic compound CHEBI:38102 Compounds based on a triazine skeleton. triazines CHEBI:38104 Any organic heterocyclic compound containing at least one ring oxygen atom. oxacycle CHEBI:38106 organosulfur heterocyclic compound CHEBI:38131 Cyclic hemiacetals formed by intramolecular addition of a hydroxy group to an aldehydic or ketonic carbonyl group. They are thus 1-oxacycloalkan-2-ols or unsaturated analogues. lactol CHEBI:38163 organic heterotetracyclic compound CHEBI:38166 CHEBI:25429 CHEBI:38075 organic heteropolycyclic compound CHEBI:38179 monocyclic heteroarene CHEBI:38180 polycyclic heteroarene CHEBI:38260 Any of a class of heterocyclic amines having a saturated five-membered ring. CHEBI:26922 CHEBI:38191 pyrrolidines CHEBI:38261 imidazolidines CHEBI:38295 azabicycloalkane CHEBI:38304 diazolidine CHEBI:38311 cephem CHEBI:38313 Any organic heterocyclic compound containing a benzene ring in which two of the C-H fragments have been replaced by isolobal nitrogens (the diazine parent structure). diazines CHEBI:38314 pyrazines CHEBI:38329 oxazolidines CHEBI:383703 The 10-methochloride salt of 3,6-diaminoacridine. Note that a mixture of this compound with 3,6-diaminoacridine (proflavine) is known as acriflavine or neutral acriflavine. 3,6-diamino-10-methylacridinium chloride CHEBI:38418 CHEBI:26949 CHEBI:38417 1,3-thiazoles CHEBI:38443 1-benzopyran CHEBI:38445 chromenone CHEBI:38532 Compounds having the structure R2C=NNR2, formally derived from aldehydes or ketones by replacing =O by =NNH2 (or substituted analogues). hydrazone CHEBI:38582 Any member of the class of fluorobenzenes containing a mono- or poly-substituted benzene ring carrying two fluorine atoms. difluorobenzene CHEBI:38770 Any organic heteropolycyclic compound based on the 1,2-diaza analogue of naphthalene and its substituted derivatives. cinnolines CHEBI:38785 Any compound containing morpholine as part of its structure. morpholines CHEBI:3907 A hydroxycoumarin antibiotic that is obtained from Streptomyces rishiriensis and exhibits potent antibacterial and anticancer activity. coumermycin A1 CHEBI:39201 Any organonitrogen heterocyclic compound based on a phenazine skeleton and derivatives. phenazines CHEBI:39206 dibenzopyridine CHEBI:39270 naphthofuran CHEBI:39410 Any compound with a 1,2,4-triazine skeleton, in which nitrogen atoms replace carbon at positions 1, 2 and 4 of the core benzene ring structure. 1,2,4-triazines CHEBI:39447 Any compound having a pyrimidine as part of its structure. CHEBI:13681 CHEBI:26448 pyrimidines CHEBI:3992 cyclic ketone CHEBI:40009 A 4-amino-1,2-oxazolidin-3-one that has R configuration. It is an antibiotic produced by Streptomyces garyphalus or S. orchidaceus and is used as part of a multi-drug regimen for the treatment of tuberculosis when resistance to, or toxicity from, primary drugs has developed. An analogue of D-alanine, it interferes with bacterial cell wall synthesis in the cytoplasm by competitive inhibition of L-alanine racemase (which forms D-alanine from L-alanine) and D-alanine--D-alanine ligase (which incorporates D-alanine into the pentapeptide required for peptidoglycan formation and bacterial cell wall synthesis). CYC Cs CHEBI:4030 D-cycloserine CHEBI:404903 Meropenem in which the one of the two methyl groups attached to the amide nitrogen is replaced by hydrogen while the other is replaced by a 3-carboxyphenyl group. The sodium salt is used for the treatment of moderate to severe susceptible infections including intra-abdominal and acute gynaecological infections, pneumonia, and infections of the skin and of the urinary tract. CHEBI:471574 ertapenem CHEBI:4309 A macrolide that is pristinamycin IIA in which the double bond between positions 26 and 26a of the pyrroline ring has been reduced and position 26R carries a [2-(diethylamino)ethyl]sulfonyl group. It is a semi-synthetic streptogramin antibiotic and often used as a mixture with quinupristin for the treatment of vancomycin-resistant Enterococcus faecium. CHEBI:42127 dalfopristin CHEBI:43968 A carbapenemcarboxylic acid in which the azetidine and pyrroline rings carry 1-hydroxymethyl and in which the azetidine and pyrroline rings carry 1-hydroxymethyl and 5-(dimethylcarbamoyl)pyrrolidin-3-ylthio substituents respectively. meropenem CHEBI:443725 Propylphosphonic acid in which one of the hydrogens at position 3 is substituted by a formyl(hydroxy)amino group. An antibiotic obtained from Streptomyces lavendulae, it specifically inhibits DXP reductoisomerase (EC 1.1.1.267), a key enzyme in the non-mevalonate pathway of isoprenoid biosynthesis. CHEBI:42526 fosmidomycin CHEBI:4454 Destomysin CHEBI:4511 A penicillin that is 6-aminopenicillanic acid in which one of the amino hydrogens is replaced by a 3-(2,6-dichlorophenyl)-5-methyl-1,2-oxazol-4-yl]formyl group. dicloxacillin CHEBI:45257 An amino cyclitol glycoside that is 4,6-diaminocyclohexane-1,2,3-triol having a 2,6-diamino-2,6-dideoxy-alpha-D-glucosyl residue attached at position 1 and a beta-D-ribosyl residue attached at position 2. It is an antibiotic produced by Streptomyces ribosidificus (formerly S. thermoflavus). ribostamycin CHEBI:45285 pyrazinamide A monocarboxylic acid amide resulting from the formal condensation of the carboxy group of pyrazinoic acid (pyrazine-2-carboxylic acid) with ammonia. A prodrug for pyrazinoic acid, pyrazinecarboxamide is used as part of multidrug regimens for the treatment of tuberculosis. Pza CHEBI:45281 CHEBI:8656 pyrazinecarboxamide CHEBI:45367 CHEBI:45364 CHEBI:8857 rifabutin CHEBI:46633 The class of beta-lactam antibiotics that whose members have a carbapenem skeleton which is variously substituted at positions 3, 4, and 6. carbapenems CHEBI:46634 carbapenemcarboxylic acid CHEBI:46770 pyrrolidinecarboxamide CHEBI:46812 1,3-oxazoles CHEBI:46845 N-alkylpiperazine CHEBI:46847 N-iminopiperazine CHEBI:46848 N-arylpiperazine CHEBI:46895 A compound consisting of a peptide with attached lipid. lipopeptide CHEBI:46920 N-methylpiperazine CHEBI:46942 Any organic heteromonocyclic compoundthat is oxane or its substituted derivatives. oxanes CHEBI:46952 oxazinane CHEBI:47017 tetrahydrofuranol CHEBI:47019 dihydroxytetrahydrofuran CHEBI:4705 double-stranded DNA double-stranded DNA CHEBI:471744 A broad-spectrum, intravenous beta-lactam antibiotic of the carbapenem subgroup. CHEBI:5879 imipenem CHEBI:472657 A third-generation cephalosporin antibiotic bearing vinyl and (2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-[(carboxymethoxy)imino]acetamido groups at positions 3 and 7, respectively, of the cephem skeleton. It is used in the treatment of gonorrhoea, tonsilitis, pharyngitis, bronchitis, and urinary tract infections. CHEBI:3487 cefixime CHEBI:474014 The hemi-aminal resulting from the condensation of the erythromycin derivative (9S)-erythromycyclamine with 2-(2-methoxyethoxy)acetaldehyde. As the oxazine ring containing the hemi-aminal group is unstable under both acidic and alkaline conditions, dirithromycin functions as a more lipid-soluble prodrug for (9S)-erythromycyclamine. Administered as enteric coated tablets to protect it from acid catalysed hydrolysis in the stomach, it is used to treat respiratory tract, skin, and soft tissue infections caused by susceptible organisms. dirithromycin CHEBI:474053 A first-generation cephalosporin compound having [(5-methyl-1,3,4-thiadiazol-2-yl)sulfanyl]methyl and (1H-tetrazol-1-ylacetyl)amino side-groups at positions 3 and 7 respectively. CHEBI:3482 cefazolin CHEBI:47622 Any carboxylic ester where the carboxylic acid component is acetic acid. CHEBI:13244 CHEBI:13799 CHEBI:22189 CHEBI:2406 acetate ester CHEBI:47779 aminoglycoside CHEBI:478164 A cephalosporin bearing (1-methylpyrrolidinium-1-yl)methyl and (2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetamido groups at positions 3 and 7, respectively, of the cephem skeleton. CHEBI:3486 CHEBI:473919 cefepime CHEBI:47880 CHEBI:26762 steroid ester CHEBI:47881 CHEBI:13600 CHEBI:1619 CHEBI:35949 3-oxo monocarboxylic acid CHEBI:47891 Any steroid substituted by at least one carboxy group. steroid acid CHEBI:47956 Any primary amide having its amide oxygen replaced by sulfur. thiocarboxamide CHEBI:4877 An ethylenediamine derivative that is ethane-1,2-diamine in which one hydrogen attached to each of the nitrogens is sutstituted by a 1-hydroxybutan-2-yl group (S,S-configuration). It is a bacteriostatic antimycobacterial drug, effective against Mycobacterium tuberculosis and some other mycobacteria. It is used (as the dihydrochloride salt) in combination with other antituberculous drugs in the treatment of pulmonary and extrapulmonary tuberculosis; resistant strains of M. tuberculosis are readily produced if ethambutol is used alone. E ETB Emb CHEBI:133410 CHEBI:659237 CHEBI:678172 ethambutol CHEBI:487869 The conjugate base of clavulanic acid. clavulanate CHEBI:48838 gypsum CHEBI:48844 Semisynthetic derivative of erythromycin A. roxithromycin CHEBI:4885 A thiocarboxamide that is pyridine-4-carbothioamide substituted by an ethyl group at position 2. A prodrug that undergoes metabolic activation by conversion to the corresponding S-oxide. ETH Eto ethionamide CHEBI:48901 An azole in which the five-membered heterocyclic aromatic skeleton contains a N atom and one S atom. thiazoles CHEBI:48924 erythromycin derivative CHEBI:48947 Antibiotic isolated from Streptomyces clavuligerus. It acts as a suicide inhibitor of bacterial beta-lactamase enzymes. CHEBI:3736 CHEBI:43442 clavulanic acid CHEBI:48975 substituted aniline CHEBI:49319 carbocyclic antibiotic CHEBI:49566 A semisynthetic penicillin antibiotic carrying a 3-(2-chlorophenyl)-5-methylisoxazole-4-carboxamido group at position 6. CHEBI:3765 CHEBI:49565 cloxacillin CHEBI:50047 A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups. organic amino compound CHEBI:50199 A quinolone that is 4-oxo-1,4-dihydroquinoline which is substituted at positions 1, 3, 6 and 7 by ethyl, carboxy, fluorine, and 4-methylpiperazin-1-yl groups, respectively. pefloxacin CHEBI:50695 Monocyclic, bacterially produced or semisynthetic beta-lactam antibiotic. It lacks the double ring construction of the traditional beta-lactam antibiotics and can be easily synthesized. monobactam CHEBI:50860 Any molecular entity that contains carbon. CHEBI:25700 CHEBI:33244 organic molecular entity CHEBI:50893 azaarene CHEBI:50896 azabicycloalkene CHEBI:50954 Compounds with structure RAs=AsR. diarsenes CHEBI:5098 A penicillin compound having a 6beta-[3-(2-chloro-6-fluorophenyl)-5-methyl-1,2-oxazole-4-carboxamido] side-chain. flucloxacillin CHEBI:50994 A compound formally derived from ammonia by replacing one hydrogen atom by an organyl group. primary amino compound CHEBI:50995 A compound formally derived from ammonia by replacing two hydrogen atoms by organyl groups. secondary amino compound CHEBI:50996 A compound formally derived from ammonia by replacing three hydrogen atoms by organyl groups. tertiary amino compound CHEBI:51026 A cyclic compound containing nine or more atoms as part of the cyclic system. macrocycle CHEBI:51069 organic halide salt CHEBI:51143 CHEBI:25556 CHEBI:7594 nitrogen molecular entity CHEBI:51151 An organic molecule that is electrically neutral carrying a positive and a negative charge in one of its major canonical descriptions. In most dipolar compounds the charges are delocalized; however the term is also applied to species where this is not the case. dipolar compound CHEBI:51454 Cyclopropane and its derivatives formed by substitution. cyclopropanes CHEBI:51689 An alpha,beta-unsaturated ketone of general formula R(1)R(2)C=CR(3)-C(=O)R(4) (R(4) =/= H) in which the C=O function is conjugated to a C=C double bond at the alpha,beta position. enone CHEBI:51721 A ketone of general formula R(1)R(2)C=CR(3)-C(=O)R(4) (R(4) =/= H) or R(1)C#C-C(=O)R(2) (R(2) =/= H) in which the ketonic C=O function is conjugated to an unsaturated C-C bond at the alpha,beta position. alpha,beta-unsaturated ketone CHEBI:51737 A carboxylic ester of general formula R(1)R(2)C=CR(3)-C(=O)OR(4) (R(4) =/= H) or R(1)C#C-C(=O)OR(2) (R(2) =/= H) in which the ester C=O function is conjugated to an unsaturated C-C bond at the alpha,beta position. alpha,beta-unsaturated carboxylic ester CHEBI:51750 A monocarboxylic amide of general formula R(1)R(2)C=CR(3)-C(=O)NR(4)R(5) or R(1)C#C-C(=O)NR(2)R(3) in which the amide C=O function is conjugated to an unsaturated C-C bond at the alpha,beta position. alpha,beta-unsaturated carboxylic acid amide CHEBI:51751 An alpha,beta-unsaturated carboxylic acid amide of general formula R(1)R(2)C=CR(3)-C(=O)NR(4)R(5) in which the amide C=O function is conjugated to a C=C double bond at the alpha,beta position. enamide CHEBI:51914 organic heterohexacyclic compound CHEBI:5195 A member of the class of oxazolidines that is 1,3-oxazolidin-2-one in which the hydrogen attached to the nitrogen is replaced by an N-{[(5-nitro-2-furyl)methylene]amino} group. It has antibacterial and antiprotozoal properties, and is used in the treatment of giardiasis and cholera. furazolidone CHEBI:51958 organic polycyclic compound CHEBI:51959 organic tricyclic compound CHEBI:52211 physiological role CHEBI:52395 A compound with the general formula R2C=O (R=/=H) where one or more of the R groups contains an oxy (-O-) group. oxyketone CHEBI:52396 An oxyketone with the general formula R2C(=O) (R=/=H) where one or more of the R groups contains an oxy (-O-) group and the oxy and carbonyl groups are bonded to the same carbon atom. alpha-oxyketone CHEBI:52429 propicillin CHEBI:5280 A monocarboxylic acid that is 4-oxo-1,4-dihydroquinoline-3-carboxylic acid which is substituted on the nitrogen by a cyclopropyl group and at positions 6, 7, and 8 by fluoro, 3-methylpiperazin-1-yl, and methoxy groups, respectively. Gatifloxacin is an antibiotic of the fourth-generation fluoroquinolone family, that like other members of that family, inhibits the bacterial topoisomerase type-II enzymes. CHEBI:101712 gatifloxacin CHEBI:52898 A cyclic macromolecule containing one or more nitrogen atoms in place of carbon either as the divalent group NH for the group CH2 or a single trivalent nitrogen atom for the group CH. azamacrocycle CHEBI:53665 Any organic heterotricyclic compound based on a skeleton comprised of an oxazine ring fused onto a quinoline system. oxazinoquinoline CHEBI:5530 gramicidin S CHEBI:553473 A parenteral third-generation cephalosporin, bearing a 2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino group at the 7beta-position. CHEBI:112105 CHEBI:3511 ceftizoxime CHEBI:55370 An imidazolidine containing one or more oxo groups. imidazolidinone CHEBI:55373 Oxazoles in which the N and O atoms are adjacent. CHEBI:46813 isoxazoles CHEBI:55374 An oxazolidine containing one or more oxo groups. oxazolidinone CHEBI:55429 Any member of the cephamycin sub-group of cephem antibiotics, differing from cephalosporins in possessing a methoxy group at the 7alpha-position of the cephem nucleus, and in being resistant to beta-lactamase. cephamycin CHEBI:5543 Grepafloxacin CHEBI:554446 A cephalosporin with acetoxymethyl and 2(pyridin-4-ylsulfanyl)acetamido substituents at positions 3 and 7, respectively, of the cephem skeleton. It is used (as its sodium salt) as an antibiotic, being effective against gram-negative and gram-positive organisms. CHEBI:3544 cephapirin CHEBI:55504 Any member of a group of synthetic antibiotics, similar to cephems but with carbon substituted for the sulfur; all possessing an acylated amine functionality at C-6 and (S,R) stereochemistry at C-6 and C-7. carbacephem CHEBI:55506 Any member of the oxacephem sub-group of cephem antibiotics, in which the thiaazabicyclo moiety of the cephalosporins is replaced by an oxaazabicyclo moiety, and where R3 is -H or -OCH3. oxacephem CHEBI:5653 A compound having the general formula RR'C(OH)OR'' (R'' =/= H). hemiacetal CHEBI:5686 A cyclic compound having as ring members atoms of at least two different elements. heterocyclic compound CHEBI:5880 Imipenem-cilastatin CHEBI:59062 Polymyxins are antibiotics with a general structure consisting of a cyclic peptide with a long hydrophobic tail. They disrupt the structure of the bacterial cell membrane by interacting with its phospholipids. Polymyxins are produced by the Gram-positive bacterium Bacillus polymyxa and are selectively toxic for Gram-negative bacteria. polymyxin CHEBI:59063 A polymyxin having a 6-methylheptanoyl group at the amino terminus. polymyxin B2 CHEBI:59064 A polymyxin having a (6R)-6-methyloctanoyl group at the amino terminus. colistin A CHEBI:59132 Any substance that stimulates an immune response in the body, such as through antibody production or by presentation to a T-cell receptor after binding to a major histocompability complex (MHC). Currently "K antigen" is a CHEBI_73772 chemical entity rather than a role. antigen K antigen CHEBI:59343 A broad spectrum, third-generation cephalosporin antibiotic with (Z)-2-(4-methyl-1,3-thiazol-5-yl)ethenyl and (2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetamido groups at positions 3 and 7, respectively, of the cephem skeleton. Generally administered as its orally absorbed pivaloyloxymethyl ester prodrug, it is used for the treatment of mild to moderate infections caused by susceptible strains of microorganisms in acute bacterial exacerbation of chronic bronchitis, community-acquired pneumonia, pharyngitis/tonsillitis, and uncomplicated skin and skin-structure infections. cefditoren CHEBI:59673 A polymyxin having a 6-methylheptanoyl group at the amino terminus. colistin B CHEBI:59769 An organooxygen compound having the structure RR'C(OR'')(OR''') (R'', R''' =/= H). Mixed acetals have R'' and R''' groups which differ. acetal CHEBI:59770 An acetal in the molecule of which the acetal carbon and one or both oxygen atoms thereon are members of a ring. cyclic acetal CHEBI:59772 A hemiacetal having the structure RR(1)C(OH)OR(2) (R, R(1), R(2) =/= H), derived from a ketone by formal addition of an alcohol to the carbonyl group. hemiketal CHEBI:59777 An acetal of formula R2C(OR)2 (R =/= H) derived from a ketone by replacement of the oxo group by two hydrocarbyloxy groups. The class name 'ketals', once abandoned by IUPAC, has been reinstated as a subclass of acetals. ketal CHEBI:59779 A ketal in the molecule of which the ketal carbon and one or both oxygen atoms thereon are members of a ring. cyclic ketal CHEBI:59780 A hemiacetal having the structure R2C(OH)OR (R =/= H), derived from a ketone by formal addition of an alcohol to the carbonyl group. The term 'cyclic hemiketals', once abandoned by IUPAC, has been reinstated as a subclass of hemiacetals. cyclic hemiketal CHEBI:59792 The sulfur analogue of 'acetal'. The term includes monothioacetals having the structure R2C(OR')(SR') (subclass monothioketals, R =/= H); and dithioacetals having the structure R2C(SR')2 (subclass dithioketals, R =/= H, R' =/= H). thioacetal CHEBI:59793 A thioacetal having the structure R2C(OR')(SR'). The term includes monothioketals, R =/= H, as a subclass. monothioacetal CHEBI:599928 A broad-spectrum oxacephem antibiotic in which the oxazine ring is substituted with a tetrazolylthiomethyl group and the azetidinone ring carries methoxy and 2-carboxy-2-(4-hydroxyphenyl)acetamido substituents. CHEBI:214506 CHEBI:44113 CHEBI:7006 moxalactam CHEBI:600103 A polypeptide comprising N-decanoyltryptophan, asparagine, aspartic acid, threonine, glycine, ornithine, aspartic acid, D-alanine, aspartic acid, glycine, D-serine, threo-3-methylglutamic acid and 3-anthraniloylalanine (also known as kynurinine) coupled in sequence and lactonised by condensation of the carboxylic acid group of the 3-anthraniloylalanine with the alcohol group of the threonine residue. CHEBI:29570 CHEBI:321017 CHEBI:478132 CHEBI:478255 daptomycin CHEBI:6030 A carbohydrazide obtained by formal condensation between pyridine-4-carboxylic acid and hydrazine. Inh isoniazid isoniazide CHEBI:60584 A commercially important azabicyclic antibiotic obtained from Streptomyces sapporonensis. It inhibits the Rho protein of E. coli. CHEBI:3091 bicozamycin CHEBI:60979 A glucoside in which the anomeric carbon of the glycosidic bond is in an alpha configuration alpha-glucoside CHEBI:6104 Kanamycin is a naturally occurring antibiotic complex from Streptomyces kanamyceticus that consists of several components: kanamycin A, the major component (also usually designated as kanamycin), and kanamycins B, C, D and X the minor components. Kan kanamycin CHEBI:61120 Any compound that has a nucleobase as a part. nucleobase-containing molecular entity CHEBI:61689 Any cyclitol having one or more alcoholic hydroxy groups replaced by substituted or unsubstituted amino groups. amino cyclitol CHEBI:61800 Any derivative of 2-deoxystreptamine. 2-deoxystreptamine derivative CHEBI:62732 An ester where the ester linkage is bonded directly to an aromatic system. aromatic ester CHEBI:62733 An amide in which the amide linkage is bonded directly to an aromatic system. aromatic amide CHEBI:62764 A family of nitrogen molecular entities which are highly reactive and derived from nitric oxide (.NO) and superoxide (O2.(-)) produced via the enzymatic activity of inducible nitric oxide synthase 2 (NOS2) and NADPH oxidase respectively. reactive nitrogen species CHEBI:63161 A carbohydrate derivative arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to an oxygen, carbon, nitrogen or sulfur atom of a separate entity. glycosyl compound CHEBI:63276 Name for a family of macrolide antibiotics with more than twenty members produced by the rare actinomycete Micromonospora griseorubida. mycinamicin CHEBI:63284 A mycinamicin composed of a 16-membered ring macrolactone core, an N,N-dimethylated deoxysugar desosamine and a 2,3-di-O-methylated 6-deoxysugar mycinose. mycinamicin IV CHEBI:63299 Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds. carbohydrate derivative CHEBI:63353 A carbohydrate derivative that is formally obtained from a disaccharide. disaccharide derivative CHEBI:63367 A carbohydrate derivative that is formally obtained from a monosaccharide. monosaccharide derivative CHEBI:63563 A carbohydrate derivative that is formally obtained from an oligosaccharide. oligosaccharide derivative CHEBI:63567 An oligosaccharide derivative that is formally obtained from a tetrasaccharide. tetrasaccharide derivative CHEBI:63598 An optically active form of ofloxacin having (S)-configuration; an inhibitor of bacterial topoisomerase IV and DNA gyrase Lfx CHEBI:6440 levofloxacin CHEBI:63607 An organofluorine compound that consists of 1,3-oxazolidin-2-one bearing an N-3-fluoro-4-(morpholin-4-yl)phenyl group as well as an acetamidomethyl group at position 5. A synthetic antibacterial agent that inhibits bacterial protein synthesis by binding to a site on 23S ribosomal RNA of the 50S subunit and prevents further formation of a functional 70S initiation complex. Lzd CHEBI:6477 linezolid CHEBI:63611 A quinolone that consists of 4-oxo-1,4-dihydroquinoline-3-carboxylic acid bearing a cyclopropyl substituent at position 1, a fluoro substitiuent at position 6, a (4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl group at position 7 and a methoxy substituent at position 8. A member of the fluoroquinolone class of antibacterial agents. MXF Mfx CHEBI:7007 moxifloxacin Mfx https://www.ncbi.nlm.nih.gov/books/NBK247415/bin/part3-m17.pdf CHEBI:63627 1H-imidazole substituted at C-1 by a (2-ethylsulfonyl)ethyl group, at C-2 by a methyl group and at C-5 by a nitro group. It is used as an antiprotozoal, antibacterial agent. CHEBI:32227 tinidazole CHEBI:63697 Any organic heterobicyclic compound containing ortho-fused pyrrolidine and piperidine rings. pyrrolidinopiperidine CHEBI:63845 A sulfonamide that is sulfanilamide acylated on the sulfonamide nitrogen. sulfacetamide CHEBI:63944 Any lactone in which the cyclic carboxylic ester group forms a part of a cyclic macromolecule. CHEBI:50333 macrocyclic lactone CHEBI:64509 A fused-ring beta-lactam system where the beta-lactam ring is fused to a 1,3-oxazolidine ring. oxapenam CHEBI:64709 Any organic molecular entity that is acidic and contains carbon in covalent linkage. organic acid CHEBI:6472 A carbohydrate-containing antibiotic produced by the actinomyces Streptomyces lincolnensis. lincomycin CHEBI:65212 A carbohydrate derivative that is any derivative of a polysaccharide. polysaccharide derivative CHEBI:6633 Mafenide CHEBI:6827 A penicillin that is 6-aminopenicillanic acid in which one of the amino hydrogens is replaced by a 2,6-dimethoxybenzoyl group. methicillin CHEBI:68452 Any monocyclic heteroarene consisting of a five-membered ring containing nitrogen. Azoles can also contain one or more other non-carbon atoms, such as nitrogen, sulfur or oxygen. azole CHEBI:68590 An 18-membered macrolide that is a fermentation product obtained from the Actinomycete Dactylosporangium aurantiacum. A narrow spectrum antibiotic used for treatment of Clostridium difficile-related infections. fidaxomicin CHEBI:6909 A member of the class of imidazoles substituted at C-1, -2 and -5 with 2-hydroxyethyl, nitro and methyl groups respectively. It has activity against anaerobic bacteria and protozoa, and has a radiosensitising effect on hypoxic tumour cells. It may be given by mouth in tablets, or as the benzoate in an oral suspension. The hydrochloride salt can be used in intravenous infusions. Metronidazole is a prodrug and is selective for anaerobic bacteria due to their ability to intracellularly reduce the nitro group of metronidazole to give nitroso-containing intermediates. These can covalently bind to DNA, disrupting its helical structure, inducing DNA strand breaks and inhibiting bacterial nucleic acid synthesis, ultimately resulting in bacterial cell death. CHEBI:39845 CHEBI:63636 metronidazole CHEBI:6919 A penicillin in which the substituent at position 6 of the penam ring is a (2R)-2-[3-(methanesulfonyl)-2-oxoimidazolidine-1-carboxamido]-2-phenylacetamido group. mezlocillin CHEBI:7025 An alpha,beta-unsaturated ester resulting from the formal condensation of the alcoholic hydroxy group of 9-hydroxynonanoic acid with the carboxy group of (2E)-4-[(2S)-tetrahydro-2H-pyran-2-yl]-3-methylbut-2-enoic acid in which the tetrahydropyranyl ring is substituted at positions 3 and 4 by hydroxy groups and at position 5 by a {(2S,3S)-3-[(2S,3S)-3-hydroxybutan-2-yl]oxiran-2-yl}methyl group. Originally isolated from the Gram-negative bacterium Pseudomonas fluorescens, it is used as a topical antibiotic for the treatment of Gram-positive bacterial infections. CHEBI:44038 mupirocin CHEBI:70718 A cephalosporin having [4-(1-methylpyridinium-4-yl)-1,3-thiazol-2-yl]sulfanyl and {(2Z)-2-(ethoxyimino)-2-[5-(phosphonoamino)-1,2,4-thiadiazol-3-yl]acetyl}amino side groups located at positions 3 and 7 respectively. The N-phospho prodrug of ceftaroline, a broad-spectrum antibiotic active against methicillin-resistant Staphylococcus aureus (MRSA). It is used for the treatment of adults with acute bacterial skin and skin structure infections. ceftaroline fosamil CHEBI:71229 A glycopeptide that is vancomycin substituted at position N-3'' by a 2-(decylamino)ethyl group and at position C-29 by a (phosphonomethyl)aminomethyl group. Used as its hydrochloride salt for treatment of adults with complicated skin and skin structure infections caused by bacteria. telavancin CHEBI:71415 An imidazolidine-2,4-dione that is hydantoin substituted at position 1 by a [(5-nitro-2-furyl)methylene]amino group. An antibiotic that damages bacterial DNA. CHEBI:7591 nitrofurantoin CHEBI:71960 Any member of a family of aminoglycosidic antibiotics produced by the bacterium Streptomyces lividus. Note that one member of this class, lividomycin A, is also known as lividomycin. lividomycins CHEBI:71961 A member of the class of lividomycins that is lividomycin B in which position 4 of the diamino-L-idopyranosyl moiety has been converted into its alpha-D-mannopyranoside. lividomycin A CHEBI:71962 A member of the class of lividomycins that is paromomycin in which the 2-amino-2-deoxyglucopyranosyl moiety is lacking the hydroxy group at position 3. lividomycin B CHEBI:72292 A quinoline-based antimycobacterial drug used (as its fumarate salt) for the treatment of pulmonary multi-drug resistant tuberculosis by inhibition of ATP synthase, an enzyme essential for the replication of the mycobacteria. Bdq bedaquiline CHEBI:72588 Any organic molecular entity derived from a natural product by partial chemical synthesis. semisynthetic derivative CHEBI:72695 Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. organic molecule CHEBI:73537 Any naphthyridine derivative that is a derivative of 1,8-naphthyridine. 1,8-naphthyridine derivative CHEBI:73539 Any organonitrogen heterocyclic compound that is a derivative of a naphthyridine. naphthyridine derivative CHEBI:73754 A carbohydrate derivative in which one or more of the oxygens or hydroxy groups of the parent carbohydrate is replaced by sulfur or -SR, where R can be hydrogen or any group. thiosugar CHEBI:73772 Any capsular polysaccharide derivative which is carried on the surface of a bacterial capsule or formed on the outer portion of a cell wall and masks somatic O antigens. Damion Dooley's note: 'K antigen' can't be a subclass of antigen as chemical entity is disjoint from role. Snomed: Concept 260824002 K antigen CHEBI:74159 A zwitterion resulting from the transfer of a proton from the ring nitrogen to the primary amino group of D-cycloserine. The major species at pH 7.3. D-cycloserine zwitterion CHEBI:7447 A penicillin in which the substituent at position 6 of the penam ring is a (2-ethoxy-1-naphthoyl)amino group. CHEBI:44256 nafcillin CHEBI:7508 A tetracyclic antibacterial agent derived from neomycin, being a glycoside ester of neamine and neobiosamine B. CHEBI:44577 framycetin CHEBI:75246 A semisynthetic member of the class of rifamycins and non-systemic gastrointestinal site-specific broad spectrum antibiotic. Used in the treatment of traveller's diarrhoea, hepatic encephalopathy and irritable bowel syndrome. rifaximin CHEBI:75606 A carboxamide that is a hydroxamic acid in which the hydrogen of the hydroxy group is replaced by an organyl group. hydroxamic acid ester CHEBI:75769 Any member of the group of eight water-soluble vitamins originally thought to be a single compound (vitamin B) that play important roles in cell metabolism. The group comprises of vitamin B1, B2, B3, B5, B6, B7, B9, and B12 (Around 20 other compounds were once thought to be B vitamins but are no longer classified as such). B vitamin CHEBI:76892 An organic anion obtained by deprotonation of the carboxy, sulfo and one of the hydroxy groups as well as protonation of the amino group of A47934; major species at pH 7.3. A47934(2-) CHEBI:7731 An oxazinoquinolone carrying carboxy, fluoro, methyl and 4-methylpiperazino substituents. A synthetic fluoroquinolone antibacterial agent, it inhibits the supercoiling activity of bacterial DNA gyrase, halting DNA replication. Ofx CHEBI:100146 ofloxacin CHEBI:78616 Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation. carbohydrates and carbohydrate derivatives CHEBI:78840 Any organic molecular entity that contains at least one C=C bond. olefinic compound CHEBI:79020 A monocarboxylic acid in which the carbon of the carboxy group is directly attached to a C=C or C#C bond. alpha,beta-unsaturated monocarboxylic acid CHEBI:7934 An amino cyclitol glycoside that is the 1-O-(2-amino-2-deoxy-alpha-D-glucopyranoside) and the 3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranoside of 4,6-diamino-2,3-dihydroxycyclohexane (the 1R,2R,3S,4R,6S diastereoisomer). It is obtained from various Streptomyces species. A broad-spectrum antibiotic, it is used (generally as the sulfate salt) for the treatment of acute and chronic intestinal protozoal infections, but is not effective for extraintestinal protozoal infections. It is also used as a therapeutic against visceral leishmaniasis. CHEBI:44703 paromomycin CHEBI:79389 Any inorganic anion with a valency of one. monovalent inorganic anion CHEBI:80016 Chalcomycin CHEBI:8232 A penicillin in which the substituent at position 6 of the penam ring is a 2-[(4-ethyl-2,3-dioxopiperazin-1-yl)carboxamido]-2-phenylacetamido group. CHEBI:472443 CHEBI:475140 CHEBI:505944 piperacillin CHEBI:8269 Pleuromutilin CHEBI:82699 A semisynthetic glycopeptide used (as its bisphosphate salt) for the treatment of acute bacterial skin and skin structure infections caused or suspected to be caused by susceptible isolates of designated Gram-positive microorganisms including MRSA. CHEBI:29553 oritavancin CHEBI:8309 A polymyxin having a (6R)-6-methyloctanoyl group at the amino terminus. polymyxin B1 CHEBI:83403 Any member of the class of chlorobenzenes containing a mono- or poly-substituted benzene ring in which only one substituent is chlorine. monochlorobenzenes CHEBI:83628 A carboxamide obtained by the formal condensation of the carboxy group of any carboxylic acid with ammonia. N-acylammonia CHEBI:83811 Any derivative of a proteinogenic amino acid resulting from reaction at an amino group, carboxy group, or a side-chain functional group, or from the replacement of any hydrogen by a heteroatom. proteinogenic amino acid derivative CHEBI:83821 Any derivative of an amino acid resulting from reaction at an amino group, carboxy group, side-chain functional group, or from the replacement of any hydrogen by a heteroatom. The definition normally excludes peptides containing amino acid residues. CHEBI:25359 amino acid derivative CHEBI:8418 Pristinamycin IB CHEBI:84186 A proteinogenic amino acid derivative resulting from reaction of L-proline at the amino group or the carboxy group, or from the replacement of any hydrogen of L-proline by a heteroatom. L-proline derivative CHEBI:8419 pristinamycin IC CHEBI:85129 A heterodetic cyclic peptide that is produced by species of Amycolatopsis and Nocardia. ristocetin CHEBI:85260 A macrolide antibiotic produced by various Streptomyces species that is used to treat toxoplasmosis and various other infections of soft tissues. CHEBI:45589 CHEBI:9236 spiramycin I CHEBI:86324 An organonitrogen heterocyclic antibiotic whose structure contains a quinolone or quinolone-related skeleton. quinolone antibiotic CHEBI:86478 Heteroorganic entities that are microbial metabolites (or compounds derived from them) which have significant antifungal properties. antibiotic antifungal agent CHEBI:87113 Any antibiotic antifungal agent used to treat fungal infections in humans or animals. antibiotic antifungal drug CHEBI:87114 Any antibiotic antifungal agent that has been used as a fungicide. antibiotic fungicide CHEBI:87211 An organonitrogen heterocyclic antibiotic containing a quinolone (or quinolone-like) moiety and which have a fluorine atom attached to the central ring system. fluoroquinolone antibiotic CHEBI:87228 A class of sulfonamides whose members generally have bacteriostatic antibiotic properties. sulfonamide antibiotic CHEBI:87230 A member of the class of furans in which the furan ring is substituted by a nitro group and which also has significant antibiotic properties. nitrofuran antibiotic CHEBI:8732 Quinupristin CHEBI:8733 Quinupristin-dalfopristin CHEBI:88187 Any penicillin which causes the onset of an allergic reaction. penicillin allergen CHEBI:88225 Any beta-lactam antibiotic which causes the onset of an allergic reaction. beta-lactam antibiotic allergen CHEBI:9016 arsphenamine CHEBI:90852 A mixed diacylamine resulting from the formal condensation of the nitrogen of a carboxamide with a sulphonic acid. N-sulfonylcarboxamide CHEBI:9212 sparfloxacin CHEBI:9215 A pyranobenzodioxin and antibiotic that is active against gram-negative bacteria and used (as its dihydrochloride pentahydrate) to treat gonorrhea. It is produced by the bacterium Streptomyces spectabilis. CHEBI:45551 spectinomycin CHEBI:9321 sulbactam CHEBI:9328 A sulfonamide consisting of pyrimidine with a 4-aminobenzenesulfonamido group at the 2-position. sulfadiazine CHEBI:9329 A sulfonamide consisting of pyrimidine having methoxy substituents at the 5- and 6-positions and a 4-aminobenzenesulfonamido group at the 4-position. In combination with the antiprotozoal pyrimethamine (CHEBI:8673) it is used as an antimalarial. sulfadoxine CHEBI:9331 A sulfonamide consisting of a 1,3,4-thiadiazole nucleus with a methyl substituent at C-5 and a 4-aminobenzenesulfonamido group at C-2. sulfamethizole CHEBI:9332 An isoxazole (1,2-oxazole) compound having a methyl substituent at the 5-position and a 4-aminobenzenesulfonamido group at the 3-position. CHEBI:102247 sulfamethoxazole CHEBI:9421 A member of the class of penicillanic acids that is sulbactam in which one of the exocyclic methyl hydrogens is replaced by a 1,2,3-triazol-1-yl group; used (in the form of its sodium salt) in combination with ceftolozane sulfate for treatment of complicated intra-abdominal infections and complicated urinary tract infections. CHEBI:45973 tazobactam CHEBI:9587 A penicillin compound having a 6beta-[(2R)-2-carboxy-2-thiophen-3-ylacetyl]amino side-group. ticarcillin CHEBI:9997 A macrolide that is (together with pristinamycin IA) a component of pristinamycin, an oral streptogramin antibiotic produced by Streptomyces pristinaespiralis. Pristinamycin exhibits bactericidal activity against Gram positive organisms including methicillin-resistant Staphylococcus aureus. CHEBI:46395 pristinamycin IIA CHMO:0000993 An independent material continuant that is self-connected and retains its identity over time. portion of material CHMO:0000999 A method that results in the separation of two or more components according to some property. FIX:0000002 partition separation method CHMO:0001019 A separation method where colloidal particles move at different speeds according to their electrophoretic mobilities in a separation medium, across which an electric field is applied. FIX:0000097 sep:00140 cataphoresis electrophoretic analysis electrophoresis CHMO:0001021 A separation method where colloidal particles move at different speeds according to their electrophoretic mobilities in a separation medium consisting of gel, across which an electric field is applied. sep:00150 gel electrophoresis CHMO:0001030 An electrophoresis method where the separation medium contains a reticulated system, for example an entangled polymer network, that further separates the analytes according to their size and shape. sieving electrophoresis CHMO:0002315 A separation method where colloidal particles move at different speeds according to their electrophoretic mobilities in a separation medium, across which a pulsed electric field is applied (a field in which the voltage changes direction). pulsed-field electrophoresis CHMO:0002316 A separation method where colloidal particles move at different speeds according to their electrophoretic mobilities in a separation medium consisting of gel, across which a pulsed electric field is applied (one in which the voltage direction is periodically switched among three directions; one that runs through the central axis of the gel and two that run at an angle of 120° either side). PFGE pulsed field gel electrophoresis pulsed-field gel electrophoresis CHMO:0002743 specimen extraction matrix Those components of a sample that are not measured by an experiment. "This observable is important where process of capturing sample can affect dna extraction." matrix CIDO:0000019 A COVID-19 nucleic acid diagnostic assay that uses RT-PCR Oliver He, Asiyah Yu Lin SARS COV-2 RT-PCR https://www.fda.gov/medical-devices/emergency-situations-medical-devices/emergency-use-authorizations#covid19ivd https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7170415/ COVID-19 RT-PCR assay CIDO:0000027 A COVID-19 diagnostic process by viral genome sequencing and identification of the SARS-CoV-2 based on the genome sequence. Oliver He, Asiyah Yu Lin, Hong Yu https://www.ncbi.nlm.nih.gov/pubmed/32245835 COVID-19 diagnostic process by viral genome sequencing CIDO:0000258 An assay that is used for COVID-19 diagnosis Oliver He, Hong Yu https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7683783/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7780074/ COVID-19 diagnostic assay CIDO:0000259 A COVID-19 diagnosti ssay that uses a nucleic acid sample Oliver He, Hong Yu COVID-19 nucleic acid diagnostic assay CIDO:0000423 A diagnostic process for detecting coronavirus disease from a patient Oliver He, Hong Yu coronavirus diagnostic process coronavirus disease diagnostic process coronavirus disease diagnostic process CIDO:0000424 A diagnostic process for detecting coronavirus from a patient Oliver He, Hong Yu COVID-19 diagnostic process CLO:0000001 cell line cell A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures. cell line cell CLO:0000019 immortal cell line cell A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. Yongqun He, Matthew Brush, Allen Xiang, Asiyah Yu Lin, Sirarat Sarntivijai, James Malone, Jie Zheng, Tomasz Adamusiak continuous cell line cell permanent cell line cell immortal cell line cell CLO:0000031 cell line A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). MB, SS, JZ, MAH, BP, CS, YH The term 'line' is used when a culture has undergone an intentional experimental process to establish a more uniform and stable population of cells (see 'establishing cell line'). This will require one or more passages, but may involve additional selection processes. Through such passaging and/or selection processes, the resulting 'line' attains some level of genetic stability and compositional homogeneity which is typically absent in primary cultures. Because of their relative homogeneity, ‘lines’ are capable of being characterized and stably propagated over a period of time. A new *type* of cell line can be established not only through the passaging/selection of a primary culture, but also through experimental modifications of existing lines (e.g. immortalization, stable genetic modifications, drug selection for a resistant subset, etc.). The definition provided here establishes the 'scale' of cell populations that qualify as cell lines - specifically those with a shared propagation history in culture. In this way, the 'cell line' class demarcates populations that represent what researchers actually use in the practice of science - e.g. as inputs to culturing, experimentation, and sharing. The definition is such that cell lines will exhibit important attributes. For example, they will have a relatively homogenous cell type composition as they have experienced similar selective pressures due to their continuous co-propagation. In addition, these populations can also be characterized by a passage number, again owing to their common passaging history.  As defined here, 'cell line' can refer to a population of cells in active culture, applied experimentally, or stored in a quiescent state for future use. cell line CLO:0000220 An immortal cell line cell that derives from kidney. Yue Liu, Yongqun He immortal kidney-derived cell line cell CLO:0000714 An immortal kidney-derived cell line cell that derives from rhesus macaque. Yue Liu, Yongqun He immortal rhesus macaque kidney-derived cell line cell CLO:0007330 LLC-MK subscript(2) LLC-MK subscript(2) cell CL:0000000 cell A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FMA:68646 GO:0005623 KUPO:0000002 VHOG:0001533 WBbt:0004017 XAO:0003012 The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell cell type CL:0000010 cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture. cultured cell CL:0000578 experimentally modified cell in vitro A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12 experimentally modified cell in vitro CL:0001034 A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. 'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells. cell in vitro CVDO:0000597 A disease existing at birth, or developping during the first month after birth. congenital disease DOID:0040001 A crustacean allergy that has_allergic_trigger shrimp. shrimp allergy DOID:0040083 A bacterial pneumonia has_material_basis_in Chlamydia pneumoniae. Chlamydia pneumonia DOID:0040084 A bacterial pneumonia has_material_basis_in Streptococcus pneumoniae. Streptococcus pneumonia DOID:0040085 A bacterial infectious disease has_material_basis_in Bacteria. bacterial sepsis DOID:0050004 A gonococcal seminal vesiculitis that is characterized by back pain, perineal pain, pain with ejaculation, hematospermia and voiding symptoms resulting from inflammation located_in the seminal vesicles caused by Neisseria gonorrhoeae infection. seminal vesicle acute gonorrhea DOID:0050025 An ehrlichiosis that results in infection located in granular leukocyte, has_material_basis_in Anaplasma phagocytophilum, which is transmitted by lone star tick (Amblyomma americanum). The infection has symptom headache, has symptom muscle aches, has symptom fatigue, has symptom fever and has symptom rash. human granulocytic anaplasmosis DOID:0050026 An ehrlichiosis that results in infection located in monocyte or located in macrophage, has_material_basis_in Ehrlichia chaffeensis, which is transmitted by black-legged tick (Ixodes scapularis), transmitted by western black-legged tick (Ixodes pacificus) or transmitted by castor bean tick (Ixodes ricinus). The infection has symptom headache, has symptom muscle aches, has symptom fatigue, has symptom fever and has symptom rash. human monocytic ehrlichiosis DOID:0050035 A spotted fever that has_material_basis_in Rickettsia africae, which is transmitted_by ticks (Amblyomma hebraeum and Amblyomma variegatum). The infection has_symptom fever, has_symptom eschar and has_symptom maculopapular rash. African tick-bite fever DOID:0050041 A spotted fever that has_material_basis_in Rickettsia conorii subsp caspia, which is transmitted_by ticks (Rhipicephalus pumilio and Rhipicephalus sanguineus). The infection has_symptom fever, has_symptom eschar (usually single), has_symptom regional adenopathy, has_symptom maculopapular rash on extremities. Astrakhan spotted fever DOID:0050042 A spotted fever that has_material_basis_in Rickettsia conorii subsp indica, which is transmitted_by ticks (Rhipicephalus sanguineus). The infection has_symptom fever, has_symptom eschar, has_symptom regional adenopathy, and has_symptom maculopapular rash on extremities. Indian tick typhus DOID:0050043 A spotted fever that has_material_basis_in Rickettsia conorii subsp israelensis, which is transmitted_by ticks (Rhipicephalus sanguineus). The infection has_symptom fever, has_symptom eschar, has_symptom regional adenopathy, and has_symptom maculopapular rash on extremities. Israeli tick typhus DOID:0050046 A spotted fever that has_material_basis_in Rickettsia heilongjiangensis, which is transmitted_by ticks (Haemaphysalis concinna). The infection has_symptom fever, has_symptom eschar, has_symptom maculopapular rash, and has_symptom regional adenopathy. Far Eastern spotted fever DOID:0050047 A spotted fever that has_material_basis_in Rickettsia honei, which is transmitted_by cayenne ticks (Amblyomma cajennense). The infection has_symptom mild spotted fever, has_symptom eschar and has_symptom adenopathy. Flinders Island spotted fever DOID:0050050 A spotted fever that has_material_basis_in Rickettsia japonica, which is transmitted_by ticks (Dermacentor taiwanensis and Haemaphysalis flava). The infection has_symptom fever, has_symptom eschars, has_symptom regional adenopathy, and has_symptom rash on extremities. Japanese spotted fever DOID:0050051 A spotted fever that has_material_basis_in Rickettsia parkeri, which is transmitted_by Gulf Coast tick (Amblyomma maculatum). The infection has_symptom fever, has_symptom headache, has_symptom eschar, and has_symptom rash. Rickettsia parkeri spotted fever DOID:0050052 A spotted fever that has_material_basis_in Rickettsia rickettsii, which is transmitted_by ticks (Dermacentor variabilis and Dermacentor andersoni). The infection has_symptom fever, has_symptom headache, has_symptom abdominal pain, and has_symptom maculopapular rash progressing into papular or petechial rash. Rocky Mountain spotted fever DOID:0050059 A gastrointestinal anthrax that results in infection located in mucosa of oropharynx, has_material_basis_in Bacillus anthracis, which is transmitted by ingestion of anthrax-infected meat. The infection has symptom lesions, has symptom vomiting of blood, has symptom severe diarrhea, has symptom loss of appetite. oropharyngeal anthrax DOID:0050061 A primary bacterial infectious disease that results_in infection located_in skin, has_material_basis_in Erysipelothrix rhusiopathiae, which is transmitted_by contact with infected animals. The infection has_symptom redness of skin, has_symptom tenderness of skin and has_symptom warmth of skin. erysipeloid DOID:0050117 A disease that is the consequence of the presence of pathogenic microbial agents, including pathogenic viruses, pathogenic bacteria, fungi, protozoa, multicellular parasites, and aberrant proteins known as prions. disease by infectious agent DOID:0050141 A botulism that involves intoxication caused by botulinum neurotoxins (BoNTA, B, E and F) in adults, has_material_basis_in Clostridium botulinum A, has_material_basis_in Clostridium botulinum B, has_material_basis_in Clostridium botulinum E and has_material_basis_in Clostridium botulinum F, which are transmitted by ingestion of bacterial spores, which then grow in the intestine and release toxins. intestinal botulism DOID:0050150 A legionellosis that involves a milder respiratory illness without pneumonia. Symptoms include fever, headache and muscle aches which last for 2 to 5 days. Pontiac fever DOID:0050152 A bacterial pneumonia which is an acute pulmonary inflammatory response that develops after the inhalation of colonized oropharyngeal material containing bacteria. It is seen in individuals with dysphagia and gastric dysmotility. The disease has_symptom tachypnea and has_symptom cough. aspiration pneumonia DOID:0050155 A nervous system disease which is located in a part of the nervous system responsible for processing sensory information that consists of sensory receptors, neural pathways, and parts of the brain involved in sensory perception. Commonly recognized sensory systems are those for vision, hearing, somatic sensation (touch), taste and olfaction (smell). sensory system disease DOID:0050160 An anthrax disease that results in infection located in lung lymph nodes brought on by breathing in the spores of the bacteria Bacillus anthracis. The first symptoms of inhalation anthrax are like cold or flu symptoms and can include a sore throat, mild fever and muscle aches. Later symptoms include cough, chest discomfort, shortness of breath, tiredness and muscle aches. inhalation anthrax DOID:0050161 A respiratory system disease which involves the lower respiratory tract. lower respiratory tract disease DOID:0050166 An urogenital tuberculosis that results_in formation of granulomas located_in fallopian tube. tuberculous salpingitis DOID:0050338 A bacterial infectious disease that results_in infection by bacteria as a result of their presence or activity within the normal, healthy host, and their intrinsic virulence is, in part, a necessary consequence of their need to reproduce and spread. primary bacterial infectious disease DOID:0050339 A bacterial infectious disease that results_in infection by bacteria which are part of the normal human flora when one or more of the defense mechanisms designed to restrict them from the usually sterile internal tissues are breached by accident, by intent (surgery), or by an underlying metabolic or an infectious disorder. commensal bacterial infectious disease DOID:0050340 A bacterial infectious disease that results_in infection by bacteria in individuals whose host defense mechanisms have been compromised. opportunistic bacterial infectious disease DOID:0050352 A botulism that involves intoxication caused by botulinum neurotoxins (BoNTA, B, E and F), which are transmitted by ingestion of food contaminated with preformed toxins, has_material_basis_in Clostridium botulinum A, has_material_basis_in Clostridium botulinum B, has_material_basis_in Clostridium botulinum E and has_material_basis_in Clostridium botulinum F. The infection has symptom blurred vision, has symptom diplopia, has symptom dysarthria, has symptom dysphonia, has symptom dysphagia and has symptom descending muscle paralysis. foodborne botulism DOID:0050353 A botulism that involves intoxication caused by botulinum neurotoxins (BoNTA, B, E and F), has_material_basis_in Clostridium botulinum A, has_material_basis_in Clostridium botulinum B, has_material_basis_in Clostridium botulinum E and has_material_basis_in Clostridium botulinum F, which are transmitted by contact of spores with the open wounds, which then reproduce in an anaerobic environment to produce toxins. wound botulism DOID:0050354 A botulism that involves intoxication caused by botulinum neurotoxins (BoNTA or B) in infants, has_material_basis_in Clostridium botulinum A or has_material_basis_in Clostridium botulinum B, which are transmitted_by ingestion of bacterial spores, which then grow in the intestine and release toxins. The infection has_symptom constipation, has_symptom lethargy, has_symptom difficulty feeding, has_symptom swallowing, has_symptom ptosis, has_symptom loss of head control, and has_symptom muscle weakness. infant botulism DOID:0050382 A tularemia that results_in swelling of regional lymph glands. glandular tularemia DOID:0050383 A tularemia that results_in bacteremia and has_symptom fever, has_symptom chills, has_symptom myalgia, has_symptom malaise, and has_symptom weight loss. typhoidal tularemia DOID:0050398 A bartonellosis that results_in infection located_in endothelial cells or located_in red blood cells, has_material_basis_in Bartonella bacilliformis, which is transmitted_by sandflies of genus Lutzomyia. The infection has acute and chronic phases. The acute phase is characterized by severe hemolytic anemia and transient immunosuppression. The chronic phase is characterized by verruga peruana lesions which may ulcerate and bleed. Carrion's disease DOID:0050456 A primary bacterial infectious disease that results_in infection located_in skin or located_in subcutaneous tissue, has_material_basis_in Mycobacterium ulcerans, which could be transmitted_by insects. The bacterium produces a toxin, named mycolactone, which causes subcutaneous fat necrosis and inhibits an immune response. The infection has_symptom nodule, which is a painless, mobile swelling in the skin. Buruli ulcer disease DOID:0050480 A typhus that has_material_basis _in Rickettsia prowazekii, which is transmitted by human body louse (Pediculus humanus corporis). The infection has_symptom high fever, has_symptom cough, has_symptom rash, has_symptom severe muscle pain, has_symptom chills, has_symptom falling blood pressure, has_symptom stupor, has_symptom sensitivity to light, and has_symptom delirium. epidemic typhus DOID:0050481 A typhus that has_material_basis_in Rickettsia typhi or has_material_basis_in Rickettsia felis, which are transmitted by fleas (Xenopsylla cheopis). The infection has symptom headache, has symptom fever, has symptom chills, has symptom myalgia, has symptom nausea, has symptom vomiting, has symptom cough and has symptom rash. endemic typhus DOID:0050484 A spotted fever that has_material_basis_in Rickettsia helvetica, which is transmitted_by ticks (Ixodes sp). The infection has_symptom fever, has_symptom headache, has_symptom myalgia. aneruptive fever DOID:0050485 A primary bacterial infectious disease that results_in infection, has_material_basis_in Neorickettsia sennetsu, which is transmitted_by ingestion of raw or under-cooked gray mullet fish infected with the trematodes. The infection has_symptom fever, has_symptom malaise, has_symptom anorexia, has_symptom lymphadenopathy, has_symptom hepatosplenomegaly, has_symptom fatigue, has_symptom chills, has_symptom headache, has_symptom backache and has_symptom myalgia. sennetsu fever DOID:0050486 A skin disease that is characterized by a rash that results from a variety of causes including bacteria, viruses, toxins, drugs and autoimmune disorders. exanthem DOID:0050487 An exanthem that is characterized by a diffuse, reddened, blanchable, finely papular, sandpaper like rash due to infection by group A streptococcus and the production of an erythrogenic toxin. bacterial exanthem DOID:0050488 A congenital syphilis that is manifested during the first 3 months of life. The infection has_symptom skin lesions, has_symptom lymphadenopathy, has_symptom hepatosplenomegaly, has_symptom failure to thrive, has_symptom blood-stained nasal discharge, has_symptom perioral fissures, has_symptom meningitis, has_symptom choroiditis, has_symptom hydrocephalus, has_symptom seizures, has_symptom intellectual disability, has_symptom osteochondritis, and has_symptom pseudoparalysis. early congenital syphilis DOID:0050490 A tertiary neurosyphilis that results when chronic meningoencephalitis causes destruction of cortical parenchyma. The infection has_symptom irritability, has_symptom difficulty concentrating, has_symptom deterioration of memory, has_symptom defective judgment, has_symptom headaches, has_symptom insomnia, has_symptom fatigue, and has_symptom lethargy. parenchymatous neurosyphilis DOID:0050491 A tertiary neurosyphilis that results in inflammation located_in arteries of the brain or located_in arteries of spinal cord. The infection has_symptom headache, has_symptom neck stiffness, has_symptom dizziness, has_symptom behavioral abnormalities, has _symptom poor concentration, has_symptom memory loss, has _symptom lassitude, has_symptom insomnia, has_symptom blurred vision, has_symptom weakness and wasting of shoulder-girdle and arm muscles, has_symptom slowly progressive leg weakness with urinary or fecal incontinence or both, and has_symptom paralysis of the legs due to thrombosis of spinal arteries. meningovascular neurosyphilis DOID:0050584 A tertiary syphilis that is characterized by granulomatous lesions, called gummas, which are characterized by a center of necrotic tissue with a rubbery texture. They form in the liver, bones, and testes but may affect any organ. gummatous syphilis DOID:0050589 An intestinal disease characterized by inflammation located in all parts of digestive tract. inflammatory bowel disease DOID:0050598 A tuberculosis that occurs at body sites other than the lung. extrapulmonary tuberculosis DOID:0050599 An extrapulmonary tuberculosis that is located_in gastrointestinal tract, located_in peritoneum, located_in omentum, located_in mesentery, located_in liver, located_in spleen or located_in pancreas. abdominal tuberculosis DOID:0050686 A cancer that is classified based on the organ it starts in. organ system cancer DOID:0050700 A heart disease and a myopathy that is characterized by deterioration of the function of the heart muscle. cardiomyopathy DOID:0050829 A cardiovascular system disease that is located_in the fibrous sac surrounding the heart. pericardium disease DOID:0060031 An autoimmune disease that is the abnormal functioning of the immune system that causes your immune system to produce antibodies or T cells against cells and/or tissues in the gastrointestinal tract. autoimmune disease of gastrointestinal tract DOID:0060057 A food allergy that develops from an immune reaction to eating gluten, a protein found in wheat, barley, rye and triticale and that is characterized by stomach cramping, diarrhea and gastrointestinal upset and is unrelated to the gluten intolerance. gluten allergy DOID:0060118 A disease of anatomical entity that is located_in the thoracic cavity. thoracic disease DOID:0060180 An inflammatory bowel disease that involves inflammation located_in colon. colitis DOID:0060345 A bartonellosis that has_material_basis_in Bartonella henselae or has_material_basis_in Bartonella quintana. The disease is characterized by the proliferation of blood vessels, resulting in them forming tumour-like masses in the skin and other organs. bacillary angiomatosis DOID:0060492 An egg allergy triggered by Gallus gallus eggs. chicken egg allergy DOID:0060495 A food allergy triggered by Crustacea or Mollusca. shellfish allergy DOID:0060502 An allergic disease that is located_in the gastrointestinal tract. gastrointestinal allergy DOID:0060503 A food allergy triggered by a plant fruit product. fruit allergy DOID:0060504 A fruit allergy triggered by Malus domestica plant fruit food product. apple allergy DOID:0060505 A fruit allergy triggered by Prunus armeniaca plant fruit food product. apricot allergy DOID:0060506 A fruit allergy triggered by Prunus avium plant fruit food product. cherry allergy DOID:0060507 A fruit allergy triggered by Ziziphus mauritiana plant fruit food product. Indian plum allergy DOID:0060508 A fruit allergy triggered by Citrus sinensis plant fruit food product. orange allergy DOID:0060509 A fruit allergy triggered by Cucumis melo plant fruit food product. melon allergy DOID:0060510 A fruit allergy triggered by Prunus persica plant fruit food product. peach allergy DOID:0060511 A fruit allergy triggered by Prunus domestica plant fruit food product. plum allergy DOID:0060512 A fruit allergy triggered by Solanum lycopersicum plant fruit food product. tomato allergy DOID:0060513 A food allergy triggered by fish. fish allergy DOID:0060514 A fish allergy triggered by Gadus morhua. Atlantic cod allergy DOID:0060515 A fish allergy triggered by Salmo salar. Atlantic salmon allergy DOID:0060516 A fish allergy triggered by Cyprinus carpio. carp allergy DOID:0060517 A fish allergy triggered by Danio rerio. zebrafish allergy DOID:0060518 A fish allergy triggered by Oncorhynchus mykiss. rainbow trout allergy DOID:0060521 A milk allergy triggered by Bos taurus milk. cow milk allergy DOID:0060522 A milk allergy triggered by Capra hircus milk. goat milk allergy DOID:0060523 A shellfish allergy triggered by Mollusca. mollusc allergy DOID:0060524 A shellfish allergy triggered by Crustacea. crustacean allergy DOID:0060525 A crustacean allergy triggered by Farfantepenaeus aztecus. brown shrimp allergy DOID:0060526 A crustacean allergy triggered by Scylla paramamosain. crab allergy DOID:0060527 A crustacean allergy triggered by Fenneropenaeus indicus. Indian prawn allergy DOID:0060528 A crustacean allergy triggered by Penaeus monodon. tiger prawn allergy DOID:0060529 A crustacean allergy triggered by Litopenaeus vannamei. white shrimp allergy DOID:0060530 A mollusc allergy triggered by snails. snail allergy DOID:0060531 A snail allergy triggered by the horned turban snail. horned turban snail allergy DOID:0060570 A tuberculosis located in the heart. cardiac tuberculosis DOID:0060859 A primary bacterial infectious disease caused by the bacteria of the genus Salmonella. It has sypmtoms diarrhea, fever, vomiting, and abdominal cramps 12 to 72 hours after infection. In most cases, the illness lasts four to seven days, and most people recover without treatment. salmonellosis DOID:0060904 A fruit allergy triggered by Fabaceae (legume) plant fruit or seed food product. legume allergy DOID:0070334 A food allergy triggered by a vegetable food product. vegetable allergy DOID:0070335 A vegetable allergy triggered by celery (Apium graveolens). celery allergy DOID:0070344 A tuberculosis that is located_in some eye, has_material_basis_in Mycobacterium tuberculosis, and has_sypmtom inflamed eyes. ocular tuberculosis DOID:0080000 A musculoskeletal system disease that affects the muscles. muscular disease DOID:0080001 A connective tissue disease that affects the structure or development of bone or causes an impairment of normal bone function. bone disease DOID:0080015 A disease that has_material_basis_in a genetic abnormality, error with embryonic development, infection or compromised intrauterine environment. physical disorder DOID:0080176 A bacterial meningitis that has_material_basis_in Neisseria meningitidis infection. meningococcal meningitis DOID:0080179 A bacterial meningitis that has_material_basis_in Haemophilus influenzae infection. haemophilus meningitis DOID:0080373 A male reproductive system disease that is located_in the epididymis. epididymis disease DOID:0080599 A viral infectious disease that has_material_basis_in Coronavirus. Coronavirus infectious disease DOID:0080784 An urinary system disease that is characterized by an infection in any part of the urinary system, including the kidneys, ureters, bladder or urethra. urinary tract infection DOID:0080995 A tuberculosis that is characterized by cerebral edema sometimes with features similar to acute disseminated encephalomyelitis (ADEM) and may manifest with a variety of symptoms ranging from focal neurological deficits to convulsions and decreased conscious state. tuberculous encephalopathy DOID:0081005 A vegetable allergy triggered by parsley (Petroselinum). parsley allergy DOID:0081006 A food allergy triggered by dill (Anethum graveolens). dill allergy DOID:10027 A tertiary neurosyphilis that results in slow degeneration of the nerve cells and nerve fibers that carry sensory information to the brain. The infection has symptom intense, stabbing pain in the back and legs that recurs irregularly, has symptom gait ataxia, has symptom hyperesthesia, has symptom paresthesia, has symptom loss of bladder sensation leading to urine retention, has symptom erectile dysfunction. tabes dorsalis DOID:10035 A tertiary neurosyphilis that results_in mild meningitis. asymptomatic neurosyphilis DOID:10039 A congenital syphilis that occurs in children at or greater than two years of age who acquired the infection trans-placentally. The infection has_symptom gummatous ulcers, has_symptom periosteal lesions, has_symptom paresis, has_symptom tabes, has_symptom optic atrophy, has_symptom interstitial keratitis, has_symptom sensorineural deafness, and has_symptom dental deformities. late congenital syphilis DOID:10073 A bacterial meningitis that is characterized by inflammation of the tissues covering the brain and spinal cord. syphilitic meningitis DOID:1022 A primary bacterial infectious disease that results_in infection located_in skin, has_material_basis_in Treponema carateum, which is transmitted_by contact with skin and mucous membrane of an infected person. The infection has_symptom pruritic plaque, which slowly enlarges and becomes pigmented and hyperkeratotic. pinta disease DOID:1023 A leprosy that results in small numerous red irregularly shaped plaques. borderline leprosy DOID:1024 A primary bacterial infectious disease that results_in infection located_in superficial peripheral nerves, located_in skin, located_in mucous membranes of the upper respiratory tract, located_in anterior chamber of the eyes, or located_in testes, has_material_basis_in Mycobacterium leprae, which is transmitted_by aerosol spread from infected nasal secretions to exposed nasal and oral mucosa. The infection has_symptom skin lesions, has_symptom sensory loss, has_symptom motor loss and has_symptom eye damage. leprosy DOID:10242 A primary bacterial infectious disease that results in infection located_in leukocyte, has_material_basis_in Ehrlichia chaffeensis or Anaplasma phagocytophilum, which are transmitted_by lone star tick and transmitted_by black-legged tick respectively. The infection has_symptom headache, has_symptom muscle aches, has_symptom fatigue and has_symptom rash. ehrlichiosis DOID:1025 A leprosy that results in one erythematous large plaque with well-defined borders that are elevated and that slope down into an atrophic center. tuberculoid leprosy DOID:10371 A primary bacterial infectious disease that results in infection located in skin, located in joint or located in bone, has_material_basis_in Treponema pallidum subsp pertenue, which is transmitted by direct skin contact with an infected person. The infection has symptom skin lesions. yaws DOID:10398 A plague that results_in infection located_in lung, which results from direct inhalation of the bacillus and has_symptom fever, has_symptom chills, has_symptom cough and has_symptom difficulty breathing. pneumonic plague DOID:10399 seminal vesicle chronic gonorrhea DOID:104 A disease by infectious agent that results_in infection, has_material_basis_in Bacteria. bacterial infectious disease DOID:10400 gonococcal seminal vesiculitis DOID:10457 A legionellosis that is characterized by severe form of infection producing pneumonia. Symptoms include fever, chills, and cough. Legionnaires' disease DOID:10458 A primary bacterial infectious disease that results_in infection located_in respiratory tract, has_material_basis_in Legionella pneumophila, which is transmitted_by inhalation of droplets containing bacteria. The symptoms include dry cough, fever, headache and diarrhea. legionellosis DOID:10567 A yaws that appears after five years of the initial infection and is characterized by disabling consequences of the nose, bones and palmar/plantar hyperkeratosis. late yaws DOID:10568 A yaws that results in initial papule at the site of entry of bacteria. Without treatment, this is followed by disseminated skin lesions over the body. Bone pain and bone lesions may also occur. early yaws DOID:106 An extrapulmonary tuberculosis that results_in lymphocyte-predominant exudative pleural effusion, located_in pleura. This results from an allergic response to tuberculoprotein causing the permeabiltity of the pleural vasculature to alter leading to a sub-pleural caseous focus rupture into the pleural sac. pleural tuberculosis DOID:10690 A breast disease characterized by painful infection of the breast tissue. mastitis DOID:10773 A plague that results_in infection located_in lymph node producing a bubo, which is an inflamed, necrotic, and hemorrhagic lymphoid tissue. The infection has_symptom enlarged, tender lymph nodes, has_symptom fever, has_symptom chills and has_symptom prostration. bubonic plague DOID:10784 A spotted fever that has_material_basis_in Rickettsia australis, which is transmitted_by ticks (Ixodes holocyclus). The infection has_symptom fever, has_symptom headache, has_symptom myalgia, has_symptom maculopapular rash, and has_symptom lymphadenopathy. Queensland tick typhus DOID:10887 A leprosy that results in early cutaneous lesions which consist of pale macules that are small, diffuse, and symmetric. This form of leprosy is characterized by hypoesthesia over extensor surfaces of the distal extremities, alopecia affecting lateral aspects of the eyebrows, saddle-nose deformity and oral lepromas. lepromatous leprosy DOID:10921 A spotted fever that has_material_basis_in Rickettsia sibirica, which is transmitted_by ticks (Dermacentor nuttalli, Dermacentor marginatus and Haemaphysalis concinna). The infection has_symptom fever, has_symptom eschar, has_symptom regional adenopathy, and has_symptom maculopapular rash. Siberian tick typhus DOID:1100 A female reproductive system disease that is located_in the ovary. ovarian disease DOID:11055 A primary bacterial infectious disease that results_in systemic infection, has_material_basis_in Pasteurella multocida, which is transmitted_by animal bite, scratch, or lick. The infection has_symptom joint pain has_symptom fever, has_symptom rigors, has_symptom pneumonia, has_symptom meningeal irritation, and has_symptom tachycardia. pasteurellosis DOID:11076 A brucellosis that involves an infection caused by Brucella suis [NCBITaxon:29461] in swine and humans. The disease has_symptom fever, has_symptom chills, has_symptom malaise, has_symptom diaphoresis, has_symptom arthralgia, has_symptom myalgia, has_symptom headache, has_symptom anorexia, and has_symptom fatigue. Brucella suis brucellosis DOID:11077 A primary bacterial infectious disease that is caused by the bacteria of the genus Brucella, when humans come in contact with contaminated animals or animal products or ingestion of infected food products. The disease has_symptom fever, has_symptom sweat, has_symptom headache, has_symptom back pain, has_symptom physical weakness, has_symptom joint pain and has_symptom fatigue. brucellosis DOID:11100 A primary bacterial infectious disease that is a zoonotic infectious disease affecting multiple organs, has_material_basis_in Coxiella burnetii, which is transmitted_by inhalation of air contaminated by barnyard dust containing dried placental material, birth fluids, or excreta of infected herd animals, transmitted_by ingestion of contaminated milk, transmitted_by tick bites and transmitted_by contact with infected person. The infection has_symptom fever, has_symptom headache, has_symptom cough, has_symptom pleuritic chest pain, has_symptom myalgia and has_symptom arthralgia. Q fever DOID:11101 A primary bacterial infectious disease that results in systemic infection, has_material_basis_in Bartonella quintana, which is transmitted by body lice (Pediculus humanus corporis). The infection has symptom relapsing fever, has symptom headache, has symptom shin pain, and has symptom soreness of the muscles of the legs and back. trench fever DOID:11102 A primary bacterial infectious disease that is caused by the bacteria of the genus Bartonella. bartonellosis DOID:11103 A spotted fever that has_material_basis_in Rickettsia akari, which is transmitted_by house mouse mite (Liponyssoides sanguineus) found on mice and other rodents. The infection has_symptom fever, has_symptom chills, has_symptom headache, has_symptom myalgia, and has_symptom papulovesicular rash. rickettsialpox DOID:11104 A primary bacterial infectious disease that results in infection, located in endothelial cell of artery or located in endothelial cell of vein, has_material_basis_in Rickettsia, which is transmitted by ticks and mites. The infection has symptom fever, has symptom headache, has symptom fatigue, has symptom muscle aches, and has symptom maculopapular or petechial rash. A distinctive eschar (blackened or crusted skin) may develop at the site of a tick bite. spotted fever DOID:1116 A commensal bacterial infectious disease that results_in inflammation located_in respiratory tract, has_material_basis_in Bordetella pertussis, or has_material_basis_in Bordetella parapertussis, which produce toxins that paralyze the cilia of the respiratory epithelial cells. The infection is characterized by a prolonged, high-pitched, deeply indrawn breath (whoop). pertussis DOID:11162 A lung disease characterized by inadequate gas exchange by the respiratory system. respiratory failure DOID:11247 disseminated intravascular coagulation DOID:11254 An epidemic typhus that is a mild form of the disease, which recurs in someone after a long period of latency due to immunosuppression, malnutrition or other illnesses. Brill-Zinsser disease DOID:11256 A primary bacterial infectious disease that refers to a group of diseases, located in endothelial cells of the small venous, arterial, and capillary vessels, has_material_basis_in Rickettsia bacteria, which are transmitted by lice, transmitted by fleas, and transmitted by mites. typhus DOID:11258 A bartonellosis that results_in infection located_in lymph node, has_material_basis_in Bartonella henselae or has_material_basis_in Bartonella clarridgeiae, which are transmitted_by scratch or bite of a kitten, or transmitted_by contact of animal's saliva with an eye or through broken skin. The infection has_symptom regional lymphadenopathy, has_symptom headache, has_symptom chills, has_symptom backache, and has_symptom abdominal pain. cat-scratch disease DOID:11262 A primary bacterial infectious disease that results_in systemic infection, has_material_basis_in Chlamydia psittaci, which is transmitted_by inhaling aerosolized dried droppings or transmitted_by contact with infected birds. The infection has_symptom fever, has_symptom headache, has_symptom rash, has_symptom chills, and has_symptom pneumonia. ornithosis DOID:11263 A commensal bacterial infectious disease that is caused by Chlamydia trachomatis. chlamydia DOID:11265 A commensal bacterial infectious disease that results_in infection located_in eye, has_material_basis_in Chlamydia trachomatis (A, B, Ba and C serovars), which is transmitted_by contact with eye discharge from the infected person and transmitted_by congenital method. The infection causes eyelid to turn inward which makes eyelashes to scratch the cornea. trachoma DOID:11336 A primary bacterial infectious disease that involves the inflammation of mucosa lining the nasal cavity, pharynx, larynx, trachea and bronchi that is characterized by the formation of granulomas, dense induration of the tissues and nodular deformity caused by Klebsiella rhinoscleromatis. rhinoscleroma DOID:11337 A commensal bacterial infectious disease that is characterized by systemic sepsis, ulcerative or necrotic lesions and multisystem abscesses caused by Fusobacterium necrophorum. The disease often first presents as a severe tonsillitis or pharyngitis with high-grade fever and chills together with leukocytosis, cervical pain and neck swelling. Lemierre's syndrome DOID:11338 A primary bacterial infectious disease that results in prolonged contraction of skeletal muscle fibers, has_material_basis_in Clostridium tetani, which produces tetanospasmin, a neurotoxin, which is carried to the brain and spinal cord, where it binds irreversibly to receptors inhibiting neurotransmission. Damaged upper motor neurons cannot control reflex responses to afferent sensory stimuli. tetanus DOID:11394 A respiratory failure that results from diffuse injury to the endothelium of the lung (as in sepsis, chest trauma, massive blood transfusion, aspiration of the gastric contents, or pneumonia) and is characterized by pulmonary edema with an abnormally high amount of protein in the edematous fluid and by difficult rapid breathing and hypoxemia. adult respiratory distress syndrome DOID:114 A cardiovascular system disease that involves the heart. heart disease DOID:11405 A primary bacterial infectious disease that is characterized by sore throat, low fever, and an adherent membrane (a pseudomembrane) on the tonsils, pharynx, and/or nasal cavity. A milder form of diphtheria can be restricted to the skin. It is caused by Corynebacterium diphtheriae, an aerobic Gram-positive bacterium. Diphtheria toxin spreads through the bloodstream and can lead to potentially life-threatening complications that affect other organs of the body, such as the heart and kidneys. diphtheria DOID:11572 A bacterial meningitis that has_material_basis_in Listeria monocytogenes infection. Listeria meningitis DOID:11573 A primary bacterial infectious disease that results_in infection, has_material_basis_in Listeria monocytogenes, which is transmitted_by ingestion of contaminated food or raw milk or transmitted_by congenital method. Ingestion of Listeria by pregnant women has_symptom nausea, has_symptom vomiting, has_symptom diarrhea, has_symptom fever, has_symptom malaise, has_symptom back pain, and has_symptom headache. Maternal infection with Listeria can result in chorioamnionitis, premature labor, spontaneous abortion, or stillbirth. listeriosis DOID:11574 A bacterial meningitis that has_material_basis_in streptococcal bacteria. streptococcal meningitis DOID:11729 A primary bacterial infectious disease that results_in infection, has_material_basis_in Borrelia burgdorferi, which is transmitted_by blacklegged tick (Ixodes scapularis) or transmitted_by western blacklegged tick (Ixodes pacificus). The infection has_symptom fever, has_symptom headache, has_symptom fatigue, and has_symptom skin rash called erythema migrans. If left untreated, infection can spread to joints, the heart, and the nervous system. Lyme disease DOID:11750 A pertussis that is a milder disease caused by the bacterium Bordetella parapertussis. The disease has_symptom coughing, has_symptom sneezing, or has_symptom runny nose . Bordetella parapertussis whooping cough DOID:11851 A leprosy that is an early form of the disease which causes one to a few hypopigmented or erythematous macules. indeterminate leprosy DOID:11963 esophagitis DOID:11976 A primary bacterial infectious disease that involves intoxication caused by botulinum neurotoxins (BoNTA, B, E and F) located in neuromuscular junction resulting in descending muscle paralysis, has_material_basis_in Clostridium botulinum A, has_material_basis_in Clostridium botulinum B, has_material_basis_in Clostridium botulinum E and has_material_basis_in Clostridium botulinum F. botulism DOID:11990 A tularemia that results_in painful regional lymphadenopathy and an ulcerated skin lesion. ulceroglandular tularemia DOID:1205 An immune system disease that is an exaggerated immune response to allergens, such as insect venom, dust mites, pollen, pet dander, drugs or some foods. allergic disease DOID:12096 A primary bacterial infectious disease that results_in infection, has_material_basis_in Spirillum minus, which is transmitted_by contact with urine or secretions from the mouth, eye, or nose of an infected animal or transmitted_by bite of an infected animal, especially rat. The infection has_symptom chills, has_symptom relapsing fever, has_symptom rash and has_symptom joint pain. sodoku disease DOID:121 A female reproductive system disease that is located_in the vagina. vaginal disease DOID:12385 A primary bacterial infectious disease that results_in infection located_in epithelium of colon, has_material_basis_in Shigella boydii, has_material_basis_in Shigella dysenteriae, has_material_basis_in Shigella flexneri, or has_material_basis_in Shigella sonnei, which produce toxins that can attack the lining of the large intestine, causing swelling, ulcers on the intestinal wall, and bloody diarrhea. The bacteria are transmitted_by ingestion of food and water contaminated with feces. shigellosis DOID:1247 A hematopoietic system disease that is characterized by abnormal blood clotting or bleeding. blood coagulation disease DOID:1251 An urogenital tuberculosis that is located_in epididymis, has_symptom pain and has_symptom scrotal swelling. tuberculous epididymitis DOID:12554 A kidney disease that is characterized by hemolytic anemia, thrombocytopenia, and renal failure caused by platelet thrombi in the microcirculation of the kidney and other organs. hemolytic-uremic syndrome DOID:12716 A respiratory failure that is characterized by deficiency of the surfactant coating the inner surface of the lungs, by failure of the lungs to expand and contract properly during breathing with resulting collapse, and by the accumulation of a protein-containing film lining the alveoli and their ducts. newborn respiratory distress syndrome DOID:1287 A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis. cardiovascular system disease DOID:13034 A primary bacterial infectious disease that results_in infection, has_material_basis_in Borrelia, which is transmitted_by tick or transmitted_by body louse. relapsing fever DOID:13035 A relapsing fever that is characterized by relapsing or recurring episodes of fever, has_material basis_in Borrelia recurrentis, which is transmitted_by body louse (Pediculus humanus). The infection has_symptom tachypnea, has_symptom tachycardia, has_symptom hepatosplenomegaly and has_symptom lymphadenopathy. louse-borne relapsing fever DOID:13036 A relapsing fever that is characterized by relapsing or recurring episodes of fever, has_material basis_in Borrelia hermsii, has_material basis_in Borrelia parkeri or has_material basis_in Borrelia duttoni, which are transmitted_by soft ticks (Ornithodoros parkeri and Ornithodoros hermsii). The infection has_symptom tachypnea, has_symptom tachycardia, has_symptom hepatosplenomegaly and has_symptom lymphadenopathy. tick-borne relapsing fever DOID:13148 A cystitis characterized by a sudden onset or severe symptoms. acute cystitis DOID:13226 A tularemia that results_in inflammation of eye and swelling of lymph glands in front of the ear. oculoglandular tularemia DOID:13238 A primary bacterial infectious disease that results_in infection, has_material_basis_in Streptobacillus moniliformis, which is transmitted_by contact with urine or secretions from the mouth, eye, or nose of an infected animal or transmitted_by bite of an infected animal, especially rat. The infection has_symptom chills, has_symptom fever, has_symptom rash and has_symptom joint pain. Haverhill fever DOID:13258 A primary bacterial infectious disease that is a communicable systemic illness, has_material_basis_in Salmonella enterica subsp enterica serovar Typhi, which is transmitted_by ingestion of food or water contaminated with the feces of an infected person. The infection has_symptom fever, has_symptom diarrhea, has_symptom prostration, has_symptom headache, has_symptom splenomegaly, has_symptom liver enlargement, has_symptom eruption of rose-colored spots, and has_symptom leukopenia. typhoid fever DOID:13272 A bacterial pneumonia involving Klebsiella pneumoniae infection. Patients with Klebsiella pneumonia tend to cough up a characteristic sputum that is said to resemble red-currant jelly. Klebsiella pneumonia tends to affect people with underlying diseases, such as alcoholism, diabetes and chronic lung disease. The symptoms include high fever, rigors and pleuritic pain, and hemoptysis. Klebsiella pneumonia DOID:13276 A bacterial pneumonia that is caused by the bacterial species Mycoplasma pneumoniae. The symptoms include chest pain, chills, dry cough which is not bloody, excessive sweating, fever, headache and sore throat. Mycoplasma pneumoniae pneumonia DOID:13282 A gastrointestinal tuberculosis that involves diffuse mucosal fold thickening, formation of ulcers and fistulae located_in intestine. The infection has_symptom abdominal pain, has_symptom gastrointestinal bleeding, has_symptom nausea and has_symptom vomiting. intestinal tuberculosis DOID:13371 A typhus that has_material_basis_in Orientia tsutsugamushi, which is transmitted by trombiculid mites (Leptotrombidium deliense). The infection has symptom fever, has symptom headache, has symptom muscle pain, has symptom cough, has symptom maculopapular rash, has symptom eschar, has symptom splenomegaly and has symptom lymphadenopathy. scrub typhus DOID:13386 An anthrax disease that results in infection located in mucosa of gastrointestinal tract, has_material_basis_in Bacillus anthracis, which is transmitted by ingestion of anthrax-infected meat. The infection has symptom lesions, has symptom vomiting of blood, has symptom severe diarrhea, has symptom loss of appetite. gastrointestinal anthrax DOID:13431 A primary bacterial infectious disease that results in infection located in mucosa of mouth, located in skin or located in bone, has_material_basis_in Treponema pallidum subsp endemicum, which is transmitted by contact or transmitted by sharing of domestic utensils. The infection has symptom moist patches in the mouth, has symptom lumps in long bones, tissues around the mouth, nose, and roof of the mouth. These lumps destroy tissue, causing bones to be deformed and disfiguring the face. bejel DOID:13444 A primary bacterial infectious disease that results in septicemic infection, has_material_basis_in Burkholderia mallei, which is transmitted by contact with tissues or body fluids of infected animals, or through mucosal surfaces such as the eyes and nose. The infection has symptom fever, has symptom chills, has symptom sweating, has symptom muscle aches, has symptom chest pain, has symptom muscle tightness, has symptom headache, has symptom mucopurulent nasal discharge, and has symptom nodular lesions in the lungs. glanders DOID:13521 A tetanus that occurs in newborn babies when the birth cord stump gets dirty through cutting it with an unclean blade or applying substances containing bacteria to it. The infection has symptom stiff body, has symptom muscle spasms, has symptom difficulty in breathing, and has symptom exhaustion. tetanus neonatorum DOID:13622 A primary bacterial infectious disease that results_in infection located_in intestine, has_material_basis_in Campylobacter jejuni, which is transmitted_by ingestion of contaminated food or water or transmitted_by contact with infected people or animals. The infection has_symptom diarrhea or has_symptom dysentery, has_symptom abdominal cramps and pain, and has_symptom fever. campylobacteriosis DOID:13778 A primary bacterial infectious disease that is a sexually transmitted infection located in skin of the genitals, has_material_basis_in Haemophilus ducreyi, which is transmitted by sexual contact. The infection has symptom painful and soft ulcers. chancroid DOID:13800 A commensal bacterial infectious disease that results_in inflammation, located_in conjunctiva of the eye, has_material_basis_in Chlamydia trachomatis, which is transmitted_by sexual contact. The infection has_symptom swollen conjunctiva and eyelids and has_symptom discharge of pus and mucus. inclusion conjunctivitis DOID:13819 A commensal bacterial infectious disease that results_in infection located_in lymph nodes, has_material_basis_in Chlamydia trachomatis, which is transmitted_by sexual contact, and transmitted_by fomites. The infection has_symptom inguinal lymphadenitis, has_symptom abscesses in the groin area, and has_symptom lymphangitis. lymphogranuloma venereum DOID:13921 bacterial esophagitis DOID:14019 A brucellosis involving an infection caused by Brucella canis [NCBITaxon:36855] in dogs and humans. The disease has_symptom fever, has_symptom sweats, has_symptom weakness, has_symptom weight loss, has_symptom headache, has_symptom lymphadenopathy and has_symptom splenomegaly. Brucella canis brucellosis DOID:14095 A spotted fever that has_material_basis_in Rickettsia conorii subsp conorii, which is transmitted_by dog tick (Rhipicephalus sanguineus). The infection has_symptom fever, has_symptom eschar (usually single), has_symptom regional adenopathy, has_symptom maculopapular rash on extremities. boutonneuse fever DOID:14115 A commensal bacterial infectious disease that results_in infection, has_material_basis_in Streptococcus pyogenes or has_material_basis_in Staphylococcus aureus , which produce toxins that are absorbed systemically and produce the systemic manifestations. The infection has_symptom fever, has_symptom rash, has_symptom hypotension, has_symptom multiorgan failure, has_symptom desquamation, has_symptom vomiting, has_symptom diarrhea, has_symptom headache, and has_symptom nonfocal neurologic abnormalities. toxic shock syndrome DOID:14239 A tularemia that results in formation of ulcerative lesions located in gastrointestinal tract. The infection has symptom fever, has symptom chills, has symptom malaise, has symptom muscle aches, and has symptom vomiting. gastrointestinal tularemia DOID:1426 A urinary system disease that is located_in the ureter. ureteral disease DOID:14456 A brucellosis that involves an infection caused by Brucella melitensis [NCBITaxon:29459] in cattle, goats, sheep and humans. The disease has_symptom fever, has_symptom malaise, has_symptom anorexia, has_symptom limb pain and has_symptom back pain. Brucella melitensis brucellosis DOID:14457 A brucellosis that involves an infection caused by Brucella abortus [NCBITaxon:235] in cattle and humans. The disease has_symptom fever, has_symptom chills, has_symptom sweats, has_symptom weight loss, has_symptom malaise, has_symptom headaches, has_symptom myalgia, and has_symptom arthralgia. Brucella abortus brucellosis DOID:14559 anaerobic meningitis DOID:14566 A disease that is characterized by abnormally rapid cell division. disease of cellular proliferation DOID:1498 A primary bacterial infectious disease that is described as an acute, diarrheal illness caused by infection of the intestine with the bacterium Vibrio cholerae, which is characterized by profuse watery diarrhea, vomiting, leg cramps, circulatory collapse and shock. cholera DOID:15 A disease of anatomical entity that is located_in reproductive system organs. reproductive system disease DOID:1532 A thoracic disease which may involve inflammation of pleura, collection of air within the pleural cavity, abnormal collection of pleural fluid, abnormal growths on the pleura (pleural tumor) and pleural plaques. The main causes of pleural diseases including pleural effusions are congestive heart failure, malignancy, parapneumonic infections and pulmonary embolism. pleural disease DOID:1579 A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm. respiratory system disease DOID:1586 A connective tissue disease that develops from an antecedent Group A Streptococcal pharyngeal infection and has_symptom carditis, has_symptom polyarthritis, has_symptom chorea, has_symptom erythema marginatum, has_symptom subcutaneous nodules, has_symptom arthralgia, has_symptom prolonged PR interval, and/or has_symptom fever. rheumatic fever DOID:16 A disease of anatomical entity that is located_in the integumentary system comprising the skin and its appendages. integumentary system disease DOID:162 A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. cancer DOID:1638 An extrapulmonary tuberculosis that results in formation of tuberculomas located_in brain or located_in spinal cord. central nervous system tuberculosis DOID:1639 An extrapulmonary tuberculosis that results in formation of lesions located in bone. skeletal tuberculosis DOID:1679 A bladder disease that is characterized by inflammation of the bladder. cystitis DOID:17 A disease of anatomical entity that occurs in the muscular and/or skeletal system. musculoskeletal system disease DOID:18 A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra. urinary system disease DOID:1962 A female reproductive system disease that is located_in the fallopian tube. fallopian tube disease DOID:2122 A tularemia that is located_in lungs. The bacteria are transmitted_by breathing dusts or aerosols containing the organisms. The infection has_symptom cough, has_symptom chest has_symptom pain, and has_symptom difficulty breathing. pneumonic tularemia DOID:2123 A primary bacterial infectious disease that has_material_basis_in Francisella tularensis, which is transmitted by dog tick bite (Dermacentor variabilis), transmitted by deer flies (Chrysops sp) or transmitted by contact with infected animal tissues. tularemia DOID:2148 An urogenital tuberculosis that results_in inflammtion located_in ovary. tuberculous oophoritis DOID:2149 An extrapulmonary tuberculosis that is located_in urogenital system. urogenital tuberculosis DOID:2170 A vaginal disease that is characterized by inflammation of the vagina. vaginitis DOID:2277 An endocrine system disease that is located_in the gonads. gonadal disease DOID:229 A reproductive system disease that impairs the ability to reproduce and is located in the uterus, vagina, cervix, ovaries or fallopian tubes. female reproductive system disease DOID:2297 A primary bacterial infectious disease that involves systemic infection, has_material_basis_in Leptospira, which is transmitted by contact with water, food, or soil containing urine from the infected animals. The infection has symptom jaundice, has symptom chills, has symptom fever, has symptom muscle pain, and has symptom hepatomegaly. leptospirosis DOID:2312 An opportunistic bacterial infectious disease that results_in disseminated infection in immunocompromised hosts, has_material_basis_in Nocardia asteroides. The infection has_symptom pneumonia, has_symptom cellulitis, has_symptom lesions in the brain or meninges, and has_symptom ascending regional lymphadenopathy. nocardiosis DOID:2326 A gastrointestinal system infectious disease that involves inflammation of the lining of the stomach and small and large intestines, which is caused by viruses, bacteria, or parasites. Chemicals and drugs also cause gastroenteritis. The symptoms include diarrhea, loss of appetite, nausea, vomiting, cramps, and discomfort in the abdomen. gastroenteritis DOID:2452 A blood coagulation disease that is characterized by an increased tendency to form clots. thrombophilia DOID:2529 splenic disease DOID:2531 An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes. hematologic cancer DOID:2755 A primary bacterial infectious disease that results_in infection, has_material_basis_in Mycobacterium avium complex (MAC), which is transmitted_by inhalation or transmitted_by ingestion of via the respiratory or gastrointestinal tract respectively. The bacteria cause disseminated infection in HIV infected people, while pulmonary disease in immunocompetent persons. Mycobacterium avium complex disease DOID:28 A disease of anatomical entity that is located_in endocrine glands which secretes a type of hormone directly into the bloodstream to regulate the body. endocrine system disease DOID:2914 A disease of anatomical entity that is located_in the immune system. immune system disease DOID:2945 A Coronavirus infection that results_in infection located_in respiratory tract, has_material_basis_in SARS coronavirus (SARS-CoV), which is transmitted_by droplet spread of respiratory secretions, transmitted_by ingestion of contaminated food, or transmitted_by fomites. The infection has_symptom fever, has_symptom headache, has_symptom body aches, has_symptom dry cough, and has_symptom hypoxia. severe acute respiratory syndrome DOID:2957 A tuberculosis that is a contagious disease located_in lungs. The infection has_symptom fever, has_symptom cough, has_symptom difficulty in breathing, has_symptom inflammatory infiltrations, has_symptom formation of tubercles, has_symptom caseation, has_symptom pleural effusion, and has_symptom fibrosis. pulmonary tuberculosis DOID:3044 A hypersensitivity reaction type I disease that is an abnormal response to a food, triggered by the body's immune system. food allergy DOID:3055 A primary bacterial infectious disease that results_in infection located_in intestine, has_material_basis_in Salmonella enterica subsp enterica serovar Paratyphi A, B or C, which are transmitted_by ingestion of contaminated food. The infection has_symptom fever, has_symptom headache, has_symptom abdominal pain, has_symptom malaise, has_symptom anorexia, has_symptom constipation, has_symptom rosy spots on the central body, has_symptom non productive cough (in early stage of illness), has_symptom bradycardia, and has_symptom hepatosplenomegaly. paratyphoid fever DOID:3091 An opportunistic bacterial infectious disease that has_material_basis_in Acinetobacter. Acinetobacter infectious disease DOID:3118 A gastrointestinal system disease that is located_in the liver and/or biliary tract. hepatobiliary disease DOID:319 spinal cord disease DOID:331 A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system. central nervous system disease DOID:3385 A vaginitis that is characterized by a grayish vaginal discharge usually of foul odor and the presence of Gardnerella vaginalis. bacterial vaginosis DOID:3463 A thoracic disease that is located_in the breast. breast disease DOID:3481 A plague that results_in infection located_in vasculature where bacterial endotoxins cause coagulation, which leads to formation of tiny clots throughout the body. The infection has_symptom fever, has_symptom chills, has_symptom prostration, has_symptom abdominal pain, has_symptom shock and has_symptom bleeding into skin and other organs. septicemic plague DOID:3482 A primary bacterial infectious disease that results_in infection, located_in lymph node, located_in vasculature or located_in lungs, has_material_basis_in Yersinia pestis, which is transmitted_by oriental rat flea (Xenopsylla cheopis) infected by feeding on rodents and other mammals, transmitted_by air, transmitted_by direct contact or transmitted_by ingestion of contaminated undercooked food. plague DOID:365 A urinary system disease that is located_in the bladder. bladder disease DOID:3660 A food allergy that develops_from exposure to and particularly consumption of wheat, and has_symptom that are both gastrointestinal and nongastrointestinal in nature, such as diarrhea, mouth and throat irritation, headache, hives, skin rashes, and anaphylaxis. wheat allergy DOID:37 An integumentary system disease that is located_in skin. skin disease DOID:3978 A cardiomyopathy that is characterized by the pathology occuring outside of the myocardium. extrinsic cardiomyopathy DOID:399 A primary bacterial infectious disease that is located_in lungs, located_in lymph nodes, located_in pericardium, located_in brain, located_in pleura or located_in gastrointestinal tract, has_material_basis_in Mycobacterium tuberculosis, which is transmitted_by droplets released into the air when an infected person coughs or sneezes. tuberculosis DOID:4 A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. http://purl.obolibrary.org/obo/OGMS_0000031 disease DOID:401 A tuberculosis that is resistant to isoniazid and rifampicin, the two most powerful first-line anti-TB drugs. multidrug-resistant tuberculosis DOID:402 A gastrointestinal tuberculosis that involves formation of painful ulcerative mucosal lesions located in tongue, located in palate, located in maxilla or located in mandible. oral tuberculosis DOID:4029 A stomach disease that is an inflammation of the lining of the stomach. gastritis DOID:403 A gastrointestinal system disease that is located_in the mouth. mouth disease DOID:4033 A gastritis that involves inflammation of the stomach lining caused by bacteria. The disease has_symptom abdominal pain, has_symptom indigestion, has_symptom ulcer formation, has_symptom abdominal bloating, has_symptom nausea and has_symptom vomiting. bacterial gastritis DOID:404 An abdominal tuberculosis that results_in infection located_in gastrointestinal tract. The infection has_symptom abdominal pain, has_symptom weight loss, has_symptom fever, has_symptom anorexia, has_symptom change in bowel habits, has_symptom nausea, and has_symptom vomiting. gastrointestinal tuberculosis DOID:407 A gastrointestinal tuberculosis that involves infection located_in liver, which results in the formation of tuberculous granulomas. The infection has_symptom fever, has_symptom anorexia, has_symptom weight loss, has_symptom abdominal pain and has_symptom jaundice. hepatic tuberculosis DOID:409 liver disease DOID:4156 A syphilis that is the first stage of syphilis, marked by the development of a chancre, which is characterized by mononuclear leukocytic infiltration, macrophages, and lymphocytes. primary syphilis DOID:4157 A syphilis that is characterized as the second stage of syphilis which appears from 2 to 6 months after primary infection, and is marked by lesions especially in the skin but also in organs and tissues, and that lasts from 3 to 12 weeks. secondary syphilis DOID:4166 A primary bacterial infectious disease that is a sexually transmitted systemic disease, has_material_basis_in Treponema pallidum subsp pallidum, which is transmitted_by sexual contact, transmitted_by blood product transfusion, transmitted_by congenital method from mother to fetus or transmitted_by contact with infectious lesions. If left untreated, produces chancres, rashes, and systemic lesions in a clinical course with three stages continued over many years. syphilis DOID:417 An immune system disease that is an overactive immune response of the body against substances and tissues normally present in the body resulting from an abnormal functioning of the immune system that results in the production of antibodies or T cell directed against the host tissues. autoimmune disease DOID:4251 An eye disease affecting the conjunctiva, which is the mucous membrane surrounding the eye and interior of the eyelids. conjunctival disease DOID:4376 A food allergy that results in adverse immune reaction to one or more of the proteins in cow's milk and/or the milk of other animals, which are normally harmless to the non-allergic individual. milk allergy DOID:4377 A food allergy that is an allergy or hypersensitivity to dietary substances from the yolk or whites of eggs, causing an overreaction of the immune system which may lead to severe physical symptoms. egg allergy DOID:4378 A legume allergy that is an allergy or hypersensitivity to dietary substances from peanuts causing an overreaction of the immune system which in a small percentage of people may lead to severe physical symptoms. peanut allergy DOID:4379 A food allergy that develops_from exposure to and particularly consumption of nuts, and has_symptom asthma, skin rashes, throat and eye irritation, and anaphylaxis. nut allergy DOID:48 A reproductive system disease that affects male reproductive organs. male reproductive system disease DOID:4889 An extrapulmonary tuberculosis that is located_in lymph node, and has_symptom lymphadenopathy, has_symptom fever, has_symptom weight loss, has_symptom fatigue, has_symptom night sweats and has_symptom cough. lymph node tuberculosis DOID:4962 An extrapulmonary tuberculosis that is located_in pericardium resulting in acute pericarditis, chronic pericardial effusion, cardiac tamponade or pericardial constriction. pericardial tuberculosis DOID:4974 A commensal bacterial infectious disease that results_in infection, has_material_basis_in Actinobacillus ureae, which is a commensal of the human respiratory tract. The pathogen causes meningitis, endocarditis, bacteremia, atrophic rhinitis, bronchitis, pneumonia, conjunctivitis, peritonitis, and otitis media. actinobacillosis DOID:5052 A primary bacterial infectious disease that results_in infection, has_material_basis_in Burkholderia pseudomallei, which is transmitted_by contact with the contaminated water or soil. The infection has_symptom fever, has_symptom respiratory distress, has_symptom chest pain, and has_symptom stomach pain. melioidosis DOID:5295 A gastrointestinal system disease that is located_in the intestine. intestinal disease DOID:5353 A intestinal disease located in the colon. colonic disease DOID:552 A lung disease that involves lung parenchyma or alveolar inflammation and abnormal alveolar filling with fluid (consolidation and exudation). It results from a variety of causes including infection with bacteria, viruses, fungi or parasites, and chemical or physical injury to the lungs. It is accompanied by fever, chills, cough, and difficulty in breathing. pneumonia DOID:557 A urinary system disease that is located_in the kidney. kidney disease DOID:5614 An eye and adnexa disease that is located_in the eye. eye disease DOID:6050 A gastrointestinal system disease that is located_in the esophagus. esophageal disease DOID:612 An immune system disease that results when one or more essential parts of the immune system is missing or not working properly at birth due to a genetic mutation. primary immunodeficiency disease DOID:6195 A conjunctival disease characterized by an inflammation of the conjunctiva, the outermost layer of the eye and the inner surface of the eyelids. conjunctivitis DOID:65 A musculoskeletal system disease that affects tissues such as skin, tendons, and cartilage. connective tissue disease DOID:7 A disease that manifests in a defined anatomical structure. disease of anatomical entity DOID:7332 A gastrointestinal tuberculosis that involves formation of tuberculous ulcers located_in esophagus. The infection has_symptom dysphagia, has_symptom cough, has_symptom chest pain, has_symptom fever and has_symptom weight loss. esophageal tuberculosis DOID:74 A disease of anatomical entity that has_material_basis_in hematopoietic cells. hematopoietic system disease DOID:7426 An anthrax disease that results_in infection located_in skin, has_material_basis_in Bacillus anthracis, which is transmitted_by contact with infected animals or animal products. The infection has_symptom skin lesion that eventually forms an ulcer with a black center. cutaneous anthrax DOID:7427 A primary bacterial infectious disease that results_in infection located_in skin, located_in lung lymph nodes or located_in gastrointestinal tract, has_material_basis_in Bacillus anthracis, transmitted_by contact with infected animals or animal products, transmitted_by airborne spores or transmitted_by ingestion of undercooked meat from infected animals and has_symptom skin ulcer, has_symptom nausea, has_symptom poor appetite, has_symptom bloody diarrhea, has_symptom fever or has_symptom shortness of breath. anthrax disease DOID:75 An immune system disease that is located_in the lymphatic system. lymphatic system disease DOID:754 An urogenital tuberculosis that is located_in urinary bladder, which results in fibrosis of bladder wall muscles. bladder tuberculosis DOID:7551 A primary bacterial infectious disease that is a sexually transmitted infection, located_in uterus, located_in fallopian tube, located_in urethra, located_in mouth, located_in throat, located_in eye or located_in anus, has_material_basis_in Neisseria gonorrhoeae, which is transmitted_by contact with the penis, vagina, mouth, or anus or transmitted_by congenitally from mother to baby during delivery. The infection has_symptom burning sensation during urination, has_symptom discharge from the penis, has_symptom increased vaginal discharge, or has_symptom vaginal bleeding between periods. gonorrhea DOID:76 A gastrointestinal system disease that is located_in the stomach. stomach disease DOID:77 A disease of anatomical entity that is located_in the gastrointestinal tract. gastrointestinal system disease DOID:820 An extrinsic cardiomyopathy that is characterized as an inflammation of the heart muscle. myocarditis DOID:8200 A syphilis that is characterized as the third stage of syphilis that develops after the disappearance of the secondary symptoms and is marked by ulcers and gummas under the skin and commonly by involvement of the skeletal, cardiovascular, and nervous systems. tertiary syphilis DOID:827 An urogenital tuberculosis that is located_in ureter resulting in ureteral strictures. ureter tuberculosis DOID:8283 A gastrointestinal system disease that involves inflammation of the peritoneum resulting from perforation of the gastrointestinal tract, which produces immediate chemical inflammation followed shortly by infection from intestinal organisms. Peritonitis can also result from appendicitis, diverticulitis, strangulating intestinal obstruction, pancreatitis, pelvic inflammatory disease, mesenteric ischemia, intraperitoneal blood, barium, or peritoneo-systemic shunts, drains, and dialysis catheters in the peritoneal cavity. The symptoms include abdominal pain and tenderness, fever, fluid in the abdomen, nausea, vomiting and low urine output. peritonitis DOID:8478 A commensal bacterial infectious disease that results in infection, which is characterized by contiguous spread, suppurative and granulomatous inflammation, and formation of multiple abscesses and sinus tracts that may discharge sulfur granules, has_material_basis_in Actinomyces israelii, has_material_basis_in Actinomyces gerencseriae, has_material_basis_in Actinomyces naeslundii, has_material_basis_in Actinomyces odontolyticus, has_material_basis_in Actinomyces viscosus, has_material_basis_in Actinomyces meyeri, has_material_basis_in Propionibacterium propionicum, which require a break in the integrity of the mucous membranes and the presence of devitalized tissue to invade deeper body structures. actinomycosis DOID:8481 rheumatic myocarditis DOID:850 A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide. lung disease DOID:8577 A colitis that is predominantly confined to the mucosa located_in colon and includes characteristic ulcers, or open sores. ulcerative colitis DOID:863 A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system. nervous system disease DOID:873 An aspiration pneumonia caused by anaerobic bacteria like Bacteroides fragilis, Peptostreptococcus, anaerobic streptococci, Fusobacterium species (Fusobacterium nucleatum and Fusobacterium necrophoram). Lung abscess and empyema are diagnosed in this disease. anaerobic pneumonia DOID:874 A pneumonia involving inflammation of the lungs caused by bacteria. bacterial pneumonia DOID:9063 A commensal bacterial infectious disease that is characterized by widespread erythema, peeling, and necrosis of the skin, that is caused by a toxin produced by a bacterium of the genus Staphylococcus (S. aureus). The infection has_symptoms redness of skin, has_symptom fluid-filled blister formation, has_symptom fever and has_symptom irritability. Ritter's disease DOID:9113 A primary bacterial infectious disease that results_in infection located_in skin or located_in mucosa of genital tract, has_material_basis_in Klebsiella granulomatis, transmitted by sexual contact or transmitted_by contact with the open sores. The infection has_symptom painless genital ulcers. granuloma inguinale DOID:9159 A commensal bacterial infectious disease that results in infection, located in muscle tissue, has_material_basis_in Clostridium perfringens, which produce gas that becomes trapped in the infected tissue. Gas gangrene usually develops after injuries or surgery. The infection has symptom large blisters, has symptom pain in the infected area, has symptom myonecrosis, has symptom gas production, and has symptom sepsis. gas gangrene DOID:9305 An abdominal tuberculosis that results_in formation of granulomas or abscesses located_in spleen. splenic tuberculosis DOID:934 A disease by infectious agent that results in infection, has_material_basis_in Viruses. viral infectious disease DOID:936 A central nervous system disease that is located_in the brain. brain disease DOID:9365 vesiculitis DOID:9470 A meningitis that has_material_basis_in a bacterial infection. bacterial meningitis DOID:9471 A central nervous system disease that is characterized by an inflammation of the pia-arachnoid meninges. It can be caused by growth of bacteria, fungi, or parasites within the subarachnoid space or by the growth of bacteria or viruses within the meningeal or ependymal cells. meningitis DOID:9531 A syphilis that is characterized as having serologic proof of infection without signs or symptoms of disease. latent syphilis DOID:9588 A brain disease that is characterized as an acute inflammation of the brain with flu-like symptoms. encephalitis DOID:96 A primary bacterial infectious disease that results_in infection located_in intestine caused by eating food contaminated with enterotoxins produced by bacteria, has_material_basis_in Staphylococcus aureus. The infection has_symptom diarrhea, has_symptom vomiting, has_symptom nausea, has_symptom cramps, and has_symptom weakness. staphyloenterotoxemia DOID:9699 A bacterial conjuctivitis that is characterized by pain and tenderness in the eyeball and conjuctival discharge. ophthalmia neonatorum DOID:9700 bacterial conjunctivitis DOID:9733 An urogenital tuberculosis that results_in formation of granulomas located_in kidney. renal tuberculosis DOID:9801 A gastrointestinal tuberculosis that results_in inflammation located_in peritoneum, which results in formation of tubercles. The infection has_symptom abdominal discomfort, has_symptom pain, has_symptom distention from gas or fluid, has_symptom digestive disturbances and has_symptom emaciation. tuberculous peritonitis DOID:9856 A syphilis that results_in a multisystem infection in the fetus via the placenta. congenital syphilis DOID:9861 An extrapulmonary tuberculosis that results in formation of tiny lesions in all the organs. miliary tuberculosis DOID:9880 A tertiary syphilis that is manifested as aneurysm formation in the ascending aorta, caused by chronic inflammatory destruction of the vasa vasorum, insufficiency of the aortic valve, or narrowing of the coronary arteries. cardiovascular syphilis DOID:9942 lymph node disease DOID:9988 A tertiary syphilis that results in infection located in brain or located in spinal cord. tertiary neurosyphilis ECTO:0600000 A exposure event involving the interaction of an exposure receptor to environmental system. environmental system exposure exposure to environmental system ECTO:1000021 A exposure event involving the interaction of an exposure receptor to construction. construction exposure exposure to construction ECTO:1000033 A exposure event involving the interaction of an exposure receptor to abattoir. abattoir exposure exposure to abattoir ECTO:1000034 A exposure event involving the interaction of an exposure receptor to farm. farm exposure exposure to farm ECTO:1000035 A exposure event involving the interaction of an exposure receptor to hospital. hospital exposure exposure to hospital ECTO:1000036 A exposure event involving the interaction of an exposure receptor to laboratory facility. laboratory facility exposure exposure to laboratory ECTO:1000037 A exposure event involving the interaction of an exposure receptor to office. office exposure exposure to office ECTO:1000040 A exposure event involving the interaction of an exposure receptor to restaurant. restaurant exposure exposure to restaurant ECTO:1000041 A exposure event involving the interaction of an exposure receptor to shop. shop exposure exposure to retail shop ECTO:3000000 A history of exposure to root. root exposure exposure to organism ECTO:3000005 A history of exposure to Homo sapiens. Homo sapiens exposure exposure to humans ECTO:5000000 A exposure event involving the interaction of an exposure receptor to geographic feature. geographic feature exposure exposure to geographic feature ECTO:5000008 A exposure event involving the interaction of an exposure receptor to petting zoo. petting zoo exposure exposure to petting zoo ECTO:5000009 A exposure event involving the interaction of an exposure receptor to campground. campground exposure exposure to campground ECTO:6000000 An exposure event involving Activity Activity exposure exposure to behavior ECTO:6000001 An exposure event involving Violence Violence exposure exposure to violence ECTO:6000030 An exposure event involving hunting behavior hunting behavior exposure exposure to hunting ENVO:00000000 https://en.wikipedia.org/wiki/Geographic_feature macroscopic spatial feature envoPolar This class is being depopulated and will be filled only with inferred subclasses. Please do not use this for direct annotation, favouring instead a more descriptive subclass. geographic feature ENVO:00000002 constructed feature An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature. FTT:78 TGN:50001 anthropogenic geographic feature ENVO:00000004 FTT:1242 FTT:1252 FTT:15 FTT:16 FTT:18 FTT:19 FTT:21 FTT:22 FTT:23 FTT:24 FTT:25 FTT:26 FTT:27 FTT:28 FTT:29 FTT:37 SWEETRealm:AdministrativeRegion TGN:80001 TGN:81099 TGN:81123 https://en.wikipedia.org/wiki/Administrative_region administrative area administrative region ENVO:00000005 state / province / territory / region lookup:http://purl.obolibrary.org/obo/GAZ_00000448 A primary administrative division of a country, such as a state in the United States. FTT:414 FTT:569 Geonames:A.ADM1 TGN:81100 first-order administrative region ENVO:00000009 A political association with effective dominion over a geographic area. FTT:424 FTT:566 FTT:567 FTT:571 SWEETRealm:Country SWEETRealm:State TGN:80006 TGN:81010 TGN:81011 TGN:81102 https://en.wikipedia.org/wiki/Nation http://purl.obolibrary.org/obo/NCIT_C25464 nation independent nation independent political entity independent sovereign nation national geopolitical entity ENVO:00000010 A construction which enables the movement of humans, their animals or their vehicles. FTT:83 transport feature ENVO:00000011 An enclosure for displaying selected plant or animal life. FTT:31 FTT:743 Geonames:S.GDN TGN:53010 https://en.wikipedia.org/wiki/Garden garden garden ENVO:00000012 A geographical feature associated with water. FTT:131 FTT:280 FTT:711 FTT:761 FTT:824 FTT:825 FTT:826 FTT:827 FTT:828 FTT:829 Geonames:H.OVF envoPolar hydrographic feature ENVO:00000014 Artificial watercourse with no flow or a controlled flow used for navigation, drainage or irrigation. EcoLexicon:canal FTT:129 FTT:395 FTT:407 FTT:408 Geonames:H.CNL SWEETRealm:Canal TGN:51252 https://en.wikipedia.org/wiki/Canal This class refers to the water contained in a canal channel, and not the channel itself. canal ENVO:00000015 A marine water body which is constitutes the majority of an astronomical body's hydrosphere. LTER:695 EcoLexicon:ocean FTT:1019 FTT:943 Geonames:H.OCN SWEETRealm:Ocean TGN:21102 https://en.wikipedia.org/wiki/Ocean Ocean ocean envoMarine envoPolar ocean ENVO:00000016 A large expanse of saline water usually connected with an ocean. EcoLexicon:sea FTT:233 FTT:830 Geonames:H.SEA TGN:21103 https://en.wikipedia.org/wiki/Sea Sea sea channel closed sea marginal sea open sea open sound open water envoMarine envoPolar sea ENVO:00000020 A body of water or other liquid of considerable size contained in a depression on a landmass. LTER:278 EcoLexicon:lake FTT:221 FTT:704 FTT:909 Geonames:H.LK Geonames:H.LKS SPIRE:Lake_or_pond SWEETRealm:Lake TGN:21114 TGN:21115 catch basin open water tarn envoPolar lake ENVO:00000022 A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply. LTER:474 EcoLexicon:river FTT:1179 FTT:251 SPIRE:River SWEETRealm:River TGN:21105 rio braided river "There are no official definitions for the generic term river as applied to geographic features, although in some countries or communities a stream is defined by its size. Many names for small rivers are specific to geographic location; examples are "run" in some parts of the United States, "burn" in Scotland and northeast England, and "beck" in northern England. Sometimes a river is defined as being larger than a creek, but not always: the language is vague." river ENVO:00000023 A watercourse which is linear and flows across the solid portion of a planetary surface. LTER:562 watercourse EcoLexicon:stream FTT:105 FTT:1221 FTT:1225 FTT:1261 FTT:303 FTT:371 FTT:593 FTT:721 Geonames:H.STM Geonames:H.STMS SWEETRealm:Stream TGN:21106 TGN:21107 TGN:21108 TGN:21109 https://en.wikipedia.org/wiki/Stream Stream stream streams braided stream fork (hydrographic lode millstream stream bend stream ENVO:00000025 An artificial body of water, often contained by a dam, constructed for the purpose of water storage. lake EcoLexicon:reservoir FTT:587 FTT:588 FTT:882 Geonames:H.RSV SWEETRealm:Reservoir TGN:51259 https://en.wikipedia.org/wiki/Reservoir reservoir covered reservoir reservoir ENVO:00000026 A cylindrical hole, pit, or tunnel drilled or dug down to a depth from which water, oil, or gas can be pumped or brought to the surface. EcoLexicon:well FTT:1032 FTT:1237 FTT:833 Geonames:H.WLL Geonames:H.WLLS SWEETRealm:Well TGN:51255 https://en.wikipedia.org/wiki/Well well ENVO:00000027 A point where groundwater or steam flows out of the ground, and is thus where the aquifer surface meets the ground surface or where there is a fissure. EcoLexicon:spring FTT:982 Geonames:H.SPNG SWEETRealm:Spring TGN:21126 SPRING Spring spring spring ENVO:00000029 A flowing body of water. EcoLexicon:brook EcoLexicon:course EcoLexicon:culvert EcoLexicon:gully EcoLexicon:ravine EcoLexicon:spillway EcoLexicon:waterway FTT:105 Geonames:H.NRWS Geonames:H.RCH Geonames:H.WTRC Geonames:S.SPLY TGN:21110 TGN:21131 TGN:21133 TGN:21137 TGN:21163 TGN:21499 https://en.wikipedia.org/wiki/Watercourse culvert dredged channel fork gulch gully gut gutter kill lode narrows overflow channel passage pup race ravine reach rill rivulet run runnel seachannel seaway spillway stream tideway wash water gap watercourse ENVO:00000032 An area of water bordered by land on three sides. EcoLexicon:bay FTT:190 FTT:232 FTT:235 Geonames:H.BAY Geonames:H.BAYS Geonames:H.BGHT SWEETRealm:Bay TGN:21121 TGN:21123 TGN:21127 bay ENVO:00000033 A body of water, usually of smaller size than a lake. LTER:975 lake EcoLexicon:pond FTT:221 FTT:902 FTT:904 FTT:905 Geonames:H.PND Geonames:H.PNDS Geonames:H.POOL SPIRE:Lake_or_pond SWEETRealm:Pond TGN:21104 TGN:21119 https://en.wikipedia.org/wiki/Pond Pond pool (water body) pond ENVO:00000037 A small, human-made channel which has been dug for draining or irrigating the land. EcoLexicon:drain FTT:129 FTT:400 FTT:403 Geomames:DTCH SWEETRealm:Drain TGN:51256 https://en.wikipedia.org/wiki/Ditch ditch ENVO:00000042 Artificial watercourse with no flow or a controlled flow used drainage. canal FTT:129 FTT:401 Geonames:H.CNLD drainage canal drainage canal ENVO:00000043 An vegetated area which overlaps a wetland ecosystem. wetland area ENVO:00000062 Place or area with clustered or scattered buildings and a permanent human population. place FTT:1097 FTT:33 Geonames:P.PPL Geonames:P.PPLS TGN:22201 TGN:83002 https://en.wikipedia.org/wiki/Populated_place inhabited place populated place populated places settlement populated place ENVO:00000063 An accumulation of water of varying size. hydrographic feature EcoLexicon:waterbody FTT:131 FTT:280 FTT:827 SWEETRealm:BodyOfWater TGN:21100 TGN:21101 https://en.wikipedia.org/wiki/Water_body aquatic feature bodies of water body of water waterbody https://en.wikipedia.org/wiki/ The term body of water most often refers to large accumulations of water, such as oceans, seas, and lakes, but it includes smaller pools of water such as ponds, wetlands, or more rarely, puddles. A body of water does not have to be still or contained; Rivers, streams, canals, and other geographical features where water moves from one place to another are also considered bodies of water. water body ENVO:00000067 Naturally formed, subterranean open area or chamber. FTT:1071 FTT:443 FTT:445 FTT:446 FTT:447 Geonames:S.CAVE SWEETRealm:Cave TGN:21485 TGN:21486 https://en.wikipedia.org/wiki/Cave cave ENVO:00000068 An underground or underwater passage. FTT:445 FTT:448 Geonames:R.TNLN SWEETRealm:Tunnel TGN:21447 https://en.wikipedia.org/wiki/Tunnel TUNNEL tunnel ENVO:00000070 A construction that has been assembled by deliberate human effort. constructed feature human construction ENVO:00000073 A permanent walled and roofed construction. FTT:42 Geonames:S.BLDG LTER:76 TGN:51011 https://en.wikipedia.org/wiki/Building BUILDING building building ENVO:00000074 A barrier constructed across a watercourse to control the flow or raise the level of water. EcoLexicon:dam FTT:599 FTT:600 Geonames:S.DAM SWEETRealm:Dam TGN:51253 https://en.wikipedia.org/wiki/Dam DAM Dam dam dam ENVO:00000076 An excavation in the Earth for the purpose of extracting earth materials. EcoLexicon:mine FTT:14 FTT:968 Geonames:L.MNA Geonames:S.MN TGN:54211 TGN:54212 mine ENVO:00000077 FTT:1246 FTT:1247 FTT:44 FTT:45 FTT:46 FTT:48 FTT:50 FTT:51 FTT:52 FTT:57 FTT:60 FTT:62 FTT:63 FTT:64 FTT:72 FTT:74 Geonames:L.AGRC Geonames:L.RESA Geonames:S.NSY TGN:55001 barn cattle dipping tank corral dairy feedlot grange grazing allotment irrigated field nursery pastoral site sheepfold stockyard As with other classes that are "features", the subclasses of this class are being moved to more informative locations. Their relation to agriculture will be modelled by something more akin to a quality or relation to an agricultural process. agricultural ecosystem ENVO:00000078 An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein. agricultural site FTT:45 FTT:58 FTT:59 FTT:69 Geonames:S.FRM Geonames:S.FRMS Geonames:S.RNCH TGN:54011 https://en.wikipedia.org/wiki/Farm FARM farm ENVO:00000080 A series of connected and aligned mountains or mountain ridges. EcoLexicon:mountain_range FTT:548 FTT:995 FTT:997 Geonamaes:MTS SWEETRealm:MountainRange TGN:21431 TGN:21432 https://en.wikipedia.org/wiki/Mountain_range MOUNT RANGE envoPolar mountain range ENVO:00000086 A region of general uniform slope, comparatively level, and of considerable extent. EcoLexicon:plain FTT:707 FTT:874 FTT:926 Geonames:T.PLN SWEETRealm:Plain TGN:21461 https://en.wikipedia.org/wiki/Plain PLAIN Plain plain plain ENVO:00000091 A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a body of water. EcoLexicon:beach EcoLexicon:to_beach FTT:237 FTT:239 Geonames:T.BCH Geonames:T.BCHS SWEETRealm:Beach TGN:21482 https://en.wikipedia.org/wiki/Beach Beach beach berm lagoon beach beach ENVO:00000097 A region rendered barren or partially barren by environmental extremes, especially by low rainfall. EcoLexicon:desert FTT:1 FTT:188 Geonames:T.DSRT LTER:147 SWEETRealm:Desert TGN:21201 https://en.wikipedia.org/wiki/Desert envoPolar desert area ENVO:00000098 Area of dry or relatively dry land surrounded by water or low wetland. EcoLexicon:island FTT:147 FTT:450 FTT:886 FTT:887 FTT:888 FTT:889 Geonames:T.ISL Geonames:T.ISLS SWEETRealm:Island TGN:21468 TGN:21469 TGN:21471 TGN:21475 https://en.wikipedia.org/wiki/Island envoPolar island ENVO:00000104 EcoLexicon:fan EcoLexicon:platform EcoLexicon:ravine FTT:1020 FTT:1137 FTT:1176 FTT:1193 FTT:1194 FTT:1195 FTT:1196 FTT:5 FTT:810 FTT:984 Geonames:FRKU Geonames:FRSU Geonames:MDVU Geonames:PLFU Geonames:RAVU Geonames:RMPU Geonames:U.BSNU Geonames:U.EDGU Geonames:U.ESCU Geonames:U.FANU Geonames:U.FLTU Geonames:U.FURU Geonames:U.GAPU Geonames:U.GLYU Geonames:U.HOLU Geonames:U.LDGU Geonames:U.LEVU Geonames:U.PLNU Geonames:U.PLTU Geonames:U.PNLU Geonames:U.PRVU Geonames:U.RDGU Geonames:U.RDSU Geonames:U.RISU Geonames:U.SDLU Geonames:U.SHVU Geonames:U.SILU Geonames:U.SPRU Geonames:U.TERU Geonames:U.VALU Geonames:U.VLSU TGN:23001 TGN:23116 TGN:23117 TGN:23118 TGN:23135 TGN:23162 TGN:23181 TGN:23182 TGN:23183 TGN:23184 TGN:23188 TGN:23192 TGN:23193 TGN:23194 TGN:23195 TGN:23196 TGN:23211 TGN:23212 TGN:23301 TGN:23411 TGN:23412 TGN:23413 TGN:23415 TGN:23421 TGN:23423 TGN:23424 TGN:23431 TGN:23453 TGN:23461 TGN:23463 TGN:23467 TGN:23550 basin escarpment fan flat fork forks furrow gap gully hole hole (seafloor) ledge levee median valley moat (seafloor) pinnacle plain plateau platform province ramp ramp (seafloor) ravine ridge ridges rise rise (seafloor) saddle shelf edge undersea bank undersea basin undersea bench undersea cliff undersea fan undersea fork undersea fracture zone undersea furrow undersea gap undersea hole undersea ledge undersea levee undersea median valley undersea moat undersea peak undersea pinnacle undersea plain undersea platform undersea ramp undersea rise undersea saddle undersea shelf undersea shelf edge undersea shelf valley undersea sill undersea slope undersea spur undersea terrace undersea tongue undersea valley undersea feature ENVO:00000106 An area in which grasses (Graminae) are a significant component of the vegetation. grassland area ENVO:00000109 Land having a cover of trees, shrubs, or both. FTT:1083 FTT:505 FTT:506 FTT:719 FTT:774 Geonames:V.GRVPN LTER:503 SWEETRealm:Break SWEETRealm:Scrub TGN:21631 TGN:21632 TGN:21641 https://en.wikipedia.org/wiki/Woodland brigalow pine grove woodland area ENVO:00000111 An area with a high density of trees. A small forest may be called a wood. EcoLexicon:forest FTT:258 FTT:506 FTT:715 FTT:717 Geonames:V.FRST LTER:2 SWEETRealm:Forest TGN:21641 TGN:21642 TGN:21645 https://en.wikipedia.org/wiki/Forest The definitions of forest can vary greatly, and different classes will be needed to support the major categories. Tree cover alone is not enough to distinguish between forests and plantations. The international definition proposed by the 2010 FAO Forestry Resource Assessment: "land spanning more than 0.5 ha with trees higher than 5 metres and canopy cover of more than 10 percent, or trees able to reach these thresholds in situ . It does not include land that is predominantly under agricultural or urban land use." - FAO. 2010. Global forest resources assessment 2010, Main report, FAO Forestry Paper 163. Rome. forested area ENVO:00000112 A vegetated area which is part of a tundra ecosystem. EcoLexicon:tundra FTT:151 FTT:152 Geonames:V.TUND LTER:605 TGN:21611 envoPolar area of tundra ENVO:00000114 A field which is located on land and used for agricultural purposes, such as the grazing of livestock or the cultivation of crops. agricultural site EcoLexicon:field FTT:45 FTT:61 Geonames:L.FLD SWEETRealm:Field TGN:21456 field agricultural field ENVO:00000117 An intentional planting of a crop, on a large scale, usually for uses other than cereal production or pasture. The term is currently most often used for plantings of trees and shrubs. The term tends also to be used for plantings maintained on economic bases other than that of subsistence farming. FTT:45 FTT:68 TGN:54041 https://en.wikipedia.org/wiki/Plantation plantation ENVO:00000121 EcoLexicon:artificial_channel artificial channel ENVO:00000123 A geographical region whose affairs and population are administered by an authority. FTT:1093 Geonames:A.PCL TGN:80002 political entity ENVO:00000127 An arid terrain with clay-rich soil that has been extensively eroded by wind and water. barren land FTT:186 FTT:187 Geonames:T.BDLD TGN:21205 https://en.wikipedia.org/wiki/Badlands badlands badland ENVO:00000130 A ridge of rocks, lying near the surface of the sea, which may be visible at low tide, but is usually covered by water. EcoLexicon:reef FTT:202 FTT:203 FTT:729 Geonames:H.RF Geonames:U.RFSU Geonames:U.RFU SPIRE:Reef TGN:21479 https://en.wikipedia.org/wiki/Reef REEF atoll reef bank reef barrier reef fringing reef shore reef submerged reef rocky reef ENVO:00000137 An opening of the sea into the land. FTT:463 TGN:21128 envoPolar coastal inlet ENVO:00000139 A ditch that supplies water to surrounding land. canal FTT:129 FTT:406 Geonames:H.DTCHI irrigation ditch irrigation ditch ENVO:00000140 A ditch that collects water from the surrounding land. EcoLexicon:drainage_ditch FTT:129 FTT:402 Geonames:H.DTCHD drainage ditch drainage ditch ENVO:00000191 A part of an astronomical body which is primarily composed of a continuous volume of solid material, shaped by one or more environmental processes. EcoLexicon:landform EcoLexicon:landforms FTT:754 FTT:96 SWEETRealm:Landform TGN:21400 TGN:21401 solid astronomical body part ENVO:00000222 An island that does not sit on a continental shelf, and is of volcanic origin. EcoLexicon:oceanic_island https://en.wikipedia.org/wiki/Oceanic_island oceanic island ENVO:00000266 A grassland ecosystem which is used for grazing of ungulate livestock as part of a farm or ranch. FTT:45 FTT:67 Geonames:L.GRAZ pasture ENVO:00000292 The separation between neighbouring drainage basins (catchments). In hilly country, the divide lies along topographical peaks and ridges, but in flat country or on a high plateau (especially where the ground is marshy) the divide may be invisible - just a more or less notional line on the ground on either side of which falling raindrops will start a journey to different rivers, and even to different sides of a country or continent. FTT:220 FTT:645 Geonames:T.DVD LTER:626 SWEETRealm:Watershed TGN:21440 https://en.wikipedia.org/wiki/Watershed divide water divide watershed ENVO:00000294 A facility in which fish are raised commercially in tanks or enclosures, usually for food. FTT:123 FTT:694 https://en.wikipedia.org/wiki/Fish_farm fish farm ENVO:00000295 A hatchery in which the eggs of fish are hatched under artificial conditions. FTT:695 https://en.wikipedia.org/wiki/Fish_hatchery fish hatchery ENVO:00000297 A flooded parcel of arable land used for growing rice and other semiaquatic crops. https://en.wikipedia.org/wiki/Paddy_field paddy field ENVO:00000300 Area covered with low-growing or stunted perennial vegetation and usually not mixed with trees. FTT:1191 FTT:262 FTT:374 FTT:473 FTT:792 FTT:991 Geonames:V.SCRB SWEETRealm:Scrub TGN:21644 TGN:21652 https://en.wikipedia.org/wiki/Scrubland scrubland scrubland area ENVO:00000309 A landform sunken or depressed below the surrounding area. EcoLexicon:depression FTT:175 FTT:215 FTT:216 Geonames:T.DPR Geonames:T.PAN Geonames:T.PANS SWEETRealm:Depression TGN:21454 TGN:21497 TGN:21521 depression ENVO:00000377 A lake purposefully constructed. https://en.wikipedia.org/wiki/Artificial_lake artificial lake ENVO:00000395 The physical confine of a river, slough or ocean strait consisting of a bed and banks. EcoLexicon:channel EcoLexicon:sea_channel FTT:1192 FTT:233 FTT:461 FTT:462 FTT:463 FTT:464 FTT:465 FTT:466 FTT:468 FTT:469 FTT:470 Geonames:H.CHN Geonames:U.SCNU Geonames:U.SCSU SWEETRealm:Channel TGN:21137 TGN:23451 channel of a watercourse ENVO:00000428 A biome is an ecosystem to which resident ecological communities have evolved adaptations. LTER:809 EcoLexicon:biome major habitat type There has been some concern raised (see Issue #143) about the usefulness of the assertion that organisms have evolved within a given biome. They may have evolved adaptations elsewhere and demonstrating one or the other is often not feasible. Consider relabelling to "environmental system determined by an ecological community" or similar. biome ENVO:00000444 A tract of land which has few or no trees and is surrounded by more heavily wooded areas. FTT:259 FTT:488 Geonames:L.CLG LTER:79 TGN:21651 CLEARING clearing forest clearing There should be a better superclass than "field" which should indicate that there are no woody plants in growth form "tree" around. woodland clearing ENVO:00000446 A biome which is primarily or completely situated on a landmass. LTER:798 SPIRE:Terrestrial terrestrial biome ENVO:00000447 An aquatic biome which is determined by a marine water body. SPIRE:Marine envoPolar This biome includes open-ocean and unprotected coastal ecosystems, characterized by exposure to wave action, tidal fluctuation, and ocean currents as well as systems that largely resemble these. Water in the marine biome is generally within the salinity range of seawater: 30 to 38 ppt. marine biome ENVO:00000450 A reservoir constructed for the purpose of providing water for irrigation. irrigation pond irrigation reservoir ENVO:00000469 A facility, permanent or temporary, on land, in air, space or water, where scientific research or measurements can be undertaken. research facility ENVO:00000475 An opening of the sea into the land, or of a lake into its shore. EcoLexicon:inlet FTT:233 FTT:463 Geonames:H.GULF Geonames:H.INLT SWEETRealm:Inlet TGN:21128 envoPolar inlet ENVO:00000478 FTT:996 envoPolar range of mounts ENVO:00000508 A step-like feature between higher and lower ground: a relatively flat or gently inclined shelf of earth, backed and fronted by steep slopes or manmade detaining walls. EcoLexicon:terrace FTT:247 FTT:248 Geonames:T.BNCH Geonames:T.TRR TGN:21498 TGN:21513 https://en.wikipedia.org/wiki/Terrace TERRACE bench ledge rock terrace terrace terrace ENVO:00000519 https://en.wikipedia.org/wiki/Agricultural_terrace agricultural terrace ENVO:00000546 Lake sediment is sediment which covers the bottom of a lake. Lake sediments are comprised mainly of clastic material (sediment of clay, silt, and sand sizes), organic debris, chemical precipitates, or combinations of these. lake sediment ENVO:00000548 Geonames:L.GVL TGN:21502 gravel field ENVO:00000562 A bounded area of land, or water, usually in its natural or semi-natural (landscaped) state and set aside for some purpose, usually to do with recreation or conservation. park ENVO:00000563 A raised walkway over water, supported by piles or pillars. EcoLexicon:pier pier ENVO:00000565 A building or region where sports activities can be carried out. sports facility ENVO:00000856 Incorporated populated place. urban area EcoLexicon:city FTT:430 FTT:483 FTT:484 FTT:485 SWEETRealm:City TGN:83020 TGN:83040 TGN:83043 https://en.wikipedia.org/wiki/City http://purl.obolibrary.org/obo/NCIT_C80234 city ENVO:00000873 An aquatic biome which is determined by a body of freshwater. SPIRE:Freshwater envoPolar freshwater biome ENVO:00001995 A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids. EcoLexicon:rock FTT:1010 FTT:145 Geonames:T.RK Geonames:T.RKS SWEETRealm:Rock TGN:21444 https://en.wikipedia.org/wiki/Rock From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure. rock ENVO:00001998 Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms. regolith LTER:535 SPIRE:Soil SWEETRealm:Soil https://en.wikipedia.org/wiki/Soil 'In engineering terms, soil is referred to as regolith, or loose rock material that lies above the 'solid geology'. Soil is commonly referred to as "earth" or "dirt"; technically, the term "dirt" should be restricted to displaced soil.' https://en.wikipedia.org/wiki/Soil " The upper limit of soil is the boundary between soil and air, shallow water, live plants, or plant materials that have not begun to decompose. Areas are not considered to have soil if the surface is permanently covered by water too deep (typically more than 2.5 meters) for the growth of rooted plants. The lower boundary that separates soil from the nonsoil underneath is most difficult to define. Soil consists of horizons near the Earth's surface that, in contrast to the underlying parent material, have been altered by the interactions of climate, relief, and living organisms over time. Commonly, soil grades at its lower boundary to hard rock or to earthy materials virtually devoid of animals, roots, or other marks of biological activity. For purposes of classification, the lower boundary of soil is arbitrarily set at 200 cm." Soil taxonomy, 2nd Ed., quoted in http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054280 soil ENVO:00001999 A significant accumulation of water which is part of a marine biome. body of marine water marine waterbody Ideas like "significant" are fuzzy and need to be modelled more accurately. The definition is a candidate for review. marine water body ENVO:00002000 A solid astronomical body part which is part of the planetary surface between the peak of an elevation or the bottom of a depression and relatively flat surrounding land. EcoLexicon:slope SWEETRealm:Slope https://en.wikipedia.org/wiki/Slope slope ENVO:00002001 Water that has been adversely affected in quality by anthropogenic influence. EcoLexicon:waste_water SWEETRealm:Wastewater https://en.wikipedia.org/wiki/Waste_water waste water ENVO:00002003 An excreta material which is composed primarily of feces, an excreta consisting of waste products expelled from an animal's digestive tract through the anus (or cloaca) during defecation. EcoLexicon:drop SPIRE:Dung SWEETRealm:Drop faeces material feces material stool ENVO bodily fluid classes differ from UBERON's treatment of bodily fluids. UBERON refers to the substance itself ("S"). We assert that UBERON's classes are the primary compositional component of the terms in ENVO ("S material"). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S. This is distinct from classes such as http://purl.obolibrary.org/obo/UBERON_0001988 in that it refers to the environmental material composed primarily of feces rather than 'just' feces. fecal material ENVO:00002005 The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth. EcoLexicon:air LTER:18 SWEETRealm:Air https://en.wikipedia.org/wiki/Air envoPolar air ENVO:00002006 An environmental material primarily composed of dihydrogen oxide in its liquid form. water EcoLexicon:water LTER:617 https://en.wikipedia.org/wiki/Water liquid water ENVO:00002007 Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid. EcoLexicon:sediment EcoLexicon:sedimentation LTER:492 LTER:493 SWEETRealm:Sediment https://en.wikipedia.org/wiki/Sediment envoPolar It is recommended to use a combination of sediment terms to describe a more specific sediment type. sediment ENVO:00002008 Minute solid particles with diameters less than 500 micrometers. Occurs in and may be deposited from, the atmosphere. EcoLexicon:dust SWEETRealm:Dust https://en.wikipedia.org/wiki/Dust envoPolar dust ENVO:00002011 Water which has a low concentration of dissolved solutes, particularly that of sodium chloride. EcoLexicon:fresh_water LTER:216 SWEETRealm:FreshWater https://en.wikipedia.org/wiki/Fresh_water freshwater envoEmpo envoPolar The lower bound of solute concentration required for water to be considered freshwater is variable, but is always less than that of seawater, and often cited as less than 1 gram of solutes per 1 litre of water. fresh water ENVO:00002018 Wastewater that is contaminated with feces or urine, SWEETRealm:Sewage https://en.wikipedia.org/wiki/Sewage sewage ENVO:00002030 A biome which is determined by a water body and which has ecological climax communities adapted to life in or on water. LTER:41 aquatic biome ENVO:00002040 wood ENVO:00002113 Sediment that accumulates in the flat or very gently sloping areas of the deep ocean basin floor. The three main types of deep marine sediment, also known as pelagic sediment, are siliceous oozes, calcareous oozes, and red clays. EcoLexicon:marine_sediment EcoLexicon:marine_sedimentation SWEETRealm:MarineSediment https://en.wikipedia.org/wiki/Marine_sediment deep marine sediments envoPolar deep marine sediment ENVO:00002127 Revise adjacent to. Consider sampled stream sediment. Dry stream sediment. stream sediment ENVO:00002170 The aerobically decomposed remnants of organic materials. https://en.wikipedia.org/wiki/Compost compost ENVO:00002173 A hospital is a building in which health care services are provided by specialized staff and equipment. https://en.wikipedia.org/wiki/Hospital hospital ENVO:00002186 EcoLexicon:water_pollution https://en.wikipedia.org/wiki/Contaminated_water polluted water contaminated water ENVO:00002191 Straw or other material strewn in an animal's enclosure (e.g. a stable) for it to sleep on and to absorb its faeces and urine. straw bedding animal litter http://opendata.inra.fr/EOL/EOL_0001601#bedding ENVO:00002221 A building in which a business presents a selection of goods and offers to trade or sell them to customers for money or other goods. https://en.wikipedia.org/wiki/Shopping retail shop retail store retailer shop ENVO:00002222 A shop in which a business offers food products for sale or trade. Whether food is the primary product offered by the business or simply one of the products it offers is not specified in this class. food shop ENVO:00002258 A soil composed of sand, silt, and clay in relatively even concentration (about 40-40-20% concentration respectively). EcoLexicon:loam SWEETRealm:Loam https://en.wikipedia.org/wiki/Loam loam ENVO:00002259 agricultural soil ENVO:00002263 A portion of soil which is found in a garden. garden soil ENVO:00002264 A material which is not the desired output of a process and which is typically the input of a process which removes it from its producer (e.g. a disposal process). EcoLexicon:waste SWEETRealm:Waste https://en.wikipedia.org/wiki/Waste waste material ENVO:00002272 WWTP waste treatment plant ENVO:00003031 This is interesting in that the "role" aspect of "waste" is (or can be) replaced by another role "fertilizer". Thus, the positioning of "manure" under waste may not be totally correct. animal manure ENVO:00003032 fresh animal manure ENVO:00003040 A house used for sheltering non-human animals. While humans are animals, this class does not refer to human houses. animal house ENVO:00003042 An animal house which is used to house pigs. https://en.wikipedia.org/wiki/Piggery piggery ENVO:00003043 https://en.wikipedia.org/wiki/Sewage_plant sewage plant ENVO:00003064 Drinking water is water which may be consumed by humans with no adverse effects on their health. EcoLexicon:drinking_water SWEETRealm:DrinkingWater https://en.wikipedia.org/wiki/Drinking_water potable water drinking water ENVO:00003074 A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products. manufactured good manufactured product ENVO:00003096 https://en.wikipedia.org/wiki/Tap_water tap water ENVO:00003859 https://en.wikipedia.org/wiki/Horse_manure horse manure ENVO:00003860 Manure which is primarily composed of pig feces. pig manure ENVO:00003861 An industrial building is a building within which goods are produced and, optionally, stored or within which services are rendered. It's possible that this will become an inferred class in the future. The United Nations' International Standard Industrial Classification should be referred to when expanding this branch. ISIC can also be used to identify processes. See http://unstats.un.org/unsd/cr/registry/regcst.asp?Cl=27&Lg=1. industrial building ENVO:00003862 A dairy is a building in which animal milk is harvested and, optionally, processed for human consumption. https://en.wikipedia.org/wiki/Dairy 'Terminology differs between countries. For example, in the United States, the entire dairy farm is commonly called a "dairy." The building or farm area where milk is harvested from the cow is often called a "milking parlor" or "parlor." The farm area where milk is stored in bulk tanks is known as the farm's "milk house." Milk is then hauled (usually by truck) to a "dairy plant," also referred to as a "dairy", where raw milk is further processed and prepared for commercial sale of dairy products. In New Zealand, farm areas for milk harvesting are also called "milking parlours", and are historically known as "milking sheds."' https://en.wikipedia.org/wiki/Dairy dairy ENVO:00003863 A food processing building is a building in which materials that contain or consist of essential body nutrients - such as carbohydrates, fats, proteins, vitamins, or minerals - and may be ingested and assimilated by an organism to produce energy, stimulate growth, and maintain life are converted alternative forms. The semantics of food are being handled by FOODON http://purl.obolibrary.org/obo/foodon.owl food processing building ENVO:00003864 A bakery is a building in which raw flour-based food is baked in an oven to produce food products such as bread, cakes, pastries, and pies. These products are often sold from the bakery itself. https://en.wikipedia.org/wiki/Bakery A bakery is a food processing building and a 'food shop' at the same time. This needs to be resolved. bakery ENVO:00003884 farmyard manure ENVO:00003885 A brewery is a building in which alcoholic beverages are produced by brewing, that is, steeping a starch source (commonly cereal grains) in water and fermenting the resulting sweet liquid with yeast. At times, the products are also sold from the brewery. brewery ENVO:00003895 paper product ENVO:00003896 currency note ENVO:00003927 stable manure ENVO:00003968 An air filter is a device that removes some substance from air. https://en.wikipedia.org/wiki/Air_filter This is a general definition derived from the definitions for particulate, chemical, and other air filters. Subclasses should be created if needed. air filter ENVO:00004638 A building within which logs are cut into lumber products. sawmill ENVO:00005747 Soil which is derived from compost. compost soil ENVO:00005749 A portion of soil which is part of a cropland or a rangeland biome. farm soil ENVO:00010483 A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. portion of environmental material Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. environmental material ENVO:00010504 A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings. EcoLexicon:surface http://sweetontology.net/reprSpaceGeometry/Surface https://en.wikipedia.org/wiki/Surface This class is distinct from a geometric surface, which is two-dimensional. The idea of "uppermost" may be problematic. Further, the definition of layer (the superclass of surface in rev 133) references surface. This may be another issue. Perhaps this can be made into an inferred class using 'bounding layer of' some material entity, note that 'bounding layer' implies containment, which may not be valid here. surface layer ENVO:00010625 A facility in which animals are confined within enclosures and displayed to the public, and in which they may also be bred. zoo zoological park zoological garden ENVO:0010001 Anthropogenic material in or on which organisms may live. anthropogenic environmental material ENVO:0010003 This is quite odd and it probably should be obsoleted. Any material that is a participant in an agricultural process can be seen as an agricultural material. agricultural environmental material ENVO:01000001 A liquid or semi-liquid mixture of water and some combination of soil, silt, and clay. EcoLexicon:mud LTER:356 SWEETRealm:Mud https://en.wikipedia.org/wiki/Mud mud ENVO:01000002 A well which provides access to groundwater held in an aquifer. https://en.wikipedia.org/wiki/Water_well water well ENVO:01000017 A naturally occurring granular material composed of finely divided rock and mineral particles. EcoLexicon:sand LTER:484 SWEETRealm:Sand https://en.wikipedia.org/wiki/Sand sand ENVO:01000018 Gravel is an environmental material which is composed of pieces of rock that are at least two millimeters (2mm) in its largest dimension and no more than 75 millimeters. EcoLexicon:gravel SWEETRealm:Gravel https://en.wikipedia.org/wiki/Gravel The logical def is a little off here - it should really suggest that a gravel is composed of many "pieces" of gravel. gravel ENVO:01000044 A prominent or distinctive aspect, quality, or characteristic of environments occurring within the marine water column. envoPolar marine pelagic feature ENVO:01000048 A marine biome which is determined by an ocean. envoPolar Ocean biomes are determined by major bodies of saline water, principal components of the hydrosphere. Approximately 71% of the Earth's surface is covered by ocean, a continuous body of water that is customarily divided into several principal oceans and smaller seas. More than half of this area is over 3,000 metres (9,800 ft) deep. Average oceanic salinity is around 35 parts per thousand (ppt) (3.5%), and nearly all seawater has a salinity in the range of 30 to 38 ppt. ocean biome ENVO:01000060 Particulate material is an environmental material which is composed of microscopic portions of solid or liquid material suspended in another environmental material. envoAtmo envoPolar particulate matter ENVO:01000155 Environmental material derived from living organisms and composed primarily of one or more biomacromolecules. EcoLexicon:organic_material biomass organic material ENVO:01000174 A forest ecosystem in which dominant ecological communities have reached their climax successional state. LTER:212 SPIRE:Forest Preliminary definition. forest biome ENVO:01000175 A woodland biome is a terrestrial biome which includes, across its entire spatial extent, woody plants spaced sufficiently far apart to allow light penetration to support communities of herbaceous plants or shrubs living closer to the woodland floor. Preliminary definition. woodland biome ENVO:01000176 A shrubland biome is a terrestrial biome which includes, across its entire spatial extent, dense groups of shrubs. Preliminary definition. shrubland biome ENVO:01000177 A grassland ecosystem in which dominant ecological communities have reached their climax successional state. SPIRE:Savannah_or_grassland grassland biome ENVO:01000179 A desert biome is a terrestrial biome which loses more liquid water by evapotranspiration than is supplied by precipitation and includes communities adapted to these conditions. SPIRE:Desert_or_dune wwfBiome Preliminary definition. desert biome ENVO:01000180 A terrestrial biome which comprises a tundra ecosystem that has reached its climax community. SPIRE:Tundra envoPolar wwfBiome Preliminary definition. tundra biome ENVO:01000181 A mangrove biome is a terrestrial biome which includes, across its spatial extent, mangrove plants (Rhizophoraceae). Mangrove plants are able to withstand high levels of salinity as well as regions of anoxia and frequent tidal inundation. Mangrove biomes often occur near tropical and sub-tropical estuaries and depositional marine coastal environments where fine sediments (often with high organic content) collect in areas protected from high energy wave action. LTER:322 wwfBiome Preliminary definition. Depending on whether mangrove trees or shrubs are present, this class could be a child of shrubland biome or woodland biome. Consider creating the appropriate classes. mangrove biome ENVO:01000219 An anthropogenic terrestrial biome is a terrestrial biome which has community structures determined by human activity. anthrome human biome Preliminary definition. anthropogenic terrestrial biome ENVO:01000245 A cropland ecosystem in which dominant ecological communities are maintained in a stable state - mimicking a climax community - by human intervention. cropland biome ENVO:01000246 A village biome is an anthropogenic terrestrial biome which contains settlements such as villages, towns, and/or small cities and which is primarily used for agricultural activity. Villages are also described as agricultural settlements with greater than 100 persons per square kilometre; however, no upper limit is defined. village biome ENVO:01000247 A rangeland biome is an anthropogenic terrestrial biome which is primarily used for the rearing and grazing of livestock. rangeland biome ENVO:01000248 A dense settlement biome is an anthropogenic terrestrial biome which is primarily used for human habitation, recreation, and industry within built structures with little other land use. dense settlement biome ENVO:01000252 A biome which is determined by a freshwater lake. freshwater lake biome ENVO:01000253 freshwater river biome ENVO:01000254 A system which has the disposition to environ one or more material entities. EcoLexicon:environment environment In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. environmental system ENVO:01000281 A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface. envoPolar Preliminary definition. layer ENVO:01000320 A marine environment and enviroment which is determined by a marine water body. envoPolar marine environment ENVO:01000324 A planetary surface is a surface layer where the solid or liquid material of a planet comes into contact with an atmosphere or outer space. a useful class: this can be used to define sub-terrestrial and sub-marine entities planetary surface ENVO:01000348 A field used for the cultivation of corn or related crop plants. Requested in Issue 112 as part of the curation of metagenome submissions in the European Nucleotide Archive. maize field ENVO:01000352 An unbroken expanse (as of ice) envoPolar This class was created to accommodate "fields" from agricultural fields to marine mesoscale eddy fields. Thus, it has a very broad definition which makes it less than informative when annotating. Please consider using or requesting an appropriate subclass. field ENVO:01000404 A (portion of) plastic is an (portion of) anthropogenic environmental material including any of numerous organic synthetic or processed materials which are primarily composed of thermoplastic or thermosetting polymers of high molecular weight. URL:http://aims.fao.org/aos/agrovoc/c_5998 URL:http://eurovoc.europa.eu/1837 envoPolar manufactured plastic ENVO:01000408 A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein. envoPolar Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition. environmental zone ENVO:01000417 A house is a building that provides a dwelling-place for a living entity. The provisioning of a dwelling-place can perhaps be modelled as a role. house ENVO:01000418 A human house is a house which provides a dwelling-place for humans. human house ENVO:01000420 A building part is a construction which is part of a building. Not recommended for annotation. This class is likely to be made into an inferred class as its subclasses are distributed among more meaningful superclasses (i.e. ceiling is_a surface layer). See for example, "building floor". The boundaries between building parts may be bona fide or fiat. building part ENVO:01000422 A bathroom is a room which contains a washbasin or other fixture, such as a shower or bath, used for bathing by humans. bathing room bathroom ENVO:01000426 A building part which is separated from other building parts by one or more interior walls and, optionally, outdoor areas by one or more exterior walls. room ENVO:01000467 A constructed barrier is a freestanding wall, berm, or fence built to limit movement of entities across a boundary. barrier constructed barrier ENVO:01000480 Glass is an amorphous (non-crystalline) solid which is often transparent. This class refers to all forms of glass. For the familiar form present in window panes and drinking glasses, consider silica-based glass. glass ENVO:01000481 Silica-based glass is a glass composed primarily of silicon dioxide, the primary constituent of sand. glass Silica-based glasses are the most common manufactured variety of glass. silica-based glass ENVO:01000486 A building floor is a surface layer which is part of a building and used for walking. To be more precise, a subfloor and a floor covering may be specified. Please request these classes and propose definitions if they are needed. building floor ENVO:01000536 A factory (previously manufactory) or manufacturing plant is an industrial site, usually consisting of buildings and machinery, or more commonly a complex having several buildings, where workers manufacture goods or operate machines processing one product into another. manufactory manufacturing plant factory ENVO:01000584 A table is a form of furniture with a flat horizontal upper surface used to support objects, for storage, show, and/or manipulation. table ENVO:01000585 A desk is a table which is intended for information-manipulation tasks, including writing and use of interactive electronics. The intentional nature of this definition is problematic, but the restricted range of activities visited upon a desk is of interest. desk ENVO:01000587 A piece of furniture is a movable object intended to support various human activities such as seating (e.g., chairs, stools and sofas) and sleeping (e.g., beds). The assumption is that furniture is manufactured, which is arguable. Further, according to Black's Law Dictionary (http://thelawdictionary.org/furniture/) many classes can be subclasses of 'piece of furntiure': "This term includes that which furnishes, or with which anything is furnished or supplied; whatever must be supplied to a house, a room, or the like, to make it habitable, convenient, or agreeable; goods, vessels, utensils, and other appendages necessary or convenient for housekeeping; whatever is added to the interior of a house or apartment, for use or convenience. Bell v. Holding, 27 Ind. 173.The term “furniture” embraces everything about the house that has been usually enjoyed there, including plate, linen, china, and pictures. 1 Endicott v. Endicott, 41N. J. Eq. 96, 3 Atl. 157.The word “furniture” made use of in the disposition of the law. or in the conventions or acts of persons, comprehends only such furniture as is intended for use and ornament of apartments, but not libraries which happen to be there, nor plate. Civ.Code La. art. 477." However, this would eventually be absurd and limit other groupings. Perhaps some sort of 'furnishing' BFO:function would be a better way to handle this. piece of furniture ENVO:01000601 A motor vehicle is a vehicle which is propelled by an engine or motor and that does not operate on rails. Subclasses will be added by inference. motor vehicle ENVO:01000602 A truck is a motor vehicle which, as its primary funcion, transports cargo rather than human passangers. lorry truck ENVO:01000604 A vehicle is a mobile machine which transports people or cargo. vehicle ENVO:01000617 A lentic water body is a water body in which the accumulated water, in its totality, has very little to no directed flow. lentic water body ENVO:01000618 A lotic water body is a water body in which the accumulated water, in its totality, is flowing. lotic water body ENVO:01000625 A manufactured structure made of interspaced structural elements such as metal or wooden bars or wires held together such that they may be used to confine, contain, or protect something. cage manufactured cage ENVO:01000626 A drylot is an enclosure of limited size usually bare of vegetation and used for fattening livestock. drylot ENVO:01000627 A feedlot is a plot of land on which livestock are fattened for market feedlot ENVO:01000635 A landmass which is part of a planet. land planetary landmass ENVO:01000658 A settlement with a high density of buildings and inhabitants. The thresholds for what makes a settlment "dense" can be determined as needed. If there is a specific threshold that should be added to ENVO, please make a new class request. dense settlement ENVO:01000685 A mass of water. water mass ENVO:01000703 Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity. precipitation "process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet) hydrological precipitation process ENVO:01000752 An area of a planet's surface which is primarily composed of bedrock, desert pavement, scarp rock, talus, material exposed by slides, volcanic material, glacial debris, sand, material exposed during strip mining, gravel, and other accumulations of earthen material in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction. Barren Land (Rock/Sand/Clay) NLCD:31 envoPolar nlcd2011 According to the NLCD 2011, areas of barren land generally have less than 15% cover of vegetation. A specific threshold is not asserted in this definition. area of barren land ENVO:01000753 A temperature that inheres in some portion of air. obsolete air temperature true ENVO:01000781 A building which is publically accessible. public building ENVO:01000797 A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely. gas gaseous environmental material ENVO:01000813 A material part of an astronomical body. envoAstro envoPolar astronomical body part ENVO:01000814 An environmental material which is in a solid state. This is a defined class: its subclasses will not be asserted, but filled by inference. solid environmental material ENVO:01000815 An environmental material which is in a liquid state. envoPolar This is a defined class: most of its subclasses will not be asserted, but filled by inference. liquid environmental material ENVO:01000875 A precipitation process is a process in which a portion of some substance segregates from a material in which that substance or its precursors were dissolved or suspended in and settles due to a force such as gravity or centrifugal force. precipitation process ENVO:01000918 An animal house which is only partially surrounded by a building envelope. open animal house ENVO:01000921 An animal house which has a complete building envelope. closed animal house ENVO:01000922 A manufactured cage which may be used to confine, contain, or protect an animal. cage chicken cage animal cage ENVO:01000923 A petting zoo is a zoological garden which contains domesticated non-human animals and some wild non-human animals that are docile enough for humans to touch and feed. petting farm Petting zoos are often nested within a zoological garden featuring wild non-human animals, not docile enough for humans to touch. petting zoo ENVO:01000924 An artificial channel which transports unwanted water or waste liquids away from their source, either to a more useful area, a receptacle, or into sewers or stormwater mains as waste discharge to be released or processed. drain drainage channel plumbing drain ENVO:01000925 A facility in which non-human animals are slaughtered and processed for human consumption. slaughterhouse abattoir ENVO:01000927 A building which is used to care for a human child during the working day by a person, outside the child's immediate family, other than that child's legal guardians. child care building This is a kind of day care facility. A facility need not be a building. day care building ENVO:01000928 A building in which fish are subject to a series of operations to prepare them for human consumption. This is a kind of fish processing facility. Facilities need not be buildings, factory ships may be considered fish processing facilities. fish processing building ENVO:01000932 A building in which nursing aides and skilled nurses provide care and treatment to residents who have significant difficulty coping with the required activities of daily living. intermediate care facility long-term care facility skilled nursing facility care home convalescent home rest home nursing home ENVO:01000933 A human house which serves as a long-term shelter for its inhabitants and within which they store personal property. This term is not to be used for hotels, hostels, inns and the like, which provides shorter-term stays. residential building ENVO:01000934 A building within which food and drink are prepared and served to customers in exchange for money or other goods and/or services. eatery restaurant ENVO:01000935 A part of an ecosystem which may be or has been used for one or more overnight stays by humans sheltering in tents, camper vans, caravans, or improvised shelters. camping ground camping pitch camping site campsite campground ENVO:01000936 A campground which has been modified by humans to provide and maintain facilities for camping such as fire pits, road access, latrines, and garbage bins. dedicated campground ENVO:01000937 A campground which has no pre-existing facilities installed or maintained by humans, usually found outside of anthropised ecosystems. impromptu campground ENVO:01000938 A manufactured product which may hold a volume of heated water suitable for one or more humans to bathe in, usually for the purposes of hydrotherapy or pleasure. spa Jacuzzi hot tub ENVO:01000964 Wastewater which is produced by industrial activity and which contains chemical contaminants other than those associated with urine and fecal matter. industrial wastewater ENVO:01000965 A construction which is designed to hold water in which humans may swim or perform other leisure activities. pool paddling pool swimming bath swimming pool wading pool constructed swimming pool ENVO:01000968 A hydraulic-engineering installation which transports water - in specified amounts, of a specified quality, and in accordance with a water-consumption plan - from a source of supply into a conduit. Sources of water include rivers, lakes, reservoirs, and other water bodies. Conduits include canals, pipelines, and tunnels. Water intakes typically transport water for purposes of hydroelectric power engineering, water supply, or irrigation. water intake ENVO:01000969 A building which provides the site for food services with little or no waiting staff furnishing table service. cafeteria ENVO:01000970 A food shop which sells a selection of food products that are not typical dietary components of the human population it is co-located with. The food products sold in a delicatessen are often considered unusual by the majority of its customers and may come from foreign food supplies which are not widely imported into its region of operation. delicatessen ENVO:01000971 A truck which is equipped to cook and sell food. Due to the facilities on board, food trucks are often larger than other trucks with comparable mechanics. food truck ENVO:01000972 A restaurant which provides prepared meals or other food products that the purchaser must eat off its premises. take out restaurant take-away take-out restaurant ENVO:01000973 A booth with an open window on one side. This definition of kiosk is characteristic of the Western hemisphere and used in English-speaking countries. kiosk ENVO:01000974 A kiosk from which food products are sold. This definition of kiosk is characteristic of the Western hemisphere and used in English-speaking countries. food kiosk ENVO:01000984 A food shop in which food products are the primary offer for sale or trade. grocery store ENVO:01000985 A part of an ecosystem which has been allocated to host a gathering of people for multiple entertainment or commercial activities. Fairgrounds, or parts thereof, may be constructed (e.g. concreted over) or be natural (e.g. clearings or heaths), thus land use is the key differentia. fairground ENVO:01000986 A fairground which is used to exhibit agricultural technology, livestock, and farm-related activity. agricultural fairground ENVO:01000987 A part of an ecosystem where people gather for the purchase and sale of provisions, livestock, and other goods. bazaar marketplace mercado palengke souk tianguis As with campgrounds and fairgrounds, land use is the key differentia here. The regularity of marketplace activities may provide a differentia for further growth of this branch. market ENVO:01000988 A food shop in which the food products on offer are restricted to those produced in a region and cultural setting other than that of the shop's locality. ethnic food store ethnic speciality shop ethnic speciality store ethnic food shop ENVO:01000989 An exchangeable device which can be connected to a plumbing system to deliver and drain water. plumbing fixture ENVO:01000990 A plumbing fixture which is bowl-shaped and used for washing hands, dishwashing, and other purposes. hand basin wash basin sink fixture ENVO:01000991 A plumbing fixture which may serve as a container for water in which humans or other animals may bathe. bathtub Of course, there are other uses for bathtubs. bathtub fixture ENVO:01000992 A plumbing fixture within which a human or other animal may bathe under a spray of water. Indoors, there is a drain in the floor. Most showers have temperature, spray pressure and adjustable showerhead nozzle. Showering is common in Western culture due to the efficiency of using it compared with a bathtub. Its use in hygiene is, therefore, common practice. A shower uses less water on average than a bath: 80 litres for a shower compared with 150 litres for a bath. shower fixture ENVO:01001110 An environmental system which includes both living and non-living components. LTER:173 This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here. ecosystem ENVO:01001199 An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it. terrestrial environmental zone ENVO:01001206 An ecosystem in which grasses (Graminae) are the dominant form of vegetation and determine the system's structure and dynamics. EcoLexicon:grassland FTT:259 FTT:760 FTT:766 Geonames:V.GRSLD LTER:232 TGN:21604 TGN:54052 GRASSLAND grassland grassland ecosystem ENVO:01001222 A building which is primarily used to facilitate the buying or selling of goods or services. "Commerce includes legal, economic, political, social, cultural and technological systems that are in operation in any country or internationally." commercial building ENVO:01001243 An ecosystem which is determined by communities of plants with a tree growth form and in which members of those communities form continuous or discontinuous regions of canopy cover. The definitions of forest can vary greatly, and different classes will be needed to support the major categories. Tree cover alone is not enough to distinguish between forests and plantations. The international definition proposed by the 2010 FAO Forestry Resource Assessment: "land spanning more than 0.5 ha with trees higher than 5 metres and canopy cover of more than 10 percent, or trees able to reach these thresholds in situ . It does not include land that is predominantly under agricultural or urban land use." - FAO. 2010. Global forest resources assessment 2010, Main report, FAO Forestry Paper 163. Rome. forest ecosystem ENVO:01001244 An ecosystem which 1) is determined by communities of annual crops, perennial woody crops, or by actively tilled land, 2) is primarily used for agricultural activity, and 3) contains no village or larger human settlement. cropland ecosystem ENVO:01001275 A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid. solid layer ENVO:01001305 A vegetated area is a geographic feature which has ground cover dominated by plant communities. envoPolar vegetated area ENVO:01001308 A geographic feature which is primarily composed of a continuous volume of liquid water held in shape or sustained by an environmental process. Similar, in spirit, to landform. hydroform ENVO:01001311 A surface layer which is composed primarily of solid environmental material. solid surface layer ENVO:01001319 A body of water which is primarily composed of saline water. saline body of water This class has its subclasses populated by inference. saline water body ENVO:01001406 A research facility in which systems of manufactured products control internal conditions and in which scientific or technological research, experiments, and measurement may be performed. laboratory facility ENVO:01001476 body of liquid ENVO:01001477 A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes. liquid astronomical body part ENVO:01001479 A part of an astronomical body which is primarily composed of a continuous volume of liquid or gaseous material, shaped by one or more environmental processes. fluid astronomical body part ENVO:01001480 A building which is primarily used for the long-term habitation of humans. domestic building ENVO:01001483 A surface layer where the solid or liquid material of an astronomical body comes into contact with an atmosphere or outer space. a useful class: this can be used to define sub-terrestrial and sub-marine entities surface of an astronomical body ENVO:01001684 A layer which separates two portions of environmental material which possess 1) differing compositions, 2) a discontinuity of some property, or 3) some derivative of some property in a direction normal to the interface. interface layer ENVO:01001780 An ecosystem in which the composition, structure, and function of resident ecological assemblages are primarily determined by a desert. desert ecosystem ENVO:01001782 A large continuous area of land, either surrounded by sea or contiguous with another landmass. landmass ENVO:01001784 A part of an astronomical body which is primarily composed of a continuous medium bearing liquid, gaseous, and solid material in varying quantities. compound astronomical body part ENVO:01001785 A surface layer of an astronomical body which is primarily composed of solid material and is not covered by oceans or other bodies of water. land ENVO:01001787 aquatic ecosystem ENVO:01001788 marine ecosystem ENVO:01001789 freshwater ecosystem ENVO:01001790 terrestrial ecosystem ENVO:01001813 A material entity which has been assembled through the intentional, instinctual, or deliberately programmed efforts of an organism or machine. construction ENVO:01001873 A construction in which eggs are hatched under artificial conditions. hatchery ENVO:02000001 A textile is a manufactured product comprised of a network of natural or artificial fibers (often referred to as thread or yarn). https://en.wikipedia.org/wiki/Textile textile ENVO:02000019 An organic material which is primarily composed of some natural bodily fluid or secretion such as blood, semen, saliva, blood plasma, intracellular and interstitial fluids. https://en.wikipedia.org/wiki/Bodily_fluid ENVO bodily fluid classes differ from UBERON's treatment of bodily fluids. UBERON refers to the substance itself ("S"). We assert that UBERON's classes are the primary compositional component of the terms in ENVO ("S material"). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S. bodily fluid material ENVO:02000022 A bodily fluid material which is composed primarily of excreta, bodily fluids consisting of matter which contains the waste products of biological processes, including urine or feces, discharged from an organism's body. ENVO bodily fluid classes differ from UBERON's treatment of bodily fluids. UBERON refers to the substance itself ("S"). We assert that UBERON's classes are the primary compositional component of the terms in ENVO ("S material"). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S. excreta material ENVO:02000047 Food material which can be used to meet nutritional requirements of animals, particularly livestock such as cattle, goats, sheep, horses, chickens and pigs. https://en.wikipedia.org/wiki/Animal_feed Most animal feed is from plants but some is of animal origin. Fodder refers particularly to food given to the animals (including plants cut and carried to them), rather than that which they forage for themselves. It includes hay, straw, silage, compressed and pelleted feeds, oils and mixed rations, and also sprouted grains and legumes. animal feed ENVO:02000048 Contaminated animal feed is an animal feed that has become contaminated with or come contact with microorganisms or toxic chemicals. contaminated animal feed ENVO:02000054 A mixture of crushed and coarsely ground bones that is used as an organic fertilizer for plants and formerly in animal feed. https://en.wikipedia.org/wiki/Bone_meal bone meal ENVO:02000055 Food material which can be used to meet nutritional requirements of plants. plant feed ENVO:02000058 A textile comprised of a pliable material made usually by weaving, felting, or knitting natural or synthetic fibers and filaments. https://en.wikipedia.org/wiki/Cloth cloth ENVO:02000140 A liquid or a gas. fluid fluid environmental material ENVO:02500000 A process in which includes the components of an environmental system as participants. This is a convenience class for organisation and should not be used for annotation. environmental system process ENVO:03000010 A process during which material is displaced from its original location and transported either to a new location or back to the original location. http://orcid.org/0000-0002-3410-4655 envoPolar Experimental class for structural purposes not recommended for annotation. material transport process ENVO:03000033 Sediment which has been transported through the marine water column, settling on the seafloor. http://orcid.org/0000-0002-3410-4655 marine sediments envoPolar Particles of marine sediment are primarily generated by 1) processes in terrestrial systems and transported to the marine realm by the action of rivers or aeolian processes (amongst other routes) , 2) marine organisms, 3) chemical processes in seawater, or 4) cosmogeneous input. marine sediment ENVO:03000117 A structure which traverses a mass of one or more environmental materials, and encloses a roughly tubular site. http://orcid.org/0000-0002-3410-4655 envoPolar channel ENVO:03501109 ENVO:03501121 ENVO:03501127 ENVO:03501130 ENVO:03501133 ENVO:03501135 ENVO:03501136 ENVO:03501145 ENVO:03501152 ENVO:03501180 ENVO:03501186 ENVO:03501194 ENVO:03501196 ENVO:03501198 ENVO:03501204 ENVO:03501208 ENVO:03501209 ENVO:03501210 ENVO:03501211 ENVO:03501212 ENVO:03501213 ENVO:03501214 ENVO:03501215 ENVO:03501216 ENVO:03501217 ENVO:03501218 ENVO:03501219 ENVO:03501220 ENVO:03501256 EO:0007027 EO:0007033 EO:0007034 EO:0007035 EO:0007036 EO:0007037 EO:0007038 EO:0007285 EO:0007286 EPO:0000016 Transmission of a disease agent (infectious pathogen, toxic chemical, etc.) from a source that is common to those who acquire the disease. Common vehicles include air, water, food, injected substances. Legionellosis is an example of common vehicle spread in air that has passed through air conditioning equipment contaminated by the causal organism. HIV disease and hepatitis B and C can be spread among illicit drug users by the common vehicle of contaminated needles and syringes. Cholera and many other waterborne diseases are spread by the common vehicle of contaminated water. common vehicle transmission ERO:0000833 ERO:0001183 ERO:0001286 ERO:0001965 A role that inheres in a material that is input as the subject of interest in a scientific technique - either as an entity about which data is generated in an assay or study, or an entity that is transformed or modified in a material processing technique (e.g. the source from which a biological sample is taken) experimental subject role ExO:0000002 An interaction between an exposure stressor and an exposure_receptor. exposure event ExO:0000038 depth:1 The condition of an organism in all aspects (e.g., functional or metabolic efficiency). See technical discussion about logic of assigning health status: https://www.w3.org/2001/sw/BestPractices/OEP/Lists-of-values-20040625/ https://en.wikipedia.org/wiki/Medical_state cmattin condition medical condition medical state Damion Dooley note: GenEpiO includes various health status descriptors here; many are annotated as included in the American AHA HIPPA or United Kingdom NHS terminologies. The challenge is to map them or order them in such a way that merged data can be analyzed. subject health status http://semanticscience.org/resource/SIO_010057 Condition Condition ExO:0000057 The process of drawing in by breathing. http://purl.obolibrary.org/obo/ExO_0000057 inhalation FIX:0000278 Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential E' oxidation-reduction potential MIxS redox potential FLU:0000976 A symptom onset date is a date-time entity that marks the start of one or more reported symptoms pertaining to an episode of human or animal illness Damion Dooley symptom onset date FOODON:00001002 A substance, usually composed primarily of carbohydrates, fats, water and/or proteins, that can be eaten or drunk by an animal or human being for nutrition or pleasure. Damion Dooley foodon product type FOODON:00001006 A food product made of meat, the skeletal muscle and associated fat, and other edible tissues such as organs, livers, skin, brains, bone marrow, kidneys, or lungs, of mammals. SUBSET_SIREN:F17332 meat food product FOODON:00001015 This food product type includes food products which are derived from or produced by a plant. plant food product FOODON:00001040 chicken meat food product FOODON:00001041 Meat from bovines, especially domestic cattle (cows). beef food product FOODON:00001092 A food product which is derived from or produced by an animal that has a vertibrae. vertebrate animal food product FOODON:00001131 A food product made from domesticated bird meat. poultry meat food product FOODON:00001134 bovine meat food product FOODON:00001143 Fungal food products include edible fungi, mushrooms, and yeast. fungal food product FOODON:00001145 A food product derived from one or more microorganisms including bacteria, mold, and yeast. microbial food product FOODON:00001176 invertebrate animal food product FOODON:00001184 This food product type includes food products which are derived from a large, diverse group of photosynthetic organisms. SUBSET_SIREN:F10419 algal food product FOODON:00001248 A fish food product includes products made from any fish species (aquatic vertebrate with gills and fins). fish food product FOODON:00001251 avian food product FOODON:00001283 A food product from a category of domestic birds kept for meat, eggs, and feathers including fowl such as chickens, turkeys, and waterfowls such as domestic ducks and geese and other meat birds such as pigeons and doves and games birds including pheasants. poultry food product FOODON:00001304 fermentation/modification process FOODON:00001714 food component FOODON:00001820 A product deriving from mahi-mahi or common dolphinfish (Coryphaena hippurus) also widely called dorado and dolphin. dolphinfish food product FOODON:00001950 herring food product FOODON:00002147 food product by consumer group FOODON:00002381 lookup food product by organism FOODON:00002403 Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience food foodstuff nourishment sustenance food material FOODON:00002404 Roasting is a baking process when the food being baked is meats roasting meat process FOODON:00002419 A food evaporation process is the process of removing water from a food. food evaporation process FOODON:00002451 A process involving the physical transformation of a food source or food product into some derived organic material or food product food transformation process FOODON:00002452 Invertebrates are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. invertebrate animal FOODON:00002462 Pan frying is a form of frying characterized by the use of minimal cooking oil or fat (compared to shallow frying or deep frying); typically using just enough oil to lubricate the pan. ... A pan fry takes place at lower heat than does a sauté. pan frying FOODON:00002470 food object quality FOODON:00002572 cut of beef, british FOODON:00002573 beef rump cut (british) FOODON:00002574 Cuts of beef are first divided into primal cuts, pieces of meat initially separated from the carcass during butchering. These are basic sections from which steaks and other subdivisions are cut. cut of beef FOODON:00002648 A method of precooking food where a liquid is heated to just below the boiling point. Often used to retard the spoiling of milk. food scalding process FOODON:00002679 A fish fillet, from the French word filet meaning a thread or strip, is the flesh of a fish which has been cut or sliced away from the bone by cutting lengthwise along one side of the fish parallel to the backbone. fish fillet FOODON:00002682 Pet food is plant or animal material intended for consumption by pets. pet food FOODON:00002698 barramundi food product FOODON:00002699 barramundi fillet FOODON:00002715 A herring fillet is a fillet cut of herring herring fillet FOODON:00002886 Synbiotic claim or use refers to food ingredients or dietary supplements combining probiotics and prebiotics in a form of synergism that beneficially affect the host. synbiotic claim or use FOODON:00002910 An organism that originated from a wild caught population. wild caught FOODON:00003001 cutlet FOODON:00003004 A multicellular eukaryotic heterotrophic organism within the kingdom Animalia. animal FOODON:00003301 A portion of meat from either the short loin, the sirloin, or the tenderloin muscle area. beef loin cut FOODON:00003302 A cut of beef corresponding to the psoas major muscle, which is very tender. beef tenderloin FOODON:00003342 A boneless cut or slice of meat or fish. fillet FOODON:00003343 A steak cut of beef taken from the smaller end of the tenderloin, or psoas major of the cow carcass, usually a steer or heifer. filet mignon FOODON:00003344 A specific cut of chicken meat that lies under the main portion of the breast just above the ribcage around the center of the sternum. Each fillet is separated from the main breast by filament. chicken fillet FOODON:00003346 A stage of plant maturity in which a plant or plant part has surpassed full maturity and is undergoing decomposition. overripe or decaying FOODON:00003347 A stage of plant development at which a plant or plant part has partly or is about to achieve full maturity and be ready for utilization. slightly ripe FOODON:00003356 A pet food that has not been heat treated or otherwise preserved. pet food (raw) FOODON:00003357 A food item intended to provide pleasure or reward to an animal, and which might not be nutritious. pet treat FOODON:03301077 SUBSET_SIREN:F1077 fish (whole or parts) FOODON:03305143 SUBSET_SIREN:F5143 fish fillet (frozen) FOODON:03305578 SUBSET_SIREN:F5578 mahi mahi fillet (raw) FOODON:03305613 SUBSET_SIREN:F5613 herring fillet (pickled) FOODON:03305734 SUBSET_SIREN:F5734 fish fillet (raw) FOODON:03307315 SUBSET_SIREN:F7315 fish fillet (smoked) FOODON:03307374 SUBSET_SIREN:F7374 herring fillet in tomato sauce FOODON:03308071 SUBSET_SIREN:F8071 fish fillet (with skin, raw, breaded, frozen) FOODON:03308082 SUBSET_SIREN:F8082 fish fillet (stuffed with crabmeat and shrimp) FOODON:03308311 SUBSET_SIREN:F8311 fish (portion cut) FOODON:03308405 SUBSET_SIREN:F8405 fish fillet (breaded, precooked) FOODON:03308407 SUBSET_SIREN:F8407 fish fillet (in tomato sauce) FOODON:03309065 SUBSET_SIREN:F9065 fish fillet (breaded) FOODON:03309079 SUBSET_SIREN:F9079 fish fillet (whitemeat, skinless, raw) FOODON:03309104 SUBSET_SIREN:F9104 herring fillet (smoked, and vegetables) FOODON:03309210 SUBSET_SIREN:F9210 herring fillet (pickled, skinless) FOODON:03309383 SUBSET_SIREN:F9383 fish fillet (breaded, frozen) FOODON:03309517 SUBSET_SIREN:F9517 herring fillet (raw) FOODON:03309527 SUBSET_SIREN:F9527 herring fillet in lemon-flavored sauce FOODON:03309997 Food product for animal covers foods intended for consumption by domesticated animals. food product for animal FOODON:03311737 lookup SUBSET_SIREN:F11737 processed food product FOODON:03316681 SUBSET_SIREN:F16681 fish fillet (quick-frozen in blocks) FOODON:03316683 SUBSET_SIREN:F16683 fish fillets and minced fish (quick-frozen in blocks) FOODON:03317478 SUBSET_SIREN:F17478 fish fillet (unprocessed, frozen) FOODON:03317479 SUBSET_SIREN:F17479 fish fillet (deep-frozen, unprocessed) FOODON:03317624 SUBSET_SIREN:F17624 fish fillet (deep-frozen) FOODON:03400361 A food product type is a class of food products that is differentiated by its food composition, processing and/or consumption characteristics. This does not include brand name products but it may include generic food dish categories. http://www.langual.org/langual_thesaurus.asp?termid=A0361 food product type FOODON:03411041 http://www.langual.org/langual_thesaurus.asp?termid=B1041 chemical food component FOODON:03411261 A member of the group of eukaryotic organisms in the kingdom Fungi that includes unicellular microorganisms such as yeasts and molds, as well as multicellular fungi that produce familiar fruiting forms known as mushrooms. http://www.langual.org/langual_thesaurus.asp?termid=B1261 fungus FOODON:03411297 A vertebrate animal is any species of organism within the subphylum Vertebrata (chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,276 species described. http://www.langual.org/langual_thesaurus.asp?termid=B1297 vertebrate animal FOODON:03411301 An informal term for a large, diverse group of photosynthetic eukaryotic organisms that are not necessarily closely related, and is thus polyphyletic. http://www.langual.org/langual_thesaurus.asp?termid=B1301 algae FOODON:03411347 A multicellular eukaryote organism of the kingdom Plantae. http://www.langual.org/langual_thesaurus.asp?termid=B1347 obsolete: plant FOODON:03411564 A food source is a plant or animal from which a food product or component is derived. http://www.langual.org/langual_thesaurus.asp?termid=B1564 food source FOODON:03412345 A composite organism that arises from algae or cyanobacteria living among filaments of multiple fungi species in a mutualistic relationship. http://www.langual.org/langual_thesaurus.asp?termid=B2345 lichen FOODON:03412846 A unicellular prokaryotic organism in the Domain Bacteria. http://www.langual.org/langual_thesaurus.asp?termid=B2846 bacteria FOODON:03412974 http://www.langual.org/langual_thesaurus.asp?termid=B2974 liquid FOODON:03420103 Edible flesh of any type of animal, including poultry and seafood. Excludes parts containing only animal fat, which is indexed under *FAT OR OIL* or under *FAT, TRIM*. http://www.langual.org/langual_thesaurus.asp?termid=C0103 meat part of animal FOODON:03420116 lookup Anatomical part of the plant or animal from which the food product or its major ingredient is derived. http://www.langual.org/langual_thesaurus.asp?termid=C0116 part of plant or animal FOODON:03420127 Includes carcass meat, organ meat, and nonmeat parts of animals, as well as the whole animal. http://www.langual.org/langual_thesaurus.asp?termid=C0127 animal body or body part FOODON:03420148 The parts of a plant that are not fruit or seed. http://www.langual.org/langual_thesaurus.asp?termid=C0148 root, stem, leaf or flower FOODON:03420164 Anatomical part of an animal; includes eggs and milk that, although separated from the animal, are produced as integral parts and are affected by the animal's food intake and metabolism. http://www.langual.org/langual_thesaurus.asp?termid=C0164 part of animal FOODON:03420174 Anatomical part of a plant, such as fruit, seed, pod, leaf, stem or flower as well as the whole plant. http://www.langual.org/langual_thesaurus.asp?termid=C0174 part of plant FOODON:03430100 http://www.langual.org/langual_thesaurus.asp?termid=E0100 divided into pieces, thickness <0.3 cm. FOODON:03430101 http://www.langual.org/langual_thesaurus.asp?termid=E0101 medium ground and sifted (bolted) FOODON:03430104 http://www.langual.org/langual_thesaurus.asp?termid=E0104 whole and pieces FOODON:03430105 http://www.langual.org/langual_thesaurus.asp?termid=E0105 whole, shape achieved by forming, thickness 1.5-7 cm. FOODON:03430106 http://www.langual.org/langual_thesaurus.asp?termid=E0106 finely ground FOODON:03430107 http://www.langual.org/langual_thesaurus.asp?termid=E0107 divided into segments or wedges FOODON:03430108 http://www.langual.org/langual_thesaurus.asp?termid=E0108 physical state, shape or form, multiple FOODON:03430111 http://www.langual.org/langual_thesaurus.asp?termid=E0111 cut into short pieces FOODON:03430113 The physical state of the food product (liquid, semiliquid, semisolid, or solid). Solid food products are further subdivided by shape or form. Terms are provided for products that have both liquid and solid components or that incorporate air or other gases. [FDA CFSAN 1995] http://www.langual.org/langual_thesaurus.asp?termid=E0113 food physical quality FOODON:03430115 http://www.langual.org/langual_thesaurus.asp?termid=E0115 divided into pieces, thickness 0.3-1.5 cm. FOODON:03430116 http://www.langual.org/langual_thesaurus.asp?termid=E0116 divided into halves FOODON:03430117 http://www.langual.org/langual_thesaurus.asp?termid=E0117 medium ground FOODON:03430122 http://www.langual.org/langual_thesaurus.asp?termid=E0122 divided or disintegrated FOODON:03430124 http://www.langual.org/langual_thesaurus.asp?termid=E0124 sliced, thick, between 0.5 and 1.5 cm. FOODON:03430125 http://www.langual.org/langual_thesaurus.asp?termid=E0125 divided into pieces, thickness more than 1.5 cm. FOODON:03430131 Refers to natural or formed shape as appropriate, regardless of size, which may vary from very large (e.g., beef carcass) to very small (e.g., poppy seed, yeast cell). http://www.langual.org/langual_thesaurus.asp?termid=E0131 whole FOODON:03430133 Divided into pieces whose shape is defined in relation to the shape of the whole, i.e., halves, quarters, or segments. It is used regardless of the size of the whole. http://www.langual.org/langual_thesaurus.asp?termid=E0133 divided into halves, quarters or segments FOODON:03430136 http://www.langual.org/langual_thesaurus.asp?termid=E0136 disintegrated or ground FOODON:03430137 http://www.langual.org/langual_thesaurus.asp?termid=E0137 sliced FOODON:03430140 http://www.langual.org/langual_thesaurus.asp?termid=E0140 whole, shape achieved by forming, thickness 0.3-1.5 cm. FOODON:03430141 http://www.langual.org/langual_thesaurus.asp?termid=E0141 cut into long pieces FOODON:03430145 http://www.langual.org/langual_thesaurus.asp?termid=E0145 sliced, thin, below 0.5 cm. FOODON:03430146 http://www.langual.org/langual_thesaurus.asp?termid=E0146 whole, shape achieved by forming, thickness bigger than 7 cm. FOODON:03430147 http://www.langual.org/langual_thesaurus.asp?termid=E0147 whole, shape achieved by forming FOODON:03430148 http://www.langual.org/langual_thesaurus.asp?termid=E0148 divided into quarters FOODON:03430150 http://www.langual.org/langual_thesaurus.asp?termid=E0150 whole, natural shape FOODON:03430152 Divided into pieces whose shape bears little or no relation to the shape of the whole. If all dimensions are below 0.2 cm., use *DISINTEGRATED OR GROUND*. Examples are: bread slice, cubed beef, sliced carrot, cut green beans, apple ring, shredded cabbage or cheese. http://www.langual.org/langual_thesaurus.asp?termid=E0152 divided into pieces FOODON:03430153 http://www.langual.org/langual_thesaurus.asp?termid=E0153 whole, shape achieved by forming, thickness <0.3 cm. FOODON:03440003 http://www.langual.org/langual_thesaurus.asp?termid=F0003 not heat-treated FOODON:03440011 Used to broadly characterize a food product based on the extent of heat applied. Heat treatment affects the flavor and textural characteristics of a food and thus consumer preparation time. Heat treatment causes chemical changes and/or reduction of enzyme and of microbial activity and thus affects food safety and shelflife. Specifics of preparation are covered by *G. COOKING METHOD* and *H. TREATMENT APPLIED*. [FDA CFSAN 1995] http://www.langual.org/langual_thesaurus.asp?termid=F0011 extent of food heat treatment FOODON:03440014 http://www.langual.org/langual_thesaurus.asp?termid=F0014 fully heat-treated FOODON:03440018 http://www.langual.org/langual_thesaurus.asp?termid=F0018 partially heat-treated FOODON:03440022 http://www.langual.org/langual_thesaurus.asp?termid=F0022 heat-treated FOODON:03440023 http://www.langual.org/langual_thesaurus.asp?termid=F0023 heat-treated, multiple components, different degrees of treatment FOODON:03450002 http://www.langual.org/langual_thesaurus.asp?termid=G0002 food cooking process FOODON:03450004 Cooked at moderate to high levels of heat in which no liquid is added and only small amounts of fat may be added to prevent sticking. http://www.langual.org/langual_thesaurus.asp?termid=G0004 cooking by dry heat FOODON:03450005 Cooked without moisture, covered or uncovered, in an oven. http://www.langual.org/langual_thesaurus.asp?termid=G0005 food baking process FOODON:03450006 Cooked without moisture under or over intense direct heat. http://www.langual.org/langual_thesaurus.asp?termid=G0006 broiling or grilling FOODON:03450007 Cooked without moisture over direct heat from a charcoal fire. http://www.langual.org/langual_thesaurus.asp?termid=G0007 charcoal broiling FOODON:03450008 Cooking on a flat surface at medium heat with only a sufficient amount of fat used to prevent sticking. http://www.langual.org/langual_thesaurus.asp?termid=G0008 griddle cooking FOODON:03450009 Cooking by agitating the food over a dry, high heat source, resulting in exploding. http://www.langual.org/langual_thesaurus.asp?termid=G0009 cooked by popping FOODON:03450010 Cooking with direct heat until the surface of the food is browned, usually associated with bread or sandwiches. http://www.langual.org/langual_thesaurus.asp?termid=G0010 food toasting process FOODON:03450011 Cooking in a microwave oven. http://www.langual.org/langual_thesaurus.asp?termid=G0011 cooking by microwave FOODON:03450012 Cooking in varying amounts of water, water-based liquid or steam. http://www.langual.org/langual_thesaurus.asp?termid=G0012 cooking by moist heat FOODON:03450013 http://www.langual.org/langual_thesaurus.asp?termid=G0013 cooking in water or water-based liquid FOODON:03450014 Cooked in boiling water at 100 degrees C (212 degrees F). http://www.langual.org/langual_thesaurus.asp?termid=G0014 boiling FOODON:03450015 Cooked in boiling water at 212 degrees F.; water that is not absorbed into the food product is discarded after cooking. http://www.langual.org/langual_thesaurus.asp?termid=G0015 boiling and then draining FOODON:03450016 Cooked in boiling water at 212 degrees F. Liquid to solid ratio is greater than 2:1. http://www.langual.org/langual_thesaurus.asp?termid=G0016 boiling in large amount of liquid FOODON:03450017 http://www.langual.org/langual_thesaurus.asp?termid=G0017 boiling in small amount of liquid FOODON:03450018 Cooked in boiling water at 212 degrees F. The water incorporates itself into the product being cooked or is not discarded when cooking is through. http://www.langual.org/langual_thesaurus.asp?termid=G0018 boiling without draining FOODON:03450019 Browned initially in fat and then tightly covered and cooked over low heat in a small amount of water. http://www.langual.org/langual_thesaurus.asp?termid=G0019 cooking by braising FOODON:03450020 Cooking in a moderate amount of liquid at just below the boiling point. http://www.langual.org/langual_thesaurus.asp?termid=G0020 cooking by simmering FOODON:03450021 http://www.langual.org/langual_thesaurus.asp?termid=G0021 cooking in steam FOODON:03450022 Cooked in a pressure cooker. http://www.langual.org/langual_thesaurus.asp?termid=G0022 steaming with pressure FOODON:03450023 Cooked suspended above boiling water. http://www.langual.org/langual_thesaurus.asp?termid=G0023 steaming without pressure FOODON:03450024 http://www.langual.org/langual_thesaurus.asp?termid=G0024 cooking with fat or oil FOODON:03450025 Cooked by adding fat or oil to those foods that do not contain fat or oil that would render during the cooking process. http://www.langual.org/langual_thesaurus.asp?termid=G0025 cooking with added fat or oil FOODON:03450026 Cooked with sufficient fat or oil to coat and moisten the food being prepared, but not cooked in enough fat or oil to immerse the food. Use *GRIDDLED* when only enough fat or oil is used to prevent sticking. http://www.langual.org/langual_thesaurus.asp?termid=G0026 cooking in small amount of fat or oil FOODON:03450027 Cooking in a very small amount of very hot fat, turning and browning the food on all sides. http://www.langual.org/langual_thesaurus.asp?termid=G0027 sautéing FOODON:03450028 Cooked by frying foods quickly over high heat, stirring constantly. Only enough cooking oil is used to coat the bottom of the pan. http://www.langual.org/langual_thesaurus.asp?termid=G0028 stir-frying FOODON:03450029 Cooked in hot fat or oil deep enough to immerse the food entirely. http://www.langual.org/langual_thesaurus.asp?termid=G0029 deep-frying process FOODON:03450030 Cooked in fat or oil rendered from the food being prepared. http://www.langual.org/langual_thesaurus.asp?termid=G0030 cooking with inherent fat or oil FOODON:03450031 http://www.langual.org/langual_thesaurus.asp?termid=G0031 cooking in container immersed in water or steam FOODON:03450032 The method by which heat is transferred to the outside of the cooking container. The most frequently used method of placing the container on an open flame, a hot metal surface or into an oven are not indexed here. http://www.langual.org/langual_thesaurus.asp?termid=G0032 cooking using heating container FOODON:03450033 Cooked in a container that is placed in another container filled with boiling water. See also *Cooked in water bath*. http://www.langual.org/langual_thesaurus.asp?termid=G0033 cooking in double boiler FOODON:03450034 Cooking in a container that is placed in another container filled with water kept near the boiling point. See also *Cooking in double boiler*. http://www.langual.org/langual_thesaurus.asp?termid=G0034 cooking in water bath FOODON:03450035 A chinese cooking technique similar to sauteing in which thick slices or chunks of floured or battered ingredients are slow seared over moderate to low heat. (Kuo, The key to chinese cooking, Knopf, 1977, p.87) http://www.langual.org/langual_thesaurus.asp?termid=G0035 shallow frying process FOODON:03450036 Extracting flavor and other components from food sources by immersion in water, usually at near-boiling temperature. http://www.langual.org/langual_thesaurus.asp?termid=G0036 steeping FOODON:03450037 Reheating is a simple process to bring an already fully cooked product to serving temperature. Do not use for a process that completes the cooking of a partially cooked food. http://www.langual.org/langual_thesaurus.asp?termid=G0037 food reheating FOODON:03450038 http://www.langual.org/langual_thesaurus.asp?termid=G0038 food reheating by microwave FOODON:03450039 http://www.langual.org/langual_thesaurus.asp?termid=G0039 food reheating by dry heat FOODON:03450040 http://www.langual.org/langual_thesaurus.asp?termid=G0040 food reheating by boil-in-bag FOODON:03450041 http://www.langual.org/langual_thesaurus.asp?termid=G0041 food reheating in pan or cooking utensil FOODON:03450043 Double steaming, also called double boiling, is a Chinese cooking technique to prepare delicate food such as bird nests, shark fins, etc. The food is covered with water and put in a covered ceramic jar and the jar is then steamed for several hours. This technique ensures there is no loss of liquid or moisture (its essences) from the food being cooked, hence it is often used with expensive ingredients like Chinese herbal medicines. [Wikipedia] http://www.langual.org/langual_thesaurus.asp?termid=G0043 double steaming FOODON:03450044 Rotisserie is a style of roasting where meat is skewered on a spit and revolves over a flame or other heat source. The rotation cooks the meat evenly in its own juices and allows easy access for continuous basting if desired. [Wikipedia] http://www.langual.org/langual_thesaurus.asp?termid=G0044 rotisserie roasting FOODON:03450045 Searing (or pan searing) is a technique used in grilling, roasting, braising, sautéing, etc. that cooks the surface of the food (usually meat, poultry or fish) at high temperature so that a brownish crust forms by Maillard reaction and denaturation of proteins. A similar technique, browning, is typically used to sear or brown all sides of a particular piece of meat, fish, poultry, etc. before finishing it in the oven. To obtain the desired brown crust, the meat surface must exceed 300 °F (150 °C), so searing requires the meat surface be free of water, which boils at around 212 °F (100 °C). http://www.langual.org/langual_thesaurus.asp?termid=G0045 searing FOODON:03450046 http://www.langual.org/langual_thesaurus.asp?termid=G0046 blind baking FOODON:03450047 http://www.langual.org/langual_thesaurus.asp?termid=G0047 pressure frying process FOODON:03460101 http://www.langual.org/langual_thesaurus.asp?termid=H0101 lactic acid fermentation process FOODON:03460102 http://www.langual.org/langual_thesaurus.asp?termid=H0102 proteolytic fermentation process FOODON:03460107 http://www.langual.org/langual_thesaurus.asp?termid=H0107 lactic acid-other agent fermentation process FOODON:03460111 Used to specifically characterize a food product based on the treatment or processes applied to the product or any indexed ingredient. The processes include adding, substituting or removing components or modifying the food or component, e.g., through fermentation. Multiple values can be assigned. http://www.langual.org/langual_thesaurus.asp?termid=H0111 food treatment process FOODON:03460119 Modified by microbial or enzymatic action resulting in molecular changes in any food component. If salt, sugar or other food additive is used to aid in the modification process, index it by the appropriate term under *INGREDIENT ADDED*. http://www.langual.org/langual_thesaurus.asp?termid=H0119 microbial/enzymatic modification process FOODON:03460123 http://www.langual.org/langual_thesaurus.asp?termid=H0123 alcohol-acetic acid fermentation process FOODON:03460127 http://www.langual.org/langual_thesaurus.asp?termid=H0127 lipolytic fermentation process FOODON:03460128 http://www.langual.org/langual_thesaurus.asp?termid=H0128 fermentation/modification process, multiple component FOODON:03460130 http://www.langual.org/langual_thesaurus.asp?termid=H0130 physical/chemical modification process FOODON:03460141 http://www.langual.org/langual_thesaurus.asp?termid=H0141 food modification process FOODON:03460200 http://www.langual.org/langual_thesaurus.asp?termid=H0200 acidification process FOODON:03460220 Treated with moist heat to soften the grain and to transfer nutrients from the bran to the endosperm. http://www.langual.org/langual_thesaurus.asp?termid=H0220 food parboiling process (grain) FOODON:03460225 http://www.langual.org/langual_thesaurus.asp?termid=H0225 food component addition process FOODON:03460230 http://www.langual.org/langual_thesaurus.asp?termid=H0230 fermentation/modification process, single component FOODON:03460232 http://www.langual.org/langual_thesaurus.asp?termid=H0232 alcohol fermentation process FOODON:03460238 A component separation process at the very least removes one component from an initial entity. The removed component may be captured as a process output for reuse if not destroyed in the process of removal. http://www.langual.org/langual_thesaurus.asp?termid=H0238 component separation process FOODON:03460253 Modified through complex enzymatic or microbial processes resulting in physicochemical changes in particular with respect to texture, flavor, color or shelf life of the food product. Such changes may be induced by the introduction of certain chemicals, such as sodium sulfite, salt, sugar, or other substances, such as phenolics, in dry or liquid form and often aided by smoke. Cheese should always be indexed by the appropriate narrower term under *LACTIC ACID-OTHER AGENT FERMENTED*. http://www.langual.org/langual_thesaurus.asp?termid=H0253 curing or aging process FOODON:03460256 http://www.langual.org/langual_thesaurus.asp?termid=H0256 carbohydrate fermentation process FOODON:03460288 http://www.langual.org/langual_thesaurus.asp?termid=H0288 curing or aging < 2 weeks FOODON:03460289 http://www.langual.org/langual_thesaurus.asp?termid=H0289 curing or aging 2 weeks to 1 month FOODON:03460290 http://www.langual.org/langual_thesaurus.asp?termid=H0290 curing or aging 1 to 2 months FOODON:03460291 http://www.langual.org/langual_thesaurus.asp?termid=H0291 curing or aging 2 to 4 months FOODON:03460292 http://www.langual.org/langual_thesaurus.asp?termid=H0292 curing or aging 4 to 6 months FOODON:03460293 http://www.langual.org/langual_thesaurus.asp?termid=H0293 curing or aging 6 to 12 months FOODON:03460294 http://www.langual.org/langual_thesaurus.asp?termid=H0294 curing or aging 12 months or over FOODON:03460300 http://www.langual.org/langual_thesaurus.asp?termid=H0300 acetic acid fermentation process FOODON:03460326 http://www.langual.org/langual_thesaurus.asp?termid=H0326 bacteria curing process FOODON:03460327 http://www.langual.org/langual_thesaurus.asp?termid=H0327 surface bacteria curing process FOODON:03460328 http://www.langual.org/langual_thesaurus.asp?termid=H0328 interior bacteria curing process FOODON:03460329 http://www.langual.org/langual_thesaurus.asp?termid=H0329 mold curing process FOODON:03460330 http://www.langual.org/langual_thesaurus.asp?termid=H0330 surface mold curing process FOODON:03460331 http://www.langual.org/langual_thesaurus.asp?termid=H0331 interior mold curing process FOODON:03460391 http://www.langual.org/langual_thesaurus.asp?termid=H0391 roasting seed process FOODON:03460396 http://www.langual.org/langual_thesaurus.asp?termid=H0396 marinading process FOODON:03470100 Preservation by adding chemical preservatives (e.g., sorbic acid, sodium benzoate, BHT, calcium proprionate) to suppress or inhibit undesirable microorganisms or enzyme activity. http://www.langual.org/langual_thesaurus.asp?termid=J0100 preservation by adding chemicals FOODON:03470102 http://www.langual.org/langual_thesaurus.asp?termid=J0102 food sterilization before filling FOODON:03470103 http://www.langual.org/langual_thesaurus.asp?termid=J0103 food salting process FOODON:03470106 Smoking is the process of flavoring, browning, cooking, or preserving food by exposing it to smoke from burning or smoldering material, most often wood. http://www.langual.org/langual_thesaurus.asp?termid=J0106 food smoking process FOODON:03470107 The methods contributing to the prevention or retardation of microbial, enzymatic or oxidative spoilage and thus to the extension of shelf life. Index all methods for which information is available, even if a corresponding descriptor has already been used in *H. TREATMENT APPLIED*. Preservation descriptors refer to the finished food as a whole with these exceptions: (1) if the components of a multi-component food, such as cream pie, are preservation by different methods, index all methods; (2) if chemical preservatives are declared on the label, always index them even if it is known that the preservative was introduced through or is only present in a component or ingredient of the food; and (3) if the preservation method for an ingredient is declared on the label (such as brie cheese made from pasteurized milk) index it. Also use *INGREDIENT preservation by THERMAL PROCESSING* or *INGREDIENT preservation by IRRADIATION* when ingredients have been pasteurized, ultrapasteurized, sterilized or irradiated. http://www.langual.org/langual_thesaurus.asp?termid=J0107 food preservation process FOODON:03470108 Preservation by immersing in or spraying with liquids (e.g., sulfite solutions) or surrounding with gases (e.g., ethylene oxide, propylene oxide or sulfur dioxide) to destroy undesirable microorganisms or inactivate enzymes. Diffusion and chemical reaction may create a residue in the food product that contributes to continuing preservation. http://www.langual.org/langual_thesaurus.asp?termid=J0108 preservation by treatment with chemicals FOODON:03470109 Preservation by use of chemical to destroy, suppress or inhibit undesirable microorganisms or enzyme activity. http://www.langual.org/langual_thesaurus.asp?termid=J0109 chemical food preservation process FOODON:03470110 http://www.langual.org/langual_thesaurus.asp?termid=J0110 food sterilization after filling FOODON:03470111 Preservation by storage in an atmosphere in which the concentrations of oxygen and carbon dioxide are different from those in air. This reduces microbial and enzymatic activity; often used commercially in conjunction with refrigeration (e.g., refrigerated rail cars) for fresh meat and produce. http://www.langual.org/langual_thesaurus.asp?termid=J0111 preservation by storage in modified atmosphere FOODON:03470112 http://www.langual.org/langual_thesaurus.asp?termid=J0112 drying under reduced pressure FOODON:03470113 http://www.langual.org/langual_thesaurus.asp?termid=J0113 sterilization by irradiation FOODON:03470114 http://www.langual.org/langual_thesaurus.asp?termid=J0114 food sterilization by hot filling and cooling FOODON:03470115 http://www.langual.org/langual_thesaurus.asp?termid=J0115 surface pasteurization or disinfection by ultraviolet irradiation FOODON:03470116 http://www.langual.org/langual_thesaurus.asp?termid=J0116 dehydration or drying process FOODON:03470117 Drying by heat. http://www.langual.org/langual_thesaurus.asp?termid=J0117 heat drying process FOODON:03470119 http://www.langual.org/langual_thesaurus.asp?termid=J0119 pasteurization by irradiation FOODON:03470120 Preservation by the use of high temperature for a time sufficient to reduce or destroy undesirable microorganisms and enzyme activity. [FDA CFSAN 1995] http://www.langual.org/langual_thesaurus.asp?termid=J0120 heat treatment food preservation process FOODON:03470121 Preservation by filtering out yeasts and molds, generally followed by aseptic packaging. FDA CFSAN 1995 http://www.langual.org/langual_thesaurus.asp?termid=J0121 food filtration process FOODON:03470122 Preservation by irradiation, primarily by gamma radiation. http://www.langual.org/langual_thesaurus.asp?termid=J0122 preservation by ionizing radiation FOODON:03470123 http://www.langual.org/langual_thesaurus.asp?termid=J0123 food sterilization by heating FOODON:03470124 Reduction of water in the product by osmosis. http://www.langual.org/langual_thesaurus.asp?termid=J0124 osmotic dehydration FOODON:03470126 http://www.langual.org/langual_thesaurus.asp?termid=J0126 aseptic filling and sealing of food FOODON:03470128 http://www.langual.org/langual_thesaurus.asp?termid=J0128 food slow freezing process FOODON:03470129 http://www.langual.org/langual_thesaurus.asp?termid=J0129 food sterilization by hot filling, held hot and cooling FOODON:03470130 Dehydration by sublimation under reduced pressure while frozen. Usually the product is not stored frozen. http://www.langual.org/langual_thesaurus.asp?termid=J0130 freeze-drying FOODON:03470131 Cooling and keeping at a temperature between 30°F and 45°F (-1°C and 7°C). Regarding food preservation regulations, the temperature range depends on national legislation. http://www.langual.org/langual_thesaurus.asp?termid=J0131 food chilling process FOODON:03470132 http://www.langual.org/langual_thesaurus.asp?termid=J0132 food quick freezing process FOODON:03470133 http://www.langual.org/langual_thesaurus.asp?termid=J0133 spray-drying FOODON:03470134 http://www.langual.org/langual_thesaurus.asp?termid=J0134 shelf-drying under normal pressure FOODON:03470135 http://www.langual.org/langual_thesaurus.asp?termid=J0135 pasteurization by heating FOODON:03470136 Preservation by freezing a food product and keeping it at a temperature below the freezing point (20-30 degrees F) without regard to the product's physical state. http://www.langual.org/langual_thesaurus.asp?termid=J0136 food freezing process FOODON:03470137 Immersed in a salt brine strong enough to suppress enzyme activity and growth of undesirable organisms. http://www.langual.org/langual_thesaurus.asp?termid=J0137 food brining process FOODON:03470138 Preservation by the use of radiation to destroy or suppress undesirable microorganisms or enzyme activity. http://www.langual.org/langual_thesaurus.asp?termid=J0138 preservation by irradiation FOODON:03470139 Packed in dry salt in sufficient quantity to suppress enzyme activity or growth of undesirable organisms. http://www.langual.org/langual_thesaurus.asp?termid=J0139 food dry salting process FOODON:03470140 http://www.langual.org/langual_thesaurus.asp?termid=J0140 drum-drying FOODON:03470141 Dried by natural heat, usually through exposure to the sun. Includes field-dried products such as grains and dry beans. These products are included also if they have been artificially dried to return them to normal dry state, e.g. grain that has been artificially dried after harvest. http://www.langual.org/langual_thesaurus.asp?termid=J0141 natural heat drying FOODON:03470142 Preservation by cooling and storage at low temperature (chilling at around 0-5°C (32 to 41°F), freezing at -18°C (0°F)) to prevent or retard microbial or enzymatic spoilage. http://www.langual.org/langual_thesaurus.asp?termid=J0142 chilling or freezing process FOODON:03470143 http://www.langual.org/langual_thesaurus.asp?termid=J0143 drying under normal pressure FOODON:03470144 Drying by the application of artificial heat. http://www.langual.org/langual_thesaurus.asp?termid=J0144 artificial heat drying FOODON:03470145 Preservation method that lowers the water activity (relative humidity) of a food product. This is accomplished by using mechanical dehydration equipment, by natural drying, by adding salt, sugar or other agents to the food or by surface drying during a refrigeration or freezing operation. This method of preservation may be used in conjunction with other preservation methods such as preservation by thermal processing. http://www.langual.org/langual_thesaurus.asp?termid=J0145 preservation by reducing water activity FOODON:03470146 Preservation by adding sugar, sugar syrup or by partial inversion of disaccharides until the sugar concentration is high enough to prevent growth of microorganisms. http://www.langual.org/langual_thesaurus.asp?termid=J0146 preservation by adding sugar FOODON:03470147 http://www.langual.org/langual_thesaurus.asp?termid=J0147 food sterilization at ultra high temperature (uht) FOODON:03470148 When used to describe a dairy product, means that such product shall have been thermally processed at or above 138° C (280° C) for at least 2 seconds, either before or after packaging so as to produce a product that has extended shelf life under refrigerated conditions (21 CFR 131.3 (c)). Used to describe liquid egg products that also have been thermally processed, but at a different temperature than for milk products. The egg product will have an extended shelf life under refrigerated conditions. http://www.langual.org/langual_thesaurus.asp?termid=J0148 ultra pasteurization (up) by heat FOODON:03470149 http://www.langual.org/langual_thesaurus.asp?termid=J0149 preservation by adding acid FOODON:03470150 Sous-vide, French for "under vacuum", is a method of cooking that is intended to maintain the integrity of ingredients by heating them for an extended period of time in vacuum sealed plastic pouches at relatively low temperatures. Food is cooked for a long time, sometimes well over 24 hours. Unlike cooking in a slow cooker, sous-vide cooking uses airtight plastic bags placed in hot water well below boiling point (usually around 60°C or 140°F). http://www.langual.org/langual_thesaurus.asp?termid=J0150 sous vide cooking process FOODON:03470151 http://www.langual.org/langual_thesaurus.asp?termid=J0151 preservation of food component by heat treatment FOODON:03470152 http://www.langual.org/langual_thesaurus.asp?termid=J0152 ingredient preservation by irradiation FOODON:03470153 Preservation by adding spices or extracts (e.g. garlic, onion, horseradish, paprika) to suppress or inhibit undesirable micro-organisms, enzyme activity, or oxidative changes. http://www.langual.org/langual_thesaurus.asp?termid=J0153 preservation by adding spices or extracts FOODON:03470154 Preservation by adding inorganic acids or salts (e.g. SO2, H2SO4, KNO4, NaNO3) to suppress or inhibit undesirable micro-organisms or enzyme activity. http://www.langual.org/langual_thesaurus.asp?termid=J0154 preservation by adding inorganic acids or salts FOODON:03470155 Preservation by adding organic acids or salts (e.g. lactic acid, acetic acid, salicylic acid) to suppress or inhibit undesirable micro organisms or enzyme activity. http://www.langual.org/langual_thesaurus.asp?termid=J0155 preservation by adding organic acids or salts FOODON:03470156 Preservation by adding antibiotics (e.g. nisin, tylosine, subtlin, bacitracin, chlorotetracyclin, oxytetracyclin) to kill micro organisms or stop their growth. http://www.langual.org/langual_thesaurus.asp?termid=J0156 preservation by adding antibiotics FOODON:03470157 Separation of colloidal or very fine solid materials by filtration through microporous or semipermeable mediums. Membranes have pores in the range 2-20 nm diameter. Some dairy product are ultrafiltrated in order to obtain a higher protein concentration and hereby, a thicker consistency or textture. http://www.langual.org/langual_thesaurus.asp?termid=J0157 food ultra-filtration process FOODON:03470158 pasteurization by heat after filling FOODON:03470159 pasteurization by heat before filling FOODON:03470160 The process of holding food at a high pressure, normally greater than 1000 bar, which leads to sterilization. Example: Fruit juice, jam. http://www.langual.org/langual_thesaurus.asp?termid=J0160 ultra high pressure sterilization process FOODON:03470161 Treated by electron accelerator radiation, for example to kill insects in cereals. http://www.langual.org/langual_thesaurus.asp?termid=J0161 preservation by electron accelerator radiation FOODON:03470162 http://www.langual.org/langual_thesaurus.asp?termid=J0162 disinfection by irradiation FOODON:03470163 http://www.langual.org/langual_thesaurus.asp?termid=J0163 drying by radiation FOODON:03470165 http://www.langual.org/langual_thesaurus.asp?termid=J0165 drying by microwave radiation FOODON:03470166 http://www.langual.org/langual_thesaurus.asp?termid=J0166 drying by infrared heat radiation FOODON:03470168 http://www.langual.org/langual_thesaurus.asp?termid=J0168 drying under over pressure FOODON:03470169 http://www.langual.org/langual_thesaurus.asp?termid=J0169 concentration by reverse osmosis FOODON:03470170 Drying by exposure to the sun. Example: cereals, spices, vegetables. http://www.langual.org/langual_thesaurus.asp?termid=J0170 sun drying FOODON:03470171 Frozen very rapidly by means of refrigerating agents such as liquid nitrogen or carbon dioxide. Example: lobster frozen in liquid nitrogen. http://www.langual.org/langual_thesaurus.asp?termid=J0171 food cryogenic freezing process FOODON:03470172 The process of food storage involving an accompanying refrigerating agent. http://www.langual.org/langual_thesaurus.asp?termid=J0172 food storage with refrigerating agent process FOODON:03470173 Preservation by storage in inert gases (e.g. nitrogen) to suppress or inhibit undesirable micro-organism growth, oxidation activity, etc. http://www.langual.org/langual_thesaurus.asp?termid=J0173 inert atmosphere storage process FOODON:03470174 Storing under reduced pressure (e.g. 1.3-2 kPa) in order to suppress or inhibit undesirable micro organism growth, oxidation activity, etc. http://www.langual.org/langual_thesaurus.asp?termid=J0174 vaccume storage process FOODON:03470175 Blanching is a cooking process wherein a food, usually a vegetable or fruit, is scalded in boiling water, removed after a brief, timed interval, and finally plunged into iced water or placed under cold running water (shocking or refreshing) to halt the cooking process. Blanching foods helps reduce quality loss over time. People often use blanching as a pre-treatment prior to freezing, drying, or canning—heating vegetables or fruits to inactivate enzymes, modify texture, remove the peel, and wilt tissue. Blanching is also utilized to preserve color, flavor, and nutritional value. The process has three stages: preheating, blanching, and cooling. The most common blanching methods for vegetables/fruits are hot water and steam, while cooling is either done using cold water or cool air. http://www.langual.org/langual_thesaurus.asp?termid=J0175 food blanching process FOODON:03470176 Storage of fruits and vegetables in an atmosphere in which the concentrations of oxygen, carbon dioxide (and often nitrogen) are different from those in air and at a low temperature. All three (four) factors are controlled at the desired levels in order to suppress the fruits' and vegetables' natural respiration. The process is also denominated CA Storage (synonym). http://www.langual.org/langual_thesaurus.asp?termid=J0176 controlled atmosphere storage process FOODON:03470177 Microfiltration is used to remove undesirable micro-organisms and molecules. The membranes have pore diameters from 10 to 10000 nm. Micro-filtration is often used instead of pateurisation, e.g. in the brewing industry. http://www.langual.org/langual_thesaurus.asp?termid=J0177 food micro-filtration process FOODON:03470178 High Temperature Short Time (HTST) pasteurization is one of the most common methods of pasteurization , which uses metal plates and hot water to raise milk temperatures to at least 72° C (161° F) for not less than 15 seconds, followed by rapid cooling. http://www.langual.org/langual_thesaurus.asp?termid=J0178 high temperature short time (htst) pasteurization FOODON:03470179 Higher Heat Shorter Time (HHST) is a process similar to HTST pasteurization, but it uses slightly different equipment and higher temperatures (83 - 127° C) for a shorter time. http://www.langual.org/langual_thesaurus.asp?termid=J0179 higher heat shorter time (hhst) pasteurization FOODON:03470180 Typically involves heating milk or cream to 135° to 150° C (275° to 302° F) for 1 or 2 seconds. The milk is then packaged in sterile, hermetically-sealed (airtight) containers (aspetic filling) and can be stored without refrigeration for up to 90 days. After opening, spoilage times for UHT products are similar to those of conventionally pasteurized products. http://www.langual.org/langual_thesaurus.asp?termid=J0180 ultra high temperature (uht) pasteurization FOODON:03470181 http://www.langual.org/langual_thesaurus.asp?termid=J0181 filling conditions for pasteurization FOODON:03470182 Low-Temperature-Long-Time Treatment (LTLT) uses low heat for a longer time to kill pathogenic bacteria. For example, milk is pasteurized at 63° C (145° F) for 30 minutes. http://www.langual.org/langual_thesaurus.asp?termid=J0182 low-temperature-long-time (ltlt) pasteurization FOODON:03480010 In the U.S., grain strength is calculated as 10 times the acid content expressed as acetic acid. For example, 40 grain vinegar = 4% acetic acid; 120 grain vinegar = 12% acetic acid. [Technically Speaking about Vinegar - A food technologist's guide to vinegar, The Vinegar Institute, 5775 Peachtree-Dunwoody Road, Atlanta, Georgia 30342, USA]. http://www.langual.org/langual_thesaurus.asp?termid=K0010 packed in vinegar with sugar FOODON:03480011 Packed in a medium that is also a food product. Ingredients that are introduced through the packing medium are indexed as appropriate under *INGREDIENT OR FOOD ADDED* found in *H. TREATMENT APPLIED*. http://www.langual.org/langual_thesaurus.asp?termid=K0011 packed in edible medium FOODON:03480012 http://www.langual.org/langual_thesaurus.asp?termid=K0012 packed in heavily sweetened liquid FOODON:03480013 http://www.langual.org/langual_thesaurus.asp?termid=K0013 packed in lightly sweetened water or juice FOODON:03480014 Packed in a modified atmosphere that contributes to preservation (e.g., applesauce packed with nitrogen in the head space or tuna salad sandwich packed in nitrogen-containing polyethylene wrapper). Also applicable to large-scale applications in shipping or storage (e.g., meat under carbon dioxide in a rail car). http://www.langual.org/langual_thesaurus.asp?termid=K0014 packed in gas other than air FOODON:03480015 Packed with a gas that is liquified under pressure and that upon release of the pressure propels and aerates the food product. See 21 CFR 173.345 and 173.360 for substances used. http://www.langual.org/langual_thesaurus.asp?termid=K0015 packed with aerosol propellant FOODON:03480016 http://www.langual.org/langual_thesaurus.asp?termid=K0016 packed in vegetable juice FOODON:03480017 http://www.langual.org/langual_thesaurus.asp?termid=K0017 packed in water FOODON:03480018 http://www.langual.org/langual_thesaurus.asp?termid=K0018 packed in salt brine FOODON:03480019 http://www.langual.org/langual_thesaurus.asp?termid=K0019 packed in sweetened brine FOODON:03480020 food packing medium The medium in which the food is packed for preservation and handling or the medium surrounding homemade foods, e.g., peaches cooked in sugar syrup. The packing medium may provide a controlled environment for the food. It may also serve to improve palatability and consumer appeal. http://www.langual.org/langual_thesaurus.asp?termid=K0020 food packing medium FOODON:03480021 http://www.langual.org/langual_thesaurus.asp?termid=K0021 packed in vegetable oil FOODON:03480022 http://www.langual.org/langual_thesaurus.asp?termid=K0022 packed in acidified salt brine FOODON:03480023 Packed in sweetened water or in sweetened and/or concentrated fruit juice. For single-strength unsweetened fruit juice, use *PACKED IN FRUIT JUICE*. When the specific terms under *PACKED IN SWEETENED LIQUID* are used, the statement seen on the product label should be used for indexing. For additional information, see 21 CFR 145. http://www.langual.org/langual_thesaurus.asp?termid=K0023 packed in sweetened liquid FOODON:03480024 http://www.langual.org/langual_thesaurus.asp?termid=K0024 packed in extra heavily sweetened liquid FOODON:03480026 http://www.langual.org/langual_thesaurus.asp?termid=K0026 packed in fat or oil FOODON:03480027 Packed in a container under high vacuum (26-29 in.). http://www.langual.org/langual_thesaurus.asp?termid=K0027 vacuum-packed FOODON:03480028 http://www.langual.org/langual_thesaurus.asp?termid=K0028 packed in carbon dioxide FOODON:03480029 In the U.S., grain strength is calculated as 10 times the acid content expressed as acetic acid. For example, 40 grain vinegar = 4% acetic acid; 120 grain vinegar = 12% acetic acid. [Technically Speaking about Vinegar - A food technologist's guide to vinegar, The Vinegar Institute, 5775 Peachtree-Dunwoody Road, Atlanta, Georgia 30342, USA]. http://www.langual.org/langual_thesaurus.asp?termid=K0029 packed in vinegar FOODON:03480030 http://www.langual.org/langual_thesaurus.asp?termid=K0030 packed in slightly sweetened water or juice FOODON:03480031 http://www.langual.org/langual_thesaurus.asp?termid=K0031 packed in nitrogen FOODON:03480032 http://www.langual.org/langual_thesaurus.asp?termid=K0032 packed in gas mixture FOODON:03480033 http://www.langual.org/langual_thesaurus.asp?termid=K0033 packed in gravy or sauce, dairy or egg component FOODON:03480034 http://www.langual.org/langual_thesaurus.asp?termid=K0034 packed in gravy or sauce FOODON:03480035 http://www.langual.org/langual_thesaurus.asp?termid=K0035 packed in gelatin FOODON:03480036 http://www.langual.org/langual_thesaurus.asp?termid=K0036 packed in gravy or sauce, meat FOODON:03480037 http://www.langual.org/langual_thesaurus.asp?termid=K0037 packed in gravy or sauce, vegetable FOODON:03480038 http://www.langual.org/langual_thesaurus.asp?termid=K0038 packed in olive oil FOODON:03480039 Packed in unsweetened single strength juice or juice prepared from concentrated fruit juice and water; if sweetener is added to the fruit juice, use the appropriate term under *PACKED IN SWEETENED LIQUID*. http://www.langual.org/langual_thesaurus.asp?termid=K0039 packed in fruit juice FOODON:03480040 http://www.langual.org/langual_thesaurus.asp?termid=K0040 packed in vinegar and oil FOODON:03480042 Packed in broth; includes meat, poultry or seafood packed in its' own juice. http://www.langual.org/langual_thesaurus.asp?termid=K0042 packed in broth FOODON:03480043 http://www.langual.org/langual_thesaurus.asp?termid=K0043 packed in cream or milk FOODON:03480044 Packed in squid or octopus ink. http://www.langual.org/langual_thesaurus.asp?termid=K0044 packed in ink FOODON:03480045 http://www.langual.org/langual_thesaurus.asp?termid=K0045 packed in gravy or sauce, fruit FOODON:03480046 http://www.langual.org/langual_thesaurus.asp?termid=K0046 packed in animal fat or oil FOODON:03480047 In the U.S., grain strength is calculated as 10 times the acid content expressed as acetic acid. For example, 40 grain vinegar = 4% acetic acid; 120 grain vinegar = 12% acetic acid. [Technically Speaking about Vinegar - A food technologist's guide to vinegar, The Vinegar Institute, 5775 Peachtree-Dunwoody Road, Atlanta, Georgia 30342, USA]. http://www.langual.org/langual_thesaurus.asp?termid=K0047 packed in vinegar with sugar and salt FOODON:03490100 Type of container or wrapping defined by the main container material, the container form, and the material of the liner lids or ends. Also type of container or wrapping by form; prefer description by material first, then by form. [FDA CFSAN 1995] http://www.langual.org/langual_thesaurus.asp?termid=M0100 food container or wrapping FOODON:03490101 http://www.langual.org/langual_thesaurus.asp?termid=M0101 plastic squeeze bottle or tube, top lined with foil FOODON:03490102 http://www.langual.org/langual_thesaurus.asp?termid=M0102 plastic squeeze bottle or tube FOODON:03490103 http://www.langual.org/langual_thesaurus.asp?termid=M0103 plastic squeeze bottle or tube, top lined with laminate FOODON:03490104 http://www.langual.org/langual_thesaurus.asp?termid=M0104 plastic squeeze bottle or tube, unlined top FOODON:03490105 http://www.langual.org/langual_thesaurus.asp?termid=M0105 plastic squeeze bottle or tube, top lined with cork FOODON:03490106 http://www.langual.org/langual_thesaurus.asp?termid=M0106 glass container, tinless steel lid FOODON:03490107 http://www.langual.org/langual_thesaurus.asp?termid=M0107 bimetal container FOODON:03490108 http://www.langual.org/langual_thesaurus.asp?termid=M0108 glass container, plastic lid, paper lining FOODON:03490109 http://www.langual.org/langual_thesaurus.asp?termid=M0109 laminate tube, ends lined with laminate FOODON:03490110 http://www.langual.org/langual_thesaurus.asp?termid=M0110 laminate tube, ends lined with foil FOODON:03490111 http://www.langual.org/langual_thesaurus.asp?termid=M0111 laminate tube, ends lined with cork FOODON:03490112 http://www.langual.org/langual_thesaurus.asp?termid=M0112 paperboard tube with lid or ends FOODON:03490113 http://www.langual.org/langual_thesaurus.asp?termid=M0113 textile or fabric stocking or casing FOODON:03490114 http://www.langual.org/langual_thesaurus.asp?termid=M0114 ceramic or earthenware bottle FOODON:03490115 http://www.langual.org/langual_thesaurus.asp?termid=M0115 ceramic or earthenware crock or jar FOODON:03490116 http://www.langual.org/langual_thesaurus.asp?termid=M0116 ceramic or earthenware container FOODON:03490117 http://www.langual.org/langual_thesaurus.asp?termid=M0117 paper bag, sack or pouch, plastic liner FOODON:03490118 http://www.langual.org/langual_thesaurus.asp?termid=M0118 paper bag, sack or pouch, foil liner FOODON:03490119 http://www.langual.org/langual_thesaurus.asp?termid=M0119 paper bag, sack or pouch, laminate liner FOODON:03490120 http://www.langual.org/langual_thesaurus.asp?termid=M0120 paper bag, sack or pouch FOODON:03490121 http://www.langual.org/langual_thesaurus.asp?termid=M0121 glass container, cork stopper FOODON:03490122 http://www.langual.org/langual_thesaurus.asp?termid=M0122 plastic tray or pan, laminate cover or wrapping FOODON:03490123 http://www.langual.org/langual_thesaurus.asp?termid=M0123 plastic tray or pan, aluminum foil cover or wrapping FOODON:03490124 http://www.langual.org/langual_thesaurus.asp?termid=M0124 plastic tray or pan, plastic cover or wrapping FOODON:03490125 http://www.langual.org/langual_thesaurus.asp?termid=M0125 plastic tray or pan, paper wrapping FOODON:03490126 http://www.langual.org/langual_thesaurus.asp?termid=M0126 plastic tray or pan FOODON:03490127 http://www.langual.org/langual_thesaurus.asp?termid=M0127 laminate tube, unlined aluminum ends FOODON:03490128 http://www.langual.org/langual_thesaurus.asp?termid=M0128 plastic wrapper FOODON:03490129 http://www.langual.org/langual_thesaurus.asp?termid=M0129 paperboard tray with wrapper FOODON:03490130 http://www.langual.org/langual_thesaurus.asp?termid=M0130 glass container FOODON:03490131 http://www.langual.org/langual_thesaurus.asp?termid=M0131 plastic tray or pan, cardboard cover FOODON:03490132 http://www.langual.org/langual_thesaurus.asp?termid=M0132 glass container, aluminum lid FOODON:03490133 http://www.langual.org/langual_thesaurus.asp?termid=M0133 glass container, plastic lid, laminate lining FOODON:03490134 http://www.langual.org/langual_thesaurus.asp?termid=M0134 glass container, plastic lid or stopper FOODON:03490135 http://www.langual.org/langual_thesaurus.asp?termid=M0135 glass container, aluminum lid, plastic lining FOODON:03490136 http://www.langual.org/langual_thesaurus.asp?termid=M0136 glass container, plastic lid, plastic lining FOODON:03490137 http://www.langual.org/langual_thesaurus.asp?termid=M0137 plastic shrink-pack FOODON:03490138 http://www.langual.org/langual_thesaurus.asp?termid=M0138 laminate tube, unlined plastic ends FOODON:03490139 http://www.langual.org/langual_thesaurus.asp?termid=M0139 aluminum tube, unlined plastic top FOODON:03490140 http://www.langual.org/langual_thesaurus.asp?termid=M0140 glass container, plastic lid, aluminum foil lining FOODON:03490141 http://www.langual.org/langual_thesaurus.asp?termid=M0141 paper bag, sack or pouch, paper liner FOODON:03490142 http://www.langual.org/langual_thesaurus.asp?termid=M0142 paperboard container with laminate liner FOODON:03490143 http://www.langual.org/langual_thesaurus.asp?termid=M0143 glass container, tin-plated steel lid FOODON:03490144 http://www.langual.org/langual_thesaurus.asp?termid=M0144 laminate bag or pouch FOODON:03490145 http://www.langual.org/langual_thesaurus.asp?termid=M0145 plastic boil-in-bag FOODON:03490146 http://www.langual.org/langual_thesaurus.asp?termid=M0146 paperboard container with plastic liner FOODON:03490147 http://www.langual.org/langual_thesaurus.asp?termid=M0147 paperboard container with aluminum foil liner FOODON:03490148 http://www.langual.org/langual_thesaurus.asp?termid=M0148 paperboard container with paper liner FOODON:03490149 http://www.langual.org/langual_thesaurus.asp?termid=M0149 tinless steel plate container FOODON:03490150 http://www.langual.org/langual_thesaurus.asp?termid=M0150 paperboard molded pack FOODON:03490151 http://www.langual.org/langual_thesaurus.asp?termid=M0151 metal container FOODON:03490152 http://www.langual.org/langual_thesaurus.asp?termid=M0152 paperboard container, waxed FOODON:03490153 http://www.langual.org/langual_thesaurus.asp?termid=M0153 paperboard container, plastic coated FOODON:03490154 http://www.langual.org/langual_thesaurus.asp?termid=M0154 paperboard container with window FOODON:03490155 http://www.langual.org/langual_thesaurus.asp?termid=M0155 paperboard container with liner FOODON:03490156 http://www.langual.org/langual_thesaurus.asp?termid=M0156 paperboard container FOODON:03490157 http://www.langual.org/langual_thesaurus.asp?termid=M0157 textile or fabric container FOODON:03490158 http://www.langual.org/langual_thesaurus.asp?termid=M0158 textile or fabric bag FOODON:03490159 http://www.langual.org/langual_thesaurus.asp?termid=M0159 paperboard or paper container FOODON:03490160 http://www.langual.org/langual_thesaurus.asp?termid=M0160 aluminum tray or pan, plastic cover or wrapping FOODON:03490161 http://www.langual.org/langual_thesaurus.asp?termid=M0161 aluminum tray or pan, cardboard cover FOODON:03490162 http://www.langual.org/langual_thesaurus.asp?termid=M0162 aluminum tray or pan, laminate cover or wrapping FOODON:03490163 http://www.langual.org/langual_thesaurus.asp?termid=M0163 aluminum tray or pan, aluminum foil cover or wrapping FOODON:03490164 http://www.langual.org/langual_thesaurus.asp?termid=M0164 aluminum tray or pan, paper wrapping FOODON:03490165 http://www.langual.org/langual_thesaurus.asp?termid=M0165 aluminum tray or pan FOODON:03490166 http://www.langual.org/langual_thesaurus.asp?termid=M0166 plastic bag or pouch FOODON:03490167 http://www.langual.org/langual_thesaurus.asp?termid=M0167 laminate tube FOODON:03490168 http://www.langual.org/langual_thesaurus.asp?termid=M0168 aluminum tube FOODON:03490169 http://www.langual.org/langual_thesaurus.asp?termid=M0169 aluminum tube, top lined with laminate FOODON:03490170 http://www.langual.org/langual_thesaurus.asp?termid=M0170 aluminum tube, top lined with foil FOODON:03490171 http://www.langual.org/langual_thesaurus.asp?termid=M0171 aluminum tube, top lined with cork FOODON:03490172 Corresponds to FSTA Thesaurus Packaging 2.2.1 Plastic container. http://www.langual.org/langual_thesaurus.asp?termid=M0172 plastic container FOODON:03490173 http://www.langual.org/langual_thesaurus.asp?termid=M0173 paper wrapper FOODON:03490174 http://www.langual.org/langual_thesaurus.asp?termid=M0174 wood container FOODON:03490175 http://www.langual.org/langual_thesaurus.asp?termid=M0175 aluminum can, drum or barrel FOODON:03490176 http://www.langual.org/langual_thesaurus.asp?termid=M0176 tin plate container FOODON:03490177 http://www.langual.org/langual_thesaurus.asp?termid=M0177 wood box FOODON:03490178 http://www.langual.org/langual_thesaurus.asp?termid=M0178 wood drum FOODON:03490179 http://www.langual.org/langual_thesaurus.asp?termid=M0179 wood barrel, cask or wheel FOODON:03490180 http://www.langual.org/langual_thesaurus.asp?termid=M0180 plastic container, molded or bubble pack FOODON:03490181 http://www.langual.org/langual_thesaurus.asp?termid=M0181 laminate container FOODON:03490182 http://www.langual.org/langual_thesaurus.asp?termid=M0182 aluminum container FOODON:03490183 http://www.langual.org/langual_thesaurus.asp?termid=M0183 plastic container, rigid or semirigid, tin-plated steel lid FOODON:03490184 http://www.langual.org/langual_thesaurus.asp?termid=M0184 plastic container, rigid or semirigid FOODON:03490185 http://www.langual.org/langual_thesaurus.asp?termid=M0185 plastic container, rigid or semirigid, tinless steel lid FOODON:03490186 http://www.langual.org/langual_thesaurus.asp?termid=M0186 plastic container, flexible or film FOODON:03490187 http://www.langual.org/langual_thesaurus.asp?termid=M0187 plastic container, rigid or semirigid, plastic lid FOODON:03490188 http://www.langual.org/langual_thesaurus.asp?termid=M0188 plastic container, rigid or semirigid, aluminum lid FOODON:03490189 http://www.langual.org/langual_thesaurus.asp?termid=M0189 steel plate container FOODON:03490190 http://www.langual.org/langual_thesaurus.asp?termid=M0190 aluminum foil wrapper FOODON:03490192 http://www.langual.org/langual_thesaurus.asp?termid=M0192 paperboard container with foil or liner overwrap FOODON:03490193 http://www.langual.org/langual_thesaurus.asp?termid=M0193 plastic container, blow-molded FOODON:03490194 http://www.langual.org/langual_thesaurus.asp?termid=M0194 can, bottle or jar FOODON:03490195 Classification corresponding to FSTA Thesaurus Packaging 3.1 Package Types http://www.langual.org/langual_thesaurus.asp?termid=M0195 container or wrapping by form FOODON:03490196 http://www.langual.org/langual_thesaurus.asp?termid=M0196 ampul FOODON:03490197 According to FSTA Thesaurus Packaging 3.1 package types, includes boil-in bag, carrier bag, flat bag, inner bag, retort pouch, shipping bag, valve bag, and valve sack http://www.langual.org/langual_thesaurus.asp?termid=M0197 bag, sack or pouch FOODON:03490198 http://www.langual.org/langual_thesaurus.asp?termid=M0198 drum (container) FOODON:03490199 A flexible container of distinctive construction and closure features used in the dispensing of tablet or powdered prescription medication; it is typically constructed of film or paper that may be coated or laminated to protect the contents [CFSAN Thesaurus]. http://www.langual.org/langual_thesaurus.asp?termid=M0199 envelope FOODON:03490200 http://www.langual.org/langual_thesaurus.asp?termid=M0200 tube FOODON:03490201 http://www.langual.org/langual_thesaurus.asp?termid=M0201 vial FOODON:03490202 Classification corresponding to FSTA Thesaurus Packaging 2.1.2 Material http://www.langual.org/langual_thesaurus.asp?termid=M0202 container or wrapping by material FOODON:03490203 http://www.langual.org/langual_thesaurus.asp?termid=M0203 bottle or jar FOODON:03490204 http://www.langual.org/langual_thesaurus.asp?termid=M0204 can (container) FOODON:03490205 http://www.langual.org/langual_thesaurus.asp?termid=M0205 leaf wrapper FOODON:03490206 http://www.langual.org/langual_thesaurus.asp?termid=M0206 husk wrapper FOODON:03490207 http://www.langual.org/langual_thesaurus.asp?termid=M0207 capsule FOODON:03490208 http://www.langual.org/langual_thesaurus.asp?termid=M0208 multicontainer package FOODON:03490209 http://www.langual.org/langual_thesaurus.asp?termid=M0209 wax container FOODON:03490210 http://www.langual.org/langual_thesaurus.asp?termid=M0210 glass container, metal lid FOODON:03490211 http://www.langual.org/langual_thesaurus.asp?termid=M0211 wrapper, material unspecified FOODON:03490212 http://www.langual.org/langual_thesaurus.asp?termid=M0212 edible container FOODON:03490213 http://www.langual.org/langual_thesaurus.asp?termid=M0213 box FOODON:03490214 http://www.langual.org/langual_thesaurus.asp?termid=M0214 bottle FOODON:03490215 http://www.langual.org/langual_thesaurus.asp?termid=M0215 jar FOODON:03490216 http://www.langual.org/langual_thesaurus.asp?termid=M0216 drawn can FOODON:03490217 http://www.langual.org/langual_thesaurus.asp?termid=M0217 three-part can FOODON:03490218 http://www.langual.org/langual_thesaurus.asp?termid=M0218 jug or demijohn FOODON:03490219 http://www.langual.org/langual_thesaurus.asp?termid=M0219 pail FOODON:03490220 Classification corresponding to FSTA Thesaurus Packaging 3.2.4 Sealing/closing means http://www.langual.org/langual_thesaurus.asp?termid=M0220 sealing/closing element FOODON:03490221 http://www.langual.org/langual_thesaurus.asp?termid=M0221 adhesive FOODON:03490222 http://www.langual.org/langual_thesaurus.asp?termid=M0222 multicomponent adhesive FOODON:03490223 http://www.langual.org/langual_thesaurus.asp?termid=M0223 multicomponent adhesive, no solvent FOODON:03490224 http://www.langual.org/langual_thesaurus.asp?termid=M0224 multicomponent adhesive, organic solvent FOODON:03490225 http://www.langual.org/langual_thesaurus.asp?termid=M0225 multicomponent adhesive, water soluble FOODON:03490226 http://www.langual.org/langual_thesaurus.asp?termid=M0226 one component adhesive FOODON:03490227 http://www.langual.org/langual_thesaurus.asp?termid=M0227 one component adhesive, organic solvent FOODON:03490228 http://www.langual.org/langual_thesaurus.asp?termid=M0228 one component adhesive, water soluble FOODON:03490229 http://www.langual.org/langual_thesaurus.asp?termid=M0229 thermoplastic adhesive FOODON:03490231 http://www.langual.org/langual_thesaurus.asp?termid=M0231 glass stopper FOODON:03490233 http://www.langual.org/langual_thesaurus.asp?termid=M0233 plastic stopper FOODON:03490234 http://www.langual.org/langual_thesaurus.asp?termid=M0234 polyethylene plug FOODON:03490235 http://www.langual.org/langual_thesaurus.asp?termid=M0235 polypropylene plug FOODON:03490236 http://www.langual.org/langual_thesaurus.asp?termid=M0236 polyvinyl chloride plug FOODON:03490237 http://www.langual.org/langual_thesaurus.asp?termid=M0237 plastic screw cap or lid FOODON:03490239 http://www.langual.org/langual_thesaurus.asp?termid=M0239 plastic screw cap/pilfer proof FOODON:03490244 http://www.langual.org/langual_thesaurus.asp?termid=M0244 crown cap FOODON:03490245 http://www.langual.org/langual_thesaurus.asp?termid=M0245 metal screw cap or lid FOODON:03490246 http://www.langual.org/langual_thesaurus.asp?termid=M0246 metal screw cap/pilfer proof FOODON:03490256 http://www.langual.org/langual_thesaurus.asp?termid=M0256 wooden cork FOODON:03490257 http://www.langual.org/langual_thesaurus.asp?termid=M0257 seal/gasket FOODON:03490258 http://www.langual.org/langual_thesaurus.asp?termid=M0258 cork wood gasket FOODON:03490259 http://www.langual.org/langual_thesaurus.asp?termid=M0259 metal gasket FOODON:03490260 http://www.langual.org/langual_thesaurus.asp?termid=M0260 plastic gasket FOODON:03490261 http://www.langual.org/langual_thesaurus.asp?termid=M0261 rubber gasket FOODON:03490262 http://www.langual.org/langual_thesaurus.asp?termid=M0262 steel solder FOODON:03490263 http://www.langual.org/langual_thesaurus.asp?termid=M0263 tin solder FOODON:03490264 http://www.langual.org/langual_thesaurus.asp?termid=M0264 ceramic or earthenware bottle, coloured FOODON:03490265 http://www.langual.org/langual_thesaurus.asp?termid=M0265 ceramic or earthenware bottle, uncoloured FOODON:03490266 http://www.langual.org/langual_thesaurus.asp?termid=M0266 ceramic or earthenware jar, coloured FOODON:03490267 http://www.langual.org/langual_thesaurus.asp?termid=M0267 ceramic or earthenware jar, uncoloured FOODON:03490273 http://www.langual.org/langual_thesaurus.asp?termid=M0273 glass container, uncoloured FOODON:03490274 http://www.langual.org/langual_thesaurus.asp?termid=M0274 glass container, uncoloured, light weight FOODON:03490275 http://www.langual.org/langual_thesaurus.asp?termid=M0275 glass container, uncoloured, normal weight FOODON:03490276 http://www.langual.org/langual_thesaurus.asp?termid=M0276 glass container, uncoloured, strengthened FOODON:03490277 http://www.langual.org/langual_thesaurus.asp?termid=M0277 glass container, uncoloured, covered/protected FOODON:03490278 http://www.langual.org/langual_thesaurus.asp?termid=M0278 glass container, coloured FOODON:03490279 http://www.langual.org/langual_thesaurus.asp?termid=M0279 glass container, coloured, light weight FOODON:03490280 http://www.langual.org/langual_thesaurus.asp?termid=M0280 glass container, coloured, normal weight FOODON:03490281 http://www.langual.org/langual_thesaurus.asp?termid=M0281 glass container, coloured, strengthened FOODON:03490282 http://www.langual.org/langual_thesaurus.asp?termid=M0282 glass container, coloured, covered/protected FOODON:03490287 http://www.langual.org/langual_thesaurus.asp?termid=M0287 aluminum box FOODON:03490288 http://www.langual.org/langual_thesaurus.asp?termid=M0288 aluminium box, plastic-coated FOODON:03490289 http://www.langual.org/langual_thesaurus.asp?termid=M0289 aluminium box, varnished FOODON:03490291 http://www.langual.org/langual_thesaurus.asp?termid=M0291 aluminium can, drum or barrel, plastic coated FOODON:03490292 http://www.langual.org/langual_thesaurus.asp?termid=M0292 aluminium can, drum or barrel, varnished FOODON:03490295 http://www.langual.org/langual_thesaurus.asp?termid=M0295 aluminium foil wrapper, coated for heat sealing FOODON:03490296 http://www.langual.org/langual_thesaurus.asp?termid=M0296 aluminium foil-paper wrapper FOODON:03490297 http://www.langual.org/langual_thesaurus.asp?termid=M0297 aluminum coextruded with paper FOODON:03490298 http://www.langual.org/langual_thesaurus.asp?termid=M0298 aluminum combined with paper and plastic FOODON:03490299 http://www.langual.org/langual_thesaurus.asp?termid=M0299 aluminum combined with regenerated cellulose FOODON:03490300 http://www.langual.org/langual_thesaurus.asp?termid=M0300 laminated aluminum combination with paper FOODON:03490301 http://www.langual.org/langual_thesaurus.asp?termid=M0301 stainless steel container FOODON:03490308 http://www.langual.org/langual_thesaurus.asp?termid=M0308 steel plate container tinned one side FOODON:03490309 http://www.langual.org/langual_thesaurus.asp?termid=M0309 steel plate container tinned both sides FOODON:03490310 http://www.langual.org/langual_thesaurus.asp?termid=M0310 varnished tin-plate container FOODON:03490320 http://www.langual.org/langual_thesaurus.asp?termid=M0320 natural polymer container FOODON:03490321 http://www.langual.org/langual_thesaurus.asp?termid=M0321 casein resin FOODON:03490322 http://www.langual.org/langual_thesaurus.asp?termid=M0322 cellulose film FOODON:03490323 http://www.langual.org/langual_thesaurus.asp?termid=M0323 acetate cellulose film FOODON:03490324 http://www.langual.org/langual_thesaurus.asp?termid=M0324 butyrate cellulose film FOODON:03490325 http://www.langual.org/langual_thesaurus.asp?termid=M0325 propyonate cellulose film FOODON:03490326 http://www.langual.org/langual_thesaurus.asp?termid=M0326 regenerated cellulose film FOODON:03490327 http://www.langual.org/langual_thesaurus.asp?termid=M0327 regenerated cellulose film, coated FOODON:03490328 http://www.langual.org/langual_thesaurus.asp?termid=M0328 regenerated cellulose film, coloured FOODON:03490329 http://www.langual.org/langual_thesaurus.asp?termid=M0329 rubber container FOODON:03490330 http://www.langual.org/langual_thesaurus.asp?termid=M0330 paper container, treated FOODON:03490331 http://www.langual.org/langual_thesaurus.asp?termid=M0331 lacquered paper container FOODON:03490332 http://www.langual.org/langual_thesaurus.asp?termid=M0332 saturated (immersed) paper container FOODON:03490333 http://www.langual.org/langual_thesaurus.asp?termid=M0333 waxed paper container FOODON:03490334 http://www.langual.org/langual_thesaurus.asp?termid=M0334 paper container, untreated FOODON:03490335 http://www.langual.org/langual_thesaurus.asp?termid=M0335 bleached paper container FOODON:03490336 http://www.langual.org/langual_thesaurus.asp?termid=M0336 kraft or brown paper container FOODON:03490337 http://www.langual.org/langual_thesaurus.asp?termid=M0337 grease proof paper container FOODON:03490338 http://www.langual.org/langual_thesaurus.asp?termid=M0338 imitation grease proof paper container FOODON:03490339 Porous, wet-strength paper, e.g. tea bag. http://www.langual.org/langual_thesaurus.asp?termid=M0339 tissue paper container FOODON:03490340 http://www.langual.org/langual_thesaurus.asp?termid=M0340 paperboard container, untreated FOODON:03490341 http://www.langual.org/langual_thesaurus.asp?termid=M0341 paperboard container, surface treated FOODON:03490342 http://www.langual.org/langual_thesaurus.asp?termid=M0342 paperboard container, surface treated both sides FOODON:03490343 http://www.langual.org/langual_thesaurus.asp?termid=M0343 paperboard container, surface treated inside FOODON:03490344 http://www.langual.org/langual_thesaurus.asp?termid=M0344 paperboard container, surface treated outside FOODON:03490345 http://www.langual.org/langual_thesaurus.asp?termid=M0345 paper combined material FOODON:03490346 http://www.langual.org/langual_thesaurus.asp?termid=M0346 impregnated/micro waxed paper FOODON:03490347 http://www.langual.org/langual_thesaurus.asp?termid=M0347 metalized paper wrapper FOODON:03490348 http://www.langual.org/langual_thesaurus.asp?termid=M0348 metalized paper coextruded with plastic FOODON:03490349 http://www.langual.org/langual_thesaurus.asp?termid=M0349 metalized paper laminated with plastic FOODON:03490350 http://www.langual.org/langual_thesaurus.asp?termid=M0350 metalized paper laminated with treated paper FOODON:03490351 http://www.langual.org/langual_thesaurus.asp?termid=M0351 paper-aluminium foil-plastic wrapper FOODON:03490352 http://www.langual.org/langual_thesaurus.asp?termid=M0352 coextruded paper-aluminium-plastic wrapper FOODON:03490353 http://www.langual.org/langual_thesaurus.asp?termid=M0353 laminated paper-aluminium-plastic wrapper FOODON:03490354 http://www.langual.org/langual_thesaurus.asp?termid=M0354 paper-paper combination FOODON:03490355 http://www.langual.org/langual_thesaurus.asp?termid=M0355 paper-plastic combination FOODON:03490356 http://www.langual.org/langual_thesaurus.asp?termid=M0356 laminate paper coextruded with plastic FOODON:03490357 Corresponds to FSTA Thesaurus Packaging 2.2.1 'Type of plastic' http://www.langual.org/langual_thesaurus.asp?termid=M0357 plastic container, according to type of plastic FOODON:03490358 http://www.langual.org/langual_thesaurus.asp?termid=M0358 thermoplastic sheet or container FOODON:03490359 http://www.langual.org/langual_thesaurus.asp?termid=M0359 polyamide container FOODON:03490360 http://www.langual.org/langual_thesaurus.asp?termid=M0360 acryl-nitrile container FOODON:03490361 http://www.langual.org/langual_thesaurus.asp?termid=M0361 nylon 11 container FOODON:03490362 http://www.langual.org/langual_thesaurus.asp?termid=M0362 nylon 6,6 container FOODON:03490363 http://www.langual.org/langual_thesaurus.asp?termid=M0363 polycarbonate container FOODON:03490364 http://www.langual.org/langual_thesaurus.asp?termid=M0364 polyester container FOODON:03490365 http://www.langual.org/langual_thesaurus.asp?termid=M0365 polyester container, glass fibre strengthened FOODON:03490366 http://www.langual.org/langual_thesaurus.asp?termid=M0366 linear polyester container FOODON:03490367 http://www.langual.org/langual_thesaurus.asp?termid=M0367 polyethylene container FOODON:03490368 http://www.langual.org/langual_thesaurus.asp?termid=M0368 high density polyethylene container FOODON:03490370 http://www.langual.org/langual_thesaurus.asp?termid=M0370 low density polyethylene container FOODON:03490371 http://www.langual.org/langual_thesaurus.asp?termid=M0371 linear low density polyethylene container FOODON:03490372 http://www.langual.org/langual_thesaurus.asp?termid=M0372 low density polyethylene container, treated FOODON:03490373 http://www.langual.org/langual_thesaurus.asp?termid=M0373 polymethylmethacrylate container FOODON:03490374 http://www.langual.org/langual_thesaurus.asp?termid=M0374 polypropylene container FOODON:03490375 http://www.langual.org/langual_thesaurus.asp?termid=M0375 biaxial oriented polypropylene container FOODON:03490376 http://www.langual.org/langual_thesaurus.asp?termid=M0376 oriented polypropylene container FOODON:03490377 http://www.langual.org/langual_thesaurus.asp?termid=M0377 polystyrene container FOODON:03490378 http://www.langual.org/langual_thesaurus.asp?termid=M0378 polyvinyl chloride container FOODON:03490379 http://www.langual.org/langual_thesaurus.asp?termid=M0379 unplasticized polyvinyl chloride container FOODON:03490380 http://www.langual.org/langual_thesaurus.asp?termid=M0380 plasticized polyvinyl chloride container FOODON:03490381 http://www.langual.org/langual_thesaurus.asp?termid=M0381 polyvinylidene chloride container FOODON:03490382 http://www.langual.org/langual_thesaurus.asp?termid=M0382 thermosetting polymer container FOODON:03490383 http://www.langual.org/langual_thesaurus.asp?termid=M0383 alkyd resin container FOODON:03490384 http://www.langual.org/langual_thesaurus.asp?termid=M0384 amin resin container FOODON:03490385 http://www.langual.org/langual_thesaurus.asp?termid=M0385 aniline-formaldehyde container FOODON:03490386 http://www.langual.org/langual_thesaurus.asp?termid=M0386 carbamide-formaldehyde container FOODON:03490387 http://www.langual.org/langual_thesaurus.asp?termid=M0387 diciandiamide-formaldehyde container FOODON:03490388 http://www.langual.org/langual_thesaurus.asp?termid=M0388 epoxy resin container FOODON:03490389 http://www.langual.org/langual_thesaurus.asp?termid=M0389 phenonile resin container FOODON:03490390 http://www.langual.org/langual_thesaurus.asp?termid=M0390 polyester resin container FOODON:03490391 http://www.langual.org/langual_thesaurus.asp?termid=M0391 plastic container, combined material FOODON:03490392 http://www.langual.org/langual_thesaurus.asp?termid=M0392 metallized polymer container FOODON:03490393 http://www.langual.org/langual_thesaurus.asp?termid=M0393 metallized polyamide container FOODON:03490394 http://www.langual.org/langual_thesaurus.asp?termid=M0394 metallized polyester container FOODON:03490395 http://www.langual.org/langual_thesaurus.asp?termid=M0395 polyethylene (high density) - polyamide container FOODON:03490396 http://www.langual.org/langual_thesaurus.asp?termid=M0396 polyethylene (high density) - nylon 11 container FOODON:03490397 http://www.langual.org/langual_thesaurus.asp?termid=M0397 polyethylene (high density) - polyester container FOODON:03490398 http://www.langual.org/langual_thesaurus.asp?termid=M0398 polyethylene (high density) - polypropylene container FOODON:03490399 http://www.langual.org/langual_thesaurus.asp?termid=M0399 polyethylene (low density) - polyamide container FOODON:03490400 http://www.langual.org/langual_thesaurus.asp?termid=M0400 polyethylene (low density) - nylon 11 container FOODON:03490401 http://www.langual.org/langual_thesaurus.asp?termid=M0401 polyethylene (low density) - polyester container FOODON:03490402 http://www.langual.org/langual_thesaurus.asp?termid=M0402 polyethylene (low density) - polyethylene (high density) container FOODON:03490403 http://www.langual.org/langual_thesaurus.asp?termid=M0403 polyethylene (low density) - polyethylene (low density) container FOODON:03490404 http://www.langual.org/langual_thesaurus.asp?termid=M0404 polyethylene (low density) - polypropylene container FOODON:03490405 http://www.langual.org/langual_thesaurus.asp?termid=M0405 polyethylene - regenerated cellulose container FOODON:03490406 http://www.langual.org/langual_thesaurus.asp?termid=M0406 polyethylene - vinyl copolymer container FOODON:03490407 http://www.langual.org/langual_thesaurus.asp?termid=M0407 polyvinyl chloride - polyvinylidene chloride container FOODON:03490409 http://www.langual.org/langual_thesaurus.asp?termid=M0409 natural textile container FOODON:03490410 http://www.langual.org/langual_thesaurus.asp?termid=M0410 animal hair container FOODON:03490411 http://www.langual.org/langual_thesaurus.asp?termid=M0411 bass fibre container FOODON:03490412 http://www.langual.org/langual_thesaurus.asp?termid=M0412 asbestos container FOODON:03490413 http://www.langual.org/langual_thesaurus.asp?termid=M0413 cotton container FOODON:03490414 http://www.langual.org/langual_thesaurus.asp?termid=M0414 leaf fibre container FOODON:03490415 http://www.langual.org/langual_thesaurus.asp?termid=M0415 polymer base textile container FOODON:03490416 http://www.langual.org/langual_thesaurus.asp?termid=M0416 polyamide container FOODON:03490417 http://www.langual.org/langual_thesaurus.asp?termid=M0417 polyester container FOODON:03490418 http://www.langual.org/langual_thesaurus.asp?termid=M0418 polyolefine container FOODON:03490419 http://www.langual.org/langual_thesaurus.asp?termid=M0419 boil-in bag FOODON:03490420 http://www.langual.org/langual_thesaurus.asp?termid=M0420 inner bag FOODON:03490423 http://www.langual.org/langual_thesaurus.asp?termid=M0423 closing cap or lid FOODON:03490424 http://www.langual.org/langual_thesaurus.asp?termid=M0424 closing capsule FOODON:03490425 http://www.langual.org/langual_thesaurus.asp?termid=M0425 screw cap or lid FOODON:03490426 http://www.langual.org/langual_thesaurus.asp?termid=M0426 peel-off lid FOODON:03490427 http://www.langual.org/langual_thesaurus.asp?termid=M0427 stopper FOODON:03490429 Example: egg box. http://www.langual.org/langual_thesaurus.asp?termid=M0429 recycled paperboard container FOODON:03490430 http://www.langual.org/langual_thesaurus.asp?termid=M0430 polyethylene terephthalate (pet) container FOODON:03490431 http://www.langual.org/langual_thesaurus.asp?termid=M0431 polyolefin container FOODON:03500010 The specific container or coating materials in direct contact with the food. Multiple values can be assigned. [FDA CFSAN 1995] http://www.langual.org/langual_thesaurus.asp?termid=N0010 food contact surface FOODON:03500011 http://www.langual.org/langual_thesaurus.asp?termid=N0011 beverage can enamel FOODON:03500012 http://www.langual.org/langual_thesaurus.asp?termid=N0012 beverage can enamel, noncarbonated beverage FOODON:03500013 http://www.langual.org/langual_thesaurus.asp?termid=N0013 beverage can enamel, carbonated soft drink FOODON:03500014 http://www.langual.org/langual_thesaurus.asp?termid=N0014 beverage can enamel, beer FOODON:03500015 Wax may be applied directly as a coating to the food product or may be used as a container material. Examples include wax-coated cheese, wax-coated cucumber, waxed fiberboard container, etc. http://www.langual.org/langual_thesaurus.asp?termid=N0015 wax FOODON:03500016 http://www.langual.org/langual_thesaurus.asp?termid=N0016 fruit enamel (f-enamel) FOODON:03500017 PE http://www.langual.org/langual_thesaurus.asp?termid=N0017 polyethylene FOODON:03500018 http://www.langual.org/langual_thesaurus.asp?termid=N0018 citrus enamel FOODON:03500019 http://www.langual.org/langual_thesaurus.asp?termid=N0019 milk enamel FOODON:03500020 http://www.langual.org/langual_thesaurus.asp?termid=N0020 meat enamel FOODON:03500021 http://www.langual.org/langual_thesaurus.asp?termid=N0021 polypropylene FOODON:03500022 http://www.langual.org/langual_thesaurus.asp?termid=N0022 polystyrene FOODON:03500023 http://www.langual.org/langual_thesaurus.asp?termid=N0023 seafood enamel FOODON:03500024 A class of coatings that contains a specially prepared vehicle, instead of raw oil. Sometimes referred to as varnish or lacquer. http://www.langual.org/langual_thesaurus.asp?termid=N0024 coating enamel FOODON:03500025 Trade name of polyvinylidene chloride copolymer film. Chief packaging uses are in film and in coatings for other flexible substrates such as cellophane and paper. http://www.langual.org/langual_thesaurus.asp?termid=N0025 saran FOODON:03500026 Trade name of polyester used in the usa. http://www.langual.org/langual_thesaurus.asp?termid=N0026 mylar FOODON:03500027 A generic term for a class of polyamides containing repeating amide groups connected by methylene units. The most common types used in food industry are ny-lon-66 and nylon-11. http://www.langual.org/langual_thesaurus.asp?termid=N0027 nylon FOODON:03500028 Trade name of a shrinkable version of pvdc used for vacuum packaging, e.g. of red meat. http://www.langual.org/langual_thesaurus.asp?termid=N0028 cryovac FOODON:03500029 PVDC http://www.langual.org/langual_thesaurus.asp?termid=N0029 vinylidene FOODON:03500030 http://www.langual.org/langual_thesaurus.asp?termid=N0030 corn enamel (c-enamel) FOODON:03500031 http://www.langual.org/langual_thesaurus.asp?termid=N0031 cellophane FOODON:03500032 A rubber hydrochloride, first introduced as a packaging film in 1936 in the U.S.A. http://www.langual.org/langual_thesaurus.asp?termid=N0032 pliofilm FOODON:03500033 http://www.langual.org/langual_thesaurus.asp?termid=N0033 polyester FOODON:03500034 CA: thermoplastic material made by the esterification of cellulose with acetic anhydride and acetic acid. http://www.langual.org/langual_thesaurus.asp?termid=N0034 cellulose acetate FOODON:03500036 http://www.langual.org/langual_thesaurus.asp?termid=N0036 plastic FOODON:03500037 PVC http://www.langual.org/langual_thesaurus.asp?termid=N0037 polyvinyl chloride FOODON:03500038 http://www.langual.org/langual_thesaurus.asp?termid=N0038 ceramic FOODON:03500039 http://www.langual.org/langual_thesaurus.asp?termid=N0039 paper or paperboard FOODON:03500040 An amorphous, inorganic, inert substance consisting of a mixture of silicates, borates or phosphates, and usually transparent or translucent. http://www.langual.org/langual_thesaurus.asp?termid=N0040 glass FOODON:03500041 http://www.langual.org/langual_thesaurus.asp?termid=N0041 metal FOODON:03500042 http://www.langual.org/langual_thesaurus.asp?termid=N0042 aluminum FOODON:03500043 http://www.langual.org/langual_thesaurus.asp?termid=N0043 tin FOODON:03500044 http://www.langual.org/langual_thesaurus.asp?termid=N0044 steel FOODON:03500045 http://www.langual.org/langual_thesaurus.asp?termid=N0045 textile or fabric FOODON:03500046 http://www.langual.org/langual_thesaurus.asp?termid=N0046 cork FOODON:03500047 Some cheeses are surrounded by a layer of ashes. http://www.langual.org/langual_thesaurus.asp?termid=N0047 ash FOODON:03500048 http://www.langual.org/langual_thesaurus.asp?termid=N0048 leaf, food contact surface FOODON:03500049 http://www.langual.org/langual_thesaurus.asp?termid=N0049 husk, food contact surface FOODON:03500050 http://www.langual.org/langual_thesaurus.asp?termid=N0050 food contact surface from natural material FOODON:03500051 http://www.langual.org/langual_thesaurus.asp?termid=N0051 food contact surface from human-made material FOODON:03500052 http://www.langual.org/langual_thesaurus.asp?termid=N0052 egg shell, food contact surface FOODON:03500053 http://www.langual.org/langual_thesaurus.asp?termid=N0053 mollusc shell, food contact surface FOODON:03500054 http://www.langual.org/langual_thesaurus.asp?termid=N0054 latex FOODON:03500055 Trade name for a polymer used to provide better protection and longer life to porous metals (nickel alloys) in coextruded sheets and films. http://www.langual.org/langual_thesaurus.asp?termid=N0055 teflon FOODON:03500056 http://www.langual.org/langual_thesaurus.asp?termid=N0056 edible casing FOODON:03500057 http://www.langual.org/langual_thesaurus.asp?termid=N0057 natural-based polymers FOODON:03510010 http://www.langual.org/langual_thesaurus.asp?termid=P0010 laboratory animal as food consumer FOODON:03510011 http://www.langual.org/langual_thesaurus.asp?termid=P0011 food fish as consumer FOODON:03510012 http://www.langual.org/langual_thesaurus.asp?termid=P0012 pet fish as consumer FOODON:03510013 http://www.langual.org/langual_thesaurus.asp?termid=P0013 non-food animal as food consumer FOODON:03510014 http://www.langual.org/langual_thesaurus.asp?termid=P0014 sheep or goat as consumer FOODON:03510015 http://www.langual.org/langual_thesaurus.asp?termid=P0015 food animal as consumer FOODON:03510017 All narrower term definitions extracted from 58 Federal Register 2302, January 6, 1993, part 101.62(b). http://www.langual.org/langual_thesaurus.asp?termid=P0017 fat special claim or use FOODON:03510018 http://www.langual.org/langual_thesaurus.asp?termid=P0018 poultry as consumer FOODON:03510019 http://www.langual.org/langual_thesaurus.asp?termid=P0019 cattle as consumer FOODON:03510020 Food produced and marketed to supply the particular dietary needs of normal infants (21 CFR 105.65) or normal toddlers (age 1 to 2 years). Junior foods are included with the strained foods for infants up to one year. Foods fall in this category only if the label bears a statement such as 'baby food', 'strained food', 'junior food' or 'toddler food'. http://www.langual.org/langual_thesaurus.asp?termid=P0020 infant or toddler as food consumer FOODON:03510021 http://www.langual.org/langual_thesaurus.asp?termid=P0021 animal as food consumer FOODON:03510023 Renamed from *FOOD FOR SPECIAL DIETARY USE* [LanguaL 2008]. These descriptors are used either for foods intended for special dietary use as defined in 21 CFR 105 or for foods that have special characteristics indicated in the name or labeling. Such claims would include 'low calorie', 'low cholesterol', 'diet' or 'dietetic', etc. Prior to february 1992, this category of descriptors was limited solely to food for adult humans. The category is now used in conjunction with any appropriate *CONSUMER GROUP* descriptor(s), for example, 'low sugar baby food' would be indexed by *INFANT OR TODDLER FOOD* as well as by *LOW SUGARS FOOD*. http://www.langual.org/langual_thesaurus.asp?termid=P0023 dietary claim or use FOODON:03510025 http://www.langual.org/langual_thesaurus.asp?termid=P0025 horse as consumer FOODON:03510026 Food produced and marketed for human use. http://www.langual.org/langual_thesaurus.asp?termid=P0026 human as food consumer FOODON:03510027 http://www.langual.org/langual_thesaurus.asp?termid=P0027 pig as consumer FOODON:03510028 http://www.langual.org/langual_thesaurus.asp?termid=P0028 pet cat as consumer FOODON:03510029 Pet animals as a consumer group; products are labeled accordingly. http://www.langual.org/langual_thesaurus.asp?termid=P0029 pet animal as consumer FOODON:03510030 http://www.langual.org/langual_thesaurus.asp?termid=P0030 pet bird as consumer FOODON:03510031 http://www.langual.org/langual_thesaurus.asp?termid=P0031 pet dog as consumer FOODON:03510032 Dietary use, where the food has special characteristics, claims or uses or is intended for individuals with particular dietary needs; and label or labeling claims, used when special dietary use factor terms were derived from actual food labels. Multiple descriptors may be used from all three categories. [FDA CFSAN 1995] http://www.langual.org/langual_thesaurus.asp?termid=P0032 dietary use/label claim FOODON:03510033 A claim that a food is low in energy, and any claim likely to have the same meaning for the consumer, may only be made where the product does not contain more than 40 kcal (170 kJ)/100 g for solids or more than 20 kcal (80 kJ)/100 ml for liquids. For table-top sweeteners the limit of 4 kcal (17 kJ)/portion, with equivalent sweetening properties to 6 g of sucrose (approximately 1 teaspoon of sucrose), applies [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having 40 calories or less per amount customarily consumed (and per 50 grams of food if the amount customarily consumed is small). Meals and main dishes contain 120 calories or less per 100 grams of food [US FDA] http://www.langual.org/langual_thesaurus.asp?termid=P0033 low energy food claim or use FOODON:03510034 A claim that a food is energy-reduced, and any claim likely to have the same meaning for the consumer, may only be made where the energy value is reduced by at least 30 %, with an indication of the characteristic(s) which make(s) the food reduced in its total energy value [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having at least 25% fewer calories per amount customarily consumed from the calories of a comparable food product. The complarable food may not be 'low calorie' [US FDA]. http://www.langual.org/langual_thesaurus.asp?termid=P0034 reduced energy food claim or use FOODON:03510035 A claim that a food is sodium-free or salt-free, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 0,005 g of sodium, or the equivalent value for salt, per 100 g. [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having less than 5 milligrams of salt or sodium per amount customarily consumed (or for meals and main dishes, less than 5 miligrams of salt or sodium per labeled serving). Such foods must not contain an ingredient that is salt or sodium or generally understood to comtain salt or sodium except where the ingredient listed is footnoted '*adds a trivial amount of {salt or sodium}' [US FDA] http://www.langual.org/langual_thesaurus.asp?termid=P0035 salt or sodium free claim or use FOODON:03510036 A claim that a food is very low in sodium/salt, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 0,04 g of sodium, or the equivalent value for salt, per 100 g or per 100 ml. This claim shall not be used for natural mineral waters and other waters [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having 35 milligrams or less salt or sodium per amount customarily consumed (and per 50 grams if the amount customarily consumed is small). Meals and main dishes contain 35 milligrams or less salt or sodium per 100 grams of food [US FDA] http://www.langual.org/langual_thesaurus.asp?termid=P0036 very low salt or sodium claim or use FOODON:03510037 http://www.langual.org/langual_thesaurus.asp?termid=P0037 reduced salt or sodium claim or use FOODON:03510038 A claim that a food is low in sodium/salt, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 0,12 g of sodium, or the equivalent value for salt, per 100 g or per 100 ml. For waters, other than natural mineral waters falling within the scope of Directive 80/777/EEC, this value should not exceed 2 mg of sodium per 100 ml [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having 140 milligrams or less salt or sodium per amount customarily consumed. Meals and main dishes have 140 milligrams or less salt or sodium per 100 grams food [US FDA] http://www.langual.org/langual_thesaurus.asp?termid=P0038 low salt or sodium claim or use FOODON:03510039 A claim that a food is low in fat, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 3 g of fat per 100 g for solids or 1,5 g of fat per 100 ml for liquids (1,8 g of fat per 100 ml for semi-skimmed milk). [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having 3 grams of fat or less per amount customarily consumed (and per 50 grams of food if the amount customarily consumed is small). Meals and main dishes contain 3 grams or less fat per 100 grams of food and not more than 30% of calories from fat [US FDA]. http://www.langual.org/langual_thesaurus.asp?termid=P0039 low fat food FOODON:03510040 Food containing at least 25% less fat per amount customarily consumed from the fat content of a comparable food product. The comparable food may not be 'low fat'. http://www.langual.org/langual_thesaurus.asp?termid=P0040 reduced fat food FOODON:03510041 All narrower term definitions extracted from 58 Federal Register 2302, January 6, 1993, part 101.62(d). http://www.langual.org/langual_thesaurus.asp?termid=P0041 cholesterol special claim or use FOODON:03510042 Food having less than 2 milligrams cholesterol per amount customarily consumed (or for meals and main dishes, less than 2 milligrams cholesterol per labeled serving). Such food must contain no ingredient that contains cholesterol except where the ingredient listed has been footnoted '*adds a trivial amount of cholesterol'. If the food contains less than 2 milligrams cholesterol per amount customarily consumed by special processing and the total fat exceeds 13 grams cholesterol per amount or labeled serving, the amount of cholesterol must be 'Substantially less' (25%) than in a comparable food with significant market share (5% of market). http://www.langual.org/langual_thesaurus.asp?termid=P0042 cholesterol free claim or use FOODON:03510043 Food having 20 miligrams or less cholesterol per amount customarily consumed (and per 50 grams of food if the amount customarily consumed is small). Meals and main dishes contain 20 milligrams or less cholesterol per 100 grams of food. If the food qualifies by special processing and total fat exceeds 13 grams per amount and labeled serving, the amount of cholesterol must be 'substantially less' (25%) than in a comparable food with significant market share (5% of market). http://www.langual.org/langual_thesaurus.asp?termid=P0043 low in cholesterol claim or use FOODON:03510044 Food having at least 25% less cholesterol per amount customarily consumed from the cholesterol content of a comparable food product. The comparable food may not be 'low cholesterol'. http://www.langual.org/langual_thesaurus.asp?termid=P0044 reduced cholesterol claim or use FOODON:03510045 All narrower term definitions are extracted from 58 Federal Register 2302, January 6, 1993, part 101.60(b) and from Corrigendum to Regulation (EC) No 1924/2006 of the European Parliament and of the Council of 20 December 2006 on nutrition and health claims made on foods. http://www.langual.org/langual_thesaurus.asp?termid=P0045 energy special claim or use FOODON:03510047 All narrower term definitions extracted from 58 Federal Register 2032, January 6, 1993, part 101.61. http://www.langual.org/langual_thesaurus.asp?termid=P0047 salt or sodium special claim or use FOODON:03510048 A claim that a food is high in fibre, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least 6 g of fibre per 100 g or at least 3 g of fibre per 100 kcal [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food that is promoted as a source of or as high in dietary fiber (often called simply 'fiber'). http://www.langual.org/langual_thesaurus.asp?termid=P0048 high fiber food FOODON:03510049 Food that is promoted as being either high or low in dietary fiber (often called simply 'fiber'). If the food is not low in total fat, total fat must be stated in conjunction with claim such as 'more fiber'. http://www.langual.org/langual_thesaurus.asp?termid=P0049 fiber special claim or use FOODON:03510054 A claim that a food is fat-free, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 0,5 g of fat per 100 g or 100 ml. However, claims expressed as "X % fat-free" shall be prohibited [REGULATION (EC) No 1924/2006 Corrigendum]. Food having less than 0.5 grams fat per amount customarily consumed. Meals and main dishes have less than 0.5 grams fat per labeled serving. Such foods must contain no ingredient that is fat or understood to contain fat except when the ingredient listed has been footnoted '*adds a trivial amount of fat'. http://www.langual.org/langual_thesaurus.asp?termid=P0054 fat free food FOODON:03510055 A claim that a food is energy-free, and any claim likely to have the same meaning for the consumer, may only be made where the product does not contain more than 4 kcal (17 kJ)/100 ml. For table-top sweeteners the limit of 0.4 kcal (1.7 kJ)/portion, with equivalent sweetening properties to 6 g of sucrose (approximately 1 teaspoon of sucrose), applies [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having less than 5 calories per amount customarily consumed. Calorie amount is not defined for meals or main dishes [US FDA] http://www.langual.org/langual_thesaurus.asp?termid=P0055 energy free food claim or use FOODON:03510056 A claim that a food is sugars-free, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 0,5 g of sugars per 100 g or 100 ml [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having less than 0.5 grams sugars per amount customarily consumed (or for meals and main dishes, less than 0.5 grams sugars per labeled serving). Such foods nust contain no ingredient that is a sugar or generally understood to contain sugars except where the ingredient listed is footnoted '*adds a trivial amount of sugars' [US FDA] http://www.langual.org/langual_thesaurus.asp?termid=P0056 sugars free food FOODON:03510057 A claim that a food is low in saturated fat, and any claim likely to have the same meaning for the consumer, may only be made if the sum of saturated fatty acids and trans-fatty acids in the product does not exceed 1.5 g per 100 g for solids or 0.75 g/100 ml for liquids and in either case the sum of saturated fatty acids and trans-fatty acids must not provide more than 10 % of energy. [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having one gram or less saturated fat per amount customarily consumed and 15% or less of calories from saturated fat. Meals and main dishes contain one gram or less saturated fat per 100 grams food and less than 10% of calories from saturated fat. http://www.langual.org/langual_thesaurus.asp?termid=P0057 low in saturated fat food FOODON:03510059 http://www.langual.org/langual_thesaurus.asp?termid=P0059 general label claim FOODON:03510060 [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18] http://www.langual.org/langual_thesaurus.asp?termid=P0060 high energy food claim or use FOODON:03510061 All narrower term definitions extracted from 58 Federal Register 2302, January 6, 1993, part 101.60(c). http://www.langual.org/langual_thesaurus.asp?termid=P0061 sugars special claim or use FOODON:03510062 A claim that a food is low in sugars, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 5 g of sugars per 100 g for solids or 2,5 g of sugars per 100 ml for liquids [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Not defined in U.S. Federal Register; no basis for a recommended intake. http://www.langual.org/langual_thesaurus.asp?termid=P0062 low sugars food FOODON:03510063 http://www.langual.org/langual_thesaurus.asp?termid=P0063 low fiber food FOODON:03510065 As defined in Corrigendum to Regulation (EC) No 1924/2006 of the European Parliament and of the Council of 20 December 2006 on nutrition and health claims made on foods, "claim" means any message or representation, which is not mandatory under Community or national legislation, including pictorial, graphic or symbolic representation, in any form, which states, suggests or implies that a food has particular characteristics; specificly, "nutrition claim" means any claim which states, suggests or implies that a food has particular beneficial nutritional properties due to: (a) the energy (calorific value) it (i) provides; (ii) provides at a reduced or increased rate; or (iii) does not provide; and/or (b) the nutrients or other substances it (i) contains; (ii) contains in reduced or increased proportions; or (iii) does not contain. http://www.langual.org/langual_thesaurus.asp?termid=P0065 nutrition-related claim or use FOODON:03510066 http://www.langual.org/langual_thesaurus.asp?termid=P0066 no or reduced energy claim or use FOODON:03510069 http://www.langual.org/langual_thesaurus.asp?termid=P0069 no or reduced fat claim or use FOODON:03510070 http://www.langual.org/langual_thesaurus.asp?termid=P0070 no fat added claim or use FOODON:03510071 All narrower term definitions extracted from 58 Federal Register 2302, January 6, 1993, part 101.62(c). http://www.langual.org/langual_thesaurus.asp?termid=P0071 saturated fat-related claim or use FOODON:03510072 http://www.langual.org/langual_thesaurus.asp?termid=P0072 no animal fat added claim or use FOODON:03510073 http://www.langual.org/langual_thesaurus.asp?termid=P0073 no tropical oils added claim or use FOODON:03510074 http://www.langual.org/langual_thesaurus.asp?termid=P0074 no palm oil added claim or use FOODON:03510075 http://www.langual.org/langual_thesaurus.asp?termid=P0075 rich in fiber claim or use FOODON:03510076 http://www.langual.org/langual_thesaurus.asp?termid=P0076 naturally rich in fiber claim or use FOODON:03510077 http://www.langual.org/langual_thesaurus.asp?termid=P0077 no or reduced salt or sodium claim or use FOODON:03510078 http://www.langual.org/langual_thesaurus.asp?termid=P0078 no salt added claim or use FOODON:03510080 Food having less than 5 milligrams salt per amount customarily consumed (or for meals and main dishes less than 5 milligrams salt per labeled serving). Such food must contain no ingredient that is salt or generally understood to contain salt except where the ingredient listed is footnoted '*adds a trivial amount of salt'. http://www.langual.org/langual_thesaurus.asp?termid=P0080 salt free claim or use FOODON:03510083 http://www.langual.org/langual_thesaurus.asp?termid=P0083 low salt claim or use FOODON:03510085 Food having less than 35 milligrams of salt per serving and per 100 grams of food. (U.S. proposed) http://www.langual.org/langual_thesaurus.asp?termid=P0085 very low salt claim or use FOODON:03510087 http://www.langual.org/langual_thesaurus.asp?termid=P0087 reduced salt claim or use FOODON:03510088 http://www.langual.org/langual_thesaurus.asp?termid=P0088 naturally sodium-free food FOODON:03510090 http://www.langual.org/langual_thesaurus.asp?termid=P0090 no or reduced sugar claim or use FOODON:03510091 A claim stating that sugars have not been added to a food, and any claim likely to have the same meaning for the consumer, may only be made where the product does not contain any added mono- or disaccharides or any other food used for its sweetening properties. If sugars are naturally present in the food, the following indication should also appear on the label: "CONTAINS NATURALLY OCCURRING SUGARS" [REGULATION (EC) No 1924/2006 Corrigendum]. No added sugars and 'without added sugars' are allowed if no sugar or sugar containing ingredient is added during processing. (28 Federal Register 2302, January 6, 1993) http://www.langual.org/langual_thesaurus.asp?termid=P0091 no sugars added claim or use FOODON:03510092 http://www.langual.org/langual_thesaurus.asp?termid=P0092 starch-related claim or use FOODON:03510093 http://www.langual.org/langual_thesaurus.asp?termid=P0093 no modified food starch added claim or use FOODON:03510094 http://www.langual.org/langual_thesaurus.asp?termid=P0094 no starch added claim or use FOODON:03510095 http://www.langual.org/langual_thesaurus.asp?termid=P0095 vitamin- or mineral-related claim or use FOODON:03510096 http://www.langual.org/langual_thesaurus.asp?termid=P0096 color-related claim or use FOODON:03510097 http://www.langual.org/langual_thesaurus.asp?termid=P0097 no artificial colors claim or use FOODON:03510098 http://www.langual.org/langual_thesaurus.asp?termid=P0098 no color added claim or use FOODON:03510099 http://www.langual.org/langual_thesaurus.asp?termid=P0099 flavor- or taste-related claim or use FOODON:03510100 http://www.langual.org/langual_thesaurus.asp?termid=P0100 no artificial flavors claim or use FOODON:03510102 http://www.langual.org/langual_thesaurus.asp?termid=P0102 no flavor added claim or use FOODON:03510103 http://www.langual.org/langual_thesaurus.asp?termid=P0103 sweetener-related claim or use FOODON:03510104 http://www.langual.org/langual_thesaurus.asp?termid=P0104 no artificial sweeteners claim or use FOODON:03510105 http://www.langual.org/langual_thesaurus.asp?termid=P0105 unsweetened claim or use FOODON:03510106 http://www.langual.org/langual_thesaurus.asp?termid=P0106 artificial ingredient-related claim or use FOODON:03510107 http://www.langual.org/langual_thesaurus.asp?termid=P0107 no artificial ingredients claim or use FOODON:03510108 http://www.langual.org/langual_thesaurus.asp?termid=P0108 no artificial additives claim or use FOODON:03510110 http://www.langual.org/langual_thesaurus.asp?termid=P0110 preservative-related claim or use FOODON:03510111 http://www.langual.org/langual_thesaurus.asp?termid=P0111 no nitrite/nitrate added claim or use FOODON:03510112 http://www.langual.org/langual_thesaurus.asp?termid=P0112 no sulfite added claim or use FOODON:03510113 http://www.langual.org/langual_thesaurus.asp?termid=P0113 no artificial preservatives claim or use FOODON:03510114 http://www.langual.org/langual_thesaurus.asp?termid=P0114 no preservatives claim or use FOODON:03510115 http://www.langual.org/langual_thesaurus.asp?termid=P0115 other ingredient- or constituent-related claim or use FOODON:03510116 http://www.langual.org/langual_thesaurus.asp?termid=P0116 no msg added claim or use FOODON:03510117 http://www.langual.org/langual_thesaurus.asp?termid=P0117 caffeine free claim or use FOODON:03510118 http://www.langual.org/langual_thesaurus.asp?termid=P0118 naturally caffeine free claim or use FOODON:03510119 http://www.langual.org/langual_thesaurus.asp?termid=P0119 processing-related claim or use FOODON:03510120 A raw food that has not been frozen, heat processed or otherwise preserved. http://www.langual.org/langual_thesaurus.asp?termid=P0120 "fresh" label claim FOODON:03510121 http://www.langual.org/langual_thesaurus.asp?termid=P0121 not pasteurized claim or use FOODON:03510122 http://www.langual.org/langual_thesaurus.asp?termid=P0122 unpurified or unrefined claim or use FOODON:03510123 http://www.langual.org/langual_thesaurus.asp?termid=P0123 unbleached claim or use FOODON:03510124 Health claim means any claim made on the label or in labeling of a food, including a dietary supplement, that expressly or by implication, including "third party" references, written statements (e.g., a brand name including a term such as "heart"), symbols (e.g., a heart symbol), or vignettes, characterizes the relationship of any substance to a disease or health-related condition. See also 21 CFR 101.14 [http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?fr=101.14]. A claim is a health claim if in the naming of the substance or category of substances, there is a description or indication of a functionality or an implied effect on health; examples: "contains antioxidants" (the function is an antioxidant effect); "containsprobiotics/prebiotics" (the reference to probiotic/prebiotic implies a health benefit). Equally, claims which refer to an indication of a functionality in the description of a nutrient or a substance (for instance as an adjective to the substance) should also beclassified as a health claim; examples: "with prebiotic fibres" or "contains prebiotic fibres". In Europe, a health claim is any statement about a relationship between food and health [http://ec.europa.eu/food/food/labellingnutrition/claims/health_claims_en.htm], and only authorized health claims are legal [see http://ec.europa.eu/food/food/labellingnutrition/claims/community_register/health_claims_en.htm]. COMMISSION REGULATION (EU) No 432/2012 of 16 May 2012 establishes a list of permitted health claims made on foods, other than those referring to the reduction of disease risk and to children"s development and health [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2012:136:0001:0040:en:PDF] http://www.langual.org/langual_thesaurus.asp?termid=P0124 health-related claim or use FOODON:03510125 http://www.langual.org/langual_thesaurus.asp?termid=P0125 tooth decay-related claim or use FOODON:03510126 http://www.langual.org/langual_thesaurus.asp?termid=P0126 religion- or customs-related claim or use FOODON:03510127 http://www.langual.org/langual_thesaurus.asp?termid=P0127 kosher claim or use FOODON:03510128 USA: The 1990 Farm Act specifies that a food labeled 'organic' must meet four requirements: 1) the food must be raised by specified methods to replenish and maintain the fertility of the soil; 2) the food must be certified as having been produced with a nationally approved list of materials and practices; 3) to be eligible for certification at least three years must have elapsed between the first organic harvest and first use of nationally approved materials on land and crops;and 4) organic foods must meet all local, state and federal regulations governing the quality and safety of the food supply. Europe: Foods produced in accordance with Council Regulation (EC) No 834/2007 of 28 June 2007 on organic production and labelling of organic products and repealing Regulation (EEC) No 2092/91. [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2007:189:0001:0023:EN:PDF] http://www.langual.org/langual_thesaurus.asp?termid=P0128 organic food claim or use FOODON:03510129 Considerations include amounts that are 'nutritionally trivial' and amounts that can be declared as zero on the nutrition label. An additional criterion based on amount per weight (e.g., per 100 grams) is not considered necessary because the amount of nutrient in a 'free' food is so low that even frequent and repeated consumption is unlikely to have physiological consequences. (U.S. proposed) http://www.langual.org/langual_thesaurus.asp?termid=P0129 "free" label claim FOODON:03510130 An amount customarily consumed contains 20% or more of the daily nutritional value to describe protein, vitamins, minerals, dietary fiber, or potassium. May be used on meals or main dishes to indicate that product contains a food that meets the definition. http://www.langual.org/langual_thesaurus.asp?termid=P0130 "high" label claim FOODON:03510131 http://www.langual.org/langual_thesaurus.asp?termid=P0131 "less" label claim FOODON:03510132 A claim stating that a product is "light" or "lite", and any claim likely to have the same meaning for the consumer, shall follow the same conditions as those set for the term "reduced", see *REDUCED {NAME OF NUTRIENT} NUTRITION CLAIM [P0132]*; the claim shall also be accompanied by an indication of the characteristic(s) which make(s) the food "light" or "lite" [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Used for foods that have 33.3% fewer calories than a comparable product and a minimum reduction of more than 40 calories per serving. Any other use of 'light' must specify whether it refers to the look, taste or smell; for example, 'light in color'. (U.S. FDA proposed) http://www.langual.org/langual_thesaurus.asp?termid=P0132 "light" label claim FOODON:03510133 http://www.langual.org/langual_thesaurus.asp?termid=P0133 "more" label claim FOODON:03510134 http://www.langual.org/langual_thesaurus.asp?termid=P0134 "source of" label claim FOODON:03510135 http://www.langual.org/langual_thesaurus.asp?termid=P0135 kosher for passover claim or use FOODON:03510136 A food consumer group is a class of organism based on their heterotrophic requirements or preferences. http://www.langual.org/langual_thesaurus.asp?termid=P0136 food consumer group FOODON:03510149 http://www.langual.org/langual_thesaurus.asp?termid=P0149 no or reduced cholesterol claim or use FOODON:03510150 http://www.langual.org/langual_thesaurus.asp?termid=P0150 (percent) fat free claim or use FOODON:03510152 Food having less than 5 miligrams sodium per amount customarily consumed (or for meals and main dishes, less than 5 milligrams sodium per labeled serving). Such food must contain no ingredient that is sodium chloride or generally understood to contain sodium except where the ingredient listed is footnoted '*adds a trivial amount of sodium'. http://www.langual.org/langual_thesaurus.asp?termid=P0152 sodium free claim or use FOODON:03510153 Food having 35 milligrams or less sodium per amount customarily consumed (and per 50 grams of food if the amount customarily consumed is small). Meals and main dishes contain 35 milligrams or less sodium per 100 grams food. http://www.langual.org/langual_thesaurus.asp?termid=P0153 very low sodium claim or use FOODON:03510154 Food containing at least 25% less sodium per amount customarily consumed than the sodium content of a comparable food product. The comparable food may not be 'low sodium'. http://www.langual.org/langual_thesaurus.asp?termid=P0154 reduced sodium claim or use FOODON:03510156 Foods having 140 milligrams or less sodium per amount customarily consumed (and per 50 grams of food if the amount customarily consumed is small). Meals and main dishes have 140 milligrams sodium per 100 grams of food. http://www.langual.org/langual_thesaurus.asp?termid=P0156 low sodium claim or use FOODON:03510157 http://www.langual.org/langual_thesaurus.asp?termid=P0157 game as consumer FOODON:03510158 http://www.langual.org/langual_thesaurus.asp?termid=P0158 rabbit as consumer FOODON:03510159 http://www.langual.org/langual_thesaurus.asp?termid=P0159 other special claim or use FOODON:03510161 http://www.langual.org/langual_thesaurus.asp?termid=P0161 label claim in food name FOODON:03510162 http://www.langual.org/langual_thesaurus.asp?termid=P0162 label claim separate from food name FOODON:03510167 http://www.langual.org/langual_thesaurus.asp?termid=P0167 no water added claim or use FOODON:03510168 http://www.langual.org/langual_thesaurus.asp?termid=P0168 pareve claim or use FOODON:03510169 http://www.langual.org/langual_thesaurus.asp?termid=P0169 noncarbonated claim or use FOODON:03510170 http://www.langual.org/langual_thesaurus.asp?termid=P0170 lactose reduced food FOODON:03510171 http://www.langual.org/langual_thesaurus.asp?termid=P0171 lactose free food FOODON:03510172 http://www.langual.org/langual_thesaurus.asp?termid=P0172 unenriched claim or use FOODON:03510173 http://www.langual.org/langual_thesaurus.asp?termid=P0173 no vitamin or mineral added claim or use FOODON:03510174 http://www.langual.org/langual_thesaurus.asp?termid=P0174 gluten free claim or use FOODON:03510175 http://www.langual.org/langual_thesaurus.asp?termid=P0175 egg free claim or use FOODON:03510176 http://www.langual.org/langual_thesaurus.asp?termid=P0176 alcohol free claim or use FOODON:03510177 http://www.langual.org/langual_thesaurus.asp?termid=P0177 kosher milchlig claim or use FOODON:03510178 The food was quickly frozen while still fresh. http://www.langual.org/langual_thesaurus.asp?termid=P0178 "fresh frozen" label claim FOODON:03510179 A claim that a food does not contain saturated fat, and any claim likely to have the same meaning for the consumer, may only be made where the sum of saturated fat and trans-fatty acids does not exceed 0,1 g of saturated fat per 100 g or 100 ml [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having less than 0.5 grams saturated fat per amount customarily consumed (or for meals and main dishes, less than 0.5 grams saturated fat per labeled serving). Trans fatty acids are not more than 1% of total fat. Such foods contain no ingredient that is understood to contain saturated fat except where the ingredient listed has been footnoted '*adds a trivial amount of saturated fat' [US FDA]. http://www.langual.org/langual_thesaurus.asp?termid=P0179 saturated fat free food FOODON:03510180 Food containing at least 25% less saturated fat per amount customarily consumed than the saturated fat content of a comparable food product. The comparable food product may not be 'low saturated fat'. http://www.langual.org/langual_thesaurus.asp?termid=P0180 reduced saturated fat food FOODON:03510181 Food having at least 25% less sugars per amount customarily consumed than the sugars content of a comparable food product. http://www.langual.org/langual_thesaurus.asp?termid=P0181 reduced sugars food FOODON:03510182 Wild or semiwild foods consumed only during periods of famine when no other food is available. http://www.langual.org/langual_thesaurus.asp?termid=P0182 aliment de disette FOODON:03510183 A food is 'enriched' when nutrients are added to it to replace those that are lost in processing. http://www.langual.org/langual_thesaurus.asp?termid=P0183 enriched claim or use FOODON:03510184 A food is 'fortified' when nutrients that were never present are added to it. http://www.langual.org/langual_thesaurus.asp?termid=P0184 fortified claim or use FOODON:03510185 http://www.langual.org/langual_thesaurus.asp?termid=P0185 iodized claim or use FOODON:03510186 http://www.langual.org/langual_thesaurus.asp?termid=P0186 unfortified claim or use FOODON:03510187 Characterized by adherence to the dietary practices required by Islamic law (Webster's). http://www.langual.org/langual_thesaurus.asp?termid=P0187 halal claim or use FOODON:03510188 http://www.langual.org/langual_thesaurus.asp?termid=P0188 adult human as food consumer FOODON:03510189 http://www.langual.org/langual_thesaurus.asp?termid=P0189 infant as food consumer, 0 - 3 months FOODON:03510190 http://www.langual.org/langual_thesaurus.asp?termid=P0190 infant as food consumer, 3 - 6 months FOODON:03510191 http://www.langual.org/langual_thesaurus.asp?termid=P0191 infant as food consumer, 6 - 12 months FOODON:03510192 http://www.langual.org/langual_thesaurus.asp?termid=P0192 toddler as food consumer, 12 months and onwards FOODON:03510193 http://www.langual.org/langual_thesaurus.asp?termid=P0193 low alcohol claim or use FOODON:03510194 http://www.langual.org/langual_thesaurus.asp?termid=P0194 probiotic claim or use FOODON:03510195 http://www.langual.org/langual_thesaurus.asp?termid=P0195 full fat claim or use FOODON:03510196 http://www.langual.org/langual_thesaurus.asp?termid=P0196 trans fat claim or use FOODON:03510197 Food Quality/Food Assurance Claim indicates, with reference to the product branding, labelling or packaging, whether the product is stamped with a quality mark, as approved by the governing authority, such as USDA for USA products [Source: GS1]. http://www.langual.org/langual_thesaurus.asp?termid=P0197 food quality claim FOODON:03510198 It should be noted that such claims are illegal in some countries, e.g. Denmark, and that other countries, e.g. United Kingdom, are calling for an end to the use of terms such as 'diabetic' or 'suitable for diabetics' on food labels. The European Commission is considering how foods intended specifically for people with diabetes can be controlled. http://www.langual.org/langual_thesaurus.asp?termid=P0198 diabetic or suitable for diabetics claim or use FOODON:03510199 http://www.langual.org/langual_thesaurus.asp?termid=P0199 vegan/vegetarian or suitability for vegan/vegetarian claim or use FOODON:03510200 http://www.langual.org/langual_thesaurus.asp?termid=P0200 no pork added claim FOODON:03510201 http://www.langual.org/langual_thesaurus.asp?termid=P0201 no beef added claim FOODON:03510202 Food that is promoted as being either high or low in protein. http://www.langual.org/langual_thesaurus.asp?termid=P0202 protein special claim or use FOODON:03510203 A claim that a food is high in protein, and any claim likely to have the same meaning for the consumer, may only be made where at least 20 % of the energy value of the food is provided by protein [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. http://www.langual.org/langual_thesaurus.asp?termid=P0203 high protein food FOODON:03510204 http://www.langual.org/langual_thesaurus.asp?termid=P0204 natural source of vitamins and or minerals FOODON:03510205 A claim that a food is a source of fibre, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least 3 g of fibre per 100 g or at least 1,5 g of fibre per 100 kcal [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. http://www.langual.org/langual_thesaurus.asp?termid=P0205 source of fibre FOODON:03510206 A claim that a food is a source of protein, and any claim likely to have the same meaning for the consumer, may only be made where at least 12 % of the energy value of the food is provided by protein. [REGULATION (EC) No 1924/2006 Corrigendum]. http://www.langual.org/langual_thesaurus.asp?termid=P0206 source of protein FOODON:03510207 A claim that a food contains a nutrient or another substance, for which specific conditions are not laid down in this Regulation, or any claim likely to have the same meaning for the consumer, may only be made where the product complies with all the applicable provisions of this Regulation, and in particular Article 5. For vitamins and minerals the conditions of the claim "source of" shall apply. [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. http://www.langual.org/langual_thesaurus.asp?termid=P0207 contains {name of the nutrient or other substance} nutrition claim FOODON:03510208 A claim stating that the content in one or more nutrients, other than vitamins and minerals, has been increased, and any claim likely to have the same meaning for the consumer, may only be made where the product meets the conditions for the claim "source of" and the increase in content is at least 30 % compared to a similar product. [Forordning (EF) nr. 1924/2006 Berigtigelse 2007-01-18]. http://www.langual.org/langual_thesaurus.asp?termid=P0208 increased {name of nutrient} nutrition claim FOODON:03510209 Where a food naturally meets the condition(s) laid down in this Annex for the use of a nutritional claim, the term "naturally/natural" may be used as a prefix to the claim [REGULATION (EC) No 1924/2006 Corrigendum2007-01-18]. http://www.langual.org/langual_thesaurus.asp?termid=P0209 "naturally/natural" label claim FOODON:03510210 A claim that a food is a source of vitamins and/or minerals, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least a significant amount as defined in the Annex to Directive 90/496/EEC or an amount provided for by derogations granted according to Article 6 of Regulation (EC) No 1925/2006 of the European Parliament and of the Council of 20 December 2006 on the addition of vitamins and minerals and of certain other substances to foods [REGULATION (EC) No 1924/2006 Corrigendum2007-01-18]. http://www.langual.org/langual_thesaurus.asp?termid=P0210 source of {name of vitamin/s} and/or {name of mineral/s} nutrition claim FOODON:03510211 A claim that a food is high in vitamins and/or minerals, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least twice the value of "source of [NAME OF VITAMIN/S] and/or [NAME OF MINERAL/S]" [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. http://www.langual.org/langual_thesaurus.asp?termid=P0211 high {name of vitamin/s} and/or {name of mineral/s} nutrition claim FOODON:03510212 A claim stating that the content in one or more nutrients has been reduced, and any claim likely to have the same meaning for the consumer, may only be made where the reduction in content is at least 30 % compared to a similar product, except for micronutrients, where a 10 % difference in the reference values as set in Directive 90/496/EEC shall be acceptable, and for sodium, or the equivalent value for salt, where a 25 % difference shall be acceptable. [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. http://www.langual.org/langual_thesaurus.asp?termid=P0212 reduced {name of nutrient} nutrition claim FOODON:03510213 http://www.langual.org/langual_thesaurus.asp?termid=P0213 food allergen labelling FOODON:03510214 Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. http://www.langual.org/langual_thesaurus.asp?termid=P0214 food allergen labelling about cereals containing gluten and products thereof FOODON:03510215 Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. http://www.langual.org/langual_thesaurus.asp?termid=P0215 food allergen labelling about crustaceans and products thereof FOODON:03510216 Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. http://www.langual.org/langual_thesaurus.asp?termid=P0216 food allergen labelling about eggs and products thereof FOODON:03510217 Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. http://www.langual.org/langual_thesaurus.asp?termid=P0217 food allergen labelling about fish and products thereof FOODON:03510218 Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. http://www.langual.org/langual_thesaurus.asp?termid=P0218 food allergen labelling about peanuts and products thereof FOODON:03510219 Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. http://www.langual.org/langual_thesaurus.asp?termid=P0219 food allergen labelling about soybeans and products thereof FOODON:03510220 Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. http://www.langual.org/langual_thesaurus.asp?termid=P0220 food allergen labelling about milk and products thereof, including lactose FOODON:03510221 Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. http://www.langual.org/langual_thesaurus.asp?termid=P0221 food allergen labelling about nuts and products thereof FOODON:03510222 Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. http://www.langual.org/langual_thesaurus.asp?termid=P0222 food allergen labelling about celery and products thereof FOODON:03510223 Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. http://www.langual.org/langual_thesaurus.asp?termid=P0223 food allergen labelling about mustard and products thereof FOODON:03510224 Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. http://www.langual.org/langual_thesaurus.asp?termid=P0224 food allergen labelling about sesame seeds and products thereof FOODON:03510225 Sulphur dioxide and sulphites are included in the EU list of allergens because they can cause adverse reactions in some people. Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. http://www.langual.org/langual_thesaurus.asp?termid=P0225 food allergen labelling about sulphur dioxide and sulphites FOODON:03510226 Contained in GS1 Allergen Code List. http://www.langual.org/langual_thesaurus.asp?termid=P0226 food allergen labelling about cocoa and products thereof FOODON:03510227 Contained in GS1 Code List. http://www.langual.org/langual_thesaurus.asp?termid=P0227 food allergen labelling about coriander and products thereof FOODON:03510228 Contained in GS1 Code List. http://www.langual.org/langual_thesaurus.asp?termid=P0228 food allergen labelling about lupine and products thereof FOODON:03510229 Contained in GS1 Code List. http://www.langual.org/langual_thesaurus.asp?termid=P0229 food allergen labelling about corn and products thereof FOODON:03510230 Contained in GS1 Code List. http://www.langual.org/langual_thesaurus.asp?termid=P0230 food allergen labelling about pod fruits and products thereof FOODON:03510231 Contained in GS1 Code List. http://www.langual.org/langual_thesaurus.asp?termid=P0231 food allergen labelling about carrot and products thereof FOODON:03510232 Contained in GS1 Code List. http://www.langual.org/langual_thesaurus.asp?termid=P0232 food allergen labelling about molluscs and products thereof FOODON:03510233 http://www.langual.org/langual_thesaurus.asp?termid=P0233 "no trans fat" claim or use FOODON:03510234 'Traditional" means proven usage on the Community market for a time period showing transmission between generations; this time period should be the one generally ascribed to one human generation, at least 25 years [COUNCIL REGULATION (EC) No 509/2006 of 20 March 2006 on agricultural products and foodstuffs as traditional specialities guaranteed]. A traditional food product is a product frequently consumed or associated to specific celebrations and/or seasons, normally transmitted from one generation to another, made with care in a specific way according to the gastronomic heritage, with little or no processing/manipulation, that is distinguished and known because of its sensory properties and associated to a certain local area, region or country. [http://www.truefood.eu/] Traditional means conforming to established practice or specifications prior to the Second World War. Traditional food is a food of a specific feature or features, which distinguish it clearly from other similar products of the same category in terms of the use of traditional ingredients (raw materials or primary products), traditional composition or traditional type of production and/or processing method. [Traditional Foods in Europe, EuroFIR Synthesis report No 6, 2009] http://www.langual.org/langual_thesaurus.asp?termid=P0234 traditional food claim or use FOODON:03510235 Ethnic food is food from countries other than the home market contributing to a different food culture than the traditional cuisine of the host country. [Ethnic Groups and Foods in Europe, EuroFIR Synthesis report No 3, 2005] "Ethnic food" has been used colloquially for a wide variety of foodstuffs, virtually any that can be identified in the public mind with a foreign source or an ethnic minority group. In the narrower ethnographic meaning, it pertains only to food prepared or consumed by members of an ethnic group as a manifestation of its ethnicity. In the end ethnic food is food that members of an ethnic group consider their own and that others attribute to them. [http://www.answers.com/topic/ethnic-cuisines] http://www.langual.org/langual_thesaurus.asp?termid=P0235 ethnic food claim or use FOODON:03510236 Raw material (species and/or varieties) or primary product either alone or as an ingredient that has been used in identifiable geographical areas and remains in use today (taking into account cases where use was abandoned for a time and then reinstated) and its characteristics are in accordance with current specifications of national and EU legislation. [Traditional Foods in Europe, EuroFIR Synthesis report No 6, 2009] http://www.langual.org/langual_thesaurus.asp?termid=P0236 traditional ingredient claim or use FOODON:03510237 The uniquely identifiable composition (in terms of ingredients) that was first established prior to the Second World War and passed down through generations by oral or other means (taking into account cases where composition was abandoned for a time and then reinstated) and when necessary is differentiated from the composition defined by the generally recognized characteristics of the wider food group to which the product belongs. [Traditional Foods in Europe, EuroFIR Synthesis report No 6, 2009] http://www.langual.org/langual_thesaurus.asp?termid=P0237 traditional composition claim or use FOODON:03510238 The production and/or processing of a food that has been transmitted from generation to generation through oral tradition or other means and has been applied prior to the Second World War and remains in use (taking into account cases where composition was abandoned for a time and then reinstated) despite its adjustment to binding rules from national or EU food hygiene regulations or the incorporation of technological progress, under the condition that production and/or processing remains in line with methods used originally and that the food"s intrinsic features such as its physical, chemical, microbiological or organoleptic features are maintained. [Traditional Foods in Europe, EuroFIR Synthesis report No 6, 2009] http://www.langual.org/langual_thesaurus.asp?termid=P0238 traditional type of production and/or processing claim or use FOODON:03510239 Authentic ethnic food is food from countries other than the home market contributing to a different food culture than the traditional cuisine of the host country. Food may be adapted by combining local and imported ingredients. [Ethnic Groups and Foods in Europe, EuroFIR Synthesis report No 3, 2005] http://www.langual.org/langual_thesaurus.asp?termid=P0239 authentic ethnic food claim or use FOODON:03510240 Modified ethnic food: a commercially-available version of a food that has been modified to suit the taste and preference of the host country. [Ethnic Groups and Foods in Europe, EuroFIR Synthesis report No 3, 2005] http://www.langual.org/langual_thesaurus.asp?termid=P0240 modified ethnic food claim or use FOODON:03510241 COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims. http://www.langual.org/langual_thesaurus.asp?termid=P0241 monounsaturated fat claim or use FOODON:03510242 COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims http://www.langual.org/langual_thesaurus.asp?termid=P0242 polyunsaturated fat claim or use FOODON:03510243 A claim that a food is high in monounsaturated fat, and any claim likely to have the same meaning for the consumer, may only be made where at least 45 % of the fatty acids present in the product derive from monounsaturated fat under the condition that monounsaturated fat provides more than 20 % of energy of the product [COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims]. http://www.langual.org/langual_thesaurus.asp?termid=P0243 high monounsaturated fat FOODON:03510244 http://www.langual.org/langual_thesaurus.asp?termid=P0244 omega-3 fatty acids claim or use FOODON:03510245 A claim that a food is high in omega-3 fatty acids, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least 0,6 g alpha-linolenic acid per 100 g and per 100 kcal, or at least 80 mg of the sum of eicosapentaenoic acid and docosahexaenoic acid per 100 g and per 100 kcal [COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims]. http://www.langual.org/langual_thesaurus.asp?termid=P0245 high omega-3 fatty acids FOODON:03510246 A claim that a food is high in polyunsaturated fat, and any claim likely to have the same meaning for the consumer, may only be made where at least 45 % of the fatty acids present in the product derive from polyunsaturated fat under the condition that polyunsaturated fat provides more than 20 % of energy of the product [COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims]. http://www.langual.org/langual_thesaurus.asp?termid=P0246 high polyunsaturated fat FOODON:03510247 http://www.langual.org/langual_thesaurus.asp?termid=P0247 unsaturated fat claim or use FOODON:03510248 A claim that a food is high in unsaturated fat, and any claim likely to have the same meaning for the consumer may only be made where at least 70 % of the fatty acids present in the product derive from unsaturated fat under the condition that unsaturated fat provides more than 20 % of energy of the product [COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims].. http://www.langual.org/langual_thesaurus.asp?termid=P0248 high unsaturated fat FOODON:03510249 A claim that a food is a source of omega-3 fatty acids, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least 0,3 g alpha-linolenic acid per 100 g and per 100 kcal, or at least 40 mg of the sum of eicosapentaenoic acid and docosahexaenoic acid per 100 g and per 100 kcal [COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims]. http://www.langual.org/langual_thesaurus.asp?termid=P0249 source of omega-3 fatty acids FOODON:03510250 US FDA Approved user group. http://www.langual.org/langual_thesaurus.asp?termid=P0250 human as food consumer, four years and above FOODON:03510251 http://www.langual.org/langual_thesaurus.asp?termid=P0251 man as food consumer FOODON:03510252 http://www.langual.org/langual_thesaurus.asp?termid=P0252 woman as food consumer FOODON:03510253 http://www.langual.org/langual_thesaurus.asp?termid=P0253 pregnant or lactating woman as food consumer FOODON:03510254 http://www.langual.org/langual_thesaurus.asp?termid=P0254 senior as food consumer FOODON:03510255 http://www.langual.org/langual_thesaurus.asp?termid=P0255 teenager as food consumer FOODON:03510256 http://www.langual.org/langual_thesaurus.asp?termid=P0256 child as food consumer, less than four years FOODON:03510257 US FDA approved language lacking for the moment. http://www.langual.org/langual_thesaurus.asp?termid=P0257 calcium and osteoporosis related claim or use FOODON:03510259 http://www.langual.org/langual_thesaurus.asp?termid=P0259 athlete as food consumer FOODON:03510260 http://www.langual.org/langual_thesaurus.asp?termid=P0260 bodybuilder as food consumer FOODON:03510261 http://www.langual.org/langual_thesaurus.asp?termid=P0261 menopaused woman as food consumer FOODON:03510262 http://www.langual.org/langual_thesaurus.asp?termid=P0262 weight-reducer as food consumer FOODON:03510263 http://www.langual.org/langual_thesaurus.asp?termid=P0263 infant as food consumer, 0 - 6 months FOODON:03510264 In the United States, these claims, usually referred to as "qualified health claims", are regulated by the Food and Drug Administration in the public interest, see 21 Code of Federal Regulations § 101.14 [http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?fr=101.14] http://www.langual.org/langual_thesaurus.asp?termid=P0264 qualified health claim FOODON:03510265 Structure/function claims describe the role of a nutrient or dietary ingredient intended to affect normal structure or function in humans, for example, "calcium builds strong bones". In addition, they may characterize the means by which a nutrient or dietary ingredient acts to maintain such structure or function, for example, "fiber maintains bowel regularity," or "antioxidants maintain cell integrity," or they may describe general well-being from consumption of a nutrient or dietary ingredient. [http://www.fda.gov/Food/LabelingNutrition/LabelClaims/StructureFunctionClaims/default.htm] http://www.langual.org/langual_thesaurus.asp?termid=P0265 structure/function claim FOODON:03510266 The term infant is typically applied to young children between the ages of 1 month and 12 months. [http://en.wikipedia.org/wiki/Infant] http://www.langual.org/langual_thesaurus.asp?termid=P0266 infant as food consumer FOODON:03510267 http://www.langual.org/langual_thesaurus.asp?termid=P0267 native american food claim or use FOODON:03510268 http://www.langual.org/langual_thesaurus.asp?termid=P0268 alaskan native food claim or use FOODON:03510269 http://www.langual.org/langual_thesaurus.asp?termid=P0269 apache food claim or use FOODON:03510270 http://www.langual.org/langual_thesaurus.asp?termid=P0270 navajo food claim or use FOODON:03510271 http://www.langual.org/langual_thesaurus.asp?termid=P0271 shoshone bannock food claim or use FOODON:03510272 http://www.langual.org/langual_thesaurus.asp?termid=P0272 pacific food claim or use FOODON:03510273 http://www.langual.org/langual_thesaurus.asp?termid=P0273 northern plains food claim or use FOODON:03510274 http://www.langual.org/langual_thesaurus.asp?termid=P0274 southwest plains food claim or use FOODON:03510275 http://www.langual.org/langual_thesaurus.asp?termid=P0275 hopi food claim or use FOODON:03510277 http://www.langual.org/langual_thesaurus.asp?termid=P0277 phytosterol claim or use FOODON:03530005 Additional groups of descriptors of a miscellaneous nature. [FDA CFSAN 1995] http://www.langual.org/langual_thesaurus.asp?termid=Z0005 adjunct characteristics of food FOODON:03530008 http://www.langual.org/langual_thesaurus.asp?termid=Z0008 cut of meat, u.s. FOODON:03530020 http://www.langual.org/langual_thesaurus.asp?termid=Z0020 brisket FOODON:03530021 http://www.langual.org/langual_thesaurus.asp?termid=Z0021 chuck FOODON:03530022 http://www.langual.org/langual_thesaurus.asp?termid=Z0022 flank FOODON:03530023 http://www.langual.org/langual_thesaurus.asp?termid=Z0023 rib (meat cut) FOODON:03530024 http://www.langual.org/langual_thesaurus.asp?termid=Z0024 round or leg (meat cut) FOODON:03530025 http://www.langual.org/langual_thesaurus.asp?termid=Z0025 fore shank FOODON:03530026 http://www.langual.org/langual_thesaurus.asp?termid=Z0026 short loin FOODON:03530027 http://www.langual.org/langual_thesaurus.asp?termid=Z0027 sirloin FOODON:03530028 http://www.langual.org/langual_thesaurus.asp?termid=Z0028 short plate FOODON:03530031 http://www.langual.org/langual_thesaurus.asp?termid=Z0031 loin FOODON:03530037 http://www.langual.org/langual_thesaurus.asp?termid=Z0037 fat back FOODON:03530040 http://www.langual.org/langual_thesaurus.asp?termid=Z0040 jowl, trimmed FOODON:03530041 http://www.langual.org/langual_thesaurus.asp?termid=Z0041 foot (meat cut) FOODON:03530043 http://www.langual.org/langual_thesaurus.asp?termid=Z0043 shoulder (meat cut) FOODON:03530045 http://www.langual.org/langual_thesaurus.asp?termid=Z0045 breast (meat cut) FOODON:03530046 http://www.langual.org/langual_thesaurus.asp?termid=Z0046 side (meat cut) FOODON:03530047 http://www.langual.org/langual_thesaurus.asp?termid=Z0047 cut of meat, composite FOODON:03530050 A stage of development of a plant or plant part. Maturity influences safety, nutrient composition and consumption characteristics. http://www.langual.org/langual_thesaurus.asp?termid=Z0050 degree of plant maturity FOODON:03530051 A stage of plant development at which a plant or plant part has not achieved full maturity. This condition does not necessarily preclude utilization, for example, green tomatoes are consumed despite their relative unripeness to red tomatoes. http://www.langual.org/langual_thesaurus.asp?termid=Z0051 unripe or immature FOODON:03530052 A stage of plant development at which a plant or plant part has achieved full maturity and is ready for utilization. http://www.langual.org/langual_thesaurus.asp?termid=Z0052 ripe or mature FOODON:03530063 Boneless skeletal meat from the lower sides of meat animals; usually belly meat is smoked and cured to produce bacon. http://www.langual.org/langual_thesaurus.asp?termid=Z0063 belly meat FOODON:03530108 http://www.langual.org/langual_thesaurus.asp?termid=Z0108 preparation establishment FOODON:03530109 http://www.langual.org/langual_thesaurus.asp?termid=Z0109 home prepared FOODON:03530110 http://www.langual.org/langual_thesaurus.asp?termid=Z0110 restaurant prepared FOODON:03530111 http://www.langual.org/langual_thesaurus.asp?termid=Z0111 fast food restaurant prepared FOODON:03530112 http://www.langual.org/langual_thesaurus.asp?termid=Z0112 food industry prepared FOODON:03530113 http://www.langual.org/langual_thesaurus.asp?termid=Z0113 commissary prepared FOODON:03530119 Foods prepared in the kitchens of restaurants or fast food restaurants and served to patrons. http://www.langual.org/langual_thesaurus.asp?termid=Z0119 restaurant or fast food prepared FOODON:03530120 Foods prepared at on- or off-site locations, commissaries (e.g., wrapped fresh sandwiches) or food industry establishments (e.g., bagged potato chips), but which are sold from vending establishments. Examples include hot dog stands, trucksandwich vendors, etc. http://www.langual.org/langual_thesaurus.asp?termid=Z0120 street vendor prepared and/or sold FOODON:03530121 http://www.langual.org/langual_thesaurus.asp?termid=Z0121 cut of meat, french FOODON:03530122 http://www.langual.org/langual_thesaurus.asp?termid=Z0122 quartier avant FOODON:03530123 http://www.langual.org/langual_thesaurus.asp?termid=Z0123 caparacon FOODON:03530124 http://www.langual.org/langual_thesaurus.asp?termid=Z0124 bavette FOODON:03530125 http://www.langual.org/langual_thesaurus.asp?termid=Z0125 flanchet FOODON:03530126 http://www.langual.org/langual_thesaurus.asp?termid=Z0126 hampe FOODON:03530127 http://www.langual.org/langual_thesaurus.asp?termid=Z0127 plat-de-cote FOODON:03530128 http://www.langual.org/langual_thesaurus.asp?termid=Z0128 poitrine FOODON:03530129 http://www.langual.org/langual_thesaurus.asp?termid=Z0129 collier FOODON:03530130 http://www.langual.org/langual_thesaurus.asp?termid=Z0130 basses-cotes FOODON:03530131 http://www.langual.org/langual_thesaurus.asp?termid=Z0131 raquette FOODON:03530132 http://www.langual.org/langual_thesaurus.asp?termid=Z0132 gite avant FOODON:03530133 http://www.langual.org/langual_thesaurus.asp?termid=Z0133 jumeau FOODON:03530134 http://www.langual.org/langual_thesaurus.asp?termid=Z0134 marcreuse FOODON:03530135 http://www.langual.org/langual_thesaurus.asp?termid=Z0135 quartier arriere FOODON:03530136 http://www.langual.org/langual_thesaurus.asp?termid=Z0136 cuisse FOODON:03530137 http://www.langual.org/langual_thesaurus.asp?termid=Z0137 gite arriere FOODON:03530138 http://www.langual.org/langual_thesaurus.asp?termid=Z0138 semelle FOODON:03530139 http://www.langual.org/langual_thesaurus.asp?termid=Z0139 tranche (meat cut) FOODON:03530140 http://www.langual.org/langual_thesaurus.asp?termid=Z0140 tranche grasse FOODON:03530141 http://www.langual.org/langual_thesaurus.asp?termid=Z0141 aloyau FOODON:03530142 http://www.langual.org/langual_thesaurus.asp?termid=Z0142 entre-cote FOODON:03530143 http://www.langual.org/langual_thesaurus.asp?termid=Z0143 faux-filet FOODON:03530144 http://www.langual.org/langual_thesaurus.asp?termid=Z0144 filet FOODON:03530145 http://www.langual.org/langual_thesaurus.asp?termid=Z0145 rumsteck FOODON:03530146 http://www.langual.org/langual_thesaurus.asp?termid=Z0146 cut of meat FOODON:03530152 http://www.langual.org/langual_thesaurus.asp?termid=Z0152 agricultural production environment FOODON:03530153 http://www.langual.org/langual_thesaurus.asp?termid=Z0153 gathered wild wild or gathered FOODON:03530154 http://www.langual.org/langual_thesaurus.asp?termid=Z0154 domestic or cultivated FOODON:03530155 http://www.langual.org/langual_thesaurus.asp?termid=Z0155 tail FOODON:03530156 http://www.langual.org/langual_thesaurus.asp?termid=Z0156 cut of poultry meat FOODON:03530157 http://www.langual.org/langual_thesaurus.asp?termid=Z0157 wing (poultry meat cut) FOODON:03530158 http://www.langual.org/langual_thesaurus.asp?termid=Z0158 breast (poultry meat cut) FOODON:03530159 http://www.langual.org/langual_thesaurus.asp?termid=Z0159 leg (poultry meat cut) FOODON:03530160 http://www.langual.org/langual_thesaurus.asp?termid=Z0160 thigh (poultry meat cut) FOODON:03530204 http://www.langual.org/langual_thesaurus.asp?termid=Z0204 semidomestic or semiwild FOODON:03530206 http://www.langual.org/langual_thesaurus.asp?termid=Z0206 production environment FOODON:03530207 http://www.langual.org/langual_thesaurus.asp?termid=Z0207 growing condition FOODON:03530208 http://www.langual.org/langual_thesaurus.asp?termid=Z0208 outdoor/open-air growing condition FOODON:03530209 Conventional outdoor/open-air production includes ICMS (Integrated Crop Management Systems) http://www.langual.org/langual_thesaurus.asp?termid=Z0209 conventional outdoor/open-air production growing condition FOODON:03530210 Organic: grown with only animal or vegetable fertilisers, as manure, bone meal, compost, etc. (Source: Webster's). Foods produced in accordance with Council Regulation (EC) No 834/2007 of 28 June 2007 on organic production and labelling of organic products and repealing Regulation (EEC) No 2092/91. [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2007:189:0001:0023:EN:PDF] http://www.langual.org/langual_thesaurus.asp?termid=Z0210 organic outdoor/open-air production growing condition FOODON:03530211 http://www.langual.org/langual_thesaurus.asp?termid=Z0211 under glass/protected growing condition FOODON:03530212 http://www.langual.org/langual_thesaurus.asp?termid=Z0212 conventional under glass/protected production growing condition FOODON:03530213 Organic: grown with only animal or vegetable fertilisers, as manure, bone meal, compost, etc. (Source: Webster's). Foods produced in accordance with Council Regulation (EC) No 834/2007 of 28 June 2007 on organic production and labelling of organic products and repealing Regulation (EEC) No 2092/91.[http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2007:189:0001:0023:EN:PDF] http://www.langual.org/langual_thesaurus.asp?termid=Z0213 organic under glass/protected production growing condition FOODON:03530214 The science of growing or the production of plants in nutrient-rich solutions or moist inert material, instead of in soil (Source: Webster's) http://www.langual.org/langual_thesaurus.asp?termid=Z0214 hydroponic growing condition FOODON:03530217 http://www.langual.org/langual_thesaurus.asp?termid=Z0217 tenderloin FOODON:03530253 Organic: grown with only animal or vegetable fertilisers, as manure, bone meal, compost, etc. (Source: Webster's). Foods produced in accordance with Council Regulation (EC) No 834/2007 of 28 June 2007 on organic production and labelling of organic products and repealing Regulation (EEC) No 2092/91. [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2007:189:0001:0023:EN:PDF] http://www.langual.org/langual_thesaurus.asp?termid=Z0253 organic growing condition FOODON:03530268 http://www.langual.org/langual_thesaurus.asp?termid=Z0268 food plant physical quality FOODON:03530291 In Europe, "organic production" means the use of the production method compliant with the rules established in Council Regulation (EC) No 834/2007 of 28 June 2007 on organic production and labelling of organic products and repealing Regulation (EEC) No 2092/91, at all stages of production, preparation and distribution.[http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2007:189:0001:0023:EN:PDF] For more on organic farming, see the European Commissions site on Organic Farming [http://ec.europa.eu/agriculture/organic/splash_en]. http://www.langual.org/langual_thesaurus.asp?termid=Z0291 organic production FOODON:03530292 The term, free range is a farming method whereby animals are given the ability to roam freely instead of being restricted to a confined area. This term can be applied to egg, dairy, poultry, and meat production.[http://www.ecolife.com/define/free-range.html] http://www.langual.org/langual_thesaurus.asp?termid=Z0292 free-range FOODON:03530293 A meat shank or shin is the portion of meat around the tibia of the animal, the leg bone beneath the knee. [http://en.wikipedia.org/wiki/Shank_(meat)] http://www.langual.org/langual_thesaurus.asp?termid=Z0293 shank (meat) FOODON:03530294 http://www.langual.org/langual_thesaurus.asp?termid=Z0294 neck (poultry meat cut) FOODON:03530295 http://www.langual.org/langual_thesaurus.asp?termid=Z0295 foot (poultry meat cut) GENEPIO:0000002 GSCID-BRC standard The GSCID-BRC Project and Sample Application Standard captures standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases. The NIAID page for specifications has a broken link for Core Project. This is the existing page: https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project Link page is: https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards Damion Dooley This standard was developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs), and NIAID and informed by discussions and input with numerous collaborating scientists. GSCID-BRC Project and Sample Application Standard GENEPIO:0000003 MIxS standard MixS is a unified standard for describing sequence data provided by the Genomic Standards Consortium (GSC) Damion Dooley Minimum Information about any (x) Sequence (MIxS) GENEPIO:0000008 MIMARKS standard The "minimum information about a marker gene sequence" (MIMARKS) is a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences. http://www.nature.com/nbt/journal/v29/n5/full/nbt.1823.html Minimum information about a marker gene sequence GENEPIO:0000009 "other (metadata choice)" indicates that for the given categorical variable, a respondent has chosen an other or additional response not listed. This class cannot be referred to directly as a subclass of more than one class without involving inference from the respective classes. Instances of it may exist as a kind of metadata. Usually a reference to a parent categorical class, but not a subordinate, carries the same information. Damion Dooley other (metadata value) GENEPIO:0000010 other relevance GENEPIO:0000011 other Other: specify the sample scope that was used. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ other specimen scope GENEPIO:0000012 other material Other: specify the material that was used. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ other material derived from specimen GENEPIO:0000013 "other capture type" is a free text description provided to indicate a target capture specification not covered by the other types. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ other capture type GENEPIO:0000014 Specify the project method Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ other project method GENEPIO:0000015 This is an organizational category for grouping parameters relevant to a biomedical sample. Damion Dooley obsolete: draft GenEpiO BioSample standard true GENEPIO:0000016 An NCBI antibiogram data item is an antimicrobial susceptibility and resistance datum related to drug resistant pathogens. This information is provided within an antibiogram table on BioSample records. Damion Dooley obsolete: NCBI antibiogram data item true GENEPIO:0000017 HIPPA PHI guideline The American HIPPA Protected Health Information (PHI) guidelines cover information, including demographic information, which relates to: - the individual’s past, present, or future physical or mental health or condition, - the provision of health care to the individual, or - the past, present, or future payment for the provision of health care to the individual, and that identifies the individual or for which there is a reasonable basis to believe can be used to identify the individual. Protected health information includes many common identifiers (e.g., name, address, birth date, Social Security Number) when they can be associated with the health information listed above." https://en.wikipedia.org/wiki/Health_Insurance_Portability_and_Accountability_Act American HIPPA Protected Health Information (PHI) guidelines GENEPIO:0000018 The natural (as opposed to laboratory) full scientific taxonomic name of a subject related to a given investigation, study and/or specimen. Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0001567 obsolete: subject species true GENEPIO:0000019 http://purl.obolibrary.org/obo/NCIT_C45908 NCBI BioSample: intersex obsolete: intersex true GENEPIO:0000020 Isolation date inferred from BCCDC interviews date the strain was isolated Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0000021 obsolete: isolation date true GENEPIO:0000021 Collection Culture isolation date suggested in metadata feedback year/month/day A culture isolation date is a date-time entity marking the end of a process in which a sample is isolated as a single colony or non-mixture culture Damion Dooley GROUP: IRIDA Ontology (Morag) GENEPIO culture isolation date GENEPIO:0000022 Collection Frozen date NML Labware LIMS year/month/day A culture frozen date is a date-time entity marking the beginning of a process in which a sample culture is frozen for preservation. Damion Dooley GROUP: IRIDA Ontology (Emma) GENEPIO culture frozen date GENEPIO:0000023 Collection Received date NML Labware LIMS year/month/day date lab received isolate NML LIMS GENEPIO isolate received date GENEPIO:0000024 Collection Upload date NML Labware LIMS month/day/year date the isolate was entered into the database NML LIMS PulseNet: UploadDate GENEPIO isolate upload date GENEPIO:0000025 Pathogen Isolate inferred from BCCDC interviews gut, spine, tongue, lung Name of body site where the specimen was obtained from, such as a specific organ or tissue. Damion Dooley's note: Although term mentions "site" in label, this cannot be placed under "site" as it is intended to refer to organism material, and leads to unsatisfiable terms otherwise. GROUP: MIxS GENEPIO subject anatomical site http://gensc.org/ns/mixs/host_body_site GENEPIO:0000026 depth:1 order: NCIT:C115935 # healthy NCIT:C25610 # pathologic NCIT:C28554 # deceased diseased Health or disease status of a given subject at time of specimen collection. Currently this does not differ from the 'subject health status (GSCID-BRC)' item. It may be revised to have more options in the future. Damion Dooley subject health status at time of specimen collection 1 1 GENEPIO:0000027 Environmental Isolate sediment, chicken feces, cheese Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. Damion Dooley NCBI Biosample specimen source context GENEPIO:0000028 Pathogen Isolate feces, cerebral spinal fluid (CSF) Substance produced by the body, e.g. stool, mucus, where the specimen was obtained from. Damion Dooley subject body product GENEPIO:0000029 Environmental Isolate Geographic location depth GROUP: MIxS value (5m) Please refer to the definitions of depth in the environmental packages GROUP: MIxS GENEPIO collection depth datum GENEPIO:0000030 The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO http://purl.obolibrary.org/obo/ENVO_00010483 obsolete: specimen source environmental material true GENEPIO:0000031 A subject sex is the phenotypic sex of given subject (human or animal) related to a given investigation, study, and/or specimen. Damion Dooley Gender is not used because it is a term referencing human social and cultural convention. subject sex specification GENEPIO:0000032 Environmental Isolate Land use where sample was taken Environment Canada Metadata descriptive; type of human use (park, farm, urban) Human use of land involving the management and modification of natural environment or wilderness into built environment. URI: http://en.wikipedia.org/wiki/Land_use GENEPIO specimen collection site land use GENEPIO:0000033 Environmental Isolate Fecal Indicator Bacteria Number Environment Canada Metadata 12,456 cfu Number of indicator micro-organisms (colony forming units) present in a sample that have been used to suggest the presence of pathogens. URI: http://www.who.int/water_sanitation_health/dwq/iwachap13.pdf GENEPIO fecal indicator bacteria count GENEPIO:0000034 Environmental Isolate Conductivity GROUP: MIxS milliSiemens per centimeter electrical conductivity of water GROUP: MIxS enviro package GENEPIO conductivity measurement datum GENEPIO:0000035 Environmental Isolate Dissolved oxygen GROUP: MIxS micromole per kilogram concentration of dissolved oxygen GROUP: MIxS enviro package GENEPIO dissolved oxygen concentration GENEPIO:0000036 GMI MDM standard The Global Microbial Identifier "Minimum data for Matching" (MDM) standard is a standard that defines essential contextual data fields to be included in genomic sequence repository records. Damion Dooley the Global Microbial Identifier Minimum Data for Matching (MDM) Standard http://www.globalmicrobialidentifier.org/-/media/Sites/gmi/News-and-events/2013/6th-meeting-2013-report.ashx?la=da GENEPIO:0000037 Environmental Isolate Soluble inorganic material GROUP: MIxS soluble organic material name;measurement value concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. GROUP: MIxS enviro package GENEPIO soluble inorganic material GENEPIO:0000038 Environmental Isolate Soluble inorganic material GROUP: MIxS GENEPIO soluble inorganic material concentration GENEPIO:0000039 Environmental Isolate Nitrite GROUP: MIxS micromole per liter concentration of nitrite GROUP: MIxS enviro package GENEPIO nitrite concentration GENEPIO:0000040 Environmental Isolate Nitrate GROUP: MIxS micromole per liter concentration of nitrate GROUP: MIxS enviro package GENEPIO nitrate concentration GENEPIO:0000041 Environmental Isolate Total phosphorous GROUP: MIxS micromole per liter total phosphorus concentration, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus. Can also be measured without filtering, reported as phosphorus GROUP: MIxS enviro package GENEPIO total phosphorous concentration 12 GENEPIO:0000042 Environmental Isolate Stream order Environment Canada Metadata value, 1-12 Stream order is a measure of the relative size of streams (The smallest tributaries are referred to as first-order streams, while the largest river in the world, the Amazon, is a twelfth-order waterway). GROUP: Environment Canada Metadata GENEPIO stream order categorical measurement datum GENEPIO:0000043 Environmental Isolate Density of bacteria in sample Environment Canada Metadata OD reading or cfu's or cells per millilitre number of bacteria in sample GROUP: Environment Canada Metadata GENEPIO bacteria density GENEPIO:0000044 Lab Analytic Host Primary Enzyme PulseNet Data Capture pick list (XbaI, BlnI) Restriction enzyme for first characterization GROUP: IRIDA Ontology (Emma) primary enzyme (LMAAI) 1 1 GENEPIO:0000045 GENEPIO PFGE test specification GENEPIO:0000046 Lab Analytic Host Primary PFGE Pattern NML LIMS First PFGE pattern from given diagnostic restriction enzyme GROUP: IRIDA Ontology (Emma) GENEPIO PFGE primary test GENEPIO:0000047 Lab Analytic Host Secondary Enzyme PulseNet Data Capture pick list (XbaI, BlnI) Restriction enzyme for second characterization GROUP: IRIDA Ontology (Emma) GENEPIO secondary enzyme (LMACI) GENEPIO:0000048 Lab Analytic Host Secondary PFGE Pattern NML LIMS Second PFGE pattern from given diagnostic restriction enzyme GROUP: IRIDA Ontology (Emma) GENEPIO PFGE secondary test GENEPIO:0000049 Lab Analytic MLST Clonal Complex inferred from BCCDC interviews and Bionumerics pick list? Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. Sequence types are grouped into clonal complexes by their similarity to a central allelic profile (genotype). As such, clonal complexes represent sequence types that share a number of identical alleles e.g. 5/7 URI: http://en.wikipedia.org/wiki/Multilocus_sequence_typing ; http://eburst.mlst.net/3.asp GENEPIO MLST clonal complex GENEPIO:0000050 Lab Analytic MLST Sequence Type inferred from BCCDC interviews and Bionumerics pick list? Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. For each housekeeping gene, the different sequences present within a bacterial species are assigned as distinct alleles and, for each isolate, the alleles at each of the loci define the allelic profile or sequence type (ST). GENEPIO MLST sequence typing GENEPIO:0000051 The process of fingerprinting the core genome of a bacteria. Add under upcomming OBI "DNA fingerprinting assay". Damion Dooley Some bacteria like E coli have a highly variable genome, and so to type them methods must focus on typing the core genome that is common to all strains. GENEPIO core genome fingerprinting assay GENEPIO:0000052 Lab Analytic CGF type inferred from BCCDC interviews pick list output of CGF GROUP: IRIDA Ontology (Emma) GENEPIO CGF type GENEPIO:0000053 Lab Analytic 16S rRNA sequencing inferred from BCCDC interviews 16S ribosomal RNA sequencing is a sequencing method used to identify and compare bacteria present within a given sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study. URI: http://www.illumina.com/applications/microbiology/microbial-sequencing-methods/16S-rrna-sequencing.html GENEPIO 16S rRNA sequencing GENEPIO:0000054 Lab Analytic Stx toxin type metadata feedback Stx1 or Stx2 pathogenic shiga toxin produced by STEC E. coli GROUP: IRIDA Ontology (Emma) GENEPIO Stx toxin type datum GENEPIO:0000055 Lab Analytic Stx toxin subtype metadata feedback stx1a, stx1c shiga toxin variant GROUP: IRIDA Ontology (Emma) GENEPIO Stx toxin subtype datum GENEPIO:0000056 Lab Analytic Stx1 Toxin PCR result NML Labware LIMS CT value? qPCR result of Stx1 gene amplification GROUP: IRIDA Ontology (Emma) GENEPIO Stx1 Toxin PCR result GENEPIO:0000057 Lab Analytic Stx1 Cell Culture NML Labware LIMS level of Stx1 toxin derived tissue culture toxicity GROUP: IRIDA Ontology (Emma) GENEPIO Stx1 cell culture level GENEPIO:0000058 Lab Analytic Stx2 Toxin PCR result NML Labware LIMS CT value? qPCR result of Stx2 gene amplification GROUP: IRIDA Ontology (Emma) GENEPIO Stx2 Toxin PCR result GENEPIO:0000059 Lab Analytic Stx2 Cell Culture NML Labware LIMS value? level of Stx2 toxin derived tissue culture toxicity GROUP: IRIDA Ontology (Emma) GENEPIO Stx2 cell culture level GENEPIO:0000060 An AccuProbe assay that uses a luminometer and DNA probe designed to identify a specific bacteria or fungus species within a culture. Damion Dooley Nucleic acid hybridization tests are based on the ability of complementary nucleic acid strands to specifically align and associate to form stable double-stranded complexes (6). The ACCUPROBE method uses a single-stranded DNA probe with a chemiluminescent label that is complementary to the ribosomal RNA of the target organism. After the ribosomal RNA is released from the target organism, the labeled DNA probe combines with the target organism’s ribosomal RNA to form a stable DNA:RNA hybrid. The Selection Reagent allows for the differentiation of non-hybridized and hybridized probes.The light signal emitted by the DNA:RNA hybrids is measured by a GEN-PROBE luminometer. A positive result is a luminometer reading equal to or greater than the cut-off. A value below this cut-off is the negative result. GENEPIO AccuProbe culture identification assay GENEPIO:0000061 An AccuProbe reagent kit for identifying Listeria monocytogenes. Damion Dooley URI: http://www.hologic.com/sites/default/files/package%20inserts/103051F-EN-RevC.pdf GENEPIO AccuProbe Listeria monocytogenes culture identification reagent kit GENEPIO:0000062 Lab Analytic NML Labware LIMS positive, negative, not done A categorical diagnostic result of an AccuProbe test. NML LIMS GENEPIO AccuProbe test result GENEPIO:0000063 Ribotyping involves the fingerprinting of genomic DNA restriction fragments that contain all or part of the genes coding for the 16S and 23S rRNA. By digesting the genes with a specific restriction enzyme, fragments of different lengths are generated. By performing a Gel electrophoresis with the digested samples, the fragments can be visualised as lines on the gel, where larger fragments are close to the start of the gel, and smaller fragments further down. After blotting onto a matrix and probing, these lines form a unique pattern for each species and can be used to identify the origin of the DNA, almost like a barcode can identify a product. GENEPIO ribotyping GENEPIO:0000064 This method is based on restriction endonuclease digestion of bacterial chromosomal DNA, followed by Southern hybridization to probes for sequences in the regions of bacterial DNA coding for the 5S-16S-23S (the Escherichia coli rrnB rRNA operon) rRNA operon. The probes have been developed that are directed to highly conserved regions of the rRNA operon present in all eubacteria and can therefore be used for ribotyping most bacteria GENEPIO riboprinting GENEPIO:0000065 an automated system that takes a purified bacterial suspension, lyses the cells, extracts the DNA, restriction endonuclease digests the DNA, separates the digest on a gel, transfers the DNA bands to a membrane, probes the bands with non-radioisotope-labeled, 5S-16S-23S rRNA-specific probes (Southern hybridization), photographs the membrane, and finally compares the bar code-like pattern to databases in order to identify the genus and species. GENEPIO Qualicon (DuPont) RiboPrinter Microbial Characterization System GENEPIO:0000066 a library of RiboPrinter recognised patterns GENEPIO DuPont identification pattern library GENEPIO:0000067 Lab Analytic Riboprinter DUP Number NML Labware LIMS DUP-PST1-1211 DuPont identification number from the DuPont identification library NML LIMS GENEPIO RiboPrinter DUP Number GENEPIO:0000068 Lab Analytic Riboprinter DUP similarity NML Labware LIMS The identification of an isolate was determined when the corresponding patterns matched one of the patterns of the DuPont Identification library of the RiboPrinter1 with a similarity of >0.85. The similarity threshold for an isolate joining a ribogroup is an adaptive value between 0.90 and 0.96, depending on the size of the ribogroup. Similarity of pattern to one of the patterns of the DuPont Identification library of the RiboPrinter GENEPIO RiboPrinter DUP similarity GENEPIO:0000069 Sequencing Sequencing Run Date NML NGS Archive yyyy/mm/dd Date the sequencing run was performed GROUP: IRIDA Ontology (Emma) GENEPIO sequencing run date GENEPIO:0000070 Sequencing Sequencing Location inferred from BCCDC interviews location the sequencing run was performed GROUP: IRIDA Ontology (Emma) GENEPIO sequencing location GENEPIO:0000071 Sequencing Platform https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._platform_descriptor_t/ Illumina (MiSeq, HiSeq), PacBio, Ion Torrent, (Roche 454), SOLiD ABI A sequencing plaform (brand) is a name of a company that produces sequencer equipment. GROUP: IRIDA Ontology (Emma) GENEPIO sequencing platform (brand) GENEPIO:0000072 Sequencing Workflow Derived from Sample Sheet Resequencing, FastQ only the workflow is the pre-defined sequence of steps to run the automated sequencing pipeline. GROUP: IRIDA Ontology (Emma) GENEPIO sequencing workflow GENEPIO:0000073 Sequencing Application Derived from Illumina Sample Sheet amplicon sequencing, WGS the sequencing application is the use or purpose of the sequencing GROUP: IRIDA Ontology (Emma) GENEPIO sequencing application GENEPIO:0000074 Derived from Illumina Sample Sheet the sequencing conditions and the analyte being measured GROUP: IRIDA Ontology (Emma) obsolete: sequencing assay true GENEPIO:0000075 Sequencing Chemistry Derived from Illumina Sample Sheet amplicon, resequencing (WGS) lab method to determine the order of nucleotides in a DNA molecule GROUP: IRIDA Ontology (Emma) GENEPIO sequencing chemistry GENEPIO:0000076 Sequencing Read Length Derived from Illumina Sample Sheet 151, 251 number of base pairs per read GROUP: IRIDA Ontology (Emma) GENEPIO read length GENEPIO:0000077 A GSCID/BRC data item is a field in one of the GSCID/BRC Project and Sample Application Standard subsets. Damion Dooley obsolete: GSCID-BRC data item true GENEPIO:0000078 Sequencing Multiplex identifiers Derived from Illumina Sample Sheet S017 Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters GROUP: MIxS GENEPIO sequencing run multiplex identifiers GENEPIO:0000079 Sequencing Sample Name Derived from Illumina Sample Sheet specification: http://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/miseq/miseq-sample-sheet-quick-ref-guide-15028392-j.pdf 1,2,3, AX234, etc. Control1, Tank1, Froglet1 A sequencing run sample identifier is an alphanumeric identifier for a sample. In bioinformatics processing this identifier is assigned to a sample in order to track it through the process of sequencing and analysis. GROUP: IRIDA Ontology (Emma) Illumina SampleSheet: Sample_ID PulseNet: SubmittedNumber sample name sample title GENEPIO sequencing run sample identifier GENEPIO:0000080 Sequencing Number of cycles Derived from Illumina Sample Sheet 500 Number of sequencing chemistry cycles GROUP: IRIDA Ontology (Emma) GENEPIO sequencing count of chemistry cycles GENEPIO:0000081 Sequencing Sequencing Kit Derived from Illumina Sample Sheet MiSeq reagent kit Pre-filled, ready-to-use reagent cartridges. Used to produce improved chemistry, cluster density and read length as well as improve quality (Q) scores. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications. GROUP: IRIDA Ontology (Emma) GENEPIO sequencing kit GENEPIO:0000082 Sequencing Sequencing Kit version Derived from Illumina Sample Sheet v2, v3 A string datum which is the version/configuration of the reagent cartidge. GROUP: IRIDA Ontology (Emma) GENEPIO sequencing kit version GENEPIO:0000083 Sequencing Adapters Derived from Illumina Sample Sheet adapter A and B sequence Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters GROUP: MIxS GENEPIO adapter sequence GENEPIO:0000084 Sequencing Adapter Trimming Derived from Illumina Sample Sheet The removal of adapter sequences from demultiplexed data reads GROUP: IRIDA Ontology (Emma) GENEPIO read adapter trimming GENEPIO:0000085 Sequencing inferred from BCCDC interviews Illumina metagenomic protocol (part 15044223), with Nextera Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids. GROUP: IRIDA Ontology (Emma) and http://applications.illumina.com/applications/sequencing/ngs-library-prep.html library preparation kit GENEPIO:0000086 Sequencing Number of base pairs inferred from BCCDC interviews 300 000 The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. GROUP: MIxS GENEPIO number of expected base pairs per genome GENEPIO:0000087 Run QC Number of Reads Passing Filter Output from MiSeq 0.92 Raw data are filtered to remove any reads that do not meet the overall quality as measured by a chastity filter. The chastity of a base call is calculated as the ratio of the brightest intensity divided by the sum of the brightest and second brightest intensities. Clusters passing filter are represented by PF in analysis reports. Clusters pass filter if no more than one base call in the first 25 cycles has a chastity of < 0.6. URI: http://support.illumina.com/sequencing/sequencing_instruments/miseq/questions.html GENEPIO number of reads passing filter GENEPIO:0000088 Run QC Cluster density Output from MiSeq 800 k/mm^2 Cluster Generation is a process by which libraries amplified into clonal clusters on a flow cell. The density of those clusters in the lane, is the cluster density. URI: https://www.broadinstitute.org/files/shared/illuminavids/clusterGenSlides.pdf sequencer flow cell cluster density GENEPIO:0000089 Run QC above 30 Qscore Output from MiSeq >75% percentage of reads with a Phred quality score over 30, which indicates less than a 1/1000 chance that the base was called incorrectly URI: http://en.wikipedia.org/wiki/Phred_quality_score GENEPIO phred quality score GENEPIO:0000090 Assembly QC Assembly Standard Term the GROUP: MIxS term encompasses assembly method; estimated error rate; method of calculation Assembly method refers to how the reads were assembled into contigs for which either a de novo or mapping (reference based) strategy is used. GROUP: MIxS GENEPIO assembly method GENEPIO:0000091 Assembly QC Assembly status from within "Finishing strategy" in GROUP: MIxS standard draft or finished "Attempting to convey the relative integrity and reliability of the data, six levels or terms have been proposed and applied to describe genome sequences." See subclass choices. Damion Dooley CITATION: Chain, P.S., Grafham, D.V., Fulton, R.S., Fitzgerald, M.G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D.C., Buhay, C., et al. (2009). Genomics. Genome project standards in a new era of sequencing. Science 326, 236-237. GENEPIO assembly status GENEPIO:0000092 Assembly QC Coverage from within "Finishing strategy" in GROUP: MIxS 30 Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence. URI: http://en.wikipedia.org/wiki/Shotgun_sequencing GENEPIO Damion Dooley's note: Wikipedia defines calculation with: "the length of the original genome (G), the number of reads(N), and the average read length(L) as N * L/G" read coverage GENEPIO:0000093 Assembly QC Number of Contigs 20 http://purl.obolibrary.org/obo/IAO_0000428 A contig count is the count of contigs that belong to a sequence assembly. Damion Dooley GENEPIO contig count GENEPIO:0000094 Assembly QC Assembly name Standard Term name and version of assemby Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community GROUP: MIxS GENEPIO assembly name (identifier) GENEPIO:0000095 Assembly QC Annotation Algorithm Standard Term Prokka Program used for annotation GROUP: IRIDA Ontology (Emma) GENEPIO genome annotation algorithm GENEPIO:0000096 Assembly QC Annotation Source Standard Term annotation source description For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter GROUP: MIxS GENEPIO genome annotation source GENEPIO:0000097 Damion Dooley obsolete: NCBI BioSample data item true GENEPIO:0000099 CDC ID GENEPIO:0000100 GENEPIO:0000101 Damion Dooley GENEPIO:0000102 Damion Dooley GENEPIO:0000103 An NCBI BioProject data item is a datum within the NCBI BioProject standard collection Damion Dooley obsolete: NCBI BioProject data item true GENEPIO:0000104 The INDISC consortium "Minimum data for Matching" standard aims to define a format to capture reads and minimum metadata. It is developed by the "Repository and storage of sequence and meta-data" workgroup 2. It is used in the Global Microbial Identifier platform. Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0000036 obsolete: INSDC MDM standard true GENEPIO:0000105 A MixS data item is a term or field defined in the Genomic Standards Consortium MIxS standard. Damion Dooley obsolete: MIxS data item true GENEPIO:0000106 The 'draft data standard' class contains draft representations of formal or defacto third party standards and related components. These representations may have been crafted without any involvement of related standards issuers and so no guarantee can be provided about their currency, accuracy or veracity. Damion Dooley draft data standard GENEPIO:0000107 obsolete: HIPPA PHI data item true GENEPIO:0000108 obsolete: PulseNet data item true GENEPIO:0000109 The I2B2 Workbench Data Protection role standard is a standard which names and lists data protection roles between a user and a given dataset that define the level of detail a user has access to. Damion Dooley Derived from the Data Protection Track of the I2B2 Workbench software specification: https://www.i2b2.org/software/files/PDF/current/IM_Architecture.pdf I2B2 Data Protection role standard GENEPIO:0000110 depth:1 order: NCIT:C115935 # healthy NCIT:C25610 # pathologic / diseased NCIT:C28554 # deceased A description of whether a given subject organism appeared healthy, sick or deceased at the time of specimen extraction. If sick or deceased, additional details should be provided in project-specific fields. Damion Dooley CS8 subject health status (GSCID-BRC) GENEPIO:0000111 The GSCID-BRC Core Sample Standard is an extension of the GMI MDM data standard Damion Dooley https://www.niaid.nih.gov/research/dmid-metadata-standards-core-sample GSCID-BRC Core Sample standard GENEPIO:0000112 A Core Project item is a field in the GSCID/BRC Project and Sample Application Core Project Standard. Damion Dooley https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project GSCID-BRC Core Project standard GENEPIO:0000113 Specimen category is a categorical variable that broadly indicates the source of a specimen in order for data processing systems like NCBI's biosample submission portal to anticipate other fields related to the source. Currently this distinguishes between "clinical or host associated" specimens and "environmental/food or other pathogen" specimens. Damion Dooley specimen category GENEPIO:0000114 day, week, month, year Age unit of the age measurement of a subject (individual organism). Damion Dooley Feb 20, 2017: GSCID-BRC calls for an explicit field here whereas NCBI Biosample and MIxS don't. Damion Dooley NIAID GSCID-BRC metadata working group subject age - unit GENEPIO:0000115 The National Center for Biotechnology Information offers standards for submitting genomic project data to their BioProject and BioSample databases. Damion Dooley National Center for Biotechnology Information standard NCBI standard GENEPIO:0000117 A datum containing the city or region or more precise geographical location identifier for the site of a specimen collection event. Damion Dooley Adapted from NIAID GSCID-BRC metadata working group Note that this is expressed in a particular format in some standards. specimen collection location - city or region lookup GENEPIO:0000118 The country of the site of a given specimen collection event. Damion Dooley NIAID GSCID-BRC metadata working group specimen collection location - country GENEPIO:0000119 The Darwin Core is body of standards. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing reference definitions, examples, and commentaries. Damion Dooley http://tdwg.github.io/dwc/terms/index.htm Darwin Core Terms GENEPIO:0000120 A datetime measurement related to a person's travel with respect to potential epidemilogical implications. Damion Dooley travel history item GENEPIO:0000121 The date of a person's departure from their primary residence (at that time) on a journey to one or more other locations. Damion Dooley travel start date GENEPIO:0000122 The date of a person's return to some residence from a journey originating at that residence. Damion Dooley travel end date GENEPIO:0000123 Infection aquired during travel is a boolean datum indicating a diagnosis of a traveller's infection during a given trip. Damion Dooley infection aquired during travel GENEPIO:0000124 This is a model of the datums involved in an epidemiology investigation. Damion Dooley draft pathogenic epidemiology case investigation record GENEPIO:0000125 The draft epi case exposure model describes datums related to the possible transmission of a pathogen between a case person and other people, places, animals etc. Damion Dooley draft pathogenic epi case exposure record GENEPIO:0000126 A description of a food item that a case patient has come in contact with. Damion Dooley draft pathogenic epi case food record GENEPIO:0000127 food brought back from travel GENEPIO:0000128 An epidemiology contact network model is a definition of the information necessary to connect pathogen transmission patterns between individuals or animals in connection with an outbreak investigation. Damion Dooley epidemiology contact network model GENEPIO:0000129 An epi contact network - human is contact information about a person who may be involved in transmitting a pathogen. Damion Dooley epi contact network model - human GENEPIO:0000130 This is a model that provides location and transportation information about an animal that may be involved in transmitting a pathogen to a human or other animal. Damion Dooley epi contact network model - animal GENEPIO:0000131 A note is text that provides human-readable information on one or more subjects. Damion Dooley note GENEPIO:0000132 An epi case general info model contains datum specifications about an epidemiology investigation case including the person involved, contact information and their demographics. Damion Dooley draft pathogenic epi case general information record GENEPIO:0000133 A record of the details around how, when, and from what an isolate was extracted. Damion Dooley draft pathogenic epi case isolate detail record GENEPIO:0000134 A specimen source substance is an organism substance or food product or environmental substance from which the specimen was extracted. Damion Dooley specimen source substance GENEPIO:0000135 An isolate sequence filename is the file name (http://edamontology.org/data_1050) of the contig assembly file created by a bioinformatics assembly process. Damion Dooley isolate sequence filename GENEPIO:0000136 A cluster identifier is an identifier that locates a genomic variant of an organism within a community of past or present genetically related organisms. Damion Dooley cluster identifier GENEPIO:0000137 A laboratory test performed on a specimen from a patient with regard to potential pathogenic disease. Damion Dooley draft pathogenic epi case test record GENEPIO:0000138 A lab test requestor is the individual or agency requesting that one or more tests be performed on a specimen. Damion Dooley contact specification - lab test requester GENEPIO:0000139 A food cultural origin datum indicates the cultural origin of a food product. Damion Dooley food cultural origin GENEPIO:0000140 A record of a patient's recent travel - departure and return, mode of travel and locations visited - as it may pertain to an outbreak pathogen transmission event. Damion Dooley draft pathogenic epi case travel record GENEPIO:0000141 Region (England) (entry subject to GAZ replacement) GENEPIO:0000142 An epi network contact is a person who may have recieved or transmitted an infectious disease related to an outbreak investigation. Damion Dooley contact specification - epi network contact GENEPIO:0000143 This model contains data type specifications for whole genome sequencing and epidemiology investigation contextual data. Damion Dooley public health lab epidemiology contextual data standard GENEPIO:0000144 This is a set of datums involved in laboratory processing of whole-genome-sequenced isolates. Damion Dooley draft whole genome sequencing lab test record GENEPIO:0000145 Damion Dooley draft WGS lab bioinformatics process record GENEPIO:0000146 Damion Dooley draft WGS lab sequencing record GENEPIO:0000147 An NCBI SRA meta information item is a field specification for a NCBI Sequence Read Archive record. Damion Dooley NCBI SRA meta information standard https://www.ncbi.nlm.nih.gov/books/NBK47529/#_SRA_Quick_Sub_BK_Experiment_ GENEPIO:0000148 An isolate raw read filename is the file name (http://edamontology.org/data_1050) of the raw read file created by a genomic sequencing assay. isolate raw read filename GENEPIO:0000149 Sequencing The version identifier of a packaged kit tailored for specific sequencing workflows. Damion Dooley library preparation kit version GENEPIO:0000150 The name and version of software used in a bioinformatics workflow to improve the quality of sequencing reads. Damion Dooley read trimming and filtering software GENEPIO:0000151 Damion Dooley bioinformatics pipeline name GENEPIO:0000152 Damion Dooley bioinformatics pipeline version GENEPIO:0000153 Damion Dooley bioinformatics pipeline protocol GENEPIO:0000154 Damion Dooley draft WGS lab sequencing quality metrics record GENEPIO:0000155 Damion Dooley draft WGS lab assembly quality metrics record GENEPIO:0000156 A general label indicating the primary study goal. These are only relevant for Primary submission projects (not Umbrella projects). Damion Dooley Damion Dooley's note: According to http://trace.ddbj.nig.ac.jp/news/2014-11-12_e.html, "A BioProject record can have multiple project data types" project data type GENEPIO:0000157 Genome assembly project utilizing already existing sequence data including data that was submitted by a different group Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ assembly project GENEPIO:0000158 A sequencing project involving clone-ends Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ clone ends project GENEPIO:0000159 A sequencing project involving DNA methylation, histone modification, and/or chromatin accessibility datasets Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ epigenomics project GENEPIO:0000160 Exome resequencing project Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ exome resequencing project GENEPIO:0000161 A whole, or partial, genome sequencing project (with or without a genome assembly) Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ genome sequencing project GENEPIO:0001000 The Relational Sequencing TB Data Platform (ReSeqTB) catalogs a vast amount of genotypic, phenotypic and related metadata from Mycobacterium tuberculosis (Mtb) strains to enable the development of clinically useful, WHO-endorsed in vitro diagnostic assays for rapid drug susceptibility testing of Mtb. Damion Dooley https://platform.reseqtb.org/ draft ReSeq Tuberculosis data platform standard GENEPIO:0001001 In expressions like: "<= 8mg/L" The measurement comparator is a sign indicating that a measurement is above, equal to, or below a given threshold. Damion Dooley test threshold measurement comparator GENEPIO:0001002 < The "less than" comparator indicates that a given substance was present at less than a given quantity or concentration. Damion Dooley < less than GENEPIO:0001003 <= The "less than or equal to" comparator indicates that a given substance was present at less than or equal to a given quantity or concentration. Damion Dooley <= less than or equal to GENEPIO:0001004 == The "equal to" comparator indicates that a given substance was present at the given quantity or concentration. Damion Dooley == equal to GENEPIO:0001005 >= The "greater than or equal to" comparator indicates that a given substance was present at greater than or equal to a given quantity or concentration. Damion Dooley >= greater than or equal to GENEPIO:0001006 > The "greater than" comparator indicates that a given substance was present at greater than a given quantity or concentration. Damion Dooley > greater than GENEPIO:0001007 order: OBI:0001616 # specimen identifier OBI:0001614 # GenBank ID GENEPIO:0001100 # antibiogram drug test model GENEPIO:0002062 # amr testing reference standard GENEPIO:0002045 # amr resistance testing method GENEPIO:0002047 # ... version or reagent GENEPIO:0002049 # amr testing platform GENEPIO:0002056 # ... vendor The NCBI antibiogram standard details the reporting specifications for antimicrobial susceptibility and resistance data derived from drug resistant pathogens. This information is submitted as an antibiogram table on BioSample records. Damion Dooley NCBI Antibiogram standard https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/ GENEPIO:0001008 http://purl.obolibrary.org/obo/GENEPIO_0001007 obsolete: NCBI isolate AMR testing model true GENEPIO:0001009 A restaurant or an eatery, is a business which prepares and serves food and drinks to customers in exchange for money. Damion Dooley https://en.wikipedia.org/wiki/Restaurant http://purl.obolibrary.org/obo/ENVO_01000934 obsolete: restaurant true GENEPIO:0001010 iPHIS standard The Canadian Integrated Public Health Information System (iPHIS) System provides a standard for holding reportable disease cases from participating jurisdictions. Damion Dooley Canadian Integrated Public Health Information System (iPHIS) Standard GENEPIO:0001011 254532233433235152213423 The MIRU24 - international standard is a mycobacterial interspersed repetitive units (MIRU) typing method that classifies Mycobacterium tuberculosis complex (MBTC) bacteria according to a multiple locus VNTR [variable number of tandem repeats] analysis (MLVA) typing scheme of counts of repeats at 24 sequence loci. The ordering of loci is as follows: MIRU 04, MIRU 26, MIRU 40, MIRU 10, MIRU 16, MIRU 31, 424 577, 2165, 401, 3690, 4156, 2163, 1955, 4052, MIRU 02, MIRU 23, MIRU 39, MIRU 20, MIRU 24, MIRU 27, 2347, 2461, 3171 MIRU24 - international standard GENEPIO:0001012 The MIRU24 - Canadian standard is a Mycobacterium tuberculosis typing method exactly like MIRU24 - international standard except that the report of the ordering of the matching loci is different. Damion Dooley The ordering of loci is as follows: MIRU 02, MIRU 04, MIRU 10, MIRU 16, MIRU 20, MIRU 23, MIRU 24, MIRU 26, MIRU 27, MIRU 31, MIRU 39, MIRU 40, 424, 577, 1955, 2163, 2165, 2347, 2401, 2461, 3171, 3690, 4052, 4156 MIRU24 - Canadian standard GENEPIO:0001013 spray-wading water GENEPIO:0001014 pool water GENEPIO:0001015 obsolete: hot tub true GENEPIO:0001016 A cafeteria is a type of food service location in which there is little or no waiting staff table service, whether a restaurant or within an institution such as a large office building or school. Damion Dooley https://en.wikipedia.org/wiki/Cafeteria http://purl.obolibrary.org/obo/ENVO_01000969 obsolete: cafeteria true GENEPIO:0001017 http://purl.obolibrary.org/obo/ENVO_00003864 obsolete: bakery true GENEPIO:0001018 A delicatessen or deli is a retail establishment that sells a selection of unusual or foreign prepared foods. Damion Dooley https://en.wikipedia.org/wiki/Delicatessen http://purl.obolibrary.org/obo/ENVO_01000970 obsolete: delicatessen true GENEPIO:0001019 A food kiosk is a kiosk (a booth with an open window on one side) that sells food. Damion Dooley http://purl.obolibrary.org/obo/ENVO_01000974 obsolete: food kiosk true GENEPIO:0001020 A grocery store is a retail store that primarily sells food. Damion Dooley http://purl.obolibrary.org/obo/ENVO_01000984 obsolete: grocery store true GENEPIO:0001021 A specialty/ethnic food store is a store specializing in a particular variety of food or food of cultural / regional origin. Damion Dooley http://purl.obolibrary.org/obo/ENVO_01000988 obsolete: specialty/ethnic store true GENEPIO:0001022 A market, or marketplace, is a location where people regularly gather for the purchase and sale of provisions, livestock, and other goods Damion Dooley http://purl.obolibrary.org/obo/ENVO_01000987 obsolete: market true GENEPIO:0001023 A time measurement datum that pertains to a patient's medical treatment. Damion Dooley treatment history datum GENEPIO:0001024 A restaurant providing prepared meals or other food items that the purchaser intends to eat elsewhere Damion Dooley https://en.wikipedia.org/wiki/Take-out http://purl.obolibrary.org/obo/ENVO_01000972 obsolete: take out restaurant true GENEPIO:0001025 A treatment start date is a date/time datum which indicates the start of a particular medical treatment for a patient. Damion Dooley treatment start date GENEPIO:0001026 canoeing / kayaking / boating GENEPIO:0001027 hiking GENEPIO:0001028 camping GENEPIO:0001029 Damion Dooley http://purl.obolibrary.org/obo/PCO_0000033 obsolete: social gathering true GENEPIO:0001030 http://purl.obolibrary.org/obo/PCO_0000035 obsolete: party true GENEPIO:0001031 http://purl.obolibrary.org/obo/PCO_0000038 obsolete: wedding true GENEPIO:0001032 http://purl.obolibrary.org/obo/PCO_0000039 obsolete: baby shower true GENEPIO:0001033 http://purl.obolibrary.org/obo/PCO_0000037 obsolete: potluck true GENEPIO:0001034 http://purl.obolibrary.org/obo/PCO_0000034 obsolete: community event true GENEPIO:0001035 A long term care facility provides a type of residential care. It is a place of residence for people who require continual nursing care and have significant difficulty coping with the required activities of daily living. Damion Dooley https://en.wikipedia.org/wiki/Nursing_home_care http://purl.obolibrary.org/obo/ENVO_01000932 obsolete: long term care facility true GENEPIO:0001036 A treatment end date is a date/time datum which indicates the end of a particular medical treatment for a patient. Damion Dooley treatment end date GENEPIO:0001037 Damion Dooley food related exposure event GENEPIO:0001038 Some bacteria are associated with particular foods. Need relationship Damion Dooley infection-specific food detail GENEPIO:0001039 A tuberculosis treatment antibiotic is an antibiotic used in the treatment of tuberculosis. Damion Dooley tuberculosis treatment drug “Treatment of Tuberculosis Guidelines”, WHO, Geneva, 2010, 30 www.who.int/tb/ - See more at: http://www.tbfacts.org/tb-drugs/#sthash.nibuzCLV.dpuf GENEPIO:0001040 vegetarian GENEPIO:0001041 A time measurement datum that pertains to an organism's physical location. Damion Dooley organism location history datum GENEPIO:0001042 This will take on a sub-herarchy of food types. food avoidance GENEPIO:0001043 special diet GENEPIO:0001044 water related exposure event GENEPIO:0001045 municipal water GENEPIO:0001046 A time measurement datum indicating the year a person immigrated to a given country. Damion Dooley immigration year of arrival GENEPIO:0001047 bottled water GENEPIO:0001048 An event (occuring at some location and for some duration of time) where Damion Dooley infectious disease exposure event GENEPIO:0001049 Damion Dooley human related exposure event GENEPIO:0001050 Damion Dooley animal related exposure event GENEPIO:0001051 Identification or description of the specific individual from which this sample was obtained Damion Dooley https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ NCBI BioSample isolate (human name or description) GENEPIO:0001052 Damion Dooley http://purl.obolibrary.org/obo/ENVO_01000923 obsolete: petting zoo true GENEPIO:0001053 Damion Dooley agricultural fair GENEPIO:0001054 An isolate passage history is a record of the cyclic growth process that led to it, including number of times its was put through the process, and the method used. Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0001835 isolate passage history datum GENEPIO:0001055 For Eschericia coli: STEC, UPEC A pathotype is a common name for a group of organisms (of the same species) that have the same pathogenicity on a specified host https://en.wiktionary.org/wiki/pathotype NCBI pathotype GENEPIO:0001056 Damion Dooley pet treat GENEPIO:0001057 Damion Dooley pet food (raw) GENEPIO:0001058 An epidemiology travel datum is a datum regarding a particular human's travel trip destination, mode, and motivation, with respect to an epidemiology investigation. Damion Dooley human exposure event - travel datum GENEPIO:0001059 boat / cruise travel GENEPIO:0001060 train travel GENEPIO:0001061 bus travel GENEPIO:0001062 car travel GENEPIO:0001063 airline travel GENEPIO:0001064 A travel mode is a type of transportation which a given human has used while travelling on a particular trip. Damion Dooley travel mode GENEPIO:0001065 A travel reason is a motivation for traveling on a particular trip expressed by the traveller. Damion Dooley travel reason GENEPIO:0001066 travel for pleasure GENEPIO:0001067 business activity GENEPIO:0001068 religious missionairy activity GENEPIO:0001069 rural backpacking activity GENEPIO:0001070 visiting relative/friends GENEPIO:0001071 travel tour GENEPIO:0001072 unsure of travel reason GENEPIO:0001073 The tuberculosis draft standard is a GenEpiO set of draft genomic and clinical data items related to Mycobacterium tuberculosis that various agencies are using in their own reporting. draft tuberculosis - specimen contextual data standard GENEPIO:0001074 Damion Dooley behavioural risk factor GENEPIO:0001075 http://purl.obolibrary.org/obo/GENEPIO_0001686 obsolete: E. coli serotype part true GENEPIO:0001076 Snomed: Concept 260827009 O antigen GENEPIO:0001077 Snomed: Concept 260823008 H antigen GENEPIO:0001078 Damion Dooley homeless status GENEPIO:0001079 A serotype or serovar is a distinct variation within a species of bacteria or virus or among immune cells of different individuals. These microorganisms, viruses, or cells are classified together based on their cell surface antigens, allowing the epidemiologic classification of organisms to the sub-species level Damion Dooley https://en.wikipedia.org/wiki/Serotype serovar/serotype common name GENEPIO:0001080 Salmonella serovar GENEPIO:0001081 Salmonella serovar name GENEPIO:0001082 Salmonella antigenic formula GENEPIO:0001083 Damion Dooley drug use status GENEPIO:0001084 Damion Dooley incarceration status GENEPIO:0001085 Damion Dooley HIV status GENEPIO:0001086 Damion Dooley HIV risk status GENEPIO:0001087 Damion Dooley A.I.D.S status GENEPIO:0001088 Damion Dooley drug abuse status GENEPIO:0001089 Damion Dooley injection drug use status GENEPIO:0001090 Damion Dooley recreational drug use status GENEPIO:0001091 Damion Dooley methadone use status GENEPIO:0001092 Damion Dooley substantial alcohol use/abuse status GENEPIO:0001093 Damion Dooley smoking status GENEPIO:0001094 A country of birth is the country that a given person (or animal) was born in. Damion Dooley country of birth GENEPIO:0001095 Tb_1 (with respect to an Illumina SampleSheet.csv spreadsheet) 13 (with respect to a ReSeqTB SNP pipeline sample report) A sequence number is a numeric identifier of a sequence with respect to a particular data table or dataset. sequence number GENEPIO:0001096 Damion Dooley The 'date last seen alive' is the date that a subject (patient) was last known (seen, heard, messaged) to be alive. date last seen alive GENEPIO:0001097 second line or reserve tuberculosis drug GENEPIO:0001098 tuberculosis infection anatomical site GENEPIO:0001099 http://purl.obolibrary.org/obo/GENEPIO_0001007 obsolete: NCBI Antibiogram model true GENEPIO:0001100 order: GENEPIO:0001187 # antimicrobial resistance test drug GENEPIO:0002112 # drug MIC GENEPIO:0002080 # drug minimum inhibitory concentration unit GENEPIO:0001001 # measurement comparator NCIT:C85539 # antimicrobial resistance phenotype GENEPIO:0002181 # antimicrobial resistance phenotype - ECOFF This is the minimal set of parameters for drug test results for a particular antimicrobial agent. Damion Dooley draft antibiogram drug test model http://the-vet.net/DVMWiz/Vetlibrary/Lab-%20Microbiology%20Guide%20to%20Interpreting%20MIC.htm https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/ GENEPIO:0001101 A date-time datum that marks the predicted start of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time. Damion Dooley predicted exposure start GENEPIO:0001102 A date-time datum that marks the predicted end of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time. Damion Dooley predicted exposure end GENEPIO:0001103 Map: - project that results in non-sequence map data such as genetic map, radiation hybrid map, cytogenetic map, optical map, and etc. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ map project GENEPIO:0001104 Metagenome: sequence analysis of environmental samples Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ metagenome project GENEPIO:0001105 Metagenome assembly: a genome assembly generated from sequenced environmental samples Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ metagenome assembly project GENEPIO:0001106 Other: a free text description is provided to indicate Other data type Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ other project data type GENEPIO:0001107 Phenotype or Genotype: project correlating phenotype and genotype Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ phenotype or genotype project GENEPIO:0001108 Proteome: large scale proteomics experiment including mass spec. analysis Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ proteome project GENEPIO:0001109 Random Survey: sequence generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ random survey project GENEPIO:0001110 Targeted locus (loci): project to sequence specific loci, such as a 16S rRNA sequencing Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ targeted locus (loci) project GENEPIO:0001111 Transcriptome or Gene expression: large scale RNA sequencing or expression analysis. Includes cDNA, EST, RNA_seq, and microarray. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ transcriptome or gene expression GENEPIO:0001112 A sequencing project with a primary goal of identifying large or small sequence variation across populations. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ variation project (Afghanistan|Albania|Algeria|American Samoa|Andorra|Angola|Anguilla|Antarctica|Antigua and Barbuda|Arctic Ocean|Argentina|Armenia|Aruba|Ashmore and Cartier Islands|Atlantic Ocean|Australia|Austria|Azerbaijan|Bahamas|Bahrain|Baltic Sea|Baker Island|Bangladesh|Barbados|Bassas da India|Belarus|Belgium|Belize|Benin|Bermuda|Bhutan|Bolivia|Borneo|Bosnia and Herzegovina|Botswana|Bouvet Island|Brazil|British Virgin Islands|Brunei|Bulgaria|Burkina Faso|Burundi|Cambodia|Cameroon|Canada|Cape Verde|Cayman Islands|Central African Republic|Chad|Chile|China|Christmas Island|Clipperton Island|Cocos Islands|Colombia|Comoros|Cook Islands|Coral Sea Islands|Costa Rica|Cote d'Ivoire|Croatia|Cuba|Curacao|Cyprus|Czech Republic|Democratic Republic of the Congo|Denmark|Djibouti|Dominica|Dominican Republic|East Timor|Ecuador|Egypt|El Salvador|Equatorial Guinea|Eritrea|Estonia|Ethiopia|Europa Island|Falkland Islands (Islas Malvinas)|Faroe Islands|Fiji|Finland|France|French Guiana|French Polynesia|French Southern and Antarctic Lands|Gabon|Gambia|Gaza Strip|Georgia|Germany|Ghana|Gibraltar|Glorioso Islands|Greece|Greenland|Grenada|Guadeloupe|Guam|Guatemala|Guernsey|Guinea|Guinea-Bissau|Guyana|Haiti|Heard Island and McDonald Islands|Honduras|Hong Kong|Howland Island|Hungary|Iceland|India|Indian Ocean|Indonesia|Iran|Iraq|Ireland|Isle of Man|Israel|Italy|Jamaica|Jan Mayen|Japan|Jarvis Island|Jersey|Johnston Atoll|Jordan|Juan de Nova Island|Kazakhstan|Kenya|Kerguelen Archipelago|Kingman Reef|Kiribati|Kosovo|Kuwait|Kyrgyzstan|Laos|Latvia|Lebanon|Lesotho|Liberia|Libya|Liechtenstein|Line Islands|Lithuania|Luxembourg|Macau|Macedonia|Madagascar|Malawi|Malaysia|Maldives|Mali|Malta|Marshall Islands|Martinique|Mauritania|Mauritius|Mayotte|Mediterranean Sea|Mexico|Micronesia|Midway Islands|Moldova|Monaco|Mongolia|Montenegro|Montserrat|Morocco|Mozambique|Myanmar|Namibia|Nauru|Navassa Island|Nepal|Netherlands|New Caledonia|New Zealand|Nicaragua|Niger|Nigeria|Niue|Norfolk Island|North Korea|North Sea|Northern Mariana Islands|Norway|Oman|Pacific Ocean|Pakistan|Palau|Palmyra Atoll|Panama|Papua New Guinea|Paracel Islands|Paraguay|Peru|Philippines|Pitcairn Islands|Poland|Portugal|Puerto Rico|Qatar|Republic of the Congo|Reunion|Romania|Ross Sea|Russia|Rwanda|Saint Helena|Saint Kitts and Nevis|Saint Lucia|Saint Pierre and Miquelon|Saint Vincent and the Grenadines|Samoa|San Marino|Sao Tome and Principe|Saudi Arabia|Senegal|Serbia|Seychelles|Sierra Leone|Singapore|Sint Maarten|Slovakia|Slovenia|Solomon Islands|Somalia|South Africa|South Georgia and the South Sandwich Islands|South Korea|South Sudan|Southern Ocean|Spain|Spratly Islands|Sri Lanka|State of Palestine|Sudan|Suriname|Svalbard|Swaziland|Sweden|Switzerland|Syria|Taiwan|Tajikistan|Tanzania|Tasman Sea|Thailand|Togo|Tokelau|Tonga|Trinidad and Tobago|Tromelin Island|Tunisia|Turkey|Turkmenistan|Turks and Caicos Islands|Tuvalu|USA|Uganda|Ukraine|United Arab Emirates|United Kingdom|Uruguay|Uzbekistan|Vanuatu|Venezuela|Viet Nam|Virgin Islands|Wake Island|Wallis and Futuna|West Bank|Western Sahara|Yemen|Zambia|Zimbabwe|Historical Country Names|Belgian Congo|British Guiana|Burma|Czechoslovakia|Former Yugoslav Republic of Macedonia|Korea|Netherlands Antilles|Serbia and Montenegro|Siam|USSR|Yugoslavia|Zaire)(:[a-zA-Z0-9 ]+)? GENEPIO:0001113 help: Consult the http://www.insdc.org/country.html country list for valid options. The INSDC country qualifier is a textual controlled vocabulary used to indicate the country of origin of a DNA sample. It can also have the following format: country:sub_region, such as: "Canada:Vancouver". Damion Dooley INSDC country qualifier GENEPIO:0001114 phenotype Phenotype: phenotypic measurements for submission to dbGaP Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ phenotype project objective GENEPIO:0001115 genome material Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ genome material from specimen GENEPIO:0001116 TB lineage 7 - Ethiopia GENEPIO:0001117 An object aggregate which has as members whole organs or parts of organs, possibly from different organisms. 2021-04-19T23:36:25Z organs or organ parts GENEPIO:0001118 A travel destination which a given human has travelled to on a particular trip and is outside Canada. 2021-05-27T04:35:17Z travel outside Canada GENEPIO:0001119 A travel destination which a given human has travelled to on a particular trip and is outside a given province/territory of interest. 2021-05-27T04:36:13Z travel outside province/territory GENEPIO:0001120 A data specification established for use by The Canadian COVID-19 Genomics Network (CanCOGeN) project for SARS-CoV-2 contextual data (metadata) harmonization and curation across data providers. https://orcid.org/0000-0002-9578-0788 2021-04-24T00:18:57Z The Canadian COVID-19 Genomics Network SARS-CoV-2 specification The Canadian COVID-19 Genomics Network severe acute respiratory syndrome coronavirus 2 specification The Canadian coronavirus 2019 Genomics Network severe acute respiratory syndrome coronavirus 2 specification CanCOGeN SARS-CoV-2 CanCOGeN SARS-CoV-2 specification https://github.com/cidgoh/pathogen-genomics-package GENEPIO:0001121 An instance of a "data field category" that contains the "bioproject accession field", "biosample accession field", and "GISAID accession field". A data field category which receives a range of one or more data fields. 2022-11-23T00:33:27.896Z data field category GENEPIO:0001122 An instance of the "database identifiers field category" that contains the "bioproject accession field". A data field category which refers to database identifier fields. database identifiers https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z database identifiers slot category Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 database identifiers field category GENEPIO:0001123 prov_rona_99 An identifier data field which describes the user-defined name for the sample. sample collector sample identifier sample_collector_sample_ID specimen collector sample ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collector sample identifier field sample collector sample identifier slot specimen collector sample ID slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Every Sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. specimen collector sample ID field GENEPIO:0001126 A livespan history item is a date-associated event pertaining to the life of a subject. Damion Dooley lifespan history item GENEPIO:0001128 SR20-12345 A data field which describes the primary identifer of a related specimen previously submitted to the repository. related specimen primary ID related specimen primary identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z related specimen primary ID slot related specimen primary identifier field related specimen primary identifier slot Monkeypox CanCOGeN SARS-CoV-2 Example Guidance: Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. related specimen primary ID field GENEPIO:0001131 prov_rona_99 A data field which describes the identifer assigned to a sequenced isolate in Integrated Rapid Infectious Disease Analysis (IRIDA) bioinformatics platform. IRIDA sample identifier IRIDA sample name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z IRIDA sample ID slot IRIDA sample identifier slot IRIDA sample name slot Integrated Rapid Infectious Disease Analysis sample ID field Integrated Rapid Infectious Disease Analysis sample ID slot Integrated Rapid Infectious Disease Analysis sample identifier field Integrated Rapid Infectious Disease Analysis sample identifier slot Integrated Rapid Infectious Disease Analysis sample name field Integrated Rapid Infectious Disease Analysis sample name slot CanCOGeN SARS-CoV-2 Example Guidance: Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). IRIDA sample name field GENEPIO:0001133 PRJNA623807 An identifier data field which describes the International Nucleotide Sequence Database Collaboration (INSDC) umbrella accession number of the BioProject to which the BioSample belongs. umbrella bioproject accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z umbrella bioproject accession slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Required if submission is linked to an umbrella BioProject. An umbrella BioProject links together related BioProjects. A valid BioProject umbrella accession has prefix PRJN, PRJE or PRJD. Your laboratory can have one or many BioProjects. umbrella bioproject accession field GENEPIO:0001136 PRJNA12345 An identifier data field which describes the International Nucleotide Sequence Database Collaboration (INSDC) accession number of the BioProject(s) to which the BioSample belongs. bioproject accession bioproject_accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z bioproject accession slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. bioproject accession field GENEPIO:0001139 SAMN14180202 A data field which describes the identifier assigned to a BioSample in International Nucleotide Sequence Database Collaboration (INSDC) archives. biosample accession biosample_accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z biosample accession slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA. biosample accession field GENEPIO:0001142 SRR11177792 A data field which describes the Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the International Nucleotide Sequence Database Collaboration (INSDC). SRA accession SRA_accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z SRA accession slot Sequence Read Archive accession field Sequence Read Archive accession slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 DDBJ = DNA DataBank of Japan Example Guidance: Store the accession assigned to the submitted .run.. NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR. SRA accession field GENEPIO:0001145 MN908947.3 A data field which describes the GenBank/ENA/DDBJ identifier assigned to the sequence in the International Nucleotide Sequence Database Collaboration (INSDC) archives. GenBank accession GenBank/ENA/DDBJ accession GenBank_accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z GenBank accession slot GenBank/ENA/DDBJ accession field GenBank/ENA/DDBJ accession slot National Genetic Sequence Data Base accession field National Genetic Sequence Data Base accession slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 GenBank = National Genetic Sequence Data Base; ENA = European Nucleotide Archive; DDBJ = DNA DataBank of Japan Example Guidance: Store the accession returned from a GenBank/ENA/DDBJ submission (viral genome assembly). GenBank accession field GENEPIO:0001147 EPI_ISL_123456 An identifier data field which describes the Global Initiative on Sharing Avian Influenza Data (GISAID) accession number assigned to the sequence. GISAID accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z GISAID accession slot Global Initiative on Sharing Avian Influenza Data accession field Global Initiative on Sharing Avian Influenza Data accession slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Store the accession returned from the GISAID submission. GISAID accession field GENEPIO:0001149 SHK123456 A data field which describes the identifier assigned to a sample by a third party service provider. third party lab sample ID third party lab sample identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z third party lab sample ID slot third party lab sample identifier field third party lab sample identifier slot CanCOGeN SARS-CoV-2 Example Guidance: Store the sample identifier supplied by the third party services provider. third party lab sample ID field GENEPIO:0001150 An instance of the "sample collection and processing field category" that contains the "sample collection date field". A data field category which refers to sample collection and processing information fields. sample collection and processing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collection and processing slot category GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 sample collection and processing field category GENEPIO:0001151 untreated water GENEPIO:0001153 Public Health Agency of Canada A data field which describes the name of the organization with which the sample collector is affiliated. sample collected by sample_collected_by https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collected by slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. sample collected by field GENEPIO:0001154 treated water - ambient temperature GENEPIO:0001156 johnnyblogs@lab.ca A data field which describes the email address of the contact responsible for follow-up regarding the sample. sample collector contact email sample_collector_contact_email https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collector contact email slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The email address can represent a specific individual or laboratory. sample collector contact email field GENEPIO:0001158 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada A data field which describes the mailing address of the agency submitting the sample. sample collector contact address https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collector contact address slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code sample collector contact address field GENEPIO:0001159 Centers for Disease Control and Prevention A data field which describes the name of the agency that generated the sequence. sequence submitted by sequence_submitted_by https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequence submitted by slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. sequence submitted by field GENEPIO:0001162 epidemiology investigation data item GENEPIO:0001163 Unclear semantics and origin obsolete distribution event true GENEPIO:0001164 obsolete supply point / event true GENEPIO:0001165 RespLab@lab.ca A data field which describes the email address of the contact responsible for follow-up regarding the sequence. sequence submitter contact email https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequence submitter contact email slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The email address can represent a specific individual or laboratory. sequence submitter contact email field GENEPIO:0001167 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada A data field which describes the mailing address of the agency submitting the sequence. sequence submitter contact address https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequence submitter contact address slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code sequence submitter contact address field GENEPIO:0001168 well water - treated GENEPIO:0001169 Well water - untreated GENEPIO:0001170 organism datum http://purl.obolibrary.org/obo/GENEPIO_0001171 http://purl.obolibrary.org/obo/OBI_0100026 http://purl.obolibrary.org/obo/PATO_0000047 GENEPIO:0001171 a role which inheres in an organism and is realized by the process of being alive organism role GENEPIO:0001172 isolate organism role GENEPIO:0001174 2020-03-19 A data field which describes the date on which the sample was collected. sample collection date sample_collection_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collection date slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Record the collection date accurately in the template. Required granularity includes year, month and day. Before sharing this data, ensure this date is not considered identifiable information. If this date is considered identifiable, it is acceptable to add .jitter. to the collection date by adding or subtracting calendar days. Do not change the collection date in your original records. Alternatively, ”received date” may be used as a substitute in the data you share. The date should be provided in ISO 8601 standard format .YYYY-MM-DD.. sample collection date field GENEPIO:0001175 animal role GENEPIO:0001177 year A data field which describes the precision to which the "sample collection date" was provided. sample collection date precision https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collection date precision slot Monkeypox CanCOGeN SARS-CoV-2 Used to further describe the .sample collection date field. [GENEPIO:0001174]. Example Guidance: Provide the precision of granularity to the .day., .month., or .year. for the date provided in the .sample collection date. field. The .sample collection date. will be truncated to the precision specified upon export; .day. for .YYYY-MM-DD., .month. for .YYYY-MM., or .year. for .YYYY.. sample collection date precision field GENEPIO:0001179 2020-03-20 A data field which describes the date on which the sample was received. sample received date sample_received_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample received date slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The date the sample was received by a lab that was not the point of collection. ISO 8601 standard .YYYY-MM-DD.. sample received date field GENEPIO:0001181 South Africa [GAZ:00001094] A data field which describes the country of origin of the sample. geo_loc name (country) geographical location country name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc name (country) slot geographical location country name field geographical location country name slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the country name from the pick list in the template geo_loc name (country) field GENEPIO:0001182 plant role GENEPIO:0001183 Damion Dooley taxonomic datum GENEPIO:0001185 Western Cape A data field which describes the state, province, or territory of origin of the sample. geo_loc name (state/province/territory) geographical location state or province or territory name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc name (state/province/territory) slot geographical location state or province or territory name field geographical location state or province or territory name slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz geo_loc name (state/province/territory) field GENEPIO:0001186 A course of treatment designed to resolve an infectious disease Damion Dooley infectious disease treatment GENEPIO:0001187 This is a collection of drugs used to test antimicrobial resistance. This is a class of chemicals by use. They are organized more indirectly in CHEBI via 'has role' some 'antimicrobial agent'. Note: NCBI provides special requirements for antibiotic test-selection for BETA-LACTAMASE, see https://www.ncbi.nlm.nih.gov/biosample/docs/beta-lactamase/ Damion Dooley note: Used http://cts.fiehnlab.ucdavis.edu/conversion/batchConvert to convert antibiotic name to CHEBI entries. 60% match, some matches off, had to curate hits manually. Note that this is a longer list of antibiotics that we will need to incorporate, perhaps through ARO: https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/?format=txt Damion Dooley antimicrobial resistance test drug GENEPIO:0001189 Vancouver A data field which describes the city of origin of the sample. geo_loc name (city) geographical location city name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc name (city) slot geographical location city name field geographical location city name slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz geo_loc name (city) field GENEPIO:0001191 Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] A data field which describes the taxonomic name of the organism. organism https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z organism slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Put the genus and species (and subspecies if applicable) of the bacteria, if known. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. organism field GENEPIO:0001192 Damion Dooley Judgements here are marked down after an agent's (doctor/veterenary) analysis of symptoms. analytic datum GENEPIO:0001193 Damion Dooley http://purl.obolibrary.org/obo/DOID_4 obsolete: type of illness true GENEPIO:0001196 A specimen which has been confirmed by laboratory test(s) to contain a disease-causing agent such as a pathogen Damion Dooley specimen with confirmed presence of disease agent GENEPIO:0001198 Diagnostic testing [GENEPIO:0100002] A data field which describes the reason that the sample was collected. purpose of sampling purpose_of_sampling https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z purpose of sampling slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select a value from the pick list in the template. purpose of sampling field GENEPIO:0001200 Screening of bat specimens in museum collections. A data field which describes additional information pertaining to the reason the sample was collected. purpose of sampling details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z purpose of sampling details slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a free text description of the sampling strategy or samples collected. purpose of sampling details field GENEPIO:0001202 Switch Health A data field which describes the name of the third party company or laboratory that provided services. third party lab service provider name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z third party lab service provider name slot CanCOGeN SARS-CoV-2 Example Guidance: Provide the full, unabbreviated name of the company or laboratory. third party lab service provider name field GENEPIO:0001204 swab A data field which describes the type of specimen submitted to the National Microbiology Laboratory (NML) for testing. NML submitted specimen type National Microbiology Laboratory submitted specimen type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z NML submitted specimen type slot National Microbiology Laboratory submitted specimen type field National Microbiology Laboratory submitted specimen type slot Monkeypox CanCOGeN SARS-CoV-2 Example Guidance: This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. NML submitted specimen type field GENEPIO:0001205 dietary restriction GENEPIO:0001206 A person which has a patient care role. Damion Dooley patient type GENEPIO:0001208 obsolete: mother true GENEPIO:0001209 Specimen sampling methods testing A data field which describes the relationship of the current specimen to the specimen/sample previously submitted to the repository. Related specimen relationship type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z Related specimen relationship type slot Monkeypox CanCOGeN SARS-CoV-2 Example Guidance: Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. Related specimen relationship type field GENEPIO:0001211 Blood [UBERON:0000178] A data field which describes the substance obtained from an anatomical part of an organism. anatomical material anatomical_material https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z anatomical material slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a descriptor if an anatomical material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank. anatomical material field GENEPIO:0001212 NCBI BioSample depth:1 lookup A subject disease outcome is an assessment of the persistence of a given disease course in a subject (patient) Damion Dooley Note that this is closely related to OGMS_0000063 "disease course" that lists chronic, progressive, transient and accute processes. subject disease outcome GENEPIO:0001214 Nasopharynx (NP) [UBERON:0001728] A data field which describes the anatomical part of an organism. anatomical part anatomical_part https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z anatomical part slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a descriptor if an anatomical part was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank. anatomical part field GENEPIO:0001216 Feces [UBERON:0001988] A data field which describes the substance excreted/secreted from an organism. body product body_product https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z body product slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a descriptor if a body product was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank. body product field GENEPIO:0001217 treated water - warm/hot GENEPIO:0001219 jacuzzi water GENEPIO:0001220 spa water GENEPIO:0001221 whirlpool water GENEPIO:0001222 A host datum is a datum that pertains to infection-related information about an organism (animal or human) who is likely bearing a pathogen Damion Dooley patient as host datum GENEPIO:0001223 Soil, water, sewage, door handle, bed handrail, face mask, etc. Example input: Face mask [OBI:0002787] A data field which describes the substance obtained from the natural or man-made environment. environmental material environmental_material https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z environmental material slot GRDI Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a descriptor if an environmental material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank. environmental material field GENEPIO:0001224 pregnancy history item GENEPIO:0001225 date of conception GENEPIO:0001226 Damion Dooley lifespan history record GENEPIO:0001227 http://purl.obolibrary.org/obo/FOODON_03450002 obsolete: food cooking method true GENEPIO:0001228 http://purl.obolibrary.org/obo/FOODON_03470107 obsolete: food preservation method true GENEPIO:0001229 infectious disease case datum GENEPIO:0001231 laboratory data GENEPIO:0001232 Hospital, wet market, bat cave, etc. Example input: Hospital [ENVO:00002173] A data field which describes an environmental location as a site in the natural or built environment. environmental site environmental_site https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z environmental site slot GRDI PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a descriptor if an environmental site was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank. environmental site field GENEPIO:0001234 Swab [GENEPIO:0100027] A data field which describes the instrument or container used to collect the sample. collection device collection_device https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z collection device slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a descriptor if a collection device was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank. collection device field GENEPIO:0001236 Damion Dooley specimen record GENEPIO:0001237 The type of material from which the specimen was obtained. Specimens are usually categorized as food, body products or tissues, or environmental material. Damion Dooley specimen type (host or environmental context) specimen source material category GENEPIO:0001238 Organism has a symbiotic relationship with host symbiotic role GENEPIO:0001239 http://purl.obolibrary.org/obo/GENEPIO_0000113 obsolete: NCBI BioSample attribute package true GENEPIO:0001240 Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0000025 http://purl.obolibrary.org/obo/GENEPIO_0000028 obsolete: host sample material true GENEPIO:0001241 Bronchoalveolar lavage (BAL) [GENEPIO:0100032] A data field which describes the process used to collect the sample. collection method collection_method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z collection method slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a descriptor if a collection method was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank. collection method field GENEPIO:0001243 SC2SamplingProtocol 1.2 A data field which describes the name and version of a particular protocol used for sampling. collection protocol https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z collection protocol slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and version of the protocol used to collect the samples. collection protocol field GENEPIO:0001244 Damion Dooley food specimen detail GENEPIO:0001245 patient specimen GENEPIO:0001246 environmental NCBI Biosample: environmental (swab or sampling) environmental specimen GENEPIO:0001247 A specimen extracted from an animal Damion Dooley animal specimen GENEPIO:0001248 built environment specimen GENEPIO:0001249 food specimen GENEPIO:0001250 natural environment specimen GENEPIO:0001251 The type of person a patient had epidemiological (i.e. close proximity) contact with. Damion Dooley exposure event person GENEPIO:0001253 Virus passage [GENEPIO:0100039] A data field which describes any processing applied to the sample during or after receiving the sample. specimen processing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z specimen processing slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in .lab host., .passage number., and .passage method. fields. If none of the processes in the pick list apply, put .not applicable.. specimen processing field GENEPIO:0001255 Vero E6 cell line [BTO:0004755] A data field which describes the name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. lab host https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z lab host slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Type of cell line used for propagation. Select a value form the pick list. If not passaged, put .not applicable.. lab host field GENEPIO:0001257 Damion Dooley An exposure group statistics record is a sumary of disease outbreak statistics on a certain date of a group of humans or animals potentially exposed to a pathogen. exposure group statistics record GENEPIO:0001258 symptom history item GENEPIO:0001259 Damion Dooley health state record GENEPIO:0001260 http://purl.obolibrary.org/obo/NCIT_C17627 obsolete: swab true GENEPIO:0001261 3 A data field which describes the number of passages. passage number https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z passage number slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide number of known passages. If not passaged, put .not applicable. passage number field GENEPIO:0001262 [WHICH DEFINITION?] See http://medical-dictionary.thefreedictionary.com/aspirate Damion Dooley obsolete: fluid - aspirate true GENEPIO:0001264 AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain. A data field which describes how the organism was passaged. passage method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z passage method slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Free text. Provide a short description. If not passaged, put .not applicable.. passage method field GENEPIO:0001266 RNA (Total) [OBI:0000895] A data field which describes the biomaterial extracted from samples for the purpose of sequencing. biomaterial extracted https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z biomaterial extracted slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the biomaterial extracted from the pick list in the template. biomaterial extracted field GENEPIO:0001267 Plant rinse is a rinse derived from plant material from one or more plants. Damion Dooley plant rinse GENEPIO:0001268 An instance of the "host information field category" that contains the "host (scientific name) field". A data field category which refers to host information fields. host information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host information slot category GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 host information field category GENEPIO:0001269 Damion Dooley outbreak animal exposure event location GENEPIO:0001270 Damion Dooley animal exposure process GENEPIO:0001271 Damion Dooley animal exposure event by material GENEPIO:0001272 Damion Dooley exposure by human contact GENEPIO:0001273 Damion Dooley unnecessary distinction obsolete: human exposure activity type true GENEPIO:0001274 Damion Dooley outbreak human exposure event location GENEPIO:0001275 A process in which one or more humans may be exposed to one or more contagious human infectious disease carriers. Damion Dooley human to human exposure process GENEPIO:0001276 water exposure by source GENEPIO:0001277 human water activity GENEPIO:0001286 This list would be customized to include organizations local to an application's software installation. It is an example of a set of ontology terms that would best be organized by a central authority if federated installations need to share investigator contact info for example. health authority GENEPIO:0001287 order: HP:0000118 # symptom FLU:0000976 # onset GENEPIO:0001789 # cessation GENEPIO:0001784 # duration Damion Dooley symptom record GENEPIO:0001289 A visual pattern caused by DNA fragments concentrated in stratefied bands in a Pulsed-field gel electrophoresis (PFGE) gel plate. PFGE pattern GENEPIO:0001291 phage type salmonella (DT) GENEPIO:0001292 phage type e-coli 0157 (PT) GENEPIO:0001293 Damion Dooley sequence record GENEPIO:0001297 A type of built structure that is suspected to be related to an outbreak investigation. Damion Dooley outbreak exposure event location http://purl.obolibrary.org/obo/ENVO_00000070 GENEPIO:0001302 Damion Dooley lab test history record GENEPIO:0001338 obsolete: earth surface true GENEPIO:0001342 A data specification is a specification of a data structure that can hold a categorical, textual or numeric variable, or that has such variables or other data structures as component parts. A data standard, may be defined as a data specification, but a data specification isn't necessarily a formal or de-facto data standard - it would have to be sanctioned by a community of users and developers to take on that status. Damion Dooley data specification GENEPIO:0001356 A specimen history item is a time-related datum about a particular specimen Damion Dooley specimen history item GENEPIO:0001386 Human [NCBITaxon:9606] A host field which describes the commonly used name of the host. host (common name) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host (common name) slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Common name or scientific name are required if there was a host. Common name examples e.g. human, bat. Select a value from the pick list. If the sample was environmental, put .not applicable.. host (common name) field GENEPIO:0001387 Homo sapiens [NCBITaxon:9606] A host field which describes the taxonomic or scientific name of the host. host (scientific name) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host (scientific name) slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Common name or scientific name are required if there was a host. Scientific name examples e.g. Homo sapiens. Select a value from the pick list. If the sample was environmental, put .not applicable.. host (scientific name) field GENEPIO:0001388 Asymptomatic [NCIT:C3833] A host field which describes the health status of the host at the time of sample collection. host health state https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host health state slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, select a value from the pick list. host health state field GENEPIO:0001389 Hospitalized (ICU) [GENEPIO:0100046] A host data field which describes additional information pertaining to the health or disease status of the host at time of collection. host health status details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host health status details slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, select a value from the pick list. host health status details field GENEPIO:0001390 Recovered [NCIT:C49498] A host data field which describes the disease outcome in the host. host health outcome https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host health outcome slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 Example Guidance: If known, select a value from the pick list. host health outcome field GENEPIO:0001391 COVID-19 [MONDO:0100096] A host data field which describes the name of the disease experienced by the host. host disease host_disease https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host disease slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: This field is only required if there was a host. If the host was a human select COVID-19 from the pick list. If the host was asymptomatic, this can be recorded under “host health state details”. .COVID-19. should still be provided if patient is asymptomatic. If the host is not human, and the disease state is not known or the host appears healthy, put “not applicable”. host disease field GENEPIO:0001392 79 A host data field which describes the age of the host at the time of sampling. host age https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host age slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, provide age. Age-binning is also acceptable. host age field GENEPIO:0001393 year [UO:0000036] A host data field which describes the units used to measure the host's age. host age unit https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host age unit slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, provide the age units used to measure the host's age from the pick list. host age unit field GENEPIO:0001394 50 - 59 [GENEPIO:0100054] A host data field which describes the age category of the host at the time of sampling. host age bin https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host age bin slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. host age bin field GENEPIO:0001395 Male [NCIT:C46109] A host data field which describes the gender of the host at the time of sample collection. host gender https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host gender slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, select a value from the pick list. host gender field GENEPIO:0001396 South Africa [GAZ:00001094] A host geographical location field which describes the country where the host resides. host residence geo_loc name (country) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host residence geo_loc name (country) slot host residence geographical location country name field host residence geographical location country name slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, select a value from the pick list. host residence geo_loc name (country) field GENEPIO:0001397 Quebec A host geographical location field which describes the state or province or territory of residence of the host. host residence geo_loc name (state/province/territory) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host residence geo_loc name (state/province/territory) slot host residence geographical location state or province or territory name field host residence geographical location state or province or territory name slot Monkeypox Monkeypox-International CanCOGeN SARS-CoV-2 Example Guidance: Select the province/territory name from pick list provided in the template. host residence geo_loc name (state/province/territory) field GENEPIO:0001398 BCxy123 A host data field which describes the unique identifier by which each host can be referred to. host subject ID host subject identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host subject ID slot host subject identifier field host subject identifier slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward. host subject ID field GENEPIO:0001399 2020-03-16 A data field which describes the date on which the symptoms began or were first noted. symptom onset date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z symptom onset date slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, provide the symptom onset date in ISO 8601 standard format .YYYY-MM-DD.. symptom onset date field GENEPIO:0001400 Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] A data field which describes the perceived change in function or sensation (loss, disturbance or appearance) indicative of a disease, reported by a patient. Generally, "symptoms" are subjective and reported by the patient, while "signs" are observed and reported by a clinician. However, data collected using case report forms are usually relayed by the patient and thus both are deamed "reported by a patient" in this definition. signs and symptoms https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z signs and symptoms slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select all of the symptoms experienced by the host from the pick list. signs and symptoms field GENEPIO:0001401 Asthma [HP:0002099] A data field which describes a medical condition that existed prior to the current infection (pre-existing condition) or a variable associated with an increased risk of disease or infection (risk factor). pre-existing conditions and risk factors https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z pre-existing conditions and risk factors slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors field GENEPIO:0001402 Acute respiratory failure [MONDO:0001208] A data field which describes medical complications that are believed to have occurred as a result of host disease. complications https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z complications slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select all of the complications experienced by the host from the pick list. complications field GENEPIO:0001403 An instance of the "host vaccination information field category" that contains the "host vaccination status field". A data field category which refers to host vaccination information fields. host vaccination information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host vaccination information slot category Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 host vaccination information field category GENEPIO:0001404 Fully Vaccinated [GENEPIO:0100100] A data field which describes the vaccination status of the host. host vaccination status https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host vaccination status slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Statuses associated with this field: fully vaccinated, partially vaccinated, or not vaccinated. Example Guidance: Select the vaccination status of the host from the pick list. host vaccination status field GENEPIO:0001406 2 A data field which describes the number of doses of the vaccine received by the host. number of vaccine doses received https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z number of vaccine doses received slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Record how many doses of the vaccine the host has received. number of vaccine doses received field GENEPIO:0001409 An instance of the "host exposure information field category" that contains the "exposure event field". A data field category which refers to host exposure information fields. host exposure information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host exposure information slot category Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 host exposure information field category GENEPIO:0001410 South Africa [GAZ:00001094] A geographical data field which describes the country where the host was likely exposed to the causative agent of the illness. location of exposure geo_loc name (country) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z location of exposure geo_loc name (country) slot location of exposure geographical location country name field location of exposure geographical location country name slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: This location pertains to the country the host was believed to be exposed, and may not be the same as the host's country of residence. If known, provide the country name from the pick list. location of exposure geo_loc name (country) field GENEPIO:0001411 New York City A geographical data field which describes the name of the city that was the destination of most recent travel. destination of most recent travel (city) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z destination city of most recent travel field destination city of most recent travel slot destination of most recent travel (city) slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz destination of most recent travel (city) field GENEPIO:0001412 California A geographical data field which describes the name of the province that was the destination of most recent travel. destination of most recent travel (state/province/territory) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z destination of most recent travel (state/province/territory) slot destination state or province or territory of most recent travel field destination state or province or territory of most recent travel slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz destination of most recent travel (state/province/territory) field GENEPIO:0001413 United Kingdom [GAZ:00002637] A geographical data field which describes the name of the country that was the destination of most recent travel. destination of most recent travel (country) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z destination of most recent travel (country) slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz destination of most recent travel (country) field GENEPIO:0001414 2020-03-16 A date field which describes the date of an individual's most recent departure from their primary residence (at time of data collection) on a journey to one or more other locations. most recent travel departure date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z most recent travel departure date slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the travel departure date in ISO 8601 standard format .YYYY-MM-DD.. most recent travel departure date field GENEPIO:0001415 2020-04-26 A date field which describes the date of an individual's most recent return to some residence from a journey originating at that residence. most recent travel return date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z most recent travel return date slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the travel return date in ISO 8601 standard format .YYYY-MM-DD.. most recent travel return date field GENEPIO:0001416 Canada, Vancouver; USA, Seattle; Italy, Milan A data field which describes an individuals travel history in last six months. travel history https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z travel history slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Specify the countries (and more granular locations if known) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semicolon. Provide as free text. travel history field GENEPIO:0001417 Mass Gathering [GENEPIO:0100237] A data field which describes an event leading to exposure. exposure event https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z exposure event slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, select the exposure event from the pick list. exposure event field GENEPIO:0001418 Direct (human-to-human contact) [TRANS:0000001] A data field which describes the exposure transmission contact type. exposure contact level https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z exposure contact level slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select direct or indirect exposure from the pick list. exposure contact level field GENEPIO:0001419 Patient [OMRSE:00000030] A data field which describes the role of the host in relation to the exposure setting. host role https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host role slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. host role field GENEPIO:0001420 Damion Dooley diagnostic test GENEPIO:0001421 Damion Dooley obsolete: sample datum true GENEPIO:0001422 A laboratory sequencing datum is a datum related to the sequencing assay process applied to an isolate. Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0001681 obsolete: laboratory sequencing datum true GENEPIO:0001423 genomic sequencing annotation datum GENEPIO:0001424 Damion Dooley ISSUE: lab test results are appropriate to lab test types. Logic around that? lab test record GENEPIO:0001425 sequencing assembly datum GENEPIO:0001426 A container id is an identifier that refers to a container object about a patient specimen. Container ids are referenced in clinical patient records reported to be suspect, or lab test results. Damion Dooley container record GENEPIO:0001427 Damion Dooley identifier of a person with the context of a health care system health care personal identifier GENEPIO:0001428 Healthcare Setting [GENEPIO:0100201] A data field which describes the setting leading to exposure. exposure setting https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z exposure setting slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. exposure setting field GENEPIO:0001429 A strain identifier is the unique microbial or eukaryotic strain name from a reference database that a sample has been matched to. Damion Dooley strain identifier GENEPIO:0001430 A line list is a collection of suspected or known disease outbreak cases. It may also include details about healthy patients associated with an exposure event (picnic, concert etc.) who have been interviewed in order to compare food intake, assess risk factors, etc. Note that the health status of people associated with an exposure event can change from healthy or unknown status, to ill patient. Damion Dooley line list object GENEPIO:0001431 Host role - Other: Bus Driver A data field which describes additional host exposure information. exposure details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z exposure details slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Free text description of the exposure. exposure details field GENEPIO:0001432 This class is a temporary holding bin for items that need a class hierarchy home, definition, and/or subclass items. Some classes have subclasses that are currently disjoint in other ontologies like ENVO, so awaiting resolution on such issues. Damion Dooley awaiting ontology review GENEPIO:0001433 The IRIDA user ID is a user account identifier provided by the IRIDA.ca system. Damion Dooley GENEPIO:0001434 An instance of the "host reinfection information field category" that contains the "prior infection isolate field". A data field category which refers to host reinfection information fields. host reinfection information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host reinfection information slot category Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 host reinfection information field category GENEPIO:0001435 Prior infection [GENEPIO:0100234] A data field which describes whether there was prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. prior SARS-CoV-2 infection https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 infection slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, provide infromation about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. prior SARS-CoV-2 infection field GENEPIO:0001436 SARS-CoV-2/human/USA/CA-CDPH-001/2020 A data field which describes the identifier of the isolate found in the prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. prior SARS-CoV-2 infection isolate https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 infection isolate ID slot prior SARS-CoV-2 infection isolate identifier field prior SARS-CoV-2 infection isolate identifier slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the isolate name of the most recent prior infection. Structure the .isolate. name to be ICTV/INSDC compliant in the following format: .SARS-CoV-2/host/country/sampleID/date.. prior SARS-CoV-2 infection isolate ID field GENEPIO:0001437 2021-01-23 A data field which describes the date of diagnosis of the prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. prior SARS-CoV-2 infection date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 infection date slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format .YYYY-MM-DD.. prior SARS-CoV-2 infection date field GENEPIO:0001438 Prior antiviral treatment [GENEPIO:0100037] A data field which describes whether there was prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) treatment with an antiviral agent. prior SARS-CoV-2 antiviral treatment https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 antiviral treatment slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, provide infromation about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. prior SARS-CoV-2 antiviral treatment field GENEPIO:0001439 Remdesivir A data field which describes the name of the antiviral treatment agent administered during the prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. prior SARS-CoV-2 antiviral treatment agent https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 antiviral treatment agent slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put .No treatment.. If multiple antiviral agents were administered, list them all separated by commas. prior SARS-CoV-2 antiviral treatment agent field GENEPIO:0001440 2021-01-28 A data field which describeds the date treatment was first administered during the prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. prior SARS-CoV-2 antiviral treatment date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 antiviral treatment date slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format .YYYY-MM-DD.. prior SARS-CoV-2 antiviral treatment date field GENEPIO:0001441 An instance of the "sequencing field category" that contains the "sequencing date field". A data field category which refers to sequencing information fields. sequencing, sequencing information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing information slot category sequencing slot category GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 sequencing field category GENEPIO:0001442 The count of healthy individuals or animals on a certain date/time from a group that was likely exposed to a pathogen Damion Dooley exposure group healthy count GENEPIO:0001443 The count of ill individuals or animals on a certain date/time from a group that was likely exposed to a pathogen Damion Dooley exposure group ill count GENEPIO:0001444 human general activity GENEPIO:0001445 Baseline surveillance (random sampling) [GENEPIO:0100005] A data field which describes the reason that the sample was sequenced. purpose of sequencing purpose_of_sequencing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z purpose of sequencing slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the .purpose of sampling. field. purpose of sequencing field GENEPIO:0001446 Screened for S gene target failure (S dropout) A data field which describes the description of why the sample was sequenced providing specific details. purpose of sequencing details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z purpose of sequencing details slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide an expanded description of why the sample was sequenced using pick list. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. purpose of sequencing details field GENEPIO:0001447 2021-04-26 A date field which describes the date the sample was sequenced. sequencing date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing date slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the sequencing date in ISO 8601 standard format .YYYY-MM-DD.. sequencing date field GENEPIO:0001448 XYZ_123345 A data field which describes user-specified identifier for the library prepared for sequencing. library ID library identifier library_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z library ID slot library identifier field library identifier slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. library ID field GENEPIO:0001449 300bp A data field which describes the length of the amplicon generated by polymerase chain reaction (PCR) amplification. amplicon size https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z amplicon size slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the amplicon size, including the units. amplicon size field GENEPIO:0001450 Nextera XT A data field which describes the name of the library preparation kit used to generate the library being sequenced. Some specification definitions may be more specific on the type of library preparation kit used (e.g. DNA). library preparation kit library_preparation_kit https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z library preparation kit slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name of the library preparation kit used. library preparation kit field GENEPIO:0001451 FAB06069 A data field which describes the barcode of the flow cell used for sequencing. flow cell barcode https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z flow cell barcode slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the barcode of the flow cell used for sequencing the sample. flow cell barcode field GENEPIO:0001452 Oxford Nanopore MinION [GENEPIO:0100142] A data field which describes the model of the sequencing instrument used. sequencing instrument sequencing_instrument https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing instrument slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select the sequencing instrument from the pick list. sequencing instrument field GENEPIO:0001453 1D_DNA_MinION, ARTIC Network Protocol V3 A data field which describes the name and version number of the sequencing protocol used. sequencing protocol name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing protocol name slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and version of the sequencing protocol. sequencing protocol name field GENEPIO:0001454 Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. A data field which describes the protocol used to generate the sequence. sequencing protocol sequencing_protocol https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing protocol slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: .Viral sequencing was performed following a tiling amplicon strategy using the <fill in> primer scheme. Sequencing was performed using a <fill in> sequencing instrument. Libraries were prepared using <fill in> library kit. . sequencing protocol field GENEPIO:0001455 AB456XYZ789 A data field which describes the manufacturer's kit number. sequencing kit number https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing kit number slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Alphanumeric value. sequencing kit number field GENEPIO:0001456 https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv A data field which describes the specifications of the primers (primer sequences, binding positions, fragment size generated, etc.) used to generate the amplicons to be sequenced. amplicon pcr primer scheme https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z amplicon pcr primer scheme slot amplicon polymerase chain reaction primer scheme field amplicon polymerase chain reaction primer scheme slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and version of the primer scheme used to generate the amplicons for sequencing. amplicon pcr primer scheme field GENEPIO:0001457 An instance of the "bioinformatics and QC metrics field category" that contains the "dehosting method field". A data field category which refers to bioinformatics and quality control (QC) metrics fields. bioinformatics and QC metrics https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z bioinformatics and QC metrics slot category bioinformatics and Quality Control metrics field category bioinformatics and Quality Control metrics slot category Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 PHA4GE QC Tag bioinformatics and QC metrics field category GENEPIO:0001458 Porechop 0.2.3 A data field which describes the method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. raw sequence data processing method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z raw sequence data processing method slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and version numbers of the software used to process the raw data. raw sequence data processing method field GENEPIO:0001459 Nanostripper 1.2.3 A data field which describes the method used to remove host reads from the pathogen sequence. dehosting method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z dehosting method slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and version number of the software used to remove host reads. dehosting method field GENEPIO:0001460 ncov123assembly3 A data field which describes the name of the consensus sequence. consensus sequence name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus sequence name slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and version number of the consensus sequence. consensus sequence name field GENEPIO:0001461 pathogenassembly123.fasta A data field which describes the user-defined filename of the FASTA file. assembly filename consensus sequence filename https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus sequence filename slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and version number of the consensus sequence FASTA file. consensus sequence filename field GENEPIO:0001462 /User/Documents/RespLab/Data/ncov123assembly.fasta A data field which describes the filepath of the consensus sequence file. consensus sequence filepath https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus sequence filepath slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the filepath of the consensus sequence FASTA file. consensus sequence filepath field GENEPIO:0001463 Ivar A data field which describes the name of the software used to generate the consensus sequence. consensus sequence software name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus sequence software name slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name of the software used to generate the consensus sequence. consensus sequence software name field GENEPIO:0001464 Damion Dooley An exposure can be narrowed down to a single date, or can be reasoned to exist with a lower and/or upper bound date. A single date exposure has lower and upper bound dates set as the same value. exposure history record GENEPIO:0001465 Damion Dooley isolate history record GENEPIO:0001466 Damion Dooley An outbreak date may have an official start, but because it might be ongoing, it may not have an end (yet). outbreak history record GENEPIO:0001467 Damion Dooley Needs to cover the various pregnancy events pregnancy history record GENEPIO:0001468 Damion Dooley Issue: a diagnosis is a set of diseases, each of which can be marked primary or secondary "Illness causality" with respect to a particular case? Requires a relation annotation. diagnosis record GENEPIO:0001469 1.3 A data field which describes the version of the software used to generate the consensus sequence. consensus sequence software version https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus sequence software version slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the version of the software used to generate the consensus sequence. consensus sequence software version field GENEPIO:0001470 Damion Dooley exposure event record GENEPIO:0001471 Damion Dooley hospitalization event record GENEPIO:0001472 95% A data field which describes the percentage of the reference genome covered by the sequenced data, to a prescribed depth. breadth of coverage value https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z breadth of coverage value slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide value as a percent. breadth of coverage value field GENEPIO:0001473 An exposure can be narrowed down to a single date, or can be reasoned to exist with a lower and/or upper bound date. A single date exposure has lower and upper bound dates set as the same value. exposure history item GENEPIO:0001474 400x A data field which describes the average number of reads representing a given nucleotide in the reconstructed sequence. depth of coverage value https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z depth of coverage value slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide value as a fold of coverage. depth of coverage value field GENEPIO:0001475 100x A data field which describes the threshold used as a cut-off for the depth of coverage. depth of coverage threshold https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z depth of coverage threshold slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the threshold fold coverage. depth of coverage threshold field GENEPIO:0001476 ABC123_S1_L001_R1_001.fastq.gz A data field which describes the user-specified filename of the read 1 (r1) FASTQ file. r1 fastq filename r1_fastq_filename https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z r1 fastq filename slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the r1 FASTQ filename. r1 fastq filename field GENEPIO:0001477 ABC123_S1_L001_R2_001.fastq.gz A data field which describes the user-specified filename of the read 2 (r2) FASTQ file. r2 fastq filename r2_fastq_filename https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z r2 fastq filename slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the r2 FASTQ filename. r2 fastq filename field GENEPIO:0001478 /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz A data field which describes the filepath of the read 1 (r1) FASTQ file. r1 fastq filepath https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z r1 fastq filepath slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the filepath of the r1 FASTQ file. r1 fastq filepath field GENEPIO:0001479 /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz A data field which describes the filepath of the read 2 (r2) FASTQ file. r2 fastq filepath https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z r2 fastq filepath slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the filepath of the r2 FASTQ file. r2 fastq filepath field GENEPIO:0001480 batch1a_sequences.fast5 A data field which describes the user-specified filename of the FAST5 file. fast5 filename fast5_filename https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z fast5 filename slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the FAST5 filename. fast5 filename field GENEPIO:0001481 /User/Documents/RespLab/Data/batch1a_sequences.fast5 A data field which describes the filepath of the FAST5 file. fast5 filepath https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z fast5 filepath slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the filepath of the FAST5 file. fast5 filepath field GENEPIO:0001482 387566 A data field which describes the number of total base pairs generated by the sequencing process. number of base pairs sequenced https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z number of base pairs sequenced slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a numerical value (no need to include units). number of base pairs sequenced field GENEPIO:0001483 38677 A data field which describes the file size of the assembled genome described as the number of base pairs. consensus genome length https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus genome length slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a numerical value (no need to include units). consensus genome length field GENEPIO:0001484 300 A data field which describes the number of N (unidentified nucleotide) symbols present in the consensus fasta sequence, per 100kbp of sequence. Ns per 100 kbp Ns per 100 kilobase pairs https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z Ns per 100 kbp slot Ns per 100 kilobase pairs field Ns per 100 kilobase pairs slot unidentified nucleotides per 100 kbp field unidentified nucleotides per 100 kbp slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a numerical value (no need to include units). Ns per 100 kbp field GENEPIO:0001485 NC_045512.2 A data field which describes the persistent, unique identifier of a genome database entry. reference genome accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z reference genome accession slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the accession number of the reference genome. reference genome accession field GENEPIO:0001486 hospital admission date GENEPIO:0001487 A date-time datum that marks the end of possible human or animal exposure to a pathogen agent, directly or indirectly. Damion Dooley exposure event end GENEPIO:0001488 A date-time datum that marks the start of a human or animal exposure event to a suspected pathogen agent, directly or indirectly. Damion Dooley This datum is NOT predicted as a function of pathogen and first symptom date. exposure event start GENEPIO:0001489 https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members A data field which describes the name and version number of the bioinformatics protocol used. bioinformatics protocol https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z bioinformatics protocol slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can be provided in an SOP or protocol. Provide the name and version number of the protocol, or a link if deposited in a protocol repository. bioinformatics protocol field GENEPIO:0001490 hospitalization history item GENEPIO:0001491 isolate history item GENEPIO:0001492 An outbreak date may have an official start, but because it might be ongoing, it may not have an end (yet). outbreak history item GENEPIO:0001493 hospital discharge date GENEPIO:0001494 A notification date is the date that an outbreak is suspected by a laboratory or other agency and is reported per outbreak detection guidelines. Damion Dooley notification date GENEPIO:0001495 An outbreak date is on which disease onset appears to have occured Damion Dooley outbreak date GENEPIO:0001496 An outbreak over date is the date on which a disease outbreak appears to have abated Damion Dooley outbreak over GENEPIO:0001497 test history item GENEPIO:0001498 An instance of the "lineage and variant information field category" that contains the "lineage/clade name field". A data field category which refers to lineage and variant information fields. lineage and variant information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z lineage and variant information slot category PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 lineage and variant information field category GENEPIO:0001499 lab test result date GENEPIO:0001500 B.1.1.7 A data field which describes the name of the lineage or clade. lineage/clade name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z lineage or clade name field lineage or clade name slot lineage/clade name slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the Pangolin or Nextstrain lineage/clade name. lineage/clade name field GENEPIO:0001501 Pangolin A data field which describe the name of the software used to determine the lineage/clade. lineage/clade analysis software name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z lineage or clade analysis software name field lineage or clade analysis software name slot lineage/clade analysis software name slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name of the software used to determine the lineage/clade. lineage/clade analysis software name field GENEPIO:0001502 2.1.10 A data field which describes the version of the software used to determine the lineage/clade. lineage/clade analysis software version https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z lineage or clade analysis software version field lineage or clade analysis software version slot lineage/clade analysis software version slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the version of the software used ot determine the lineage/clade. lineage/clade analysis software version field GENEPIO:0001503 Variant of Concern (VOC) [GENEPIO:0100083] A data field which describes the variant classification of the lineage/clade. variant designation https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z variant designation slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank. variant designation field GENEPIO:0001504 RT-qPCR RT-qPCR TaqPath assay: S gene target failure A data field which describes the evidence used to make the variant determination. variant evidence variant evidence details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z variant evidence details slot variant evidence slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: List the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. Example Guidance: Select whether the sample was screened using RT-qPCR or by sequencing from the pick list. variant evidence details field variant evidence field GENEPIO:0001506 An instance of the "pathogen diagnostic testing field category" that contains the "diagnostic pcr protocol field". A data field category which refers to pathogen diagnostic testing information fields. pathogen diagnostic testing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z pathogen diagnostic testing slot category Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 pathogen diagnostic testing field category GENEPIO:0001516 An instance of the "contributor acknowledgement field category" that contains the "authors field". A data field category which refers to contributor acknowledgement information fields. contributor acknowledgement https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z contributor acknowledgement slot category Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 contributor acknowledgement field category GENEPIO:0001517 Tejinder Singh, Fei Hu, Johnny Blogs A data field which describes the names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. authors https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z data authors slot data contributors fields data contributors slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Include the first and last names of all individuals that should be attributed, separated by a comma. data authors field GENEPIO:0001518 DataHarmonizer v1.4.3, PHA4GE v1.0.0 A data field which describes the DataHarmonizer software and template version provenance. DataHarmonizer provenance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z DataHarmonizer provenance slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The current software and template version information will be automatically generated in this field after the user utilizes the .validate. function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer provenance field GENEPIO:0001522 A data item that is a set of entities, referenced by mention, that don't necessarily have something in common. 0000-0002-8844-9165 0000-0002-9578-0788 2022-01-31T03:45:04Z While "enumeration" is a "data item" not everything referenced within an enumeration qualifies as a "data item". Not to be confused with "data set" which describes "data item"s of the same type that have something in common. data enumeration GENEPIO:0001523 An analytic datum which describes the observed or detectable signs, and experienced symptomps of an illness, injury, or condition. 0000-0002-9578-0788 https://en.wikipedia.org/wiki/Signs_and_symptoms 2022-01-31T23:08:50Z signs & symptoms signs and symptoms GENEPIO:0001532 A particular attribute (feature, quality or process history) of a food sample. Damion Dooley The underlying facets will be supplied from the FoodOn food ontology. food specimen datum GENEPIO:0001533 order: FOODON:03411564 # food source FOODON:00002381 # food product by organism FOODON:03311737 # processed food product NCIT:C71898 # brand name A food specimen type is a categorization of a food specimen, by the organism it is or came from, or by a class of food products. Damion Dooley food specimen specification GENEPIO:0001534 An agency that has reported a disease cluster. Damion Dooley disease cluster notification agency GENEPIO:0001535 This is a subset of OBI investigation identifier. It pertains only to NCBI Biosample projects Damion Dooley http://purl.obolibrary.org/obo/OBI_0001628 obsolete: NCBI BioProject ID true GENEPIO:0001536 The count of individuals or animals for which no health status is available on a certain date/time from a group that was likely exposed to a pathogen. Damion Dooley exposure group unknown health status count GENEPIO:0001537 A role which inheres in a person and is realized by the process of being in the context of civilization Damion Dooley person role GENEPIO:0001538 An exposed person role is the role a person takes on who has been exposed to a pathogen. In serious situations this may call for special treatment, e.g. quarantine. Damion Dooley exposed person role GENEPIO:0001541 Redundant with "term replaced by" entity. obsolete: parent-guardian role parent-guardian role true GENEPIO:0001543 Damion Dooley illness causality GENEPIO:0001548 pre-existing condition GENEPIO:0001550 To restore to the normal state after some pathologic process. Damion Dooley Dorland's Illustrated Medical Dictionary, 30th ed. improving recovering resolving health trend GENEPIO:0001551 Damion Dooley close interpersonal relationship exposure GENEPIO:0001552 Damion Dooley Found to be redudant with another term, deprecrated in favor of said term. obsolete: household exposure true GENEPIO:0001553 Damion Dooley exposure to individual with diarrhea GENEPIO:0001554 Damion Dooley other human exposure GENEPIO:0001555 Damion Dooley sexual contact exposure GENEPIO:0001556 Damion Dooley exposure via diaper changing (human fecal) GENEPIO:0001558 container identifier GENEPIO:0001559 PulseNet: Outbreak outbreak identifier GENEPIO:0001560 GENEPIO reference genome size GENEPIO:0001561 The assembly genome size is the sum of all lengths of a sequence assembly's contigs. Damion Dooley GENEPIO As noted in Quast documentation: " The total assembly size may increase (and in some cases exceeds the genome size) due to contaminants (see Chitsaz et al. (2011)), misassembled contigs, repeats, and hubs that contribute to multiple contigs. " assembly genome size GENEPIO:0001562 Identifier for a reference genome (used to build or compare an assembly) that is used in the genome browsers and in the community Damion Dooley GENEPIO reference genome identifier GENEPIO:0001563 Assembly QC The 'genome size delta ratio' is a ratio of the difference between a sample's genome assembly size and the size of a given reference genome, over the reference genome size. The formula: | (reference_genome_size - assembly_genome_size) | / reference_genome_size This yeilds a decimal / percentage ranging from 0 = exact length, to say .1 which is equivalent to a 10% variance. If the ratio is too far from a quality control ratio that depends on the species in question, this indicates a bad assembly or a mis-identified sample. Damion Dooley GENEPIO genome size delta ratio GENEPIO:0001564 Assembly QC This is the upper acceptable limit of the 'genome size delta ratio' with respect to a particular species. For Salmonella a 0.10 variance in length between an assembly size and a reference genome size may be acceptable. For E-coli a more generous 0.30 or .40 variance should be allowed, given the pathogenic subspecies’ highly dynamic genome. GENEPIO genome size delta ratio QC threshold GENEPIO:0001565 Assembly QC http://purl.obolibrary.org/obo/IAO_0000428 The contig N50 length QC threshold is a minimum length threshold that a contig N50 length datum should be above for good QC. A lower length is indicative of assembly problems (insufficient read depth) or a mismatched reference genome. Damion Dooley GENEPIO contig N50 length QC threshold GENEPIO:0001566 Assembly QC 2000 The contig N99 length QC threshold is the minimum length that a contig N99 or NG99 length datum can be for satisfactory QC. This threshold avoids having too many gene coding regions prematurely clipped inside short contigs. An assembly having 1% or more of its content in less than 2Kbp chunks is cause for concern. Bacterial genes are generally about 1Kbp in length. Damion Dooley GENEPIO contig N99 length QC threshold GENEPIO:0001567 lookup Homo sapiens The species of the host organism from which a specimen (pathogen) organism was obtained. Use the full taxonomic name, eg, "Homo sapiens". Damion Dooley subject organism (host) taxonomic species lookup GENEPIO:0001568 Assembly QC A single datum having to do with a metric for genomic sequence assembly quality control. A "quality control measurement" can be defined as a measurement that has some norm within a definable context, e.g. for a certain subspecies. It may be a calculated quantity. A "quality control metric" is an upper or lower bound threshold that a measurement is compared to. Surpassing the threshold may indicate an error situation. A "measure" can indicate an amount of activity, consumption, transformation, etc. but doesn't itself convey an over-stepping of bounds in the way that a metric does. Damion Dooley GENEPIO assembly quality control datum GENEPIO:0001569 Damion Dooley GSCID-BRC:Clinical/host-associated pathogen NCBI:Pathogen.cl clinical or host-associated pathogen Clinical/host-associated pathogen Pathogen.cl GENEPIO:0001570 Assembly QC http://purl.obolibrary.org/obo/IAO_0000428 The N99 length definition is identical to the N50 definition except that the threshold for determining the contigs is 1% of the nucleotides. This contig basepair length can be compared to a minimum threshold to determine if gene annotation (where contigs greater than say 2000bp are necessary) would generally succeed. Damion Dooley GENEPIO contig N99 GENEPIO:0001571 Assembly QC http://purl.obolibrary.org/obo/IAO_0000428 The upper threshold of contig counts that are acceptable in a genome assembly. This may vary based on the overall genome length and depth of coverage. A large contig count may indicate insufficient read coverage. Damion Dooley contig count QC threshold GENEPIO:0001572 Indicates how the knowledge derived from the project can be applied, and to what field(s). Damion Dooley's note: NAIAD GRCID-BRC has Project Relevance map to OBO Foundry Study Design (http://purl.obolibrary.org/obo/OBI_0500000) but this is a bit of a stretch. Damion Dooley https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project project relevance GENEPIO:0001573 agricultural project relevance GENEPIO:0001574 medical knowledge relevance GENEPIO:0001575 industrial processing relevance GENEPIO:0001576 evolution modelling relevance GENEPIO:0001577 environmental project relevance GENEPIO:0001578 model organism relevance GENEPIO:0001579 The NCBI BioProject model includes all datums associated with the current NCBI BioProject specification. Damion Dooley obsolete: NCBI BioProject model true GENEPIO:0001580 http://purl.obolibrary.org/obo/GENEPIO_0000147 obsolete: NCBI SRA model true GENEPIO:0001581 http://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ http://www.ncbi.nlm.nih.gov/biosample/docs/packages/Pathogen.cl.1.0/ Damion Dooley notes: NCBI doesn't quite make the distinction but it may be helpful to distinguish sample submission facilitator vs submitter/repository organization contact? So should we have a BioSample_submission_facilitator field and a BioSample_contact_information field? Damion Dooley Damion's note: There are a few different kinds of biosample, and required fields depend on the type selected. draft NCBI BioSample model - mixed clinical and environmental/food/other GENEPIO:0001582 monoisolate A monoisolate sample scope involves specimens from a single animal, cultured cell-line, inbred population, or possibly a heterogeneous population when a single genome assembly is generated from a pooled sample because multiple individuals are needed to collect enough material and an inbred line is not available; however, this situation is not preferred. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ monoisolate monoisolate sample scope GENEPIO:0001583 multiisolate A multiisolate sample scope contains multiple individuals that represent distinct specimen collections, a population (representative of a species). Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ This is often used for variation or phenotype and genotype studies. This should not be used when multiple genomes will be annotated. Eventually, multiple locus_tag prefixes will be able to be assigned to a single multiisolate genome sequencing project, but currently only a single prefix can be registered per project. Therefore, individual monoisolate projects need to be registered when more than one genome will be annotated. multiisolate sample scope GENEPIO:0001584 multispecies A multi-species sample scope involves a sample representing multiple species. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ multispecies sample scope GENEPIO:0001585 environment An environment sample scope indicates that the species content of the sample is not known. Generally, nucleic acid is directly isolated from an environmental sample for analysis. This is used for metagenome studies. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ environment sample scope GENEPIO:0001586 A synthetic sample scope involves a sample synthesized in a laboratory. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ synthetic sample scope GENEPIO:0001587 Damion Dooley single cell GENEPIO:0001588 other Other project objective: specify an objective not listed above Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ other project objective GENEPIO:0001590 Damion Dooley GSCID-BRC:environmental/food/other NCBI:Pathogen.env environmental, food or other pathogen environmental/food/other Pathogen.env GENEPIO:0001591 whole Whole: the project makes use of the whole sample material (most common case). Use this for whole genome sequencing studies, transcriptome studies that are not targeting specific loci, epigenetic studies of a genome, and metagenomes or unbiased transcriptome studies of metagenomes. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ whole genomic data capture GENEPIO:0001592 raw sequence reads A raw sequence reads project objective has the goal of submission of raw reads to SRA or Trace repositories Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ raw sequence read objective GENEPIO:0001593 sequence A sequence project objective has a goal of submission of sequence data to standard archival sequence databases (yielding accession.version identifiers; e.g., whole genome shotgun, cDNA sequences, transcript shotgun assemblies) Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ sequence project objective GENEPIO:0001594 analysis An "analysis project objective" indicates there was an other analysis not otherwise indicated, includes submission of BAM files. This defn. could be a negation of the "not otherwise indicated". Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ analysis objective GENEPIO:0001595 assembly Submission of genome assembly (AGP data) Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ assembly objective GENEPIO:0001596 annotation Sequence annotation data Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ sequence annotation objective GENEPIO:0001597 sequence variation Variation: identification of sequence variation data for submission to dbSNP or dbVAR Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ sequence variation project objective GENEPIO:0001598 epigenetic markers DNA methylation, histone modification, chromatin accessibility datasets Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ epigenetic markers objective GENEPIO:0001599 expression Expression: assays of transcript or protein existence or abundance Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ transcript or protein expression objective GENEPIO:0001600 maps Maps: non-sequence based map data; e.g., genetic, radiation hybrid, cytogenetic, etc. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ mapping objective GENEPIO:0001601 Phenotypic descriptive data. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ phenotypic observation data from specimen GENEPIO:0001602 select sequence if any sequence data is generated from this project. sequencing Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ sequencing project method GENEPIO:0001603 array Select Array if that is the primary method and no sequence data is submitted Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ array project method GENEPIO:0001604 mass spectrometry Select Mass Spectrometry if that is the primary method Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ mass spectrometry project method GENEPIO:0001606 order: NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C42775 # email address GENEPIO:0001756 # phone contact specification - person GENEPIO:0001607 A categorical investigation datum is a datum pertaining to some entity examined for scientific research or diagnostic purposes and which has a scope that is broader than one of the clinical, environmental or epidemiological domains. Damion Dooley investigation datum GENEPIO:0001608 An organism and its host share physical space but no evidence exists to determine if one benefits from this arrangement. commensal role GENEPIO:0001609 draft isolate details model GENEPIO:0001610 A subject age is the age since birth of a given organism that is involved in an investigation or study at a given time. Damion Dooley subject age GENEPIO:0001611 draft NCBI component model GENEPIO:0001612 draft IRIDA BioSample model GENEPIO:0001613 draft GenEpiO epidemiology case record GENEPIO:0001614 A subject description is a field containing additional information about an organism (related to an investigation, study and/or specimen) that is not included in other defined vocabulary fields. Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0001835 subject description host description GENEPIO:0001615 NCBI BioSample The host profile or identifiers text is the "identification or description of the specific individual from which this sample was obtained". Damion Dooley NCBI BioSample: isolate host profile or identifers GENEPIO:0001616 A subject identifier is an identifier of a subject organism within the context of a particular investigation, study, or specimen extraction event. Damion Dooley This varies in its type (numeric or string) and its central repository depending on its context (use in a particular application/instance). Note: GSCID-BRC specification states " 'Host' is not the preferred term since some specimens may lack any detectable pathogen". In other words, a person would technically (logically) only have a host identifier AFTER they have been diagnosed as having a pathogen. A health care personal identifier, or a case identifier would be better than a more ephemeral "host id" subject identifier GENEPIO:0001617 Name of disease in a subject that is related to a given investigation, study and/or specimen. Damion Dooley NIAID GSCID-BRC metadata working group Controlled vocabulary. Human specimen source: https://bioportal.bioontology.org/ontologies/DOID or https://www.ncbi.nlm.nih.gov/mesh/1000067 subject disease GENEPIO:0001618 INSDC term (top level) A categorical choice recorded when a measurement value was known to be recorded in the past but the observed value cannot be located or retrieved for some reason. NCBI Biosample: missing missing GENEPIO:0001619 INSDC term (top level) 'not applicable' is an appropriate value for the measure of femur length for a patient with a missing limb A categorical choice recorded when a measurable datum does not apply to a given context. Damion Dooley not applicable GENEPIO:0001620 INSDC term (lower level) A categorical choice recorded when a datum was not measured with respect to some entity during some process. NCBI Biosample: not collected not collected GENEPIO:0001621 draft isolate identifier model GENEPIO:0001622 draft GenEpiO isolate testing model GENEPIO:0001623 draft NCBI isolate source location model GENEPIO:0001624 draft GenEpiO isolate environment model GENEPIO:0001625 A subject disease stage is a measure of the acuteness of a subject organism's diagnosed disease, if any, at a given time in an investigation, study or specimen extraction event. Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0001835 subject disease stage GENEPIO:0001626 environmental datum GENEPIO:0001627 temperature of sample GENEPIO:0001628 de-novo assembly GENEPIO:0001629 http://purl.obolibrary.org/obo/GENEPIO_0000025 obsolete: sample body source true GENEPIO:0001630 contig pre-analysis minimum length QC threshold A 'contig length QC threshold' is an integer setting which can be applied by an algorithm to an array of assembly and annotation contig lengths to remove (filter out) all items less than the threshold value. The reduced array is used for calculation of statistics. Damion Dooley http://quast.bioinf.spbau.ru/manual.html QUAST specifies which of its report stats are affected by the "--min-contig" minimum contig length parameter. contig length QC threshold GENEPIO:0001631 The NG50 length is the same as the N50 length except that the length of the reference genome is used in the calculation rather than the assembly genome size. Damion Dooley "Note that N50 is calculated in the context of the assembly size rather than the genome size. Therefore, comparisons of N50 values derived from assemblies of significantly different lengths are usually not informative, even if for the same genome. To address this, the authors of the Assemblathon competition derived a new measure called NG50. The NG50 statistic is the same as N50 except that it is 50% of the known or estimated genome size that must be of the NG50 length or longer. This allows for meaningful comparisons between different assemblies. In the typical case that the assembly size is not more than the genome size, the NG50 statistic will not be more than the N50 statistic." - wikipedia contig NG50 GENEPIO:0001632 A contig length is the count of base pairs in a given sequence assembly contig. Damion Dooley contig length GENEPIO:0001633 Assembly QC http://purl.obolibrary.org/obo/IAO_0000428 Contig L50 is the number of contigs equal to or longer than contig N50. The length of the assembly itself is used in the calculation. Damion Dooley QUAST manual contig L50 GENEPIO:0001634 Assembly QC http://purl.obolibrary.org/obo/IAO_0000428 The LG99 count is like the L99 count except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths. Damion Dooley contig LG99 GENEPIO:0001635 An organism isolate datum is any datum pertaining to an isolate organism Damion Dooley obsolete: specimen from subject datum true GENEPIO:0001636 A product of an animal, as in blood, feces, sputum, etc. that has no particular anatomical site Damion Dooley animal body product GENEPIO:0001637 This is the scientific role or category that the subject organism or material has with respect to an investigation. Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0001237 obsolete: specimen source material category true GENEPIO:0001638 draft GenEpiO general information record GENEPIO:0001639 An antigenic formula is a string composed of codes representing categorized results of tests performed on various viral, bacterial or immune cell surface antigens. Damion Dooley antigenic formula http://medical-dictionary.thefreedictionary.com/antigen GENEPIO:0001640 lookup This is the taxonomic species descriptor of a specimen isolate (an organism found within a specimen.) Damion Dooley specimen organism taxonomy (species) GENEPIO:0001641 An identifier moe3l indicates an identifier, the organization it has been issued by, and the status of the identifier - whether it is a primary one, active or archaic. Damion Dooley identifier model GENEPIO:0001642 help:This should be populated with a selection from INSDC.org controlled vocabulary for providers: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/coll_dump.txt The curator organization name is the name of an organization that manages a given repository of entities (samples, isolates, sequences ...) Damion Dooley curator organization name GENEPIO:0001643 INSDC:institution_code:BRS IRIDA:ACK Agriculture and Agri-Food Canada GENEPIO:0001644 An isolate identifier is an identifier assigned to a given isolate by a particular agency that is handling or storing it. Damion Dooley isolate identifier GENEPIO:0001645 An identifier status describes the principle role of an identifier assigned to an entity by its curator or handler. An entity may have a number of identifiers assigned to it over time. An identifier may be phased-out as can happen when its content is transferred to another curator. Damion Dooley identifier status GENEPIO:0001646 GenEpiO A data protection role is a role (or user permission) that a user has with respect to particular data. A data server may be able to provide a protected(modified) dataset with metadata indicating what parts have a protection role with respect to the user requesting this information. A data protection role would be inherited from a user's relation to an entitiy to the entity's components or subclasses. Damion Dooley data protection role GENEPIO:0001647 An identifier used in the initial submission of content to a repository. original submission GENEPIO:0001648 This was created to help define a contributing organization to a repository. However this still needs organizing. The "collected_by" field is free text but contact name AND organization could be associated with this in controlled vocabulary. NCBI Contributing organization / project GENEPIO:0001649 food - liquid GENEPIO:0001650 draft NCBI BioSample identifier model GENEPIO:0001651 An INSDC institution code is an identifier of an organization from a list of sequence repository organizations managed by INSDC. Damion Dooley http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier INSDC institution code GENEPIO:0001652 draft IRIDA epidemiological case model GENEPIO:0001653 An identifier that had been used previously but is no longer promoted. Damion Dooley previous (archaic) identifier GENEPIO:0001654 A geographical location datum is a datum that refers to a real, hypothesized or fanciful spatial location Damion Dooley geographic location datum GENEPIO:0001655 A categorical tree specification datum is a categorical value specification which takes its value from the ontology URI identifier of any one of its subclass items; these may be organized in a hierarchy. Damion Dooley http://purl.obolibrary.org/obo/OBI_0001930 A categorical tree specification datum may have its own URI identifier as its value. This could be interpreted to mean that the datum was recorded but that no particular categorical subclass distinction was observed. This in effect makes the datum act as a boolean variable. obsolete: categorical tree specification true GENEPIO:0001656 Damion Dooley A geographic coordinate entity composed of both latitude and longitude components. latitude and longitude coordinate (ISO 6709) GENEPIO:0001657 order: NCIT:C25464 # country ENVO:00000005 # state / province etc. Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps" Damion Dooley draft NCBI BioSample geo_loc_name model GENEPIO:0001658 draft GenEpiO isolate sequencing model GENEPIO:0001659 A case ID is a unique identifier associated with a particular episode of care for an individual or animal. Damion Dooley case identifier GENEPIO:0001660 An animal that has had a substantial part of its reproductive organs removed surgically. Damion Dooley NCBI BioSample: neuter Not a PATO phenotypic sex catigorical value. neuter GENEPIO:0001661 NCBI BioSample 'pooled male and female' is a categorical value used when the male and female categories or levels of a factor are combined. If used to describe a single organism, then the organism will be one or the other. Not a PATO phenotypic sex catigorical value. Damion Dooley NCBI BioSample: 'pooled male and female' pooled male and female GENEPIO:0001662 A categorical choice recorded while the data for a given measurable datum has not finished being collected, is awaiting a conclusion, or has not yet been communicated. Damion Dooley undetermined in process GENEPIO:0001663 swimming / wading GENEPIO:0001664 Damion Dooley NECESSARY? : What details are categorical and what are freehand? This item was originally too broad; moved sub-items to Treatment. infection detail datum GENEPIO:0001665 This is problematic - its not clear if this is reporting that antibiotics were administered, or whether they are recommended as a result of diagnosis. Damion Dooley antibiotics required GENEPIO:0001666 The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. INSDC covers the spectrum of data raw reads, though alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations. Damion Dooley International Nucleotide Database Collaboration standard INSDC INSDC standard GENEPIO:0001667 Damion Dooley outcome of pregnancy associated with illness GENEPIO:0001668 INSDC term (lower level) a categorical choice indicating that information of an expected format was not given; a value may be given at the later stage. not provided GENEPIO:0001669 Damion Dooley stable health status http://purl.obolibrary.org/obo/GENEPIO_0002026 GENEPIO:0001670 induced abortion GENEPIO:0001671 live birth GENEPIO:0001672 Damion Dooley http://purl.obolibrary.org/obo/VT_0002292 obsolete: gestation duration (weeks) true GENEPIO:0001673 date of pregnancy outcome GENEPIO:0001674 contact specification - physician GENEPIO:0001675 obsolete: matrix - solid true GENEPIO:0001676 contact specification - parent/guardian GENEPIO:0001677 contact specification - patient GENEPIO:0001678 draft GenEpiO case epidemiology record GENEPIO:0001679 order: NCIT:C25464 # Country ENVO:00000005 # major administrative subdivision aka state/province/territory/region (via GenEpiO -> GAZ ) NCIT:C80234 # Municipality (via GenEpiO -> GAZ cities) NCIT:C25690 # Street Address NCIT:C25621 # postal code The address component of a contact specification. contact specification - address GENEPIO:0001680 GENEPIO_0001829 obsolete: draft IRIDA model true GENEPIO:0001681 A datum related to the sequencing assay process applied to an isolate. Damion Dooley laboratory sequencing datum http://purl.obolibrary.org/obo/OBI_0001901 http://purl.obolibrary.org/obo/OBI_0400103 GENEPIO:0001682 Damion Dooley host illness associated with GENEPIO:0001683 draft subject demographic specification K(1|2a|2ac|3|4|5|6|7|8|9|10|11|12|13|14|15|16|18a|18ab|19|20|22|23|24|26|27|28|29|30|31|34|37|39|40|41|42|43|44|45|46|47|49|50|51|52|53|54|56|96|55|74|82|84|85ab|85ac|87|92|93|95|97|98|100|101|102|103|X104|X105|X106) GENEPIO:0001684 E. coli K antigen specification 1 6 GENEPIO:0001685 other antigen specification GENEPIO:0001686 E. coli serotype specification GENEPIO:0001687 Damion's note: This will be converted to a categorical tree specification list of serovars by name or id asap. Salmonella serovar specification GENEPIO:0001688 A lab test specification indicates the inputs and outputs (results / conclusions) of a test. Damion Dooley test specification (1/2|1/2a|1/2b|1/2c|3a|3b|3c|4a|4ab|4b|4c|4d|4e|1|7) GENEPIO:0001689 listeria antigen GENEPIO:0001690 obsolete: matrix - fluid true GENEPIO:0001691 listeria serotype 1/2a GENEPIO:0001692 listeria serotype 1/2b GENEPIO:0001693 listeria serotype 1/2c GENEPIO:0001694 listeria serotype 1/2 GENEPIO:0001695 listeria serotype 3a GENEPIO:0001696 listeria serotype 3b GENEPIO:0001697 listeria serotype 4a GENEPIO:0001698 listeria serotype 4b GENEPIO:0001699 listeria serotype 4c GENEPIO:0001700 listeria serotype 4d GENEPIO:0001701 listeria serotype 4e GENEPIO:0001702 non-monocytogenes listeria antigen GENEPIO:0001703 listeria serotype 3c GENEPIO:0001704 textual test result GENEPIO:0001705 This is an organizational category for grouping parameters relevant to biomedical research projects. Damion Dooley obsolete: draft GenEpiO BioProject standard true GENEPIO:0001706 Damion Dooley NCBI BioSample: collection_code NCBI BioSample collection code GENEPIO:0001707 draft NCBI BioSample host model GENEPIO:0001708 food - solid GENEPIO:0001709 lab test datum GENEPIO:0001710 Xbal GENEPIO:0001711 Ascl GENEPIO:0001712 Smal GENEPIO:0001713 Blnl GENEPIO:0001714 Apal GENEPIO:0001715 Kpnl GENEPIO:0001716 Taxonomy below subspecies; sometimes used in viruses to denote subgroups taken from a single isolate. Damion Dooley NCBI Biosample subgroup GENEPIO:0001717 help:This is an optional additional subtype classification as per organism convention A viral subtype is a classification name for a virus according to some protocol. Damion Dooley NCBI BioSample viral subtype 1 1 GENEPIO:0001718 serotype specification GENEPIO:0001719 IRIDA An integer and character referring to a pattern of opaque or confluent lysis caused by a panel of bacteriophage infections e.g. 14a. Damion Dooley SNOMED: http://www.snomedbrowser.com/Codes/Details/272405002 phage type specification GENEPIO:0001720 obsolete: swab - food contact surface true GENEPIO:0001721 ATCC:26370 An NCBI culture collection is a composite identifier containing “institution code:collection code”. Annotation with a culture_collection qualifier implies that the sequence was obtained from a sample retrieved (by the submitter or a collaborator) from the indicated culture collection, or that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in the indicated culture collection. See the description for the proper format and list of allowed institutes, http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier. NCBI culture collection GENEPIO:0001722 UAM:Mamm:52179 The NCBI specimen voucher is an identifier composed of “institution code:collection code:specimen id” parts. In addition to a specimen identifier, it includes an institution-code (and optional collection-code) taken from a controlled vocabulary maintained by the INSDC that denotes the museum or herbarium collection where the specimen resides. INSDC:specimen_voucher NCBI specimen voucher http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier. GENEPIO:0001723 culture identifier GENEPIO:0001724 human; dog; horse The natural language (non-taxonomic) name of the type of organism (human or animal) that is the subject of a given investigation, study and/or specimen. Damion Dooley's note: as of 2017 this is a problematic field for NCBI Biosample because it is slotted into "host" field, yet field is listed as "host common name" which does not fit with requirement that scientific name be provided. Person: Damion Dooley subject organism common name GENEPIO:0001725 temperature of air - average daily GENEPIO:0001726 obsolete: swab - inanimate object surface true GENEPIO:0001727 obsolete: swab - meat true GENEPIO:0001728 obsolete: swab - rectal swab true GENEPIO:0001729 obsolete: swab - tissue true GENEPIO:0001730 unknown source GENEPIO:0001731 patient sample human clinical specimen GENEPIO:0001732 "environment (swab or sampling)" is a specific response for NCBI BioSample that could be mapped or unified with "environment sample" used elsewhere in GenEpiO Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0001246 obsolete: environmental (swab or sampling) true GENEPIO:0001733 avian - wild GENEPIO:0001734 avian - domesticated GENEPIO:0001735 human clinical specimen - invasive GENEPIO:0001736 In chemistry, pH is a numeric scale used to specify the acidity or basicity(alkalinity) of an aqueous solution Damion Dooley Wikipedia Normally falls within the bounds of 0 - 14 pH measurement GENEPIO:0001737 precipitation GENEPIO:0001738 The assembly and annotation objective is the set of objectives that assembly and annotation techniques (including instruments and software platforms) applied to a sample are meant to satisfy. This impacts on the quality control thresholds applied to the sequencing project. Damion Dooley assembly and annotation project objective GENEPIO:0001740 Damion Dooley line list row record GENEPIO:0001741 This class contains components under development for fulfilling GenEpiO and other standard data specifications. Components are relevant to epidemiological, laboratory, clinical or environmental pathogen sample data collection and analysis. Damion Dooley draft GenEpiO component record GENEPIO:0001742 region lookup:http://purl.obolibrary.org/obo/GAZ_00000448 A subnational region is a type of subnational entity similar to a nation's state, province, or territory. Damion Dooley subnational region GENEPIO:0001743 A data standard related to public health research and service delivery. Damion Dooley public health data standard GENEPIO:0001744 Damion Dooley 0D space GENEPIO:0001747 Reagent: material studied was obtained by chemical reaction, precipitation. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ reagent derived material from specimen GENEPIO:0001748 transcriptome Transcriptome: transcript and/or expression data. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ transcriptome data from specimen GENEPIO:0001749 proteome Proteome material is protein or peptide sequences. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ proteome data derived from specimen GENEPIO:0001750 purified chromosome Purified chromosome: one or more chromosomes or replicons were experimentally purified. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ purified chromosome from specimen GENEPIO:0001751 targeted locus/loci TargetedLocusLoci: capturing specific loci (gene, genomic region, bar code standard). Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ Targeted Locus Loci data capture GENEPIO:0001752 clone ends CloneEnds: capturing clone end data. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ clone end data capture GENEPIO:0001753 exome Exome: capturing exon-specific data. Damion Dooley NCBI BioSample https://www.ncbi.nlm.nih.gov/books/NBK54364/ exome specific data capture GENEPIO:0001754 random survey Sequences generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material Is this with respect to an isolate or a specimen derived culture? Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ random survey data capture GENEPIO:0001755 This is a collection of various human (and animal contact location) contact information specifications used in data standards. Damion Dooley contact specification GENEPIO:0001756 order: NCIT:C40978 # phone GENEPIO:0001896 # phone type contact specification - phone GENEPIO:0001757 Damion Dooley millimetres per day GENEPIO:0001758 obsolete: millisiemens true GENEPIO:0001759 Damion Dooley millisiemens per centimetre GENEPIO:0001760 Damion Dooley cubic metre per second GENEPIO:0001761 umol/kg Damion Dooley micromole per kilogram GENEPIO:0001762 Damion Dooley micromole per litre GENEPIO:0001764 Damion Dooley quality control record GENEPIO:0001765 Standard draft: describing the minimum information needed for submission to a public database. Damion Dooley 1 - standard draft GENEPIO:0001766 High quality draft: describing sequences with little to no manual review. Damion Dooley 2 - high quality draft GENEPIO:0001767 Improved high quality draft: in which data is either reviewed by people or machines to some extent to indicate that most of the genetic data is assembled correctly, but some errors may still be present. Damion Dooley 3 - improved high quality draft GENEPIO:0001768 Annotation-directed improvement: in which genetic information in various gene regions is represented as accurately as possible. Damion Dooley 4 - annotation-directed improvement GENEPIO:0001769 Non-contiguous finished: which includes sequences that have been reviewed by both people and machines and would be considered complete except for “recalcitrant regions” that are proving problematic for genome closure. Damion Dooley 5 - non-contiguous finished GENEPIO:0001770 Finished: which describes un-gapped complete sequences that have minimal errors, if any. The biology of the microbe will determine whether this finished genome consists of more than one chromosome. Damion Dooley 6 - finished GENEPIO:0001771 Assembly QC http://purl.obolibrary.org/obo/IAO_0000428 The NG99 length is the same as the N99 length except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths. Damion Dooley GENEPIO contig NG99 GENEPIO:0001773 Assembly QC http://purl.obolibrary.org/obo/IAO_0000428 Contig L50 is the number of contigs equal to or longer than contig N50. The length of the assembly itself is used in the calculation. Damion Dooley contig LG50 GENEPIO:0001774 Assembly QC http://purl.obolibrary.org/obo/IAO_0000428 Contig L99 is the number of contigs equal to or longer than contig N99. The length of the assembly itself is used in the calculation. Damion Dooley contig L99 GENEPIO:0001775 A subject age at time of specimen extraction is the age (since birth) of the organism at the time a given specimen was extracted. Damion Dooley subject age at time of specimen collection GENEPIO:0001776 A public health related data standard involving a particular species of pathogen. Damion Dooley pathogen specific data standard GENEPIO:0001777 The draft tuberculosis contextual data standard is a data standard for the collection of contextual information of a given tuberculosis case that pertain to typing, clinical treatment, and potential research questions. Damion Dooley draft tuberculosis contextual data standard 1 PulseNet:Outbreak GENEPIO:0001778 The PulseNet Canada Salmonella submission standard details the fields required in a PuseNet Canada pathogen submission report for Salmonella in spreadsheet format Damion Dooley draft PulseNet Canada Salmonella submission standard http://www.pulsenetinternational.org/assets/PulseNet/uploads/wgs/PND18-NCBI-Biosample-Submission.pdf GENEPIO:0001779 A PFGE pattern resulting from DNA fragmentation induced by the Xbal enzyme. PFGE Xbal pattern GENEPIO:0001780 A PFGE pattern resulting from DNA fragmentation induced by the Blnl enzyme. PFGE Blnl pattern GENEPIO:0001781 NLEP ID An NLEP ID is a unique identifier code for a sample registered with the Canadian "National Laboratory for Enteric Pathogens" (NLEP) Damion Dooley Pulsenet Canada spreadsheet. National Laboratory for Enteric Pathogens Identifier GENEPIO:0001782 PulseNet spreadsheet Date an uploaded sample was re-uploaded or had its metadata modified. Damion Dooley PulseNet: UploadModifiedDate upload modified date GENEPIO:0001783 A travel destination is a destination city (or populated place of some scale) which a given human has travelled to on a particular trip. Damion Dooley travel destination GENEPIO:0001784 A symptom duration is a date-time entity which is the duration (in hours or days or weeks etc.) that one or more symptoms persist for in a particular human or animal Damion Dooley This may be a calculated field if symptoms are reported to cease on a particular date. Often however symptom duration is reported more generally as a date or time range since cesation date is less certain. symptom duration GENEPIO:0001785 The city where a specimen was collected (taken) from a subject or environment Damion Dooley specimen collection location - city lookup GENEPIO:0001786 Damion Dooley obsolete: sample city true GENEPIO:0001787 This is the genus-level taxonomic name of an organism playing a pathogen role Damion Dooley genus of pathogen GENEPIO:0001788 This is the species-level taxonomic name of an organism playing a pathogen role Damion Dooley species of pathogen GENEPIO:0001789 A symptom cessation date is a date-time entity that marks the end of one or more reported symptoms pertaining to an episode of human or animal illness Damion Dooley symptom cessation date GENEPIO:0001790 This is a catch-all category for listing specimen related terms Damion Dooley specimen datum http://purl.obolibrary.org/obo/GENEPIO_0002105 http://purl.obolibrary.org/obo/OBI_0001616 GENEPIO:0001791 isolate identifier specification GENEPIO:0001792 The 'data obfuscated' role between a user and given data entails that the user is authorized to see particular fields that have been transformed consistently such that statistics performed on those fields would yeild the same results as statistics applied to the un-obfuscated data. The purpose of obfuscation is to prevent related individuals or organizations from being identified. Damion Dooley data obfuscated https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/ GENEPIO:0001793 The 'data aggregated' role between a user and given data entails that the user is authorized to see aggregated results (like the patient count) via preset reports, queries or views. The results are not obfuscated. Damion Dooley data aggregated GENEPIO:0001794 A 'limited data set' role between a user and given data entails that a user is authorized to see some of the fields but the remainder are withheld (or encrypted). Damion Dooley limited data set GENEPIO:0001795 help:In this dataset, selected data have been de-identified (anonymized) for access by dataset users. A 'de-identified data' role between a user and given data entails that the user is authorized to see only those fields (including those that are encrypted) which do not contain information that could be use to identify particular individuals (whether patients or medical practitioners) or potentially organizations in the case where an investigation may implicate them. Damion Dooley's note: There is a case in the "draft tuberculosis contextual data standard" that has this be a boolean selection. If a categorical field is linked directly, and it has no underlings, this indicates that it is being treated as a boolean feature. Damion Dooley Generally de-identified data should include HIPAA patient privacy fields as indicated in https://www.hipaa.com/hipaa-protected-health-information-what-does-phi-include/ de-identified data GENEPIO:0001796 A 'data protected' role between a user and given data entails that a user must be authorized in order to view that data. Damion Dooley data protected 1 1 GENEPIO:0001797 A datum containing the name of persons or institute who collected a given specimen. Damion Dooley https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ specimen collector GENEPIO:0001798 Damion Dooley NCBI BioSample culture identifier GENEPIO:0001799 A user identifier is an identifier provided as part of an authentication process of a client (user) to a service (server). User identifiers normally persist over time, in contrast to session identifiers which are temporary. Damion Dooley user identifier GENEPIO:0001800 sequence identifier GENEPIO:0001801 metagenomic species identification GENEPIO:0001802 Note: REPLACE WITH Citation: SIO_000174 ???? document citation identifier GENEPIO:0001803 organization identifier GENEPIO:0001804 collection identifier GENEPIO:0001805 variant calling / pathogen identification and clustering GENEPIO:0001806 isolate (pathogen) identification GENEPIO:0001807 http://purl.obolibrary.org/obo/OBI_0001616 obsolete: NCBI BioSample ID - true GENEPIO:0001808 1) Escherichia coli O104:H4 str. C227-11 clinical isolate 2010_333_NC-6 2) CD8+ T cells from female TSG6-knockout BALB/c mouse 3) Human metagenome isolated from urine of healthy female A specimen (or sample) title should be short and informative. Each specimen title must be unique in a submission. NCBI BioSample record documentation refers to a "BioSample title", stating that it is "auto-generated if one is not supplied by the submitter." This is distinct from any assigned BioSession accession, or other "external sample identifier" that may have been issued by the source database or repository. Damion Dooley specimen title GENEPIO:0001809 draft GenEpiO isolate source context GENEPIO:0001810 INSDC term (lower level) A categorical choice recorded when the data for a given measurable datum is available but not shared publicly because of information privacy concerns. restricted access GENEPIO:0001811 State (United States of America) GENEPIO:0001812 A health status trend is a short-term prognosis about whether health is improving, worsening or unchanging Damion Dooley health status trend datum GENEPIO:0001813 http://www.itis.gov The Integrated Taxonomic Information System (ITIS) contains authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. Damion Dooley Integrated Taxonomic Information System ITIS ITIS GENEPIO:0001818 https://www.nlm.nih.gov/mesh/meshhome.html MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. Damion Dooley Medical Subject Headings MSH MESH GENEPIO:0001819 https://ncit.nci.nih.gov/ncitbrowser/ The National Cancer Institute Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities. Damion Dooley National Cancer Institude Thesaurus NCI_Thesaurus NCIt NCIT GENEPIO:0001820 The NIFSTD ontology of the Neuroscience Information Framework is composed of a collection of OWL modules with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, organism, function and dysfunction. Damion Dooley https://wiki.nci.nih.gov/display/VKC/NIFSTD+Ontology NIFSTD GENEPIO:0001821 SNOMED CT is a large clinical health terminology product owned and distributed by SNOMED International. Damion Dooley http://www.snomed.org/snomed-ct SNOMEDCT SNOMEDCT GENEPIO:0001822 http://www.fao.org/fishery/collection/asfis/en ASFIS is a database curated by the United Nations Food And Agriculture Organization (FAO) Fisheries and Aquaculture Statistics and Information Branch (FIPS). It contains over 12,700 species items selected according to their interest or relation to fisheries and aquaculture. Damion Dooley UN FAO Fisheries and Aquaculture Statistics and Information Branch database FAO ASFIS ASFIS GENEPIO:0001823 FTT GENEPIO:0001824 TGN GENEPIO:0001825 Wikipedia is a free online encyclopedia that aims to allow anyone to edit articles. Damion Dooley https://en.wikipedia.org/wiki/Wikipedia Wikipedia GENEPIO:0001826 SWEETRealm GENEPIO:0001827 The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge. Damion Dooley http://www.geonames.org/ Geonames GENEPIO:0001828 http://ecolexicon.ugr.es/en/index.htm EcoLexicon is a terminological resource developed by the LexiCon Research Group at the University of Granada. Damion Dooley EcoLexicon GENEPIO:0001829 A standard established for use by the Integrated Rapid Infectious Disease Analysis (IRIDA) project, which is a Canadian-led initiative to build an open source, end-to-end platform for infectious disease genomic epidemiology. Damion Dooley http://www.irida.ca/ draft IRIDA standard GENEPIO:0001830 ISO 3166-1 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for the names of countries, dependent territories, and special areas of geographical interest. Damion Dooley https://en.wikipedia.org/wiki/ISO_3166-2 ISO3166-1 GENEPIO:0001831 ISO 3166-2 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for identifying the principal subdivisions (e.g., provinces or states) of all countries coded in ISO 3166-1. Damion Dooley https://en.wikipedia.org/wiki/ISO_3166-1 ISO3166-2 GENEPIO:0001832 Information Technology – Codes For The Identification Of The States And Equivalent Areas Within The United States, Puerto Rico, And The Insular Areas Damion Dooley American National Standards Institute ANSI INCITS 38 GENEPIO:0001833 Damion Dooley The Geographic Names Information System (GNIS), developed by the U.S. Geological Survey in cooperation with the U.S. Board on Geographic Names, contains information about physical and cultural geographic features in the United States and associated areas, both current and historical. https://nhd.usgs.gov/gnis.html GNISID GENEPIO:0001834 LTER GENEPIO:0001835 order: OBI:0001628 # investigation identifier OBI:0001616 # specimen identifier GENEPIO:0001808 # specimen title GENEPIO:0000113 # specimen category sep:00196 # specimen description OBI:0001479 # specimen from organism GENEPIO:0001640 # specimen organism taxonomy (species) GENEPIO:0000027 # specimen source context GENEPIO:0001722 # NCBI specimen voucher GENEPIO:0001429 # strain identifier GENEPIO:0001798 # NCBI BioSample culture identifier GENEPIO:0001717 # viral subtype OMP:0000207 # serotype phenotype SO:0001027 # genotype GENEPIO:0001079 # serovar GENEPIO:0001716 # subgroup GENEPIO:0001055 # NCBI pathotype GENEPIO:0001054 # isolate passage history GENEPIO:0001656 # latitude and longitude coordinate GENEPIO:0001657 # NCBI BioSample geo_loc_name model GENEPIO:0001051 # NCBI BioSample isolate (human name or description) GENEPIO:0001648 # NCBI Contributing organization / project GENEPIO:0001797 # specimen collector OBI:0001619 # specimen collection date OBI:0001888 # sequencing facility contact person GENEPIO:0001651 # INSDC institution code GENEPIO:0001721 # NCBI culture collection GENEPIO:0001567 # subject (host) taxonomic species GENEPIO:0001724 # subject organism common name GENEPIO:0001775 # subject age at time of specimen collection GENEPIO:0000026 # subject health status at time of specimen extraction GENEPIO:0000031 # subject sex GENEPIO:0001614 # subject description GENEPIO:0001617 # subject disease GENEPIO:0001625 # subject disease stage GENEPIO:0001212 # subject disease outcome A National Center for Biotechnology Information BioSample specification defines fields and terms that provide "descriptions of biological source materials used in experimental assays". Damion Dooley http://www.ncbi.nlm.nih.gov/biosample/ NCBI BioSample Pathogen.cl standard https://www.ncbi.nlm.nih.gov/biosample/docs/packages/Pathogen.cl.1.0/ 1 1 GENEPIO:0001836 The National Center for Biotechnology Information BioProject standard is a collection of datums that describe biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. Damion Dooley http://www.ncbi.nlm.nih.gov/bioproject/ NCBI lists project data type and other controlled vocabulary fields at : https://www.ncbi.nlm.nih.gov/books/NBK54364/ NCBI BioProject standard 1 1 1 Objective The format of the BioProject Accession is five alpha-letters followed by one to six numbers. For example PRJNA43021 Project Accession Methodology GENEPIO:0001837 http://www.aha.org/content/00-10/overview0302.pdf http://www.webcitation.org/5VBWPbFgY The American Hospital Association has issued HIPAA Updated Guidelines for Releasing Information on the Condition of Patients Damion Dooley American Hospital Association HIPAA Standard AHA HIPPA AHA HIPPA standard GENEPIO:0001838 http://www.ncbi.nlm.nih.gov/pubmed/ PubMed comprises more than 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. NCBI PubMed PMID PubMed GENEPIO:0001839 PulseNet, a national and international surveillance system used to identify and respond to foodborne disease outbreaks, has a standardized laboratory method and data submission standard for pathogen isolate typing test results and related isolate contextual data. From this information clusters of disease can be identified that might represent unrecognized outbreaks. Pulse Net International BioSample Metadata PulseNet PulseNet submission standard GENEPIO:0001840 AHA HIPPA: http://www.aha.org/content/00-10/overview0302.pdf Good - Vital signs are stable and within normal limits. Patient is conscious and comfortable. Indicators are excellent. Damion Dooley AHA Hippa: Good good health status Good satisfactory GENEPIO:0001841 Fair - Vital signs are stable and within normal limits. Patient is conscious, but may be uncomfortable. Indicators are favorable. Damion Dooley fair health status fair Stable GENEPIO:0001842 Serious - Vital signs may be unstable and not within normal limits. Patient is acutely ill. Indicators are questionable. Damion Dooley serious health status Serious GENEPIO:0001843 A health status history datum is a record of the longer-term pattern or presence of a given patient's health status. Damion Dooley health status history datum GENEPIO:0001844 (0,0) is the origin of the cartesian coordinate system. "In mathematics, the origin of a Euclidean space is a special point, usually denoted by the letter O, used as a fixed point of reference for the geometry of the surrounding space. In physical problems, the choice of origin is often arbitrary, meaning any choice of origin will ultimately give the same answer. This allows one to pick an origin point that makes the mathematics as simple as possible, often by taking advantage of some kind of geometric symmetry." Damion Dooley https://en.wikipedia.org/wiki/Origin_(mathematics) origin GENEPIO:0001845 https://en.wikipedia.org/wiki/Medical_state United Kingdom National Health Service trusts, boards, etc. have some terminology in common for public disclosure of patient health conditions. Damion Dooley National Health Service terminology NHS standard GENEPIO:0001846 Damion Dooley Damion Dooley's note: This is a contentious term. AHA calls for it never to be used, since the common phrase "critical but stable" is misleading by the very nature of "critical". The NHS however has it as one of its central terms. The use of "stable" also points to a health trend, rather than a state. A separate "health status trend datum" has been set up to capture this. critical but stable health status critical but stable GENEPIO:0001847 NHS Terms: https://en.wikipedia.org/wiki/Medical_state Damion Dooley comfortable health status Comfortable GENEPIO:0001848 Damion Dooley progressing well health status progressing well GENEPIO:0001849 Damion Dooley Damion Dooley note: This term (weakly) implies that the patient is recovered enough to be released from hospital. Technically this isn't a health status though, it is a patient medical service state. discharged from hospital discharged GENEPIO:0001850 A data item which is about the collection state of a datum at some point in time. Damion Dooley note: We'll need to incorporate NIAID GSCID-BRC Sample data standards mention: Unknown/Not Applicable/Censored Allowed Unknown/not applicable/not available/ available upon request Damion Dooley A given datum's datum status value is metadata, i.e. a statement about a particular datum, often when no actual data entry or categorical choice for that datum has been made. datum status INSDC missing value reporting terms: http://www.ebi.ac.uk/ena/about/missing-values-reporting GENEPIO:0001851 A categorical choice indicating that a datum is available for retrieval. Damion Dooley In theory any datum that has a recorded value has 'recorded' for its datum status. recorded GENEPIO:0001852 Patient is awaiting physician and/or assessment. Very similar to 'datum status' 'in process' status. Damion Dooley undetermined health status - awaiting assessment GENEPIO:0001853 Damion Dooley deteriorating worsening health trend GENEPIO:0001854 Damion Dooley An N-dimensional space consists of n dimensions, each with an origin. It can be translated via various coordinate systems, and can be populated with N and lesser dimensional vectors. n-dimensional space GENEPIO:0001855 Damion Dooley A distance metric exists between any two members of a one-dimensional set. Should have vector as subclass? 1D space GENEPIO:0001856 This data type is for an item that can map to a point, line, set or area on a surface (2 dimensional space) or to the surface itself. It can be a slice of a higher dimensional space. It can be defined by a cartesian or radial coordinate system. Damion Dooley 2D space GENEPIO:0001857 Damion Dooley 3D space GENEPIO:0001858 Damion Dooley n-dimensional coordinate GENEPIO:0001859 This covers the description of data and abstract structure in n-dimensional space. Within space there are coordinate systems, coordinates, and entities made up of coordinates. Damion Dooley n-dimensional concept 1 1 GENEPIO:0001860 Damion Dooley This should cover all interval data 1D coordinate 2 GENEPIO:0001861 Damion Dooley 2D coordinate -90.0 90.0 GENEPIO:0001862 /^[N+](:<lat>\d(\.\d+)?)$/, $lat /^S(:<lat>\d(\.\d+)?)$/, '-' + $lat /^(:<lat>[-S+N])?(:<degree>[1-8]?[0-9](:<decimal>\.\d{1,6})?)$/, $lat$degree.$decimal /^(:<lat>[-S+N])?(:<degree>90(:<decimal>\.0{1,6})?))$/, $lat$degree.$decimal /^(\d(\.\d+)?)$/, '+\1' A decimal latitude measurement in degrees in conformance with the ISO 6709 standard. This is failing Hermit reasoner since it rejects totalDigits, and fractionDigits: 'has primitive data type' exactly 1 xsd:decimal[>= -90.0 , <= 90.0 , totalDigits 8 , fractionDigits 6]' Damion Dooley latitude specification (ISO 6709) -180.0 180.0 GENEPIO:0001863 /^(:<long>[-W+E])?(:<degree>(1[0-7]|[1-9])?[0-9])(:<decimal>\.\d{1,6})?)$/, $long$degree.$decimal /^(:<long>[-W+E])?(:<degree>180(:<decimal>\.0{1,6})?)$,$long$degree.$decimal A decimal longitude measurement in degrees in conformance with the ISO 6709 standard. Damion Dooley longitude specification (ISO 6709) 1 GENEPIO:0001864 Damion Dooley 1D coordinate system 2 GENEPIO:0001865 A 2D coordinate system is a coordinate system in 2 dimensional space. Each coordinate is composed of an offset from the origin of each dimension Damion Dooley 2D coordinate system 3 GENEPIO:0001866 Damion Dooley 3D coordinate system 1 1 GENEPIO:0001867 Damion Dooley A coordinate system composed of a radius from the origin of one dimension combined with angular offsets from the origins of the remaining dimensions. radial coordinate system 1 GENEPIO:0001868 Damion Dooley's note: IAO lat/long can't be made a subclass of "angular coordinate" or disjoint contradiction arises with "immaterial entity" Damion Dooley angular coordinate 1 GENEPIO:0001869 Damion Dooley A coordinate composed of a given dimension and the offset from the origin of the dimension to some point linear coordinate 1 GENEPIO:0001870 An area calculation datum is a functional mapping of a two dimensional surface area (can be anything from an abstract polygon, to a postal code or country) to a 1 dimensional scalar. The original surface area may be curved, e.g. spheroid. The surface area can also be described using only one input - for example the radius scalar of a polar coordinate plane described by pi*r^2. Damion Dooley area calculation 1 1 1 GENEPIO:0001871 Damion Dooley geographic coordinate GENEPIO:0001872 Damion Dooley removed date GENEPIO:0001873 A datetime range intermediate datum is a datetime item grouped under a process, and occuring after some process start and before some process end. Damion Dooley datetime range intermediate GENEPIO:0001874 Damion Dooley updated date GENEPIO:0001875 This seems to be covered by 'datetime range intermediate' Damion Dooley datetime range member - UNUSED? GENEPIO:0001876 Damion Dooley datetime range item GENEPIO:0001877 The ending date of a process datetime range end GENEPIO:0001878 Damion Dooley The starting date of a process datetime range start GENEPIO:0001879 Wikipedia: "The significant figures of a number are digits that carry meaning contributing to its measurement resolution." Damion Dooley significant digits 1 GENEPIO:0001880 As mentioned here: http://www.datypic.com/sc/xsd11/t-xsd_dateTimeStamp.html , we could change this to dateTimeStamp if we need to enforce a time zone? Damion Dooley Some dates don't belong to a range other than the overall timeline. Other dates associated with a process fall within a range that has a start and end bound. datetime linear coordinate GENEPIO:0001881 $year/$month/$day /^(:<year>(19|20)\d\d)([- /.])(:<month>0[1-9]|1[012])\2(:<day>0[1-9]|[12][0-9]|3[01])$/ /^(:<month>0[1-9]|1[012])([- /.])(:<day>0[1-9]|[12][0-9]|3[01])\2(:<year>(19|20)\d\d)$/ /^(:<day>0[1-9]|[12][0-9]|3[01])([- /.])(:<month>0[1-9]|1[012])\2(:<year>(19|20)\d\d)$/ $year/$month/$day A datetime set item is a datetime that has been grouped semantically under a given type of process Damion Dooley The instant is subject to the level of granularity of the observed time. Year / Month / Day / Hour / Minute / Second datetime set item GENEPIO:0001882 Damion Dooley created date GENEPIO:0001883 Damion Dooley entity history item GENEPIO:0001884 Damion Dooley n-dimensional entity 1 GENEPIO:0001885 Damion Dooley Generic term allowing for different geometries. Can encompass the infinite surface area of a plane, or some portion bounded by a circumference or polygon for example. surface area GENEPIO:0001886 A designated area on earth is one or more areas defined by one or more boundaries. A boundary can be defined by a polygon perimeter, a lat/long and radius, or a fiat-boundary geographic featureset like a named river channel or mountain ridge; it may have one or more names associated with it. Note that areas associated with a name may change their boundary definitions over time. Damion Dooley designated area on Earth GENEPIO:0001887 Damion Dooley landmark GENEPIO:0001888 /^((:<FSA>[ABCEGHJKLMNPRSTVXY][0-9][ABCEGHJKLMNPRSTVWXYZ])) ?(:<LDU>[0-9][ABCEGHJKLMNPRSTVWXYZ][0-9])$/i, $FSA $LDU A Canadian postal code is a postal code that pertains to a geographic region of Canada. Note that a Canadian postal code can cover multiple communities. Secondly, postal codes can be retired, and then reintroduced elsewhere. Historical data associations may need to take the date of postal code mapping into account. Canada postal code GENEPIO:0001889 /^((:<FSA>[ABCEGHJKLMNPRSTVXY][0-9][ABCEGHJKLMNPRSTVWXYZ]))$/i, $FSA The "Canadia postal code FSA" is the leading FSA (Forward Sortation Area) 3 character portion of a full 6 character Canadian postal code. It can be used to reduce the geographic granularity of a postal code for data generalization or obfuscation. Damion Dooley Canada postal code FSA GENEPIO:0001890 A "USA zip code" is a five digit (Zone Improvement Plan) or 9 digit postal code pertaining to a region of the United States of America. The optional trailing 4 digits of a 9 digit zip code provide greater granularity of delivery target. Damion Dooley http://purl.obolibrary.org/obo/NCIT_C25720 obsolete: US postal code true GENEPIO:0001891 /^([a-zAA-Z0-9 _-')*$/ alphanumeric phrase GENEPIO:0001892 Damion Dooley entity history record GENEPIO:0001893 Damion Dooley generic range history record GENEPIO:0001894 Damion Dooley lingual set GENEPIO:0001895 Damion Dooley non-lingual set GENEPIO:0001896 phone type GENEPIO:0001898 mobile phone type - mobile GENEPIO:0001899 work phone type - work GENEPIO:0001900 Damion Dooley A set does not have a direct distance metric between its members. set GENEPIO:0001901 Damion Dooley This data type is for items that have a unique order or rank with respect to each other in a set BUT NO meaningful DISTANCE metric exists between items aside from their position in the full set. "Favorite soft drinks" or "Favorite colours" or "Closest friends" are examples. Letters of the alphabet cannot be interpreted as ordinal with respect to their use in words, since no uniform rules exist about their placement in words. But they can be ordinal insofar as they are stated in a particular order in listing off the alphabet. A distance metric becomes possible if the items have units, e.g. 5cm or 10degrees celcius. The set's elements can then be mapped to one dimension. ordered set GENEPIO:0001902 An unordered set is a set of elements which have no intrinsic (semantic) order with respect to each other. The set of all living people is not intrinsically ordered; an ordering can only be provided by looking at some partiular feature of the given set elements. Damion Dooley The set can have a very large or infinite (open-ended) number of values. Because the elements are essentially open-ended, we can only offer a lookup-as-you-type function for selecting past-used items. Use "Categorical" for unordered sets where items are finite, pre-defined and not too numerous. Strings are only indirectly ordered insofar as strings can be sorted by character - but this requires picking apar the name strings, an examination which has no inherent semantic relation to the things being named. That one email address or name comes before another is arbitrary. Only numbers are directly ordered. unordered set GENEPIO:0001903 Damion Dooley Subclasses here are types of string that have a particular syntactic structure or constraint to them that should be expressable using regular expressions. set of unordered strings GENEPIO:0001904 /^(:<area>(\([0-9]{3})\)|[0-9]{3})(:<sep>[- ])?(:<central>\d{3})\2(:<station>\d{4})$/, $area $central $station ($area) $central-$station Damion Dooley phone number (North America) 1 GENEPIO:0001905 A set of points that exist in a 2-dimensional plane. (This plane may be a cross-section of points defined in n > 2 dimensions). Damion Dooley points in 2 dimensions GENEPIO:0001906 In Euclidean space, quadrics have dimension D = 2, and are known as quadric surfaces. Damion Dooley https://en.wikipedia.org/wiki/Quadric quadratic surface GENEPIO:0001907 A spheroid, or ellipsoid of revolution, is a quadric surface obtained by rotating an ellipse about one of its principal axes; in other words, an ellipsoid with two equal semi-diameters. Damion Dooley https://en.wikipedia.org/wiki/Spheroid spheroid GENEPIO:0001908 In mathematics, a plane is a flat, two-dimensional surface. A plane is the two-dimensional analogue of a point (zero dimensions), a line (one dimension) and three-dimensional space. Planes can arise as subspaces of some higher-dimensional space, as with the walls of a room, or they may enjoy an independent existence in their own right, as in the setting of Euclidean geometry." "When working exclusively in two-dimensional Euclidean space, the definite article is used, so, the plane refers to the whole space. Damion Dooley https://en.wikipedia.org/wiki/Plane_(geometry) plane GENEPIO:0001909 Issue: this implicitly affects 'significant digits' datum. quantity unit GENEPIO:0001910 ^([+-]?[1-9]\d*|0)(\.\d+)?$ Damion Dooley decimal GENEPIO:0001911 ^([-+]?[1-9]\d*|0)$ Damion Dooley integer GENEPIO:0001912 ones GENEPIO:0001913 tens GENEPIO:0001914 hundreds GENEPIO:0001915 thousands GENEPIO:0001916 tenths GENEPIO:0001917 hundredths GENEPIO:0001918 millions GENEPIO:0001919 Damion Dooley Number types can have min / max limits for validation. Regular expressions would be used mostly for data entry transformation and display. number GENEPIO:0001921 A product name and model number of a manufacturer's genomic (dna) sequencer. Damion Dooley sequencing instrument model 1 1 GENEPIO:0001922 A circle is a simple closed shape in Euclidean geometry. It is the set of all points in a plane that are at a given distance from a given point, the centre; equivalently it is the curve traced out by a point that moves so that its distance from a given point is constant. Damion Dooley https://en.wikipedia.org/wiki/Circle circle GENEPIO:0001923 NCBI SRA: ILLUMINA Illumina platform GENEPIO:0001924 NCBI SRA: COMPLETE_GENOMICS Damion Dooley's note: This platform is in-house and not a product per se. Complete Genomics states: "Complete Genomics’ sequencing platform employs high-density DNA nanoarrays that are populated with DNA nanoballs (DNBs™). Base identification is performed using an unchained ligation-based read technology known as combinatorial probe-anchor ligation (cPAL™). The sequencing instrumentation is custom-developed to support this process. Details are described in our Science publication (Drmanac et al., 2010)." Complete Genomics platform 0 1 GENEPIO:0001925 Damion Dooley earth area boundary census GENEPIO:0001926 NCBI SRA: LS454 Roche LS454 platform GENEPIO:0001927 NCBI SRA: PACBIO_SMRT PacBio platform GENEPIO:0001928 NCBI SRA: AB SOLiD 4hq SOLiD 4hq System GENEPIO:0001929 NCBI SRA: AB SOLiD 5500 SOLiD 5500 GENEPIO:0001930 NCBI SRA: AB SOLiD 5500xl SOLiD 5500xl GENEPIO:0001931 NCBI SRA: AB SOLiD PI System SOLiD PI System GENEPIO:0001932 NCBI SRA: AB SOLiD System 2.0 SOLiD System 2.0 GENEPIO:0001933 NCBI SRA: AB SOLiD System 3.0 SOLiD System 3.0 GENEPIO:0001934 A two dimensional entity is an entity composed of one or more points on a two dimensional surface. Damion Dooley 2D entity GENEPIO:0001935 Redundant with "term replaced by" entity. NCBI SRA: Ion Torrent PGM obsolete: Ion Torrent PGM true GENEPIO:0001936 NCBI SRA: 454 GS FLX Titanium 454 Genome Sequencer FLX Titanium GENEPIO:0001937 NCBI SRA: 454 GS 454 Genome Sequencer GENEPIO:0001938 NCBI SRA: 454 GS Junior 454 Genome Sequencer Junior GENEPIO:0001939 Redundant with "term replaced by" entity. obsolete: Illumina HiSeq Sequencer true GENEPIO:0001940 https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly Whether any method was used to select for or against, enrich, or screen the material being sequenced. Damion Dooley NCBI SRA: LIBRARY_SELECTION library selection GENEPIO:0001941 Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C). NCBI SRA: 5-methylcytidine antibody 5-methylcytidine antibody method GENEPIO:0001942 Cap-analysis gene expression. NCBI SRA: CAGE CAGE method GENEPIO:0001943 Cot-filtered highly repetitive genomic DNA NCBI SRA: CF-H CF-H method GENEPIO:0001944 Cot-filtered moderately repetitive genomic DNA NCBI SRA: CF-M CF-M method GENEPIO:0001945 Cot-filtered single/low-copy genomic DNA NCBI SRA: CF-S CF-S method GENEPIO:0001946 Cot-filtered theoretical single-copy genomic DNA NCBI SRA: CF-T CF-T method GENEPIO:0001947 Chromatin immunoprecipitation NCBI SRA: ChIP ChIP method GENEPIO:0001948 Deoxyribonuclease (MNase) digestion NCBI SRA: DNAse DNAse method GENEPIO:0001949 Hypo-methylated partial restriction digest NCBI SRA: HMPR HMPR method GENEPIO:0001950 Selection by hybridization in array or solution. NCBI SRA: Hybrid Selection Hybrid Selection method GENEPIO:0001951 Enrichment by methyl-CpG binding domain. NCBI SRA: MBD2 protein methyl-CpG binding domain MBD2 protein methyl-CpG binding domain method GENEPIO:0001952 Methyl Filtrated NCBI SRA: MF MF method GENEPIO:0001953 Micrococcal Nuclease (MNase) digestion NCBI SRA: MNase MNase method GENEPIO:0001954 Methylation Spanning Linking Library NCBI SRA: MSLL MSLL method GENEPIO:0001955 Source material was selected by designed primers. NCBI SRA: PCR PCR method GENEPIO:0001956 Rapid Amplification of cDNA Ends. NCBI SRA: RACE RACE method GENEPIO:0001957 Source material was selected by randomly generated primers. NCBI SRA: RANDOM PCR RANDOM PCR method GENEPIO:0001958 Random selection by shearing or other method. NCBI SRA: RANDOM RANDOM method GENEPIO:0001959 Source material was selected by reverse transcription PCR NCBI SRA: RT-PCR RT-PCR method GENEPIO:0001960 Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling. NCBI SRA: Reduced Representation Reduced Representation method GENEPIO:0001961 DNA fractionation using restriction enzymes. NCBI SRA: Restriction Digest Restriction Digest method GENEPIO:0001962 PolyA selection or enrichment for messenger RNA (mRNA). complementary DNA. NCBI SRA: cDNA cDNA method GENEPIO:0001963 Physical selection of size appropriate targets. NCBI SRA: size fractionation size fractionation method GENEPIO:0001964 Other library enrichment, screening, or selection process. NCBI SRA: other other library method GENEPIO:0001965 https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly The library source specifies the type of source material that is being sequenced. Damion Dooley library source GENEPIO:0001966 Genomic DNA (includes PCR products from genomic DNA). Damion Dooley NCBI SRA: GENOMIC genomic source GENEPIO:0001967 Mixed material from metagenome. Damion Dooley NCBI SRA: METAGENOMIC metagenomic source GENEPIO:0001968 Transcription products from community targets Damion Dooley NCBI SRA: METATRANSCRIPTOMIC metatranscriptomic source GENEPIO:0001969 Other, unspecified, or unknown library source material. Damion Dooley NCBI SRA: OTHER other library source GENEPIO:0001970 Synthetic DNA. Damion Dooley NCBI SRA: SYNTHETIC synthetic source GENEPIO:0001971 Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries). Damion Dooley NCBI SRA: TRANSCRIPTOMIC transcriptomic source GENEPIO:0001972 Viral RNA. Damion Dooley NCBI SRA: VIRAL RNA viral RNA source GENEPIO:0001973 Sequencing technique intended for this library. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly library strategy GENEPIO:0001974 Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA NCBI SRA: AMPLICON amplicon strategy GENEPIO:0001975 MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status. NCBI SRA: Bisulfite-Seq Bisulfite-Seq strategy GENEPIO:0001976 Clone end (5', 3', or both) sequencing. NCBI SRA: CLONEEND clone end strategy GENEPIO:0001977 Genomic clone based (hierarchical) sequencing. NCBI SRA: CLONE clone strategy GENEPIO:0001978 Concatenated Tag Sequencing NCBI SRA: CTS CTS strategy GENEPIO:0001979 Direct sequencing of chromatin immunoprecipitates. NCBI SRA: ChIP-Seq ChIP-Seq strategy GENEPIO:0001980 Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI. NCBI SRA: DNase-Hypersensitivity DNase-Hypersensitivity strategy GENEPIO:0001981 Single pass sequencing of cDNA templates NCBI SRA: EST EST strategy GENEPIO:0001982 Sequencing intended to finish (close) gaps in existing coverage. NCBI SRA: FINISHING finishing strategy GENEPIO:0001983 Full-length sequencing of cDNA templates NCBI SRA: FL-cDNA FL-cDNA strategy GENEPIO:0001984 Direct sequencing of methylated fractions sequencing strategy. NCBI SRA: MBD-Seq MBD-Seq strategy GENEPIO:0001985 Direct sequencing following MNase digestion. NCBI SRA: MNase-Seq MNase-Seq strategy GENEPIO:0001986 Methylation-Sensitive Restriction Enzyme Sequencing strategy. NCBI SRA: MRE-Seq MRE-Seq strategy GENEPIO:0001987 Methylated DNA Immunoprecipitation Sequencing strategy. NCBI SRA: MeDIP-Seq MeDIP-Seq strategy GENEPIO:0001988 Library strategy not listed. NCBI SRA: OTHER other library strategy GENEPIO:0001989 Shotgun of pooled clones (usually BACs and Fosmids). NCBI SRA: POOLCLONE pool clone strategy GENEPIO:0001990 Random sequencing of whole transcriptome. NCBI SRA: RNA-Seq RNA-Seq strategy GENEPIO:0001991 Random sequencing of a whole chromosome or other replicon isolated from a genome. NCBI SRA: WCS WCS strategy GENEPIO:0001992 Random sequencing of the whole genome. NCBI SRA: WGS WGS strategy GENEPIO:0001993 Random sequencing of exonic regions selected from the genome. NCBI SRA: WXS WXS strategy GENEPIO:0001994 Free form text describing the protocol by which the sequencing library was constructed. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly library construction protocol GENEPIO:0001995 The submitter's name for this library. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly NCBI SRA: LIBRARY_NAME library name GENEPIO:0001996 A two dimensional boundary is a continuous path (loop) defined on a two dimensional surface. Damion Dooley 2D boundary GENEPIO:0001997 cfu/100mL A colony forming unit count which is a count of viable bacterial numbers in 100 milliliters of liquid. Should this be deprecated? Need to find working examples that actually use / 100mL. Damion Dooley colony forming unit per 100 milliliter GENEPIO:0001998 A multiplier in the decimal number system that has been applied to an accompanying number or set of numbers often to simplfy their appearance. Numbers described by multipliers may have lost significant digits through rounding or trimming. Damion Dooley decimal quantity unit GENEPIO:0001999 draft tuberculosis - dataset features and provenance GENEPIO:0002000 draft tuberculosis - case specimen characteristics GENEPIO:0002001 draft tuberculosis - case subject characteristics GENEPIO:0002002 draft tuberculosis - case risk factors GENEPIO:0002003 draft tuberculosis - case clinical presentation GENEPIO:0002004 draft tuberculosis - case laboratory testing GENEPIO:0002005 draft tuberculosis - case medication GENEPIO:0002006 draft isolate whole genome sequencing model GENEPIO:0002007 draft tuberculosis - case model GENEPIO:0002008 A Mycobacterium tuberculosis lineage is a named family of strains of tuberculosis, named usually with reference to their shared geographic origin. Damion Dooley Mycobacterium tuberculosis lineage A TB-Lineage identification tool using spoligotypes and MIRU data: http://tbinsight.cs.rpi.edu/run_tb_lineage.html Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans http://www.nature.com/ng/journal/v45/n10/full/ng.2744.html GENEPIO:0002009 TB lineage 2 - East-Asian, includes Bejing GENEPIO:0002010 TB lineage 3 - East-African Indian, includes CAS/Delhi GENEPIO:0002011 TB lineage 4 - Euro-American, includes Haarlem, LAM3, X, T, F11, H37Rv GENEPIO:0002012 TB lineage 1 - Indo-Oceanic GENEPIO:0002013 TB lineage 5 - West African 1 GENEPIO:0002014 TB lineage 6 - West African 2 GENEPIO:0002015 Damion Dooley An isolate preparation facility is a type of organization that provides the service of isolating organisms of interest from provided specimens. isolate preparation facility GENEPIO:0002016 plant product GENEPIO:0002017 geospatial name GENEPIO:0002018 A personal health datum is a datum that pertains to the health situation or history of an individual. Personal health datum covers the following information 'has member' some 'analytic datum' 'has member' some 'behavioural risk factor' 'has member' some 'country of birth' 'has member' some 'dietary restrictions' 'has member' some 'Disease Attributes' 'has member' some 'health status history datum' 'has member' some 'health status trend datum' 'has member' some 'host hospital service status' 'has member' some 'subject disease stage' 'has member' some 'subject health status' 'has member' some 'subject health status (AHA)' 'has member' some 'subject health status (GSCID-BRC)' 'has member' some 'subject health status (NCIT)' 'has member' some 'subject health status (UK NHS)' 'has member' some 'subject health status at time of specimen extraction' 'has member' some 'tuberculosis disease anatomical site' 'has member' some comorbidity 'has member' some disease 'has member' some symptom Damion Dooley personal health datum GENEPIO:0002019 A host hospital service status indicates the state of a host's interaction with hospital medical services. Damion Dooley host hospital service status GENEPIO:0002020 Damion Dooley admitted to hospital GENEPIO:0002021 Received treatment but not admitted. treated and released (not admitted to hospital) Treated and Released GENEPIO:0002022 Received treatment. Transferred to a different facility. treated and transferred Treated and Transferred GENEPIO:0002023 Damion Dooley satisfactory health status satisfactory GENEPIO:0002024 depth:1 subject health status (UK NHS) GENEPIO:0002025 depth:1 subject health status (AHA) http://purl.obolibrary.org/obo/GENEPIO_0002019 GENEPIO:0002026 stable health trend http://purl.obolibrary.org/obo/GENEPIO_0001669 GENEPIO:0002027 An ordinal variable is a categorical variable whose values have sequential order, but no distance metric between them. Damion Dooley http://purl.obolibrary.org/obo/STATO_0000228 obsolete: ordinal variable true GENEPIO:0002028 mapping (reference based) GENEPIO:0002029 data protection item GENEPIO:0002030 subject provided consent GENEPIO:0002031 Damion Dooley An ordinal tree specification is a value specification entity whose subclasses each represent a possible value selection, and which have a linear order with respect to their siblings. ordinal value specification GENEPIO:0002032 consent datum GENEPIO:0002033 agency provided consent GENEPIO:0002034 2019-11-17T00:43:00Z draft ISO sequence repository field GENEPIO:0002035 Centre of circle, ellipse or parabola; centre of mass. A centre point is a point used in the description of an n-dimentional entity from which other (given) aspects of the entity are most efficienty described. A point of symmetry. The entity must have only one such point. Probably a better formal math defn? Damion Dooley centre point GENEPIO:0002036 This covers the following entities: 'has member' some 'antimicrobial phenotype' 'has member' some 'antimicrobial resistance test drug' 'has member' some 'antimicrobial resistance test platform' 'has member' some 'antimicrobial resistance testing method' 'has member' some 'antimicrobial resistance testing method version or reagent' 'has member' some 'antimicrobial resistance testing reference standard' 'has member' some 'antimicrobial resistance testing reference standard version' 'has member' some 'antimicrobial resistance tissue specificity' 'has member' some 'antimicrobial resistant plasmid type' 'has member' some 'automated testing platform vendor' 'has member' some 'draft antibiogram drug test model' 'has member' some 'in-vitro microbial susceptibility test' 'has member' some 'measurement comparator' 'has member' some 'MIC unit' 'has member' some 'MIC value' 'has member' some 'Minimum Inhibitory Concentration Test' 'has member' some 'test drug maximum concentration' 'has member' some 'test drug minimum concentration' 'has member' some 'tuberculosis treatment drug' Damion Dooley This is a collection of antibiotic resistance process parameters and outputs phenotypic antimicrobial drug susceptibility test datum GENEPIO:0002037 The resistance phenotype of an isolate represents the interpretation of an MIC value with regard to some breakpoint threshold e.g. resistant (R), sensitive (S), intermediate (I), wild type (WT), or non-wild type (NWT) Damion Dooley http://purl.obolibrary.org/obo/NCIT_C85539 obsolete: antimicrobial resistance phenotype true GENEPIO:0002038 Intermediate resistance indicates that an isolate is observed to offer an intermediate level of resistance to a given antibiotic. Damion Dooley http://purl.obolibrary.org/obo/NCIT_C85560 obsolete: antibiotic intermediate resistance (I) true GENEPIO:0002039 Non-susceptible indicates that an isolate is observed to offer complete resistance to a given antibiotic. Damion Dooley http://purl.obolibrary.org/obo/NCIT_C85561 obsolete: antibiotic nonsensitive (high resistance) true GENEPIO:0002040 A not defined resistance indicates that an isolate was not tested against a given antibiotic, or the result of the test was inconclusive. Damion Dooley note: Is this the same as "indeterminate"? Damion Dooley N ND antibiotic resistance not defined GENEPIO:0002041 Resistant indicates that an isolate is observed to offer a greater than intermediate level of resistance to a given antibiotic. Damion Dooley http://purl.obolibrary.org/obo/NCIT_C85562 obsolete: antibiotic resistant (R) true GENEPIO:0002042 Susceptible indicates that an isolate is observed to offer a detectable but less than intermediate level of resistance to a given antibiotic. Damion Dooley http://purl.obolibrary.org/obo/NCIT_C85563 obsolete: antibiotic sensitive (S) true GENEPIO:0002043 Susceptible - dose dependent indicates that an isolate is observed to offer resistance to a given antibiotic when a sufficient dose is given. Damion Dooley http://purl.obolibrary.org/obo/NCIT_C85559 obsolete: sensitive - dose dependent true GENEPIO:0002044 A MIC test measurement resulting from a laboratory dilution method. Damion Dooley's note: is this still useful? Currently "MIC dilution measurement specification' refers directly via 'is about' to "broth dilution method" but that may be too specific. Damion Dooley MIC dilution measurement datum GENEPIO:0002045 The type of assay used to determine the minimum inhibitory concentration. Damion Dooley http://purl.obolibrary.org/obo/NCIT_C85540 obsolete: antimicrobial resistance testing method true GENEPIO:0002046 http://purl.obolibrary.org/obo/NCIT_C85555 obsolete: agar dilution evidence true GENEPIO:0002047 The commercial kit or product used to determine the MIC e.g. E-Test. If a commercial product was not used, include the type of media used. Damion Dooley antimicrobial resistance testing method device or reagent GENEPIO:0002048 antimicrobial resistant plasmid type GENEPIO:0002049 The instrumentation used to determine minimum inhibitory concentration values. Damion Dooley http://purl.obolibrary.org/obo/ARO_3004390 obsolete: antimicrobial resistance testing platform true GENEPIO:0002050 http://purl.obolibrary.org/obo/ARO_3004400 obsolete: Microscan true GENEPIO:0002051 http://purl.obolibrary.org/obo/ARO_3004401 obsolete: Phoenix true GENEPIO:0002052 http://purl.obolibrary.org/obo/ARO_3004402 obsolete: Sensititre true GENEPIO:0002053 http://purl.obolibrary.org/obo/ARO_3004403 obsolete: Vitek true GENEPIO:0002054 http://purl.obolibrary.org/obo/ARO_3004409 obsolete: Trek true GENEPIO:0002055 obsolete: manual - noncommercial true GENEPIO:0002056 The manufacturer of an antibiotic resistance lab typing platform Damion Dooley http://purl.obolibrary.org/obo/ARO_3004404 obsolete: antimicrobial resistance testing platform vendor true GENEPIO:0002057 http://purl.obolibrary.org/obo/ARO_3004407 obsolete: Siemens true GENEPIO:0002058 http://purl.obolibrary.org/obo/ARO_3004406 obsolete: Biomérieux true GENEPIO:0002059 http://purl.obolibrary.org/obo/ARO_3004405 obsolete: Becton Dickinson true GENEPIO:0002060 A manual in vitro diagnostic device used by laboratories to determine the MIC (Minimum Inhibitory Concentration) and whether or not a specific strain of bacterium or fungus is susceptible to the action of a specific antimicrobial. Damion Dooley E-Test Epsilometer test Etest (device) GENEPIO:0002061 GM-NEG GENEPIO:0002062 The clinical and laboratory guidelines or standards that prescribe the threshold values for determining resistance phenotypes. Damion Dooley http://purl.obolibrary.org/obo/ARO_3004360 obsolete: antimicrobial resistance testing reference standard true GENEPIO:0002063 BSAC is a British inter-professional organisation involved in antibiotic education, research and leadership Damion Dooley BSAC obsolete: British Society for Antimicrobial Chemotherapy (BSAC) true GENEPIO:0002064 The Clinical and Laboratory Standards Institute develops and implements clinical laboratory testing standards Damion Dooley NCCLS http://clsi.org CLSI On January 1, 2005 the National Committee on Clinical Laboratory Standards (NCCLS) changed its name to CLSI obsolete: Clinical and Laboratory Standards Institute (CLSI) true GENEPIO:0002065 DIN is recognized by the Federal Government of Germany as the competent standards organization for Germany and as the national standards body representing Germany in non-governmental international standards organizations. Damion Dooley http://www.din.de/en/din-and-our-partners/din-e-v DIN Deutsches Institut für Normung obsolete: German Institute for Standardization (DIN) true GENEPIO:0002066 EUCAST is a standing committee jointly organized by ESCMID, ECDC and European national breakpoint committees; it deals with breakpoints and technical aspects of phenotypic in vitro antimicrobial susceptibility testing. Damion Dooley http://www.eucast.org/ EUCAST obsolete: European Committe on Antimicrobial Susceptibility Testing (EUCAST) true GENEPIO:0002067 Damion Dooley NCCLS obsolete: National Committee on Clinical Laboratory Standards (NCCLS) true GENEPIO:0002068 La SFM a vocation à rassembler les microbiologistes de France et des pays francophones, travaillant dans les différents domaines de la microbiologie médicale, industrielle, et environnementale, en physiologie, génétique, taxonomie, hygiène, agents antimicrobiens, ...concernant les bactéries, virus, champignons et parasites. The French Society of Microbiology (SFM) is a non-profit association which aims to bring together microbiologists from French-speaking countries, working in the domains of bacteria, viruses, Fungi and parasites, and related medical, industrial and environmental microbiology, physiology, genetics, taxonomy, hygiene, and antimicrobial agents. This isn't at moment considered a valid EBI antibiogram choice? Damion Dooley http://www.sfm-microbiologie.org/ SFM obsolete: Société Française de Microbiologie (SFM) true GENEPIO:0002069 Replaced by domain appropriate term created in the Comprehensive Antibiotic Resistance Database (CARD). obsolete: SIR true GENEPIO:0002070 Replaced by domain appropriate term created in the Comprehensive Antibiotic Resistance Database (CARD). obsolete: WRG true GENEPIO:0002071 first line tuberculosis drug GENEPIO:0002072 last resort antibiotic GENEPIO:0002073 NIAID standard NIAID provides The GSCID/BRC Project and Sample Application Standard. It is designed to capture standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases. Damion Dooley https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards National Institute of Allergy and Infectious Disease standard GENEPIO:0002074 A RefSeq accession identifier is an accession identifier for selected NCBI-curated genomic, transcript and protein sequences. These identifiers are distinct from DDBJ/EMBL/GenBank identifiers. Damion Dooley RefSeq accession identifier http://www.ncbi.nlm.nih.gov/refseq/about/ GENEPIO:0002075 A Genomic Standards Consortium standard is an international, community-driven standard to facilitate genomic data integration, discovery and comparison. Damion Dooley Genomic Standards Consortium (GSC) standard http://gensc.org/ GENEPIO:0002076 A landform, biome or built environment at site that a given specimen was collected from. Damion Dooley specimen collection site - geographic feature GENEPIO:0002077 A particular human patient, or a given animal or plant. An investigative subject which is an organism. Damion Dooley subject organism GENEPIO:0002078 help=The number of passages should be expressed as a numerical value. The number of serial iterations that an isolate is grown in one environment. Damion Dooley number of passages GENEPIO:0002079 help:The passage protocol should include, when applicable, inoculum size, media type, temperature and duration of incubation. A passage protocol should detail the number of serial iterations that an isolate is grown in one environment, and the conditions of that environment. Damion Dooley passage protocol GENEPIO:0002080 The unit provided for an antibiotic drug test dosage. Damion Dooley http://purl.obolibrary.org/obo/ARO_3004372 obsolete: drug minimum inhibitory concentration unit true GENEPIO:0002081 order: GENEPIO:0001237 # specimen type (host or environmental context) OBI:0001619 # specimen collection date OBI:0000659 # specimen collection process GENEPIO:0002094 # specimen collection device GENEPIO:00001600 # draft sequence repository data - geographic location ENVO:00010483 # environmental material ENVO:00002297 # environmental feature GENEPIO:0001567 # subject (host) taxonomic species GENEPIO:0000110 # subject health status GENEPIO:0001617 # subject disease GENEPIO:0000028 # subject body product GENEPIO:0000025 # specimen source anatomical site FOODON:03411564 # draft sequence repository data - food processing draft sequence repository data - specimen collection GENEPIO:0002082 order: GENEPIO:0002105 # Specimen processing organization role NCIT:C93874 # organization name NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C93582 # job title NCIT:C42775 # email address GENEPIO:0001756 # phone NCIT:C25464 # Country ENVO:00000005 # major administrative subdivision -> GAZ state/province/territory/region) NCIT:C80234 # Municipality” (via GenEpiO -> GAZ cities) NCIT:C25690 # Street Address Contact information for an organization related to specimen collection, processing or storage. Damion Dooley contact specification - specimen related organization GENEPIO:0002083 dateFormat:ISO 8601 order: GENEPIO:0002082 # specimen related organization GENEPIO:0002081 # specimen collection GENEPIO:0002086 # geographic location GENEPIO:0002084 # isolate GENEPIO:0002087 # isolate history GENEPIO:0002106 # food specimen GENEPIO:0002088 # antibiogram GENEPIO:0002085 # sequencing GENEPIO:0002090 # sequencing QC GENEPIO:0002089 # virulence GENEPIO:0002092 # submission to EBI GENEPIO:0002091 # submission to NCBI/DDBJ This draft specification provides a collection of fields related to the contextual data of a specimen, its genomic sequencing, and its pathogenic epidemiology. Damion Dooley draft sequence repository contextual data standard GENEPIO:0002084 order: GENEPIO:0001640 # specimen taxonomy GENEPIO:0001429 # strain identifier GENEPIO:0001644 # isolate identifier OBI:0000079 # culture medium GENEPIO:0002107 # isolation medium draft sequence repository data - isolate GENEPIO:0002085 order: GENEPIO:0000069 # sequencing date OBI:0000079 # culture medium” (via MicrO, yields a list of formulas). GENEPIO:0002093 # sequencing dna extraction method EFO:0000683 # replicate GENEPIO:0000085 # library preparation kit GENEPIO:0000149 # library preparation kit version GENEPIO:0000075 # sequencing chemistry GENEPIO:0001921 # sequencing instrument model GENEPIO:0000150 # read trimming and filtering software GENEPIO:0000084 # read adapter trimming software GENEPIO:0002095 # read paired-end merging software GENEPIO:0000090 # assembly method GENEPIO:0000151 # bioinformatics pipeline name GENEPIO:0000153 # bioinformatics pipeline protocol GENEPIO:0000152 # bioinformatics pipeline version GENEPIO:0000095 # genome annotation algorithm draft sequence repository data - sequencing GENEPIO:0002086 order: GENEPIO_0001656 # latitude and longitude ISO 6709 GENEPIO:0000118 # specimen collection country GENEPIO:0002097 # specimen collection state/prov/ter/region GENEPIO:0001785 # specimen collection city The geographical origin of the sample by city, region, country or latitude and logitude. Damion Dooley draft sequence repository data - geographic location GENEPIO:0002087 order: GENEPIO:0002078 # number of passages GENEPIO:0002079 # passage protocol draft sequence repository data - isolate passage history GENEPIO:0002088 order: GENEPIO:0001100 # antimicrobial drug tests GENEPIO:0002101 # test drug minimum concentration GENEPIO:0002100 # test drug maximum concentration GENEPIO:0002045 # antimicrobial resistance testing method GENEPIO:0002047 # antimicrobial testing method version or reagent GENEPIO:0002062 # antimicrobial resistance testing reference standard GENEPIO:0002049 # antimicrobial resistance testing platform A dataset of the minimal inhibitory concentrations (value, unit, sign (<,>, =)) and resistance phenotypes (resistant, sensitive or undetermined) of the sequenced isolate against different antibiotics tested. Damion Dooley draft sequence repository data - antibiogram GENEPIO:0002089 order: GENEPIO:0002130 # Virulence factor name GENEPIO:0002131 # Virulence testing protocol GENEPIO:0002132 # detection limit The virulence factors determined to be present in the sequenced isolate by phenotypic or target amplification methods e.g. Shiga toxins, hemolysins. Damion Dooley draft sequence repository data - virulence GENEPIO:0002090 order: OBI:0001941 # N50 GENEPIO_0000092 # sequencing depth / read coverage Measurements or calculated quantities used to assess the extent and success of the sequence assembly process. Metric thresholds are species-specific. Damion Dooley draft sequence repository data - sequencing quality control GENEPIO:0002091 order: OBI:0001616 # specimen identifier GENEPIO:0001644 # isolate identifier GENEPIO:0001429 # strain identifier GENEPIO:0001640 # specimen organism taxonomy GENEPIO:0000113 # specimen category OBI:0001619 # specimen collection date GENEPIO:0001797 # specimen collector GENEPIO:0001657 # geo_loc_name GENEPIO:0001656 # latitude and longitude coord GENEPIO:0000027 # specimen source context GENEPIO:0001567 # subject organism taxonomy GENEPIO:0001724 # subject organism common name GENEPIO:0001617 # subject disease Damion Dooley draft sequence repository data - submission to NCBI/DDBJ GENEPIO:0002092 order: GENEPIO:0001644 # isolate identifier GENEPIO:0001429 # strain identifier GENEPIO:0001640 # specimen organism taxonomy GENEPIO:0001079 # serovar GENEPIO:0002135 # EBI environmental feature GENEPIO:0000113 # specimen category OBI:0001619 # specimen collection date GENEPIO:0001797 # specimen collector GENEPIO:0002086 # geographic location GENEPIO:0000027 # specimen source context GENEPIO:0002076 # geographic feature GENEPIO:0001567 # subject taxonomy GENEPIO:0000110 # subject health status Damion Dooley draft sequence repository data - submission to EBI https://www.ebi.ac.uk/ena/submit/pathogen-data GENEPIO:0002093 The procedure used to obtain genomic DNA from a sample through chemical, physical or mechanical means. Damion Dooley sequencing dna extraction method datum GENEPIO:0002094 Moved term to OBI, deprecated in favour of the OBI version. obsolete: specimen collection device true GENEPIO:0002095 The name and version of the software used to merge paired-end reads before assembly. read paired-end merging software GENEPIO:0002096 Sequencing The name and version of the software product used for removal of adapter sequences from demultiplexed data reads GROUP: IRIDA Ontology (Emma) GENEPIO read adapter trimming software GENEPIO:0002097 An ontology identifier or textual name of the most precise geographical location available for the site of a specimen collection event. Damion Dooley Adapted from NIAID GSCID-BRC metadata working group Note that this is expressed in a particular format in some standards. specimen collection location - state/province/territory/region lookup GENEPIO:0002098 A wild type (WT) resistance phenotype indicates a bacterial pathogen belongs to a "Naïve", susceptible wild-type population with respect to a given antimicrobial. No acquired or mutational resistance mechanisms are present to the antimicrobial in question. Damion Dooley https://sisu.ut.ee/sites/default/files/amr/files/pab_new_legislation_on_amr.pdf http://purl.obolibrary.org/obo/ARO_3004432 obsolete: wild type (WT) true GENEPIO:0002099 A non-wild type (WT) resistance phenotype indicates a bacterial pathogen has an acquired or mutational resistance mechanism present with respect to the antimicrobial in question. The bacteria has a reduced susceptibility to this agent. Damion Dooley https://sisu.ut.ee/sites/default/files/amr/files/pab_new_legislation_on_amr.pdf http://purl.obolibrary.org/obo/ARO_3004433 obsolete: non-wild type (NWT) true GENEPIO:0002100 This is the maximum concentration of a drug applied during an an assay. Damion Dooley test drug maximum concentration GENEPIO:0002101 This is the minimum concentration of a drug applied during an an assay. Damion Dooley test drug minimum concentration GENEPIO:0002102 The tissue type used to select breakpoints from a particular standard, for the interpretation of MIC results. Damion Dooley http://purl.obolibrary.org/obo/ARO_3004430 obsolete: antimicrobial resistance tissue specificity true GENEPIO:0002103 depth:1 order: NCIT:C115935 # healthy NCIT:C126054 # non-pathalogical NCIT:C25610 # pathologic NCIT:C82508 # life threatening NCIT:C28554 # deceased subject health status (NCIT) GENEPIO:0002104 order: NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C93582 # job title NCIT:C42775 # email address GENEPIO:0001756 # phone contact specification - professional role GENEPIO:0002105 An organization related to the collection, isolate production, sequencing or storage of specimen material or data. Damion Dooley specimen processing organization type GENEPIO:0002106 order: GENEPIO:0001533 # food specimen type FOODON:03450002 # food cooking method FOODON:03440011 # extent of heat treatment FOODON:03430113 # physical state, shape or form FOODON:03470107 # food preservation method FOODON:03490100 # container or wrapping FOODON:03480020 # food packing medium FOODON:03500010 # food contact surface GENEPIO:0000139 # food cultural origin FOODON:03460111 # treatment applied to food This specification offers food source, product type, packaging and processing attributes relevant to describing a food specimen. draft sequence repository data - food specimen GENEPIO:0002107 An isolation medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment. Chris has proposed this term for OBI as "enrichment culture medium" Damion Dooley isolation medium GENEPIO:0002108 order: GENEPIO:0000121 # start date GENEPIO:0000122 # end date GENEPIO:0001783 # travel destination GENEPIO:0001064 # travel mode GENEPIO:0001065 # travel reason This record details a person's travel movement and duration for epidemiological analysis. Damion Dooley draft travel log specification GENEPIO:0002109 order: OBI:0001616 # BioSample_ID GENEPIO:0001640 # Species GENEPIO:0001187 # Antibiotic_Name GENEPIO:0002062 # AST_Standard GENEPIO:0002111 # Breakpoint_version NCIT:C85540 # Laboratory_typing_method GENEPIO:0002112 # Measurement GENEPIO:0002080 # Measurement_units GENEPIO:0001001 # Measurement_sign NCIT:C85539 # Resistance_phenotype GENEPIO:0002181 # Resistance_phenotype - ECOFF GENEPIO:0002049 # Platform A standard for European Bioinformatics Institute (EBI) antibiogram data submission Damion Dooley draft EBI antimicrobial susceptibility test V. 2017-08-30 https://github.com/EBI-COMMUNITY/compare-amr/blob/master/Antimicrobial-susceptibility-testing-data-submission_V_2017-08-30.pdf GENEPIO:0002110 A MIC test measurement resulting from a laboratory diffusion method. Damion Dooley's note: is this still useful? Currently "MIC diffusion measurement specification' refers directly via 'is about' to "Disk Diffusion Method". Damion Dooley MIC diffusion measurement datum GENEPIO:0002111 The version of the antimicrobial reistance testing reference standard protocol used in assessing an isolate. Damion Dooley antimicrobial resistance testing reference standard version GENEPIO:0002112 This is a component of an antibiogram that enables a choice of MIC measurements based on either the diffusion or dilution method. These methods call for different numeric input ranges and units. draft sequence repository data - antibiogram MIC measurement 1 GENEPIO:0002113 time value specification GENEPIO:0002114 The process of collecting a portion of feces from an organism. Emma Griffiths stool collection feces collection GENEPIO:0002115 The process of collecting a portion of urine from an organism. Emma Griffiths sputum collection GENEPIO:0002116 The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids. Emma Griffiths rinsing for specimen collection GENEPIO:0002117 The process of collecting specimen material using a swab collection device. Emma Griffiths swabbing for specimen collection GENEPIO:0002118 The process of collecting bodily fluids that have been discharged from blood vessels usually arising from inflammation or injury. Emma Griffiths exudate collection GENEPIO:0002119 The removal or collection of specimen material through the use of suction. Emma Griffiths vacuuming for specimen collection GENEPIO:0002120 Emma Griffiths NOTE: there are different types of tubes with coloured caps indicating different preservatives etc. tube containing media or preservative GENEPIO:0002121 Emma Griffiths NOTE: there are different types of tubes with coloured caps indicating different preservatives etc. tube containing antimicrobial GENEPIO:0002122 A sterilized sampling bag that is puncture proof tabs for protection from damage due to wire-end protrusion and leak-proof closures. Emma Griffiths Whirlpak sampling bag GENEPIO:0002123 Emma Griffiths spoon GENEPIO:0002124 Emma Griffiths fork GENEPIO:0002125 A shovel-like utensil that has a deep curved dish and a short handle and is used for digging into a soft substance for lifting out a portion. Emma Griffiths 2023-06-21T13:54:32Z hand scoop GENEPIO:0002126 Emma Griffiths trier GENEPIO:0002127 A device which generates a vacuum to provide suction of material. Emma Griffiths vaccum device GENEPIO:0002128 investigation identifier specification GENEPIO:0002129 order: GENEPIO:0001640 # taxonomy GENEPIO:0002086 # geographic location GENEPIO:0002076 # geographic feature GENEPIO:0002106 # food FOODON:03510136 # food consumer GENEPIO:0002094 # specimen collection device GENEPIO:0000025 # anatomical site GENEPIO:0000028 # body product GENEPIO:0001724 # host organism common name GENEPIO:0001567 # host taxonomy UBERON:0000105 # life cycle GENEPIO:0001639 # antigenic formula GENEPIO:0001718 # serotype specification GENEPIO:0000045 # PFGE test specification This is a draft (under development) collection of fields for capturing the contextual data for Enterobase (https://enterobase.warwick.ac.uk/) records. Damion Dooley draft Enterobase contextual data standard GENEPIO:0002130 The name of the virulence factor molecule produced by a pathogen that specifically causes disease, or that influences the host's function to allow the pathogen to thrive. Emma Griffiths virulence factor name GENEPIO:0002131 help:The protocol for determining virulence should include, when applicable, inoculum preparation, platforms and instrumentation, conditions, cell lines and animal models. The laboratory protocol used to determine virulence phenotypes and markers. Emma Griffiths virulence testing protocol name GENEPIO:0002132 help:Detection limits should include the numerical cut-off (threshold) value and units for determining positive results e.g. qPCR value, CFUs. The detection limit denotes the smallest measure that can be detected with reasonable certainty for a given analytical procedure. Emma Griffiths detection limit GENEPIO:0002133 A disease cluster is an unusually high incidence of a particular disease or disorder occurring in close proximity in terms of both time and geography. Damion Dooley https://en.wikipedia.org/wiki/Disease_cluster disease cluster GENEPIO:0002134 A disease cluster in which two or more cases have been linked by an infectious disease transmission process. Damion Dooley infectious disease cluster GENEPIO:0002135 help:used only with the source feature key; source feature keys containing the /environmental_sample qualifier should also contain the /isolation_source qualifier. entries including /environmental_sample must not include the /strain qualifier Identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism. Environmental samples include clinical samples, gut contents, and other sequences from anonymous organisms that may be associated with a particular host. They do not include endosymbionts that can be reliably recovered from a particular host, organisms from a readily identifiable but uncultured field sample (e.g., many cyanobacteria), or phytoplasmas that can be reliably recovered from diseased plants (even though these cannot be grown in axenic culture). ENA Webin:environmental_feature EBI ENA Webin environmental feature GENEPIO:0002136 The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. Webin is an ENA interface and standard for sequence submissions. https://www.ebi.ac.uk/ena EBI European Nucleotide Archive Webin https://www.ebi.ac.uk/ena/WebFeat/ GENEPIO:0002137 help:Breadth of coverage should be reported as a percentage value (e.g. 95%) to a fold of coverage (e.g. 10X). breadth of coverage Eighty percent of the reference genome was covered by sequence fragments with a coverage depth of 4X; therefore, the breadth of coverage was 80% (4:5). Eighty percent of the reference genome was covered by sequence fragments with a coverage depth of 4X; therefore, the breadth of coverage was 80% (4:5). A data item which is the amount of a reference sequence covered by a sequence of interest. A data item which is the amount of a reference sequence covered by a sequence of interest. https://orcid.org/0000-0002-1107-9135 Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 OBI:0002879 breadth of coverage breadth of coverage GENEPIO:0002138 The mean contig length is the count of base pairs in the average size contig of the sequence assembly. Emma Griffiths mean contig length GENEPIO:0002139 order: GENEPIO:0000084 # read adapter trimming (y/n) GENEPIO:0002096 # read adapter trimming software GENEPIO:0002095 # read paired-end merging software GENEPIO:0000150 # read trimming and filtering software The procedures used to remove adapters from raw sequence reads, trim low quality bases and where applicable, merge paired-end reads. Emma Griffiths raw sequence data processing datum GENEPIO:0002140 Name of strain from which sample was obtained OR name of isolate from which sample was obtained. Damion Dooley specimen strain or isolate identifier \s*(\d(.\d{1,4})?|[1-8]\d(.\d{1,4})?|90(.0{1,4})?)\s*[WEwe]\s*(\d(.\d{1,4})?|[1-9]\d(.\d{1,4})?|1[0-7]\d(.\d{1,4})?|180(.0{1,4})?)\s*[NSns]\s* GENEPIO:0002141 The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W Damion Dooley https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ latitude and longitude coordinate (NCBI BioSample format) GENEPIO:0002142 decimal value specification GENEPIO:0002143 floating point value specification GENEPIO:0002144 unsigned integer A 32 bit number having a range 0 - 4294967295. unsigned integer value specification 1 1 GENEPIO:0002145 date value specification 1 GENEPIO:0002146 A specification for the size of an assembled genome as measured in base pairs. This is a decimal because the megabasepair unit may involve a fractional component. assembly genome size specification GENEPIO:0002147 sequencing facility name specification GENEPIO:0002148 date (ISO 8601) A date should be recorded as YYYY-MM-DD according to ISO 8601. HOWEVER ... OWL 2.0 does not include xsd:date as a permitted data type, so this value specification only accepts xsd:dateTime date value specification (ISO 8601) GENEPIO:0002149 strain identifier specification 1 5 100 GENEPIO:0002150 A MIC test measurement resulting from a laboratory diffusion method. Damion Dooley MIC diffusion measurement specification GENEPIO:0002151 unsigned short A 16 bit integer ranging from 0 - 65535 unsigned short integer value specification 1 GENEPIO:0002152 genomic sequence length specification 1 0.01 2048.0 GENEPIO:0002153 A MIC test measurement resulting from a laboratory dilution method. Damion Dooley MIC dilution measurement specification GENEPIO:0002154 The date on which a specimen was collected, in ISO 8601 format. specimen collection date (ISO 8601) GENEPIO:0002155 date of diagnosis (ISO 8601) 1 0 GENEPIO:0002156 A subject age is the age since birth of a given organism that is involved in an investigation or study at a given time. Damion Dooley subject age specification GENEPIO:0002157 subject age at time of specimen collection specification 1 GENEPIO:0002158 boolean A boolean value specification indicates a presence (true value) or absence (false value) of a given feature. Damion Dooley boolean value specification GENEPIO:0002159 specimen identifier specification [A-Za-z0-9]+([_.\-][A-Za-z0-9]+)*\@[A-Za-z0-9]+([.\-][A-Za-z0-9]+){1,3} GENEPIO:0002160 email address specification GENEPIO:0002161 region, province, state or territory specification GENEPIO:0002162 A specification for a geographic location that a specimen was collected at. specimen collection site specification GENEPIO:0002163 subject organism common name specification GENEPIO:0002164 A subject identifier specification is a specification including datatype pertaining to a given standard's subject identifier field. Damion Dooley subject identifier specification GENEPIO:0002165 Name of disease in a subject that is related to a given investigation, study and/or specimen. Damion Dooley NIAID GSCID-BRC metadata working group Controlled vocabulary. Human specimen source: https://bioportal.bioontology.org/ontologies/DOID or https://www.ncbi.nlm.nih.gov/mesh/1000067 subject disease specification GENEPIO:0002166 unsigned long integer A 64 bit integer ranging from 0 - 18446744073709551615 unsigned long integer value specification GENEPIO:0002167 The physical location that a specimen was collected at. The location may be described by geographic coordinates, city or other geopolitical entity, biome, etc. Damion Dooley specimen collection site GENEPIO:0002168 The unit provided for an antibiotic drug test dosage. Damion Dooley drug MIC unit specification GENEPIO:0002169 Damion Dooley A datum specification for the maximum concentration of a drug applied during an an assay. test drug maximum concentration specification GENEPIO:0002170 This is the minimum concentration of a drug applied during an an assay. Damion Dooley test drug minimum concentration specification (1/2|1/2a|1/2b|1/2c|3a|3b|3c|4a|4ab|4b|4c|4d|4e|1|7) GENEPIO:0002171 listeria antigen specification 1 url GENEPIO:0002172 URL specification GENEPIO:0002173 A travel destination is a destination city (or populated place of some scale) which a given human has travelled to on a particular trip. Damion Dooley travel destination specification GENEPIO:0002174 A specimen source substance is an organism substance or food product or environmental substance from which the specimen was extracted. Damion Dooley specimen source substance specification GENEPIO:0002175 Damion Dooley note: OBI has a variety of subclasses like "blood specimen" and "colon specimen" etc. which we have not added here. The are mapped to UBERON terms indirectly through the logic "derives from some [uberon term]". GenEpiO takes a different approach in describing this class with lists for "subject anatomical site", "subject body product", and "plant anatomy". specimen from organism specification 1 0 GENEPIO:0002176 duration specification GENEPIO:0002178 A field specification is the specification of a data field used in a data standard or database table. This includes at least a database field name, and optionally display name, description, and data type (binary blob, numeric, categorical, textual or cross-reference). Damion Dooley 2019-04-17T23:04:53Z obsolete: field specification true GENEPIO:0002181 Damion Dooley http://purl.obolibrary.org/obo/ARO_3004431 obsolete: antimicrobial resistance phenotype - epidemiological cut-off values true GENEPIO:0002185 Damion Dooley 2019-04-17T23:41:35Z PulseNet Canada field GENEPIO:0002186 Damion Dooley 2019-04-17T23:41:56Z PulseNet Canada Salmonella field GENEPIO:0002222 Damion Dooley 2019-05-03T02:44:38Z specimen collection service GENEPIO:0002223 Damion Dooley 2019-05-03T02:49:24Z bioinformatics analysis service GENEPIO:0002224 An isolate preparation service prepares isolates for molecular sequencing. Damion Dooley 2019-05-03T02:51:51Z isolate preparation service GENEPIO:0002225 order: GENEPIO:0002222 # specimen collection service GENEPIO:0002226 # specimen repository/biobank service GENEPIO:0002224 # isolate preparation service OBI:0001904 # sequencing service OBI:0000992 # DNA sequencing service GENEPIO:0002223 # bioinformatics analysis service Damion Dooley 2019-05-03T02:52:19Z specimen related service GENEPIO:0002226 Damion Dooley 2019-05-03T03:24:33Z specimen repository/biobank service GENEPIO:0002228 Vital signs are unstable and not within normal limits. Patient may be unconscious. Indicators are unfavorable. 2019-11-19T22:17:43Z grave critical health status critical critical GENEPIO:0002230 A datum indicating one of six defined subspecies of Salmonella. 2019-11-25T08:45:41Z Salmonella subspecies GENEPIO:0002231 A PFGE pattern resulting from DNA fragmentation induced by the Spel enzyme. 2019-11-25T09:07:26Z PFGE Spel pattern GENEPIO:0002232 A collection of organisms that is indicative of faecal contamination. 2020-02-08T20:15:43Z Fecal indicator organism collections include bacterial groups such as thermotolerant coliforms or E. coli. Hence, they only infer that pathogens may be present fecal indicator GENEPIO:0002233 An isolate derived from a food sample. Damion Dooley 2019-06-28T23:41:26Z food isolate GENEPIO:0002234 A method for typing The RNA component of the small (30S) subunit of prokaryotic ribosomes. 2020-04-24T19:06:05Z microbial 16S RNA typing h(1|2|3|4|5|6|7|8|9|10|11|12|14|15|16|17|18|19|21|23|24|26|27|28|29|30|31|32|33|34|35|36|37|38|39|40|41|42|43|44|45|46|47|48|49|51|52|53|54|55|56) GENEPIO:0002464 E. coli H antigen specification O([1-9][0-9][0-9]) GENEPIO:0002465 E. coli O antigen specification 1 GENEPIO:0002468 string string value specification GENEPIO:0002682 A sequencing platform brand provided by Helicos corporation (now defunct). 2020-04-24T22:50:49Z Helicos platform GENEPIO:0002683 A sequencing platform provided by the Ion Torrent company. 2020-04-24T22:54:06Z Ion Torrent platform GENEPIO:0002684 A sequencing platform provided by Life Technologies Corporation Sequencing by Oligonucleotide Ligation and Detection 2020-04-24T22:55:31Z SOLiD sequening platform GENEPIO:0002713 obsolete: drag swab true GENEPIO:0002749 Rinse is the liquid output of rinsing plant, animal or other material with liquid with the objective of extracting specimen material from that liquid. Damion Dooley 2019-06-28T20:07:25Z rinse GENEPIO:0002750 Animal rinse is a rinse derived from animal material of one or more animals. Damion Dooley 2019-06-28T20:11:45Z animal rinse GENEPIO:0003358 obsolete: surface wipe true GENEPIO:0004318 A low flat-bottomed laboratory container for growing a layer of organisms such as bacteria, molds, and cells on a thin layer of nutrient medium. https://en.wikipedia.org/wiki/Culture_plate 2022-09-23T10:59:09Z culture plate GENEPIO:0004323 A fluid that is obtained from rinsing meat for the purpose of collecting materials and organisms that are on its surface. 2022-09-23T11:24:53Z fluid from meat rinse GENEPIO:0004324 A sequencing platform provided by the BGI Genomics company. https://en.wikipedia.org/wiki/BGI_Group 2022-09-23T11:41:23Z BGI Genomics platform GENEPIO:0004325 A sequencing platform provided by the MGI company. https://en.wikipedia.org/wiki/MGI_(company) 2022-09-23T11:43:21Z MGI platform GENEPIO:0004326 A fecal specimen collection method in which feces is obtained by inserting the collection device into the anus of the host, or the feces is captured as it is excreted. Emma J Griffiths 2022-09-23T11:47:33Z fecal grab GENEPIO:0004432 A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. 2023-06-21T12:33:56Z Illumina NextSeq 1000 GENEPIO:0004433 An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://store.nanoporetech.com/flongle.html 2023-06-21T13:02:13Z Oxford Nanopore Flongle GENEPIO:0100000 A severe acute respiratory syndrome-related coronavirus which is 1) bat-derived, 2) sharing 93.3% nucleotide identity with SARS-CoV-2, and 3) contains an insertion at the S1/S2 cleavage site in the spike protein. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://en.wikipedia.org/wiki/RmYN02 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 RmYN02 GENEPIO:0100001 A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Cluster/Outbreak investigation https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 The terms cluster and outbreak both describe the occurrence of new disease cases within a particular location and time period. The number of cases within a cluster are not necessarily greater than what is expected, however in an outbreak the number of cases does exceed the usual norm. In an outbreak the cases are confirmed to be epidemiologically linked while in a cluster an epidemiological connection is only suspected. Not all clusters are outbreaks, however each cluster needs to be investigated. [Source: https://covid19evidencereviews.saskhealthauthority.ca/en/permalink/coviddoc153] cluster/outbreak investigation strategy GENEPIO:0100002 A sampling strategy in which individuals are sampled in the context of diagnostic testing. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Diagnostic testing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 diagnostic testing strategy GENEPIO:0100003 A sampling strategy in which individuals are sampled in order to perform research. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Research https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 research strategy GENEPIO:0100004 A sampling strategy in which individuals are sampled for surveillance investigations. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Surveillance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 surveillance strategy GENEPIO:0100005 A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Baseline surveillance (random sampling) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z random sampling Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Such that each possible unit has a fixed and known or equal probability of selection. [Source: "Random Sample" (p.238) in Porta, M. (2014). A Dictionary of Epidemiology (6th ed.). Oxford University Press, Incorporated.] baseline surveillance strategy GENEPIO:0100006 A surveillance sampling strategy in which an aspired outcome is explicity stated. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Targeted surveillance (non-random sampling) Target" (p.279) in Porta, M. (2014). A Dictionary of Epidemiology (6th ed.). Oxford University Press, Incorporated. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z non-random sampling Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 targeted surveillance strategy GENEPIO:0100007 A targeted surveillance strategy which is considered important and/or urgent. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Priority surveillance project https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 priority surveillance project strategy GENEPIO:0100008 A targeted surveillance strategy in which the aim is early detection of variants of concern (VoC) in individuals. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Screening for Variants of Concern (VoC) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z screening for VOC screening for VoC PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 screening for Variants of Concern strategy GENEPIO:0100009 A priority surveillance strategy in which subsets of a defined population can be identified who are, have been, or in the future may be exposed or not exposed - or exposed in different degrees - to a disease of interest and are selected to under go repeat sampling over a defined period of time. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Longitudinal surveillance (repeat sampling of individuals) Cohort Study" (p.50) in Porta, M. (2014). A Dictionary of Epidemiology (6th ed.). Oxford University Press, Incorporated. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z repeat sampling of individuals Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 longitudinal surveillance strategy GENEPIO:0100010 A priority surveillance strategy in which a population that previously tested positive for a disease of interest, and since confirmed to have recovered via a negative test, are monitored for positive test indication of re-infection with the disease of interest within a defined period of time. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Re-infection surveillance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 re-infection surveillance strategy GENEPIO:0100011 A priority surveillance strategy in which individuals are monitored for investigation into vaccine escape, i.e., identifying variants that contain mutations that counteracted the immunity provided by vaccine(s) of interest. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Vaccine escape surveillance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 vaccine escape surveillance strategy GENEPIO:0100012 A priority surveillance strategy in which individuals are selected if they have a travel history outside of the reporting region within a specified number of days before onset of symptoms. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Travel-associated surveillance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 travel-associated surveillance strategy GENEPIO:0100013 A travel-associated surveillance strategy in which individuals are selected if they have an intranational travel history within a specified number of days before onset of symptoms. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Domestic travel surveillance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 domestic travel surveillance strategy GENEPIO:0100014 A travel-associated surveillance strategy in which individuals are selected if they have a travel history outside of the reporting country in a specified number of days before onset of symptoms. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. International travel surveillance https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.37.2001641 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 international travel surveillance strategy GENEPIO:0100015 An international travel-associated surveillance strategy in which individuals are selected if they have a travel history of crossing an international border via air travel or ground transport. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Surveillance of international border crossing by air travel or ground transport https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 surveillance of international border crossing by air travel or ground transport strategy GENEPIO:0100016 An international travel-associated surveillance strategy in which individuals are selected if they have a travel history of crossing an international border via air travel. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Surveillance of international border crossing by air travel https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 surveillance of international border crossing by air travel strategy GENEPIO:0100017 An international travel-associated surveillance strategy in which individuals are selected if they have a travel history of crossing an international border via ground transport. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Surveillance of international border crossing by ground transport https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 surveillance of international border crossing by ground transport strategy GENEPIO:0100018 A travel-associated surveillance strategy in which individuals are selected if they have a travel history outside of the reporting country in a specified number of days before onset of symptoms. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Surveillance from international worker testing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 surveillance from international worker testing strategy GENEPIO:0100019 obsolete: cluster/outbreak investigation strategy true GENEPIO:0100020 An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that has connections to two or more jurisdictions. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Multi-jurisdictional outbreak investigation https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 multi-jurisdictional outbreak investigation strategy GENEPIO:0100021 An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that only has connections within a single jurisdiction. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Intra-jurisdictional outbreak investigation https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 intra-jurisdictional outbreak investigation strategy GENEPIO:0100022 obsolete: research strategy true GENEPIO:0100023 A research sampling strategy in which individuals are sampled in order to perform a viral passage experiment. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Viral passage experiment https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 viral passage experiment strategy GENEPIO:0100024 A research sampling strategy in which samples are collected in order to test a method or protocol. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Protocol testing Protocol testing experiment https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 protocol testing strategy GENEPIO:0100025 personal protective gown A personal protective clothing item which is a gown worn in order to provide a barrier between a person and the external environment. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-9578-0788 PPE gown personal protective equipment gown protective gown Rhiannon Cameron personal protective gown GENEPIO:0100026 A device which is used to collect liquid samples. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 collection cup GENEPIO:0100027 swab A device which is a soft, absorbent material mounted on one or both ends of a stick. A device which is a soft, absorbent material mounted on one or both ends of a stick. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-8395-2570 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 swab swab GENEPIO:0100028 An aspiration process which involves putting a needle through the skin just above the pubic bone into the bladder to take a urine sample. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z suprapubic aspiration GENEPIO:0100029 An aspiration process which collects tracheal secretions. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z tracheal aspiration GENEPIO:0100030 An aspiration process which uses a vacuum source to remove a sample. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z vacuum aspiration GENEPIO:0100031 A filtration process which removes solid particulates from the air via an air filtration device. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z air filtration GENEPIO:0100032 The collection of bronchoalveolar lavage fluid (BAL) from the lungs. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z BAL bronchoalveolar lavage GENEPIO:0100033 The administration and evacuation of small volumes of liquid through an orogastric tube to remove toxic substances within the stomach. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z gastric lavage GENEPIO:0100034 A collecting specimen from organism process in which a salt water solution is taken into the oral cavity, rinsed around, and gargled before being deposited into an external collection device. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z mouth rinse and gargle saline gargle GENEPIO:0100035 A specimen collection process in which a sample is collected by scraping a surface with a sterile sampling device. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z scraping GENEPIO:0100036 A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z finger prick GENEPIO:0100037 Antiviral treatment administered prior to the current regimen or test. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z prior antiviral treatment GENEPIO:0100038 A collecting specimen from organism process in which fluid is added to the eye prior to sample collection, effectively "washing out" ocular surface molecules. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z washout tear collection GENEPIO:0100039 The process of growing a virus in serial iterations. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z virus passage GENEPIO:0100040 A secondary RNA extraction after performing reverse transcription polymerase chain reaction (RT-PCR). The desired output is RNA. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z RNA re-extraction (post reverse transcription-polymerase chain reaction) RNA re-extraction (post RT-PCR) GENEPIO:0100041 293 cells stably expressing the SARS-CoV receptor protein, angiotensin-converting enzyme 2 (ACE2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z 293/hACE2 cell line 293/ACE2 cell line GENEPIO:0100042 Eptesicus fucus (big brown bat) kidney 3B cells. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Efk-3B clone 3B cell Efk3B cell Eptesicus fucus kidney 3B cell EFK3B cell line GENEPIO:0100043 Normal human primary renal cortical epithelial cells. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z human renal cortical epithelial cell line HRCE cell line GENEPIO:0100044 VeroE6 cells expressing the transmembrane serine protease TMPRSS2. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?ID=8668 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Vero E6/TMPRSS2 cell Vero-E6/TMPRSS2 cell VeroE6/TMPRSS2 cell line GENEPIO:0100045 The condition of being treated as a patient in a hospital without admission to an intensive care unit (ICU). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Hospitalized (Non-ICU) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Hospitalized (non-intensive care units) hospitalized (non-ICU) datum GENEPIO:0100046 The condition of being treated as a patient in a hospital intensive care unit (ICU). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Hospitalized (ICU) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Hospitalized (intensive care units) hospitalized (ICU) datum GENEPIO:0100047 Separation of people with a contagious disease from population to reduce the spread of the disease. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Mechanical Ventilation https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7338113/ https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z medically isolated datum GENEPIO:0100048 Medical isolation in a negative pressure environment: 6 to 12 air exchanges per hour, and direct exhaust to the outside or through a high efficiency particulate air filter. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Medically Isolated https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z medically isolated (negative pressure) datum GENEPIO:0100049 An age group that stratifies the age of a case to be between 0 to 9 years old (inclusive). 0 - 9 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (0 - 9) GENEPIO:0100050 An age group that stratifies the age of a case to be between 10 to 19 years old (inclusive). 10 - 19 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (10 - 19) GENEPIO:0100051 An age group that stratifies the age of a case to be between 20 to 29 years old (inclusive). 20 - 29 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (20 - 29) GENEPIO:0100052 An age group that stratifies the age of a case to be between 30 to 39 years old (inclusive). 30 - 39 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (30 - 39) GENEPIO:0100053 An age group that stratifies the age of a case to be between 40 to 49 years old (inclusive). 40 - 49 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (40 - 49) GENEPIO:0100054 An age group that stratifies the age of a case to be between 50 to 59 years old (inclusive). 50 - 59 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (50 - 59) GENEPIO:0100055 An age group that stratifies the age of a case to be between 60 to 69 years old (inclusive). 60 - 69 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (60 - 69) GENEPIO:0100056 An age group that stratifies the age of a case to be between 70 to 79 years old (inclusive). 70 - 79 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (70 - 79) GENEPIO:0100057 An age group that stratifies the age of a case to be between 80 to 89 years old (inclusive). 80 - 89 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (80 - 89) GENEPIO:0100058 An age group that stratifies the age of a case to be between 90 to 99 years old (inclusive). 90 - 99 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (90 - 99) GENEPIO:0100059 An age group that stratifies the age of a case to be greater than or equal to 100 years old. 100+ https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (100+) GENEPIO:0100060 Age of host at the time of sampling, expressed as an age group in years. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin GENEPIO:0100061 Inability to arouse in response to one or more external stimuli. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Inability to arouse (inability to stay awake) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z inability to stay awake inability to arouse GENEPIO:0100062 Persistent blue discoloration of the lips. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Cyanotic face (bluish face) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z bluish face cyanotic face GENEPIO:0100063 Generalized bluish discoloration of the body and the visible mucous membranes, which occurs due to inadequate oxygenation secondary to conditions that lead to an increase in deoxygenated hemoglobin or presence of abnormal hemoglobin. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z central cyanosis GENEPIO:0100064 Persistent blue discoloration of the lips. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Cyanotic lips (bluish lips) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z bluish lips cyanotic lips GENEPIO:0100065 Bluish discoloration of the distal extremities (hands, fingertips, toes), and can sometimes involve circumoral and periorbital areas. Mucous membranes are generally not involved. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z peripheral cyanosis GENEPIO:0100066 Fever that exceeds 38 degrees centigrade. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z fever (>=100.4°F) fever (>=38°C) GENEPIO:0100067 Focal or diffuse areas of ill-defined, hazy, increased lung attenuation, which cause pulmonary vascular indistinctness, yet through which vessels can still be identified via high-resolution computed tomography or the conventional radiograph. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Ground Glass Opacities (GGO) PMID: 12465687 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z GGO ground glass opacities GENEPIO:0100068 Abnormally low blood oxygen level without the presence of dyspnea/dyspnoea. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Silent hypoxemia https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397783/ https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z silent hypoxemia GENEPIO:0100069 Inflammation of infection of the ear. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Otitis https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z otitis GENEPIO:0100070 Fluid exuded from the pharynx posterior wall. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Pharyngeal exudate https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z pharyngeal exudate GENEPIO:0100071 Replaced with entity from an appropriate domain ontology. obsolete: prostration true GENEPIO:0100072 Inflammatory chilblain-like nodules on the hands and/or fingers. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Pseudo-chilblains on fingers (covid fingers) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z covid fingers pseudo-chilblains on fingers GENEPIO:0100073 Inflammatory chilblain-like nodules on the feet and/or toes. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Pseudo-chilblains on toes (covid toes) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z covid toes pseudo-chilblains on toes GENEPIO:0100074 Trauma to the cardiac muscle or valves. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C45430 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z cardiac injury GENEPIO:0100075 A reflex action of the respiratory tract that is used to clear the upper airways, lasting for more than 8 weeks Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z chronic cough GENEPIO:0100076 A persistent disease that affects the gastrointestinal tract. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z chronic gastrointestinal disease GENEPIO:0100077 The period of time less than or equal to six weeks after labor and delivery. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z postpartum (≤6 weeks) GENEPIO:0100078 The use of a drug for a reason other than which it was intended or in a manner or in quantities other than directed. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z drug abuse GENEPIO:0100079 The use of an injection drug for a reason other than which it was intended or in a manner or in quantities other than directed. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z injection drug abuse GENEPIO:0100080 An individual who is receiving or has received a transplant of a heart. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z cardiac transplant GENEPIO:0100081 An individual who is receiving or has received a transplant of a liver. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z liver transplant GENEPIO:0100082 A variant designation which is 1) a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), 2) believed to have genetic mutations that increase binding affinity to human cells, 3) linked to rapid spread in human populations, and 4) is being monitored. Variant of Concern (VOC) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z VOC VoC PHA4GE Definition: A category used for indicating that a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) containing genetic mutations believed to increase binding affinity to human cells and linked to rapid spread in human populations is being monitored. variant of concern (SARS-CoV-2) GENEPIO:0100083 A variant designation which is 1) a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), 2) demonstrated to have genetic mutations that increase binding affinity to human cells, 3) linked to rapid spread in human populations, and 4) is under surveillance. Variant of Interest (VOI) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z VOI PHA4GE Definition: A category used for indicating that a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) containing genetic mutations demonstrated to increase binding affinity to human cells and linked to rapid spread in human populations is under surveillance. variant of interest (SARS-CoV-2) GENEPIO:0100084 A disorder characterized by an arrhythmia with an above normal rate. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=21.09d&ns=ncit&code=C110938&key=n2078840696&b=1&n=null https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z tachyarrhythmia GENEPIO:0100085 A disease process that results in acute hypoxia secondary to a rapid deterioration in respiratory status.Increased capillary permeability and changes in pressure gradients within the pulmonary capillaries and vasculature are mechanisms for which noncardiogenic pulmonary edema occurs. To differentiate from cardiogenic pulmonary edema, pulmonary capillary wedge pressure is not elevated and remains less than 18 mmHg. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z noncardiogenic pulmonary edema GENEPIO:0100086 A clinical syndrome characterized by the acute onset of pulmonary edema following a significant central nervous system (CNS) insult. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z NPE neurogenic pulmonary edema GENEPIO:0100087 Redundant with "term replaced by" entity. obsolete: cardiac injury true GENEPIO:0100088 An acute form of myocarditis, whose main characteristic is a rapidly progressive clinical course with the need for hemodynamic support. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z fulminant myocarditis GENEPIO:0100089 A diagnosis of Kawasaki disease (KD) based on the fulfillment of a set of clinical signs including fever of five or more days' duration with at least four of the following five signs: (i) bilateral conjunctival injection, (ii) cervical lymphadenopathy, (iii) polymorphous skin rash, (iv) changes in the lips or oral mucosa, and (v) changes of the distal extremities.Usual laboratory findings in KD patients include elevated erythrocyte sedimentation rate and C-reactive protein, hypoalbuminemeia, elevated serum hepatic transaminases and leukocytosis with thrombocytosis noted later in the course of the illness. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z complete Kawasaki syndrome complete Kawasaki disease GENEPIO:0100090 A diagnosis of Kawasaki disease (KD) when patients fail to meet “classic” clinical features but have laboratory findings usually associated with KD and no reasonable alternate diagnosis, they are said to have incomplete or atypical KD. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z incomplete Kawasaki syndrome incomplete Kawasaki disease GENEPIO:0100091 A condition of liver damage that is characterized by coagulopathy with no signs of encephalopathy. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://doi.org/10.1016/j.aohep.2018.11.009 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z acute liver injury GENEPIO:0100092 A lung injury that results from mechanical stress and strain that occur during tidal ventilation in the susceptible lung. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z VILI ventilation induced lung injury GENEPIO:0100093 An injury in muscle tissue caused by bruising, spraining or laceration. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z muscle injury GENEPIO:0100094 An organ dysfunction to such a degree that normal homeostasis cannot be maintained without external clinical intervention. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://en.wikipedia.org/wiki/Organ_dysfunction https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z organ failure GENEPIO:0100095 A infection caused by staphylococcus bacteria, bearing the secondary infection role Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z If a secondary staphylococcus infection was identified during or after treatment of the primary infection. secondary staph infection GENEPIO:0100096 A infection caused by streptococcal bacteria, bearing the secondary infection role Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z If a secondary streptococcal infection was identified during or after treatment of the primary infection. secondary strep infection GENEPIO:0100097 A systemtic inflammatory response to infectious and/or non-fectious etiologies, resulting in life-threatening, generalized form of acute circulatory failure associated with inadequate oxygen utilization by the cells. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Descriptive of both infectious and non-infectious etiologies. hyperinflammatory shock GENEPIO:0100098 A persistent form of cardiogenic shock that presents as persistent tissue hyoperfusion despite administration of adequote doses of vasoactive medications and treatmenft of the underlying aetiology. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z refractory cardiogenic shock GENEPIO:0100099 A persistent form of cardiogenic shock that presents simultaneously with vasoplegic shock. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z refractory cardiogenic plus vasoplegic shock GENEPIO:0100100 A vaccination status in which an individual has completed a full series of an authorized vaccine according to the regional health institutional guidance. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z PHA4GE Definition: A category used for indicating that a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) containing genetic mutations demonstrated to increase binding affinity to human cells and linked to rapid spread in human populations is under surveillance. fully vaccinated GENEPIO:0100101 A vaccination status in which an individual has started but not yet fully completed a vaccine series authorized and administered according to the regional health institutional guidance. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z In general, people are considered partially vaccinated 2 weeks after their first dose in a single-dose or multi-dose vaccine series. partially vaccinated GENEPIO:0100102 A vaccination status in which an individual has not completed or initiated a vaccine series authorized and administered according to the regional health institutional guidance. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z unvaccinated In general, people are considered not vaccinated if they have not received a single dose or have not yet completed the 2 weeks after their first dose in a single-dose or multi-dose vaccine series. not vaccinated GENEPIO:0100103 A manufactured product which separates solids from fluids by adding a medium through which only a fluid can pass. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. http://purl.obolibrary.org/obo/NCIT_C41199 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 filter GENEPIO:0100104 An extract which is the output of an extraction process in which messenger RNA molecules are isolated from a specimen. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. mRNA (messenger RNA) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z messenger RNA extract mRNA extract GENEPIO:0100105 A DNA sequencer manufactured by the Illumina corporation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina sequencing instrument model GENEPIO:0100106 A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina Genome Analyzer GENEPIO:0100107 Rehomed in OBI obsolete: Illumina Genome Analyzer II true GENEPIO:0100108 Rehomed in OBI obsolete: Illumina Genome Analyzer IIx true GENEPIO:0100109 A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an "SQ Module" to support microfluidics. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina HiScanSQ GENEPIO:0100110 A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina HiSeq GENEPIO:0100111 A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that oenabled sufficent depth and coverage to produce the first 30x human genome for $1000. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina HiSeq X GENEPIO:0100112 A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina HiSeq X 5 Illumina HiSeq X Five GENEPIO:0100113 A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina HiSeq X 10 Illumina HiSeq X Ten GENEPIO:0100114 Rehomed in OBI obsolete: Illumina HiSeq 1000 true GENEPIO:0100115 A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina HiSeq 1500 GENEPIO:0100116 Rehomed in OBI obsolete: Illumina HiSeq 2000 true GENEPIO:0100117 Rehomed in OBI obsolete: Illumina HiSeq 2500 true GENEPIO:0100118 Rehomed in OBI obsolete: Illumina HiSeq 3000 true GENEPIO:0100119 Rehomed in OBI obsolete: Illumina HiSeq 4000 true GENEPIO:0100120 A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina iSeq GENEPIO:0100121 A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina iSeq 100 GENEPIO:0100122 A DNA sequencer manufactured by the Illunina corporation using sequence-by-synthesis chemistry that has an output capacirty of 6 Tb and 20 billion reads in dual flow cell mode. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina NovaSeq GENEPIO:0100123 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina NovaSeq 6000 GENEPIO:0100124 A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina MiniSeq GENEPIO:0100125 Rehomed in OBI obsolete: Illumina MiSeq true GENEPIO:0100126 A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina NextSeq GENEPIO:0100127 Rehomed in OBI obsolete: Illumina NextSeq 500 true GENEPIO:0100128 A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina NextSeq 550 GENEPIO:0100129 A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina NextSeq 2000 GENEPIO:0100130 A DNA sequencer manufactured by the Pacific Biosciences corporation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Pacific Biosciences sequencing instrument model GENEPIO:0100131 A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z PacBio RS GENEPIO:0100132 Rehomed in OBI obsolete: PacBio RS II true GENEPIO:0100133 A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z PacBio Sequel GENEPIO:0100134 A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z PacBio Sequel II GENEPIO:0100135 A DNA sequencer manufactured by the Ion Torrent corporation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Ion Torrent sequencing instrument model GENEPIO:0100136 A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Ion Torrent PGM GENEPIO:0100137 A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Ion Torrent Proton GENEPIO:0100138 A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Ion Torrent S5 XL GENEPIO:0100139 A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Ion Torrent S5 GENEPIO:0100140 A DNA sequencer manufactured by the Oxford Nanopore corporation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Oxford Nanopore sequencing instrument model GENEPIO:0100141 A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Oxford Nanopore GridION GENEPIO:0100142 A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Oxford Nanopore MinION GENEPIO:0100143 A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Oxford Nanopore PromethION GENEPIO:0100144 A DNA sequencer manufactured by the BGI Genomics corporation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z BGI Genomics sequencing instrument model GENEPIO:0100145 A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z BGI Genomics BGISEQ-500 GENEPIO:0100146 A DNA sequencer manufactured by the MGI corporation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z MGI sequencing instrument model GENEPIO:0100147 A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1~6TB of data per day. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z MGI DNBSEQ-T7 GENEPIO:0100148 A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB~1440GB per run. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z MGI DNBSEQ-G400 GENEPIO:0100149 A DNA sequencer manufactured by the MGI corporation with an outout capacity of 55GB~330GB per run, which enables faster sequencing than the DNBSEQ-G400. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z MGI DNBSEQ-G400RS FAST GENEPIO:0100150 A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z MGI DNBSEQ-G50 GENEPIO:0100151 A gene encoding the envelope protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf4 gene (SARS-CoV-2) E gene (SARS-CoV-2) GENEPIO:0100152 A gene encoding the membrane glycoprotrein M protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf5 gene (SARS-CoV-2) M gene (SARS-CoV-2) GENEPIO:0100153 A gene encoding the nucleocapsid phosphoprotein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf9 gene (SARS-CoV-2) N gene (SARS-CoV-2) GENEPIO:0100154 A gene encoding the Spike protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf2 gene (SARS-CoV-2) Spike gene (SARS-CoV-2) GENEPIO:0100155 A gene encoding the replicase polyprotein 1ab of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z rep gene (SARS-CoV-2) orf1ab gene (SARS-CoV-2) GENEPIO:0100156 A gene encoding the polyprotein 1a of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z pp1a gene (SARS-CoV-2) orf1a gene (SARS-CoV-2) GENEPIO:0100157 A gene encoding the nonstructural protein 11 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp11 gene (SARS-CoV-2) GENEPIO:0100158 A gene encoding the nonstructural protein 1 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp1 gene (SARS-CoV-2) GENEPIO:0100159 A gene encoding the nonstructural protein 2 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp2 gene (SARS-CoV-2) GENEPIO:0100160 A gene encoding the nonstructural protein 3 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp3 gene (SARS-CoV-2) GENEPIO:0100161 A gene encoding the nonstructural protein 4 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp4 gene (SARS-CoV-2) GENEPIO:0100162 A gene encoding the nonstructural protein 5 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp5 gene (SARS-CoV-2) GENEPIO:0100163 A gene encoding the nonstructural protein 6 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp6 gene (SARS-CoV-2) GENEPIO:0100164 A gene encoding the nonstructural protein 7 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp7 gene (SARS-CoV-2) GENEPIO:0100165 A gene encoding the nonstructural protein 8 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp8 gene (SARS-CoV-2) GENEPIO:0100166 A gene encoding the nonstructural protein 9 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp9 gene (SARS-CoV-2) GENEPIO:0100167 A gene encoding the nonstructural protein 10 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp10 gene (SARS-CoV-2) GENEPIO:0100168 A gene encoding the RNA-dependent RNA polymerase (RdRp) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp12 gene (SARS-CoV-2) RdRp gene (SARS-CoV-2) GENEPIO:0100169 A gene encoding the helicase (hel) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp13 gene (SARS-CoV-2) hel gene (SARS-CoV-2) GENEPIO:0100170 A gene encoding the nonstructural protein 14 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp14 gene (SARS-CoV-2) exoN gene (SARS-CoV-2) GENEPIO:0100171 A gene encoding the nonstructural protein 15 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp15 gene (SARS-CoV-2) GENEPIO:0100172 A gene encoding the nonstructural protein 16 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp16 gene (SARS-CoV-2) GENEPIO:0100173 A gene encoding the viroporin ORF3a of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf3a gene (SARS-CoV-2) GENEPIO:0100174 A gene encoding the polyprotein ORF3b of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf3b gene (SARS-CoV-2) GENEPIO:0100175 A gene encoding the nonstructural protein 6 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z ns6 gene (SARS-CoV-2) orf6 gene (SARS-CoV-2) GENEPIO:0100176 A gene encoding a transmembrane protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf7a gene (SARS-CoV-2) GENEPIO:0100177 A gene encoding the polyprotein ORF7b of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z ns7b gene (SARS-CoV-2) orf7b gene (SARS-CoV-2) GENEPIO:0100178 A gene encoding the nonstructural protein 8 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z ns8 gene (SARS-CoV-2) orf8 gene (SARS-CoV-2) GENEPIO:0100179 A gene encoding the viral accessory protein ORF9b of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf9b gene (SARS-CoV-2) GENEPIO:0100180 A gene encoding the membrane-associated protein ORF9c of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf9c gene (SARS-CoV-2) GENEPIO:0100181 A gene encoding the polyprotein ORF10 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf10 gene (SARS-CoV-2) GENEPIO:0100182 A gene encoding the uncharacterized protein ORF14 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf14 gene (SARS-CoV-2) GENEPIO:0100183 A genomic region that is untranslated at the 5' end of the genome of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. SARS-COV-2 5' UTR https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z SARS-CoV-2 5' untranslated region SARS-CoV-2 5'-UTR 5' UTR (SARS-CoV-2) GENEPIO:0100184 A process occuring within or in the vicinity of a human with a confirmed case of COVID-19 that exposes the recipient organism to SARS-CoV-2. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Contact with Known COVID-19 Case https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z contact with known COVID19 case contact with known COVID-19 case exposure process GENEPIO:0100185 A process occuring within or in the vicinity of a human patient that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Contact with Patient https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z contact with patient exposure process GENEPIO:0100186 A process occuring within or in the vicinity of a human with a probable case of COVID-19 that exposes the recipient organism to SARS-CoV-2. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Contact with Probable COVID-19 Case https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z contact with probable COVID19 case contact with probable COVID-19 case exposure process GENEPIO:0100187 A process occuring within or in the vicinity of a human with acute respiratory illness that exposes the recipient organism to said acute respiratory illness. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Contact with Person with Acute Respiratory Illness https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z contact with person with acute respiratory illness exposure process GENEPIO:0100188 A process occuring within or in the vicinity of a human with a fever and/or cough that exposes the recipient organism to the causative agent. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Contact with Person with Fever and/or Cough https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z contact with person with fever and/or cough exposure process GENEPIO:0100189 A process occuring within or in the vicinity of a human, who recently travelled, that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Contact with Person who Recently Travelled https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z contact with person who recently travelled exposure process GENEPIO:0100190 A process occuring within or in the vicinity of a human residential environment that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Occupational, Residency or Patronage Exposure https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z occupational, residency or patronage exposure process GENEPIO:0100191 A process occuring within or in the vicinity of an animal rescue facility that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Animal Rescue https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z animal rescue exposure process GENEPIO:0100192 A process occuring within or in the vicinity of a human childcare environment that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Childcare https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z childcare exposure process GENEPIO:0100193 A process occuring within or in the vicinity of a human daycare environment that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Daycare https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z daycare exposure process GENEPIO:0100194 A process occuring within or in the vicinity of a human nursery that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Nursery https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nursery exposure process GENEPIO:0100195 A process occuring within or in the vicinity of a community service centre that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Community Service Centre https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z community service centre exposure process GENEPIO:0100196 A process occuring within or in the vicinity of a correctional facility that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Correctional Facility https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z correctional facility exposure process GENEPIO:0100197 A process occuring within or in the vicinity of a dormitory that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Dormitory https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z dormitory exposure process GENEPIO:0100198 A process occuring within or in the vicinity of a first nations reserve that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. First Nations Reserve https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z first nations reserve exposure process GENEPIO:0100199 A process occuring within or in the vicinity of a fgroup home that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Funeral Home https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z funeral home exposure process GENEPIO:0100200 A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Group Home https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z group home exposure process GENEPIO:0100201 A process occuring within or in the vicinity of a healthcare environment that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Healthcare Setting https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z healthcare setting exposure process GENEPIO:0100202 A process occuring within or in the vicinity of an ambulance that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Ambulance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z ambulance exposure process GENEPIO:0100203 A process occuring within or in the vicinity of an acute care facility that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Acute Care Facility https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z acute care facility exposure process GENEPIO:0100204 A process occuring within or in the vicinity of a medical clinic that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Clinic https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z clinic exposure process GENEPIO:0100205 A process occuring within or in the vicinity of a community health centre that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Community Health Centre https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z community health centre exposure process GENEPIO:0100206 A process occuring within or in the vicinity of an emergency department that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Emergency Department https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z emergency department exposure process GENEPIO:0100207 A process occuring within or in the vicinity of an ICU that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. ICU https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z ICU intensive care unit exposure process GENEPIO:0100208 A process occuring within or in the vicinity of a hospital ward that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Ward https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z ward exposure process GENEPIO:0100209 A process occuring within or in the vicinity of a long-term care facility that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Long-Term Care Facility https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z LTC facility long-term care facility exposure process GENEPIO:0100210 A process occuring within or in the vicinity of a pharmacy that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Pharmacy https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z pharmacy exposure process GENEPIO:0100211 A process occuring within or in the vicinity of a physician's office that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Physician's Office https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z physician's Office exposure process GENEPIO:0100212 A process occuring within or in the vicinity of a household that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Household https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z household exposure process GENEPIO:0100213 A process occuring that exposes the recipient organism to a material entity as a consequence of said organism having insecure housing. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Insecure Housing (Homeless) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z homeless insecure housing exposure process GENEPIO:0100214 A process occuring within or in the vicinity of a human occupational environment that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Occupational Exposure https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z occupational exposure process GENEPIO:0100215 A process occuring within or in the vicinity of an office that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Worksite https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z worksite exposure process GENEPIO:0100216 A process occuring outdoors that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Outdoors https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z outdoors exposure process GENEPIO:0100217 A process that exposes the recipient organism to a material entity as a consequence of hiking. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Hiking Trail https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z hiking trail exposure process GENEPIO:0100218 A process occuring within or in the vicinity of a ski resort that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Ski Resort https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z ski resort exposure process GENEPIO:0100219 A directive information entity which realizes sample strategy specifications. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z sampling strategy specification GENEPIO:0100220 A process occuring within or in the vicinity of a place of worship that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Place of Worship https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z place of worship exposure process GENEPIO:0100221 A process occuring within or in the vicinity of a church that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Church https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z church exposure process GENEPIO:0100222 A process occuring within or in the vicinity of a mosque that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Mosque https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z mosque exposure process GENEPIO:0100223 A process occuring within or in the vicinity of a temple that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Temple https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z temple exposure process GENEPIO:0100224 A process occuring within or in the vicinity of a school that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. School https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z school exposure process GENEPIO:0100225 A process occuring within or in the vicinity of a temporary residence that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Temporary Residence https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z temporary residence exposure process GENEPIO:0100226 A process occuring within or in the vicinity of a homeless shelter that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Homeless Shelter https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z homeless shelter exposure process GENEPIO:0100227 A process occuring within or in the vicinity of a hotel exposure that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Hotel https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z hotel exposure process GENEPIO:0100228 A process occuring within or in the vicinity of a veterinary facility that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Veterinary Care Clinic https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z veterinary care clinic exposure process GENEPIO:0100229 A process occuring as a result of travel that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Travel Exposure https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z travel exposure process GENEPIO:0100230 A process occuring within or in the vicinity of a cruise ship that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Travelled on a Cruise Ship https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z travelled on a cruise ship exposure process GENEPIO:0100231 A process occuring within or in the vicinity of an airplane that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Travelled on a Plane https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z travelled on a plane exposure process GENEPIO:0100232 A process occuring within or in the vicinity of ground transport that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Travelled on Ground Transport https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z travelled on ground transport exposure process GENEPIO:0100233 An absence of antiviral treatment administered prior to the current regimen or test. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z no prior antiviral treatment GENEPIO:0100234 An infection that occurred within a host prior to the current infection. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z prior infection GENEPIO:0100235 A process occuring that exposes the recipient organism to a material entity. Other Exposure Setting https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z other exposure setting exposure process GENEPIO:0100236 An absence of infection that occurred within a host prior to the current infection. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z no prior infection GENEPIO:0100237 A type of social behavior in which a sufficent number of humans gather together such that there is potential strain on community resources. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Mass Gathering https://en.wikipedia.org/wiki/Mass_gathering https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z mass gathering exposure datum GENEPIO:0100238 A human mass gathering in which humans meet at an arranged place and time in order to discuss or engage in some common interest. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Convention https://en.wikipedia.org/wiki/Convention_(meeting) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z convention exposure datum GENEPIO:0100239 A human social gathering in which a group of humans formally assemble for a specific purpose. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Convocation https://en.wikipedia.org/wiki/Convocation https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z convocation exposure datum GENEPIO:0100240 A human social gathering at which humans gather for a planned or social occasion to carry out activities relevant to agriculture. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Agricultural Event https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z agricultural event exposure datum GENEPIO:0100241 A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage in a religious activity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Religious Gathering https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z religious gathering exposure datum GENEPIO:0100242 A human eucharistic liturgical gathering in which humans perform public worship. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Mass https://en.wikipedia.org/wiki/Mass_(liturgy) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z mass exposure datum GENEPIO:0100243 A human social event in which human family members congregate. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Family Gathering https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z family gathering exposure datum GENEPIO:0100244 A human social event in which many human members of an extended family congregate. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Family Reunion https://en.wikipedia.org/wiki/Family_reunion https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z family reunion exposure datum GENEPIO:0100245 A human social event in which humans gather for a ceremony connected with the final disposition of a corpse, such as a burial or cremation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Funeral https://en.wikipedia.org/wiki/Funeral https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z funeral exposure datum GENEPIO:0100246 Contact via airborne transmission or contact with contaminated surfaces. A type of contact in which an individual does not come in direct contact with a source of infection. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z indirect contact GENEPIO:0100247 A type of indirect contact where an individual sustains unprotected exposure by being within 6 feet of an infected individual over a sustained period of time. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z face-to-face contact close indirect contact GENEPIO:0100248 A type of indirect contact where an individual may at the same location at the same time as a positive case; however, they may have been there only briefly, or it may have been a location that carries a lower risk of transmission. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z casual indirect contact GENEPIO:0100249 A role inhering in a person that is realized when the bearer is present on a given occasion or at a given place. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Attendee https://www.merriam-webster.com/dictionary/attendee https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z attendee role GENEPIO:0100250 A role inhering in a person that is realized when the bearer travels in a vehicle but bears little to no responsibility for vehicle operation nor arrival at its destination. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Passenger https://en.wikipedia.org/wiki/Passenger https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z passenger role GENEPIO:0100251 A role inhering in a person that is realized when the bearer maintains residency in a given place. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Resident https://en.wikipedia.org/wiki/Resident https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z resident role GENEPIO:0100252 A role inhering in a person that is realized when the bearer pays a visit to a specific place or event. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Visitor https://en.wikipedia.org/wiki/Resident https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z visitor role GENEPIO:0100253 A role inhering in a person that is realized when the bearer enters into any service of their own free will. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Volunteer https://en.wiktionary.org/wiki/visitor https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z volunteer role GENEPIO:0100254 A role inhering in a person that is realized when the bearer performs labor for a living. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Work https://en.wiktionary.org/wiki/volunteer https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z work role GENEPIO:0100255 A role inhering in a person that is realized when the bearer is engaged in administration or administrative work. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Administrator https://en.wiktionary.org/wiki/worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z administrator role GENEPIO:0100256 A role inhering in a person that is realized when the bearer is among the first to arrive at the scene of an emergency and has specialized training to provide assistance. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. First Responder https://en.wikipedia.org/wiki/First_responder https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z first responder role GENEPIO:0100257 A role inhering in a person that is realized when the bearer is a rescuer extensively trained in firefighting. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Firefighter https://en.wikipedia.org/wiki/Firefighter https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z firefighter role GENEPIO:0100258 A role inhering in a person that is realized when the bearer is a healthcare professional who responds to emergency calls for medical help outside of a hospital. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Paramedic https://en.wikipedia.org/wiki/Paramedic https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z paramedic role GENEPIO:0100259 A role inhering in a person that is realized when the bearer is a warranted law employee of a police force. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Police Officer https://en.wikipedia.org/wiki/Police_officer https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z police officer role GENEPIO:0100260 A role inhering in a person that is realized when the bearer is an individual who performs cleaning duties and/or is responsible for the supervision of cleaning staff. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Housekeeper https://en.wikipedia.org/wiki/Housekeeper_(domestic_worker) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z housekeeper role GENEPIO:0100261 A role inhering in a person that is realized when the bearer is an employee that performs labor in a kitchen. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Kitchen Worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z kitchen worker role GENEPIO:0100262 A role inhering in a person that is realized when the bearer is an employee that performs labor in a laboratory. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Laboratory Worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z laboratory worker role GENEPIO:0100263 A role inhering in a person that is realized when the bearer works to help another person complete their daily activities. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Personal Care Aid https://www.careerexplorer.com/careers/personal-care-aide/#:~:text=A%20personal%20care%20aide%20is,as%20in%2Dhome%20caretakers). https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z personal care aide role personal care aid role GENEPIO:0100264 A role inhering in a person that is realized when the bearer is a health professional who specializes in dispensing prescription drugs at a healthcare facility. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Pharmacist https://en.wiktionary.org/wiki/pharmacist https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z pharmacist role GENEPIO:0100265 A role inhering in a person that is realized when the bearer is a professional who practices veterinary medicine. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Veterinarian https://en.wikipedia.org/wiki/Veterinarian https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z veterinarian role GENEPIO:0100266 A role inhering in a person that is realized when the bearer is in a state of being acquainted with a person. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Acquaintance of case https://en.wiktionary.org/wiki/acquaintance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z acquaintance role GENEPIO:0100267 A role inhering in a person that is realized when the bearer is a relative of the case. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Relative of case https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z relative role GENEPIO:0100268 A role inhering in a person that is realized when the bearer is a person younger than the age of majority. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Child of case https://en.wikipedia.org/wiki/Child https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z child role GENEPIO:0100269 A role inhering in a person that is realized when the bearer is a caregiver of the offspring of their own species. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Parent of case https://en.wikipedia.org/wiki/Parent https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z guardian of case role parent of caserole parent-guardian role GENEPIO:0100270 A role inhering in a person that is realized when the bearer is the male parent of a child. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Father of case https://en.wikipedia.org/wiki/Father https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z father role GENEPIO:0100271 A role inhering in a person that is realized when the bearer is the female parent of a child. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Mother of case https://en.wikipedia.org/wiki/Mother https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z mother role GENEPIO:0100272 A role inhering in a person that is realized when the bearer is a significant other in a marriage, civil union, or common-law marriage. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Spouse of case https://en.wikipedia.org/wiki/Spouse https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z spouse role GENEPIO:0100273 A variant surveillance strategy in which a sample is sequenced because the individual from which the sample is derived has a known epidemiological link to a variant case. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Sample has epidemiological link to Variant of Concern (VoC) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z sample has epidemiological link to VoC PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 sample has epidemiological link to Variant of Concern strategy GENEPIO:0100274 A variant surveillance strategy in which a sample is sequenced because the individual from which the sample is derived has a known epidemiological link to an Omicron variant case. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Sample has epidemiological link to Omicron Variant https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 sample has epidemiological link to Omicron variant strategy GENEPIO:0100275 A domestic travel-associated surveillance strategy in which individuals are selected if their travel occurred within a state/province within a nation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Interstate/ interprovincial travel surveillance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 interstate/ interprovincial travel surveillance strategy GENEPIO:0100276 A domestic travel-associated surveillance strategy in which individuals are selected if their travel occurred between states/provinces within a nation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Intra-state/ intra-provincial travel surveillance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 intra-state/ intra-provincial travel surveillance strategy GENEPIO:0100277 Yes [NCIT:C49488] A data field which describes whether the sample was collected from an individual in quarantine. sample collected in quarantine https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collected in quarantine slot PHA4GE SARS-CoV-2 Example Guidance: Whether a sample was collected under quarantine conditions (e.g. self-quarantining, medically isolated, staying at a quarantine hotel) can inform public health measure assessments. Use the picklist provided in the template. sample collected in quarantine field GENEPIO:0100278 Jitter added to publicly shared collection dates to prevent re-identifiability. A data field which describes how any data elements were altered to preserve patient privacy. data abstraction details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z data abstraction details slot PHA4GE SARS-CoV-2 Example Guidance: If applicable, provide a description of how each data element was abstracted. data abstraction details field GENEPIO:0100279 A variant designation which is 1) a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), 2) containing genetic mutates that may increase binding affinity to human cells, 3) linked to rapid spread in human populations, 4) is being monitored, and 5) denoted as a lower risk than a Variant of Interest (VOI). Variant Under Monitoring (VUM) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z VBM VUM Variant Being Monitored PHA4GE Definition: A category used for indicating that a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) containing genetic mutations that may increase binding affinity to human cells and linked to rapid spread in human populations is being monitored. This category denotes less risk than a Variant of Interest (VOI). variant under monitoring (SARS-CoV-2) GENEPIO:0100280 Derbyshire A data field which describes the county or region of origin of the sample. geo_loc name (county/region) geographical location county or region name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc name (county/region) slot geographical location county or region name field geographical location county or region name slot PHA4GE SARS-CoV-2 Example Guidance: Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz geo_loc name (county/region) field GENEPIO:0100281 ABCD1234 A data field which describes the identifier used to specify an epidemiologically detected case of disease. case ID case identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z case ID slot case identifier field case identifier slot Monkeypox Monkeypox-International CanCOGeN SARS-CoV-2 Example Guidance: Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. epidemiology case ID field GENEPIO:0100282 hCoV-19/Canada/prov_rona_99/2020 An identifier data field which describes the user-defined Global Initiative on Sharing Avian Influenza Data (GISAID) virus name assigned to the sequence. GISAID virus name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z GISAID virus name slot Global Initiative on Sharing Avian Influenza Data virus name field Global Initiative on Sharing Avian Influenza Data virus name slot Monkeypox PHA4GE SARS-CoV-2 Example Guidance: GISAID virus names should be in the format .hCoV-19/Country/Identifier/year.. GISAID virus name field GENEPIO:0100283 URI example: http://portal.vertnet.org/o/fmnh/mammals?id=33e55cfe-330b-40d9-aaae-8d042cba7542, INSDC triplet example: UAM:Mamm:52179 A data field which describes the identifier for the physical specimen. host specimen voucher https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host specimen voucher ID slot host specimen voucher identifier field host specimen voucher identifier slothost specimen voucher ID field host specimen voucher slot PHA4GE SARS-CoV-2 Example Guidance: Include a URI (Uniform Resource Identifier) in the form of a URL providing a direct link to the physical host specimen. If the specimen was destroyed in the process of analysis, electronic images (e-vouchers) are an adequate substitute for a physical host voucher specimen. If a URI is not available, a museum-provided globally unique identifier (GUID) can be used. If no persistent unique identifier is available, follow the INSDC guidance for populating the voucher_specimen attribute using standard triplets for institution codes (i.e., /specimen_voucher=.[<institution-code>:[<collection-code>:]]<specimen_id>.): http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier host specimen voucher field GENEPIO:0100284 /culture_collection="ATCC:26370 A data field which describes the name of the source collection and unique culture identifier. culture collection https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z culture collection slot PHA4GE SARS-CoV-2 Example Guidance: Format: .<institution-code>:[<collection-code>:]<culture_id>.. For more information, see http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier. culture collection ID field GENEPIO:0100285 CanCOGeN Sampling Strategy 1.0 A data field which describes the name of the sample plan implemented for sample collection. sample plan name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample plan name slot PHA4GE SARS-CoV-2 Example Guidance: Provide the name and version of the sample plan outlining the sample strategy. sample plan name field GENEPIO:0100286 A specimen datum which describes the collection, isolate production, sequencing, or storage of specimen material or data. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z specimen processing GENEPIO:0100288 An organism datum which contains additional contextual details regarding the health or disease status of a host at the time of sample collection. 2022-01-19T18:23:15.862Z host health status details at time of specimen collection GENEPIO:0100289 A personal health datum which specifies host health complications at time of specimen collection. 0000-0002-9578-0788 2022-01-31T23:52:14Z host health complications at time of specimen collection GENEPIO:0100290 A personal health datum which specifies host pre-existing conditions and risk factors at time of specimen collection. 0000-0002-9578-0788 2022-01-31T23:52:41Z pre-existing conditions and risk factors at time of specimen collection GENEPIO:0100291 A personal health datum which specifies host signs and symptoms at time of specimen collection. 0000-0002-9578-0788 2022-01-31T23:53:13Z signs and symptoms at time of specimen collection GENEPIO:0100293 An infection detail datum which is used for classifying a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), determined by the risk it poses based on available scientific evidence. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z variant designation (SARS-CoV-2) GENEPIO:0100294 A material entity encoding a genomic region of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z SARS-CoV-2 genomic region GENEPIO:0100295 A data item that describes an event in which exposure to a stressor may have occurred. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z exposure datum GENEPIO:0100296 A process in which a recipient organism is exposed to a material entity. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z exposure process GENEPIO:0100297 Redundant with "term replaced by" entity. obsolete: cell line cell true GENEPIO:0100298 A patient as host datum which indicates the vaccination status of the patient. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z vaccination status GENEPIO:0100299 A genomic region encoding a gene of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z SARS-CoV-2 gene GENEPIO:0100300 A data enumeration which references a set of named signs and symptoms entities. signs and symptoms https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z health signs and symptoms enumeration GENEPIO:0100301 A data enumeration which references a set of named pre-existing conditions and risk factors entities. pre-existing conditions and risk factors https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z pre-existing conditions and risk factors enumeration GENEPIO:0100302 A data enumeration which references a set of named complications entities. complications https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z health complications enumeration GENEPIO:0100303 A data enumeration which references a set of named person role entities. host role https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 person role enumeration GENEPIO:0100309 38.98 N A data field which describes the latitude coordinates of the geographical location of sample collection. geo_loc latitude geographical location latitude https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc latitude slot geographical location latitude field geographical location latitude slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 Example Guidance: Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format .d[d.dddd] N|S.. geo_loc latitude field GENEPIO:0100310 77.11 W A data field which describes the longitude coordinates of the geographical location of sample collection. geo_loc longitude geographical location longitude https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc longitude slot geographical location longitude field geographical location longitude slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 Example Guidance: Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format .d[dd.dddd] W|E.. geo_loc longitude field GENEPIO:0100311 25 swabs were pooled and further prepared as a single sample during library prep. A data field which describes detailed information regarding the processing applied to a sample during or after receiving the sample. specimen processing details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z specimen processing details slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a free text description of any processing details applied to a sample. specimen processing details field GENEPIO:0100312 Indigenous, European A host data field which describes the self-identified ethnicity(ies) of the host. host ethnicity https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host ethnicity slot PHA4GE SARS-CoV-2 Example Guidance: If known, provide the self-identified ethnicity or ethnicities of the host as a free text description. This is highly sensitive information which must be treated respectfully and carefully when sharing. The information may have implications for equitable access and benefit sharing. Consult your privacy officer, data steward and/or cultural services representative. host ethnicity field GENEPIO:0100313 Pfizer-BioNTech (Comirnaty) A data field which describes the name of the vaccine administered as the first dose of a vaccine regimen. vaccination dose 1 vaccine name vaccination dose one vaccine name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 1 vaccine name slot vaccination dose one vaccine name field vaccination dose one vaccine name slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list vaccination dose 1 vaccine name field GENEPIO:0100314 2021-03-01 A host data field which describes the date the first dose of a vaccine was administered. vaccination dose 1 vaccination date vaccination dose one vaccination date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 1 vaccination date slot vaccination dose one vaccination date field vaccination dose one vaccination date slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format .YYYY-MM-DD.. vaccination dose 1 vaccination date field GENEPIO:0100315 Pfizer-BioNTech (Comirnaty) A data field which describes the name of the vaccine administered as the second dose of a vaccine regimen. vaccination dose 2 vaccine name vaccination dose two vaccine name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 2 vaccine name slot vaccination dose two vaccine name field vaccination dose two vaccine name slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list vaccination dose 2 vaccine name field GENEPIO:0100316 2021-09-01 A host data field which describes the date the second dose of a vaccine was administered. vaccination dose 2 vaccination date vaccination dose two vaccination date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 2 vaccination date slot vaccination dose two vaccination date field vaccination dose two vaccination date slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format .YYYY-MM-DD.. vaccination dose 2 vaccination date field GENEPIO:0100317 Pfizer-BioNTech (Comirnaty) A data field which describes the name of the vaccine administered as the third dose of a vaccine regimen. vaccination dose 3 vaccine name vaccination dose three vaccine name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 3 vaccine name slot vaccination dose three vaccine name field vaccination dose three vaccine name slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the third dose by selecting a value from the pick list vaccination dose 3 vaccine name field GENEPIO:0100318 2021-12-30 A host data field which describes the date the third dose of a vaccine was administered. vaccination dose 3 vaccination date vaccination dose three vaccination date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 3 vaccination date slot vaccination dose three vaccination date field vaccination dose three vaccination date slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the date the third dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format .YYYY-MM-DD.. vaccination dose 3 vaccination date field GENEPIO:0100319 Pfizer-BioNTech (Comirnaty) A data field which describes the name of the vaccine administered as the fourth dose of a vaccine regimen. vaccination dose 4 vaccine name vaccination dose four vaccine name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 4 vaccine name slot vaccination dose four vaccine name field vaccination dose four vaccine name slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the fourth dose by selecting a value from the pick list vaccination dose 4 vaccine name field GENEPIO:0100320 2022-01-15 A host data field which describes the date the fourth dose of a vaccine was administered. vaccination dose 4 vaccination date vaccination dose four vaccination date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 4 vaccination date slot vaccination dose four vaccination date field vaccination dose four vaccination date slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the date the fourth dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format .YYYY-MM-DD.. vaccination dose 4 vaccination date field GENEPIO:0100321 Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 A host data field which describes the description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. vaccination history https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination history slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. vaccination history field GENEPIO:0100334 A role inhering in a person that is realized when the bearer is an employee that performs labor in a healthcare setting. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Healthcare Worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z healthcare worker role GENEPIO:0100354 A role inhering in a person that is realized when the bearer is an employee that performs labor which rotates according to a schedule. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Rotational Worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z rotational worker role GENEPIO:0100355 A role inhering in a person that is realized when the bearer is an employee that performs labor according to a seasonal schedule. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Seasonal Worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z seasonal worker role GENEPIO:0100356 A sampling strategy in which stored samples from past events are sequenced. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Retrospective sequencing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-02-25T05:13:49.123Z Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 retrospective sequencing strategy GENEPIO:0100357 A type of contact in which an individual comes in contact with an infected person, either directly or indirectly. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-02-28T05:08:07.274Z contact with infected individual GENEPIO:0100413 Air A data field which describes the type of entry point a traveler arrives through. travel point of entry type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z travel point of entry type slot CanCOGeN SARS-CoV-2 Example Guidance: Select the point of entry type. travel point of entry type field GENEPIO:0100414 day 1 A data field which describes the day a traveller was tested on or after arrival at their point of entry. border testing test day type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z border testing test day type slot CanCOGeN SARS-CoV-2 Example Guidance: Select the test day. border testing test day type field GENEPIO:0100415 A process occuring within or in the vicinty of a the individual home where the patient or client is living and health care or supportive care is being being delivered, as opposed to care provided in group accommodations like clinics or nursing home. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Community Healthcare (At-Home) Setting https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z at-home community healthcare exposure process GENEPIO:0100416 Public Health Ontario (PHO) A data field which describes the name of the agency that generated the sequence. sequenced by sequenced_by https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequenced by slot GRDI Monkeypox-International Monkeypox Example Guidance: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the .National Microbiology Laboratory (NML).. sequenced by field GENEPIO:0100417 A mass gathering event where the primary emphasis is on recreation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Recreational Event https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z CanCOGeN SARS-CoV-2 recreational event datum GENEPIO:0100418 A recreational event where the primary emphasis is on a concert performance. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Concert https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z CanCOGeN SARS-CoV-2 concert event datum GENEPIO:0100419 A recreational event where the primary emphasis is a sporting deemonstration or athletic competition. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Sporting Event https://www.lawinsider.com/dictionary/sporting-and-recreational-event#:~:text=Related%20Definitions&text=Sporting%20and%20Recreational%20Event%20means,yoga%2C%20and%20other%20exercise%20gatherings. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z CanCOGeN SARS-CoV-2 sporting event datum GENEPIO:0100420 A role inhering in a person that is realized when the bearer a professional caregiver that provides health care or supportive care in the individual home where the patient or client is living, as opposed to care provided in group accommodations like clinics or nursing home. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Community Healthcare Worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z community healthcare worker GENEPIO:0100422 RespLab@lab.ca A data field which describes the email address of the contact responsible for follow-up regarding the sequence. sequenced by contact email sequenced_by_contact_email https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequenced by contact email slot GRDI Monkeypox-International Monkeypox Example Guidance: The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca sequenced by contact email field GENEPIO:0100423 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada A data field which describes the mailing address of the agency submitting the sequence. sequenced by contact address https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequenced by contact address slot Monkeypox-International Monkeypox Example Guidance: The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country sequenced by contact address field GENEPIO:0100427 bvn5567, RA1-HH789 A data field which describes an alternative sample identifier assigned to the sample by another organization. alternative sample ID alternative sample identifier alternative_sample_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z alternative sample ID slot alternative sample identifier field alternative sample identifier slot GRDI Example Guidance: Provide any alternative identifiers for the sample here, separated by commas. Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. If the information is unknown or cannot be provided, leave blank or provide a null value. alternative sample ID field GENEPIO:0100428 Topp Lab A data field which describes the specific laboratory affiliation of the sample collector. sample collected by laboratory name sample_collected_by_laboratory_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collected by laboratory name slot GRDI Example Guidance: Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. sample collected by laboratory name field GENEPIO:0100429 Watershed Project (HA-120) A data field which describes the project/initiative/program for which the sample was collected. sample collection project name sample_collection_project_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collection project name slot GRDI Example Guidance: Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. sample collection project name field GENEPIO:0100430 National Microbiological Baseline Study in Broiler Chicken A data field which describes the name of the study design for a surveillance project. sample plan name sample_plan_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample plan name slot GRDI Example Guidance: Provide the name of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. sample plan name field GENEPIO:0100431 2001_M205 A data field which describes the identifier of the study design for a surveillance project. sample plan ID sample plan identifier sample_plan_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample plan ID slot sample plan identifier field sample plan identifier slot GRDI Example Guidance: Provide the identifier of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. sample plan ID field GENEPIO:0100432 Enterics Lab Manager A data field which describes the name or job title of the contact responsible for follow-up regarding the sample. sample collector contact name sample_collector_contact_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collector contact name slot GRDI Example Guidance: Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. sample collector contact name field GENEPIO:0100433 Antimicrobial pre-treatment [GENEPIO:0100537] A data field which describes the activities or variables introduced upstream of sample collection that may affect the sample collected. presampling activity presampling_activity https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z presampling activity slot GRDI Example Guidance: If there was presampling activity that would affect the sample prior to collection (this is different than sample processing which happens after the sample is collected), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. presampling activity field GENEPIO:0100434 Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter. A data field which describes the details of the activities or variables introduced upstream of sample collection that may affect the sample collected. presampling activity details presampling_activity_details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z presampling activity details slot GRDI Example Guidance: Briefly describe the presampling activity details using free text. presampling activity details field GENEPIO:0100435 Samples pooled [OBI:0600016] A data field which describes the processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures. specimen processing specimen_processing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z specimen processing slot GRDI Example Guidance: Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. specimen processing field GENEPIO:0100436 Credit River" as opposed to "river A data field which describes the name of a specific geographical location (i.e. toponym). geo_loc name (site) geographical location site name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc name (site) slot geographical location site name field geographical location site name slot GRDI Example Guidance: Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). geo_loc name (site) field GENEPIO:0100437 United States of America [GAZ:00002459] A data field which describes the country of origin of a food product. food product origin geo loc name (country) food product origin geographical location country name food_product_origin geo_loc_name (country) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food product origin geo loc name (country) slot food product origin geographical location country name field food product origin geographical location country name slot GRDI Example Guidance: If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. food product origin geo loc name (country) field GENEPIO:0100438 South Africa [GAZ:00001094] A host geographical location field which describes the country of origin of the host. host origin geo loc name (country) host origin geographical location name host_origin geo_loc_name (country) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host origin geo loc name (country) slot host origin geographical location name field host origin geographical location name slot GRDI Example Guidance: If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. host origin geo loc name (country) field GENEPIO:0100439 RTE Prosciutto from deli A data field which describes the original sample description provided by the sample collector. original sample description original_sample_description https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z original sample description slot GRDI Example Guidance: Provide the sample description provided by the original sample collector. The original description is useful as it may provide further details, or can be used to clarify higher level classifications. original sample description field GENEPIO:0100440 5 m A data field which describes the depth of some water. water depth water_depth https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z water depth slot GRDI Example Guidance: Provide the depth of water with a value and unit. water depth field GENEPIO:0100441 25C A data field which describes the temperature of some air. air temperature air_temperature https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z air temperature slot GRDI Example Guidance: Provide the temperature of the air with a value and unit. Do not provide a symbol for degree e.g. oC air temperature field GENEPIO:0100442 Rain [ENVO:01001564] A data field which describes the state of the atmosphere at a place and time. Regarding heat, dryness, sunshine, wind, rain, etc. weather type weather_type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z weather type slot GRDI Example Guidance: Provide the weather conditions at the time of sample collection. weather type field GENEPIO:0100443 Turkey [NCBITaxon:9103] A data field which describes the type of animal or plant population inhabiting an area. animal or plant population animal_or_plant_population https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z animal or plant population slot GRDI Example Guidance: This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank. animal or plant population field GENEPIO:0100444 Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] A data field which describes material consumed and digested for nutritional value or enjoyment. food product food_product https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food product slot GRDI Example Guidance: This field includes animal feed. If applicable, provide the standardized term and ontology ID for the anatomical material. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/foodon. If not applicable, leave blank. food product field GENEPIO:0100445 Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] A data field which describes any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers. food product properties food_product_properties https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food product properties slot GRDI Example Guidance: Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). food product properties field GENEPIO:0100446 Chicken [NCBITaxon:9031] A data field which describes the animal from which the food product was derived. animal source of food animal_source_of_food https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z animal source of food slot GRDI Example Guidance: Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma. animal source of food field GENEPIO:0100447 Plastic tray or pan [FOODON:03490126] A data field which describes the type of packaging used to contain a food product. food packaging food_packaging https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food packaging slot GRDI Example Guidance: If known, provide information regarding how the food product was packaged. food packaging field GENEPIO:0100448 Frozen at -20C A data field which describes the way that a specimen is or was stored. sample storage method sample_storage_method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample storage method slot GRDI Example Guidance: Provide a description of how the same was stored. sample storage method field GENEPIO:0100449 PBS + 20% glycerol A data field which describes the material or matrix in which a sample is stored. sample storage medium sample_storage_medium https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample storage medium slot GRDI Example Guidance: Provide a description of the material or matrix used to store the sample. sample storage medium field GENEPIO:0100450 Sea ecotype A host field which describes the biotype resulting from selection in a particular habitat. host (ecotype) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host (ecotype) slot GRDI Example Guidance: Provide the name of the ecotype of the host organism. host (ecotype) field GENEPIO:0100451 Holstein A host field which describes a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. host (breed) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host (breed) slot GRDI Example Guidance: Provide the name of the breed of the host organism. host (breed) field GENEPIO:0100452 Calf [FOODON:03411349] A host field which describes the name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. host (food production name) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host (food production name) slot GRDI Example Guidance: Select the host's food production name from the pick list. host (food production name) field GENEPIO:0100453 An instance of the "strain and isolation information field category" that contains the "isolate received date field". An instance of the "strain and isolation information field category" that contains the "microbiological method field". A data field category which refers to strain and isolation information fields. strain and isolation information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z 2022-06-25T03:32:51.876Z strain and isolation information slot category GRDI strain and isolation information field category GENEPIO:0100454 MFHPB-30 A data field which describes the laboratory method used to grow, prepare, and/or isolate the microbial isolate. microbiological method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z microbiological method slot GRDI Example Guidance: Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. microbiological method field GENEPIO:0100455 K12 A data field which describes the strain identifier. strain https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z strain slot GRDI Example Guidance: A population or type of organisms that is genetically different from others of the same species and possessing a set of defined characteristics. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. strain field GENEPIO:0100456 SARS-CoV-2/human/USA/CA-CDPH-001/2020 A data field which describes the identifier of the specific isolate. isolate isolate ID isolate identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolate ID slot isolate field isolate identifier field isolate identifier slot isolate slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the .isolate. name is propagated throughtout different databases. As such, structure the .isolate. name to be ICTV/INSDC compliant in the following format: .SARS-CoV-2/host/country/sampleID/date.. isolate ID field GENEPIO:0100457 PHAC_45678 A data field which describes an isolate identifier assigned to the isolate by another organization. alternative isolate ID alternative isolate identifier alternative_isolate_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z alternative isolate ID slot alternative isolate identifier field alternative isolate identifier slot GRDI Example Guidance: If one or more alternative isolate_IDs are available, record them all here, separated by a comma. alternative isolate ID field GENEPIO:0100458 SUB_ON_1526 A data field which describes the identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. progeny isolate ID progeny isolate identifier progeny_isolate_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z progeny isolate ID slot progeny isolate identifier field progeny isolate identifier slot GRDI Example Guidance: If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. progeny isolate ID field GENEPIO:0100459 GRDI_LL_12345 A data field which describes the identifier of the isolate in the Integrated Rapid Infectious Disease Analysis (IRIDA) platform. IRIDA isolate ID IRIDA isolate identifier IRIDA_isolate_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z IRIDA isolate ID slot IRIDA isolate identifier field IRIDA isolate identifier slot Integrated Rapid Infectious Disease Analysis isolate ID field Integrated Rapid Infectious Disease Analysis isolate ID slot Integrated Rapid Infectious Disease Analysis isolate identifier field Integrated Rapid Infectious Disease Analysis isolate identifier slot GRDI Example Guidance: Provide the .sample ID. used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices. IRIDA isolate ID field GENEPIO:0100460 666 A data field which describes the identifier of the project in the Integrated Rapid Infectious Disease Analysis (IRIDA) platform. IRIDA project ID IRIDA project identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z IRIDA project ID slot IRIDA project identifier field IRIDA project identifier slot Integrated Rapid Infectious Disease Analysis project ID field Integrated Rapid Infectious Disease Analysis project ID slot Integrated Rapid Infectious Disease Analysis project identifier field Integrated Rapid Infectious Disease Analysis project identifier slot GRDI Example Guidance: Provide the IRIDA .project ID.. IRIDA project ID field GENEPIO:0100461 Public Health Agency of Canada (PHAC) [GENEPIO:0100551] A data field which describes the name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. isolated by isolated_by https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolated by slot GRDI Example Guidance: Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. isolated by field GENEPIO:0100462 Topp Lab A data field which describes the specific laboratory affiliation of the individual who performed the isolation procedure. isolated by laboratory name isolated_by_laboratory_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolated by laboratory name slot GRDI Example Guidance: Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. isolated by laboratory name field GENEPIO:0100463 Enterics Lab Manager A data field which describes the name or title of the contact responsible for follow-up regarding the isolate. isolated by contact name isolated_by_contact_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolated by contact name slot GRDI Example Guidance: Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. isolated by contact name field GENEPIO:0100464 enterics@lab.ca A data field which describes the email address of the contact responsible for follow-up regarding the isolate. isolated by contact email isolated_by_contact_email https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolated by contact email slot GRDI Example Guidance: Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. isolated by contact email field GENEPIO:0100465 2020-10-30 A date field which describes the date on which the isolate was isolated from a sample. isolation date isolation_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolation date slot GRDI Example Guidance: Provide the date according to the ISO 8601 standard .YYYY-MM-DD., .YYYY-MM. or .YYYY.. isolation date field GENEPIO:0100466 2020-11-15 A date field which describes the date on which the isolate was received by the laboratory. isolate received date isolate_received_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolate received date slot GRDI Example Guidance: Provide the date according to the ISO 8601 standard .YYYY-MM-DD., .YYYY-MM. or .YYYY.. isolate received date field GENEPIO:0100467 Heidelberg A data field which describes the serovar of the organism. serovar https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z serotype field serotype slot serovar slot GRDI Example Guidance: Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. serovar field GENEPIO:0100468 SISTR 1.0.1 A data field which describes the method used to determine the serovar. serotyping method serotyping_method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z serotyping method slot GRDI Example Guidance: If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. serotyping method field GENEPIO:0100469 47 A data field which describes the phagetype of the organism. phagetype https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z phagetype slot GRDI Example Guidance: Provide if known. If unknown, put “missing”. phagetype field GENEPIO:0100470 Topp Lab A data field which describes the specific laboratory affiliation of those responsible for sequencing the isolate's genome. sequenced by laboratory name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequenced by laboratory name slot GRDI Example Guidance: Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. sequenced by laboratory name field GENEPIO:0100471 Enterics Lab Manager A data field which describes the name or title of the contact responsible for follow-up regarding the sequence. sequenced by contact name sequenced_by_contact_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequenced by contact name slot GRDI Example Guidance: Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. sequenced by contact name field GENEPIO:0100472 AMR-GRDI (PA-1356) A data field which describes the name of the project/initiative/program for which sequencing was performed. sequencing project name sequencing_project_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing project name slot GRDI Example Guidance: Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. sequencing project name field GENEPIO:0100473 Illumina [GENEPIO:0001923] A data field which describes the platform technology used to perform the sequencing. sequencing platform sequencing_platform https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing platform slot GRDI Example Guidance: Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. sequencing platform field GENEPIO:0100474 Enterics Lab Manager A data field which describes the name or title of the contact responsible for follow-up regarding the submission of the sequence to a repository or database. sequence submitted by contact name sequence_submitted_by_contact_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z sequence submitted by contact name slot GRDI Example Guidance: Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. sequence submitted by contact name field GENEPIO:0100475 PMID: 33205991 A data field which describes the identifier for a publication. publication ID publication identifier publication_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z publication ID slot publication identifier field publication identifier slot GRDI Example Guidance: If the isolate is associated with a published work which can provide additional information, provide the PubMed identifier of the publication. Other types of identifiers (e.g. DOI) are also acceptable. publication ID field GENEPIO:0100476 Pathogen.env A data field which describes the attribute package used to structure metadata in an International Nucleotide Sequence Database Collaboration (INSDC) BioSample. attribute package attribute_package https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z attribute package slot GRDI Example Guidance: If the sample is from a specific human or animal, put “Pathogen.cl”. If the sample is from an environmental sample including food, feed, production facility, farm, water source, manure etc, put “Pathogen.env”. attribute package field GENEPIO:0100477 An instance of the "public repository information field category" that contains the "publication ID field". A data field category which refers to public repository information fields. public repository information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-06-25T03:32:51.876Z public repository information slot category GRDI public repository information field category GENEPIO:0100478 An instance of the "risk assessment information field category" that contains the "prevalence metrics field". A data field category which refers to risk assessment information fields. risk assessment information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-06-25T03:32:51.876Z risk assessment information slot category GRDI risk assessment information field category GENEPIO:0100479 An instance of the "antimicrobial resistance field category" that contains the "AMR* laboratory typing method field". *AMR = antimicrobial resistance A data field category which refers to antimicrobial resistance fields. antimicrobial resistance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-06-25T03:32:51.876Z antimicrobial resistance slot category GRDI antimicrobial resistance field category GENEPIO:0100480 Number of total samples collected, Number of positive samples A data field which describes metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. prevalence metrics prevalence_metrics https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z prevalence metrics slot GRDI Example Guidance: Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are . Number of total samples collected., .Number of positive samples., .Average count of hazard organism., .Average count of indicator organism.. You do not need to provide the actual values, just indicate that the information is available. prevalence metrics field GENEPIO:0100481 Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. A data field which describes the details pertaining to the prevalence metrics from a surveillance project. prevalence metrics details prevalence_metrics_details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z prevalence metrics details slot GRDI Example Guidance: If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. prevalence metrics details field GENEPIO:0100482 Abattoir [ENVO:01000925] A data field which describes the stage of food production. stage of production stage_of_production https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z stage of production slot GRDI Example Guidance: Provide the stage of food production from which the sample was taken. Select a value form the pick list provided. stage of production field GENEPIO:0100483 Vaccination [NCIT:C15346] A data field which describes the category of the experimental intervention applied in the food production system. experimental intervention experimental_intervention https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z experimental intervention slot GRDI Example Guidance: In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. experimental intervention field GENEPIO:0100484 2% cranberry solution mixed in feed a data field which describes the details of the experimental intervention applied in the food production system. experiment intervention details experiment_intervention_details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z experiment intervention details slot GRDI Example Guidance: If an experimental intervention was applied in the survey, provide details in this field as free text. experiment intervention details field GENEPIO:0100485 A role inhering in a person that is realized when the bearer is engaged in child care or education work. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Child Care/Education Worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z CanCOGeN SARS-CoV-2 child care or education worker GENEPIO:0100486 A role inhering in a person that is realized when the bearer is engaged in operations and services that are essential to ensure the continuity of critical infrastructure operations. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Essential Worker http://purl.obolibrary.org/obo/NCIT_C179411 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z CanCOGeN SARS-CoV-2 essential worker GENEPIO:0100487 A role inhering in a person that is realized when the bearer is an employee that performs labor internationally. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. International worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z CanCOGeN SARS-CoV-2 international worker GENEPIO:0100488 A role inhering in a person that is realized when the bearer is engaged in transportation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Transport Worker https://www.lawinsider.com/dictionary/transportation-worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z CanCOGeN SARS-CoV-2 transport worker GENEPIO:0100489 A transport worker role inhering in a person that is realized when the bearer is the driver of a transport truck. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Transport Truck Driver https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z CanCOGeN SARS-CoV-2 transport truck driver GENEPIO:0100500 A role inhering in a person that is realized when the bearer is a sexual partner of the case. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Sexual partner of case https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z sexual partner role GENEPIO:0100501 A process occuring within or in the vicinity of a human with a confirmed case of COVID-19 that exposes the recipient organism to Monkeypox. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Contact with Known Monkeypox Case https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z contact with known Monkeypox case Monkeypox-International Monkeypox contact with known Monkeypox case exposure process GENEPIO:0100502 A process occuring within or in the vicinity of a human with a probable case of COVID-19 that exposes the recipient organism to Monkeypox. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Contact with Probable Monkeypox Case https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z contact with probable Monkeypox case Monkeypox-International Monkeypox contact with probable Monkeypox case exposure process GENEPIO:0100511 Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] A data field which describes the name of the organization that performed the antimicrobial resistance (AMR) testing. AMR testing by AMR_testing_by antimicrobial resistance testing by https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing by slot antimicrobial resistance testing by field antimicrobial resistance testing by slot GRDI Example Guidance: Provide the name of the agency, organization or institution that performed the AMR testing, in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. AMR testing by field GENEPIO:0100512 Topp Lab A data field which describes the name of the lab within the organization that performed the antimicrobial resistance (AMR) testing. AMR testing by laboratory name AMR_testing_by_laboratory_name antimicrobial resistance testing by laboratory name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing by laboratory name slot antimicrobial resistance testing by laboratory name field antimicrobial resistance testing by laboratory name slot GRDI Example Guidance: Provide the name of the specific laboratory that performed the AMR testing (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. AMR testing by laboratory name field GENEPIO:0100513 Enterics Lab Manager A data field which describes the name of the individual or the individual's role in the organization that performed the antimicrobial resistance (AMR) testing. AMR testing by contact name AMR_testing_by_contact_name antimicrobial resistance testing by contact name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing by contact name slot antimicrobial resistance testing by contact name field antimicrobial resistance testing by contact name slot GRDI Example Guidance: Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR testing by contact name field GENEPIO:0100514 johnnyblogs@lab.ca A data field which describes the email of the individual or the individual's role in the organization that performed the antimicrobial resistance (AMR) testing. AMR testing by contact email AMR_testing_by_contact_email antimicrobial resistance testing by contact email https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing by contact email slot antimicrobial resistance testing by contact email field antimicrobial resistance testing by contact email slot GRDI Example Guidance: Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR testing by contact email field GENEPIO:0100515 2022-04-03 A data field which describes the date the antimicrobial resistance (AMR) testing was performed. AMR testing date AMR_testing_date antimicrobial resistance testing date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing date slot antimicrobial resistance testing date field antimicrobial resistance testing date slot GRDI Example Guidance: Provide the date according to the ISO 8601 standard .YYYY-MM-DD., .YYYY-MM. or .YYYY.. AMR testing date field GENEPIO:0100516 8 An antimicrobial resistance (AMR) field which describes the maximum measurement for a sample to be considered “sensitive” to this antibiotic. Dependent on the units specified in the 'AMR measurement units field' [GENEPIO:0100523]. AMR testing susceptible breakpoint AMR_testing_susceptible_breakpoint antimicrobial resistance testing susceptible breakpoint https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing susceptible breakpoint slot antimicrobial resistance testing susceptible breakpoint field antimicrobial resistance testing susceptible breakpoint slot GRDI Example Guidance: This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. AMR testing susceptible breakpoint field GENEPIO:0100517 16 An antimicrobial resistance (AMR) field which describes intermediate measurement(s) where a sample would be considered to have an “intermediate” phenotype for this antibiotic. Dependent on the units specified in the 'AMR measurement units field' [GENEPIO:0100523]. AMR testing intermediate breakpoint AMR_testing_intermediate_breakpoint antimicrobial resistance testing intermediate breakpoint https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing intermediate breakpoint slot antimicrobial resistance testing intermediate breakpoint field antimicrobial resistance testing intermediate breakpoint slot GRDI Example Guidance: This field should only contain a number (either an integer or a number with decimals), since the qualifier is implied. AMR testing intermediate breakpoint field GENEPIO:0100518 32 An antimicrobial resistance (AMR) field which describes minimum measurement for a sample to be considered “resistant” to this antibiotic. Dependent on the units specified in the 'AMR measurement units field' [GENEPIO:0100523]. AMR testing resistant breakpoint AMR_testing_resistant_breakpoint antimicrobial resistance testing resistant breakpoint https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing resistant breakpoint slot antimicrobial resistance testing resistant breakpoint field antimicrobial resistance testing resistant breakpoint slot GRDI Example Guidance: This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. AMR testing resistant breakpoint field GENEPIO:0100520 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. An antimicrobial resistance (AMR) field which describes additional details associated with the testing standard used for determination of resistance phenotype. AMR testing standard details AMR_testing_standard_details antimicrobial resistance testing standard details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing standard details slot antimicrobial resistance testing standard details field antimicrobial resistance testing standard details slot GRDI Example Guidance: This information may include the year or location where the testing standard was published. If not applicable, leave blank. AMR testing standard details field GENEPIO:0100521 Amoxicillin-clavulanic [ARO:3003997] A data field which describes the name of the agent that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. antimicrobial agent name antimicrobial_agent_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z antimicrobial agent name slot GRDI Example Guidance: The names of the drug have already been matched with measurement, breakpoint, and phenotype fields in the template. No need to add these unless the drug of interest is not present. Use the Term Request System to request the addition of other agents. antimicrobial agent name field GENEPIO:0100522 4 A data field which describes the measured value of antimicrobial resistance (AMR). Dependent on the value specified in the 'antimicrobial agent name field' [GENEPIO:0100521] AMR measurement AMR_measurement antimicrobial resistance measurement https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR measurement slot antimicrobial resistance measurement field antimicrobial resistance measurement slot GRDI Example Guidance: This field should only contain a number (either an integer or a number with decimals). AMR measurement field GENEPIO:0100523 mg/L A data field which describes the units of the antimicrobial resistance (AMR) measurement. Dependent on the numerical value specified in the 'AMR measurement field' [GENEPIO:0100522] AMR measurement units AMR_measurement_units antimicrobial resistance measurement units https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR measurement units slot antimicrobial resistance measurement units field antimicrobial resistance measurement units slot GRDI Example Guidance: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. AMR measurement units field GENEPIO:0100524 == A data field which describes the qualifier associated with the antibiotic resistance (AMR) measurement. Dependent on the units specified in the 'AMR measurement units field' [GENEPIO:0100523]. AMR measurement sign AMR_measurement_sign antimicrobial resistance measurement sign https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR measurement sign slot antimicrobial resistance measurement sign field antimicrobial resistance measurement sign slot GRDI Example Guidance: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. AMR measurement sign field GENEPIO:0100525 Susceptible antimicrobial phenotype [ARO:3004302] A data field which describes an antimicrobial resistance (AMR) phenotype, as determined by the antibiotic susceptibility measurement and testing standard for the antibiotic specified. Dependent on the value specified in the 'antimicrobial agent name field' [GENEPIO:0100521] AMR phenotype AMR_phenotype antimicrobial resistance phenotype https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR phenotype slot antimicrobial resistance phenotype field antimicrobial resistance phenotype slot GRDI Example Guidance: Select a phenotype from the pick list provided. AMR phenotype field GENEPIO:0100526 Broth dilution [ARO:3004397] An antimicrobial resistance (AMR) field which describes the general method used for antibiotic susceptibility testing. AMR laboratory typing method AMR_laboratory_typing_method antimicrobial resistance laboratory typing method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR laboratory typing method slot antimicrobial resistance laboratory typing method field antimicrobial resistance laboratory typing method slot GRDI Example Guidance: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. AMR laboratory typing method field GENEPIO:0100527 Sensitire [ARO:3004402] An antimicrobial resistance (AMR) field which describes the brand/platform used for antibiotic susceptibility testing. AMR laboratory typing platform AMR_laboratory_typing_platform antimicrobial resistance laboratory typing platform https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR laboratory typing platform slot antimicrobial resistance laboratory typing platform field antimicrobial resistance laboratory typing platform slot GRDI Example Guidance: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. AMR laboratory typing platform field GENEPIO:0100528 CMV3AGNF An antimicrobial resistance (AMR) field which describes the specific name and version of the plate, panel, or other platform used for antibiotic susceptibility testing. AMR laboratory typing platform version AMR_laboratory_typing_platform_version antimicrobial resistance laboratory typing platform version https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR laboratory typing platform version slot antimicrobial resistance laboratory typing platform version field antimicrobial resistance laboratory typing platform version slot GRDI Example Guidance: Include any additional information about the antimicrobial susceptibility test such as the drug panel details. AMR laboratory typing platform version field GENEPIO:0100529 Sensititre An antimicrobial resistance (AMR) field which describes the name of the vendor of the testing platform used. AMR vendor name AMR_vendor_name antimicrobial resistance vendor name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR vendor name slot antimicrobial resistance vendor name field antimicrobial resistance vendor name slot GRDI Example Guidance: Provide the full name of the company (avoid abbreviations). AMR vendor name field GENEPIO:0100530 Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] An antimicrobial resistance (AMR) field which describes testing standard used for determination of resistance phenotype. AMR testing standard AMR_testing_standard antimicrobial resistance testing standard https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing standard slot antimicrobial resistance testing standard antimicrobial resistance testing standard field antimicrobial resistance testing standard slot GRDI Example Guidance: Select a testing standard from the pick list provided. AMR testing standard field GENEPIO:0100531 M100 An antimicrobial resistance (AMR) field which describes version number associated with the testing standard used for determination of resistance phenotype. If applicable, include a version number for the testing standard used. AMR testing standard version AMR_testing_standard_version antimicrobial resistance testing standard version https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing standard version slot antimicrobial resistance testing standard version field antimicrobial resistance testing standard version slot GRDI Example Guidance: If applicable, include a version number for the testing standard used. AMR testing standard version field GENEPIO:0100532 Prior infection A data field which describes the absence or presence of a prior Monkeypox infection. prior Monkeypox infection https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior Monkeypox infection slot Monkeypox-International Monkeypox Example Guidance: If known, provide information about whether the individual had a previous Monkeypox infection. Select a value from the pick list. prior Monkeypox infection field GENEPIO:0100533 2022-06-20 A data field which describes the date of diagnosis of the prior Monkeypox infection. prior Monkeypox infection date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior Monkeypox infection date slot Monkeypox-International Monkeypox Example Guidance: Provide the date that the most recent prior infection was diagnosed. Provide the prior Monkeypox infection date in ISO 8601 standard format .YYYY-MM-DD.. prior Monkeypox infection date field GENEPIO:0100534 Prior antiviral treatment A data field which describes the absence or presence of antiviral treatment for a prior Monkeypox infection. prior Monkeypox antiviral treatment https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior Monkeypox antiviral treatment slot Monkeypox-International Monkeypox Example Guidance: If known, provide information about whether the individual had a previous Monkeypox antiviral treatment. Select a value from the pick list. prior Monkeypox antiviral treatment field GENEPIO:0100535 AZT was administered for HIV infection during the prior Monkeypox infection. A data field which describes the antiviral treatment for any infection during the prior Moneypox infection period. prior antiviral treatment during prior Monkeypox infection https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior antiviral treatment during prior Monkeypox infection slot Monkeypox-International Monkeypox Example Guidance: Provide a description of any antiviral treatment administered for viral infections (not including Monkeypox treatment) during the prior Monkeypox infection period. This field is meant to capture concurrent treatment information. prior antiviral treatment during prior Monkeypox infection field GENEPIO:0100548 A sampling strategy in which environments are sampled in the context of testing for the presence of, or change in the levels of, chemicals, pathogens or other phenomena. A sampling strategy in which samples are taken during real-life experiments which test directly whether proposed interventions actually work. Environmental testing 2023-01-23T00:42:19.315Z GRDI environmental testing sampling strategy environmental testing strategy GENEPIO:0100549 A sampling strategy in which individuals are sampled in the context of experiments or observations performed as part of clinical research. Clinical trial 2022-09-23T11:08:21Z 2023-01-23T00:42:19.315Z GRDI clinical trial sampling strategy clinical trial strategy GENEPIO:0100550 A sampling strategy in which samples are taken during real-life experiments which test directly whether proposed interventions actually work. Field experiment https://en.wikipedia.org/wiki/Field_experiment 2022-09-23T11:12:34Z 2023-01-23T00:42:19.315Z GRDI field experiment sampling strategy field experiment strategy GENEPIO:0100557 ncov-tools A data field which describes the name of the method used to assess whether a sequence passed a predetermined quality control threshold. quality control method name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc method name field qc method name slot quality control method name field quality control method name slot PHA4GE QC Tag quality control method name field GENEPIO:0100558 1.2.3 A data field which describes the version number of the method used to assess whether a sequence passed a predetermined quality control threshold. quality control method version https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc method version field qc method version slot quality control method version field quality control method version slot PHA4GE QC Tag quality control method version field GENEPIO:0100559 sequence failed quality control [GENEPIO:0100564] A data field which describes the determination of a quality control assessment. quality control determination https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc determination field qc determination slot quality control determination field quality control determination slot PHA4GE QC Tag quality control determination field GENEPIO:0100560 low average genome coverage [GENEPIO:0100570] A data field which describes the reason contributing to, or causing, a low quality determination in a quality control assessment. quality control issues https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc issues field qc issues slot quality control issues field quality control issues slot PHA4GE QC Tag quality control issues field GENEPIO:0100561 CT value of 39. Low viral load. Low DNA concentration after amplification. A data field which describes the details surrounding a low quality determination in a quality control assessment. quality control details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc details field qc details slot quality control details field quality control details slot PHA4GE QC Tag quality control details field GENEPIO:0100562 A data item which is a statement confirming that quality control processes were carried out and no quality issues were detected. no quality control issues identified https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z PHA4GE QC Tag Example: This statement may be used in conjunction with the quality control determination statement "sequence passed quality control" to confirm that no issues were identified. It is possible that a sequence may pass QC but still have some issues worthy of noting e.g. novel indel detected. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment. no quality control issues identified datum GENEPIO:0100563 A data item which is a statement confirming that quality control processes were carried out and that the sequence met the assessment criteria. sequence passed quality control https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z PHA4GE QC Tag Example: Use this statement to indicate that quality control processes were carried out and that the sequence met the assessment criteria. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment. sequence passed quality control datum GENEPIO:0100564 A data item which is a statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria. sequence failed quality control https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z PHA4GE QC Tag Example: Use this statement to indicate that quality control processes were carried out and that the sequence failed to meet the assessment criteria. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment. sequence failed quality control datum GENEPIO:0100565 A data item which is a statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor. minor quality control issues identified https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z PHA4GE QC Tag Example: This statement may be used in conjunction with the quality control determination statement "sequence failed quality control" to communicate that the reasons why the sequence did not meet the assessment criteria. Minor issues may include phenomena that the analyst should review e.g. amplicons detected in the negative control sequence or more mutations than expected based on the reference sequence. The details of the issues can be described in the "quality control details" field. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment. minor quality control issues identified datum GENEPIO:0100566 A data item which is a statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review. sequence flagged for potential quality control issues https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z PHA4GE QC Tag Example: This statement may be used in conjunction with other quality control determination statements to indicate potential sequence quality issues. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment. sequence flagged for potential quality control issues datum GENEPIO:0100567 A data item which is a statement confirming that quality control processes have not been carried out. quality control not performed https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z PHA4GE QC Tag Example: Use this statement to indicate that quality control processes have not been performed. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment. quality control not performed datum GENEPIO:0100568 A data item that describes sequence data that does not meet quality control thresholds. low quality sequence https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z PHA4GE QC Tag low quality sequence datum GENEPIO:0100569 A data item that describes sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source. sequence contaminated https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z PHA4GE QC Tag sequence contaminated datum GENEPIO:0100570 A data item that describes sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage). low average genome coverage https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z PHA4GE QC Tag low average genome coverage datum GENEPIO:0100571 A data item that describes sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage). low percent genome captured https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z PHA4GE QC Tag low percent genome captured datum GENEPIO:0100572 A data item that describes average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions. read lengths shorter than expected https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z PHA4GE QC Tag read lengths shorter than expected datum GENEPIO:0100573 A data item that describes sequence data containing errors generated during the polymerase chain reaction (PCR) amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts). sequence amplification artifacts https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z PHA4GE QC Tag sequence amplification artifacts datum GENEPIO:0100574 A data item that describes sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal). low signal to noise ratio https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z PHA4GE QC Tag low signal to noise ratio datum GENEPIO:0100575 A data item that describes sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence. low coverage of characteristic mutations https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z PHA4GE QC Tag low coverage of characteristic mutations datum GENEPIO:0100580 Tecovirimat used to treat current Monkeypox infection; AZT administered for concurrent HIV infection A data field which describes treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function. antiviral therapy https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z antiviral therapy slot Monkeypox-International Monkeypox Example Guidance: Provide details of all current antiviral treatment during the current Monkeypox infection period. Consult with the data steward prior to sharing this information. antiviral therapy field GENEPIO:0100581 A collection of contextual data attributes pertaining to a pathogen in an environmental sample, as specified by the International Nucleotide Sequence Database Collaboration (INSDC). 2022-09-23T10:54:21Z Environmental Pathogen Attribute Package (Pathogen.env) GENEPIO:0100582 A sampling strategy in which individuals and/or materials are sampled for surveillance performed for research purposes. Survey study 2022-09-23T11:04:13Z 2023-01-23T00:42:19.315Z GRDI survey study survey study sampling strategy GENEPIO:0100583 PCR assay [OBI:0002740] A data field which describes the type of planned process by which an organismal entity is associated with a taxon or taxa. taxonomic identification process taxonomic_identification_process https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z taxonomic identification process slot GRDI Example Guidance: Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. taxonomic identification process field GENEPIO:0100584 Biolog instrument A data field which describes the details of the process used to determine the taxonomic identification of an organism. taxonomic identification process details taxonomic_identification_process_details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z taxonomic identification process details slot GRDI Example Guidance: Briefly describe the taxonomic identififcation method details using free text. taxonomic identification process details field GENEPIO:0100586 The "specimen collector sample ID" is where one can store sample identifiers given by the specimen collector. A data item which is a location for a predetermined type of data. https://analystanswers.com/what-is-a-data-field-definition-types-examples/ 2022-11-23T00:33:27.896Z data slot data field GENEPIO:0100587 A data specification established for use by The Public Health Alliance for Genomic Epidemiology (PHA4GE) project for SARS-CoV-2 contextual data (metadata) harmonization and curation across data providers. PHA4GE SARS-CoV-2 contextual data specification https://orcid.org/0000-0002-9578-0788 2022-12-09T20:18:38.910Z Public Health Alliance for Genomic Epidemiology SARS-CoV-2 specification Public Health Alliance for Genomic Epidemiology severe acute respiratory syndrome coronavirus 2 specification PHA4GE SARS-CoV-2 PHA4GE SARS-CoV-2 specification Manuscript: https://doi.org/10.1093/gigascience/giac003 GitHub: https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification GENEPIO:0100588 A data specification established for pathogen genomics contextual data (metadata) harmonization and curation across Canadian data providers. https://orcid.org/0000-0002-9578-0788 2022-12-09T20:18:38.910Z Canadian pathogen genomics specification https://github.com/cidgoh/pathogen-genomics-package GENEPIO:0100589 A data specification established for use by The Canadian Genomics Research & Development Initiative (GRDI) Antimicrobial Resistance (AMR) project for contextual data (metadata) harmonization and curation across data providers. https://orcid.org/0000-0002-9578-0788 2022-12-09T20:18:38.910Z Genomics Research & Development Initiative Antimicrobial Resistance One Health specification GRDI GRDI AMR One Health specification https://github.com/cidgoh/GRDI_AMR_One_Health GENEPIO:0100590 A data specification established for Monkeypox pathogen genomics contextual data (metadata) harmonization and curation across Canadian data providers. https://orcid.org/0000-0002-9578-0788 2022-12-09T20:18:38.910Z Monkeypox Canadian Monkeypox specification https://github.com/cidgoh/pathogen-genomics-package GENEPIO:0100591 A data specification established for Monkeypox pathogen genomics contextual data (metadata) harmonization and curation across international data providers. https://orcid.org/0000-0002-9578-0788 2022-12-09T20:18:38.910Z Monkeypox-International International Monkeypox specification https://github.com/cidgoh/pathogen-genomics-package GENEPIO:0100592 specimen storage duration A data item which is a duration for which a specimen is stored before analysis. https://orcid.org/0000-0002-8844-9165 sample storage duration http://gensc.org/ns/mixs/samp_store_dur https://github.com/obi-ontology/obi/issues/1577 specimen storage duration GENEPIO:0100593 specimen storage temperature The refrigerator provided a sample storage temperature of -80 degree Celsius A data item which is a temperature at which a specimen is stored. https://orcid.org/0000-0002-8844-9165 sample storage temperature http://gensc.org/ns/mixs/samp_store_temp https://github.com/obi-ontology/obi/issues/1577 specimen storage temperature GENEPIO:0100594 specimen storage location molecular lab was recorded as the sample storage location. A data item which indicates the location where a specimen is stored, usually of a room or freezer. https://orcid.org/0000-0002-8844-9165 sample storage location http://gensc.org/ns/mixs/samp_store_loc https://github.com/obi-ontology/obi/issues/1577 specimen storage location GENEPIO:0100595 sequence file name The sequence data for "Zika virus envelope protein (E) gene, partial cds" is stored in a file named "AF372422-1.fasta". A sequence data item which is the name of a file containing molecular sequence data. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 input file name Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 sequence file name GENEPIO:0100596 contig number identifier When a new genome is sequenced, it is constructed from a series of overlapping sequences known as contigs. Each contig receives an identifier code that contains a unique numerical identifier, in addition to project and assembly information, to differentiate an individual contig from others within a squence collection. A sequence data which specifies a particular contig in a sequence collection. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 contig identifier contig ID Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 contig number identifier GENEPIO:0100597 genomic orientation The "123" gene ORF is oriented in the 5' -> 3' direction on the DNA sense (coding) strand. A sequence data which is the orientation of a genomic element on a double stranded molecule. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 strand orientation strand http://purl.obolibrary.org/obo/NCIT_C48673 https://github.com/obi-ontology/obi/issues/1579 genomic orientation GENEPIO:0100598 gene symbol gyrA A sequence data which is the short name of a gene typically derived from the gene name. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 http://edamontology.org/data_1026 https://github.com/obi-ontology/obi/issues/1579 gene symbol GENEPIO:0100599 gene name Gyrase A A sequence data which is the name of a gene (typically) assigned by a person and/or according to a naming scheme. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 http://edamontology.org/data_2299 https://github.com/obi-ontology/obi/issues/1579 gene name GENEPIO:0100600 breadth of coverage percentage The breadth of coverage of the sequence of interest to the reference sequence was 75%. A data item which is breadth of coverage datum as a percentage. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 % coverage (breadth) breadth of coverage % coverage (breadth) Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 breadth of coverage percentage GENEPIO:0100601 breadth of coverage ratio The breadth of coverage of the sequence of interest to the reference sequence was 3:4. A data item which is breadth of coverage datum as a ratio. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 breadth of coverage ratio GENEPIO:0100602 sequence identity percentage The BLAST results for two sequences of interest resulted in a sequence identity of 50%; i.e. only 50% of the sequences matched in both nucleotide content and corresponding positions when performing a theoretically optimal local alignment. A data item which is the number of matches (identical characters) in positions from an alignment of two molecular sequences as a percentage. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 http://edamontology.org/data_1412 https://github.com/obi-ontology/obi/issues/1579 sequence identity percentage GENEPIO:0100603 reference database name I used the NCBI reference sequence "RefSeq" database as a reference database for the identification and characterization of novel prokaryote sequences. A data item which is an identifier of a reference bioinformatics database. See editor note of http://purl.obolibrary.org/obo/IAO_0000650 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 http://edamontology.org/data_1048 https://github.com/obi-ontology/obi/issues/1579 reference database name GENEPIO:0100604 reference sequence The reference SARS-CoV-2 genome provided a basis for the design of PCR primers and probes to be utilized in SARS-CoV-2 detection. A sequence data which is any sequence that is used as a basis for comparison against another sequence. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 reference sequence GENEPIO:0100605 accession number A sequence Accession number without a version suffix always refers to the latest version of the sequence. A unique identifier given to a sequence record to allow for tracking of different versions of that sequence record and the associated sequence over time in a single data repository. https://orcid.org/0000-0002-1107-9135 accession identifier https://en.wikipedia.org/wiki/Accession_number_(bioinformatics) https://github.com/obi-ontology/obi/issues/1579 accession number GENEPIO:0100606 reference sequence accession number The "Homo sapiens DRD2 mRNA" sequence has the NCBI reference sequence identifier NM_000795. A centrally registered identifier symbol that specifies an individual sequence record in a public sequence repository and used as a basis for comparison against another sequence. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 reference sequence accession identifier reference accession Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 reference sequence accession number GENEPIO:0100607 sequence length measurement datum The sequence length measurement datum for the Zika virus E protein gene (AF372422.1) is 830 bp. A length measurement datum which is the number of base pairs in a sequence. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 sequence length measurement datum GENEPIO:0100608 reference sequence length measurement datum The sequence length measurment datum for the SARS-CoV-2 reference sequence (NC_045512.2) is 29903 bp. A sequence length measurement datum which describes the number of base pairs of a reference sequence. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 reference sequence length measurement datum GENEPIO:0100609 reference gene sequence length datum The sequence length measurment datum for the SARS-CoV-2 reference sequence (NC_045512.2) ORF1ab gene (43740578) is 21289 bp. A reference sequence length measurement datum which describes the number of base pairs of a gene retrieved from a reference sequence. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 reference gene length Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 reference gene sequence length datum GENEPIO:0100610 reference protein sequence length datum The sequence length measurment datum for the SARS-CoV-2 reference sequence (NC_045512.2) nps13_ZBD protein (YP_009725308.1) is 1802 bp. A reference sequence length measurement datum which describes the number of positions of a reference protein. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 reference protein length Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 reference protein sequence length datum GENEPIO:0100611 input sequence length measurement datum 701bp A sequence length measurement datum about a input sequence being analyzed. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 input sequence length measurement datum GENEPIO:0100612 input gene sequence length measurement datum 1802bp A sequence length measurement datum which describes the number of base pairs of a gene of interest undergoing analysis. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 input gene length Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 input gene sequence length measurement datum GENEPIO:0100613 input protein sequence length measurement datum 638bp A sequence length measurement datum which describes the number of positions of a protein undergoing analysis. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 input protein length Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 input protein sequence length measurement datum GENEPIO:0100614 virus transport medium A processed material which is a medium designed to promote longevity of a viral sample. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-8844-9165 https://github.com/obi-ontology/obi/issues/1194 virus transport medium GENEPIO:0100615 2020-05-25 A data field which describes the date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. food quality date food_quality_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food quality date slot GRDI Example Guidance: This date is typically labeled on a food product as .best if used by., best by., .use by., or .freeze by. e.g. 5/24/2020. If the date is known, leave blank or provide a null value. food quality date field GENEPIO:0100616 2020-05-25 A data field which descibes the food product's packaging date as marked by a food manufacturer or retailer. food packaging date food_packaging_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food packaging date slot GRDI Example Guidance: The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. food packaging date field GENEPIO:0100628 A data item which describes an organism bearing a host role. https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z host column host slot; host organism field; host organism slot host field GENEPIO:0100629 A data field which describes a geographical location. geo_loc field geo_loc slot https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z geographical location column geographical location slot geographical location field GENEPIO:0100630 A field that describes the host country of reisdence. A data field which describes the geographical location of a host organism. host geo_loc https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z host geographical location column host geographical location slot host geographical location field GENEPIO:0100631 third party lab sample ID field A data field which describes a symbol that is part of a centrally registered identifier database (CRID) and that is sufficient to look up a record from the CRID's registry. http://purl.obolibrary.org/obo/IAO_0000577 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z ID column identifier column ID field ID slot identifier slot identifier field GENEPIO:0100632 A data field which describes the particular day, month and/or year an event has happened or will happen. https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z date column date slot date field GENEPIO:0100633 A data field which describes the vaccination information of a host organism. https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z host vaccination column host vaccination slot host vaccination field GENEPIO:0100634 This "or" class is just to represent an equivalency with a commonly used classification, it should not have subclasses under it. (2022-12-22) 2022-12-22T22:56:03.687Z State or Province or Territory GENEPIO:0100635 A data field which describes antimicrobial information. https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z antimicrobial column antimicrobial slot antimicrobial field GENEPIO:0100636 A data field which describes antimicrobial resistance information. https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR column antimicrobial resistance column AMR field AMR slot antimicrobial resistance slot antibiotic field antimicrobial resistance field GENEPIO:0100637 A data field which describes the exposure information of a host organism. https://orcid.org/0000-0002-9578-0788 2023-01-01T03:32:48.197Z exposure column exposure slot exposure field GENEPIO:0100638 A data field which describes prior infection information of a host organism. https://orcid.org/0000-0002-9578-0788 2023-01-01T03:32:48.197Z prior infection column prior infection slot prior infection field GENEPIO:0100655 E gene (orf4) [GENEPIO:0100151] A data field which describes the name of the gene used in the diagnostic reverse transcription polymerase chain reaction (RT-PCR) test. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z gene name slot gene name field GENEPIO:0100656 PCREGene 2.0 A data field which describes the name and version number of the reverse transcription polymerase chain reaction (RT-PCR) protocol used for diagnostic marker amplification. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr protocol slot diagnostic polymerase chain reaction protocol field diagnostic polymerase chain reaction protocol slot diagnostic pcr protocol field GENEPIO:0100657 21 A data field which describes the cycle threshold (Ct) value result from a diagnostic reverse transcription polymerase chain reaction (RT-PCR) test. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr Ct value slot diagnostic polymerase chain reaction cycle threshold field diagnostic polymerase chain reaction cycle threshold slot diagnostic pcr Ct value field GENEPIO:0100658 wet wipe A small moistened piece of plastic or cloth fabric. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-8395-2570 https://en.wikipedia.org/wiki/Wet_wipe wet wipe GENEPIO:0100659 A data specification established by the Public Health Alliance for Genomic Epidemiology (PHA4GE) for genomics contextual data (metadata) harmonization and curation. https://orcid.org/0000-0002-9578-0788 2023-01-22T23:12:40.795Z Public Health Alliance for Genomic Epidemiology specification PHA4GE genomics specification GitHub: https://github.com/pha4ge GENEPIO:0100660 A data specification established by the Public Health Alliance for Genomic Epidemiology (PHA4GE) for genomics contextual data (metadata) harmonization and curation. PHA4GE QC contextual data tags specification PHA4GE QC tags specification PHA4GE quality control contextual data tags specification https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-22T23:12:40.795Z PHA4GE QC specification Public Health Alliance for Genomic Epidemiology quality control specification PHA4GE QC Tag PHA4GE quality control specification GitHub: https://github.com/pha4ge/contextual_data_QC_tags GENEPIO:0100661 A data field which describes quality control information. https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc column quality control column qc field qc slot quality control slot quality control field GENEPIO:0100662 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z quality control datum GENEPIO:0100663 A data enumeration which references a set of named quality control determination entities. quality control determination https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z PHA4GE QC Tag quality control determination enumeration GENEPIO:0100664 A data enumeration which references a set of named quality control issues entities. quality control issues https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z PHA4GE QC Tag quality control issues enumeration GENEPIO:0100665 A role inhering in a person that is realized when the bearer is engaged in child care work. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z childcare worker role GENEPIO:0100666 A role inhering in a person that is realized when the bearer is engaged in education work. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z education worker role 1 GEO:000000788 A coordinate system, and a set of reference points, used to locate places on the Earth (or similar objects). Josh Hanna William R. Hogan Damion Dooley's note: This coordinate system must reference the particulars of a spheroid - its "radius = fn(lat,long)" formula - in order to yeild any distance metrics. Alternate definition: A geographic coordinate system is a 2 dimensional coordinate system superimposed onto the surface of a spheroid. geodetic datum GO:0000003 The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GO:0019952 GO:0050876 NCIt:C21173 SNOMEDCT:272515006 Wikipedia:Reproduction reproductive physiological process reproduction GO:0006810 The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. GO:0015457 GO:0015460 GO:0044765 Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. transport GO:0007610 The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. GO:0023032 GO:0044708 GO:0044709 GO:0007610 MeSH:D001519 NCIt:C16326 Wikipedia:Behavior behavioral response to stimulus behaviour behavioural response to stimulus 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). behavior GO:0008150 biological_process A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. GO:0000004 GO:0007582 GO:0044699 GO:0008150 MeSH:D055705 NCIt:C17828 Wikipedia:Biological_process biological process physiological process A biological process is an evolved process Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological process biological_process GO:0032501 Any biological process, occurring at the level of a multicellular organism, pertinent to its function. GO:0044707 GO:0050874 organismal physiological process multicellular organismal process GO:0035176 Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. Wikipedia:Social_behavior social behaviour Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. social behavior GO:0035314 Formation of hardened covering (a scab) at a wound site. The scab has multiple functions including limiting blood loss, providing structural stability to the wound and guarding against infection. scab formation GO:0044409 Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. entry into host GO:0046903 The controlled release of a substance by a cell or a tissue. secretion GO:0051179 Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation establishment and maintenance of cellular component location establishment and maintenance of substance location establishment and maintenance of substrate location localization GO:0051234 Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. establishment of localisation establishment of localization GO:0051703 Any process in which an organism has an effect on an organism of the same species. intraspecies interaction between organisms intraspecies interaction with other organisms biological process involved in intraspecies interaction between organisms GSSO:000127 An umbrella term often used in medical literature to include transgender persons and gender nonconforming people who may or may not be transgender. transgender and gender nonconforming GSSO:000129 An umbrella term often used in research to covered genderqueer and gender nonbinary identities, as well as gender nonconforming persons. genderqueer, gender non-conforming, and gender nonbinary genderqueer, gender nonconforming and gender nonbinary genderqueer, gender nonconforming, and gender nonbinary GSSO:000132 Either, a specific gender identity which is not male or female; or, more broadly, an umbrella term for gender identities not considered male or female. https://en.wikipedia.org/wiki/Category:Non-binary_gender gender non-binary "Non-binary" (with the hyphen) is more common in the United Kingdom, whereas "nonbinary" (as one word) is more common in the United States. Note that "nonbinary" as itself is preferable if the context in relationship to gender is known. Most therefore "nonbinary persons" not "gender nonbinary persons" can be used. gender nonbinary GSSO:003565 Equitable representation of persons of different genders. https://en.wikipedia.org/wiki/Gender_diversity https://www.wikidata.org/wiki/Q1501335 diversité de genre gender diversity gender diversity GSSO:004004 Having a feminine gender (identity) which is different from the sex one was assigned at birth. https://en.wikipedia.org/wiki/Transfeminine https://mogai-genders.fandom.com/wiki/Transfeminine https://www.wikidata.org/wiki/Q27679684 trans feminine transfemenino transfeminin transfeminine GSSO:004005 Having a masculine gender (identity) which is different from the sex one was assigned at birth. https://mogai-genders.fandom.com/wiki/Transmasculine https://www.wikidata.org/wiki/Q27679766 trans masculine transmasculine transmasculino transmaskulin GSSO:012492 https://lgbta.fandom.com/wiki/Cisn%27t noncisgender gender modality non-cisgender gender modality HANCESTRO:0004 Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data ancestral group ancestry category HANCESTRO:0005 Includes individuals who either self-report or have been described by authors as European, Caucasian, White or one of the sub-populations from this region (e.g Dutch). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CEU, FIN, GBR, IBS and TSI populations. Caucasian white European HANCESTRO:0006 Includes individuals who either self-report or have been described by authors as South Asian or one of the sub-populations from this region (e.g Asian Indian). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap BEB, GIH, ITU, PJL and STU populations. South Asian HANCESTRO:0007 Includes individuals who either self-report or have been described by authors as South East Asian or one of the sub-populations from this region (e.g Vietnamese). This category also includes includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes KHV population. We note that East Asian and South East Asian populations are often conflated. However, recent studies indicate a unique genetic background for South East Asian populations. South East Asian HANCESTRO:0008 Includes individuals that either self-report or have been described as Asian but there was not sufficient information to allow classification as East Asian, Central Asian, South Asian or South-East Asian. Asian unspecified Asian HANCESTRO:0009 Includes individuals who either self-report or have been described by authors as East Asian or one of the sub-populations from this region (e.g Chinese). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CDX, CHB, CHS and JPT populations. East Asian HANCESTRO:0010 Includes individuals that either self-report or have been described as African, but there was not sufficient information to allow classification as African American, AfroCaribbean or Sub-Saharan African. African unspecified African HANCESTRO:0011 Includes individuals who either self-report or have been described by authors as SubSaharan African or one of the subpopulations from this region (e.g. Yoruban). This category also includes individuals who genetically cluster with reference populations from this region for example 1000 Genomes and/or HapMap ESN, LWK, GWD, MSL, MKK and YRI populations. Sub-Saharan African HANCESTRO:0013 Includes indigenous individuals of North, Central and South America, descended from the original human migration into the Americas from Siberia. We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap. American Indian Native American HANCESTRO:0014 Includes individuals who either self-report or are described by authors as Hispanic, Latino, Latin American or one of the sub-populations from this region. This category includes individuals with known admixture of primarily European, African and Native American ancestries, though some may have also a degree of Asian (e.g. Peru). We also note that the levels of admixture vary depending on the country, with Caribbean countries carrying higher levels of African admixture when compared to South American countries, for example. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CLM, MXL, PEL and PUR populations Jackie MacArthur Joannella Morales Hispanic or Latin American HANCESTRO:0015 Includes individuals who self-report or were described by authors as Middle Eastern, North African, Persian or one of the subpopulations from this region (e.g. Saudi Arabian). We note there is heterogeneity in this category with different degrees of admixture as well as levels of genetic isolation. We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap. Middle Eastern/North African Greater Middle Eastern (Middle Eastern or North African or Persian) HANCESTRO:0016 Includes individuals who either self-report or have been described by authors as African American or Afro-Caribbean. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap ACB or ASW populations. We note that there is likely to be significant admixture with European ancestry populations. African American or Afro-Caribbean HANCESTRO:0017 Includes individuals that either self-report or have been described by authors as Oceanian or one of the sub-populations from this region (e.g. Native Hawaiian). We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap. Oceanian HANCESTRO:0018 A population for which specific ancestry information is known but that does not fall into any of the defined ancestry categories uncategorised population HANCESTRO:0019 Japanese HANCESTRO:0020 non-aboriginal Taiwanese Taiwanese HANCESTRO:0021 Chinese HANCESTRO:0022 Korean HANCESTRO:0023 Mongolian HANCESTRO:0024 Macanese HANCESTRO:0025 Singaporean Chinese HANCESTRO:0026 Hong Kong Chinese HANCESTRO:0027 Han Chinese HANCESTRO:0286 Includes individuals who either self-report or have been described by authors as Central Asian. We note that there does not appear to be a suitable reference population for this population and efforts are required to fill this gap. Central Asian HANCESTRO:0290 A population with increased genetic homogeneity and reduced genetic variation due to cultural or geographic isolation founder population population isolate genetically isolated population HANCESTRO:0307 Italian HANCESTRO:0309 Sardinian HANCESTRO:0310 Val Borbera HANCESTRO:0311 Friuli Venezia Giulia HANCESTRO:0312 Carlantino HANCESTRO:0313 Old Order Amish HANCESTRO:0314 Sorbian HANCESTRO:0315 Hutterite HANCESTRO:0316 Amish HANCESTRO:0317 Erasmus Rucphen HANCESTRO:0318 Orcadian HANCESTRO:0319 Korculan HANCESTRO:0320 Dutch HANCESTRO:0321 Finnish HANCESTRO:0322 Finnish founder HANCESTRO:0323 Dutch founder HANCESTRO:0324 Ashkenazi Jew HANCESTRO:0331 Sudanese HANCESTRO:0332 Sahrawi HANCESTRO:0333 Anguillan HANCESTRO:0334 Antiguan or Barbudan HANCESTRO:0335 Barbadian HANCESTRO:0336 Haitian HANCESTRO:0337 Jamaican HANCESTRO:0338 Tajikistani HANCESTRO:0339 Turkmen HANCESTRO:0340 Uzbekistani HANCESTRO:0341 Afghan HANCESTRO:0342 Kazakhstani HANCESTRO:0343 Kyrgyzstani HANCESTRO:0344 Albanian HANCESTRO:0345 Andorran HANCESTRO:0346 Australian HANCESTRO:0347 Austrian HANCESTRO:0348 Belarusian HANCESTRO:0349 Belgian HANCESTRO:0350 Bermudian HANCESTRO:0351 Bosnian or Herzegovinian HANCESTRO:0352 Brazilian HANCESTRO:0353 Bulgarian HANCESTRO:0354 Canadian HANCESTRO:0355 Channel Islander HANCESTRO:0356 Chilean HANCESTRO:0357 Croatian HANCESTRO:0358 Czech HANCESTRO:0359 Danish HANCESTRO:0360 Estonian HANCESTRO:0361 Faroese HANCESTRO:0362 Falkland Islander HANCESTRO:0363 French HANCESTRO:0364 German HANCESTRO:0365 Gibraltarian HANCESTRO:0366 Greek HANCESTRO:0367 Greenlander HANCESTRO:0368 Hungarian HANCESTRO:0369 Icelandic HANCESTRO:0370 Manx HANCESTRO:0371 Latvian HANCESTRO:0372 Liechtensteiner HANCESTRO:0373 Lithuanian HANCESTRO:0374 Luxembourgish HANCESTRO:0375 Maltese HANCESTRO:0376 Monegasque HANCESTRO:0377 Montenegrin HANCESTRO:0378 New Zealandish HANCESTRO:0379 Norfolk Islander HANCESTRO:0380 Norwegian HANCESTRO:0381 Polish HANCESTRO:0382 Portugese HANCESTRO:0383 Irish HANCESTRO:0384 Moldovan HANCESTRO:0385 Romanian HANCESTRO:0386 Russian HANCESTRO:0387 Saint-Pierrais or Miquelonnais HANCESTRO:0388 Sammarinese HANCESTRO:0389 Serb HANCESTRO:0390 Slovak HANCESTRO:0391 Slovene HANCESTRO:0392 Spanish HANCESTRO:0393 Swedish HANCESTRO:0394 Swiss HANCESTRO:0395 Macedonian HANCESTRO:0396 Ukrainian HANCESTRO:0397 Argentine HANCESTRO:0398 Bahamian HANCESTRO:0399 Belizean HANCESTRO:0400 Bolivian HANCESTRO:0401 British Virgin Islander HANCESTRO:0402 Caymanian HANCESTRO:0403 Colombian HANCESTRO:0404 Costa Rican HANCESTRO:0405 Cuban HANCESTRO:0406 Dominican HANCESTRO:0407 Ecuadorian HANCESTRO:0408 Salvadoran HANCESTRO:0409 French Guianese HANCESTRO:0410 Grenadian HANCESTRO:0411 Guatemalan HANCESTRO:0412 Guyanese HANCESTRO:0413 Honduran HANCESTRO:0414 Martinican HANCESTRO:0415 Mexican HANCESTRO:0416 Montserratian HANCESTRO:0417 Nicaraguan HANCESTRO:0418 Panamanian HANCESTRO:0419 Paraguayan HANCESTRO:0420 Peruvian HANCESTRO:0421 Puerto Rican HANCESTRO:0422 Kittitian or Nevisian HANCESTRO:0423 Saint Lucian HANCESTRO:0424 Saint Vincentian HANCESTRO:0425 Surinamer Surinamese HANCESTRO:0426 Trinidadian or Tobagonian HANCESTRO:0427 Turks and Caicos Islander HANCESTRO:0428 Virgin Islander HANCESTRO:0429 Uruguayan HANCESTRO:0430 Venezuelan HANCESTRO:0431 Algerian HANCESTRO:0432 Armenian HANCESTRO:0433 Azerbaijani HANCESTRO:0434 Bahraini HANCESTRO:0435 Cypriote HANCESTRO:0436 Egyptian HANCESTRO:0437 Georgian HANCESTRO:0438 Iranian HANCESTRO:0439 Iraqi HANCESTRO:0440 Israeli HANCESTRO:0441 Jordanian HANCESTRO:0442 Kuwaiti HANCESTRO:0443 Lebanese HANCESTRO:0444 Libyan HANCESTRO:0445 Moroccan HANCESTRO:0446 Palestinian HANCESTRO:0447 Omani HANCESTRO:0448 Qatari HANCESTRO:0449 Saudi Arab Saudi HANCESTRO:0450 Tunisian HANCESTRO:0451 Turkish HANCESTRO:0452 Emirati HANCESTRO:0453 Yemeni HANCESTRO:0454 Aruban HANCESTRO:0455 Christmas Islander HANCESTRO:0456 Cocos Islander HANCESTRO:0457 Curacaoan HANCESTRO:0458 Kosovar HANCESTRO:0459 Northern Mariana Islander HANCESTRO:0460 South Sudanese HANCESTRO:0461 Syrian HANCESTRO:0462 British HANCESTRO:0463 American HANCESTRO:0464 American Samoan HANCESTRO:0465 Cook Islander HANCESTRO:0466 Fijian HANCESTRO:0467 French Polynesian HANCESTRO:0468 Guamanian HANCESTRO:0469 I-Kiribati HANCESTRO:0470 Marshallese HANCESTRO:0471 Micronesian HANCESTRO:0472 Nauruan HANCESTRO:0473 New Caledonian HANCESTRO:0474 Niuean HANCESTRO:0475 Palauan HANCESTRO:0476 Papua New Guinean HANCESTRO:0477 Pitcairn Islander HANCESTRO:0478 Samoan HANCESTRO:0479 Solomon Islander HANCESTRO:0480 Tokelauan HANCESTRO:0481 Tongan HANCESTRO:0482 Tuvaluan HANCESTRO:0483 Ni-Vanuato HANCESTRO:0484 Wallis and Futuna Islander HANCESTRO:0485 Bangladeshi HANCESTRO:0486 Bhutanese HANCESTRO:0487 Asian Indian Indian Asian Indian HANCESTRO:0488 Maldivian HANCESTRO:0489 Nepalese HANCESTRO:0490 Pakistani HANCESTRO:0491 Sri Lankan HANCESTRO:0492 Bruneian HANCESTRO:0493 Cambodian HANCESTRO:0494 Indonesian HANCESTRO:0495 Lao HANCESTRO:0496 Malaysian HANCESTRO:0497 Burmese HANCESTRO:0498 Filipino HANCESTRO:0500 Thai HANCESTRO:0501 Timorese HANCESTRO:0502 Vietnamese HANCESTRO:0503 Cameroonian HANCESTRO:0504 Cape Verdean HANCESTRO:0505 Chadian HANCESTRO:0506 Ethiopian HANCESTRO:0507 Kenyan HANCESTRO:0508 Liberian HANCESTRO:0509 Malagasy HANCESTRO:0510 Mauritanian HANCESTRO:0511 Mauritian HANCESTRO:0512 Mahoran HANCESTRO:0513 Namibian HANCESTRO:0514 Sao Tomean HANCESTRO:0515 Senegalese HANCESTRO:0516 Seychellois HANCESTRO:0517 Sierra Leonean HANCESTRO:0518 Somali HANCESTRO:0519 South African HANCESTRO:0520 St. Helenian HANCESTRO:0521 Ugandan HANCESTRO:0522 Angolan HANCESTRO:0523 Beninese HANCESTRO:0524 Motswana HANCESTRO:0525 Burkinabe HANCESTRO:0526 Burundian HANCESTRO:0527 Central African HANCESTRO:0528 Comoran HANCESTRO:0529 Congolese HANCESTRO:0530 Ivoirian HANCESTRO:0531 Djiboutian HANCESTRO:0532 Equatorial Guinean HANCESTRO:0533 Eritrean HANCESTRO:0534 Gabonese HANCESTRO:0535 Gambian HANCESTRO:0536 Ghanaian HANCESTRO:0537 Guinean HANCESTRO:0538 Bissau-Guinean HANCESTRO:0539 Mosotho HANCESTRO:0540 Malawian HANCESTRO:0541 Malian HANCESTRO:0542 Mozambican HANCESTRO:0543 Nigerien HANCESTRO:0544 Nigerian HANCESTRO:0545 Rwandan HANCESTRO:0546 Swazi HANCESTRO:0547 Togolese HANCESTRO:0548 Tanzanian HANCESTRO:0549 Zambian HANCESTRO:0550 Zimbabweian HANCESTRO:0551 Irish founder genetically homogenous Irish HANCESTRO:0552 Includes individuals who either self-report or have been described by authors as Australian Aboriginal. These are expected to be descendents of early human migration into Australia from Eastern Asia and can be distinguished from other Asian populations by mtDNA and Y chromosome variation. Aboriginal Australian HANCESTRO:0554 Silk Road founder HANCESTRO:0555 Israeli Arab Arab Israeli founder HANCESTRO:0556 Cilento HANCESTRO:0557 Costa Rican founder HANCESTRO:0558 French Canadian founder HANCESTRO:0559 Italian founder HANCESTRO:0560 Northern Finnish founder HANCESTRO:0561 Romanian founder HANCESTRO:0563 South Tyrolean HANCESTRO:0564 Vis founder HANCESTRO:0565 Split founder HANCESTRO:0566 Population for which insufficient information is available to allocate it to a specific ancestral group or which contain individuals from a range of known ancestry categories, eg American undefined ancestry population HANCESTRO:0567 African Caribbean Afro-Caribbean HANCESTRO:0568 African American HANCESTRO:0569 Talana HANCESTRO:0570 Pima Indian HANCESTRO:0571 Plains American Indian HANCESTRO:0572 Kosraen HANCESTRO:0573 Native Hawaiian HANCESTRO:0574 Pacific Islander HANCESTRO:0575 Yoruban HANCESTRO:0576 West African HANCESTRO:0577 Dai Chinese HANCESTRO:0578 Hui Chinese HANCESTRO:0579 Jingpo Chinese HANCESTRO:0580 Malaysian Chinese HANCESTRO:0581 Uigur Chinese Uygur Chinese HANCESTRO:0582 Tibetan HANCESTRO:0583 Han Taiwanese Taiwanese Han HANCESTRO:0584 Sri Lankan Sinhalese HANCESTRO:0585 Tatar HANCESTRO:0586 Bashkir HANCESTRO:0587 Includes individuals who either self-report or have been described by authors as Aboriginal Australian of Martu ancestry. The Martu Australian Aboriginal people are from the Western Desert region located across the Pilbara in Western Australia Mardu Aboriginal Australian Mardu Australian Aboriginal Martu Aboriginal Australian PMID:27070114 Martu Australian Aboriginal HANCESTRO:0588 Jewish Israeli HANCESTRO:0589 Punjabi Sikh HANCESTRO:0590 American of European ancestry European American HANCESTRO:0591 The Esan people are one of the major ethnic groups in Edo State, Nigeria who speak the Esan language. (PMID:10146569) Samples from this population were studied as part of the full 1000 Genomes project (https://www.coriell.org/1/NHGRI/Collections/1000-Genomes-Collections/Esan-in-Nigeria-ESN) Esan HANCESTRO:0592 The Luhya are the second-largest ethnic group in Kenya and are comprised of subgroups that speak a common Bantu language. (PMID: 27813082) The Luhya ancestry group was assembled as part of phase III of the HapMap project and used in a number of rare variant density studies (PMID:22373165, PMID:26673965) Luhya HANCESTRO:0593 The Maasai are an indigenous African ethnic group of semi-nomadic people located in northern Tanzania and Kenya. (PMID:29868928) The Maasai ancestry group was assembled as part of phase III of the HapMap project and used as reference in a range of population genetic studies (PMID:28049708). Maasai HANCESTRO:0594 The Mende people are one of the largest ethnic groups in Sierra Leone who speak a language of the Mande branch of the Niger-Congo family. (PMID:15761855) Samples from this population were studied as part of the full 1000 Genomes project (https://www.coriell.org/1/NHGRI/Collections/1000-Genomes-Collections/Mende-in-Sierra-Leone-MSL) Mende HANCESTRO:0595 Native people residing in the Arctic of Alaska, northern Canada, Greenland, or eastern Siberia PMID:25884279 PMID:29220501 Class previously labelled as "Eskimo", which is outdated and culturally inappropriate. Outdated label may be added as an appropriately flagged synonym at a later stage. Inuit HANCESTRO:0596 Includes individuals with ethnic origins in the Semitic people populating the Arabian Peninsula and other countries in the Middle East and Northern Africa PMID:27393651 PMID:28106113 Arab HANCESTRO:0597 Includes individuals who either self-report or have been described by authors as Singaporean Malay. PMID:19700652 PMID:31626772 Singaporean Malay HANCESTRO:0598 Includes individuals who either self-report or have been described by authors as Singaporean Indian. PMID:19700652 PMID:31626772 Singaporean Indian HP:0000001 UMLS:C0444868 Root of all terms in the Human Phenotype Ontology. All HP:0000005 The pattern in which a particular genetic trait or disorder is passed from one generation to the next. HP:0001425 HP:0001453 HP:0001461 HP:0010985 UMLS:C1708511 Inheritance While there is a close conceptual relationship between allelic requirement and inheritance, they serve different purposes; allelic requirement is necessary for variant annotation pipelines and to determine if a given variant in a specific context is relevant to the phenotype of the patient e.g. a heterozygous variant (in the absence of compound heterozygosity) is relevant for dominant but not for recessive disease; while inheritance is used for describing the mode of inheritance of a phenotype and is particularly applicable in the clinical setting for communicating recurrence risk, to guide family screening, and to guide reproductive advice. Mode of inheritance HP:0000077 An abnormality of the kidney. MSH:D007674 SNOMEDCT_US:44513007 SNOMEDCT_US:90708001 UMLS:C0022658 UMLS:C0266292 Abnormal kidney Abnormality of the kidney Renal anomalies Renal anomaly The kidney is a paired organ whose primary function is the production of urine. Abnormality of the kidney HP:0000079 An abnormality of the urinary system. UMLS:C4021821 Urinary tract abnormalities Urinary tract abnormality Urinary tract anomalies Abnormality of the urinary system HP:0000083 A reduction in the level of performance of the kidneys in areas of function comprising the concentration of urine, removal of wastes, the maintenance of electrolyte balance, homeostasis of blood pressure, and calcium metabolism. HP:0000084 HP:0004723 MSH:D051437 SNOMEDCT_US:236423003 SNOMEDCT_US:42399005 UMLS:C0035078 UMLS:C1565489 UMLS:C1839604 Renal failure Renal failure in adulthood Renal insufficiency HP:0000118 symptom A phenotypic abnormality. UMLS:C4021819 http://purl.obolibrary.org/obo/SYMP_0000462 Organ abnormality This is the root of the phenotypic abnormality subontology of the HPO. Phenotypic abnormality HP:0000119 The presence of any abnormality of the genitourinary system. HP:0008658 HP:0008688 HP:0008704 HP:0008713 MSH:D014564 SNOMEDCT_US:287085006 SNOMEDCT_US:42030000 UMLS:C0042063 UMLS:C0080276 UMLS:C4020895 Abnormality of the GU system Genitourinary abnormality Genitourinary tract anomalies Genitourinary tract malformation Urogenital abnormalities Urogenital anomalies Abnormality of the genitourinary system HP:0000152 An abnormality of head and neck. UMLS:C4021817 Abnormality of head or neck Head and neck abnormality Abnormality of head or neck HP:0000153 An abnormality of the mouth. MSH:D009056 SNOMEDCT_US:128334002 UMLS:C0026633 Abnormal mouth Abnormality of the mouth Abnormality of the mouth HP:0000157 Any abnormality of the tongue. UMLS:C0878638 Abnormal tongue Abnormality of the tongue Glossal abnormality Lingual abnormality Tongue abnormality Abnormality of the tongue HP:0000163 Abnormality of the oral cavity, i.e., the opening or hollow part of the mouth. UMLS:C4025887 Abnormality of the oral cavity Abnormal oral cavity morphology HP:0000206 Inflammation of the tongue. MSH:D005928 SNOMEDCT_US:45534005 UMLS:C0017675 Inflammation of the tongue Lingual inflammation Smooth swollen tongue Glossitis HP:0000217 Dryness of the mouth due to salivary gland dysfunction. HP:0002709 HP:0100756 Decreased salivary flow MSH:D014987 SNOMEDCT_US:300268000 SNOMEDCT_US:56893005 SNOMEDCT_US:87715008 UMLS:C0043352 Dry mouth Dry mouth syndrome Reduced salivation Xerostomia HP:0000223 UMLS:C4025879 Abnormality of taste sensation Abnormality of taste sensation HP:0000224 A decreased ability to perceive flavor. MSH:D000370 SNOMEDCT_US:697990000 UMLS:C0151934 Decreased taste Decreased taste sensation Hypogeusia HP:0000234 An abnormality of the head. UMLS:C4021812 Abnormal head Abnormality of the head Head abnormality Abnormality of the head HP:0000271 An abnormality of the face. Abnormality of the countenance Abnormality of the physiognomy Abnormality of the visage Disorder of face SNOMEDCT_US:118930001 SNOMEDCT_US:32003007 SNOMEDCT_US:398206004 SNOMEDCT_US:398302004 UMLS:C0266617 UMLS:C1290857 UMLS:C4025871 Abnormal face Abnormality of the face Facial abnormality Disorder of the face Abnormality of the face HP:0000315 HP:0000284 UMLS:C4025863 Abnormality of the eye region Abnormality of the region around the eyes Anomaly of the orbital region of the face Deformity of the orbital region of the face Malformation of the orbital region of the face Abnormality of the orbital region HP:0000366 An abnormality of the nose. SNOMEDCT_US:128274005 SNOMEDCT_US:72089000 UMLS:C0240547 UMLS:C0265736 UMLS:C2235909 Abnormality of the nose Anomaly of the nose Nasal abnormality Nasal anomaly Deformity of the nose Malformation of the nose Nasal deformity Nasal malformation Abnormality of the nose HP:0000421 Epistaxis, or nosebleed, refers to a hemorrhage localized in the nose. COHD:318556 EFO:0003895 ICD10:R04.0 ICD9:784.7 MSH:D004844 NCIT:C26766 SNOMEDCT_US:12441001 SNOMEDCT_US:249366005 UMLS:C0014591 Bloody nose Frequent nosebleeds Nasal haemorrhage Nasal hemorrhage Nose bleed Nose bleeding Nosebleed Epistaxis HP:0000458 An inability to perceive odors. This is a general term describing inability to smell arising in any part of the process of smelling from absorption of odorants into the nasal mucous overlying the olfactory epithelium, diffusion to the cilia, binding to olfactory receptor sites, generation of action potentials in olfactory neurons, and perception of a smell. MSH:D000857 SNOMEDCT_US:44169009 UMLS:C0003126 Loss of smell Lost smell Anosmia HP:0000464 An abnormality of the neck. SNOMEDCT_US:298390003 SNOMEDCT_US:40052002 UMLS:C0266623 UMLS:C0575167 UMLS:C4280628 Abnormality of the neck Anomaly of the neck Deformity of the neck Malformation of the neck Abnormality of the neck HP:0000478 Any abnormality of the eye, including location, spacing, and intraocular abnormalities. MSH:D005124 MSH:D005128 SNOMEDCT_US:19416009 SNOMEDCT_US:371405004 SNOMEDCT_US:371409005 UMLS:C0015393 UMLS:C0015397 Abnormal eye Abnormality of the eye Abnormality of the eye HP:0000492 An abnormality of the eyelids. HP:0000285 UMLS:C4021803 Abnormality of the eyelid Abnormality of the eyelids Abnormal eyelid morphology HP:0000502 An abnormality of the conjunctiva. UMLS:C4025847 The conjunctiva is a thin, sparsely vascularized transparent membrane that covers and protects the sclera (the bulbar conjunctiva), and forms the inner lining of the eyelids (the tarsal conjunctiva). Abnormal conjunctiva morphology HP:0000504 Abnormality of eyesight (visual perception). UMLS:C4025846 Abnormality of sight Abnormality of vision Vision issue Abnormality of vision HP:0000508 The upper eyelid margin is positioned 3 mm or more lower than usual and covers the superior portion of the iris (objective); or, the upper lid margin obscures at least part of the pupil (subjective). MSH:D001763 SNOMEDCT_US:11934000 UMLS:C0005745 Blepharoptosis Drooping upper eyelid Eyelid ptosis Ptosis HP:0000509 Inflammation of the conjunctiva. MSH:D003231 SNOMEDCT_US:9826008 UMLS:C0009763 UMLS:C1864156 Pink eye Conjunctivitis HP:0000598 An abnormality of the ear. SNOMEDCT_US:275259005 UMLS:C0266589 Abnormality of the ear Ear anomaly Either a morphological abnormality or hearing deficit. This should be split more cleanly in the future. Abnormality of the ear HP:0000600 An anomaly of the pharynx, i.e., of the tubular structure extending from the base of the skull superiorly to the esophageal inlet inferiorly. UMLS:C4025838 The pharynx is tubular structure extending from base of skull superiorly to esophageal inlet inferiorly, and is composed of three distinct areas: the nasopharynx, the oropharynx, and the hypopharynx, with the pharyngeal walls being composed of the superior, middle, and inferior pharyngeal constrictor muscles. It is part of the digestive system and of the conducting zone of the respiratory system. Abnormality of the pharynx HP:0000622 Lack of sharpness of vision resulting in the inability to see fine detail. HP:0007723 SNOMEDCT_US:111516008 SNOMEDCT_US:246636008 UMLS:C0344232 Blurred vision This is a very nonspecific term and it is preferable to describe the correlates of blurred vision with the corresponding terms if possible. Blurred vision HP:0000707 An abnormality of the nervous system. HP:0001333 HP:0006987 Brain and/or spinal cord issue MSH:D009421 SNOMEDCT_US:88425004 UMLS:C0497552 Abnormality of the nervous system Neurologic abnormalities Neurological abnormality The nervous system comprises the neuraxis (brain, spinal cord, and ventricles), the autonomic nervous system, the enteric nervous system, and the peripheral nervous system. Abnormality of the nervous system HP:0000708 An abnormality of mental functioning including various affective, behavioral, cognitive, and perceptual abnormalities. HP:0000715 HP:0002368 HP:0002456 MSH:D000066553 MSH:D001526 SNOMEDCT_US:25786006 SNOMEDCT_US:277843001 UMLS:C0004941 UMLS:C0233514 Behavioral abnormality Behavioral changes Behavioral disorders Behavioral disturbances Behavioral problems Behavioral symptoms Behavioral/psychiatric abnormalities Behavioural abnormality Behavioural changes Behavioural disorders Behavioural disturbances Behavioural problems Behavioural symptoms Behavioural/Psychiatric abnormality Psychiatric disorders Psychiatric disturbances Atypical behavior HP:0000737 A proneness to anger, i.e., a condition of being easily bothered or annoyed. UMLS:C2700617 Irritability Irritable Irritability HP:0000790 The presence of blood in the urine. Hematuria may be gross hematuria (visible to the naked eye) or microscopic hematuria (detected by dipstick or microscopic examination of the urine). High urine occult blood MSH:D006417 SNOMEDCT_US:34436003 SNOMEDCT_US:53298000 UMLS:C0018965 Blood in urine Hematuria HP:0000818 An abnormality of the endocrine system. MSH:D004700 SNOMEDCT_US:362969004 UMLS:C0014130 UMLS:C4025823 The endocrine system is composed of glands that secrete hormones directly into the bloodstream and includes the following glands: thyroid, parathyroids, adrenals, pancreas, gonads (testicles and ovaries), and pituitary. Many other organs, such as the kidney, liver, and heart, have secondary endocrine functions. Abnormality of the endocrine system HP:0000819 A group of abnormalities characterized by hyperglycemia and glucose intolerance. HP:0004908 HP:0008217 HP:0008234 HP:0008260 MSH:D003920 SNOMEDCT_US:73211009 UMLS:C0011849 Diabetes mellitus HP:0000822 The presence of chronic increased pressure in the systemic arterial system. HP:0004949 HP:0005126 MSH:D006973 SNOMEDCT_US:24184005 SNOMEDCT_US:38341003 UMLS:C0020538 UMLS:C0497247 Arterial hypertension Systemic hypertension Hypertension is sustained elevation of resting systolic BP (140 mm Hg or higher), diastolic BP (90 mm Hg or higher), or both. Hypertension HP:0000924 An abnormality of the skeletal system. UMLS:C4021790 Abnormality of the skeletal system Skeletal abnormalities Skeletal anomalies Abnormality of the skeletal system HP:0000951 An abnormality of the skin. HP:0001478 HP:0001479 HP:0005591 HP:0006736 HP:0007415 HP:0007580 MSH:D012868 MSH:D012871 SNOMEDCT_US:199879009 SNOMEDCT_US:95320005 UMLS:C0037268 UMLS:C0037274 Abnormality of the skin Dermatopathy Dermopathy Abnormality of the skin HP:0000961 Bluish discoloration of the skin and mucosa due to poor circulation or inadequate oxygenation of arterial or capillary blood. MSH:D003490 SNOMEDCT_US:119419001 SNOMEDCT_US:3415004 UMLS:C0010520 Blue discoloration of the skin Cyanosis HP:0000964 Eczema is a form of dermatitis. The term eczema is broadly applied to a range of persistent skin conditions and can be related to a number of underlying conditions. Manifestations of eczema can include dryness and recurring skin rashes with redness, skin edema, itching and dryness, crusting, flaking, blistering, cracking, oozing, or bleeding. HP:0001481 MSH:D004485 SNOMEDCT_US:281104002 SNOMEDCT_US:43116000 UMLS:C0013595 Eczema Eczema has several forms including atopic dermatitis, contact dermatitis, dyshidrotic eczema, nummular eczema, seborrheic dermatitis, and stasis dermatitis. Eczema HP:0000969 An abnormal accumulation of fluid beneath the skin, or in one or more cavities of the body. HP:0000990 MSH:D004487 SNOMEDCT_US:20741006 SNOMEDCT_US:267038008 SNOMEDCT_US:423666004 SNOMEDCT_US:79654002 UMLS:C0013604 Dropsy Fluid retention Hydrops Oedema Water retention Edema may be related to one or more of the following factors: 1) increased capillary hydrostatic pressure, 2) decreased osmotic pressure of plasma, 3) decreased tissue tension and lymphatic drainage, 4) increased osmotic pressure of tissue fluids, and 5) increased capillary permeability. Edema HP:0000988 A red eruption of the skin. Rash MEDDRA:10037844 MSH:D005076 SNOMEDCT_US:112625008 SNOMEDCT_US:271807003 UMLS:C0015230 Skin rash Skin rash HP:0001005 UMLS:C4025812 Dermatological manifestations of systemic disorders HP:0001063 Bluish discoloration of the skin of the hands or feet. SNOMEDCT_US:25003006 UMLS:C0221347 Persistent blue color of hands or feet Persistent blue colour of hands or feet Cyanosis is caused by increased levels of deoxygenated hemoglobin. Acrocyanosis HP:0001081 Hard, pebble-like deposits that form within the gallbladder. MSH:D002769 SNOMEDCT_US:266474003 UMLS:C0008350 Gallstones Gallstones range in size from as small as a grain of sand to as large as a golf ball. Cholesterol gallstones are the most common type of gallstone. Gallstones resulting from too much bilirubin in the bile are referred to as pigment stones. Cholelithiasis HP:0001197 An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities. UMLS:C4025797 Abnormality of prenatal development or birth Because of the close link between prenatal developmental abnormalities and abnormalities of the birth process, a single term is chosen to subsume both classes of abnormality. Abnormality of prenatal development or birth HP:0001250 A seizure is an intermittent abnormality of nervous system physiology characterised by a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain. HP:0001275 HP:0001303 HP:0002125 HP:0002182 HP:0002279 HP:0002306 HP:0002348 HP:0002391 HP:0002417 HP:0002430 HP:0002431 HP:0002432 HP:0002434 HP:0002437 HP:0002466 HP:0002479 HP:0002794 HP:0006997 HP:0010520 MSH:D004827 MSH:D012640 SNOMEDCT_US:128613002 SNOMEDCT_US:246545002 SNOMEDCT_US:313307000 SNOMEDCT_US:84757009 SNOMEDCT_US:91175000 UMLS:C0014544 UMLS:C0036572 Epileptic seizure Seizures A type of electrographic seizure has been proposed in neonates which does not have a clinical correlate, it is electrographic only. The term epilepsy is not used to describe recurrent febrile seizures. Epilepsy presumably reflects an abnormally reduced seizure threshold. Seizure HP:0001259 Complete absence of wakefulness and content of conscience, which manifests itself as a lack of response to any kind of external stimuli. ICD-10:R40.2 MSH:D003128 SNOMEDCT_US:371632003 UMLS:C0009421 Coma Coma is generally a result of diffuse or extensive involvement of both hemispheres of the brain or lesions in the brainstem. Coma HP:0001287 Inflammation of the meninges. MSH:D008581 SNOMEDCT_US:7180009 UMLS:C0025289 Meningitis HP:0001289 Lack of clarity and coherence of thought, perception, understanding, or action. HP:0000731 MSH:D003221 SNOMEDCT_US:286933003 UMLS:C0009676 Confusion Disorientation Easily confused Mental disorientation Confusion HP:0001297 Sudden impairment of blood flow to a part of the brain due to occlusion or rupture of an artery to the brain. HP:0002452 MSH:D020521 SNOMEDCT_US:230690007 UMLS:C0038454 Cerebral vascular events Cerebrovascular accident Stroke Stroke HP:0001298 Encephalopathy is a term that means brain disease, damage, or malfunction. In general, encephalopathy is manifested by an altered mental state. MSH:D001927 SNOMEDCT_US:81308009 UMLS:C0085584 This term and its children are general and bundled terms that are kept for convenience. For new annotations, it is recommended that the specific phenotypic abnormalities be noted. Encephalopathy HP:0001324 Reduced strength of muscles. HP:0002309 HP:0008979 HP:0009012 HP:0009061 MSH:D018908 SNOMEDCT_US:26544005 UMLS:C0151786 Muscle weakness Muscular weakness It is important clinical to distinguish between muscle weakness, fatigue, and asthenia. Fatigue describes the inability to continue performing a task after multiple repetitions; in contrast, a patient with primary weakness is unable to perform the first repetition of the task. Asthenia is a sense of weariness or exhaustion in the absence of muscle weakness. Conditions that result in intrinsic muscle weakness can be divided into several main categories: infectious, neurologic, endocrine, inflammatory, rheumatologic, genetic, metabolic, electrolyte-induced, or drug-induced. Muscle weakness HP:0001350 Abnormal coordination of muscles involved in speech. SNOMEDCT_US:289195008 UMLS:C0234518 Slurred speech Slurred speech HP:0001367 An abnormal structure or form of the joints, i.e., one or more of the articulations where two bones join. MSH:D007592 SNOMEDCT_US:399269003 UMLS:C0022408 UMLS:C0240083 Abnormal shape of joints Abnormality of the joints Anomaly of the joints Abnormal joint morphology HP:0001376 A reduction in the freedom of movement of one or more joints. HP:0003101 UMLS:C1857108 Decreased joint mobility Decreased mobility of joints Limitation of joint mobility Limited joint mobility Limited joint motion Limitation of joint mobility HP:0001386 SNOMEDCT_US:271771009 UMLS:C0152031 Joint swelling Joint swelling HP:0001387 Joint stiffness is a perceived sensation of tightness in a joint or joints when attempting to move them after a period of inactivity. Joint stiffness typically subsides over time. HP:0002775 HP:0003033 SNOMEDCT_US:84445001 UMLS:C0162298 Joint stiffness Stiff joint Stiff joints Joint stiffness HP:0001392 An abnormality of the liver. MSH:D008107 SNOMEDCT_US:235856003 UMLS:C0023895 UMLS:C4021780 Abnormal liver Abnormality of the liver Liver abnormality Abnormality of the liver HP:0001397 Steatosis is a term used to denote lipid accumulation within hepatocytes. HP:0002252 HP:0200121 MSH:D005234 SNOMEDCT_US:197321007 SNOMEDCT_US:442191002 UMLS:C2711227 Fatty infiltration of liver Fatty liver Liver steatosis Steatosis Although steatosis is the hallmark of the fatty liver disease, it is not a specific feature because it can be seen as part of other disease processes, such as drug injury, Wilson disease, or hepatitis C virus infection (especially genotype-3). Involvement of less than 5% of the hepatocytes by steatosis is considered clinically insignificant and within reference range. Based on the morphologic appearance and the size of the lipid droplets within the cytoplasm of the hepatocytes, steatosis is characterized as macrovesicular or microvesicular. Macrovesicular steatosis is characterized by large lipid droplets occupying the cytoplasm, displacing the nucleus to the periphery (large droplet macrovesicular steatosis) or multiple small lipid droplets of variable size occupying the cytoplasm with the nucleus maintaining its central location (small droplet macrovesicular steatosis). Microvesicular steatosis is characterized by innumerable tiny, relatively uniform lipid vacuoles that result in a bubbly appearance of the hepatocytes. Hepatic steatosis HP:0001410 Reduced ability of the liver to perform its functions. HP:0004393 HP:0005228 HP:0006570 MSH:D008107 SNOMEDCT_US:75183008 SNOMEDCT_US:77981007 UMLS:C0086565 UMLS:C0232744 UMLS:C3279149 Decreased liver function Liver dysfunction Decreased liver function HP:0001507 HP:0008904 UMLS:C0262361 Abnormal growth Growth abnormality Growth issue Growth abnormality HP:0001513 Accumulation of substantial excess body fat. MSH:D009765 SNOMEDCT_US:414915002 SNOMEDCT_US:414916001 UMLS:C0028754 Having too much body fat Obesity Obesity HP:0001538 A thrusting or bulging out of the abdomen. UMLS:C1854928 Abdominal protuberance Belly sticks out Extended belly Protuberant abdomen HP:0001574 An abnormality of the integument, which consists of the skin and the superficial fascia. UMLS:C4025761 Abnormality of skin, hair, or nails. Abnormality of the integument HP:0001608 UMLS:C4021776 Abnormality of the voice Voice abnormality This term describes any abnormality of the voice, i.e., of the sounds produced by humans by the passage of air through the larynx and over the vocal cords, and then modified by the resonance organs, the nasopharynx, and the mouth. Abnormality of the voice HP:0001612 SNOMEDCT_US:2120003 UMLS:C0234860 Weak cry HP:0001626 Any abnormality of the cardiovascular system. HP:0003116 MSH:D002318 MSH:D018376 SNOMEDCT_US:49601007 UMLS:C0007222 UMLS:C0243050 Abnormality of the cardiovascular system Cardiovascular abnormality The cardiovascular system consists of the heart, vasculature, and the lymphatic system. Abnormality of the cardiovascular system HP:0001627 Any structural anomaly of the heart. HP:3000001 MSH:D006330 SNOMEDCT_US:13213009 UMLS:C0018798 UMLS:C0152021 Abnormality of cardiac morphology Abnormality of the heart Abnormally shaped heart Cardiac abnormality Cardiac anomalies Cardiac anomaly Congenital heart defect Congenital heart defects Heart defect Abnormal heart morphology HP:0001635 The presence of an abnormality of cardiac function that is responsible for the failure of the heart to pump blood at a rate that is commensurate with the needs of the tissues or a state in which abnormally elevated filling pressures are required for the heart to do so. Heart failure is frequently related to a defect in myocardial contraction. HP:0006686 MSH:D006333 SNOMEDCT_US:42343007 SNOMEDCT_US:84114007 UMLS:C0018801 UMLS:C0018802 CHF Cardiac failure Cardiac failures Cardiac insufficiency Chronic heart failure Heart failure Congestive heart failure HP:0001637 A structural anomaly of the muscle layer of the heart wall. UMLS:C4025758 Abnormality of the myocardium Abnormal myocardium morphology HP:0001638 A myocardial disorder in which the heart muscle is structurally and functionally abnormal, in the absence of coronary artery disease, hypertension, valvular disease and congenital heart disease sufficient to cause the observed myocardial abnormality. Fyler:1840 MSH:D009202 SNOMEDCT_US:57809008 SNOMEDCT_US:85898001 UMLS:C0878544 Disease of the heart muscle Cardiomyopathy HP:0001649 A rapid heartrate that exceeds the range of the normal resting heartrate for age. HP:0001673 HP:0001720 MSH:D013610 SNOMEDCT_US:3424008 SNOMEDCT_US:86651002 UMLS:C0039231 UMLS:C4020868 Fast heart rate Heart racing Racing heart Tachycardia HP:0001695 An abrupt loss of heart function. MSH:D006323 SNOMEDCT_US:397829000 SNOMEDCT_US:410429000 UMLS:C0018790 Heart stops beating Cardiac arrest HP:0001700 Irreversible damage to heart tissue (myocardium) due to lack of oxygen after a heart attack (myocardial infarction). SNOMEDCT_US:251061000 UMLS:C1442837 Myocardial necrosis HP:0001742 Reduced ability to pass air through the nasal cavity often leading to mouth breathing. MSH:D015508 SNOMEDCT_US:232209000 SNOMEDCT_US:267100006 SNOMEDCT_US:68235000 UMLS:C0027424 UMLS:C0027429 Blockage of nose Nasal blockage Nasal obstruction Obstruction of nose Stuffy nose Congestion of nose Nasal congestion HP:0001751 An abnormality of the functioning of the vestibular apparatus. HP:0006917 HP:0007921 UMLS:C1843865 Impaired vestibular function Interictal vestibular dysfunction Vestibular function defect The vestibular apparatus is the nonauditory portion of the inner ear that mediates the subjective sensation of motion and spatial orientation of the head, adjusts muscular activity and body position to maintain posture, and stabilizes in space the fixation point of the eyes when the head moves, in order to provide a stable image upon the retina. The functioning of the vestibular system is often checked clinically by means of the caloric test, in which the head is tilted backward by about 60 degrees and either warm or cold water is introduced into the external auditory meatus on one side. The immediate results are usually vertigo, nausea, nystagmus, and twisting of the head and body. Abnormal vestibular function HP:0001787 An abnormality of the birth process. SNOMEDCT_US:274127000 UMLS:C0549629 Abnormal delivery Delivery complication Abnormal delivery HP:0001824 Reduction of total body weight. MSH:D015431 SNOMEDCT_US:161832001 SNOMEDCT_US:262285001 SNOMEDCT_US:89362005 UMLS:C1262477 Loss of weight Weight loss HP:0001871 An abnormality of the hematopoietic system. HP:0003135 MSH:D006402 SNOMEDCT_US:191124002 SNOMEDCT_US:34093004 UMLS:C0018939 UMLS:C0850715 UMLS:C4020864 Abnormality of blood and blood-forming tissues Abnormality of the haematopoietic system Abnormality of the hematopoietic system Haematological abnormality Hematological abnormality The hematopoietic system comprises the organs that are involved in the production of blood, primarily the bone marrow, spleen, tonsils, and lymph nodes. Abnormality of blood and blood-forming tissues HP:0001877 Any structural abnormality of erythrocytes (red-blood cells). HP:0010973 SNOMEDCT_US:12222001 UMLS:C0391870 UMLS:C4020862 Abnormality of erythrocytes Abnormality of red blood cells Abnormal erythrocyte morphology HP:0001892 An abnormal susceptibility to bleeding, often referred to as a bleeding diathesis. A bleeding diathesis may be related to vascular, platelet and coagulation defects. HP:0004830 HP:0004834 HP:0004849 HP:0004862 HP:0004865 HP:0008183 SNOMEDCT_US:248250000 SNOMEDCT_US:64779008 UMLS:C1458140 Bleeding diathesis Bleeding tendency Hemorrhagic diathesis This term is kept for historical reasons. If possible, a more exact description of the phenotype (i.e., whether there is a vascular, platelet and coagulation defect) should be attempted. Abnormal bleeding HP:0001903 A reduction in erythrocytes volume or hemoglobin concentration. HP:0001926 HP:0003136 HP:0005509 MSH:D000740 SNOMEDCT_US:165397008 SNOMEDCT_US:271737000 UMLS:C0002871 UMLS:C0162119 Anaemia Low number of red blood cells or haemoglobin Low number of red blood cells or hemoglobin Anemia is not a specific entity but can result from many underlying pathologic processes. The three main causes of anemia are blood loss, decreased or faulty red blood cell production, and increased destruction of red blood cells. Various classifications are in clinical use including a classification according to the mean corpuscular volume (MCV) of the erythrocytes: microcytic, macrocytic, or normocytic. Anemias can also be classified according to variations in cell size and shape, as reflected by the red-cell distribution width (RDW). Additionally, anemias can be classified into those of inadequate production and hemolytic anemias. Anemia HP:0001919 Sudden loss of renal function, as manifested by decreased urine production, and a rise in serum creatinine or blood urea nitrogen concentration (azotemia). MSH:D058186 SNOMEDCT_US:14350001000004108 SNOMEDCT_US:14669001 UMLS:C0022660 UMLS:C2609414 Acute kidney failure Acute renal failure Acute renal failure is usually classified into prerenal (response to severe volume depletion), intrinsic (response to acute cytotoxic, ischemic, or inflammatory insults) and postrenal (response to obstruction of the passage of urine) etiologies. Acute kidney injury HP:0001939 HP:0002146 HP:0004355 HP:0004367 UMLS:C4021768 Laboratory abnormality Metabolism abnormality Abnormality of metabolism/homeostasis HP:0001944 MSH:D003681 SNOMEDCT_US:34095006 UMLS:C0011175 Dehydration Exsiccosis Dehydration HP:0001945 Body temperature elevated above the normal range. MSH:D005334 SNOMEDCT_US:386661006 SNOMEDCT_US:50177009 UMLS:C0015967 Fever Hyperthermia Pyrexia Fever has been defined as a state of elevated core temperature, which is often, but not necessarily, part of the defensive responses of multicellular organisms (host) to the invasion of live (microorganisms) or inanimate matter recognized as pathogenic or alien by the host. The febrile response (of which fever is a component) is a complex physiologic reaction to disease, involving a cytokine-mediated rise in core temperature, generation of acute phase reactants, and activation of numerous physiologic, endocrinologic, and immunologic systems. The rise in temperature during fever is to be distinguished from that occurring during episodes of hyperthermia. Unlike fever, hyperthermia involves an unregulated rise in body temperature in which pyrogenic cytokines are not directly involved and against which standard antipyretics are ineffective. It represents a failure of thermoregulatory homeostasis, in which there is uncontrolled heat production, inadequate heat dissipation, or defective hypothalamic thermoregulation. Fever HP:0001952 Glucose intolerance (GI) can be defined as dysglycemia that comprises both prediabetes and diabetes. It includes the conditions of impaired fasting glucose (IFG) and impaired glucose tolerance (IGT) and diabetes mellitus (DM). HP:0000833 Abnormal glucose tolerance UMLS:C0235401 Glucose intolerance Glucose intolerance HP:0001977 Venous or arterial thrombosis (formation of blood clots) of spontaneous nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis). UMLS:C4025731 Abnormal blood clot Abnormal blood clotting Abnormal thrombosis HP:0002011 A structural abnormality of the central nervous system. HP:0002405 HP:0002413 HP:0002481 HP:0007319 MSH:D002493 SNOMEDCT_US:23853001 UMLS:C0007682 UMLS:C4021765 Abnormality of the central nervous system Morphological abnormality of the CNS Morphological abnormality of the central nervous system Morphological central nervous system abnormality HP:0002012 An abnormality of the viscera of the abdomen. UMLS:C4021764 Abnormality of the abdominal organs Gastrointestinal tract defects The abdominal organs comprise the stomach, small and large intestines, liver, pancreas, bile tract, and spleen. Abnormality of the abdominal organs HP:0002013 Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions. MEDDRA:10047700 MSH:D014839 SNOMEDCT_US:249497008 SNOMEDCT_US:300359004 SNOMEDCT_US:422400008 UMLS:C0042963 Emesis Throwing up Vomiting Vomiting HP:0002014 Abnormally increased frequency (usually defined as three or more) loose or watery bowel movements a day. MSH:D003967 SNOMEDCT_US:267060006 SNOMEDCT_US:62315008 UMLS:C0011991 Diarrhea Diarrhoea Watery stool Diarrhea HP:0002015 Difficulty in swallowing. HP:0002569 MEDDRA:10013950 MSH:D003680 SNOMEDCT_US:288939007 SNOMEDCT_US:40739000 UMLS:C0011168 Difficulty swallowing Poor swallowing Swallowing difficulties Swallowing difficulty Dysphagia HP:0002017 Nausea is a commonly encountered symptom that has been defined as an unpleasant painless subjective feeling that one will imminently vomit. Vomiting has been defined as the forceful expulsion of the contents of the stomach, duodenum, or jejunum through the oral cavity. While nausea and vomiting are often thought to exist on a temporal continuum, this is not always the case. There are situations when severe nausea may be present without emesis and less frequently, when emesis may be present without preceding nausea. SNOMEDCT_US:16932000 UMLS:C0027498 Nausea and vomiting Nausea and vomiting HP:0002018 A sensation of unease in the stomach together with an urge to vomit. MEDDRA:10028813 MSH:D009325 SNOMEDCT_US:422587007 UMLS:C0027497 Nausea Nausea HP:0002019 Infrequent or difficult evacuation of feces. HP:0002241 HP:0003786 MSH:D003248 SNOMEDCT_US:14760008 SNOMEDCT_US:225595004 UMLS:C0009806 UMLS:C0237326 Constipation Costiveness Dyschezia Constipation HP:0002027 An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) and perceived to originate in the abdomen. Gastro pain Gastrointestinal pain MEDDRA:10000081 MSH:D015746 SNOMEDCT_US:21522001 UMLS:C0000737 Abdominal pain Pain in stomach Stomach pain Abdominal pain can be crampy, achy, dull, intermittent or sharp. The terms stomach ache and stomach cramps are nonmedical terms often used to describe pain in the mid- or upper abdominal area, even though it is not the case that the (smooth) muscles of the stomach or the abdomen have cramps. Stomach pain is another layperson term commonly used to refer to abdominal pain. Abdominal pain HP:0002028 The presence of chronic diarrhea, which is usually taken to mean diarrhea that has persisted for over 4 weeks. SNOMEDCT_US:236071009 UMLS:C0401151 Chronic diarrhea Chronic diarrhoea Chronic diarrhea HP:0002033 An inadequate sucking reflex, resulting in the difficult of newborns to be breast-fed. UMLS:C1837142 Poor suck Poor sucking Sucking weakness Poor suck HP:0002037 Inflammation, or an inflammatory state in the large intestine. MSH:D015212 SNOMEDCT_US:24526004 SNOMEDCT_US:302168000 UMLS:C0021390 UMLS:C0578878 Inflammation of the large intestine Inflammation of the large intestine HP:0002038 UMLS:C1839531 Protein avoidance HP:0002039 A lack or loss of appetite for food (as a medical condition). MSH:D000855 SNOMEDCT_US:79890006 UMLS:C0003123 Anorexia Note that this term does not refer to the condition anorexia nervosa (A disorder characterized by an obsessive desire to lose weight by refusing to eat). Anorexia HP:0002041 UMLS:C0743178 Intractable diarrhoea Intractable diarrhea HP:0002060 Any structural abnormality of the telencephalon, which is also known as the cerebrum. UMLS:C4021762 Abnormality of the cerebrum Abnormality of the telencephalon Cerebral lesion Abnormal cerebral morphology HP:0002076 Migraine is a chronic neurological disorder characterized by episodic attacks of headache and associated symptoms. HP:0007194 MSH:D008881 SNOMEDCT_US:37796009 UMLS:C0149931 UMLS:C0744641 Intermittent migraine headaches Migraine Migraine headache Migraine headaches Migraine HP:0002086 An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles. UMLS:C4018871 Respiratory abnormality Abnormality of the respiratory system HP:0002087 An abnormality of the upper respiratory tract. UMLS:C4025727 Abnormality of the upper respiratory tract Upper respiratory tract issues Abnormality of the upper respiratory tract HP:0002088 Any structural anomaly of the lung. MSH:D008171 SNOMEDCT_US:19829001 UMLS:C0024115 UMLS:C4021760 Abnormality of lung structure Abnormality of the lungs Abnormally shaped lung Unusal lung shape Abnormal lung morphology HP:0002090 Inflammation of any part of the lung parenchyma. MSH:D011014 SNOMEDCT_US:233604007 UMLS:C0032285 Pneumonia Pneumonia HP:0002093 HP:0004893 HP:0005937 HP:0006542 MSH:D012131 SNOMEDCT_US:409623005 UMLS:C0035229 UMLS:C4020855 Respiratory impairment Respiratory insufficiency HP:0002094 Difficult or labored breathing. Dyspnea is a subjective feeling only the patient can rate, e.g., on a Borg scale. MSH:D004417 SNOMEDCT_US:230145002 SNOMEDCT_US:267036007 UMLS:C0013404 Abnormal breathing Breathing difficulty Difficult to breathe Difficulty breathing Dyspnoea Shortness of breath Trouble breathing Dyspnea HP:0002097 HP:0006534 MSH:D011656 SNOMEDCT_US:87433001 UMLS:C0034067 Pulmonary emphysema Emphysema HP:0002099 Asthma is characterized by increased responsiveness of the tracheobronchial tree to multiple stimuli, leading to narrowing of the air passages with resultant dyspnea, cough, and wheezing. HP:0002112 MSH:D001249 SNOMEDCT_US:195967001 SNOMEDCT_US:991000119106 UMLS:C0004096 UMLS:C3714497 Asthma Bronchial asthma Asthma HP:0002103 An abnormality of the pulmonary pleura, the thin, transparent membrane which covers the lungs and lines the inside of the chest walls. UMLS:C4025726 Abnormality of the pleura Abnormal pleura morphology HP:0002105 Coughing up (expectoration) of blood or blood-streaked sputum from the larynx, trachea, bronchi, or lungs. MSH:D006469 SNOMEDCT_US:66857006 SNOMEDCT_US:6686005 UMLS:C0019079 Coughing up blood Haemoptysis Hemoptysis HP:0002107 Accumulation of air in the pleural cavity leading to a partially or completely collapsed lung. MSH:D011030 SNOMEDCT_US:36118008 UMLS:C0032326 Collapsed lung Pneumothorax HP:0002108 Pneumothorax occurring without traumatic injury to the chest or lung. MSH:D011030 SNOMEDCT_US:80423007 UMLS:C0149781 Spontaneous collapsed lung Spontaneous pneumothorax HP:0002140 Acute ischemic stroke (AIS) is defined by the sudden loss of blood flow to an area of the brain with the resulting loss of neurologic function. It is caused by thrombosis or embolism that occludes a cerebral vessel supplying a specific area of the brain. During a vessel occlusion, there is a core area where damage to the brain is irreversible and an area of penumbra where the brain has lost function owing to decreased blood flow but is not irreversibly injured. SNOMEDCT_US:422504002 UMLS:C0948008 Ischaemic stroke Ischemic stroke HP:0002167 Abnormalities in the sound of a person's speech or vocalization not necessarily associated with a known physical cause or due to stuttering or stammering. MSH:D013064 UMLS:C0037822 Abnormal speech Abnormal vocalisation Abnormal vocalization Abnormality of speech or vocalization HP:0002202 The presence of an excessive amount of fluid in the pleural cavity. MSH:D010996 SNOMEDCT_US:60046008 UMLS:C0032227 Fluid around lungs Pleural effusion HP:0002204 An embolus (that is, an abnormal particle circulating in the blood) located in the pulmonary artery and thereby blocking blood circulation to the lung. Usually the embolus is a blood clot that has developed in an extremity (for instance, a deep venous thrombosis), detached, and traveled through the circulation before becoming trapped in the pulmonary artery. MSH:D011655 SNOMEDCT_US:59282003 UMLS:C0034065 Blood clot in artery of lung Pulmonary embolism HP:0002206 Replacement of normal lung tissues by fibroblasts and collagen. HP:0006523 MSH:D011658 SNOMEDCT_US:51615001 UMLS:C0034069 Pulmonary fibrosis leads to an irreversible impairment of alveolar oxygen transfer. Pulmonary fibrosis HP:0002239 Hemorrhage affecting the gastrointestinal tract. MSH:D006471 SNOMEDCT_US:74474003 UMLS:C0017181 GI haemorrhage GI hemorrhage Gastrointestinal bleeding Gastrointestinal haemorrhage Gastrointestinal hemorrhage HP:0002242 An abnormality of the intestine. The closely related term enteropathy is used to refer to any disease of the intestine. HP:0002628 MSH:D007410 SNOMEDCT_US:85919009 UMLS:C0021831 Abnormality of the intestine Enteropathy Abnormal intestine morphology HP:0002249 The passage of blackish, tarry feces associated with gastrointestinal hemorrhage. Melena occurs if the blood remains in the colon long enough for it to be broken down by colonic bacteria. One degradation product, hematin, imbues the stool with a blackish color. Thus, melena generally occurs with bleeding from the upper gastrointestinal tract (e.g., stomach ulcers or duodenal ulcers), since the blood usually remains in the gut for a longer period of time than with lower gastrointestinal bleeding. MSH:D008551 SNOMEDCT_US:249627005 SNOMEDCT_US:267055007 SNOMEDCT_US:269899009 SNOMEDCT_US:2901004 SNOMEDCT_US:35064005 UMLS:C0025222 UMLS:C0474585 Black faeces Black feces Melena HP:0002250 Any abnormality of the large intestine. UMLS:C4025715 Abnormality of the large intestine The large intestine comprises the cecum and colon. Abnormal large intestine morphology HP:0002254 Repeated episodes of diarrhea separated by periods without diarrhea. UMLS:C0239181 Episodic diarrhea Episodic diarrhoea Intermittent diarrhoea Intermittent diarrhea HP:0002315 Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve. HP:0000266 HP:0001354 MSH:D006261 SNOMEDCT_US:25064002 UMLS:C0018681 Headache Headaches Headache is one of the most common types of recurrent pain as well as one of the most frequent symptoms in neurology. In addition to occasional headaches, there are well-defined headache disorders that vary in incidence, prevalence and duration and can be divided into two broad categories. In secondary headache disorders, headaches are attributed to another condition, such as brain tumor or head injury; for the primary disorders the headache is not due to another condition. Headache HP:0002321 An abnormal sensation of spinning while the body is actually stationary. MSH:D004244 MSH:D014717 SNOMEDCT_US:271789005 SNOMEDCT_US:399090003 SNOMEDCT_US:399153001 SNOMEDCT_US:404640003 UMLS:C0012833 UMLS:C0042571 Dizzy spell Vertigo HP:0002371 UMLS:C0542223 Loss of speech Loss of speech HP:0002383 A disorder of the brain caused by an infectious agent that presents with fever, headache, and an altered level of consciousness. There may also be focal or multifocal neurologic deficits, and focal or generalized seizure activity. MSH:D004660 SNOMEDCT_US:45170000 UMLS:C0014038 Brain inflammation Infectious encephalitis HP:0002572 Paroxysmal, recurrent episodes of vomiting. UMLS:C1838993 UMLS:C1857202 Episodic vomiting Episodic vomiting HP:0002573 The passage of fresh (red) blood per anus, usually in or with stools. Most rectal bleeding comes from the colon, rectum, or anus. HP:0002255 HP:0002609 MSH:D006471 SNOMEDCT_US:236068001 SNOMEDCT_US:405729008 UMLS:C0018932 Rectal bleeding Bright red blood in stool, most frequentoly caused by hemorrhoids or diverticulosis. Hematochezia HP:0002574 An intermittent form of abdominal pain. UMLS:C0262527 UMLS:C3808022 Episodic abdominal pain HP:0002583 Colitis refers to an inflammation of the colon and is often used to describe an inflammation of the large intestine (colon, cecum and rectum). Colitides may be acute and self-limited or chronic, and broadly fit into the category of digestive diseases. MSH:D003092 SNOMEDCT_US:64226004 UMLS:C0009319 Colitis HP:0002587 Vomiting that ejects the gastric contents with great force. SNOMEDCT_US:8579004 UMLS:C0221151 Projectile vomiting Projectile vomiting HP:0002597 An abnormality of the vasculature. UMLS:C0241657 Abnormality of blood vessels Abnormality of the vasculature Vascular abnormalities Abnormality of the vasculature HP:0002615 Low Blood Pressure, vascular hypotension. HP:0005127 HP:0006701 MSH:D007022 SNOMEDCT_US:45007003 UMLS:C0020649 Arterial hypotension Low blood pressure Hypotension HP:0002625 Formation of a blot clot in a deep vein. The clot often blocks blood flow, causing swelling and pain. The deep veins of the leg are most often affected. MSH:D020246 SNOMEDCT_US:128053003 UMLS:C0149871 Blood clot in a deep vein Deep vein thrombosis Multiple deep venous thrombosis Deep venous thrombosis HP:0002633 Inflammation of blood vessel. MSH:D014657 SNOMEDCT_US:31996006 UMLS:C0042384 Angiitis Inflammation of blood vessel Vasculitis HP:0002637 Restriction of arterial blood supply to the brain associated with insufficient oxygenation to support the metabolic requirements of the tissue. MSH:D002545 SNOMEDCT_US:287731003 SNOMEDCT_US:389100007 UMLS:C0007786 UMLS:C0917798 Brain ischemia Cerebrovascular ischemia Disruption of blood oxygen supply to brain Cerebral ischemia HP:0002664 An organ or organ-system abnormality that consists of uncontrolled autonomous cell-proliferation which can occur in any part of the body as a benign or malignant neoplasm (tumor). HP:0003008 HP:0006741 Abnormal tissue mass MSH:D009369 NCIT:C3262 SNOMEDCT_US:108369006 SNOMEDCT_US:363346000 UMLS:C0006826 UMLS:C0027651 Neoplasia Oncological abnormality Tumor Tumour The World Health Organization (WHO) classifies neoplasms into four main groups: (i) benign neoplasm, (ii) in situ neoplasm, (iii) malignant neoplasm, and (iv) neoplasm of uncertain or unknown behavior. A malignant neoplasm is also known as cancer. Neoplasm HP:0002715 An abnormality of the immune system. HP:0003257 HP:0003346 HP:0010986 UMLS:C4021753 Abnormality of the immune system Immunological abnormality The immune system is composed of organs and interdependent cell types that collectively protect the body from infections and from the growth of tumor cells. The organs of the immune system comprise the bone marrow, the spleen, the thymus,the lymph nodes, and the cell types comprise B cells, T cells, natural killer cells, granulocytes,dendritic cells, and macrophages. Abnormality of the immune system HP:0002716 Enlargment (swelling) of a lymph node. HP:0002735 MSH:D000072281 SNOMEDCT_US:30746006 UMLS:C0497156 Lymph node hyperplasia Swollen lymph nodes Lymphadenopathy HP:0002733 A structural lymph node abnormality. HP:0008149 UMLS:C0149727 Abnormal lymph node histology Abnormality of the lymph nodes Abnormal lymph node morphology HP:0002789 Very rapid breathing. HP:0002874 HP:0004346 MSH:D059246 SNOMEDCT_US:271823003 UMLS:C0231835 Increased respiratory rate or depth of breathing Polypnea In adults, a beathing rate of between 12-20 breaths per minute is normal and tachypnea is present with a ventilatory rate greater than 20 breaths per minute. Tachypnea HP:0002793 An anomaly of the rhythm or depth of breathing. UMLS:C1837388 Abnormal pattern of respiration Abnormal respiratory patterns Unusual breathing patterns Abnormal pattern of respiration HP:0002795 HP:0005952 Fyler:4200 UMLS:C4025677 Abnormal respiration Functional respiratory abnormality Abnormal respiratory system physiology HP:0002829 Joint pain. MSH:D018771 SNOMEDCT_US:57676002 UMLS:C0003862 Arthralgias Joint pain Arthralgia is distinct from Arthritis, which is not a symptom but a diagnosis with articular inflammation or signs of osteoarthritis. Arthralgia HP:0002878 A severe form of respiratory insufficiency characterized by inadequate gas exchange such that the levels of oxygen or carbon dioxide cannot be maintained within normal limits. HP:0004877 MSH:D012131 SNOMEDCT_US:409622000 UMLS:C1145670 Respiratory failure Respiratory failure is classified as type 1 with hypoxemia (arterial partial pressure of oxygen less than 60 mmHg) without hypercapnea, and type 2 with hypoxemia in the present of hypercapnea (partial pressure of carbon dioxide over 50 mmHg). Respiratory failure HP:0002900 An abnormally decreased potassium concentration in the blood. MSH:D007008 SNOMEDCT_US:166690008 SNOMEDCT_US:43339004 UMLS:C0020621 Low blood potassium levels Hypokalemia HP:0002901 An abnormally decreased calcium concentration in the blood. MSH:D006996 SNOMEDCT_US:5291005 UMLS:C0020598 Hypocalcaemia Low blood calcium levels Hypocalcemia HP:0002917 An abnormally decreased magnesium concentration in the blood. HP:0003284 SNOMEDCT_US:190855004 UMLS:C0151723 Low blood Mg levels Low blood magnesium levels Hypomagnesemia HP:0003011 Abnormality originating in one or more muscles, i.e., of the set of muscles of body. HP:0003197 HP:0003708 HP:0040290 UMLS:C4021745 Muscular abnormality Abnormality of the musculature HP:0003110 An abnormality of the composition of urine or the levels of its components. HP:0011865 HP:0011866 UMLS:C4025655 Pee issues Urine issues Abnormality of urine homeostasis HP:0003111 Abnormality of the homeostasis (concentration) of a monoatomic ion. HP:0003253 SNOMEDCT_US:237840007 UMLS:C1704431 UMLS:C4025654 Abnormality of ion homeostasis Electrolyte disorders Electrolyte disturbance Abnormal blood ion concentration HP:0003201 Breakdown of muscle fibers that leads to the release of muscle fiber contents (myoglobin) into the bloodstream. MSH:D012206 SNOMEDCT_US:240131006 SNOMEDCT_US:89010004 UMLS:C0035410 Breakdown of skeletal muscle Rhabdomyolysis HP:0003270 Distention of the abdomen. HP:0001542 HP:0003364 SNOMEDCT_US:41931001 SNOMEDCT_US:60728008 UMLS:C0000731 Abdominal bloating Abdominal distension Abdominal swelling Belly bloating Bloating Distended abdomen Abdominal distention can be a secondary feature associated with a number of conditions such as bowel obstruction. Abdominal distention HP:0003326 Pain in muscle. HP:0003718 MSH:D063806 SNOMEDCT_US:68962001 UMLS:C0231528 Muscle ache Muscle pain Myalgia HP:0003470 Paralysis of voluntary muscles means loss of contraction due to interruption of one or more motor pathways from the brain to the muscle fibers. Although the word paralysis is often used interchangeably to mean either complete or partial loss of muscle strength, it is preferable to use paralysis or plegia for complete or severe loss of muscle strength, and paresis for partial or slight loss. Motor paralysis results from deficits of the upper motor neurons (corticospinal, corticobulbar, or subcorticospinal). Motor paralysis is often accompanied by an impairment in the facility of movement. MSH:D010243 SNOMEDCT_US:44695005 UMLS:C0522224 Inability to move Paralysis Paralysis HP:0003674 The age group in which disease manifestations appear. HP:0003588 HP:0003590 HP:0003597 HP:0003602 HP:0003603 HP:0003618 HP:0003626 HP:0003628 HP:0003630 HP:0003663 HP:0003664 HP:0003668 HP:0011007 MSH:D017668 MeSH:D017668 UMLS:C0206132 Age of onset Age symptoms begin Adolescent is defined by WHO as a person between 10-19 years of age. Onset HP:0003745 Cases of the disease in question occur without a previous family history, i.e., as isolated cases without being transmitted from a parent and without other siblings being affected. HP:0001420 HP:0003747 HP:0003769 UMLS:C1853237 Isolated cases No previous family history Sporadic HP:0003750 An abnormal, increased fatiguability of the musculature. MSH:D018763 SNOMEDCT_US:80449002 UMLS:C0242979 UMLS:C4025573 Increased muscle fatiguability HP:0003826 Death of the fetus in utero after at least 22 weeks of gestation. HP:0001624 HP:0001625 MSH:D005313 MSH:D050497 SNOMEDCT_US:237364002 SNOMEDCT_US:276507005 UMLS:C0015927 UMLS:C0595939 Late fetal death Late foetal death Stillbirth Stillborn The age at which fetal demise is legally classified asa a miscarriage varies between countries with the US being 20 gestational weeks and the UK being 24 gestational weeks. The HPO chooses the average of these age ranges. Stillbirth HP:0004297 An abnormality of the biliary system. UMLS:C0940767 Abnormality of the biliary system HP:0004308 SNOMEDCT_US:44103008 UMLS:C0085612 Ventricular arrhythmias Ventricular arrhythmia HP:0004323 An abnormal increase or decrease of weight or an abnormal distribution of mass in the body. HP:0010718 UMLS:C0878621 UMLS:C4025357 Abnormality of body weight Abnormality of body weight HP:0004324 Abnormally increased body weight. HP:0045083 MSH:D015430 SNOMEDCT_US:161831008 SNOMEDCT_US:262286000 SNOMEDCT_US:8943002 UMLS:C0043094 Increased body weight Increased body weight HP:0004325 Abnormally low body weight. HP:0001823 HP:0001826 MSH:D013851 MSH:D015431 SNOMEDCT_US:161832001 SNOMEDCT_US:248342006 SNOMEDCT_US:262285001 SNOMEDCT_US:89362005 UMLS:C0041667 UMLS:C1262477 UMLS:C1844806 Decreased body weight Decreased weight Low body weight Low weight Weight less than 3rd percentile Decreased body weight HP:0004363 Any deviation from the normal concentration of calcium in the blood circulation. HP:0040077 Abnormal blood calcium concentration Abnormal blood calcium levels Abnormal circulating Ca concentration Abnormal circulating Ca2+ concentration Abnormal circulating calcium concentration HP:0004370 An abnormality of temperature homeostasis. MSH:D001832 UMLS:C0005904 UMLS:C1832160 Abnormality of temperature regulation Poor temperature regulation Abnormality of temperature regulation HP:0004372 SNOMEDCT_US:3006004 UMLS:C0234428 Disturbances of consciousness Lowered consciousness Reduced consciousness/confusion Reduced consciousness/confusion HP:0004385 SNOMEDCT_US:236077008 UMLS:C0473133 Protracted diarrhoea Protracted diarrhea HP:0004386 Inflammation of the alimentary part of the gastrointestinal system. UMLS:C1535950 GI inflammation Gastrointestinal inflammation Gastrointestinal inflammation HP:0004395 A deficiency in the intake of energy and nutrients. MSH:D044342 SNOMEDCT_US:248325000 SNOMEDCT_US:2492009 SNOMEDCT_US:47563007 SNOMEDCT_US:65404009 SNOMEDCT_US:70241007 UMLS:C0162429 Malnutrition Malnutrition HP:0004396 A reduced desire to eat. SNOMEDCT_US:64379006 UMLS:C0232462 Decreased appetite Loss of appetite Poor appetite Poor appetite HP:0004408 An anomaly in the ability to perceive and distinguish scents (odors). HP:0004410 UMLS:C4021655 Abnormal sense of smell Abnormality of olfaction Abnormality of the sense of smell Smell defect Abnormality of the sense of smell HP:0004409 A decreased sensitivity to odorants (that is, a decreased ability to perceive odors). SNOMEDCT_US:83156004 UMLS:C2364082 Decreased smell sensation Sense of smell impaired Hyposmia HP:0004420 The formation of a blood clot inside an artery. SNOMEDCT_US:65198009 UMLS:C0151942 Blood clot in artery Arterial thrombosis HP:0004469 Chronic inflammation of the bronchi. MSH:D029481 SNOMEDCT_US:63480004 UMLS:C0008677 Chronic bronchitis HP:0004756 A tachycardia originating in the ventricles characterized by rapid heart rate (over 100 beats per minute) and broad QRS complexes (over 120 ms). Fyler:7160 MSH:D017180 SNOMEDCT_US:25569003 UMLS:C0042514 Ventricular tachycardia (VT) is a potentially life-threatening ventricular arrhythmia that presents as a wide QRS complex tachycardia, and is defined as three or more consecutive QRS complexes with a duration longer than 120 milliseconds (ms) and a rate of 100 beats per minute or more, whereby the complexes have a ventricular origin. VT can be subdivided as follows: (i) sustained VT persists for 30 seconds or more; (ii) non-sustained VT lasts less than 30 seconds; (iii) monomorphic VT displays a uniform QRS morphology; and (iv) polymorphic VT displays QRS morphologies that variy from beat to beat. VT is observed most commonly in individuals with structural heart disease or acute myocardial infarction (MI). VT may also be observed in in the setting of drug toxicity or electrolyte abnormalities or in individuals with Mendelian disease. Ventricular tachycardia HP:0004887 A state of respiratory distress that requires a life saving intervention in the form of gaining airway access and instituting positive pressure ventilation. HP:0004883 UMLS:C4025279 Respiratory distress necessitating mechanical ventilation Respiratory distress requiring endotracheal intubation Respiratory distress requiring mechanical ventilation Respiratory failure requiring assisted ventilation HP:0004921 An abnormality of magnesium ion homeostasis. HP:0008274 UMLS:C4020826 UMLS:C4025274 Abnormal Mg concentration Abnormality of magnesium homeostasis Abnormal magnesium concentration HP:0004936 Formation of a blood clot (thrombus) inside a vein, causing the obstruction of blood flow. MSH:D020246 SNOMEDCT_US:111293003 UMLS:C0042487 Blood clot in vein Venous thrombosis HP:0005208 Watery voluminous diarrhea resulting from an imbalance between ion and water secretion and absorption. SNOMEDCT_US:15699003 UMLS:C0267557 Secretory diarrhoea Secretory diarrhea HP:0005264 An abnormality of the gallbladder. SNOMEDCT_US:253803008 SNOMEDCT_US:49714001 UMLS:C0266249 Abnormality of the gallbladder Anomaly of the gallbladder Abnormality of the gallbladder HP:0005268 A pregnancy that ends at a stage in which the fetus is incapable of surviving on its own, defined as the spontaneous loss of a fetus before the 22th week of pregnancy. MSH:D000022 SNOMEDCT_US:17369002 UMLS:C0000786 Early fetal demise Early foetal demise Spontaneous abortion The age at which fetal demise is legally classified asa a miscarriage varies between countries with the US being 20 gestational weeks and the UK being 24 gestational weeks. The HPO chooses the average of these age ranges. Miscarriage HP:0005978 A type of diabetes mellitus initially characterized by insulin resistance and hyperinsulinemia and subsequently by glucose interolerance and hyperglycemia. HP:0005965 HP:0100652 MSH:D003924 SNOMEDCT_US:44054006 UMLS:C0011860 Diabetes mellitus Type II Diabetes mellitus, noninsulin-dependent NIDDM NIDDM diabetes mellitus Non-insulin dependent diabetes Noninsulin dependent diabetes mellitus Noninsulin-dependent diabetes Type 2 diabetes Type II diabetes Persons with type II diabetes mellitus rarely develop ketoacidosis. Type II diabetes mellitus HP:0005986 Limited neck mobility MSH:D009127 SNOMEDCT_US:161882006 SNOMEDCT_US:405947006 UMLS:C0151315 UMLS:C1320474 UMLS:C1847392 Limitation of neck motion Restricted neck movement Limitation of neck motion HP:0006510 An anomaly that is characterized progressive airflow obstruction that is only partly reversible, inflammation in the airways, and systemic effects or comorbities. HP:0006541 MSH:D029424 SNOMEDCT_US:13645005 UMLS:C0024117 COPD Chronic obstructive pulmonary disease COPD is usually conceptualized as a disease entity. It is heterogeneous histologically and pathogenically, and conventionally includes emphysema and chronic bronchitis, It is included as a phenotype term as COPD is often annotated as a feature of other diseases. Chronic pulmonary obstruction HP:0006528 According to the definitions of the American and British Thoracic Societies, including pulmonary functional tests, X-rays, and CT scans for items such as fibrosis, bronchiectasis, bullae, emphysema, nodular or lymphomatous abnormalities. SNOMEDCT_US:413839001 UMLS:C0746102 Chronic lung disease Chronic lung disease HP:0006530 Abnormality of the lung parenchyma extending to the pulmonary interstitium and leading to diffuse pulmonary fibrosis. HP:0006513 HP:0006547 MSH:D017563 SNOMEDCT_US:233703007 UMLS:C0206062 Abnormal lung parenchyma morphology Abnormality in area between air sacs in lung Interstitial lung disease Interstitial pulmonary disease Abnormal pulmonary interstitial morphology HP:0006536 Obstruction of conducting airways of the lung. HP:0006512 MSH:D008173 UMLS:C0600260 Obstructive lung disease Pulmonary obstruction Airway obstruction HP:0006561 UMLS:C1837257 Lipid accumulation in hepatocytes HP:0008047 UMLS:C4024752 Abnormality of eye blood vessels Abnormality of the vasculature of the eye HP:0008872 Impaired feeding performance of an infant as manifested by difficulties such as weak and ineffective sucking, brief bursts of sucking, and falling asleep during sucking. There may be difficulties with chewing or maintaining attention. HP:0002016 HP:0002022 HP:0002568 UMLS:C2674608 Feeding difficulties in infancy HP:0010750 Loss of elasticity of the upper and lower eyelids causing the skin to sag and bulge. SNOMEDCT_US:246815009 UMLS:C0423124 UMLS:C2674149 Baggy eyes Droopy eyelid skin Extra eyelid skin Eyelid dermatochalasia Redundant eyelid skin Dermatochalasis HP:0010927 An abnormality of divalent inorganic cation homeostasis. UMLS:C4023648 Abnormality of divalent inorganic cation homeostasis Abnormal blood inorganic cation concentration HP:0010929 An abnormality of cation homeostasis. UMLS:C4023646 Abnormality of cation homeostasis Abnormal blood cation concentration HP:0010930 An abnormality of monovalent inorganic cation homeostasis. UMLS:C4023645 Abnormality of monovalent inorganic cation homeostasis Abnormal blood monovalent inorganic cation concentration HP:0010935 An abnormality of the upper urinary tract. UMLS:C4023641 Abnormality of the upper urinary tract The upper urinary tract is a subdivision of urinary system which consists of the kidney and the ureters. Abnormality of the upper urinary tract HP:0010978 A functional abnormality of the immune system. UMLS:C4023616 Abnormality of immune system physiology HP:0011008 The speed at which disease manifestations appear and develop. UMLS:C4021204 Speed of onset Temporal pattern HP:0011009 Sudden appearance of disease manifestations over a short period of time. SNOMEDCT_US:272118002 UMLS:C0205178 Acute onset The word acute is applied to different time scales depending on the disease or manifestation and does not have an exact definition in minutes, hours, or days. Acute HP:0011014 Abnormality of glucose homeostasis. UMLS:C4023598 An abnormality of any process involved in the maintenance of an internal steady state of glucose within an organism or cell. Abnormal glucose homeostasis HP:0011024 An abnormality of the gastrointestinal tract. MSH:D004066 MSH:D005767 SNOMEDCT_US:119292006 SNOMEDCT_US:25374005 SNOMEDCT_US:53619000 UMLS:C0012242 UMLS:C0017178 UMLS:C4023588 Abnormality of the GI tract Abnormality of the gastrointestinal tract Abnormality of the gastrointestinal tract HP:0011025 Abnormal functionality of the cardiovascular system. UMLS:C4023587 Abnormality of cardiovascular system physiology Abnormal cardiovascular system physiology HP:0011028 An abnormality of blood circulation. UMLS:C4020760 UMLS:C4023585 Abnormality of blood circulation HP:0011029 The presence of hemorrhage within the body. UMLS:C1390214 Internal bleeding Internal haemorrhage Internal hemorrhage HP:0011032 An abnormality of the regulation of body fluids. SNOMEDCT_US:1860003 SNOMEDCT_US:190902006 UMLS:C2364164 Abnormality of fluid regulation Fluid imbalance Abnormality of fluid regulation HP:0011042 An abnormal concentration of potassium. UMLS:C4023575 Abnormal blood K concentration Abnormality of potassium homeostasis Abnormal blood potassium concentration HP:0011097 A sudden flexion, extension, or mixed extension-flexion of predominantly proximal and truncal muscles that is usually more sustained than a myoclonic movement but not as sustained as a tonic seizure. Limited forms may occur: Grimacing, head nodding, or subtle eye movements. Epileptic spasms frequently occur in clusters. Infantile spasms are the best known form, but spasms can occur at all ages MSH:D013036 SNOMEDCT_US:28055006 UMLS:C0037769 UMLS:C1527366 Epileptic spasms Salaam convulsion Salaam convulsions Salaam seizure Salaam seizures The maximum age of onset is between 3 and 12 months, the peak being at 6 months. However, spasms may start from birth, or appear long after the age of 12 months, including into adulthood. Infantile spasms represent a specific type of seizure seen in an epilepsy syndrome of infancy and childhood known as West Syndrome. West Syndrome is characterized by infantile spasms, developmental regression, and hypsarrhythmia (as demonstrated by electroencephalography). Epileptic spasm HP:0011121 Any morphological abnormality of the skin. Fyler:4133 UMLS:C4023528 Abnormal skin morphology Abnormal skin structure Abnormality of skin morphology HP:0011122 Any abnormality of the physiological function of the skin. UMLS:C4023527 Abnormality of skin physiology Abnormality of skin physiology HP:0011123 The presence of inflammation of the skin. That is, an abnormality of the skin resulting from the local accumulation of fluid, plasma proteins, and leukocytes. HP:0002727 HP:0007423 MP:0004947 MSH:D003872 SNOMEDCT_US:703938007 UMLS:C0011603 UMLS:C3875321 Abnormal tendency to infections of the skin Inflammatory abnormality of the skin Skin inflammation Inflammatory abnormality of the skin HP:0011277 UMLS:C4023437 Abnormality of the urinary system physiology HP:0011354 An abnormality of the skin that is not localized to any one particular region. UMLS:C4021157 Generalised abnormality of skin Generalized abnormality of skin Generalized abnormality of skin HP:0011389 An abnormality of the function of the inner ear. UMLS:C4023382 Functional abnormality of the inner ear The inner ear comprises the cochlea, three semicircular canals and the vestibule (labyrinth), and is directly responsible for hearing. Additionally, the vestibule and semicircular canals function to maintain balance or equilibrium. Functional abnormality of the inner ear HP:0011410 Delivery of a fetus through surgical incisions made through the abdominal wall (laparotomy) and the uterine wall (hysterotomy). SNOMEDCT_US:200144004 UMLS:C1384674 Caesarian section Caesarian section HP:0011420 The age group when the cessation of life happens. UMLS:C1546180 Age of death HP:0011442 An anomaly of the control or production of movement in the central nervous system. UMLS:C4023354 Abnormality of central motor function Abnormal central motor function HP:0011443 UMLS:C4023353 Abnormality of coordination Coordination issue Abnormality of coordination HP:0011446 Cognitive, psychiatric or memory anomaly. UMLS:C4023352 Abnormality of higher mental function HP:0011450 A type of infection of the central nervous system that can be regarded as a sign of a pathological susceptibility to infection. MSH:D002494 SNOMEDCT_US:128117002 UMLS:C0007684 Central nervous system infection Unusual CNS infection HP:0011458 A subjective manifestation of disease localized to the abdomen. UMLS:C0740651 Abdominal symptom HP:0011469 Regurgitation of milk through the nose. SNOMEDCT_US:85023004 UMLS:C0232608 Nasal regurgitation HP:0011470 Feeding problem necessitating nasogastric tube feeding. UMLS:C4023343 This is a severe form of feeding problems in infancy. Nasogastric tube feeding in infancy HP:0011471 Feeding problem necessitating gastrostomy tube feeding. UMLS:C4020748 UMLS:C4023342 This is an extremely severe form of feeding problems in infancy. Gastrostomy tube feeding in infancy HP:0011675 Any cardiac rhythm other than the normal sinus rhythm. Such a rhythm may be either of sinus or ectopic origin and either regular or irregular. An arrhythmia may be due to a disturbance in impulse formation or conduction or both. HP:0001656 HP:0001661 HP:0001665 HP:0001666 HP:0001675 HP:0001687 HP:0001721 HP:0004351 HP:0005158 MSH:C562490 MSH:D001145 SNOMEDCT_US:102594003 SNOMEDCT_US:44808001 SNOMEDCT_US:698247007 UMLS:C0003811 UMLS:C0264886 UMLS:C0522055 UMLS:C0855329 UMLS:C1832603 UMLS:C1842820 Abnormal heart rate Arrhythmias Cardiac arrhythmia Cardiac arrhythmias Cardiac rhythm disturbances Heart rhythm disorders Irregular heart beat Irregular heartbeat Arrhythmia HP:0011729 An abnormality in the range and ease of motion of joints across their normal range. UMLS:C4023216 Abnormality of joint mobility HP:0011793 Neoplasm categorized according to the anatomical site of origin of the neoplasm. UMLS:C4023185 Neoplasm by anatomical site HP:0011804 A functional abnormality of a skeletal muscle. UMLS:C4023182 Abnormality of muscle physiology Issue with muscle function Abnormal muscle physiology HP:0011805 A structural abnormality of a skeletal muscle. HP:0003735 UMLS:C4023181 Abnormal muscle morphology Abnormality of muscle morphology Abnormally shaped muscle Issue with muscle structure Abnormal skeletal muscle morphology HP:0011842 An abnormality of the form, structure, or size of the skeletal system. UMLS:C4023165 Abnormality of skeletal morphology Abnormally shaped skeletal Abnormal skeletal morphology HP:0011843 An abnormality of the function of the skeletal system. UMLS:C4023164 Abnormality of musculoskeletal physiology Abnormal musculoskeletal physiology HP:0011848 A type of abdominal pain that comes and goes in waves, most often starting and ending suddenly and being of severe intensity. MSH:D003085 SNOMEDCT_US:9991008 UMLS:C0232488 Colicky abdominal pain can be caused by kidney stones and gallstones, among other etiologies. This type of pain is thought to be caused by spasm, obstruction, or distension of any of the hollow viscera of the gastrointestinal system. Abdominal colic HP:0011947 An infection of the upper or lower respiratory tract. MSH:D012141 SNOMEDCT_US:275498002 UMLS:C0035243 Respiratory infection Respiratory tract infection Respiratory tract infection HP:0011968 Impaired ability to eat related to problems gathering food and getting ready to suck, chew, or swallow it. SNOMEDCT_US:78164000 UMLS:C0232466 Feeding difficulties Feeding problems Poor feeding Feeding difficulties HP:0012211 An abnormal functionality of the kidney. HP:0000082 HP:0000087 HP:0005566 HP:0008646 SNOMEDCT_US:39539005 UMLS:C0151746 Abnormal kidney function Abnormal renal function Abnormality of renal physiology Kidney function issue Renal functional abnormality Abnormal renal physiology HP:0012252 A structural anomaly of the respiratory system. Fyler:4235 UMLS:C4022992 Abnormal respiratory system morphology HP:0012337 An anomaly in the processes involved in the maintenance of an internal equilibrium. MP:0001764 UMLS:C4022950 Abnormal homeostasis HP:0012372 A structural anomaly of the globe of the eye, or bulbus oculi. HP:0000489 HP:0012374 Fyler:4863 UMLS:C4022925 Abnormal eye structure Abnormality of the globe Abnormally shaped eye previously: Abnormal globe morphology Abnormal eye morphology HP:0012373 A functional anomaly of the eye. UMLS:C4022924 Abnormal eye physiology Abnormal eye physiology HP:0012378 A subjective feeling of tiredness characterized by a lack of energy and motivation. MSH:D005221 SNOMEDCT_US:248274002 SNOMEDCT_US:84229001 UMLS:C0015672 Fatigue Tired Tiredness Fatigue is distinct from muscle weakness. Fatigue HP:0012381 A delay in the development of skills required to feed oneself in the toddler period (between one and three years of age). UMLS:C4022920 Delayed self-feeding during toddler years HP:0012387 Inflammation of the large airways in the lung including any part of the bronchi from the primary bronchi to the tertiary bronchi. MSH:D001991 SNOMEDCT_US:32398004 UMLS:C0006277 Bronchitis HP:0012415 An abnormality of the partial pressure of oxygen or carbon dioxide in the arterial blood. SNOMEDCT_US:312391003 UMLS:C0476337 Abnormal blood gas level Abnormal blood gas level HP:0012417 Abnormally reduced blood carbon dioxide (CO2) level. MSH:D016857 SNOMEDCT_US:61031008 UMLS:C0085383 Hypocarbia Reduced carbon dioxide in the blood Hypocapnia HP:0012418 An abnormally low level of blood oxygen. MSH:D000860 SNOMEDCT_US:389087006 UMLS:C0700292 Low blood oxygen level Note that hypoxemia is defined as a condition where arterial oxygen tension is below normal (80-100mmHg). Hypoxia is defined as the failure of oxygenation at the tissue level. Hypoxia is not measured directly by a standard laboratory value. Hypoxemia HP:0012437 A structural anomaly of the gallbladder. UMLS:C4022904 Abnormal gallbladder structure Abnormal shape of gallbladder Abnormal gallbladder morphology HP:0012443 A structural abnormality of the brain, which has as its parts the forebrain, midbrain, and hindbrain. UMLS:C4021085 Abnormal shape of brain Abnormality of the brain Abnormality of brain morphology HP:0012450 Constipation for longer than three months with fewer than 3 bowel movements per week, straining, lumpy or hard stools, and a sensation of anorectal obstruction or incomplete defecation. SNOMEDCT_US:236069009 UMLS:C0401149 Chronic constipation Infrequent bowel movements Chronic constipation HP:0012451 Constipation of sudden onset and lasting for less than three months. SNOMEDCT_US:197119006 UMLS:C0401148 Acute constipation HP:0012531 An unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage. MSH:D010146 SNOMEDCT_US:22253000 UMLS:C0030193 Pain Pain HP:0012614 An anomalous finding in the examination of the urine for cells. SNOMEDCT_US:310439007 UMLS:C0587955 Abnormal urine cytology HP:0012622 Functional anomaly of the kidney persisting for at least three months. HP:0000106 HP:0001918 HP:0008671 MSH:D051436 SNOMEDCT_US:709044004 UMLS:C0748318 UMLS:C1561643 Chronic kidney disease Chronic kidney disease HP:0012638 A functional anomaly of the nervous system. UMLS:C4022811 Abnormality of nervous system physiology Abnormal nervous system physiology HP:0012639 A structural anomaly of the nervous system. Fyler:4135 Fyler:4300 UMLS:C4022810 Abnormal shape of nervous system Abnormality of nervous system morphology Abnormal nervous system morphology HP:0012647 Any anomaly of the inflammatory response, a response to injury or infection characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. UMLS:C4022805 Abnormal inflammatory response Abnormal inflammatory response HP:0012649 A abnormal increase in the inflammatory response to injury or infection. UMLS:C4022803 Increased inflammatory response HP:0012718 Abnormal structure of the gastrointestinal tract. UMLS:C4021073 Abnormal shape of the digestive system Morphological abnormality of the GI tract Morphological anomaly of the digestive system Morphological abnormality of the gastrointestinal tract HP:0012719 Abnormal functionality of the gastrointestinal tract. UMLS:C4022755 Functional abnormality of the GI tract GI dysfunction Functional abnormality of the gastrointestinal tract HP:0012735 A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation. MSH:D003371 SNOMEDCT_US:263731006 SNOMEDCT_US:272039006 SNOMEDCT_US:49727002 UMLS:C0010200 Cough Coughing The European Respiratory Society Task Force recommended two possible definitions of cough: (1) A three-phase expulsive motor act characterized by an inspiratory effort (inspiratory phase) followed by a forced expiratory effort against a closed glottis (compressive phase) and then by opening of the glottis and rapid expiratory airflow (expulsive phase);and (2) A forced expiratory manoeuvre, usually against a closed glottis and associated with a characteristic sound. The term Cough or any of its more specific descendents can be modified by the terms Acute (HP:0011009), Subacute (HP:0011011), and Chronic (HP:0011010). In adults, an acute cough lasts less than 3 weeks, a subacute cough from 3 to 8 weeks, and a chronic cough longer than 8 weeks. In children aged less than 15 years a chronic cough is defined as a daily cough lasting for over 4 weeks. Cough HP:0012823 This subontology is designed to provide terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. HP:0000004 UMLS:C4021064 Phenotypic modifier Note that some of the terms, such as Intellectual disability, have children terms such as Severe intellectual disability that represent precomposed combinations of modifiers and phenotypic abnormality terms. This done where the medical community commonly uses these terms with a fixed meaning (for instance, the Intellectual disability terms are used with specific IQ ranges). For computational reasoning, the semantics are intended to be the same as if there was a combination of the phenotype term and the clinical modifier term. Clinical modifier HP:0012830 position of phenotype abnormality HP:0020219 A motor seizure is a type of seizure that is characterized at onset by involvement of the skeletal musculature. The motor event could consist of an increase (positive) or decrease (negative) in muscle contraction to produce a movement. This term describes the initial semiology of the seizure without specifying whether the onset is focal or generalized. Motor seizure HP:0025015 Abnormal vascular morphology HP:0025031 Any anomaly of the digestive system, a collection of organs that is made up of the gastrointestinal tract and the liver, pancreas, and gallbladder. The gastrointestinal tract is a series of hollow organs joined in a long, twisting tube from the mouth to the anus, including the mouth, esophagus, stomach, small intestine, large intestine and anus. Abnormality of the digestive system HP:0025032 A functional anomaly of the digestive system. Abnormality of digestive system physiology HP:0025033 A structural anomaly of the digestive system. Abnormality of digestive system morphology HP:0025063 The anterior abdominal wall is sunken and presents a concave rather than a convex contour. Scaphoid abdomen can be observed in diseases such as congenital diaphragmatic hernia (since the abdominal contents can be in the thorax). Scaphoid abdomen HP:0025085 Passage of many stools containing blood. Blood in stool Bloody stool Bloody bowel movement Bloody diarrhea Bloody diarrhoea Diarrhea that contains bright red or maroon-colored blood may be referred to as hematochezia, while melena is used to describe black, tarry, and smelly diarrhea. Bloody diarrhea HP:0025086 Passage of many stools containing blood and mucus. Bloody mucoid diarrhoea Bloody mucoid diarrhea HP:0025089 Vomiting of material that is of fecal origin. Faecal vomiting Fecal vomiting Stercoraceous vomiting Vomiting faecal matter Vomiting fecal matter Feculent vomiting is usually due to mechanical intestinal obstruction but it can be due to paralytic obstruction (adynamic ileus). Feculent vomiting HP:0025095 A sudden violent, spasmodic, audible expiration of breath through the nose and mouth. Sneeze HP:0025142 A symptom or manifestation indicating a systemic or general effect of a disease and that may affect the general well-being or status of an individual. Note that we use the preferred term label constitutional symptom because this reflects common usage, but we do not restrict the term or its descendents to the narrow meaning of symptom, i.e., a complaint related by a patient to a physician. There is no generally accepted classification of what defines a constitutional symptom, but examples include weight loss, fatigue, general weakness, night sweats, shaking, chills, fever, and vomiting. Constitutional symptom HP:0025143 A sudden sensation of feeling cold. Chills The word chills can also refer to an episode of shivering, accompanied by paleness and feeling cold. Chills HP:0025144 Involuntary contraction or twitching of the muscles. Shivering Shuddering Shivering is a physiologic method of heat production in man and other mammals. Shivering is a bodily function in response to fever, early hypothermia or feeling cold. Shivering HP:0025145 Severe chills with violent shivering. A rigor is an episode of shaking or exaggerated shivering which can occur with a high fever. Rigours A sudden attack of severe shivering accompanied by chills (a feeling of coldness) is called a rigor and may be associated with a marked rise in body temperature. Patients often describe rigors as an attack of uncontrollable shaking. Rigors are often a sign of infection, particularly bacterial infection. Rigors HP:0025155 A functional anomaly of the hepatobiliary system Abnormality of hepatobiliary system physiology HP:0025270 Any physiological abnormality of the esophagus. Abnormality of esophagus physiology Abnormality of oesophagus physiology Functional abnormality of the esophagus Functional abnormality of the oesophagus Abnormal esophagus physiology HP:0025323 An anomaly of arterial function. Abnormal arterial physiology HP:0025337 A reddish appearance over the white part (sclera) of the eye ranging from a few enlarged blood vessels appearing as wiggly lines over the sclera to a bright red color completely covering to sclera. Red eye Red eyes Red eye HP:0025406 A state characterized by a feeling of weakness and loss of strength leading to a generalized weakness of the body. Lack of energy and strength Weakness Asthenia is to be distinguished from fatigue, because asthenia refers to a sensation of exhaustion which occurs before any effort. Asthenia is to be distinguished from myasthenia, which means a specific weakness of one or more muscles. Asthenia and fatigue can coexist. Asthenia HP:0025429 Any anomaly of the vocalizing of an infant's crying, i.e.,the typically loud voice production that is accompanied by tears and agitation. Abnormal cry HP:0025439 Inflammation (due to infection or irritation) of the pharynx. Pharyngitis HP:0025615 Abscess HP:0025669 Any functional anomaly of the neck region. Abnormal neck physiology HP:0025722 A necrotic lesion in the cerebrum resulting from a sudden insufficiency of arterial or venous blood supply due to emboli, thrombi or mechanical factors. Cerebral infarct HP:0030142 An anomaly of the amount or nature of abdominal sounds. Abdominal sounds (bowel sounds) are made by the movement of the intestines as they promote passage of abdominal contents by peristalsis. SNOMEDCT_US:60612008 UMLS:C0159060 Abnormal bowel sounds Abnormal bowel sounds HP:0030143 Abnormally increased gurgling/rumbling sounds made by the movement of fluid and gas in the intestines. SNOMEDCT_US:18101008 UMLS:C0232694 Borborygmi Increased bowel sounds Hyperactive bowel sounds HP:0030144 An decreased amount of bowel sounds. SNOMEDCT_US:15280003 UMLS:C0232695 Decreased bowel sounds Hypoactive bowel sounds HP:0030145 Complete lack of abdominal sounds as assayed by examination of the abdomen with a stethoscope. UMLS:C4022606 Lack of bowel sounds This feature reflects lack of intestinal activity. Lack of bowel sounds HP:0030149 Severely decreased cardiac output with evidence of inadequate end-organ perfusion (i.e., tissue hypoxia) in the presence of adequate intravascular volume. MSH:D012770 SNOMEDCT_US:89138009 UMLS:C0036980 Cardiovascular shock Cardiogenic shock can result from a number of different of cardiac insults, the most common of which is acute myocardial infarction. Cardiogenic shock HP:0030163 Abnormality of vascular function. UMLS:C4022603 Abnormal vascular physiology HP:0030669 A structural anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva. UMLS:C4073120 Abnormal ocular adnexa morphology HP:0030680 Any structural anomaly of the heart and great vessels. HP:0001632 HP:0002564 HP:0002565 UMLS:C4049796 Cardiovascular malformations Abnormality of cardiovascular system morphology HP:0030809 Any structural anomaly of the tongue. UMLS:C4280755 Abnormal tongue morphology HP:0030810 Any functional anomaly of the tongue. UMLS:C4280754 Abnormal tongue physiology HP:0030829 An anomalous (adventitious) sound produced by the breathing process. SNOMEDCT_US:301273002 UMLS:C0231856 Abnormal lung auscultation finding Abnormal breath sound HP:0030875 A functional anomaly of that portion of the cardiosvascular system that carries deoxygenated blood from the heart to the lungs and returns oxygenated blood back to the heart. UMLS:C4280730 Abnormal pulmonary circulation Abnormality of respiratory circulation Abnormality of pulmonary circulation HP:0030884 Feeding problem necessitating gastrojejunal tube feeding. UMLS:C4280681 Gastro-jejunal tube feeding in infancy The rationale for gastrojejunal tube feeding is that placing the tip of the tube beyond the ligament of Treitz prevented duodenogastric reflux or gastro-esophageal reflux. Gastrojejunal feeding tubes have since been used in children who are deemed too unfit for antireflux surgery or where fundoplication has failed. Gastrojejunal tube feeding in infancy HP:0030953 Dilatation of the blood vessels of the conjunctiva leading to a red appearance of the sclera. Conjunctival hyperaemia Conjunctival injection Conjunctival vascular congestion Conjunctival hyperemia HP:0030956 An anomaly of the electrical conduction physiology of the heart. Abnormality of cardiovascular system electrophysiology HP:0030972 A chronic deviation from normal pressure in the systemic arterial system. Abnormal systemic BP Abnormal systemic blood pressure HP:0031137 Hepatocytes (liver parenchymal cells) exhibit a bloated appearance because of expansion of the cytoplasm by accumulated material. Storage in hepatocytes HP:0031179 Resistance of the extensor muscles of the neck to being bent forwards (i.e., impaired neck flexion) as a result of muscle spasm of the extensor muscles of the neck. Nuchal rigidity is not a fixed rigidity. Nuchal rigidity has been used as a bedside test for meningism, although its sensitivity for this purpose has been debated. Meningism is resistance to neck flexion due to painful spasm of extensor muscles resulting from meningeal irritation. The diagnosis of meningism is made in someone whose symptoms simulate meningitis, but in which no actual inflammation of these membranes is present. Nuchal rigidity can thus be observed in individuals with meningitis or with meningism. Nuchal rigidity HP:0031245 A cough that produces phlegm or mucus. Cough with mucus production Wet cough Productive cough HP:0031246 A cough that does not produce phlegm or mucus. Dry cough Dry coughing Nonproductive cough HP:0031249 A distortion of the sense of taste, often characterized by the sensation of a metallic taste. Altered sense of taste Dysgeusia Metallic taste Metallic taste in mouth Parageusia HP:0031258 A state of sudden and severe confusion. Delirium HP:0031273 The state in which profound and widespread reduction of effective tissue perfusion leads first to reversible, and then if prolonged, to irreversible cellular injury. Shock HP:0031292 A circumscribed area of pus or necrotic debris in the skin. Skin abscess Cutaneous abscess HP:0031352 An unpleasant sensation of tightness or pressure in the chest. Tightness in chest Tightness of chest Chest tightness HP:0031416 Any deviation from the normal quantity of secretion of nasal mucus, a thick viscous liquid produced by the mucous membranes of the nose. Abnormal nasal mucus secretion HP:0031417 Increased discharge of mucus from the nose. Nasal Discharge Runny Nose Rhinorrhea HP:0031677 A type of ventricular tachycardia that is characterized by variable QRS complexes within each lead (i.e., QRS complexes may be different from beat to beat). Polymorphic ventricular tachycardia HP:0031704 Any functional anomaly of the ear. Abnormal ear physiology HP:0031797 The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual. Clinical course HP:0031815 A functional anomaly of the mouth (which is also known as the oral cavity). The physiological functions of the mouth include salivary gland secretory function, mastication (chewing) and preparation of food for swallowing. Abnormal oral physiology HP:0031816 Any structural anomaly of the mouth, which is also known as the oral cavity. Abnormal oral morphology HP:0032016 Abnormal appearance of material expectorated (coughed up) from the respiratory system and that is composed of mucus but may contain other substances such as pus, blood, microorganisms, and fibrin. Abnormal sputum morphology Abnormal sputum HP:0032039 An anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva. Abnormality of the ocular adnexa HP:0032101 A type of infection that is regarded as a sign of a pathological susceptibility to infection. There are five general subtypes. (i) Opportunistic infection, meaning infection by a pathogen that is not normally able to cause infection in a healthy host (e.g., pneumonia by Pneumocystis jirovecii or CMV); (ii) Unusual location (focus) of an infection (e.g., an aspergillus brain abscess); (iii) a protracted course or lack of adequate response to treatment (e.g., chronic rhinosinusitis); (iv) Unusual severity or intensity of an infection; and (v) unusual recurrence of infections. Unusual infection HP:0032148 Intermittent pain, i.e., pain that occurs occasionally and at irregular intervals. Episodic pain HP:0032155 A type of abdominal pain characterized by a feeling of contractions and typically fluctuating in intensity. Abdominal cramps HP:0032158 An unusual infection classified by the affected body part. Unusual infection by anatomical site HP:0032180 An abnormal level of an analyte measured in the blood. Abnormal circulating metabolite concentration HP:0032243 Any deviation from the normal concentration of a metabolite in a tissue. Abnormal tissue metabolite concentration HP:0032251 Abnormal immune system morphology HP:0032263 Abnormal increase in blood pressure. An individual measurement of increased blood pressure does not necessarily imply hypertension. In practical terms, multiple measurements are recommended to diagnose the presence of hypertension. Increased BP Increased blood pressure HP:0032545 Involuntary tightening of the abdominal musculature that occurs in response to touching the abdomen to avoid pain. Rigidity can occur in the presence of abdominal inflammation and usually involves only the inflamed area. Rigid abdomen Abdominal rigidity HP:0032546 A voluntary contraction of the abdominal wall musculature to avoid pain. Abdominal guarding tends to be generalized over the entire abdomen. In contrast to abdominal rigidity, guarding can often be overcome by having the patient purposely relax the muscles; rigidity cannot be. Abdominal guarding HP:0032556 Persistent blue color of the skin that surrounds the mouth. Bluish around mouth Circumoral cyanosis may be a sign of peripheral or of central cyanosis. Circumoral cyanosis HP:0032674 A cutaneous wound is a defined as a disruption of normal anatomic structure and function of the skin that occured owing to an injury of the skin. Wound healing is a dynamic, interactive processinvolving soluble mediators, blood cells, extracellularmatrix, and parenchymal cells. Wound healing has three phases: inflammation, tissue formation, and tissue remodeling, that overlap in time. Skin wound Cutaneous wound HP:0032675 A cutaneous wound that is proceeding through an orderly and timely reparative process that results in sustained restoration of the anatomic and functional integrity of the skin. Wound healing accors in multiple overlapping stages, with re=-eipthelialization normally beginning on day one or two. In most clinical settings, closure of acute and chronic wounds is considered the wound healing end point, but wounds can continue to undergo remodeling or tissue maturation for several months or even years. Acute cutaneous wound HP:0032676 A cutaneous wound that has failed to proceed through the orderly and timely process to produce an atomic and functional integrity, or proceeded through the repair process without establishing a sustained anatomic and functional result. Chronic nonhealing cutaneous wound Chronic cutaneous wound HP:0033127 An anomaly of the musculoskeletal system, which consists of the bones of the skeleton, muscles, cartilage, tendons, ligaments, joints, and other connective tissue. The musculoskeletal system supports the weight of the body, maintains body position and produces movements of the body or of parts of the body. Abnormality of the musculoskeletal system HP:0033151 A structural anomaly of the pharynx. Abnormal pharynx morphology HP:0033310 Osmotic diarrhea results from the presence of osmotically active, poorly absorbed solutes in the bowel lumen that inhibit normal water and electrolyte absorption. Osmotic diarrhea involves an unabsorbed substance that draws water from the plasma into the intestinal lumen along osmotic gradients. Secretory diarrhea results from disordered electrolyte transport and, despite the term, is more commonly caused by decreased absorption rather than net secretion. Inflammatory diseases cause diarrhea with exudative, secretory, or osmotic components. Osmotic diarrhea HP:0033343 Passage of an increased number of stools containing mucus, a thick fluid substance secreted by mucous membranes. Mucous diarrhea Mucous diarrhoea Mucoid diarrhea HP:0033353 Any structural anomaly of a blood vessel (artery, arteriole, capillary, venule, or vein). Abnormal blood vessel morphology HP:0033400 A sudden onset of abdominal pain with associated nausea or vomiting. The acute abdomen may be caused by an infection, inflammation, vascular occlusion, or obstruction. Acute abdominal pain Acute abdomen HP:0033401 Ischemia is defined as a restriction of arterial blood supply to a tissue associated with insufficient oxygenation to support the metabolis requirements of the tissue. Depending on the involved tissues, clinical manifestations may include pain, pallor, lack of pulse, coldness, paresthesia, and paralysis. Additional associated manifestations include hemodynamic parameters (reduced blood pressure distal to the site of restricted arterial supply) and angiographic evidence of arterial occclusion. Tissue ischemia HP:0033454 Feeding problem necessitating food and nutrient delivery via a tube. Tube feeding HP:0033589 Passage of excessive amounts of gas and the feeling of abdominal fullness and bloating. Flatulence HP:0033628 Intermittent abdominal pain with diarrhea and/or constipation. Bowel irritability HP:0033677 Acute respiratory distress syndrome (ARDS) is defined as an acute disorder that starts within seven days of the inciting event and is characterized by bilateral lung infiltrates and severe progressive hypoxemia in the absence of any evidence of cardiogenic pulmonary edema. ARDS is defined by the patient's oxygen in arterial blood (PaO2) to the fraction of the oxygen in the inspired air (FiO2). These patients have a PaO2/FiO2 ratio of less than 300. ARDS Acute respiratory distress syndrome (ARDS) is a life-threatening condition of seriously ill patients, characterized by poor oxygenation, pulmonary infiltrates, and acuity of onset. On a microscopic level, the disorder is associated with capillary endothelial injury and diffuse alveolar damage. Once ARDS develops, patients usually have varying degrees of pulmonary artery vasoconstriction and may subsequently develop pulmonary hypertension. ARDS carries a high mortality, and few effective therapeutic modalities exist to combat this condition. ARDS can be observed as a complication of many diseases including pulmonary infection or aspiration, sepsis, trauma, massive transfusion, drowning, drug overdose, fat embolism, inhalation of toxic fumes, and pancreatitis. Acute respiratory distress syndrome HP:0033696 Acral areas of erythema with vesicles or pustules. The lesions resemble chilblains and have purpuric areas, affecting hands and feet. Chilblain-like lesion This condition is termed pseudo-chilblain because of the similar appearance of these lesions to chilblains. Pseudochilblains may be observed in persons with COVID-19 without documented exposure to cold or other risk factors for chilblains. Pseudo-chilblain HP:0033709 An increase in the amount of airway mucus. This feature may be characterized by frequent or excessive throat clearing (exhalation through tightly constricted laryngopharyngeal tissues accompanied by vibration of the palatoglossal arch and the vocal folds serving to clear mucus from the airway). Increased phlegm If excessive sputum production is manifested by frequent and often involuntary coughing, the HPO term Productive cough should be used. Increased sputum production HP:0033771 Pleuritic chest pain is characterized by sudden and intense sharp, stabbing, or burning pain in the chest when inhaling and exhaling. Pleuritic chest pain HP:0033834 A feeling of general discomfort, weakness, or lack of health. Malaise HP:0033842 The condition of being unable to eat a full meal because of a feeling of fullness (satiety), or or feeling very full after eating only a small amount of food. Feeling full quickly when eating Not able to finish a normal-sized meal Early satiety HP:0033843 Feeling excessively full after meals. Postprandial fullness HP:0033994 Inability to ingest sufficient quantities of nutrition by mouth or by tube-feeding with the corresponding requirement for intravenous administration of nutrition. Dependency on parenteral nutrition HP:0034031 Bluish discoloration of one or more regions of the face. Bluish face Cyanotic face Facial cyanosis HP:0034033 Bluish discoloration of the distal extremities (hands, fingertips, toes), and can sometimes involve circumoral and periorbital areas. Mucous membranes are generally not involved. Peripheral cyanosis HP:0034241 Death of a fetus in the uterus. Death before birth Intrauterine death Prenatal death HP:0034430 Abnormal joint physiology HP:0034644 The concentration of a metabolite in the liver is above or below the limits of normal. Abnormal liver metabolite concentration HP:0034753 Murphy's sign is elicited in patients with acute cholecystitis by asking the patient to take in and hold a deep breath while palpating the subcostal region. In practice, Murphy's sign is performed by palpating the subcostal region during inspiration. If pain is elicited and the patient suddenly stops their inspiratory effort, a positive Murphy's sign has been elicited. Murphy's sign Murphy's sign positive Sweeney's sign Positive Murphy sign HP:0034754 Vomiting whereby the vomit has the color of bile, yellowish-green. Bilious emesis HP:0034782 Obstipation is the inability to pass either stool or flatus (gas). Lack of flatulence No gas passage Obstipation can be a sign of an acute obstruction of the GI tract, either of the small or large bowel. Obstipation HP:0034783 Vomiting following a coughing spell. Individuals with gastroesophageal reflux disease (GERD) will frequently vomit when coughing for a non-GI reason. Vomiting occurs during these coughing spells because the intrabdominal pressure is high from the coughing and the propensity to reflux results in stomach contents emerging as vomit. This is a historical question that allows a parent to impart information suggesting GERD at an age when it is difficult to obtain a reliable GERD history from the child. Posttussive emesis HP:0040006 UMLS:C4022499 Mortality/Aging HP:0040202 Abnormal and compulsive consumption of food, liquid, or objects that could have negative consequences for the individual. UMLS:C4073150 Abnormal consumption behaviour Abnormal consumption behavior HP:0040288 The condition of inability to eat normally treated by placement of a thin tube through the nose into the stomach that is then used to carry food. Nasogastric tube feeding HP:0041051 A rare condition that is characterized by a complete loss of taste function of the tongue. Absent sense of taste Impaired taste sensation Lost taste Ageusia HP:0100279 A chronic inflammatory bowel disease that includes characteristic ulcers, or open sores, in the colon. The main symptom of active disease is usually constant diarrhea mixed with blood, of gradual onset and intermittent periods of exacerbated symptoms contrasting with periods that are relatively symptom-free. In contrast to Crohn's disease this special form of colitis begins in the distal parts of the rectum, spreads continually upwards and affects only mucose and submucose tissue of the colon. MSH:D003093 SNOMEDCT_US:64766004 UMLS:C0009324 Colitis ulcerosa Ulcerative colitis HP:0100280 A chronic granulomatous inflammatory disease of the intestines that may affect any part of the gastrointestinal tract from mouth to anus, causing a wide variety of symptoms. It primarily causes abdominal pain, diarrhea which may be bloody, vomiting, or weight loss, but may also cause complications outside of the gastrointestinal tract such as skin rashes, arthritis, inflammation of the eye, tiredness, and lack of concentration. Crohn's disease is thought to be an autoimmune disease, in which the body's immune system attacks the gastrointestinal tract, causing inflammation. MSH:D003424 SNOMEDCT_US:34000006 UMLS:C0010346 Granulomatous enteritis and colitis Morbus Crohn Crohn's disease HP:0100281 A chronic inflammatory disease of the large intestine (colon, cecum and rectum). SNOMEDCT_US:54597004 UMLS:C0267375 Chronic colitis HP:0100326 Immunological states where the immune system produces harmful responses upon reexposure to sensitising antigens. UMLS:C0237653 Immunologic hypersensitivity HP:0100533 Inflammation of the eye, parts of the eye or the periorbital region. HP:0007891 UMLS:C4020969 Inflammatory abnormality of the eye Ocular inflammation Inflammatory abnormality of the eye HP:0100543 Abnormal cognition with deficits in thinking, reasoning, or remembering. HP:0002128 HP:0002129 HP:0002302 HP:0002337 HP:0002441 HP:0006972 HP:0006998 HP:0007211 MSH:D060825 SNOMEDCT_US:386806002 UMLS:C0338656 UMLS:C0683322 Abnormality of cognition Cognitive abnormality Cognitive defects Cognitive deficits Cognitive impairment Intellectual impairment An individual with cognitive impairment may have trouble remembering, learning new things, concentrating, or making decisions. Cognitive impairment HP:0100547 An abnormality of the forebrain, which has as its parts the telencephalon, diencephalon, lateral ventricles and third ventricle. UMLS:C4020967 Abnormal shape of forebrain Abnormality of forebrain morphology Abnormality of the forebrain Abnormal forebrain morphology HP:0100613 Death between the age of 16 and 40 years. UMLS:C4022012 Death in early adulthood Death in early adulthood HP:0100651 A chronic condition in which the pancreas produces little or no insulin. Type I diabetes mellitus is manifested by the sudden onset of severe hyperglycemia with rapid progression to diabetic ketoacidosis unless treated with insulin. MSH:D003922 SNOMEDCT_US:46635009 UMLS:C0011854 Diabetes mellitus Type I Juvenile diabetes mellitus Type 1 diabetes Type I diabetes The onset of type 1 diabetes is typically during adolescence, but it can develop at any age. Type I diabetes mellitus HP:0100659 An anomaly of the cerebral blood vessels. UMLS:C4022001 Abnormality of the cerebral blood vessels Abnormality of the cerebral vasculature Abnormal cerebral vascular morphology HP:0100738 Abnormal eating habit with excessive or insufficient consumption of food or any other abnormal pattern of food consumption. UMLS:C4021982 Abnormal eating behavior Abnormal eating behaviour Note that this HPO term refers to an abnormal eating habit but does not directly refer to an eating disorder, which is a psychological disorder that is characterized by one or more abnormal eating behaviors. Abnormal eating behavior HP:0100749 An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the chest. MSH:D002637 SNOMEDCT_US:29857009 UMLS:C0008031 Chest pain Thoracic pain Chest pain HP:0100755 UMLS:C4021978 Abnormal spit Abnormality of salivation Abnormality of salivation HP:0100763 An anomaly of the lymphatic system, a network of lymphatic vessels that carry a clear fluid called lymph unidirectionally towards either the right lymphatic duct or the thoracic duct, which in turn drain into the right and left subclavian veins respectively. HP:0003012 MSH:D008206 SNOMEDCT_US:111590001 SNOMEDCT_US:234087005 SNOMEDCT_US:3305006 SNOMEDCT_US:362971004 UMLS:C0024228 UMLS:C4021976 Abnormality of the lymphatic system HP:0100806 Systemic inflammatory response to infection. MSH:D018805 UMLS:C0036690 Infection in blood stream Sepsis HP:0100851 An abnormality of emotional behaviour. UMLS:C4020949 Abnormal emotion/affect behaviour Abnormal emotion/affect behavior HP:0200039 A small elevation of the skin containing cloudy or purulent material usually consisting of necrotic inflammatory cells. MEDDRA:10037578 SNOMEDCT_US:103605005 SNOMEDCT_US:271760008 SNOMEDCT_US:285305004 SNOMEDCT_US:47002008 UMLS:C0241157 UMLS:C0542346 Pimple Pustula Pustular lesion Pustules Skin pustule Skin pustules Pustule HP:0410042 Any structural anomaly of the bile-secreting organ that is important for detoxification, for fat, carbohydrate, and protein metabolism, and for glycogen storage. Fyler:4447 Abnormal liver morphology HP:0410281 A heterogeneous group of symptoms that are localized in the epigastric region. Typical dyspeptic symptoms include postprandial fullness, early satiation, epigastric pain and epigastric burning, but other upper gastrointestinal symptoms such as nausea, belching or abdominal bloating often occur. Indigestion Dyspepsia HP:0500164 An abnormality of carbon dioxide (CO2) in the arterial blood. Abnormal CO2 levels in blood Abnormal blood carbon dioxide level Abnormal blood carbon dioxide level HP:0500165 An abnormality of the partial pressure of oxygen in the arterial blood. Abnormal O2 blood concentration Abnormal blood O2 level Abnormal blood oxygen levels Abnormal blood oxygen level HP:5200045 Reduced ability to control, or a failure to resist a temptation, urge, or impulse. Impaired self-restraint Impulse control disorders Reduced impulse control IAO:0000003 measurement unit label A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label IAO:0000005 objective specification A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification IAO:0000007 A directive information entity that describes an action the bearer will take. Alan Ruttenberg OBI Plan and Planned Process branch action specification IAO:0000009 datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label GROUP: IAO datum label IAO:0000010 software Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI software IAO:0000027 data item data item An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Chris Stoeckert PERSON: Jonathan Rees PERSON: Jonathan Rees data data item IAO:0000028 symbol An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol IAO:0000029 numeral A symbol that denotes a number. PERSON: Jonathan Rees numeral IAO:0000030 information content entity A generically dependent continuant that is about some thing. An information entity is an entity that represents information about some other entity. For example, a measurement, a clustered data set. an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. James Malone PERSON: Chris Stoeckert PERSON: Chris Stoeckert OBI_0000142 OBI_0000142 information content entity information content entity information entity IAO:0000031 integer numeral A numeral that denotes an integer PERSON: Jonathan Rees integer numeral IAO:0000032 scalar measurement datum A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum IAO:0000033 An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity IAO:0000078 curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification IAO:0000100 data set A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set IAO:0000102 data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part IAO:0000104 plan specification A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg Clint Dowland OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification IAO:0000109 measurement datum A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. person:Chris Stoeckert OBI_0000305 group:OBI http://www.ebi.ac.uk/efo/EFO_0001444 measurement datum IAO:0000140 A settings datum is a datum that denotes some configuration of an instrument. setting datum IAO:0000300 textual entity A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. PERSON: Lawrence Hunter textual entity IAO:0000314 document part An information content entity that is part of a document. PERSON: Lawrence Hunter document part IAO:0000408 A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg length measurement datum IAO:0000414 A scalar measurement datum that is the result of measurement of mass quality Person:Alan Ruttenberg mass measurement datum IAO:0000416 A scalar measurement datum that is the result of measuring a temporal interval Person:Alan Ruttenberg Damion Dooley's note: See https://www.w3.org/TR/NOTE-datetime for ISO 8601 time standards time measurement datum IAO:0000429 email address Person:Alan Ruttenberg Person:Chris Stoeckart email address IAO:0000577 A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot Original proposal from Bjoern, discussions at IAO calls Damion notes: Subclasses can actually have two components - the identifier, and the agency it is associated with. Under the general concept of "postal code" one can place particular national postal code systems like the US Postal code. centrally registered identifier symbol IAO:0000582 time stamped measurement datum IAO:0000594 A software application is software that can be directly executed by some processing unit. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software application IAO:0000634 notes section A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc. PERSON: Bill Baumgartner notes section ICO:0000288 2020-04-24T22:38:17Z pregnant woman IDO:0000414 A pathogen host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell By this definition, vectors and other organisms that may not be infected are bearers of the infectious agent host role. infectious agent host role IDO:0000415 A host role borne by an organism in virtue of the fact that its extended organism contains a pathogen. Albert Goldfain Alexander Diehl Lindsay Cowell Bearing the infectious agent host role implies bearing the pathogen host role, but the reverse is not true. See comment for infectious agent host role. pathogen host role IDO:0000416 An infectious agent host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent, the infectious agent has the infectious disposition towards the host, and the host has no symptoms of the infectious disease caused by the infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent carrier role IDO:0000444 A disposition that inheres in a material entity in virtue of the fact that the entity has a part (e.g. a gene product), which itself has a disposition to mitigate damage to the entity. Albert Goldfain Alexander Diehl Lindsay Cowell Examples include the following: CCR5 mutations protect T cells from HIV invasion. A tumor cell's resistance to chemotherapy protects the cell from damage by the drug (although this harms the patient). An insect's resistance to insecticide protects it from the insecticide. The disposition is realized in a process that mitigates damage to the bearer and has the part as a participant. protective resistance IDO:0000445 A protective resistance that mitigates the damaging effects of a drug. Albert Goldfain Alexander Diehl Lindsay Cowell drug resistance resistance to drug IDO:0000451 A disposition borne by an infectious agent that is the disposition to penetrate the epithelial barriers of an organism of another Species. Albert Goldfain Alexander Diehl Lindsay Cowell invasive disposition IDO:0000477 An infectious disease course that begins soon after infection is established and progresses rapidly to severe stages. Albert Goldfain Alexander Diehl Lindsay Cowell acute infectious disease course IDO:0000495 A disease course that is the realization of an infectious disease. Albert Goldfain Alexander Diehl Lindsay Cowell infectious disease course IDO:0000496 A chronic infectious disease course that does not progress to severe stages for a long period of time. Albert Goldfain Alexander Diehl Lindsay Cowell long-term non-progressing infectious disease course IDO:0000502 A process of infectious disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population. Albert Goldfain Alexander Diehl Lindsay Cowell infectious disease outbreak infectious disease epidemic IDO:0000504 An infection that is clinically abnormal. Albert Goldfain Alexander Diehl Lindsay Cowell infectious disorder IDO:0000509 An aggregate of organisms of the same Species. Albert Goldfain Alexander Diehl Lindsay Cowell The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age. organism population IDO:0000511 An organism population whose members have an infection. Albert Goldfain Alexander Diehl Lindsay Cowell infected population IDO:0000512 An organism population in whose members an infectious disease is being realized. Albert Goldfain Alexander Diehl Lindsay Cowell diseased population IDO:0000513 An organism population whose members each have an infectious disposition. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent population IDO:0000514 An organism population whose members are not infected with an infectious agent and who lack immunity to the infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell at-risk population susceptible population IDO:0000515 An organism population whose members are participating in non-parasitic symbiosis with a particular host. Albert Goldfain Alexander Diehl Lindsay Cowell normal resident microflora population normal resident microbiota population IDO:0000531 An organism bearing a host role. Albert Goldfain Alexander Diehl Lindsay Cowell host IDO:0000537 An organism bearing an infectious agent host role. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent host IDO:0000538 An organism bearing a pathogen host role. Albert Goldfain Alexander Diehl Lindsay Cowell pathogen host IDO:0000540 An organism bearing an infectious agent vector role. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent vector IDO:0000543 A material entity bearing an infectious agent vehicle role. Albert Goldfain Alexander Diehl Lindsay Cowell vehicle of infectious agent IDO:0000547 A biological macromolecule produced by a pathogen and that has a virulence factor disposition. Albert Goldfain Alexander Diehl Lindsay Cowell virulence factor IDO:0000567 An infection bearing the secondary infection role. Albert Goldfain Alexander Diehl Lindsay Cowell secondary infection IDO:0000569 An organism that is host to an infectious agent and has no symptoms of the infectious disease associated with the infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell asymptomatic host of infectious agent IDO:0000573 An organism who is host to an infectious agent and has symptoms of the infectious disease associated with the infectious agent Albert Goldfain Alexander Diehl Lindsay Cowell symptomatic host of infectious agent IDO:0000581 A resistance to drug that mitigates the damaging effects of an antibiotic. Albert Goldfain Alexander Diehl Lindsay Cowell antibiotic resistance IDO:0000586 A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population. Albert Goldfain Alexander Diehl Lindsay Cowell The organism corresponding to the extended organism is host to the infectious agents. By this definition, parts of the host can be considered part of the infection. infection IDO:0000590 An infectious disease course that unfolds over a long period of time. Albert Goldfain Alexander Diehl Lindsay Cowell persistent infectious disease course chronic infectious disease course IDO:0000592 An organism population whose members have acquired immunity to an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell immune population IDO:0000615 An organism population persisting in a site it has colonized. Albert Goldfain Alexander Diehl Lindsay Cowell colony IDO:0000616 A colony whose members are infectious agents. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent colony IDO:0000629 A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism. Albert Goldfain Alexander Diehl Lindsay Cowell host role IDO:0000636 A process that is a systemic inflammatory response to infection. Albert Goldfain Alexander Diehl Lindsay Cowell sepsis IDO:0000659 An organism that is not infected with an infectious agent and lacks protective immunity to the infectious agent. Alex Diehl Lindsay Cowell susceptible organism IDO:0100629 domestic animal that bears a food production role. YL Livestock refers to one or more domesticated animals raised in an agricultural setting to produce commodities such as food, fiber and labor. The term "livestock" as used in this article does not include poultry or farmed fish; however the inclusion of these, especially poultry, within the meaning of "livestock" is common. (http://en.wikipedia.org/wiki/Livestock) livestock MI:0489 http://www.ontobee.org/ontology/MI data source Database that originally provided the interaction record for exchange purposes. PMID:14755292 Damion Dooley's note: GenEpiO is using members of this class for the first part of the hasDbXref relation. This is where we are keeping the mapping between a code and its source database. Depending on its context, hasDbXref annotations may point directly to metadata field names in the target database, and may be annotated with additional information that guides any additional specifications that impact on data conversion of these fields. source database MMO:0000000 The manner, procedure or technique by which a morphological or physiological state or property in a single individual or sample or a group of individuals or samples is assessed and a quantitative or qualitative value assigned. measurement method MMO:0000343 A postmortem examination of a body to determine the cause of death or the character and extent of changes produced by disease. autopsy MMO:0000344 tissue collection (necropsy) A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease. A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease. [database_cross_reference: Merriam-Webster:Merriam-Websters_Online_Dictionary--11th_Ed] necropsy necropsy MONDO:0000001 A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. DOID:4 EFO:0000408 ICD9:799.9 MESH:D004194 NCIT:C2991 OGMS:0000031 Orphanet:377788 SCTID:64572001 UMLS:C0012634 condition disease disease or disorder disease or disorder, non-neoplastic diseases diseases and disorders disorder disorders medical condition other disease disease MONDO:0000270 A disease involving the lower respiratory tract. DOID:0050161 ICD9:478.1 ICD9:478.19 SCTID:128272009 UMLS:C1290325 disease of lower respiratory tract disease or disorder of lower respiratory tract disorder of lower respiratory tract lower respiratory tract disease lower respiratory tract disease or disorder lower respiratory tract disorder MONDO:0000314 DOID:0050338 primary bacterial infectious disease MONDO:0000376 A malignant neoplasm involving the respiratory system DOID:0050615 ICD9:165.8 ICD9:165.9 SCTID:449096009 UMLS:C3164456 cancer of respiratory system malignant neoplasm of respiratory system malignant respiratory system neoplasm respiratory system cancer respiratory system cancer MONDO:0000429 A monogenic disease that is has material basis in a mutation in a single gene on one of the non-sex chromosomes. DOID:0050739 ICD9:758.5 SCTID:1899006 UMLS:C0265384 autosomal hereditary disorder autosomal inherited disease autosomal inherited disorder autosomal genetic disease MONDO:0000590 A hypersensitivity reaction type II disease that involves the peripheral nervous system. DOID:0060033 peripheral nervous system autoimmune disease peripheral nervous system hypersensitivity reaction type II disease autoimmune disorder of peripheral nervous system MONDO:0001208 Life-threatening respiratory failure that develops rapidly. Causes include injury, sepsis, drug overdose, and pancreatitis. It manifests with dyspnea and cyanosis and may lead to cardiovascular shock. ICD9:518.81 NCIT:C27043 SCTID:65710008 UMLS:C0264490 acute respiratory failure respiratory failure, acute acute respiratory failure MONDO:0002025 A disorder characterized by behavioral and/or psychological abnormalities, often accompanied by physical symptoms. The symptoms may cause clinically significant distress or impairment in social and occupational areas of functioning. Representative examples include anxiety disorders, cognitive disorders, mood disorders and schizophrenia. DOID:150 MESH:D001523 MFOMD:0000004 NCIT:C2893 SCTID:74732009 Psychiatric disease Psychiatric disorder disease of mental health mental disorder mental dysfunction mental illness psychiatric disorder MONDO:0002037 A non-neoplastic or neoplastic disorder that affects the pleura. Representative examples include pleural infection, pleural mesothelioma, and pleural solitary fibrous tumor. DOID:1532 ICD9:518.89 MESH:D010995 NCIT:C26859 SCTID:88075009 UMLS:C0032226 disease of pleura disease or disorder of pleura disorder of pleura pleura disease pleura disease or disorder pleural disorder pleural disorders non-neoplastic pleural disease pleural disorder MONDO:0002046 The use of alcoholic beverages to excess, either on individual occasions ("binge drinking") or as a regular practice. DOID:1574 ICD9:305.0 ICD9:305.00 MESH:D000437 SCTID:15167005 alcohol abuse ethanol abuse alcohol abuse MONDO:0002052 Acute or chronic inflammation of one or more lymph nodes. It is usually caused by an infectious process. DOID:1602 HP:0002840 ICD9:289.1 ICD9:683 MESH:D008199 NCIT:C26821 SCTID:41174002 UMLS:C0024205 UMLS:C0154304 UMLS:C0157705 Inflammation of lymph node adenitis inflammation of lymph node lymph node inflammation lymph nodeitis lymphadenitis lymphadenitis (disease) acute adenitis acute lymphadenitis chronic adenitis chronic lymphadenitis lymphadenitis MONDO:0002075 DOID:1672 ICD10CM:J93.0 ICD9:512.0 SCTID:196102003 UMLS:C0155907 spontaneous tension pneumothorax MONDO:0002076 Abnormal presence of air in the pleural cavity. DOID:1673 HP:0002107 ICD9:512.8 MESH:D011030 NCIT:C38006 SCTID:36118008 pneumothorax pneumothorax (disease) pneumothorax MONDO:0002081 A disease involving the musculoskeletal system. DOID:17 ICD9:729.99 MESH:D009140 NCIT:C107377 SCTID:928000 UMLS:C0026857 disease of musculoskeletal system disease or disorder of musculoskeletal system disorder of musculoskeletal system musculoskeletal disease musculoskeletal system disease musculoskeletal system disease or disorder musculoskeletal system disorder musculoskeletal system disorder MONDO:0002118 A disease involving the renal system. DOID:18 ICD9:V47.4 MESH:D014570 NCIT:C3430 SCTID:128606002 UMLS:C1335051 disease of renal system disease or disorder of renal system disease, urinary tract disease, urologic disease, urological diseases, urinary tract diseases, urologic diseases, urological disorder of renal system disorder of the urinary system disorder of urinary system non-neoplastic urinary tract disease renal system disease renal system disease or disorder urinary disease urinary system disease urinary system disorder urinary tract disease urinary tract diseases urinary tract disorder urologic disease urologic disorder urological disease urological diseases urological disorder urological disorders urinary system disorder MONDO:0002254 A group of signs, symptoms, and clinicopathological characteristics that may or may not have a genetic basis and collectively define an abnormal condition. DOID:225 MESH:D013577 NCIT:C28193 OGMS:0000086 UMLS:C0039082 cluster, symptom clusters, symptom symptom cluster symptom clusters syndrome syndrome associated with disease or disorder syndromes syndromic disease syndromic disease or disorder syndromic disease MONDO:0002280 A reduction in the number of red blood cells, the amount of hemoglobin, and/or the volume of packed red blood cells. Clinically, anemia represents a reduction in the oxygen-transporting capacity of a designated volume of blood, resulting from an imbalance between blood loss (through hemorrhage or hemolysis) and blood production. Signs and symptoms of anemia may include pallor of the skin and mucous membranes, shortness of breath, palpitations of the heart, soft systolic murmurs, lethargy, and fatigability. DOID:2355 EFO:0004272 HP:0001903 ICD9:285.8 ICD9:285.9 MESH:D000740 NCIT:C2869 SCTID:271737000 anaemia anemia anemia (disease) anemia MONDO:0002491 The use of a drug for a reason other than which it was intended or in a manner or in quantities other than directed. DOID:302 ICD9:305.90 SCTID:66214007 substance abuse MONDO:0002494 A category of psychiatric disorders which include disorders related to the taking of a drug of abuse (including alcohol, prescribed medications and recreational drugs). DOID:303 ICD10CM:F10-F19 MESH:D019966 NCIT:C92203 substance induced mood disorders substance-related disorder substance-related disorder MONDO:0002515 A non-neoplastic or neoplastic disorder that affects the liver, bile ducts, and gallbladder. Representative examples of non-neoplastic disorders include hepatitis, cirrhosis, cholangitis, and cholecystitis. Representative examples of neoplastic disorders include hepatocellular adenoma, hepatocellular carcinoma, and cholangiocarcinoma. DOID:3118 NCIT:C3959 UMLS:C0267792 disease of hepatobiliary system disease or disorder of hepatobiliary system disorder of hepatobiliary system hepatobiliary disorder hepatobiliary system disease hepatobiliary system disease or disorder liver and biliary disease liver and biliary disorder liver and biliary system disorder liver and biliary tract disease hepatobiliary disorder MONDO:0002516 A primary or metastatic malignant neoplasm involving any part of the digestive system. GI tumor DOID:3119 ICD10CM:C15-C26 ICD9:239.0 NCIT:C4890 cancer of digestive system digestive system cancer gastrointestinal system cancer gastrointestinal tract cancer malignant digestive system neoplasm malignant gastrointestinal neoplasm malignant gastrointestinal system neoplasm malignant neoplasm of digestive system digestive system cancer MONDO:0002602 A disease involving the central nervous system. DOID:331 MESH:D002493 NCIT:C2934 SCTID:23853001 UMLS:C0007682 CNS disorder central nervous disease central nervous system disease central nervous system disease or disorder central nervous system disorder disease of central nervous system disease of the central nervous system disease or disorder of central nervous system disorder of central nervous system central nervous system disorder MONDO:0002657 A disease involving the breast. DOID:3463 ICD10CM:N60-N65 ICD9:610-612.99 ICD9:611.8 ICD9:611.9 MESH:D001941 NCIT:C26709 SCTID:79604008 UMLS:C0006145 breast disease breast disease or disorder breast diseases breast disorder disease of breast disease or disorder of breast disorder of breast breast disorder MONDO:0002977 A disorder characterized by the degeneration of the nervous system due to autoimmunity. Representative examples include multiple sclerosis, Guillain-Barre syndrome, and myasthenia gravis. DOID:438 MESH:D020274 NCIT:C99383 UMLS:C0751871 UMLS:C0751872 autoimmune disease of nervous system autoimmune disease, neurologic autoimmune diseases, nervous system autoimmune diseases, neurologic autoimmune disorders of the nervous system autoimmune disorders, nervous system autoimmune nervous system diseases autoimmune nervous system disorder disease, neurologic autoimmune diseases, neurologic autoimmune immune diseases, nervous system immune disorders, nervous system nervous system autoimmune disease nervous system autoimmune diseases nervous system hypersensitivity reaction type II disease nervous system immune diseases nervous system immune disorders neurologic autoimmune disease neurologic autoimmune diseases autoimmune disorder of the nervous system MONDO:0003274 A primary or metastatic malignant neoplasm affecting the tissues of the thorax. thoracic tumor thorax neoplasm tumor of thorax DOID:5093 ICD9:195.1 NCIT:C3576 SCTID:188361007 UMLS:C0153661 cancer of thoracic segment of trunk malignant neoplasm of the thorax malignant neoplasm of thoracic segment of trunk malignant neoplasm of thorax malignant thoracic neoplasm malignant thoracic segment of trunk neoplasm malignant thoracic tumor malignant tumor of the thorax malignant tumor of thorax thoracic segment of trunk cancer thorax cancer thoracic cancer MONDO:0003346 Vasculitis affecting the blood vessels of the brain and/or spinal cord. DOID:525 MESH:D020293 NCIT:C84622 UMLS:C0751878 central nervous system vasculitis vasculitis of central nervous system central nervous system vasculitis MONDO:0003620 A disease involving the peripheral nervous system. DOID:574 ICD9:350-359.99 ICD9:356.9 MESH:D010523 NCIT:C27580 SCTID:42658009 PNS (peripheral nervous system) diseases PNS disease PNS diseases disease of peripheral nervous system disease or disorder of peripheral nervous system disorder of peripheral nervous system disorder of the peripheral nervous system peripheral nervous system disease peripheral nervous system disease or disorder peripheral nervous system disorder peripheral nervous system disorders nerve disease, peripheral nerve diseases, peripheral neuropathy, peripheral peripheral Neuropathies peripheral nerve disease peripheral nerve diseases peripheral neuropathy peripheral nervous system disorder MONDO:0003780 A broad classification of disorders that affect the cell-mediated aspect of the immune response. Circulating numbers of T lymphocytes are decreased or ineffective. DOID:613 NCIT:C27145 SCTID:402792003 UMLS:C1274233 T-cell immunodeficiency T-lymphocyte deficiency (finding) T-lymphocyte immunodeficiency T-cell immunodeficiency MONDO:0003847 A disease that is caused by genetic modifications where those modifications are inherited from a parent's genome. genetic condition genetic disease genetic disorder DOID:630 EFO:0000508 ICD9:799.89 MESH:D030342 NCIT:C3101 SCTID:32895009 UMLS:C0019247 hereditary disease hereditary disease or disorder hereditary diseases inherited disease inherited genetic disease molecular disease Mendelian disease Usage note: this is intended only for diseases with an inherited genetic etiology. Somatic genetic mutations are excluded. Some ontologies use the term 'genetic disease' in the sense of inherited disorders only, we are here careful to distinguish. hereditary disease MONDO:0003900 A disease involving the connective tissue. DOID:65 MESH:D003240 NCIT:C26729 SCTID:105969002 UMLS:C0009782 connective tissue disease connective tissue disease or disorder connective tissue diseases connective tissue disorder connective tissue disorders disease of connective tissue disease or disorder of connective tissue disease, connective tissue disorder of connective tissue primary disorder of connective tissue tissue disease, connective Following clinical usage of the term 'connective tissue disorder' this grouping excludes some diseases affecting tissues classically considered to be connective tissue, such as bone. connective tissue disorder MONDO:0003916 An imbalanced nutritional status resulting from excessive intake of nutrients. Generally, overnutrition generates an energy imbalance between food consumption and energy expenditure leading to disorders such as obesity. DOID:654 ICD9:278.8 MESH:D044343 SCTID:302872003 UMLS:C1257763 overnutrition MONDO:0003939 A disease involving the muscle tissue. DOID:0080000 DOID:66 EFO:0002970 ICD10CM:M60-M63 MESH:D009135 disease of muscle organ disease of muscle tissue disease or disorder of muscle organ disease or disorder of muscle tissue disorder of muscle organ disorder of muscle tissue muscle organ disease muscle organ disease or disorder muscle tissue disease muscle tissue disease or disorder muscular disorder muscle tissue disorder MONDO:0004335 A disease or disorder that involves the digestive system. DOID:77 EFO:0000405 ICD10CM:K00-K95 ICD9:520-579.99 ICD9:V47.3 MESH:D005767 NCIT:C2990 SCTID:53619000 alimentary system disease digestive disease digestive system disease digestive system disease or disorder digestive system disorder disease of digestive system disease or disorder of digestive system disorder of digestive system gastroenterological system disease gastroenterological system disorder gastroenteropathy gastrointestinal disease gastrointestinal disorder gastrointestinal system disease gastrointestinal system disorder git disease stomach or intestinal disorder digestive system disorder MONDO:0004670 An autoimmune, connective tissue chronic inflammatory disorder affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood cells. It is more commonly seen in women than men. Variants include discoid and systemic lupus erythematosus. DOID:8857 ICD10CM:L93 ICD9:695.4 NCIT:C27153 SCTID:200936003 UMLS:C0409974 lupus lupus erythematosus lupus erythematosus MONDO:0004781 Necrosis of the myocardium, as a result of interruption of the blood supply to the area. It is characterized by a severe and rapid onset of symptoms that may include chest pain, often radiating to the left arm and left side of the neck, dyspnea, sweating, and palpitations. DOID:9408 EFO:0008583 ICD10CM:I21.9 ICD9:410 ICD9:410.80 ICD9:410.81 ICD9:410.82 ICD9:410.9 ICD9:410.90 ICD9:410.91 ICD9:410.92 NCIT:C35204 SCTID:57054005 UMLS:C0155626 acute myocardial infarction (disease) myocardial infarction (disease), acute acute myocardial infarction MONDO:0004928 Any disorder of the lymph nodes. DOID:9942 NCIT:C35346 SCTID:76616003 UMLS:C0272394 disease of lymph node disease or disorder of lymph node disorder of lymph node lymph node disease lymph node disease or disorder lymph node disorder lymph node disorder MONDO:0004992 A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas. DOID:0050686 DOID:0050687 DOID:162 EFO:0000311 GARD:0011960 ICD9:195.8 ICD9:199 ICD9:199.1 ICDO:8000/3 NCIT:C9305 NIFSTD:birnlex_406 ONCOTREE:MT SCTID:363346000 UMLS:C0006826 CA cancer cell type cancer malignancy malignant Growth malignant neoplasm malignant neoplasm (disease) malignant neoplastic disease malignant tumor neoplasm (disease), malignant neoplasm, malignant organ system cancer primary cancer cancer MONDO:0004995 A disease involving the cardiovascular system. DOID:1287 EFO:0000319 ICD9:390-459.99 ICD9:420-429.99 ICD9:423 ICD9:423.8 ICD9:424 ICD9:429 ICD9:429.2 ICD9:429.7 ICD9:429.8 ICD9:429.81 ICD9:429.89 ICD9:459.89 ICD9:459.9 MESH:D002318 NCIT:C2931 SCTID:49601007 UMLS:C0007222 cardiovascular disease cardiovascular disease (CVD) cardiovascular disorder cardiovascular system disease cardiovascular system disease or disorder disease of cardiovascular system disease of subdivision of hemolymphoid system disease or disorder of cardiovascular system disorder of cardiovascular system cardiovascular disorder MONDO:0005020 A non-neoplastic or neoplastic disorder that affects the small or large intestine. DOID:5295 ICD9:520-579.99 ICD9:560-569.99 ICD9:564 ICD9:564.4 ICD9:569 ICD9:569.4 ICD9:569.49 ICD9:569.89 ICD9:569.9 ICD9:570-579.99 ICD9:575 MESH:D007410 NCIT:C26801 SCTID:85919009 disease of intestine disease or disorder of intestine disorder of intestine intestinal disease intestinal disorder intestine disease intestine disease or disorder intestinal disorder MONDO:0005027 A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions. DOID:1826 EFO:0000474 ICD10CM:G40 ICD10WHO:G40 ICD9:345 ICD9:345.8 ICD9:345.80 ICD9:345.9 ICD9:345.90 ICD9:345.91 MESH:D004827 NCIT:C3020 NIFSTD:birnlex_12718 SCTID:84757009 epilepsy seizure disorder epilepsy MONDO:0005039 A disease involving the reproductive system. DOID:15 EFO:0000512 NCIT:C4875 SCTID:362968007 UMLS:C0178829 Wikipedia:Reproductive_system_disease disease of reproductive system disease or disorder of reproductive system disorder of reproductive system genital disorders genital system disease reproductive disease reproductive system disease reproductive system disease or disorder reproductive system disorder reproductive system disorder MONDO:0005046 A disorder resulting from an abnormality in the immune system. DOID:2914 EFO:0000540 ICD9:279 ICD9:279.1 ICD9:279.10 ICD9:279.19 ICD9:279.4 ICD9:279.49 ICD9:279.8 ICD9:279.9 MESH:D007154 NCIT:C3507 SCTID:414029004 disease of immune system disease or disorder of immune system disorder of immune system immune disease immune disorder immune dysfunction immune system disease or disorder immune system disorder immune system disorder MONDO:0005068 Gross necrosis of the myocardium, as a result of interruption of the blood supply to the area, as in coronary thrombosis. DOID:5844 EFO:0000612 HP:0001658 ICD10CM:I21 MESH:D009203 NCIT:C27996 SCTID:22298006 UMLS:C0027051 MI MI, myocardial infarction heart attack infarction (MI), myocardial myocardial infarct myocardial infarction myocardial infarction (disease) myocardial infarction, (MI) myocardial infarction MONDO:0005070 A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias. cell process disease DOID:14566 EFO:0000616 HP:0002664 ICD10CM:C00-D49 ICD10CM:C7A-C7A ICD10CM:C7B-C7B ICD9:140-239.99 ICD9:239.8 ICD9:239.9 MESH:D009369 NCIT:C3262 ONCOTREE:OTHER SCTID:55342001 UMLS:CN236628 disease of cellular proliferation neoplasia neoplasm neoplasm (disease) neoplastic disease neoplastic growth tumor tumor disease other neoplasm neoplasm MONDO:0005071 A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves. DOID:863 EFO:0000618 ICD10CM:G00-G99 ICD9:349.89 ICD9:349.9 MESH:D009422 NCIT:C26835 SCTID:118940003 UMLS:C0027765 Wikipedia:Nervous_system_disease disease of nervous system disease or disorder of nervous system disorder of nervous system nervous system disease nervous system disease or disorder nervous system disorder neurologic disease neurologic disorder neurological disease neurological disorder 'psychiatric disorder' is not classified as a 'nervous system disorder' in Mondo (though it is often as such): the hallmarks of psychiatric disorders are based in behavior and emotional state, and the relation with nervous system malfunction or damage is not always clearly determined. nervous system disorder MONDO:0005087 A non-neoplastic or neoplastic disorder that affects the respiratory system. Representative examples include pneumonia, chronic obstructive pulmonary disease, pulmonary failure, lung adenoma, lung carcinoma, and tracheal carcinoma. DOID:1579 EFO:0000684 ICD10CM:J00-J99 ICD9:460-519.99 ICD9:500-508.99 ICD9:503 ICD9:508 ICD9:508.1 ICD9:508.8 ICD9:508.9 ICD9:510-519.99 ICD9:516 ICD9:516.8 ICD9:516.9 ICD9:517 ICD9:517.8 ICD9:519 ICD9:519.1 ICD9:519.3 ICD9:519.8 ICD9:519.9 ICD9:V12.60 ICD9:V47.2 MESH:D012140 NCIT:C26871 SCTID:50043002 disease of respiratory system disease or disorder of respiratory system disorder of respiratory system respiratory disease respiratory disorder respiratory system disease respiratory system disease or disorder respiratory system disorder respiratory system disorder MONDO:0005108 Any disease caused by a virus. DOID:934 EFO:0000763 ICD9:060-066.99 ICD9:066.9 ICD9:078.89 ICD9:079.99 MESH:D014777 NCIT:C3439 SCTID:34014006 Viruses caused disease or disorder Viruses disease or disorder Viruses infection Viruses infectious disease infection, viral viral disease viral disorder viral infection virus infection viral infectious disease MONDO:0005109 An infection caused by the human immunodeficiency virus. DOID:526 EFO:0000764 ICD10CM:B20-B20 ICD9:042 ICD9:042-042.99 MESH:D015658 NCIT:C3108 SCTID:86406008 UMLS:C0019693 HIV infection Human immunodeficiency virus caused disease or disorder Human immunodeficiency virus disease or disorder Human immunodeficiency virus infectious disease HIV infectious disease MONDO:0005113 An acute infectious disorder that is caused by gram positive or gram negative bacteria; representative examples include pneumococcal, streptococcal, salmonella, and meningeal infections. DOID:104 EFO:0000771 ICD9:040.89 ICD9:041.89 ICD9:041.9 MESH:D001424 NCIT:C2890 SCTID:87628006 UMLS:C0004623 Bacteria caused disease or disorder Bacteria disease or disorder Bacteria infectious disease bacterial disease bacterial disorder bacterial infection bacterial infectious disease infection, bacterial bacterial infectious disease MONDO:0005137 Any condition related to a disturbance between proper intake and utilization of nourishment. DOID:374 EFO:0001069 ICD9:783.9 MESH:D009748 NCIT:C26836 SCTID:2492009 UMLS:C3714509 nutritional disorder nutritional disorder MONDO:0005139 An excess of body weight, normally defined as an individual with a body mass index greater than 35 or a body weight greater than one hundred percent of ideal body weight. DOID:11981 EFO:0001074 ICD9:278.01 MESH:D009767 NIFSTD:nlx_dys_20090303 SCTID:83911000119104 UMLS:C0028756 severe obesity morbid obesity MONDO:0005151 A disease involving the endocrine system. DOID:28 EFO:0001379 ICD9:259.8 ICD9:259.9 MESH:D004700 NCIT:C3009 SCTID:362969004 UMLS:C0014130 disease of endocrine system disease or disorder of endocrine system disorder of endocrine system endocrine disease endocrine disorder endocrine system disease endocrine system disease or disorder endocrine system disorder endocrinopathy thyroid or other glandular disorders endocrine system disorder MONDO:0005154 A disease involving the liver. DOID:409 EFO:0001421 ICD10CM:K70-K77 ICD9:573.8 ICD9:573.9 MESH:D008107 NCIT:C3196 SCTID:235856003 UMLS:C0023895 disease of liver disease or disorder of liver disorder of liver hepatic disease hepatic disorder liver and intrahepatic bile duct disorder liver disease liver disease or disorder liver disorder liver disorder MONDO:0005240 A disease involving the kidney. DOID:557 EFO:0003086 ICD9:583.81 MESH:D007674 NCIT:C3149 SCTID:90708001 UMLS:C0022658 disease of kidney disease or disorder of kidney disorder of kidney kidney disease kidney disease or disorder kidney disorder renal disease renal disorder kidney disorder MONDO:0005265 A spectrum of small and large bowel inflammatory diseases of unknown etiology. It includes Crohn's disease, ulcerative colitis, and colitis of indeterminate type. DOID:0050589 EFO:0003767 ICD9:558.9 MESH:D015212 NCIT:C3138 OMIMPS:266600 SCTID:24526004 UMLS:C0021390 IBD autoimmune bowel disorder inflammatory bowel disease inflammatory bowel disease MONDO:0005267 A disease involving the heart and/or pericardium. DOID:114 EFO:0003777 ICD9:429.89 ICD9:429.9 ICD9:V47.2 MESH:D006331 NCIT:C3079 SCTID:56265001 UMLS:C0018799 UMLS:CN236661 UMLS:CN239852 cardiac disease disease of heart disease or disorder of heart disorder of heart disorder of heart/pericardium heart disease heart disease or disorder heart disorder heart trouble heart/pericardial disease heart/pericardial disease or disorder heart/pericardial disorder heart/pericardial trouble heart disorder MONDO:0005275 A disease involving the lung. DOID:850 EFO:0003818 ICD9:518.89 MESH:D008171 NCIT:C3198 SCTID:19829001 disease of lung disease or disorder of lung disorder of lung lung disease lung disease or disorder lung disorder lung disorders pulmonary disease pulmonary diseases pulmonary disorder pulmonary disorders lung disorder MONDO:0005335 A benign or malignant neoplasm that affects the colon or rectum. Representative examples of benign neoplasms include lipoma and leiomyoma. Representative examples of malignant neoplasms include carcinoma, lymphoma, and sarcoma. Colorectal adenomas always exhibit epithelial dysplasia and are considered premalignant neoplasms. MONDO:0021236 EFO:0004142 MESH:D015179 NCIT:C2956 colorectal neoplasm colorectal tumor colorectum neoplasm colorectum neoplasm (disease) colorectum tumor large bowel neoplasm large bowel tumor large intestinal neoplasm large intestine neoplasm large intestine tumor neoplasm of colorectum neoplasm of large bowel neoplasm of the large bowel tumor of colorectum tumor of large bowel tumor of the large bowel colorectal neoplasm MONDO:0005385 A general term used to describe any disease affecting blood vessels]. It includes vascular abnormalities caused by degenerative, metabolic and inflammatory conditions, embolic diseases, coagulative disorders, and functional disorders such as posteri or reversible encephalopathy syndrome. DOID:178 EFO:0004264 ICD10CM:I00-I99 ICD10CM:I70-I79 ICD9:442.9 MESH:D014652 NCIT:C35117 SCTID:27550009 UMLS:C0042373 disease of vasculature disease or disorder of vasculature disorder of vasculature vascular disorder vascular tissue disease vasculature disease vasculature disease or disorder The etiology of vasculopathy is generally unknown and the condition is frequently not pathologically proven. Vasculitis, on the other hand, is a more specific term and is defined as inflammation of the wall of a blood vessel. However, the term vasculopathy is also used for “vasculitis” that has not been pathologically established. vascular disorder MONDO:0005404 A medical condition characterized by long-term fatigue and other symptoms that limit a person's ability to carry out ordinary daily activities. DOID:8544 EFO:0004540 ICD9:780.71 ICD9:780.79 MESH:D015673 NCIT:C3037 Orphanet:1983 SCTID:51771007 UMLS:C0015674 CFS Postviral fatigue syndrome chronic fatigue immune dysfunction syndrome chronic fatigue syndrome myalgic encephalitis myalgic encephalomyelitis systemic exertion intolerance disease myalgic encephalomeyelitis/chronic fatigue syndrome MONDO:0005550 A disorder directly resulting from the presence and activity of a microbial, viral, or parasitic agent in humans. It can be transmitted by direct or indirect contact. DOID:0050117 EFO:0005741 ICD10CM:A00-B99 ICD9:079.0 ICD9:136.8 ICD9:136.9 IDO:0000436 MESH:D003141 NCIT:C26726 SCTID:40733004 communicable disease infection infectious infectious disease infectious diseases and manifestations infectious disorder transmissible disease clinical infection Replaces 'infection' in disease hierarchy. OBI imported term infection is moved to pathologic process. This class is a container class for infectious diseases, not the process of infection itself. infectious disease MONDO:0005554 Inflammatory and degenerative diseases of connective tissue structures, such as arthritis. DOID:1575 EFO:0005755 ICD9:729.0 MESH:D012216 NCIT:C27204 SCTID:396332003 UMLS:C0035435 Wikipedia:Rheumatism rheumatic disease rheumatologic disorder This is an umbrella term encompassing conditions causing chronic, often intermittent pain affecting the joints and/or connective tissue rheumatic disorder MONDO:0005560 A disease affecting the brain or part of the brain. DOID:936 EFO:0005774 ICD9:348.3 ICD9:348.30 ICD9:348.8 ICD9:348.9 MESH:D001927 NCIT:C96413 SCTID:81308009 UMLS:C0006111 UMLS:C0085584 brain disease brain disease or disorder disease of brain disease or disorder of brain disorder of brain encephalopathy Editor note: NCIT has different classes for brain disease and encephalopathy brain disorder MONDO:0005570 A disease involving the hematopoietic system. DOID:74 EFO:0005803 GTR:AN1320635 ICD10CM:D50-D89 ICD9:280-289.99 ICD9:289.8 ICD9:289.9 MESH:D006402 NCIT:C26323 Orphanet:97992 SCTID:414022008 UMLS:C0018939 UMLS:CN206939 UMLS:CN882913 blood disease blood disorder blood dyscrasia disease of hematopoietic system disease of the blood and blood-forming organs disease or disorder of hematopoietic system disorder of hematopoietic system hematologic and lymphocytic disorder hematologic disorder hematological disease hematological disorder hematological system disease hematopoietic disease hematopoietic system disease hematopoietic system disease or disorder rare hematologic disease placeholder for lymphoid disease hematologic disorder MONDO:0005575 A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma. DOID:5672 DOID:9256 EFO:0005842 NCIT:C4978 OMIM:114500 Orphanet:466667 SCTID:363510005 UMLS:C1527249 cancer of colorectum cancer of large bowel cancer of large intestine cancer of the large bowel colon cancer, advanced, somatic colon cancer, somatic colorectal cancer colorectal cancer with chromosomal instability, somatic colorectal cancer, autosomal dominant, somatic mutation colorectal cancer, somatic colorectal cancer, susceptibility to, autosomal dominant, somatic mutation colorectum cancer malignant colorectal neoplasm malignant colorectal tumor malignant colorectum neoplasm malignant large bowel neoplasm malignant large bowel tumor malignant large intestine neoplasm malignant large intestine tumor malignant neoplasm of colorectum malignant neoplasm of large bowel malignant neoplasm of large intestine malignant neoplasm of the large bowel malignant neoplasm of the large intestine malignant tumor of large bowel malignant tumor of large intestine malignant tumor of the large bowel malignant tumor of the large intestine Editor note: some sources make distinct classes for colorectal vs large intestine. We follow NCIT and make these equivalent colorectal cancer MONDO:0005718 Virus diseases caused by coronaviridae. EFO:0007223 UMLS:C0010078 Coronaviridae infectious disease MONDO:0005814 A malignant neoplasm involving the intestine DOID:10155 EFO:0007330 ICD9:159.0 MESH:D007414 NCIT:C4572 SCTID:363508008 UMLS:C0346627 bowel cancer cancer of intestine cancer of the intestine intestinal cancer intestinal neoplasms, malignant intestinal tumors, malignant intestine cancer malignant intestinal neoplasm malignant intestinal neoplasms malignant intestinal tumor malignant intestinal tumors malignant intestine neoplasm malignant intestine tumor malignant neoplasm of intestine malignant neoplasm of the intestine malignant tumor of intestine malignant tumor of the intestine intestinal cancer MONDO:0005833 A disease involving the lymphatic part of lymphoid system. DOID:75 EFO:0007352 MESH:D008206 NCIT:C50764 SCTID:362971004 UMLS:C0024228 disease of lymphatic part of lymphoid system disease or disorder of lymphatic part of lymphoid system disorder of lymph node and lymphatics disorder of lymphatic part of lymphoid system disorder of lymphatic system glands, swollen lymphatic disease lymphatic disorder lymphatic part of lymphoid system disease lymphatic part of lymphoid system disease or disorder swollen gland swollen glands lymphadenopathy lymphangiopathy Editor note: check alignment to anatomy, consider lymphoid system disease lymphatic system disorder MONDO:0005876 Infections with viruses of the order nidovirales. The concept includes arterivirus infections and coronaviridae infections. EFO:0007396 MESH:D030341 UMLS:C0969753 Nidovirales caused disease or disorder Nidovirales disease or disorder Nidovirales infectious disease MONDO:0006025 Autosomal recessive form of disease. DOID:0050737 EFO:1000017 ICD9:758.5 SCTID:85995004 UMLS:C0265388 autosomal recessive disease or disorder autosomal recessive hereditary disease autosomal recessive hereditary disorder autosomal recessive inherited disease autosomal recessive inherited disorder disease or disorder, autosomal recessive disease, autosomal recessive autosomal recessive disease MONDO:0006502 Progressive and life-threatening pulmonary distress in the absence of an underlying pulmonary condition, usually following major trauma or surgery. Cases of neonatal respiratory distress syndrome are not included in this definition. EFO:1000637 GARD:0005698 ICD10CM:J80 MedDRA:10001052 NCIT:C3353 ARDS acute respiratory distress syndrome shock lung This disease can present as a mild ARDS (PaO2/FiO2 of 201–300 mmHg) moderate ARDS (PaO2/FiO2 of 101–200 mmHg) and severe ARDS (PaO2/FiO2 ≤100 mmHg). [PMID:30872586] acute respiratory distress syndrome MONDO:0007179 A disorder resulting from loss of function or tissue destruction of an organ or multiple organs, arising from humoral or cellular immune responses of the individual to their own tissue constituents. It may be systemic (e.g., systemic lupus erythematosus), or organ specific, (e.g., thyroiditis). DOID:417 EFO:0005140 ICD9:279.4 ICD9:279.49 ICD9:720 MESH:D001327 NCIT:C2889 OBI:1110054 OMIM:109100 SCTID:85828009 UMLS:C0004364 autoimmune disease autoimmune disease or disorder autoimmune disorder disease, autoimmune Editor note: check OMIM autoimmune disease MONDO:0007254 A primary or metastatic malignant neoplasm involving the breast. The vast majority of cases are carcinomas arising from the breast parenchyma or the nipple. Malignant breast neoplasms occur more frequently in females than in males. breast tumor mammary tumor DOID:1612 ICD10CM:C50 ICD9:174.8 NCIT:C9335 SCTID:254837009 breast cancer cancer of breast malignant breast neoplasm malignant breast tumor malignant neoplasm of breast malignant neoplasm of the breast malignant tumor of breast malignant tumor of the breast mammary cancer primary breast cancer breast cancer MONDO:0008903 A malignant neoplasm involving the lung. DOID:1324 ICD9:162.3 ICD9:162.4 ICD9:162.5 ICD9:162.8 ICD9:162.9 NCIT:C7377 OMIM:211980 SCTID:363358000 adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation adenocarcinoma of lung, somatic cancer of lung lung cancer lung cancer, protection against, autosomal dominant, somatic mutation lung cancer, resistance to, autosomal dominant, somatic mutation lung cancer, somatic lung cancer, susceptibility to, autosomal dominant, somatic mutation malignant lung neoplasm malignant lung tumor malignant neoplasm of lung malignant neoplasm of the lung malignant tumor of lung malignant tumor of the lung nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation nonsmall cell lung cancer, somatic nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation lung cancer MONDO:0009061 Cystic fibrosis (CF) is a genetic disorder characterized by the production of sweat with a high salt content and mucus secretions with an abnormal viscosity. DOID:1485 GARD:0006233 ICD10CM:E84 ICD9:277.0 MESH:D003550 MedDRA:10011762 NCIT:C2975 OMIM:219700 Orphanet:586 SCTID:190905008 UMLS:C0010674 CF cystic fibrosis cystic fibrosis lung disease, modifier of mucoviscidosis pseudomonas aeruginosa, susceptibility to chronic infection by, in cystic fibrosis cystic fibrosis MONDO:0009971 Infant acute respiratory distress syndrome is a lung disorder that affects premature infants caused by developmental insufficiency of surfactant production and structural immaturity of the lungs. The symptoms usually appear shortly after birth and may include tachypnea, tachycardia, chest wall retractions (recession), expiratory grunting, nasal flaring and cyanosis during breathing efforts. RDS respiratory distress syndrome EFO:1000644 GARD:0000112 MESH:C566881 OMIM:267450 Orphanet:70587 UMLS:C1968593 RDS of prematurity respiratory distress syndrome in premature infants respiratory distress syndrome in premature infants MONDO:0011057 A disorder resulting from inadequate blood flow in the vessels that supply the brain. Representative examples include cerebrovascular ischemia, cerebral embolism, and cerebral infarction. DOID:6713 EFO:0003763 ICD10CM:I60-I69 ICD9:430-438.99 ICD9:434.91 ICD9:437.8 ICD9:437.9 MESH:D002561 NCIT:C2938 SCTID:62914000 UMLS:C0007820 cerebrovascular disease cerebrovascular disorder CVA CVA (cerebral vascular accident) cerebral infarction cerebrovascular accident stroke cerebrovascular disorder MONDO:0011122 A disorder involving an excessive amount of body fat. DOID:9970 EFO:0001073 HP:0001513 ICD9:278.0 ICD9:278.00 NCIT:C3283 NIFSTD:nlx_dys_20090302 Orphanet:521399 SCTID:414916001 UMLS:C0028754 obesity obesity disease Obesity is a complex disease that may involve multiple environmental and genetic causes. See the subclass monogenic disease for genetic subtypes obesity disorder MONDO:0011382 Sickle cell anemias are chronic hemolytic diseases that may induce three types of acute accidents: severe anemia, severe bacterial infections, and ischemic vasoocclusive accidents (VOA) caused by sickle-shaped red blood cells obstructing small blood vessels and capillaries. Many diverse complications can occur. DOID:10923 EFO:1001797 GARD:0008614 ICD9:282.6 ICD9:282.60 ICD9:282.63 MESH:D000755 MedDRA:10040641 NCIT:C34383 OMIM:603903 Orphanet:232 UMLS:C0002895 UMLS:C0019034 Hb SC disease Hb-S/Hb-C disease Hb-SS disease without crisis Hemoglobin S disease without crisis drepanocytosis hemoglobin SC disease sickle cell anemia sickle cell disease sickle-cell/Hb-C disease without crisis sickling disorder due to Hemoglobin S sickle cell anemia MONDO:0012268 A syndrome resulting from the acquired deficiency of cellular immunity caused by the human immunodeficiency virus (HIV). It is characterized by the reduction of the Helper T-lymphocytes in the peripheral blood and the lymph nodes. Symptoms include generalized lymphadenopathy, fever, weight loss, and chronic diarrhea. Patients with AIDS are especially susceptible to opportunistic infections (usually pneumocystis carinii pneumonia, cytomegalovirus (CMV) infections, tuberculosis, candida infections, and cryptococcosis), and the development of malignant neoplasms (usually non-Hodgkin lymphoma and Kaposi sarcoma). The human immunodeficiency virus is transmitted through sexual contact, sharing of contaminated needles, or transfusion of contaminated blood. DOID:635 EFO:0000765 MESH:D000163 NCIT:C2851 SCTID:62479008 AIDS AIDS, acquired immunodeficiency syndrome acquired immune deficiency acquired immunodeficiency disease acquired immunodeficiency syndrome, AIDS AIDS MONDO:0012727 Kawasaki disease (KD) is a febrile, systemic, self-limiting vasculitis affecting children and characterized by inflammation in the medium sized vessels associated with coronary arterial aneurysms (CAA) that may be life threatening when untreated. KD is the most common cause of acquired heart disease in children in developed countries and is a risk factor for ischemic heart disease in adulthood. DOID:13378 EFO:0004246 GARD:0006816 ICD9:446.1 MESH:D009080 MedDRA:10023320 NCIT:C34825 OMIM:611775 Orphanet:2331 SCTID:75053002 UMLS:C0026691 Kawasaki's disease MLNS acute febrile MCLS acute febrile mucocutaneous lymph node syndrome acute febrile mucocutaneous lymph node syndrome [MCLS] infantile polyarteritis nodosa mucocutaneous lymph node syndrome mucocutaneous lymph node syndrome MONDO:0013792 Bleeding into one or both cerebral hemispheres including the basal ganglia and the cerebral cortex. It is often associated with hypertension and craniocerebral trauma. EFO:0005669 ICD9:431 MESH:D002543 OMIM:614519 SCTID:274100004 stroke, hemorrhagic Editor note: consider separate subclass for OMIM ID intracerebral hemorrhage MONDO:0015489 Orphanet:156143 predominantly medium-vessel vasculitis MONDO:0015796 A condition of lung damage that is characterized by bilateral pulmonary infiltrates (pulmonary edema) rich in neutrophils, and in the absence of clinical heart failure. This can represent a spectrum of pulmonary lesions, endothelial and epithelial, due to numerous factors (physical, chemical, or biological). EFO:0004610 MESH:D055371 MedDRA:10069351 NCIT:C155766 Orphanet:178320 SCTID:315345002 acute lung injury MONDO:0015925 A diverse group of lung diseases that affect the lung parenchyma. They are characterized by an initial inflammation of pulmonary alveoli that extends to the interstitium and beyond leading to diffuse pulmonary fibrosis. Interstitial lung diseases are classified by their etiology (known or unknown causes), and radiological-pathological features. DOID:3082 EFO:0004244 GARD:0013336 ICD10CM:J80-J84 MESH:D017563 MedDRA:10022611 NCIT:C164315 Orphanet:182095 SCTID:233703007 UMLS:C0206062 ILD interstitial lung disease interstitial lung disease MONDO:0016218 A spectrum of rare post-infectious neuropathies that usually occur in otherwise healthy patients. GBS is clinically heterogeneous and encompasses acute inflammatory demyelinating polyradiculoneuropathy (AIDP), acute motor axonal neuropathy (AMAN) and acute motor-sensory axonal neuropathy (AMSAN), Miller-Fisher syndrome (MFS) and some other regional variants. DOID:12842 EFO:0007292 GARD:0006554 ICD10CM:G61.0 MESH:D020275 MedDRA:10018767 NCIT:C116345 Orphanet:2103 SCTID:40956001 UMLS:C0018378 GBS Guillain Barre syndrome Guillain Barré syndrome Guillain-Barre-Strohl syndrome Guillain-Barré syndrome Guillain-Barré-Strohl syndrome acute postinfectious polyneuropathy post-infectious polyneuritis post-infective polyneuritis postinfectious polyneuritis Guillain-Barre syndrome MONDO:0017014 A interstitial lung disease that occurs during childhood. Orphanet:264656 SCTID:328661000119108 UMLS:CN202324 ILD specific to childhood chILD chILD syndrome childhood interstitial lung disease interstitial lung disease of childhood pediatric interstitial lung disease The terms chILD or chILD syndrome (not preferred) have been coined to memorize easily and to identify a phenotype that requires prompt and expert evaluation. interstitial lung disease specific to childhood MONDO:0017015 GARD:0010559 Orphanet:264665 UMLS:CN202326 primary ILD specific to childhood primary interstitial lung disease specific to childhood primary interstitial lung disease specific to childhood MONDO:0017026 Orphanet:264735 UMLS:CN202338 ILD specific to adulthood interstitial lung disease specific to adulthood MONDO:0017027 Orphanet:264740 UMLS:CN202339 primary ILD specific to adulthood primary interstitial lung disease specific to adulthood MONDO:0017146 Orphanet:275752 UMLS:CN202572 Reason: out of scope. MONDO:excludeGroupingClass. Term to consider:MONDO:0011382 sickle cell anemia sickle cell disease and related diseases MONDO:0018076 A chronic, recurrent infection caused by the bacterium Mycobacterium tuberculosis. Tuberculosis (TB) may affect almost any tissue or organ of the body with the lungs being the most common site of infection. The clinical stages of TB are primary or initial infection, latent or dormant infection, and recrudescent or adult-type TB. Ninety to 95% of primary TB infections may go unrecognized. Histopathologically, tissue lesions consist of granulomas which usually undergo central caseation necrosis. Local symptoms of TB vary according to the part affected; acute symptoms include hectic fever, sweats, and emaciation; serious complications include granulomatous erosion of pulmonary bronchi associated with hemoptysis. If untreated, progressive TB may be associated with a high degree of mortality. This infection is frequently observed in immunocompromised individuals with AIDS or a history of illicit IV drug use. DOID:399 GARD:0007827 ICD10CM:A15-A19 ICD9:017.90 ICD9:017.92 ICD9:017.94 ICD9:017.96 MESH:D014376 MedDRA:10044755 NCIT:C3423 Orphanet:3389 SCTID:56717001 UMLS:C0041296 UMLS:C0151332 tuberculosis disease active tuberculosis tuberculosis MONDO:0018882 Vasculitis represents a clinically heterogenous group of diseases of multifactorial etiology characterized by inflammation of either large-sized vessels (large-vessel vasculitis, e.g. Giant-cell arteritis and Takayasu arteritis), medium-sized vessels (medium-vessel vasculitis e.g. polyarteritis nodosa and Kawasaki disease), or small-sized vessels (small-vessel vasculitis, e.g. granulomatosis with polyangiitis, microscopic polyangiitis, immunoglobulin A vasculitis, and cutaneous leukocytoclastic angiitis). Vasculitis occurs at any age, may be acute or chronic, and manifests with general symptoms such as fever, weight loss and fatigue, as well as more specific clinical signs depending on the type of vessels and organs affected. The degree of severity is variable, ranging from life or sight threatening disease (e.g. BehC'et disease) to relatively minor skin disease. DOID:865 EFO:0006803 GARD:0009565 MESH:D014657 MedDRA:10036023 MedDRA:10047115 NCIT:C26912 Orphanet:280369 Orphanet:52759 SCTID:31996006 UMLS:C0042384 Wikipedia:Vasculitis systemic vasculitis vasculitis MONDO:0019050 An inherited disorder characterized by structural alterations of a globin chain within the hemoglobin molecule. DOID:2860 GARD:0012455 ICD10CM:D58.0 ICD10CM:D58.1 ICD9:282.7 MESH:D006453 MedDRA:10060892 NCIT:C3092 Orphanet:68364 SCTID:427306008 UMLS:C0019045 UMLS:C1960031 Hemoglobinopathies / iron metabolism hemoglobinopathies hereditary hemoglobinopathy inherited hemoglobinopathy MONDO:0019056 Any disease that impairs the functioning of the muscles, either directly, being pathologies of the voluntary muscle, or indirectly, being pathologies of nerves or neuromuscular junctions DOID:440 EFO:1001902 ICD9:358 ICD9:358.9 MESH:D009468 MedDRA:10029323 Orphanet:68381 UMLS:C0027868 nerve and muscle disorder neuromuscular disease neuromuscular disease MONDO:0020010 A infectious disease that involves the nervous system. ICD9:349.89 NCIT:C27590 Orphanet:98010 SCTID:128116006 UMLS:C0597039 nervous system infectious disease nervous system infectious disorder infectious disorder of the nervous system MONDO:0020590 Infection due to organisms from the genus Mycobacteria. MESH:D009164 NCIT:C26831 SCTID:88415009 UMLS:C0026918 mycobacterial infection mycobacteriosis mycobacterium infection mycobacterial infectious disease MONDO:0020641 A benign or malignant, primary or metastatic neoplasm involving the respiratory tract. EFO:0003853 ICD10CM:C30-C39 MESH:D012142 NCIT:C3355 SCTID:126667002 neoplasm of respiratory tract neoplasm of the respiratory tract neoplasm, respiratory tract neoplasms, respiratory tract respiratory system neoplasm respiratory tract neoplasm respiratory tract tumor tract neoplasm, respiratory tract neoplasms, respiratory tumor of respiratory tract tumor of the respiratory tract respiratory tract neoplasm MONDO:0020683 Disease having a short and relatively severe course. ICD9:799.89 MESH:D000208 SCTID:2704003 UMLS:C0001314 acute disease acute diseases disease, acute acute disease MONDO:0020753 Infectious disease causes by viruses in the subfamily Orthocoronavirinae (coronaviruses). In humans, coronaviruses cause respiratory tract infections that can be mild, such as some cases of the common cold (among other possible causes, predominantly rhinoviruses), and others that can be lethal, such as SARS, MERS, and COVID-19. DOID:0080599 coronavirus infectious disease Orthocoronavirinae infectious disease MONDO:0021094 Disease in which there is a deficiency or defect in the mechanisms of immunity, either cellular or humoral. ICD9:279.3 NCIT:C3131 OMIMPS:300755 SCTID:234532001 UMLS:C0021051 immuno-deficiency immunodeficiency immunodeficiency disorder immunodeficiency disease MONDO:0021100 A benign or malignant neoplasm of the breast parenchyma. It can originate from the ducts, lobules or the breast adipose tissue. Breast neoplasms are much more common in females than males. EFO:0003869 ICD9:239.3 MESH:D001943 NCIT:C2910 ONCOTREE:BREAST SCTID:126926005 UMLS:CN236627 breast neoplasm breast neoplasm (disease) breast tumor neoplasm of breast neoplasm of the breast neoplasm, breast tumor of breast tumor of the breast breast neoplasm MONDO:0021113 The significant impairment of gas exchange within the lungs resulting in hypoxia, hypercarbia, or both, to the extent that organ tissue perfusion is severely compromised. Causes include chronic obstructive pulmonary disease, asthma, emphysema, acute respiratory distress syndrome, pneumonia, pulmonary edema, pneumothorax, and congestive heart failure. Treatment requires intubation and mechanical ventilation until the time the lungs recover sufficient function. DOID:11162 ICD9:518.81 ICD9:518.83 MESH:D012131 NCIT:C26872 SCTID:39871006 UMLS:C1145670 failure, respiratory respiratory failure respiratory insufficiency/failure acute respiratory failure chronic respiratory failure respiratory failure MONDO:0021117 A benign or malignant, primary or metastatic neoplasm involving the lungs. Representative examples of benign neoplasms include adenoma, papilloma, chondroma, and endobronchial lipoma. Representative examples of malignant neoplasms include carcinoma, carcinoid tumor, sarcoma, and lymphoma. MESH:D008175 NCIT:C3200 ONCOTREE:LUNG lung neoplasm lung neoplasm (disease) lung neoplasms lung tumor neoplasm of lung neoplasm of the lung tumor of lung tumor of the lung lung neoplasm MONDO:0021118 A benign or malignant neoplasm involving the small or large intestine. DOID:4610 NCIT:C3141 ONCOTREE:BOWEL SCTID:126769007 intestinal neoplasm intestinal neoplasms intestinal tumor intestinal tumors intestine growth intestine neoplasm intestine neoplasm (disease) intestine tumor neoplasm of intestinal tract neoplasm of intestine neoplasm of intestines neoplasm of the intestines tumor of intestine tumor of intestines tumor of the intestines intestinal neoplasm MONDO:0021166 A disease involving a pathogenic inflammatory response in the anatomical structure. ICD9:799.89 NCIT:C93210 SCTID:128139000 UMLS:C1290884 anatomical structure inflammation inflammation of anatomical structure inflammatory disease inflammatory disorder inflammatory disease MONDO:0021178 Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity. EFO:0000546 MESH:D014947 NCIT:C3671 injury trauma traumatic injury wound injury MONDO:0021223 A neoplasm (disease) that involves the digestive system. EFO:0008549 MESH:D005770 NCIT:C3052 GI neoplasm GI system neoplasm GI system tumor GI tumor digestive neoplasm digestive system neoplasm (disease) digestive system tumor digestive tumor gastrointestinal neoplasm gastrointestinal system neoplasm gastrointestinal system tumor gastrointestinal tumor neoplasm of GI system neoplasm of digestive system neoplasm of gastrointestinal system neoplasm of the GI system neoplasm of the digestive system neoplasm of the gastrointestinal system tumor of GI system tumor of digestive system tumor of gastrointestinal system tumor of the GI system tumor of the digestive system tumor of the gastrointestinal system digestive system neoplasm MONDO:0021350 A neoplasm (disease) that involves the thoracic segment of trunk. ICD10CM:C30-C39 ICD9:239.89 NCIT:C3406 SCTID:255058005 UMLS:C0039981 neoplasm of the thorax neoplasm of thoracic segment of trunk thoracic neoplasm thoracic segment of trunk neoplasm thoracic segment of trunk neoplasm (disease) thoracic segment of trunk tumor thoracic tumor tumor of the thorax tumor of thoracic segment of trunk tumor of thorax neoplasm of thorax MONDO:0021669 A disorder that follows infection but is distinct from the infection itself and its usual manifestations. ICD10CM:B90-B94 ICD9:139.8 SCTID:123976001 sequela of infectious disorder post-infectious disorder MONDO:0021674 A post-infectious disorder that follows viral infection but is distinct from the viral infection itself and its usual manifestations. ICD9:139.8 SCTID:123948009 sequela of viral disease post-viral disorder MONDO:0021681 A Disease due to or propagated by sexual contact. ICD10CM:A50-A64 ICD9:099.8 ICD9:099.9 MESH:D012749 NCIT:C3365 SCTID:8098009 UMLS:C0036916 STD VD VD, venereal disease disease (VD), venereal sexually Transmitted disorder sexually transmitted disease venereal disease (VD) sexually transmitted disease MONDO:0021682 Viral diseases which are potentially transmitted or propagated by sexual conduct. MESH:D015229 UMLS:C0036918 viral sexually transmitted disease viral sexually transmitted disease MONDO:0021698 Disorders related to or resulting from abuse or mis-use of alcohol. MESH:D019973 SCTID:29212009 alcohol-related disorders MONDO:0022034 Virus diseases caused by the Lentivirus genus. They are multi-organ diseases characterized by long incubation periods and persistent infection. EFO:1001357 MESH:D016180 UMLS:C0079680 lentivirus infection MONDO:0023370 Either an isolated neoplasm or a syndrome with neoplasm as a major feature. neoplastic disease or syndrome MONDO:0024619 An infectious process that affects the brain and/or spinal cord. Representative examples include encephalitis, poliomyelitis, arachnoiditis, and meningitis. EFO:1001456 ICD9:349.89 MESH:D002494 NCIT:C27582 SCTID:128117002 UMLS:C0007684 central nervous system infectious disease central nervous system infectious disorder infectious disease of central nervous system central nervous system infectious disorder MONDO:0024634 A disease that involves the large intestine. SCTID:119523007 UMLS:C0341321 disease of large intestine disease or disorder of large intestine disorder of large intestine large intestine disease or disorder large intestine disorder MONDO:0024643 A disorder that affects the muscle tissue of the heart. Representative examples include myocardial infarction, myocarditis, and cardiomyopathy. NCIT:C35544 SCTID:57809008 disease of myocardium disease or disorder of myocardium disorder of myocardium myocardial disease myocardial disorder myocardium disease myocardium disease or disorder myocardial disorder MONDO:0024880 A malignant tumor that has spread from its original (primary) site of growth to another site close to or distant from the primary site. NCIT:C36263 malignant metastatic neoplasm metastatic cancer metastatic malignant neoplasm metastatic neoplasm, malignant Note that we currently treat secondary neoplasms as being neoplastic diseases that are derived from neoplasm; classes such as 'neoplasm', 'carcinoma' are implicitly primary. This may change in future. metastatic malignant neoplasm MONDO:0024881 A malignant neoplasm that arises from a pre-existing lower grade lesion, or as a result of a primary lesion that has spread to secondary sites, or due to a complication of a cancer treatment. ICD9:198.89 ICD9:199.1 NCIT:C4968 SCTID:128462008 secondary cancer secondary malignancy secondary malignant neoplasm Note that we currently treat secondary neoplasms as being neoplastic diseases that are derived from neoplasm; classes such as 'neoplasm', 'carcinoma' are implicitly primary. This may change in future. secondary malignant neoplasm MONDO:0024882 A neoplasm that arises from a pre-existing lower grade lesion, or as a result of a primary lesion that has spread to secondary sites, or due to a complication of a cancer treatment. NCIT:C36255 secondary neoplasm secondary tumor Note that we currently treat secondary neoplasms as being neoplastic diseases that are derived from neoplasm; classes such as 'neoplasm', 'carcinoma' are implicitly primary. This may change in future. secondary neoplasm MONDO:0024883 A tumor that has spread from its original (primary) site of growth to another site, close to or distant from the primary site. Metastasis is characteristic of advanced malignancies, but in rare instances can be seen in neoplasms lacking malignant morphology. ICDO:8000/6 NCIT:C3261 metastatic disease metastatic neoplasm metastatic tumor Note that we currently treat secondary neoplasms as being neoplastic diseases that are derived from neoplasm; classes such as 'neoplasm', 'carcinoma' are implicitly primary. This may change in future. metastatic neoplasm MONDO:0035375 Orphanet:598363 MIS-C/A multisystem inflammatory syndrome in children and adults MONDO:0041656 A very serious type of heart attack during which one of the heart’s major arteries (one of the arteries that supplies oxygen and nutrient-rich blood to the heart muscle) is blocked. ST-segment elevation is an abnormality detected on the 12-lead ECG. EFO:0008585 MESH:D000072657 SCTID:401303003 ST segment elevation myocardial infarction STEMI acute-ST segment elevation myocardial infarction ST-elevation myocardial infarction MONDO:0043218 A disorder of the nervous system related to a vascular etiology. NCIT:C117007 UMLS:C3898144 disease of nervous system vasculature nervous system disorder of vasculature neurovascular disorder vasculature nervous system disorder neurovascular disorder MONDO:0044347 A disease or disorder that involves the erythrocyte. ICD9:289.9 SCTID:38292009 UMLS:C0221016 disease of erythrocyte disease or disorder of erythrocyte disorder of erythrocyte erythrocyte disease erythrocyte disease or disorder red blood cell disease red blood cell disorder erythrocyte disorder MONDO:0044348 ICD9:282.7 SCTID:80141007 hemoglobinopathy hemoglobinopathy MONDO:0044986 A disease or disorder that involves the lymphoid system. SCTID:111590001 disease of lymphoid system disease or disorder of lymphoid system disorder of lymphoid system lymphoid system disease lymphoid system disease or disorder lymphoid system disorder MONDO:0045024 Any disorder that features disrupted cell proliferation. Includes hyperplasia, neoplastic syndrome and isolated neoplasm diseases as well as precancerous conditions. cell proliferation disorder neoplasm cancer or benign tumor MONDO:0100096 A disease caused by infection with severe acute respiratory syndrome coronavirus 2. DOID:0080600 ICD10CM:U07.1 MESH:C000657245 MESH:D000086382 SCTID:840539006 2019 novel coronavirus infection 2019-nCoV infection coronavirus disease 2019 severe acute respiratory syndrome coronavirus 2 infectious disease COVID-19 MONDO:0100131 Acute respiratory distress syndromet that occurs in pediatric patients and includes findings of new infiltrates (unilateral or bilateral) consistent with acute parenchymal disease, edema not fully explained by fluid overload or cardiac failure, and may present as new acute lung disease in setting of chronic lung disease and/or heart disease, and perinatal lung disease is excluded. PARDS pediatric acute respiratory distress syndrome MONDO:0100163 A inflammatory syndrome in children infected by the SARS-CoV-2 with similarities to Kawasaki disease. Clinical manifestations range from fever and inflammation to myocardial injury, shock, and development of coronary artery aneurysms. DOID:0080711 NCIT:C172127 COVID-19 -related pediatric inflammatory multisystem syndrome COVID-19 Kawasaki-like syndrome COVID-19 associated multisystem inflammatory syndrome in children MIS-C PIMS PIMS-TS PMIS SARS-CoV-2 Kawasaki-like syndrome multisystem inflammatory syndrome in children multisystem inflammatory syndrome in children associated with COVID-19 multisystem inflammatory syndrome in children associated with coronavirus disease 2019 paediatric inflammatory multisystem syndrome: temporally associated with SARS-CoV-2 pediatric inflammatory multisystem syndrome pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 pediatric multi-system inflammatory syndrome potentially associated with COVID-19 pediatric multisystem inflammatory syndrome The clinical presentation of MIS-C includes fever, severe illness, and the involvement of two or more organ systems, in combination with laboratory evidence of inflammation and laboratory or epidemiologic evidence of SARS-CoV-2 infection. Some features of MIS-C resemble Kawasaki Disease, toxic shock syndrome, and secondary hemophagocytic lymphohistiocytosis/macrophage activation syndrome. COVID-19–associated multisystem inflammatory syndrome in children MONDO:0100192 A liver disease characterized by the liver losing or has lost all of its function. MESH:D017093 NCIT:C26922 hepatic failure liver failure MONDO:0100233 A chronic disease triggered by acute COVID-19 infection that is characterized by persistent symptoms following the acute phase of the SARS-CoV-2 infection, which may include fatigue, coughing, dyspnea, clouding of mentation, sleep disturbances, exercise intolerance and autonomic symptoms including tachycardia upon mild exercise or standing, night sweats, temperature dysregulation, gastroparesis, constipation or loose stools, and peripheral vasoconstriction. DOID:0080848 MESH:D000094024 MedDRA:10085503 MedDRA:10085504 NCIT:C179263 UMLS:C5433293 PASC long haul COVID-19 long-haul COVID-19 post-acute sequelae of COVID-19 post-acute sequelae of SARS-CoV-2 infection sequelae of COVID-19 long COVID-19 MONDO:0100319 A inflammatory syndrome in adults infected by the SARS-CoV-2 with severe illness requiring hospitalization in a person aged ≥21 years; a positive test result for current or previous SARS-CoV-2 infection (nucleic acid, antigen, or antibody) during admission or in the previous 12 weeks; severe dysfunction of one or more extrapulmonary organ systems (e.g., hypotension or shock, cardiac dysfunction, arterial or venous thrombosis or thromboembolism, or acute liver injury); laboratory evidence of severe inflammation (e.g., elevated CRP, ferritin, D-dimer, or interleukin-6); and absence of severe respiratory illness (to exclude patients in which inflammation and organ dysfunction might be attributable simply to tissue hypoxia). MIS-A COVID-19–associated multisystem inflammatory syndrome in adults MONDO:0100320 A SARS-CoV-2-related disease that is caused by infection by SARS-CoV-2, and manifests after the original primary infection. post-COVID-19 disorder MONDO:0100329 The initial viral infectious disase that causes illness. primary viral infectious disease MONDO:0600008 A syndrome that occurs after therapeutic infusion of antibodies into the blood and is characterized by nausea, headache, tachycardia, hypotension, rash, and shortness of breath. It is caused by the release of cytokines from the cells that are targeted by the antibodies. Most patients experience a mild to moderate reaction; however, the reaction may be severe and life-threatening. MESH:D000080424 NCIT:C78251 CRS cytokine storm cytokine-associated toxicity cytokine release syndrome MONDO:0700081 A condition beginning in the first day of life that results from inadequate surfactant production, causing increased work of breathing and impaired gas exchange. RDS respiratory distress syndrome DOID:12716 GARD:0000112 ICD9:769 NCIT:C27560 SCTID:46775006 UMLS:C0020192 UMLS:C0035220 HMD - hyaline membrane disease RDS Of newborns RDS, respiratory distress syndrome Of newborns hyaline membrane disease infant ARDS infant acute respiratory distress syndrome infant respiratory distress syndrome neonatal respiratory distress neonatal respiratory distress syndrome newborns (RDS), respiratory distress syndrome Of pulmonary hyaline membrane disease pulmonary hypoperfusion syndrome of newborn respiratory distress syndrome Of newborns respiratory distress syndrome Of newborns (RDS) respiratory distress syndrome in the newborn respiratory distress syndrome of newborn syndrome Of newborns (RDS), respiratory distress RDS of prematurity respiratory distress syndrome in premature infants newborn respiratory distress syndrome MONDO:0700096 human disease or disorder human disease MPATH:0 Pathological structure or process pathological entity MPATH:1000 Phenotypic observation of the presence or absence of a pathological entity. pathological phenotype observation MPATH:105 Lesions leading to or consequent on failure of, or atypical movement of, blood throughout the body. circulatory disorder MPATH:108 A syndrome consequent to uncontrolled activation of blood clotting factors leading to disseminated platelet lysis, and fibrin deposition, ultimately leading to bleeding and necrosis as a consequence of inhibition of fibrin polymerisation by degradation products. Diagnosed by microthrombi in many organs. disseminated intravascular coagulation MPATH:603 Anatomically located instance of pathological response or entity. pathological anatomical entity MP:0000001 the observable morphological, physiological, behavioral and other characteristics of mammalian organisms that are manifested through development and lifespan mammalian phenotype MP:0000313 any anomaly in the cessation of function at the cellular level MP:0001647 abnormal cell viability abnormal cellular death abnormal cell death MP:0000316 pathologic death of cells, usually from irreversible damage cellular necrosis MP:0001790 deviation from the normal function of the immune system MP:0001789 GO:0006955 immune system/response abnormalities immune system: response/ function abnormalities abnormal immune system physiology MP:0001845 aberrant reaction of the microcirculation characterized by movement of fluid and leukocytes from the blood into extravascular tissues inflammation inflammatory response abnormal inflammatory response MP:0001846 greater than expected response to injury, infection, or insult increased inflammatory response MP:0001866 local accumulation of fluid, plasma proteins, and leukocytes in the proximal portion of the respiratory passages nasal inflammation MP:0001867 inflammation of the mucous membrane of the nose MP:0001113 nasal catarrh rhinitis MP:0002133 any functional anomaly of the pulmonary system; inability or reduced ability to intake and exchange oxygen and carbon dioxide with the environment MGI:2173593 respiratory system dysfunction respiratory system physiology abnormalities respiratory system: respiratory distress/failure/functional anomalies abnormal respiratory system physiology MP:0002405 local accumulation of fluid, plasma proteins, and leukocytes in the respiratory system respiratory system inflammation MP:0005384 the observable morphological and physiological characteristics of the basic structural and functional unit of all mammalian organisms that are manifested through development and lifespan cell phenotype cellular phenotype MP:0005387 the observable morphological and physiological characteristics of the mammalian system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies that are manifested through development and lifespan immune system phenotype MP:0005388 the observable morphological and physiological characteristics of the mammalian system responsible for the exchange of oxygen and carbon dioxide with the environment that are manifested through development and lifespan respiratory system phenotype MP:0005621 any functional anomaly of the vital processes of the cell abnormal cell physiology MP:0031126 necrosis or death of soft tissue due to lack of blood flow resulting from injury, infection or other conditions that affect blood circulation gangrenous necrosis gangrene MP:0031127 a form of coagulative necrosis that develops in ischemic tissue, where the blood supply is inadequate to keep tissue viable, in the absence of superimposed microbial infection; can be due to peripheral artery disease or acute limb ischemia; the affected body part is dry, shrunken, and dark reddish-black and can fall off (autoamputate) if not removed surgically The term dry is used only when referring to a limb or to the gut; in other locations, this same type of necrosis is called an infarction, such as myocardial infarction dry gangrene NBO:0000313 "The action, reaction, or performance of an organism in response to external or internal stimuli." [GO:GO\:0007610] NBO:0000000 behavior behaviour behavior process NBO:0001845 Behavior related to the intake of substances. ingest consumption behavior NBO:0015005 Consumption behavior that involves burning a substance and inhaling the particulate and gas suspension emitted. smoking behavior NCBITaxon:1 root root NCBITaxon:10090 Mus musculus house mouse mouse Mus musculus NCBITaxon:10091 Mus musculus castaneus southeastern Asian house mouse Mus musculus castaneus NCBITaxon:10092 Mus musculus domesticus western European house mouse Mus musculus domesticus NCBITaxon:10141 Cavia porcellus domestic guinea pig guinea pig Cavia porcellus NCBITaxon:10239 Viruses Viruses NCBITaxon:10244 Monkeypox virus monkey pox virus Monkeypox virus NCBITaxon:1045010 Escherichia coli O157 Escherichia coli O157 NCBITaxon:1055535 Escherichia coli O111 Escherichia coli O111 NCBITaxon:1055536 Escherichia coli O103 Escherichia coli O103 NCBITaxon:1078021 Escherichia coli O113:H21 Escherichia coli O113:H21 NCBITaxon:1078032 Escherichia coli O45:H2 Escherichia coli O45:H2 NCBITaxon:108619 Salmonella enterica subsp. enterica serovar Newport Salmonella enterica subsp. enterica serovar Newport NCBITaxon:1095706 Escherichia coli O18 Escherichia coli O18 NCBITaxon:116058 Mus musculus brevirostris Mus musculus brevirostris NCBITaxon:1224 Proteobacteria purple bacteria purple bacteria and relatives purple non-sulfur bacteria purple photosynthetic bacteria purple photosynthetic bacteria and relatives Proteobacteria NCBITaxon:1232152 Escherichia coli O103:H11 Escherichia coli O103:H11 NCBITaxon:1266728 Mus musculus domesticus x M. m. molossinus Mus musculus domesticus x M. m. molossinus NCBITaxon:131567 cellular organisms cellular organisms NCBITaxon:1365258 Escherichia coli 151_06 Escherichia coli 151_06 NCBITaxon:1385377 Mus musculus gansuensis Mus musculus gansuensis NCBITaxon:1437010 Boreoeutheria Boreoeutheria NCBITaxon:149385 Salmonella enterica subsp. enterica serovar Hadar Salmonella enterica subsp. enterica serovar Hadar NCBITaxon:149539 Salmonella enterica subsp. enterica serovar Enteritidis Salmonella enterica serovar Enteritidis Salmonella enterica subsp. enterica serovar Enteritidis NCBITaxon:1549675 Galloanserae Galloanserae NCBITaxon:1637 Listeria Listeria NCBITaxon:1639 Listeria monocytogenes Listeria monocytogenes NCBITaxon:1643390 Mus musculus helgolandicus Mus musculus helgolandicus NCBITaxon:1773 Mycobacterium tuberculosis Mycobacterium tuberculosis NCBITaxon:1783272 Terrabacteria group Terrabacteria group NCBITaxon:179238 Mus musculus homourus Mus musculus homourus NCBITaxon:1879032 Mus musculus isatissus Mus musculus isatissus NCBITaxon:192953 Salmonella enterica subsp. enterica serovar Stanley Salmonella enterica subsp. enterica serovar Stanley NCBITaxon:194 Campylobacter Campylobacter NCBITaxon:197 Campylobacter jejuni Campylobacter jejuni NCBITaxon:2 Bacteria eubacteria Bacteria NCBITaxon:2157 Archaea The Archaea constitute a domain and kingdom of single-celled microorganisms Damion Dooley https://en.wikipedia.org/wiki/Archaea Archaea NCBITaxon:244317 Escherichia coli O128:H2 Escherichia coli O128:H2 NCBITaxon:244319 Escherichia coli O26:H11 Escherichia coli O26:H11 NCBITaxon:2697049 Severe acute respiratory syndrome coronavirus 2 2019-nCoV COVID-19 virus HCoV-19 Human coronavirus 2019 SARS-2 SARS-CoV2 SARS2 Severe acute respiratory syndrome coronavirus 2 NCBITaxon:2709072 Bat coronavirus RaTG13 Bat coronavirus Ra4991 Bat coronavirus isolate RaTG13 Bat coronavirus RaTG13 NCBITaxon:2759 Eukaryota eucaryotes eukaryotes Eukaryota NCBITaxon:28901 Salmonella enterica Salmonella enterica NCBITaxon:314145 Laurasiatheria Laurasiatheria NCBITaxon:314146 Euarchontoglires Euarchontoglires NCBITaxon:314147 Glires Rodents and rabbits Glires NCBITaxon:32524 Amniota amniotes Amniota NCBITaxon:33090 Viridiplantae Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants Viridiplantae NCBITaxon:33213 Bilateria Bilateria NCBITaxon:33317 Protostomia Protostomia NCBITaxon:33554 Carnivora carnivores Carnivora NCBITaxon:35531 Mus musculus bactrianus southwestern Asian house mouse Mus musculus bactrianus NCBITaxon:363569 Salmonella enterica subsp. enterica serovar Javiana Salmonella enterica subsp. enterica serovar Javiana NCBITaxon:376725 Escherichia coli O103:H2 Escherichia coli O103:H2 NCBITaxon:379583 Feliformia Feliformia NCBITaxon:379584 Caniformia Caniformia NCBITaxon:39442 Mus musculus musculus eastern European house mouse Mus musculus musculus NCBITaxon:397454 Escherichia coli O142:H6 Escherichia coli O142:H6 NCBITaxon:404394 Escherichia coli O26:NM Escherichia coli O26:NM NCBITaxon:404399 Escherichia coli O26 Escherichia coli O26 NCBITaxon:43738 Schizophora Schizophora NCBITaxon:452646 Neogale vison American mink mink Neogale vison NCBITaxon:46456 Mus musculus wagneri Mus musculus wagneri NCBITaxon:477815 Mus musculus musculus x M. m. domesticus Mus musculus musculus x M. m. domesticus NCBITaxon:477816 Mus musculus musculus x Mus musculus castaneus Mus musculus musculus x Mus musculus castaneus NCBITaxon:48409 Salmonella enterica subsp. enterica serovar Virchow Salmonella enterica subsp. enterica serovar Virchow NCBITaxon:543 Enterobacteriaceae Enterobacteriaceae NCBITaxon:54736 Salmonella bongori Salmonella bongori NCBITaxon:562 Escherichia coli E. coli Escherichia/Shigella coli Escherichia coli NCBITaxon:57486 Mus musculus molossinus Japanese wild mouse Mus musculus molossinus NCBITaxon:58055 Rhinolophidae Old World leaf-nosed bats Rhinolophidae NCBITaxon:590 Salmonella Salmonella NCBITaxon:59201 Salmonella enterica subsp. enterica Salmonella enterica subsp. enterica NCBITaxon:59477 Rhinolophus affinis intermediate horseshoe bat Rhinolophus affinis NCBITaxon:595 Salmonella enterica subsp. enterica serovar Infantis Salmonella enterica subsp. enterica serovar Infantis NCBITaxon:611 Salmonella enterica subsp. enterica serovar Heidelberg Salmonella enterica subsp. enterica serovar Heidelberg NCBITaxon:6447 Mollusca clam, squid, octopus molluscs mollusks Mollusca NCBITaxon:694009 Severe acute respiratory syndrome-related coronavirus Human coronavirus (strain SARS) SARS-like coronavirus SARS-related coronavirus Severe acute respiratory syndrome-related coronavirus NCBITaxon:7215 Drosophila <flies,genus> Drosophila fruit flies fruit fly Drosophila <flies,genus> NCBITaxon:7370 Musca domestica house fly Musca domestica NCBITaxon:7742 Vertebrata <vertebrates> Vertebrata vertebrates Vertebrata <vertebrates> NCBITaxon:7776 Gnathostomata <vertebrates> Gnathostomata jawed vertebrates Gnathostomata <vertebrates> NCBITaxon:7777 Chondrichthyes cartilaginous fishes fish fishes Chondrichthyes NCBITaxon:80274 Mus musculus gentilulus Mus musculus gentilulus NCBITaxon:816 Bacteroides Bacteroides NCBITaxon:8782 Aves birds Aves NCBITaxon:8825 Neognathae Neognathae NCBITaxon:8839 Anas platyrhynchos duck mallard mallard duck mallard ducks Anas platyrhynchos NCBITaxon:8930 Columbidae pigeons Columbidae NCBITaxon:9005 Phasianidae turkeys Phasianidae NCBITaxon:9031 Gallus gallus Gallus domesticus bantam chicken chickens Gallus gallus NCBITaxon:90371 Salmonella enterica subsp. enterica serovar Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium NCBITaxon:9091 Coturnix coturnix Common quail Coturnix coturnix NCBITaxon:9103 Meleagris gallopavo common turkey turkey wild turkey Meleagris gallopavo NCBITaxon:91561 Artiodactyla whales, hippos, ruminants, pigs, camels etc. Artiodactyla NCBITaxon:9397 Chiroptera bats Chiroptera NCBITaxon:947985 Mus musculus albula Mus musculus albula NCBITaxon:9605 Homo humans Homo NCBITaxon:9606 Homo sapiens human Homo sapiens NCBITaxon:9615 Canis lupus familiaris dog dogs Canis lupus familiaris NCBITaxon:9673 Viverridae civets Viverridae NCBITaxon:9681 Felidae cat family Felidae NCBITaxon:9685 Felis catus cat cats domestic cat Felis catus NCBITaxon:9688 Panthera Panthera NCBITaxon:9689 Panthera leo lion Panthera leo NCBITaxon:9694 Panthera tigris tiger Panthera tigris NCBITaxon:9796 Equus caballus domestic horse equine horse Equus caballus NCBITaxon:9825 Sus scrofa domesticus domestic pig Sus scrofa domesticus NCBITaxon:9895 Bovidae Bovidae NCBITaxon:9913 Bos taurus bovine cattle cow dairy cow domestic cattle domestic cow ox oxen Bos taurus NCBITaxon:991913 Escherichia coli O103:H25 Escherichia coli O103:H25 NCBITaxon:991915 Escherichia coli O121:H19 Escherichia coli O121:H19 NCBITaxon:991919 Escherichia coli O145:NM Escherichia coli O145:NM NCBITaxon:9922 Capra Capra NCBITaxon:9923 Capra aegagrus bezoar ibex wild goat Capra aegagrus NCBITaxon:9925 Capra hircus domestic goat goat goats Capra hircus NCBITaxon:9940 Ovis aries domestic sheep lambs sheep wild sheep Ovis aries NCBITaxon:9963 Caprinae Caprinae NCBITaxon:9973 Manis Manis NCBITaxon:9974 Manis javanica Javan pangolin Malayan pangolin Sunda pangolin Manis javanica NCBITaxon:9986 Oryctolagus cuniculus European rabbit Japanese white rabbit domestic rabbit rabbit rabbits Oryctolagus cuniculus NCBITaxon:9989 Rodentia rodent Rodentia NCBITaxon:genus genus genus NCBITaxon:species species species NCBITaxon:subspecies subspecies NCIT:85595 A method to determine microbial susceptibility to antibiotics wherein bacteria are inoculated onto agar plates and the antimicrobial agent diffused onto the agar plate from a filter paper disk. An approximate, but not exact, MIC is determined by the diameter of growth inhibition zones. This method has been found to have good correlation between in-vivo data and in-vitro data. Kirby-Bauer disk assay disk-diffusion method NCIT:85596 A method to determine microbial susceptibility to antibiotics in which a plastic strip impregnated with the antibiotic of interest is placed on an agar plate that has been inoculated with bacteria. The antibiotic diffuses from the strip producing a concentration gradient of drug on the agar. The point at which the elliptical shaped area of growth inhibition meets the strip is the minimum inhibitory concentration of the drug of interest. antimicrobial gradient method (E-test) NCIT:85701 A method to determine the minimum inhibitory concentration (MIC) of antibiotics in which growth media is pipetted into a multi-well plate. Each well contains a known concentration of drug which is inoculated with a known quantity of bacteria. The plate is incubated for a specified period of time and each well is assessed for bacterial cell growth. The drug concentration in the first well showing no growth is known as the MIC for that antibiotic. Minimum 2 mL total broth dilution volume. macro broth dilution method NCIT:C100128 A person that is associated with another person in some manner or action. Partner Partner NCIT:C100811 An individual who provides support to a pregnant individual. PREGNANCY PARTNER Pregnancy Partner Pregnancy Partner NCIT:C100812 A person with whom one has had sexual relations. SEXUAL PARTNER Sexual Partner Sexual Partner NCIT:C103180 A statement that defines conventions, guidelines, characteristics or methods for consistent data handling to facilitate exchange or processing of the data. This set of criteria are reviewed by and agreed upon by the user community or a governing body before they are released and adopted for use. Data Standard data standards Data Standard NCIT:C103245 A vial used to store specimens in a cryopreservative at very low temperatures. Cryovial Cryovial NCIT:C105370 The RNA component of the small (30S) subunit of prokaryotic ribosomes. Damion Dooley's note: this term was mistakenly placed in a list of GenEpiO diagnostic tests; in fact it references a material entity 16S Ribosomal RNA 16S rRNA Bacterial 16S RNA Bacterial 16S Ribosomal RNA Bacterial 16S rRNA Bacterial 16S RNA NCIT:C106515 The fluid which runs through a dialysis machine and captures, for discard or analysis, the excess water and waste from the blood stream through diffusion and ultrafiltration. DIALYSIS FLUID Dialysate Dialysis Fluid Dialysis Fluid NCIT:C106561 An indicator as to whether the female subject is pregnant during the study period. PREGST Pregnant During the Study Pregnant During the Study NCIT:C107103 An unexpected death without warning. Sudden Death Sudden Death, NOS Sudden Death NCIT:C110959 Indicates that no answer was given. Not Answered Not answered Not Answered NCIT:C111853 Unexpected death of an infant less than one year of age, whose cause of death is not immediately obvious prior to investigation. SUID Sudden Unexplained Infant Death Sudden Unexplained Infant Death NCIT:C111854 Unexpected death of a child over one year of age, which remains unexplained when all known and possible causes of death have been ruled out. Sudden Unexplained Death in Childhood Sudden Unexplained Death in Childhood NCIT:C111858 Death resulting from conditions or complications which are unique to pregnancy and occur during the antepartum, intrapartum, or postpartum period. Direct Maternal Death Direct Maternal Death NCIT:C111859 Death resulting from previously existing disease or a disease developing during pregnancy which was not associated with gestation, but which was aggravated by the unique physiologic changes of pregnancy. Examples of indirect deaths include those associated with epilepsy, diabetes, cardiac disease and hormone-dependent malignancies. Indirect Maternal Death Indirect Maternal Death NCIT:C111860 The death of a woman while pregnant or within 42 days of the end of the pregnancy, irrespective of the duration or anatomic site of the pregnancy, due to any cause related to or aggravated by the pregnancy or its management, but not from accidental or incidental causes. Maternal Death Maternal Mortality Maternal Mortality NCIT:C113122 A test tube, capillary tube, or other tube designed for the collection of blood. BCT Blood Collection Tube Blood Collection Tube NCIT:C113124 A blood collection tube that contains a vacuum, allowing it to draw blood through a needle to fill the tube. Evacuated Blood Specimen Collection Tube Evacuated Blood Specimen Collection Tube NCIT:C113419 A person who shares a house with another person. Housemate Housemate NCIT:C113609 Hepatic necrosis, inflammation, or scarring due to any cause that persists for more than 6 months. Manifestations may include signs and symptoms of cholestasis, portal hypertension, and/or abnormal liver function tests. Chronic Liver Disease Chronic_Liver_Disease Chronic Liver Disease NCIT:C113644 An identifying designation assigned to an individual that corresponds with their function. Person Role Person Role Title Role Title Title title Person Role Title NCIT:C114551 A title that describes the function of a designated group, governing body, or institution. Organization Role Organization Role NCIT:C114870 A fetus of 16-20 weeks gestational age that shows signs of life at birth but dies after delivery. Post-Natal Death at 16-20 Weeks Gestation Post-Natal Death at 16-20 Weeks Gestation NCIT:C114930 An age group comprised of infants delivered after full 37 weeks gestation whose 5 minute Apgar score was above 7, has no major congenital anomalies and was discharged home with mother without any additional diagnoses except for physiologic hyperbilirubinemia. Healthy Term Newborn Healthy Term Newborn NCIT:C114931 An age group comprised of healthy newborns whose only diagnoses are those related to prematurity. Healthy Preterm Newborn Healthy Preterm Newborn NCIT:C114938 An age group comprised of infants greater than or equal to 34 weeks, 0 days and less than 37 weeks, 0 days gestational age. Late Preterm Infant Near Term Infant Late Preterm Infant NCIT:C114939 An age group comprised of infants less than 28 weeks, 0 days gestational age. Extreme Immaturity Extremely Preterm Infant Extremely Preterm Infant NCIT:C114947 An age group comprised of infants greater than or equal to 42 weeks, 0 days gestational age. Post Dates Postmature Postterm Infant Postterm Infant NCIT:C115935 healthy Having no significant health-related issues. Healthy Well Healthy NCIT:C116117 A laboratory test to determine the concentration of a substance that will inhibit a biological or biochemical function, such as microorganism growth or enzymatic activity. Inhibitory Concentration Test Inhibitory Concentration Test NCIT:C116340 Irreversible absence of cortical and brain stem functioning. Brain Death Brain Death NCIT:C116518 Interventions or procedures not otherwise categorized. Other Intervention or Procedure Other Intervention or Procedure NCIT:C116772 Death of a live newborn during the first 7 days of life. Early Neonatal Death Early Neonatal Mortality Early Neonatal Death NCIT:C116773 Death of live newborn between 7and 27 days after birth. Late Neonatal Death Late Neonatal Mortality Late Neonatal Death NCIT:C117720 Symptoms, physical examination results, and/or laboratory test results related to the female reproductive system. Female Reproductive System Finding Female Reproductive System Finding NCIT:C118676 Fetal or infant death during the period of time that includes the antepartum, intrapartum, and neonatal stages. Perinatal Death Perinatal Mortality Perinatal Mortality NCIT:C118677 An age group comprised of infants greater than 28 weeks, 0 days and less than 34 weeks, 0 days. Very Preterm Infant Very Preterm Infant NCIT:C120592 Death of a live newborn during the first 24 hours of life Very Early Neonatal Death Very Early Neonatal Death NCIT:C121303 Death between 28 days and 1 year of life. Post Neonatal Death Post Neonatal Death NCIT:C121416 A response indicating that a person has lost their ability for fine movement: cannot button, write, eat, etc., or minor loss of sensitivity. Loss of Fine Movements Loss of fine movements Loss of Fine Movements NCIT:C12219 A human biological structure, fluid or other substance; excludes single molecular entities. Anatomic Structure, System, or Substance Anatomic Structures and Systems Anatomic Structure, System, or Substance NCIT:C1225 A bacterial toxin produced by Shigella dysenteriae and by some strains of E. coli that inhibits protein synthesis by blocking the interaction of ribosomal RNA with peptide elongation factors. The non-catalytic beta subunit of Shiga toxin may be useful as a fusion vector for induction of antigen-specific cytotoxic T lymphocyte responses. Shiga Toxin Shiga Toxin NCIT:C124295 Observed to be or have been pregnant. PREGNANT Pregnant Pregnant NCIT:C124600 A death of the embryo occurring inside the uterus. EARLY INTRAUTERINE DEATH Early IUD Early Intrauterine Death Early Intrauterine Death NCIT:C124643 A death of the fetus occurring inside the uterus. LATE INTRAUTERINE DEATH Late IUD Late Intrauterine Death Late Intrauterine Death NCIT:C12471 A general term comprising tissue that is not hardened or calcified; including muscle, fat, blood vessels, nerves, tendons, ligaments and fascia. SOFT TISSUE Soft Tissue soft tissue Soft Tissue NCIT:C125203 Death due to complications following an organ transplant. TRM Transplant Related Death Transplant Related Mortality Transplant-Related Death Transplant-Related Mortality Transplant-Related Mortality NCIT:C126054 The absence of disease or pathology. NON-PATHOLOGICAL Non-Pathological Non-Pathological NCIT:C127784 Any individual with whom the subject attends or attended the same school. SCHOOLMATE Schoolmate Schoolmate NCIT:C12801 An anatomical structure consisting of similarly specialized cells and intercellular matrix, aggregated according to genetically determined spatial relationships, performing a specific function. Normal Normal Tissue TISSUE Tissue Tissue, NOS Tissues tissue Tissue NCIT:C128042 An age group comprised of infants born alive with a gestational age between 32 to less than 37 weeks. Moderate to Late Preterm Infant Moderate to Late Preterm Infant NCIT:C128985 A laboratory test to determine the lowest concentration of a substance that will inhibit a biological or biochemical function, such as microorganism growth or enzymatic activity. NCIT offers this alternate definition which GenEpiO intends: "A measurement that specifies the minimum concentration of the agent at which organism growth was inhibited." MIC MIC Minimum Inhibitory Concentration Minimum Inhibitory Concentration Test Minimum Inhibitory Concentration Test Clinical and Laboratory Standards Institute MIC antimicrobial testing standards at http://em100.edaptivedocs.info/GetDoc.aspx?doc=CLSI%20M100%20S27:2017&scope=user NCIT:C12964 The supporting connective tissue of an organ. Connective and Soft Tissue Connective and Soft Tissue NCIT:C130200 An individual who is receiving a transplant of a solid organ. Solid Organ Transplant Recipient Solid Organ Transplantation Recipient Solid Organ Transplant Recipient NCIT:C131759 An individual receiving a bone marrow transplant. Bone Marrow Transplant Recipient Bone Marrow Transplantation Recipient Bone Marrow Transplant Recipient NCIT:C13229 A body part, organ or organ component that is formed during the embryonic stage of life of an organism. Embryologic Structure Embryonic Structure Embryonic Structure NCIT:C13235 An unborn or unhatched vertebrate in the later stages of development showing the main recognizable features of the mature being. FETUS Fetal Fetus fetus Fetus NCIT:C132450 A female who is married to a spouse with children whom are not biologically related to her. MOTHER, STEP Step Mother Stepmother Stepmother NCIT:C13308 Pertaining to, affecting, or associated with the liver. Hepatic hepatic Hepatic NCIT:C13347 Fluid withdrawn from a body cavity, organ, cyst, or tumor. ASPIRATE Aspirate aspirate Aspirate NCIT:C13442 An adjectival term used to specify a region of the body or other concepts associated with the body. Anatomy Qualifier Anatomy Qualifiers Anatomy Qualifier NCIT:C13717 Named locations of or within the body. Anatomic Location Anatomic Site Anatomic Sites Anatomical Location Anatomical_Location CDISC Location Site Topographic (Anatomic) Site Topographic Site Anatomic Site NCIT:C141241 An indication that death occurred on or within 90 days of a patient's initial admission to a hospital. Death During, or within 90 Days of, Index Hospital Admission Death Less than 90 Days or During Index Hospital Admission Death During, or within 90 Days of, Index Hospital Admission NCIT:C14139 A loss of any arm of immune functions, resulting in potential or actual increase in infections. This state may be reached secondary to specific genetic lesions, syndromes with unidentified or polygenic causes, acquired deficits from other disease states, or as result of therapy for other diseases or conditions. Immunocompromised Immunocompromised Host Immunocompromised Patient Immunosuppressed Immunosuppressed Host Immunosuppressed Patient immunocompromised Immunocompromised NCIT:C14182 A living organism that has membranous cell walls, requires oxygen and organic foods, and is capable of voluntary movement, as distinguished from a plant or mineral. ANIMAL Animal Animalia Animals Animal NCIT:C14197 A large order of insects having a single pair of wings and sucking or piercing mouths; includes true flies and mosquitoes and gnats and crane flies. Diptera Flies Diptera NCIT:C14227 A taxonomic class of arthropods that includes praying mantises, dragonflies, grasshoppers, true bugs, flies, bees, wasps, ants, butterflies, moths, and beetles. Insect Insecta Invertebrates, Insects Insect NCIT:C14250 A living entity. BiologicEntity Organism Organismal Organisms Taxon organism Organism NCIT:C14376 A non-taxonomic grouping of organisms based on a shared characteristic. Other Organism Groupings Other Organism Groupings NCIT:C14419 A population or type of organisms that is genetically different from others of the same species and possessing a set of defined characteristics. Organism Strain STRAIN Strain Strain Number strain Organism Strain NCIT:C147908 Any agent that can alter hormone levels or modulate hormone effects. Hormonal Therapy Agent Hormone Therapy Hormone Therapy Agent Hormone Therapy Agent NCIT:C147914 A plan of action intended to accomplish a specific goal. Strategy Strategy NCIT:C150895 A heterogeneous and variable aggregate of body fluids, tissues, cells, microorganisms, and other materials that are collected from a swab biospecimen collection procedure. SWABBED MATERIAL Swabbed Material Swabbed Material NCIT:C15189 The removal of tissue specimens or fluid from the living body for microscopic examination, performed to establish a diagnosis. BIOPSY BIOPSY_TYPE Biopsy Bx biopsy Biopsy NCIT:C15221 A procedure to remove toxic substances from the blood that is used in patients with end-stage chronic kidney disease or acute kidney failure. This includes hemodialysis and peritoneal dialysis. Dialysis Dialysis Procedure Dialysis Therapy dialysis Dialysis NCIT:C15248 A therapeutic procedure used in patients with kidney failure. It involves the extracorporeal removal of harmful wastes and fluids from the blood using a dialysis machine. Following the dialysis, the blood is returned to the body. Artificial Kidney Dialysis Extracorporeal Dialysis HEMODIALYSIS Hemodialysis Kidney Dialysis Renal Dialysis Hemodialysis NCIT:C15258 Inoculating an individual with either killed or live agents to prevent contraction of a disease. Immunization immunization Immunization NCIT:C15306 Prevention of disease or mental disorders in susceptible individuals or populations through promotion of health, including mental health, and specific protection, as in immunization, as distinguished from the prevention of complications or after-effects of existing disease. PRIMARY PREVENTION Prevention, Primary Primary Prevention Primary Prevention NCIT:C15310 The removal of excess fluid via needle puncture from any body cavity. Paracentesis paracentesis Paracentesis NCIT:C15327 An invasive procedure in which a hollow needle is introduced through an intervertebral space in the lower back to access the subarachnoid space in order to sample cerebrospinal fluid or to administer medication. LP Lumbar Puncture Spinal Tap lumbar puncture spinal tap Lumbar Puncture NCIT:C15329 A diagnostic or treatment procedure performed by manual and/or instrumental means, often involving an incision and the removal or replacement of a diseased organ or tissue; of or relating to or involving or used in surgery or requiring or amenable to treatment by surgery. Operation SURGERY Surgery Surgery Type Surgical Surgical Intervention Surgical Interventions Surgical Procedure Surgical Procedures Surgically Type of Surgery surgery Surgical Procedure NCIT:C15346 Administration of vaccines to stimulate the host's immune response. This includes any preparation intended for active immunological prophylaxis or treatment. Vaccination vaccination Vaccination NCIT:C15360 Chemotherapy that is administered subsequent to the main treatment plan to minimize or prevent disease recurrence. Adjuvant Adjuvant Chemotherapy Adjuvant Chemotherapy NCIT:C15384 An intentional cut made to an individual's body with the intent of performing a diagnostic or therapeutic intervention. Incision Incisional Otomy Surgical Incision incision Surgical Incision NCIT:C15392 The removal of excess fluid via needle puncture from the thoracic cavity. Chest Aspiration Pleural Cavity Tap Pleural Tap Pleurocentesis Puncture of Pleural Cavity for Aspiration THORACENTESIS Thoracentesis Thoracic Paracentesis thoracentesis Thoracentesis NCIT:C15416 Deliberate stimulation of a host's immune response via administration of antigens or immunologic adjuvants. Active Immunization Active Immunization NCIT:C154851 A male that is related to a child or children through marriage to their biological parent. FATHER, STEP Step Father Stepfather Step Father NCIT:C15511 Treat infections with antibacterial, antifungal, antiparasite or antiviral drugs Infection Prophylaxis and Management Infectious Diseases / Treatment, General Treatment of Infectious Disease infectious diseases treatment management, infection prophylaxis Infection Prophylaxis and Management NCIT:C15631 Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue. ASPIRATION Aspiration aspiration Aspiration NCIT:C15632 The use of synthetic or naturally-occurring chemicals for the treatment of diseases. CHEMO CHEMOTHERAPY Chemo Chemotherapy Chemotherapy (NOS) Chemotherapy, Cancer, General chemotherapy Chemotherapy NCIT:C156427 A death attributed to the progression of a cancer-related pathologic condition. Cancer Death Cancer Related Cancer Related Death Cancer-Related Death Cancer-Related Death NCIT:C156428 A death attributed to any cause other than the progression of a cancer-related pathologic condition. Non-Cancer Death Non-Cancer Related Non-Cancer Related Death Not Cancer Related Non-Cancer Related Death NCIT:C15655 Any surgery performed inside the thoracic cavity. Chest Surgery Thoracic Surgery Thoracic Surgical Procedure Thoracic Surgical Procedures Thoracic Surgical Procedure NCIT:C15657 General term for hemodialysis, plasmapheresis, blood transfusions, and related procedures involving autologous removal, alteration, and replacement of patients' blood or blood components. Blood Treatment Hematologic Procedure Therapeutic Procedures Hematopoietic System Blood Treatment NCIT:C156660 A non-neoplastic or neoplastic disorder that affects the genitourinary system. Genitourinary Disorder Genitourinary System Disorder Urogenital Disease Genitourinary System Disorder NCIT:C15675 Any therapy that is administered to augment or stimulate other treatment modalities or to minimize or prevent disease recurrence subsequent to the main treatment plan. AJ-Adjuvant Therapy Adjuvant Therapy adjunct therapy adjunctive therapy adjuvant therapy Adjuvant Therapy NCIT:C157332 An individual who is receiving or has received a transplant of a kidney. Kidney Transplant Recipient Kidney Transplantation Recipient Kidney Transplant Recipient NCIT:C157740 Surgical procedures targeted at minimizing or eliminating a neoplastic process. Cancer Surgery Cancer Surgery NCIT:C15843 Therapeutic, nutritional, environmental, social and/or behavioral interventions at the societal, community, organizational or individual levels to reduce, modify or stop the course of a disease. PREVENTATIVE PRYLX Prevention Prevention Measures Preventive Intervention Prophylaxis prevention prophylaxis Preventive Intervention NCIT:C159659 An individual receiving a transplant. Transplant Recipient Transplantation Recipient Transplant Recipient NCIT:C15986 Treatment of disease through the use of drugs. Drug Therapy Pharmaceutical Therapy Pharmaceutical Therapy, NOS Pharmacological Treatment Pharmacological Treatments Pharmacotherapy Treatment With Medication drug therapy Pharmacotherapy NCIT:C16118 Treatment of human immunodeficiency virus (HIV) infections with medications that target the virus directly, limiting the ability of infected cells to produce new HIV particles. AIDS anti-HIV therapy Anti-HIV Therapy therapy, AIDS anti-HIV therapy, anti-HIV Anti-HIV Therapy NCIT:C16119 Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function. Antiviral Therapy Infectious Diseases / Treatment, Viral Treatment of Infectious Diseases, Viral treatment of viral infectious disease Antiviral Therapy NCIT:C161420 Any individual related biologically to another individual and considered immediate family as in the case of a parent, sibling or child. First Degree Biological Relative RELATIVE, BIOLOGICAL, FIRST DEGREE First Degree Biological Relative NCIT:C16143 A facility where items can be deposited for storage or safekeeping. Bank Repository Repository NCIT:C161601 A categorization of surgical procedures by type or purpose. PROCEDURE_TYPE Surgical Procedure by Type Surgical Procedure by Type NCIT:C16203 Any specific activity undertaken during the course of a clinical study or research protocol. Clinical or Research Activity Clinical or Research Activity NCIT:C16205 The actions of prevention, treatment, and management of illness and the preservation of mental and physical well-being through the services offered by the medical and allied health professions. Health Care Activity Healthcare Healthcare Activity Healthcare Activity NCIT:C16212 Any intervention for management of a malignant neoplasm. Cancer Therapeutic Procedure Cancer Therapy Cancer Treatment Malignant Neoplasm Therapy Malignant Neoplasm Treatment anticancer therapy Cancer Therapeutic Procedure NCIT:C16268 An age group comprised of individuals 65 years of age and older. Aged 65 and Over ELDERLY Elderly Elderly (Over 65) Senior Citizen Elderly NCIT:C16326 The actions or reactions of an object or organism, usually in relation to the environment or surrounding world of stimuli. Attitude Behavior Behavioral Conduct Behavior NCIT:C1636 Synthetically made hormones possessing the steroid ring system; e.g., androgens, estrogens, and adrenocortical hormones. Steroid Hormone Synthetic Steroids Therapeutic Steroid Hormone steroid drug Therapeutic Steroid Hormone NCIT:C16423 An age group comprised of individuals who are not yet an adult. The specific cut-off age will vary by purpose. CHILD Child Children Children (0-21) Child NCIT:C165131 Study Country Code StudyCountry.countryCode Study Country Code NCIT:C165587 A sample containing a mixture of multiple individual specimens of interest that were collected in a study. Composite Sample Pooled Pooled Sample Pooled Specimen Pooled Sample NCIT:C16576 A person who belongs to the sex that normally produces ova. The term is used to indicate biological sex distinctions, or cultural gender role distinctions, or both. F FEMALE Female female Female NCIT:C165792 A male foster parent. Foster Father Foster Father NCIT:C165793 A female foster parent. Foster Mother Foster Mother NCIT:C166092 The biological father of the offspring of the female subject. Biological Father of Subject's Child FATHER, BIOLOGICAL OF SUBJECT'S CHILD Biological Father of Subject's Child NCIT:C166093 The biological mother of the offspring of the male subject. Biological Mother of Subject's Child MOTHER, BIOLOGICAL OF SUBJECT'S CHILD Biological Mother of Subject's Child NCIT:C166114 The male who supplied the sperm or the female who supplied the egg which resulted in one's conception. Biological Parent Natural Parent Biological Parent NCIT:C166116 A non-biological parent through current or prior marriage to the subject's biological or legal parent. Step Parent Step Parent NCIT:C166129 A parent in the parent-child relationship established by a legal adoption proceeding. Adoptive Parent Adoptive Parent NCIT:C166133 A male parent in the parent-child relationship established by a legal adoption proceeding. Adoptive Father Adoptive Father NCIT:C166134 A female parent in the parent-child relationship established by a legal adoption proceeding. Adoptive Mother Adoptive Mother NCIT:C166165 A death that is considered to be causally linked to a treatment. TRM Treatment-Related Mortality Treatment-Related Mortality NCIT:C16632 Any demarcated area of the Earth; may be determined by both natural and human boundaries. Area Geographic Area Geographic Location Geographic Region Region Geographic Area NCIT:C16729 Any disease or condition resulting in postnatal death before age 1 yr. (NCI) Infant Death Infant Mortality Infant Mortality Total Infant Mortality NCIT:C16731 An age group comprised of infants during the first month after birth. NEONATE Neonatal Neonate Newborn Newborn NCIT:C16742 Any object, or item of electrical or electronic equipment, which is designed to carry out a specific function or set of functions. Instrument Instrumentation Instrumentation NCIT:C16830 Any physical object that is useful for prevention, diagnosis, monitoring, or treatment of disease or other conditions. DEVICE Device Medical Device Medical Devices medical device Medical Device NCIT:C168498 A difficulty or problem that occurs at or just after delivery of an infant that can jeopardize the health of the infant. Neonatal Complication Neonatal Complications Neonatal Complication NCIT:C16866 A representation of something, often idealized or modified to make it conceptually easier to understand. Model Model System Modeling System Models model Model NCIT:C168830 An indication that the mortality of the individual was related to the stem cell treatment. Mortality related to Stem Cell Treatment Mortality related to Stem Cell Treatment NCIT:C168970 An indication that the subject has died due to the progression of their disease. Death due to Disease Progression Disease Progression Terminal Disease Progression Death due to Disease Progression NCIT:C16960 A person who receives medical attention, care, or treatment, or who is registered with medical professional or institution with the purpose to receive medical care when necessary. LAY USER/PATIENT PATIENT PT Patient Patients patient Patient NCIT:C17005 A group of individuals united by a common factor (e.g., geographic location, ethnicity, disease, age, gender) Group Population Population Group Subpopulation population Population Group NCIT:C171087 A word or phrase that imparts a distinctive characteristic or attribute to the word or phrase it is modifying. Person/Individual Attribute Person/Individual Attribute NCIT:C171256 A manufactured object designed for non-medical use. Non-Medical Object or Device Non-Medical Object or Device NCIT:C171550 Pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is characterized by the presence of ground glass opacities on CT scan images. COVID-19-Associated Pneumonia SARS-CoV-2 -Associated Pneumonia COVID-19-Associated Pneumonia NCIT:C171551 Acute respiratory distress syndrome caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19-Associated Acute Respiratory Distress Syndrome SARS-CoV-2-Associated Acute Respiratory Distress Syndrome COVID-19-Associated Acute Respiratory Distress Syndrome NCIT:C171562 Coagulation disorder caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19-Associated Coagulation Disorder COVID-19-Associated Coagulopathy SARS-CoV-2-Associated Coagulation Disorder SARS-CoV-2-Associated Coagulopathy COVID-19-Associated Coagulation Disorder NCIT:C17357 Characteristics of people that are socially constructed, including norms, behaviors, and roles based on sex. As a social construct, gender varies from society to society and can change over time. (Adapted from WHO.) Gender gender Gender NCIT:C173621 Inhaling the vapor produced by an electronic cigarette or similar device. Vape Vaping Vaping NCIT:C173641 A biospecimen collected from the rectum by swabbing. Rectal Swab Rectal Swab Specimen Rectal Swab Specimen NCIT:C173767 A plan used to minimize the effects of a deleterious phenomenon. Mitigation Strategy Mitigation Strategy NCIT:C173768 A method used by an individual to be kept apart in seclusion from others for a period of time in an attempt to minimize the risk of transmission of an infectious disease. Self-Isolation Self-Isolation NCIT:C17445 The primary person in charge of the care of a patient, usually a family member or a designated health care professional. CAREGIVER Caregiver Caretaker caregiver Caregiver NCIT:C17456 Experimental Model Experimental Models, Other Experimental Model NCIT:C17471 The time of life between childhood and maturity. This period overlaps with adolescence. Youth Youth 10-21 Youth NCIT:C17598 A device which is an artificial substitute for a missing body part or function; used for functional or cosmetic reasons, or both. Prostheses Prosthesis prosthesis Prosthesis NCIT:C17600 An age group comprised of humans who have reached reproductive age. ADULT Adult Adult Human (21+) Human, Adult Adult NCIT:C17627 A portion of an absorbent material attached to one end of a small stick for the purpose of applying or collecting material. A tuft of material on the end of a stick for applying solutions and suspensions Emma Griffiths SWAB Swab Swab NCIT:C17734 Population groups with an increased likelihood of a disease or other health issue, eg smoking, drug use, teen pregnancy. At-Risk Population Population at Risk At-Risk Population NCIT:C17828 An activity occurring within an organism, between organisms or among organisms and the mechanisms underlying such events. Biological Function Biological Process Biological Process NCIT:C18020 Any procedure or test to diagnose a disease or disorder. Diagnostic Method Diagnostic Procedure Diagnostic Technique Diagnostic Test diagnostic procedure diagnostic technique Diagnostic Procedure NCIT:C188268 The name or names between a person's first name and their surname (last name, family name). Middle Name Middle Name NCIT:C18850 infant death due to causes other than AIDS Infant Mortality, Non-AIDS Infant Mortality, Non-AIDS NCIT:C19067 An identifying designation. Title title Title NCIT:C1908 An organic or inorganic substance, element, isotope, food or other materials derived from microorganism, plant, or animal sources. They can be used for the prevention, diagnosis, treatment or research of disease states, for industrial purposes, or for the promotion or maintenance of organism viability or health. Drug, Food, Chemical or Biomedical Material Drug, Food, Chemical or Biomedical Material NCIT:C1909 Any natural, endogenously-derived, synthetic or semi-synthetic compound with pharmacologic activity. A pharmacologic substance has one or more specific mechanism of action(s) through which it exerts one or more effect(s) on the human or animal body. They can be used to potentially prevent, diagnose, treat or relieve symptoms of a disease. Formulation specific agents and some combination agents are also classified as pharmacologic substances. Agent DRUG Drug Drug Substance Pharmaceutical Agent Pharmaceuticals Pharmacologic Agent Pharmacologic Substance Pharmacological Substance drug therapeutic agents therapeutic_agents Pharmacologic Substance NCIT:C19148 In Vivo Model In Vivo Model NCIT:C19157 A part of a thing, or of several things, taken to demonstrate or to determine the character of the whole, e.g. a substance, or portion of material obtained for use in testing, examination, or study; particularly, a preparation of tissue or bodily fluid taken for examination or diagnosis. Research Specimen Sample Specimen Specimen NCIT:C19160 A grouping of occupations and fields of study. Occupation or Discipline Occupation or Discipline NCIT:C19238 A manufactured object that is used to perform diagnostic, therapeutic or research activities. Diagnostic, Therapeutic, and Research Equipment Diagnostic, Therapeutic, or Research Equipment Equipment Hardware Diagnostic, Therapeutic, or Research Equipment NCIT:C19239 infant death due to AIDS AIDS, Infant Mortality Infant Mortality, AIDS Infant Mortality, AIDS NCIT:C19254 Occupations within the field of medicine. Health Care Occupation Medical Occupation Medical Occupation NCIT:C1932 A chemical that influences the properties of another chemical or biological function. (NCI) Chemical Modifier Modifier Chemical Modifier NCIT:C19332 The distinguishing qualities or prominent aspects of an individual person. The distinguishing qualities or prominent aspects of an individual person. Personal Personal Attribute Subject Characteristics Personal Attribute personal attribute NCIT:C19498 A physical object, or electronic counterpart, that is characterized by containing writing which is meant to be human-readable. Document Document Type documentation Document NCIT:C19683 The observable response of a person. Personal Behavior Personal Conduct Personal Behavior NCIT:C19988 A biologic function, activity, or process involving either specialized organ functions, individual organs, organ systems, body parts, or whole organisms. Organism-Level Process Organismal Process Physiological Process Organismal Process NCIT:C20108 An alphanumeric system designed to identify countries. The ISO 3166 standard includes a two letter representation, a three letter representation, and a 3 number representation. The last two are identical to the UN system. The US State Department system maintains a separate two letter representation code set. Country Country Code countryCode Country Code NCIT:C20181 An organizational header for concepts representing mostly abstract entities. Conceptual Entity Conceptual Entity NCIT:C20189 A distinguishing quality or prominent aspect of a person, object, action, process, or substance. Property or Attribute Property or Attribute NCIT:C20192 A listing of occupations that don't fall under another major heading. Miscellaneous Occupation Miscellaneous Occupation NCIT:C20197 A person who belongs to the sex that normally produces sperm. The term is used to indicate biological sex distinctions, cultural gender role distinctions, or both. Human, Male M MALE Male male Male NCIT:C20200 The result of an action. Outcome Result outcome result Outcome NCIT:C20587 Subgroups of populations based on age. Age Group Age Group NCIT:C211 Corticosteroids Therapeutic Corticosteroid corticosteroid Therapeutic Corticosteroid NCIT:C21173 A Reproductive System Process involves a function of cellular, cell, or tissue components of the organ system involved in generation of offspring that includes the ovaries, fallopian tubes, uterus, cervix, and vagina in women or the prostate, testes, and penis in men. Reproductive Process Reproductive System Process Reproductive Process NCIT:C21480 A person related by blood or marriage. RELATIVE Relation Relative Relative NCIT:C21481 Any relative who is one meiosis away from a particular individual in a family; a relative with whom one half of an individual's genes is shared (i.e., parent, sibling, offspring) (from Genetics Home Reference glossary) FDR First Degree Relative RELATIVE, FIRST DEGREE first-degree relative First Degree Relative NCIT:C21514 Terms used to indicate units of time or other terms associated with time. Temporal Qualifier Temporal Qualifier NCIT:C2364 Pharmacological agents which affect the function of the adrenal glands. Adrenal Agent Adrenal Drugs Adrenal Agent NCIT:C25155 The event of being born. Birth Born Delivery Birth NCIT:C25160 A large and densely populated urban area; a city specified in an address. City City NCIT:C25162 A symbol or combination of symbols which is assigned to the members of a collection. CODE Code Code Name Coding System code Code NCIT:C25164 The particular day, month and year an event has happened or will happen. Date Date (MM/DD/YYYY) Dated date Date NCIT:C25174 A male parent. FATHER Father Father NCIT:C25179 The condition of being treated as a patient in a hospital. HOSPITALIZATION Hospitalization Hospitalized Hospitalization NCIT:C25182 A patient who is residing in the hospital where he is being treated. Inpatient Inpatient NCIT:C25189 A female parent. MOTHER Mother Mother NCIT:C25190 A human being. Individual Person Person NCIT:C25191 A word or group of words indicating the identity of a person usually consisting of a first (personal) name and a last (family) name with an optional middle name. In some cultural traditions the family name comes first. Contact Name Individual's Name Name Name of Person Person Name Person.name Person Name NCIT:C25193 The principal activity that a person does to earn money. EMPJOB Employee Job Employment Category Job OCCUPATION Occupation Occupation Type Occupation NCIT:C25198 Anything (e.g., a document) providing permanent evidence of or information about past events. Record record Record NCIT:C25218 An activity that produces an effect, or that is intended to alter the course of a disease in a patient or population. This is a general term that encompasses the medical, social, behavioral, and environmental acts that can have preventive, therapeutic, or palliative effects. Intervention Intervention Strategies Intervention or Procedure Interventional Procedure intervention interventionDescription procedure treatment type treatment_type Intervention or Procedure NCIT:C25251 Occurring first in time or sequence; original; of greatest rank or importance or value. Primary Primary NCIT:C25254 Advancing in extent or severity. Progressive Progressive NCIT:C25269 Exhibiting the symptoms of a particular disease. Currently has symptoms Is_Symptomatic SYMPTOMS Symptomatic symptomatic Symptomatic NCIT:C25294 Any procedure that involves testing or manipulating a sample of blood, urine, or other body substance in a laboratory setting. Lab Test Lab Tests Laboratory Procedure Laboratory Test Test Tests lab exam lab_exam laboratory test laboratory_test Laboratory Procedure NCIT:C25337 A numeral or string of numerals expressing value, quantity, or identification. Number Numeric Numerical number {Number} Number NCIT:C25341 A position, site, or point in space where something can be found. LOC Location Location NCIT:C25381 A woman's surname before marriage. Maiden Maiden Name Maiden Name NCIT:C25392 A person, enterprise, or entity that produces finished goods. MANUF MANUFACTURER Make Maker Manufacturer Manufacturer Name Manufacturing Manufacturer Manufacturer NCIT:C25407 A standardized representation of the location of a person, business, building, or organization. Address Physical Address physicalAddress Address NCIT:C25414 Pertaining to a portion of the whole; any one of two or more samples of something, of the same volume or weight. Aliquot Aliquot NCIT:C25447 The distinguishing qualities or prominent aspect of a person, object, action, process, or substance. characteristic NCIT:C25464 A collective generic term that refers here to a wide variety of dependencies, areas of special sovereignty, uninhabited islands, and other entities in addition to the traditional countries or independent states. COUNTRY Country Country http://purl.obolibrary.org/obo/GEO_000000396 NCIT:C25499 Something that happens at a given place and time. Event Event NCIT:C25577 Nearest to the present. Most Recent Most Recent NCIT:C25610 diseased Caused by or altered by or manifesting disease or pathology. PATHOLOGICAL Pathologic sick Pathologic NCIT:C25621 Any system designed to expedite the sorting and delivery of mail by assigning a series of alphanumeric codes to each delivery area. Also used to refer to any individual delivery area code. Postal Code Postal code Postal Code NCIT:C25632 lookup:http://purl.obolibrary.org/obo/GAZ_00000448 A region, district or division of a country; a tract; a portion a state, especially one remote from the capital. Province Province NCIT:C25667 Derived as a result of a primary condition; not direct or immediate; of second rank or importance or value. Secondary Secondary NCIT:C25677 The spatial arrangement of something as distinct from its substance. SHAPE Shape Shape NCIT:C25690 The street name and building number where a person or organization can be found. STREET Street Street Address Street Address NCIT:C25709 A named quantity in terms of which other quantities are measured or specified, used as a standard measurement of like kinds. U UOM Unit Unit of Measure Unit of Measurement Unit(s) Units medication units of measure medication_units_of_measure unit unit(s) Unit of Measure NCIT:C25717 The state or condition of being living or deceased; also includes the case where the vital status is unknown. SURVSTAT Survival Status Vital Status Vital Status (at date of last contact) Vital_Status vital status vital_status Vital Status [A-Za-z0-9]+([_.\-][A-Za-z0-9]+)*\@[A-Za-z0-9]+([.\-][A-Za-z0-9]+){1,3} NCIT:C25720 /^(:<zip>\d{5}(-\d{4})?)/, $zip A system designed to expedite the sorting and delivery of mail by assigning a series of numbers to each delivery area in the United States. Also used to refer to any individual delivery area code. ZIP Zip Code Zip Code NCIT:C25741 A doctor; a person who has been educated, trained, and licensed to practice the art and science of medicine; a practitioner of medicine, as contrasted with a surgeon. DR Doctor PHYSICIAN Physician physician Physician NCIT:C25742 The state or condition of having a developing embryo or fetus in the body (uterus), after union of an ovum and spermatozoon, during the period from conception to birth. Gestation PREGNANCY Pregnancy pregnancy Pregnancy NCIT:C25796 Organism or cells with a nucleus separated from the cytoplasm by a two membrance nuclear envelope and compartmentalization of function into distinct cytoplasmic organelles. Eukaryota Eukaryote Eukaryotida Eukaryota NCIT:C26323 A neoplastic or non-neoplastic disorder that affects the production and proliferation of the hematopoietic cells including lymphoid cells, the synthesis of hemoglobin, and/or the mechanisms of coagulation. Blood Disease Blood Disorder Hematologic Disorder Hematologic and Lymphocytic Disorder Hematological Disorder Hematologic and Lymphocytic Disorder NCIT:C26324 A disorder that arises from the bone marrow or lymphoid system and is characterized by the absence of a clonal cellular component. It rarely progresses to a malignant neoplasm. Non-Malignant Hematologic and Lymphocytic Disorder Non-Neoplastic Hematologic and Lymphocytic Disorder nonmalignant hematologic disorder Non-Neoplastic Hematologic and Lymphocytic Disorder NCIT:C26548 A protein, RNA or a complex that contains proteins and/or RNA. Gene Product Genome Encoded Entity Gene Product NCIT:C26549 The product of so-called RNA genes; a functional RNA represents the final product of a gene rather than a transient molecule that will be translated into protein. Functional RNA Non-Coding RNA Noncoding RNA Untranslated RNA ncRNA Untranslated RNA NCIT:C26726 A disorder resulting from the presence and activity of a microbial, viral, fungal, or parasitic agent. It can be transmitted by direct or indirect contact. Clinical Infection ID INFECTION Infection Infectious Infectious Disease Infectious Diseases and Manifestations Infectious Disorder Unspecified Infection infection Infectious Disorder NCIT:C26871 A non-neoplastic or neoplastic disorder that affects the respiratory system. Representative examples include pneumonia, chronic obstructive pulmonary disease, pulmonary failure, lung adenoma, lung carcinoma, and tracheal carcinoma. Disorder of Respiratory System Respiratory Disorder Respiratory System Disorder Unspecified Respiratory Problem Respiratory System Disorder NCIT:C27197 Acute inflammation of the lung parenchyma caused by viruses, bacteria, fungi, radiation treatment, or exposure to chemicals. Signs and symptoms include cough, shortness of breath, fevers, chills, chest pain, headache, sweating, and weakness. Acute Pneumonia Acute Pneumonia NCIT:C27550 A non-neoplastic disorder that affects the gastrointestinal tract, anus, liver, biliary system, and pancreas. Representative examples include infections, ulcers, cirrhosis, and diverticulosis. Non-Neoplastic Digestive System Disorder Non-Neoplastic Gastrointestinal Disorder Non-Neoplastic Gastrointestinal System Disorder Non-Neoplastic Digestive System Disorder NCIT:C27551 A term that refers to the classification of a disorder according to the anatomic site that is involved in the pathologic process. Disease by Site Disorder by Site Disorder by Site NCIT:C27557 A lung disorder not caused by a neoplasm. Representative examples include chronic obstructive pulmonary disease, atelectasis, lung infections, pulmonary fibrosis, and pneumoconiosis. Non-Neoplastic Lung Disorder Non-Neoplastic Pulmonary Disorder Non-neoplastic Lung Disorders Non-neoplastic Pulmonary Disease Non-neoplastic Pulmonary Diseases Non-Neoplastic Lung Disorder NCIT:C27583 Infectious Disorder by Site Infectious Disorder by Site NCIT:C27669 A non-neoplastic or neoplastic disorder that affects the respiratory system or the thoracic organs. Respiratory and Thoracic Disease Respiratory and Thoracic Disorder Respiratory, Thoracic, and Mediastinal Disease Respiratory, Thoracic, and Mediastinal Disorder Respiratory and Thoracic Disorder NCIT:C27954 An age group comprised of juveniles between the onset of puberty and maturity; in the state of development between puberty and maturity. ADOLESCENT Adolescent Adolescents Adolescent NCIT:C27956 An age group comprised of individuals between one month and two years of age. INFANT Infant Infant NCIT:C27992 An adjectival term used to specify and describe a disease appearance or processes. Disease Qualifier Disease Qualifier NCIT:C27993 A term that helps define and render another concept unique. General Modifier General Qualifier General Qualifiers General Qualifier NCIT:C28102 Disease Clinical Qualifier Disease Clinical Qualifier NCIT:C28147 An organism in its initial stage of development following fertilization. The human embryonic period lasts approximately eight weeks, during which time organogenesis takes place. EMBRYO Embryo Embryologic Human Embryo embryo Embryo NCIT:C28193 A group of signs, symptoms, and clinicopathological characteristics that may or may not have a genetic basis and collectively define an abnormal condition. Syndrome syndrome Syndrome NCIT:C28221 The collection of blood from a vein, most commonly via needle venipuncture. Phlebotomy Venipuncture phlebotomy venipuncture Phlebotomy NCIT:C28293 A patient who comes to a healthcare facility for diagnosis or treatment but is not admitted for an overnight stay. Outpatient outpatient Outpatient NCIT:C28554 deceased The cessation of life. DEAD DEATH DIED Dead Death Death NOS Deceased Died EXPIRED EXPIRED/DEATH Patient Deceased dead deceased Dead deceased NCIT:C2902 A condition in which there is a deviation from or interruption of the normal coagulation properties of the blood. Coagulation Defect Coagulation Disorder Coagulopathy Coagulopathy, specify Coagulation Disorder NCIT:C2931 A non-neoplastic or neoplastic disorder affecting the heart or the vessels (arteries, veins and lymph vessels). Representative examples of non-neoplastic cardiovascular disorders are endocarditis and hypertension. Representative examples of neoplastic cardiovascular disorders are endocardial myxoma and angiosarcoma. Cardiovascular Disease Cardiovascular Disease (CVD) Cardiovascular Disorder Cardiovascular Disorder, NOS Cardiovascular_Disease Disorder of Cardiovascular System Cardiovascular Disorder NCIT:C2959 Any disease or disorder that occurs during the course of, or because of, another disease, treatment, or procedure. Complication Complications Medical Complication complication Complication NCIT:C296 Bacterial Toxin bacterial toxin Bacterial Toxin NCIT:C2990 A non-neoplastic or neoplastic disorder that affects the gastrointestinal tract, anus, liver, biliary system, and pancreas. Digestive Disease Digestive System Disease Digestive System Disorder Disorder of Digestive System GI Disorder Gastrointestinal Disorder Gastrointestinal System Disease Gastrointestinal System Disorder Unspecified Gastrointestinal Problem stomach or intestinal disorder Digestive System Disorder NCIT:C2991 Any abnormal condition of the body or mind that causes discomfort, dysfunction, or distress to the person affected or those in contact with the person. The term is often used broadly to include injuries, disabilities, syndromes, symptoms, deviant behaviors, and atypical variations of structure and function. Diagnosis Disease Disease or Disorder Disease or Disorder, Non-Neoplastic Diseases Diseases and Disorders Disorder Disorders Other Disease condition disease disease term disease type disease_term disease_type disorder Disease or Disorder NCIT:C30103 Subject to little fluctuation; showing little if any change. STABLE Stable Stable NCIT:C3079 A non-neoplastic or neoplastic disorder that affects the heart and/or the pericardium. Representative examples include endocarditis, pericarditis, atrial myxoma, cardiac myeloid sarcoma, and pericardial malignant mesothelioma. Cardiac Disease Heart Disease Heart Disorder Heart trouble Unspecified Heart Problem Heart Disorder NCIT:C308 Any substance that induces, enhances, restores or suppresses the host's immune system, or an agent that utilizes or is derived from a component of the immune system. BRM Biological Response Modifier Biomodulators Immune Mediators Immune Modulators Immune Regulators Immunomodulating Agent Immunomodulators Immunomodulatory Agent Immunopotentiators Immunotherapeutic Agent Immunotherapy Immunotherapy Agent Immunotherapeutic Agent NCIT:C3149 A neoplastic or non-neoplastic condition affecting the kidney. Representative examples of non-neoplastic conditions include glomerulonephritis and nephrotic syndrome. Representative examples of neoplastic conditions include benign processes (e.g., renal lipoma and renal fibroma) and malignant processes (e.g., renal cell carcinoma and renal lymphoma). Kidney Disease Kidney Disorder Kidney disease Renal Disease Renal Disorder Renal Disorder, NOS Kidney Disorder NCIT:C3196 A non-neoplastic or neoplastic disorder that affects the liver parenchyma and intrahepatic bile ducts. Representative examples of non-neoplastic disorders include hepatitis, cirrhosis, cholangitis, and polycystic liver disease. Representative examples of neoplastic disorders include hepatocellular adenoma, hepatocellular carcinoma, intrahepatic cholangiocarcinoma, lymphoma, and angiosarcoma. Hepatic Disorder Liver Disease Liver Disorder Liver and Intrahepatic Bile Duct Disorder Liver disease Liver and Intrahepatic Bile Duct Disorder NCIT:C3198 A non-neoplastic or neoplastic disorder affecting the lung. Representative examples of non-neoplastic disorders include chronic obstructive pulmonary disease and pneumonia. Representative examples of neoplastic disorders include benign processes (e.g., respiratory papilloma) and malignant processes (e.g., lung carcinoma and metastatic cancer to the lung). Disorder of Lung Lung Disorder Lung Disorders Pulmonary Disease Pulmonary Diseases Pulmonary Disorder Pulmonary Disorders Lung Disorder NCIT:C32221 Any part of an organism. Body Part Body Structure Body Part NCIT:C3333 An acute, acute and chronic, or chronic inflammation focally or diffusely affecting the lung parenchyma, due to infections (viruses, fungi, mycoplasma, or bacteria), treatment (e.g. radiation), or exposure (inhalation) to chemicals. Symptoms include cough, shortness of breath, fevers, chills, chest pain, headache, sweating, and weakness. Patient_developed_pneumonia Pneumonia Pneumonia, NOS pneumonia Pneumonia NCIT:C3353 Progressive and life-threatening pulmonary distress in the absence of an underlying pulmonary condition, usually following major trauma or surgery. Cases of neonatal respiratory distress syndrome are not included in this definition. ARDS Acute Respiratory Distress Syndrome Adult RDS Adult Respiratory Distress Syndrome Adult respiratory distress syndrome Acute Respiratory Distress Syndrome NCIT:C33556 A recess, cavity, or channel. SINUS Sinus sinus Sinus NCIT:C3364 The presence of pathogenic microorganisms in the blood stream causing a rapidly progressing systemic reaction that may lead to shock. Symptoms include fever, chills, tachycardia, and increased respiratory rate. It is a medical emergency that requires urgent medical attention. Sepsis Sepsis Syndrome Septicemia Systemic Sepsis blood poisoning sepsis septicemia toxemia Septicemia NCIT:C3367 Clinical, laboratory or molecular evidence, or absence of evidence of disease. Finding Observable Entity finding Finding NCIT:C33904 Other Anatomic Concept Other Anatomy Concept Other Anatomic Concept NCIT:C34144 Body tissue, region, surface, cavity, fluid, organ, or collection of organs present in, or associated with, an embryo. Embryologic Structure or System Embryonic Structure or System Embryonic Structure or System NCIT:C3426 A circumscribed inflammatory and often suppurating lesion on the skin or an internal mucous surface resulting in necrosis of tissue. ULCER Ulcer Ulcerated Ulceration Ulcerative Ulcers ulcer Ulcer NCIT:C3430 Disorders of any part of the urologic system. Disorder of Urinary System Urinary System Disorder Urinary Tract Disease Urinary Tract Disorder Urologic Disorder Urological Disorders urinary tract disorder Urinary System Disorder NCIT:C34433 Any disease of the bone marrow. Bone Marrow Disease Bone Marrow Disorder Bone Marrow Disorder NCIT:C35016 A life-threatening condition that requires immediate medical intervention. It is characterized by reduced blood flow that may result in damage of multiple organs. Types of shock include cardiogenic, hemorrhagic, septic, anaphylactic, and traumatic shock. Circulatory Collapse Shock Shock NCIT:C35018 A state of acute circulatory failure characterized by persistent arterial hypotension despite adequate fluid resuscitation or by tissue hypoperfusion unexplained by other causes. Septic Shock Systemic Septic Shock Septic Shock NCIT:C35461 A term that refers to the nature and/or clinical outcome of a disease (e.g., acute or chronic disease, aggressive or indolent disease, recurrent disease, etc.). Clinical Course Clinical Course of Disease LONGCRSE Longitudinal Course Clinical Course of Disease NCIT:C35552 Symptoms, physical examination results, and/or laboratory test results related to the cardiovascular system. CARDIOVASCULAR SYSTEM Cardiovascular Finding Cardiovascular System Finding Cardiovascular System Finding NCIT:C35708 Accumulated material from the secretions of an organ. It is solid and representative examples include gallbladder stones, kidney stones, and salivary gland stones. CALCULUS Calculi Calculus Stone Stone NCIT:C35742 A non-neoplastic or neoplastic disorder that affects the thorax and/or the organs of the thoracic cavity. Representative examples include pleural infection, mediastinitis, thymoma, mediastinal lymphoma, and pleural mesothelioma. Thoracic Disease Thoracic Disorder Thoracic Disorder NCIT:C35743 A non-neoplastic disorder that affects the thorax and/or the organs of the thoracic cavity. Representative examples include pleural infection, mediastinitis, pneumonia, and chronic obstructive pulmonary disease. Non-Neoplastic Thoracic Disease Non-Neoplastic Thoracic Disorder Non-Neoplastic Thoracic Disorder NCIT:C35755 A non-neoplastic disorder that affects the respiratory system. Representative examples include pneumonia, chronic obstructive pulmonary disease, pulmonary failure, tracheitis, and tracheal agenesis. Non-Neoplastic Respiratory System Disorder Non-Neoplastic Respiratory System Disorder NCIT:C35773 Bile Duct Calculus Bile Duct Stone Bile Duct Stone NCIT:C35814 Any deviation from the normal structure or function of the blood or lymphatic system that is manifested by a characteristic set of symptoms and signs. Hematopoietic and Lymphoid System Disease Hematopoietic and Lymphoid System Disorder Hematopoietic and Lymphoid System Disorder NCIT:C36278 A term that refers to the classification of a clinical or laboratory finding according to the anatomic site or system that is involved. Finding by Site or System Finding by Site or System NCIT:C36284 Symptoms, physical examination results, and/or laboratory test results related to the reproductive system. REPRODUCTIVE SYSTEM Reproductive System Finding Reproductive System Finding NCIT:C36288 Symptoms, physical examination results, and/or laboratory test results related to the connective and soft tissue. Connective and Soft Tissue Finding MUSCULOSKELETAL SYSTEM Connective and Soft Tissue Finding NCIT:C36291 Finding by Cause Finding by Cause NCIT:C3671 Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity. Injury Trauma Traumatic Injury Wound trauma wound Injury NCIT:C37984 A facility equipped and competent to conduct scientific experiments, observations, tests, investigations, and/or to manufacture chemicals or medical products. LABORATORY Lab Laboratory Laboratory NCIT:C37987 Showing characteristics of life; displaying signs of life. ALIVE Alive Live Living alive Alive NCIT:C38186 Clinical or Research Facility Clinical or Research Facility NCIT:C3833 Without clinical signs or indications that raise the possibility of a particular disorder or dysfunction. Asymptomatic NO SYMPTOMS asymptomatic Asymptomatic NCIT:C3959 A non-neoplastic or neoplastic disorder that affects the liver, bile ducts, and gallbladder. Representative examples of non-neoplastic disorders include hepatitis, cirrhosis, cholangitis, and cholecystitis. Representative examples of neoplastic disorders include hepatocellular adenoma, hepatocellular carcinoma, and cholangiocarcinoma. Hepatobiliary Disorder Liver Disease Liver and Biliary Disease Liver and Biliary Disorder Liver and Biliary System Disorder Hepatobiliary Disorder NCIT:C40974 A word or group of words indicating a person's first (personal or given) name; the name that precedes the surname. First Name Forename Given Name pi first name pi_first_name First Name NCIT:C40975 A word or group of words indicating a person's last (family) name. Family Name Last Name Surname pi last name pi_last_name Last Name NCIT:C40978 phone A sequence of decimal digits (0-9) that is used for identifying a destination telephone line or other device in a telephone network. Phone Phone Number Telephone Telephone Number Telephone Number NCIT:C41009 A term that helps define and render a concept unique. Modifier Qualifier Qualifier NCIT:C41075 A prosthesis placed permanently in tissue. Implant Implantable Implanted implant Implant NCIT:C41085 Information regarding the person who is acting as a channel for communication between groups. Contact Info Person Contact Information Person Contact Information NCIT:C41256 Any of the individuals who are descended from a common progenitor, related by marriage or other legal tie, or by a feeling of closeness. FAMILY MEMBER Family Member Family Member NCIT:C41275 A small, often stoppered glass or plastic bottle for holding fluids. Phial Vial Vial NCIT:C41277 A hollow cylinder, especially one for holding or conveying liquids. A hollow cylinder, especially one for holding or conveying liquids; anything shaped like such a hollow cylinder, e.g. an organic structure having the shape or function of a tube such as channel within a plant or animal body (e.g. fallopian tube). Damion Dooley Tube Tube NCIT:C42568 Unit by Category Unit by Category NCIT:C42579 An indication of the type of unit of measure being used to express a mass. Unit of Mass Unit of Mass NCIT:C42614 The words or language units by which a thing is known. Name name Name NCIT:C42694 The account name used by a person to access a computer system. Account Name Login Name User ID User Name Username Login Name NCIT:C42709 A mother or a father; an immediate progenitor. PARENT Parent Parental Parent NCIT:C42775 A text string identifier for a location to which e-mail can be delivered. Damion Dooley's note: It can also be used as an authorization token in some identification processes. E-mail E-mail Address Electronic Mail Address Email Email Address E-mail Address NCIT:C42856 A soft flexible, absorbent pad usually made from natural material such as gauze or cotton, used to absorb blood and other fluids, as in surgery or the dressing of a wound. The term also refers to a small absorbent contraceptive pad that contains a spermicide and is placed against the cervix of the uterus before sexual intercourse. Sponge Sponge NCIT:C43164 Kinds of packages that bulk drug substances and final drug dosage forms are contained in, including both the immediate (or primary) and secondary containers. Package Type Package Type NCIT:C43167 A sac or pouch. BAG Bag Bag NCIT:C43169 A vessel with a narrow neck designed to accept a specific closure. BOTTLE Bottle Bottle NCIT:C43186 An object that can be used to hold things. CONTAINER Container Container NCIT:C43209 A glass container designed for use with parenteral drug products. Glass Vial VIAL, GLASS Glass Vial NCIT:C43214 A plastic container designed for use with parenteral drug products. Plastic Vial VIAL, PLASTIC Plastic Vial NCIT:C43359 Any number of entities (members) considered as a unit. Group Panel Group NCIT:C43431 An active process; excludes processes and mechanisms which fulfill biological functions. Activity General activity Activity NCIT:C45322 A physical structure or device capable of holding objects or samples. Storage Device Storage Unit StorageEquipment Unit Storage Unit NCIT:C45908 A person (one of unisexual specimens) who is born with genitalia and/or secondary sexual characteristics of indeterminate sex, or which combine features of both sexes. Intersex Intersexed UNDIFFERENTIATED Intersex NCIT:C45910 A mix of specimens from multiple individuals representing multiple sex groups. Damion Dooley's note: here "sample" means more than one specimen merged together. Pooled Sample Sex Pooled Sample Sex Pooled Specimen pooled Sex Pooled Sample NCIT:C46109 An individual who reports belonging to the cultural gender role distinction of male. Male Male Gender Male Gender, Self Report Male Gender, Self Reported Male Gender NCIT:C46110 An individual who reports belonging to the cultural gender role distinction of female. Female Female Gender Female Gender, Self Report Female Gender, Self Reported Female Gender NCIT:C47955 A way of doing something; how a result is obtained or an end is achieved. Means Means NCIT:C48187 The tangible substance that goes into the makeup of a physical object. Material Material NCIT:C48191 Knowledge derived from study, experience, or instruction that has been gathered or received by communication. Info Information Information NCIT:C48443 An established procedure to be followed in carrying out a given operation or in a given situation. SOP Standard Operating Procedure standard operating procedures (SOPs) Standard Operating Procedure NCIT:C48470 The basic quantity or increment used to describe the strength of a product or amount of product in a package. POTENCY UNIT Potency Unit Unit of Potency Potency Unit NCIT:C48519 The traditional unit of mass. The avoirdupois ounce is equal to 1/16 pound, or 28.349 5 grams, or 0.911 457 troy ounce. Avoirdupois Ounce International Ounce OUNCE OZ Ounce [oz_av] ounce oz oz avdp Ounce NCIT:C48531 The traditional unit of mass. By international agreement, one avoirdupois pound is equal to exactly 0.453 592 37 kilogram, 16 ounces, or 1.215 28 troy pounds. Avoirdupois Pound LB POUND Pound Pounds [lb_av] lb pound Pound NCIT:C48655 A specific reason explaining why a meaningful value is not available. A meaningful value answers the question posed by a Data Element Concept. In contrast, a Missing Value Reason answers the implicit question "Why is there no 'meaningful' value?", when there is none. MVR Missing Value Reason Missing Value Reason NCIT:C48835 The usual or expected function of something; the part something plays in an action or event. Functional Role Generic Role Role Role, Generic Role NCIT:C49163 Surgical Procedure by Site or System Surgical Procedure by Site or System NCIT:C49165 A categorization of surgical procedures based on surgical techniques. Surgical Procedure by Method Surgical Procedure by Method NCIT:C49188 A laboratory procedure to detect microorganisms in a sample. Laboratory Testing, Microbiology Microbiology Test Microbiology Test NCIT:C49236 An action or administration of therapeutic agents to produce an effect that is intended to alter or stop a pathologic process. TREAT TX Therapeutic Interventions Therapeutic Method Therapeutic Procedure Therapeutic Technique Therapy Treatment any therapy any_therapy therapy treatment treatment or therapy treatment_or_therapy Therapeutic Procedure NCIT:C49237 A laboratory test designed for the quantification of an organic or inorganic chemical within a biological specimen. Chemistry Measurement Chemistry Procedure Chemistry Technique Chemistry Test Chemistry Test NCIT:C49493 Clinical Course Adverse Event Clinical Course Adverse Event NCIT:C49498 One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated. Patient recovered RECOVERED/RESOLVED Recovered Recovered from Adverse Event Recovered from Adverse Event NCIT:C49641 The period of time during which the embryo or fetus is present in the uterus of the female. Also describes the location of the embryo or fetus as being in the uterus in contrast to outside the uterus (ex utero). In Utero In Utero NCIT:C49642 An age group comprised of infants less than 37 weeks, 0 days gestational age. Premature Infant Preterm Infant Preterm Infant NCIT:C49643 An age group comprised of individuals between 28 days to 23 months of age. Infant And Toddler Infant And Toddler (28 Days to 23 Months) Infant And Toddler NCIT:C49683 An age group comprised of individuals between 2 to 11 years of age. Children (2-11) Children 2-11 Years Old Children 2-11 Years Old NCIT:C49685 An age group comprised of individuals from 18 years to 65 years of age. Adult (18-65) Adult 18-65 Years Old Adult 18-65 Years Old NCIT:C49755 A physical object that is a device or a component or accessory of a device. Device Component or Accessory Sleeve Device Component or Accessory NCIT:C49844 A device consisting of a narrow loop of material moving over shafts or pulleys. Belt Belt Device Belt Device NCIT:C5044 Fluid and Electrolyte Manifestation Fluid and Electrolyte Manifestation NCIT:C50911 An unexpected natural death from a cardiac cause within a short time period from the onset of symptoms. SCD Sudden Cardiac Death Sudden Cardiac Death NCIT:C52009 A prenatal diagnostic procedure in which a small sample of amniotic fluid is removed from the uterus by a needle inserted into the abdomen. This procedure is used to detect various genetic abnormalities in the fetus and/or the sex of the fetus. Amniocentesis Amniocentesis NCIT:C53268 A person who gets something. Recipient recipient Recipient NCIT:C53287 A person qualified to be engaged in activity directed at preservation of mental and physical health by diseases prevention and treatment as a source of livelihood. HEALTH CARE PROFESSIONAL Health Care Professional Health Professional Health Care Professional NCIT:C53471 A specific individual microbe and its genetically identical progeny separated on a single occasion from a sample taken from a host or culture system. ISOLATE Isolate Microbial Isolate Isolate NCIT:C53529 Any disorder other than abnormal tissue growth resulting from uncontrolled cell proliferation. NON-NEOPLASTIC Non-Neoplastic Disease Non-Neoplastic Disorder Non-neoplastic Disorder Non-neoplastic condition, NOS Non-neoplastic disorder, NOS Non-Neoplastic Disorder NCIT:C53531 Non-Neoplastic Disease by Site Non-Neoplastic Disorder by Site Non-Neoplastic Disorder by Site NCIT:C53547 Non-Neoplastic Disease by Special Category Non-Neoplastic Disorder by Special Category Non-Neoplastic Disorder by Special Category NCIT:C53550 A non-neoplastic disorder that affects the liver parenchyma and the intrahepatic bile ducts. Representative examples include hepatitis, cirrhosis, and cholangitis. Non-Neoplastic Hepatic Disease Non-Neoplastic Hepatic Disorder Non-Neoplastic Liver and Intrahepatic Bile Duct Disorder Non-Neoplastic Liver and Intrahepatic Bile Duct Disorder NCIT:C54014 A female individual who has had her ovaries removed. Castrated Female Spayed Female Castrated Female NCIT:C54196 The cessation of life due to heart abnormalities or disease. Cardiac Death Cardiac Death NCIT:C54197 An expected natural death from a cardiac cause. This condition usually occurs in persons with pre-existing cardiac abnormalities or disease. Non-Sudden Cardiac Death Non-Sudden Cardiac Death NCIT:C54640 The numeric, three-digit country codes specified by the ISO 3166-1 country code standard. ISO 3166-1 Numeric Country Code Numeric Country Code Numeric Country Code NCIT:C54641 The two-letter country codes specified by the ISO 3166-1 country code standard. Alpha-2 Country Code ISO 3166-1 Alpha-2 Country Code Alpha-2 Country Code NCIT:C54642 The three-letter country codes specified by the ISO 3166-1 country code standard. Alpha-3 Country Code ISO 3166-1 Alpha-3 Country Code Alpha-3 Country Code NCIT:C548 Any synthetic or animal-derived agent that is chemically identical or similar to an endogenous hormone with therapeutic application. Synthetic Hormone Therapeutic Hormone Therapeutic Hormone NCIT:C574 Immunosuppressant Immunosuppressive Agents immunosuppressant immunosuppressive immunosuppressive treatment type immunosuppressive_treatment_type Immunosuppressant NCIT:C60776 Information regarding the means of contacting a person or group. Contact Info Contact Information Contact Information NCIT:C60811 Death of a fetus, neonate, or patient 20 years or younger. PEDIATRIC DEATH Pediatric Death Pediatric Death NCIT:C62103 An object contrived for a specific purpose. Device device Device NCIT:C62263 The degree of differences in identifying features among the members of a purposefully defined group. Variety; quality, state, fact, or instance of being different. https://en.wikipedia.org/wiki/Diversity_(politics) https://www.wikidata.org/wiki/Q1230584 diversitet diversity NCIT:C62574 Services and space and equipment provided for a particular purpose; a building or place that provides a particular service or is used for a particular industry. Facility Facility NCIT:C62649 A person's partner in marriage. SPOUSE Spouse Spouse NCIT:C63362 A brand of of test tube specifically designed for venipuncture; the tube contains a vacuum allowing it to suck blood though a needle and fill itself. The tube may contain additives to facilitate downstream processing and testing of the blood samples; the tube cap is color-coded to indicate the type of additive present. Evacuated Blood Specimen Collection Tube Vacutainer Vacutainer NCIT:C64979 Diagnostic Surgical Procedure Diagnostic Surgical Procedure NCIT:C64989 The withdrawal of fluid via a needle for microscopic examination for the purpose of diagnosing a disease/disorder. Diagnostic Aspiration Diagnostic Aspiration NCIT:C68615 The calendar date on which a person was born. Damion Dooley BD BRTHDAT Birth Date DOB Date of Birth birthDate Birth Date NCIT:C69218 The pregnancy status of an individual. PREGSTAT Pregnancy Status Pregnancy Status NCIT:C69257 The name of the individual of interest. Subject Name patient first name patient_first_name Subject Name NCIT:C7057 A condition that is relevant to human neoplasms and non-neoplastic disorders. This includes observations, test results, history and other concepts relevant to the characterization of human pathologic conditions. Disease, Disorder or Finding Disease, Disorder or Finding NCIT:C70699 Any material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes, including a sample obtained from a living organism or taken from the biological object after halting of all its life functions. Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products. BIOSPECIMEN Bio-Specimen BiologicSpecimen Biological Sample Biological Specimen Biospecimen Sample Specimen biospecimen sample specimen Biospecimen NCIT:C70806 The value for a particular telecommunication address used as the contact telecommunication information for a person or organization. Telecommunication Address telecomAddress Telecommunication Address NCIT:C70810 The calendar date of subject's death. Damion Dooley DOD Date of Death Date of Death (If Deceased) Death Date deathDate Date of Death NCIT:C70909 A method to mechanically assist or replace spontaneous breathing in patients by use of a powered device that forces oxygenated air into the lungs. MECHANICAL VENTILATION Mechanical Ventilation Mechanical Ventilation NCIT:C71164 An animal that is amenable to experimentation and whose physiological or pathologic mechanisms are sufficiently similar to those of a human for the animal to serve as a model. Animal Model Animal Model, Generic Research Model, Animal Animal Model NCIT:C71384 A person related by descent rather than by marriage or law. BIOLOGICALLY RELATED Biological Relative Blood Relation Blood Relative Consanguinity Natural Relative consanguinity Biological Relative NCIT:C71392 Family members related by secondary marriage or other legal arrangement. Legal Relation Legal Relative Legal Relative NCIT:C71393 Unrelated persons who are part of the same foster family. Foster Relation Foster Relative Foster Relative NCIT:C71394 A family relation established by a legal proceeding that creates a parent-child relation between persons not related by blood. Adoptive Relation Adoptive Relative Adoptive Relative NCIT:C71395 A family relation established through a subsequent marriage of your parent. Step Relation Step Relative Step Relative NCIT:C71898 brand name The part of the name or logo associated with a specific product or service identifying and distinguishing it from varieties of the same product or service marketed by competing companies. Brand Brand Name Proprietary Name TRADENAM Trade Name brand name proprietary name Proprietary Name NCIT:C73706 A term used to indicate an object's position in space or it's relationship in space to another object. Spatial Qualifier Spatial Qualifier NCIT:C74723 The determination of the opacity of a sample. TURB Turbidity Turbidity Measurement Turbidity Measurement NCIT:C74944 A laboratory procedure that involves the examination of blood, urine, other fluids, and stool for diagnostic or research purposes. Clinical Pathology Procedure Clinical Pathology Procedure NCIT:C74957 A laboratory procedure that is performed in more than one of these laboratory specializations: anatomic pathology, clinical pathology, or molecular pathology. Mixed Category Laboratory Procedure Mixed Category Laboratory Procedure NCIT:C77683 The anatomic site of a cut made during surgery. The term may also refer to the resultant scar from the surgical procedure. Incision Site SITE, SURGICAL Incision Site NCIT:C77917 The taxonomic phylum whose members are invertebrates with hard exoskeletons and segmented joints. Organisms in this phylum include the Arachnids, Centipedes, Crustaceans, Insects and the extinct Trilobites. Arthropod Arthropoda Arthropods Arthropoda NCIT:C79426 Cancer Diagnostic or Therapeutic Procedure Cancer Diagnostic or Therapeutic Procedure NCIT:C79916 An entity, either biologic or otherwise, of interest in an investigation. [def-source: NCI] Damion Dooley NCIT Thesaurus investigative subject NCIT:C80082 Death of a live newborn during the first 28 days of life. Death neonatal Neonatal Death Neonatal Death NCIT:C80234 lookup:http://purl.obolibrary.org/obo/GAZ_00000448 A political unit, such as a city, town, or village, incorporated for local self-government. Municipality Municipality http://semanticscience.org/resource/SIO_000665 NCIT:C80244 A fictitious name used when the person performs a particular social role. Pseudonym Pseudonym NCIT:C80519 Systems designed to elucidate facts about complex biological phenomena, usually in a less complex or theoretical test environment. Biological Model Biological Models Model Model System Biological Model NCIT:C80693 The inability of the bone marrow to produce hematopoietic elements. Bone Marrow Failure Bone Marrow Failure NCIT:C814 An RNA molecule that does not contain protein-coding sequence information and constitutes the majority of the cellular RNA (~80%). This nucleic acid associates with multiple proteins to form ribosomes, which are the organelles that drive mRNA-directed protein synthesis. RIBOSOMAL RNA Ribosomal RNA rRNA Ribosomal RNA NCIT:C81893 A document, established by consensus and approved by a recognized body, that provides, for common and repeated use, rules, guidelines or characteristics for activities or their results. Standard standard technical standard Standard NCIT:C82465 Death that is attributed to the progression of a disease or pre-existing condition, and which is not attributable to any outside action or force. DIED - NATURALLY Death by Natural Cause Death by Natural Cause NCIT:C82466 Death resulting from an unknown cause. DIED - UNDETERMINED Death Due to Indeterminate Cause Death by Undetermined Cause Unknown Cause of Death Death by Undetermined Cause NCIT:C82508 A situation that imperils the existence of an entity. Life Threatening SLIFE Life Threatening NCIT:C84327 A refrigerated cabinet or room for preserving materials at or below 32F (0C). Freezer Freezer NCIT:C84328 A framework for holding objects. Rack Rack NCIT:C85173 Unexpected death in infancy which remains unexplained following autopsy, review of the medical history, and investigation of the death circumstances and death scene. SIDS Sudden Infant Death Syndrome crib death sudden infant death syndrome Sudden Infant Death Syndrome NCIT:C85405 An age group comprised of individuals between 5 and 12 years of age. School Age Child School Age Child NCIT:C85540 antimicrobial resistance testing method A method to determine whether microbial growth is affected by an antimicrobial compound. MICROSUS MSTEST Microbial Susceptibility Microbial Susceptibility Test Microbiology Susceptibility Test Microbial Susceptibility Test NCIT:C85555 A method to determine microbial susceptibility to antibiotics in which test bacteria is inoculated onto agar plates with serial dilutions of know quantities of antibiotics. The minimum inhibitory concentration of antibiotic is assessed. AGAR DILUTION Agar Dilution Method Agar Dilution Method NCIT:C85596 E-test (Epsilometry) A method to determine microbial susceptibility to antibiotics in which a plastic strip impregnated with the antibiotic of interest is placed on an agar plate that has been inoculated with bacteria. The antibiotic diffuses from the strip producing a concentration gradient of drug on the agar. The point at which the elliptical shaped area of growth inhibition meets the strip is the minimum inhibitory concentration of the drug of interest. E-Test EPSILOMETER Epsilometry Epsilometry NCIT:C85697 A method to determine the minimum inhibitory concentration (MIC) of antibiotics in which growth media is pipetted into a test tube. Each tube contains a known concentration of drug and is inoculated with a known quantity of bacteria. The tubes are incubated for a specified period of time and each is assessed for bacterial cell growth. The drug concentration in the first tube showing no growth is known as the MIC for that antibiotic. MACRO BROTH DILUTION Macro Broth Dilution Method Macro Broth Dilution Method NCIT:C87194 lookup:http://purl.obolibrary.org/obo/GAZ_00000448 A constituent administrative district of a nation. State Territory State NCIT:C87500 Ascaris conosoma Degeeria dawsoni Degeeria obscura House Fly MUSCA DOMESTICA Musca analis Musca antiquissima Musca atrifrons Musca aurifacies Musca aurulans Musca australia Musca australis Musca basilaris Musca campicola Musca chilensis Musca consanguinea Musca contigua Musca cuthbertsoni Musca determinata Musca divaricata Musca divisa Musca domestica Musca domestica major Musca flavifacies Musca flavinervis Musca flavipennis Musca frontalis Musca fulvescens Musca harpyia Musca minor Musca multispina Musca nancauriensis Musca nigricans Musca oceanica Musca pampasiana Musca pellucens Musca rivularis Musca rufifrons Musca rufiventris Musca sanctae-helenae Musca sordidissima Musca soror Musca stomoxidea Musca taitensis Musca tiberina Musca umbraculata Musca vaccina Musca vagatoria Musca vicaria Musca vicina Sphora australis Sphora nigricans Volucella domestica Musca domestica NCIT:C87913 A site where a microbiology specimen is collected. MBLOC Microbiology Specimen Origin Microbiology Specimen Origin NCIT:C89084 A term referring to the lack of definitive clinical or pathologic criteria for a tumor to predict its clinical course or to classify it as benign or malignant. UNDETERMINED Undetermined Undetermined NCIT:C89333 An age group comprised of infants greater than or equal to 37 weeks, 0 days and less than or equal to 41 weeks, 6 days gestational age. Full Term Infant Full Term Neonate Term Infant Term Neonate Term Infant NCIT:C89342 An age group comprised of individuals between 12 and 18 months of age. Toddler Toddler NCIT:C894 A chemical, physical, or biological agent that causes disease or some alteration of the normal structure and function of an organism. Usually refers to poisonous substance produced during the metabolism and growth of certain microorganisms and some higher plant and animal species, or any poisonous isomer, homolog, or derivative of such a substance. It causes either permanent or reversible injury to the health of a living thing on contact or absorption, typically by interacting with biological macromolecules such as enzymes and receptors. Onset of effects may be immediate or delayed, and impairments may be slight or severe. (NCI) Toxin Toxins toxin Toxin NCIT:C89811 lookup:http://purl.obolibrary.org/obo/GAZ_00000448 A geographical area under the jurisdiction of a sovereign state and marked off for administrative or other purposes. Territory Territory NCIT:C90351 An indication that the subject's death was due to a mishap. ACCIDENTAL DEATH Accidental Death Accidental Death NCIT:C90481 The cessation of life at an unplanned time. Unscheduled Death Unscheduled Death NCIT:C91106 A statement (either spoken or written) that is made in reply to a clinical research assessment question. Clinical or Research Assessment Answer Clinical or Research Assessment Question Response Clinical or Research Assessment Response Clinical or Research Assessment Answer NCIT:C91107 An age group comprised of individuals who have reached sexual maturity but whose character and personality are still developing. In psychology this generally covers the age range of 20-40. Young Adult Young Adult NCIT:C91108 An age group comprised of individuals between young adult and elderly, approximately 40-60 years of age. Middle Adult Middle Age Middle Adult NCIT:C92720 Symptoms, signs, diagnostic examinations or a test results in a pregnant mother. Pregnancy Finding Pregnancy Finding NCIT:C92743 Uterine contractions resulting in cervical change (dilation and/or effacement). (reVITALize) Birthing Labor Labor Birthing Labor NCIT:C93044 Index Case index case Index Case NCIT:C93210 An infectious or non infectious disorder characterized by signs and symptoms derived from focal or extensive tissue infiltration by acute (e.g., polymorphonuclear) or chronic (e.g., lymphocytic-plasmacytic) inflammatory cells. Representative examples of infectious disorders include viral infections, bacterial infections, and parasitic infections. Representative examples of non-infectious inflammatory disorders include inflammatory bowel disease and inflammatory polyps. Inflammatory Disease Inflammatory Disorder Inflammatory_Disease Inflammatory Disorder NCIT:C93582 A local name for an individual's occupation. http://purl.obolibrary.org/obo/ncit.owl Job Title jobTitle Job Title NCIT:C93874 organization name A textual identifier for an organization. Damion Dooley NCI Thesaurus Organization Organization Name Organization.name Organization Name NCIT:C94631 Treatment of retroviral infections with medications that target the virus directly, limiting the ability of infected cells to produce new virus particles. ART Anti-Retroviral Therapy Anti-retroviral therapy Antiretroviral Therapy antiretroviral therapy Antiretroviral Therapy NCIT:C96572 A male who contributes to the genetic makeup of his offspring through the fertilization of an ovum by his sperm. Biological Father FATHER, BIOLOGICAL Father Natural Father Biological Father NCIT:C96580 A female who contributes to the genetic makeup of her offspring from the fertilization of her ovum. Biological Mother MOTHER, BIOLOGICAL Mother Natural Mother Biological Mother NCIT:C96853 A non-neoplastic disorder that affects the liver, bile ducts, and gallbladder. Representative examples include hepatitis, cirrhosis, cholangitis, and cholecystitis. Non-Neoplastic Hepatobiliary Disorder Non-Neoplastic Liver and Biliary Disorder Non-Neoplastic Liver and Biliary System Disorder Non-Neoplastic Hepatobiliary Disorder NCIT:C97325 A physical object created by hand or machine. Manufactured Object Manufactured Object NCIT:C97331 Creations of the mind, such as those created by musicians, authors, artists, and inventors. Intellectual Product Intellectual Property Intellectual Property NCIT:C98904 Damage inflicted on the soft tissues and their supporting structures as the direct or indirect result of an external force, with or without disruption of structural continuity. Connective and Soft Tissue Injury Unspecified Tissue Injury Connective and Soft Tissue Injury NCIT:C99944 The patient died while in a medical center such as a hospital, skilled nursing facility (SNF), intermediate care facility (ICF), or a freestanding hospice center. (ACC) Died in a Medical Facility EXPIRED IN A MEDICAL FACILITY Died in a Medical Facility NCRO:0000230 antibiotic treatment OAE:0002678 fetal death (miscarriage/still birth) OBA:2001000 The age at which Alzheimer disease manifestations first appear. age Alzheimer disease symptoms begin age at onset of Alzheimer disease age of onset of Alzheimer disease OBA:2001001 The age at which asthma manifestations first appear. age asthma symptoms begin age at onset of asthma age of onset of asthma OBA:2001002 The age at which urinary bladder carcinoma manifestations first appear. age at onset of urinary bladder carcinoma age urinary bladder carcinoma symptoms begin age of onset of urinary bladder carcinoma OBA:2001004 The age at which cataract manifestations first appear. age at onset of cataract age cataract symptoms begin age of onset of cataract OBA:2001007 The age at which hyperlipidemia manifestations first appear. age at onset of hyperlipidemia age hyperlipidemia symptoms begin age of onset of hyperlipidemia OBA:2001008 The age at which osteoarthritis manifestations first appear. age at onset of osteoarthritis age osteoarthritis symptoms begin age of onset of osteoarthritis OBA:2001009 The age at which Parkinson disease manifestations first appear. age Parkinson disease symptoms begin age at onset of Parkinson disease age of onset of Parkinson disease OBA:2001010 The age at which essential hypertension manifestations first appear. age at onset of essential hypertension age essential hypertension symptoms begin age of onset of essential hypertension OBA:2001011 The age at which schizophrenia manifestations first appear. age at onset of schizophrenia age schizophrenia symptoms begin age of onset of schizophrenia OBA:2001012 The age at which type 1 diabetes mellitus manifestations first appear. age at onset of type 1 diabetes mellitus age type 1 diabetes mellitus symptoms begin age of onset of type 1 diabetes mellitus OBA:2001013 The age at which type 2 diabetes mellitus manifestations first appear. age at onset of type 2 diabetes mellitus age type 2 diabetes mellitus symptoms begin age of onset of type 2 diabetes mellitus OBA:2001015 The age at which childhood onset asthma manifestations first appear. age at onset of childhood onset asthma age childhood onset asthma symptoms begin age of onset of childhood onset asthma OBA:2001016 The age at which alcohol dependence manifestations first appear. age alcohol dependence symptoms begin age at onset of alcohol dependence age of onset of alcohol dependence OBA:2001017 The age at which allergic disease manifestations first appear. age allergic disease symptoms begin age at onset of allergic disease age of onset of allergic disease OBA:2001018 The age at which amyotrophic lateral sclerosis manifestations first appear. age amyotrophic lateral sclerosis symptoms begin age at onset of amyotrophic lateral sclerosis age of onset of amyotrophic lateral sclerosis OBA:2001019 The age at which bipolar disorder manifestations first appear. age at onset of bipolar disorder age bipolar disorder symptoms begin age of onset of bipolar disorder OBA:2001020 The age at which Buruli ulcer disease manifestations first appear. age Buruli ulcer disease symptoms begin age at onset of Buruli ulcer disease age of onset of Buruli ulcer disease OBA:2001022 The age at which frontotemporal dementia manifestations first appear. age at onset of frontotemporal dementia age frontotemporal dementia symptoms begin age of onset of frontotemporal dementia OBA:2001024 The age at which Huntington disease manifestations first appear. age Huntington disease symptoms begin age at onset of Huntington disease age of onset of Huntington disease OBA:2001026 The age at which migraine disorder manifestations first appear. age at onset of migraine disorder age migraine disorder symptoms begin age of onset of migraine disorder OBA:2001027 The age at which migraine with aura manifestations first appear. age at onset of migraine with aura age migraine with aura symptoms begin age of onset of migraine with aura OBA:2001028 The age at which migraine without aura manifestations first appear. age at onset of migraine without aura age migraine without aura symptoms begin age of onset of migraine without aura OBA:2001029 The age at which multiple sclerosis manifestations first appear. age at onset of multiple sclerosis age multiple sclerosis symptoms begin age of onset of multiple sclerosis OBA:2001030 The age at which myopia manifestations first appear. age at onset of myopia age myopia symptoms begin age of onset of myopia OBA:2001031 The age at which refractive error manifestations first appear. age at onset of refractive error age refractive error symptoms begin age of onset of refractive error OBA:2001032 The age at which narcolepsy-cataplexy syndrome manifestations first appear. age at onset of narcolepsy-cataplexy syndrome age narcolepsy-cataplexy syndrome symptoms begin age of onset of narcolepsy-cataplexy syndrome OBA:2001033 The age at which coronary atherosclerosis manifestations first appear. age at onset of coronary atherosclerosis age coronary atherosclerosis symptoms begin age of onset of coronary atherosclerosis OBA:2040153 The age at which cancer manifestations first appear. age at onset of cancer age cancer symptoms begin age of onset of cancer OBA:2040154 The age at which glaucoma manifestations first appear. age at onset of glaucoma age glaucoma symptoms begin age of onset of glaucoma OBA:2040155 The age at which stroke disorder manifestations first appear. age at onset of stroke disorder age stroke disorder symptoms begin age of onset of stroke disorder OBA:2040156 The age at which coronary stenosis manifestations first appear. age at onset of coronary stenosis age coronary stenosis symptoms begin age of onset of coronary stenosis OBA:2040157 The age at which glioblastoma manifestations first appear. age at onset of glioblastoma age glioblastoma symptoms begin age of onset of glioblastoma OBA:2040158 The age at which systemic lupus erythematosus manifestations first appear. age at onset of systemic lupus erythematosus age systemic lupus erythematosus symptoms begin age of onset of systemic lupus erythematosus OBA:2040159 The age at which hypertensive disorder manifestations first appear. age at onset of hypertensive disorder age hypertensive disorder symptoms begin age of onset of hypertensive disorder OBA:2040160 The age at which Machado-Joseph disease manifestations first appear. age Machado-Joseph disease symptoms begin age at onset of Machado-Joseph disease age of onset of Machado-Joseph disease OBA:2040161 The age at which major depressive disorder manifestations first appear. age at onset of major depressive disorder age major depressive disorder symptoms begin age of onset of major depressive disorder OBA:2040165 The age at which cognitive disorder manifestations first appear. age at onset of cognitive disorder age cognitive disorder symptoms begin age of onset of cognitive disorder OBA:2040166 The age at which depressive disorder manifestations first appear. age at onset of depressive disorder age depressive disorder symptoms begin age of onset of depressive disorder OBA:2040167 The age at which cervical dystonia manifestations first appear. age at onset of cervical dystonia age cervical dystonia symptoms begin age of onset of cervical dystonia OBA:2050099 The age at which anorexia nervosa manifestations first appear. age anorexia nervosa symptoms begin age at onset of anorexia nervosa age of onset of anorexia nervosa OBI:0000011 planned process planned process A process that realizes a plan which is the concretization of a plan specification. A processual entity that realizes a plan which is the concretization of a plan specification. Bjoern Peters branch derived CHMO:0001840 planned process planned process OBI:0000018 material supplier role a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. PERSON:Jennifer Fostel material supplier role OBI:0000047 processed material Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material OBI:0000066 investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived investigation OBI:0000070 assay A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived assay OBI:0000079 culture medium a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. Person: Jennifer Fostel, Jie Zheng OBI culture medium OBI:0000093 patient role a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider GROUP:Role Branch OBI, CDISC patient role OBI:0000094 material processing A planned process which results in physical changes in a specified input material A planned process which results in physical changes in a specified input material. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra OBI branch derived CHMO:0001131 CHMO:0001267 CHMO:0001461 FIX:0000258 material transformations preparative method sample preparation sample preparation step sample preparative method material processing material processing OBI:0000112 specimen role a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation GROUP: Role Branch OBI specimen role OBI:0000136 incubator A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled Frank Gibson http://www.medterms.com/script/main/art.asp?articlekey=18426 incubator OBI:0000181 population a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area PERSON: Philippe Rocca-Serra adapted from Oxford English Dictionnary population OBI:0000245 organization An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization OBI:0000257 DNA extraction A DNA extraction is a nucleic acid extraction where the desired output material is DNA. PlanAndPlannedProcess Branch OBI branch derived DNA extraction OBI:0000423 extract an extract is a material entity which results from an extraction process PERSON: Philippe Rocca-Serra GROUP: OBI Biomatrial Branch extract OBI:0000427 enzyme (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity) person: Melanie Courtot GROUP:OBI enzyme OBI:0000430 plasmid plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467 person:Melanie Courtot group:OBI plasmid OBI:0000436 needle A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture. Philippe Rocca-Serra OBI Instrument needle OBI:0000571 manufacturer role Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. GROUP: Role Branch OBI manufacturer role OBI:0000626 DNA sequencing assay A sequencing assay which determines information on the sequence of a DNA molecule. Philippe Rocca-Serra url:https://en.wikipedia.org/wiki/DNA_sequencing DNA sequencing assay OBI:0000648 clustered data set A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. PERSON: James Malone PERSON: Monnie McGee data set with assigned discovered class labels clustered data set OBI:0000652 material combination is a material processing with the objective to combine two or more material entities as input into a single material entity as output. bp bp material combination OBI:0000658 data representational model Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax. Melanie Courtot GROUP: OBI data representational model OBI:0000659 specimen collection process A planned process with the objective of collecting a specimen. Bjoern Peters specimen collection process OBI:0000679 average value A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. PERSON: James Malone PERSON: Monnie McGee average value OBI:0000689 454 Genome Sequence 20 is a DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. Philippe Rocca-Serra NCBI SRA: 454 GS 20 454 Genome Sequence 20 OBI:0000691 ABI 377 automated sequencer is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers. Philippe Rocca-Serra Applied Biosystems ABI 377 automated sequencer OBI:0000696 AB SOLiD System is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation Philippe Rocca-Serra Applied Biosystems NCBI SRA: AB SOLiD System AB SOLiD System OBI:0000702 454 Genome Sequencer FLX is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. Philippe Rocca-Serra adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay NCBI SRA: 454 GS FLX 454 Genome Sequencer FLX OBI:0000703 Illumina Genome Analyzer II is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology Philippe Rocca-Serra Illumina Corporation NCBI SRA: Illumina Genome Analyzer II Illumina Genome Analyzer II OBI:0000710 Li-Cor 4300 DNA Analysis System is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing Philippe Rocca-Serra OBI and Li-Cor Li-Cor 4300 DNA Analysis System OBI:0000717 HeliScope Single Molecule Sequencer is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry Philippe Rocca-Serra NCBI SRA: Helicos HeliScope HeliScope Single Molecule Sequencer OBI:0000718 pathogen role pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role GROUP: Role Branch OBI pathogen role OBI:0000732 restriction enzyme an enzyme that has a specific target cleavage sites within nucleic acids Kevin Clancy, Bjoern Peters restriction enzyme OBI:0000740 material sample role A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. material sample role OBI:0000832 measurement device A device in which a measure function inheres. GROUP:OBI Philly workshop OBI measurement device OBI:0000869 polyA RNA extract A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group polyA RNA extract OBI:0000880 RNA extract an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. PERSON: Chris Stoeckert PERSON: Jie Zheng Group: UPenn Group RNA extract OBI:0000893 real time polymerase chain reaction assay An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. Bjoern Peters Melanie Courtot url:http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction real time polymerase chain reaction assay OBI:0000895 total RNA extract A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group total RNA extract OBI:0000925 infectious agent is a material entity bearing the disposition to infect an organism IEDB IEDB Note: testing use of 'transmitted by' relation; issue to be resolved is whether appropriate domain and range are involved. This use would place 'transmitted by' as a subclass of 'participates in' infectious agent OBI:0000938 categorical measurement datum A measurement datum that is reported on a categorical scale Bjoern Peters Bjoern Peters categorical measurement datum OBI:0000947 service provider role is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person PERSON:Helen Parkinson service provider role OBI:0000953 processed specimen A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. processed specimen OBI:0000963 categorical label A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters Bjoern Peters categorical label OBI:0000967 container A device that can be used to restrict the location of material entities over time PERSON: Bjoern Peters container OBI:0000968 device A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. PERSON: Helen Parkinson OBI development call 2012-12-17. device OBI:0000973 sequence data A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. Person:Chris Stoeckert GROUP: OBI sequence data OBI:0000992 DNA sequencing service A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized. DNA sequencing service OBI:0001010 nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. PERSON: Jie Zheng UPenn Group nucleic acid extract OBI:0001034 environmental control device An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity. Helen Parkinson OBI environmental control device OBI:0001128 micropipette A microinjection device that is used to measure very small volumes of liquids. PERSON: Erik Segerdell http://www.answers.com/topic/micropipette micropipette OBI:0001141 individual organism identifier a CRID symbol used to distinguish one individual organism from another. PERSON: Chris Stoeckert, Jie Zheng MO_169 Individual individual organism identifier OBI:0001167 age measurement datum A time measurement datum that is the result of measurement of age of an organism PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng MO_178 Age age measurement datum OBI:0001169 age since birth measurement datum An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. PERSON:Chris Stoeckert, Jie Zheng MO_710 birth age since birth measurement datum OBI:0001173 service A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. Carlo; Matt OBI workshop San Diego 2011 service OBI:0001177 RNA sequencing assay An assay that determines the sequence of an RNA molecule. Bjoern Peters Bjoern Peters RNA sequencing assay OBI:0001479 specimen from organism A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). Damion Dooley note: OBI has a variety of subclasses like "blood specimen" and "colon specimen" etc. which we have not added here. The are mapped to UBERON terms indirectly through the logic "derives from some [uberon term]". GenEpiO takes a different approach in describing this class with lists for "subject anatomical site", "subject body product", and "plant anatomy". PERSON: Chris Stoeckert, Jie Zheng MO_954 organism_part specimen from organism OBI:0001508 sampling time measurement datum A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point. Person: Chris Stoeckert MO_738 timepoint sampling time measurement datum OBI:0001515 material maintenance service A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process. material maintenance service OBI:0001528 material service A service which has a material entity as specified input and/or specified output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai material service OBI:0001547 material analysis service A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush material analysis service OBI:0001557 material storage service A storage service in which a service consumer provides some material as input which a service provider stores and returns as output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush material storage service OBI:0001614 ^SAM[NED](\w)?\d+$ GenBank ID A CRID symbol uniquely indentifies the submitted GeneBank sequence record. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group GenBank ID http://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000350 http://www.ncbi.nlm.nih.gov/Sequin/acc.html https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/ OBI:0001615 investigation description A textual entity that describes an investigation. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NCBI BioProject investigation description Project Description Description* OBI:0001616 specimen identifier A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group sample identifier specimen identifier OBI:0001617 PubMed ID A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information. Person: Chris Stoeckert, Jie Zheng Website: http://en.wikipedia.org/wiki/Wikipedia:PMID PubMed ID OBI:0001619 specimen collection date specimen collection time measurement datum A time measurement datum that is the measure of the time when the specimens are collected. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group specimen collection time measurement datum OBI:0001620 help:Latitude should not be abstracted to the centre of a city, province/state or country as this may falsely implicate an existing location. latitude coordinate measurement datum A measurement datum that is the measure of the latitude coordinate of a site. Damion Dooley's note: IAO lat/long can't be made a subclass of "angular coordinate" or disjoint contradiction arises. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group See http://www.csgnetwork.com/gpscoordconv.html See http://www.geomidpoint.com/latlon.html See http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org/obo/OBI_0001621 See http://www.w3.org/2003/01/geo/wgs84_pos latitude coordinate measurement datum OBI:0001621 longitude coordinate measurement datum A measurement datum that is the measure of the longitude coordinate of a site. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group longitude coordinate measurement datum OBI:0001622 investigation title A textual entity that denotes an investigation. Person:Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NCBI BioProject NIAID GSCID-BRC investigation title OBI:0001627 country name A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Website: http://en.wikipedia.org/wiki/Country Damion Dooley's note: A 'sovereign state' entity should have attribute or relationships to measurables - population, size, name, etc. So e.g. " 'country name' inheres in some 'sovereign state/country'". Also note historical name issue (Myanmar vs Burma) and diplomatic name issue (Taiwan vs "Republic of China"). Both point to needing a single entity with multiple names. country name OBI:0001628 investigation identifier A CRID symbol used to identify an investigation. Person: Chris Stoeckert, Jie Zhneg NIAID GSCID-BRC metadata working group http://purl.obolibrary.org/obo/OMIABIS_0000006 investigation identifier OBI:0001629 grant identifier A CRID symbol used to identify a grant. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group grant identifier OBI:0001687 contact representative role A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent. Person: Chris Stoeckert contact representative role OBI:0001866 secondary cultured cell A cultured cell that has been passaged or derives from a cell that has been passaged in culture. Person: Matthew Brush PERSON: Matthew Brush A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture. secondary cultured cell OBI:0001879 reagent A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output. PERSON:Matthew Brush PERSON:Matthew Brush (copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). reagent OBI:0001880 specimen provider PI organization organization of specimen provider principal investigator An organization that is the affiliation of the principal investigator providing the specimens for the investigation PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group organization of specimen provider principal investigator OBI:0001882 target material target material in specimen specification A plan specification which specifies the type of material that will be assayed in an investigation. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NCBI BioProject: Material Used in NCBI BioProject specifcation target material in specimen specification OBI:0001884 specimen sample scope specimen-based scope of investigation specification A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group specimen-based scope of investigation specification OBI:0001885 specimen repository organization An organization that provides a service to store and distribute specimens PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group specimen repository organization OBI:0001888 sequencing facility contact person A person who is the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group sequencing facility contact person OBI:0001889 specimen provider principal investigator A person who is a principal investigator and provides the specimen NIAID GSCID-BRC metadata working group Sample Provider Principal Investigator (PI) Name specimen provider principal investigator OBI:0001891 sequencing facility sequencing facility organization An organization that provides sequence determination service PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group sequencing facility organization OBI:0001892 project objective specification of data to be generated in an investigation An objective specification which indicates the type of data that will be generated and submitted to a database. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NCBI BioProject: Objective specification of data to be generated in an investigation OBI:0001893 organization of specimen collector An organization that is the affiliation of the person collecting the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group organization of specimen collector OBI:0001894 email address of sequencing facility contact person An email address of the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group email address of sequencing facility contact person OBI:0001896 project method investigation assay specification A plan specification which indicates the assay type used to obtain data. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group investigation assay specification OBI:0001897 organization of sequencing facility contact person An organization that is the affiliation of the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group organization of sequencing facility contact person OBI:0001898 comment on investigation A textual entity that is about any of the aspects of an investigation worth noting PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group comment on investigation OBI:0001899 target capture specification A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group target capture specification OBI:0001900 specimen identifier assigned by specimen repository A specimen identifier which is assigned by a specimen repository PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group specimen identifier assigned by specimen repository OBI:0001901 specimen identifier assigned by sequencing facility A specimen identifier which is assigned by a sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group specimen identifier assigned by sequencing facility OBI:0001903 specimen provider PI email email address of specimen provider principal investigator An email address of the principal investigator providing the specimens for the investigation PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group email address of specimen provider principal investigator OBI:0001904 sequencing service A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized. Person: Jie Zheng Adpated from 'DNA sequencing service' sequencing service OBI:0001905 secondary cultured cell population A cultured cell population that is derived through one or more passages in culture. PERSON:Matthew Brush secondary cell culture sample PERSON:Matthew Brush The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally. secondary cultured cell population 1 OBI:0001930 categorical categorical value specification A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification OBI:0001931 scalar scalar value specification A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification OBI:0001933 value specification An information content entity that specifies a value within a classification scheme or on a quantitative scale. PERSON:Bjoern Peters Damion Dooley's note: Often a value specification may need to allow for a "data item state" that indicates that a given datum doesn't have a recorded or observed or retrievable value, and the general reason for this state. value specification OBI:0001940 N50 the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly Alejandra Gonzalez-Beltran Philippe Rocca-Serra adapted from: "http://genome.cshlp.org/content/21/12/2224.full?sid=74019122-f944-4ccc-bffe-d16fdd0e7d6c" (from table 7) and from "http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html" N50 OBI:0001941 Assembly QC contig N50 N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list. Alejandra Gonzalez-Beltran Damion Dooley Philippe Rocca-Serra adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html http://www.nature.com/nature/journal.../409860a0.html GENEPIO contig N50 OBI:0001942 grant agency An organization that provides funding support for projects such as investigations. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group grant agency OBI:0002000 Genome Analyzer IIx An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg ENCODE group NCBI SRA: Illumina Genome Analyzer IIx Genome Analyzer IIx OBI:0002001 Illumina HiSeq 2000 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf Illumina HiSeq 2000 OBI:0002002 Illumina HiSeq 2500 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf Illumina HiSeq 2500 OBI:0002003 MiSeq A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf NCBI SRA: Illumina MiSeq MiSeq OBI:0002007 SOLiD 3 Plus System A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf NCBI SRA: AB SOLiD 3 Plus System SOLiD 3 Plus System OBI:0002012 PacBio RS II A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg http://www.pacificbiosciences.com/products/ NCBI SRA: PacBio RS PacBio RS II OBI:0002021 NextSeq 500 A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng http://systems.illumina.com/systems/nextseq-sequencer.html NCBI SRA: Illumina NextSeq NextSeq 500 OBI:0002022 Illumina HiSeq 1000 A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf Illumina HiSeq 1000 OBI:0002024 SOLiD 4 System An AB SOLid System which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/next-generation-systems/solid-4-system.html?CID=FL-091411_solid4 NCBI SRA: AB SOLiD 4 System SOLiD 4 System OBI:0002027 Genome Analyzer IIe An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf NCBI SRA: Illumina Genome Analyzer IIe Genome Analyzer IIe OBI:0002048 Illumina HiSeq 3000 A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. PERSON: Sagar Jain, Richard Scheuermann http://www.illumina.com/systems/hiseq-3000-4000.html Illumina HiSeq 3000 OBI:0002049 Illumina HiSeq 4000 A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. PERSON: Sagar Jain, Richard Scheuermann http://www.illumina.com/systems/hiseq-3000-4000.html Illumina HiSeq 4000 OBI:0002088 specimen container A container with the function of containing a specimen. Chris Stoeckert Duke Biobank, OBIB specimen container OBI:0002128 Illumina Genome Analyzer A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. Person: Chris Stoeckert, Jason Hilton http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html Illumina Genome Analyzer OBI:0002129 Illumina HiSeq X Ten A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html Illumina HiSeq X Ten OBI:0002198 molecular analysis facility organization An organization that provides molecular analysis service. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB molecular analysis facility organization OBI:0002565 adapter-sequence trimming A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed). Dan Berrios Dan Berrios adapter-sequence trimming OBI:0002585 sequence trimming A data transformation in which subsequences of a molecular sequence are cut (removed). sequence trimming OBI:0002599 swab specimen A specimen that is stored on a swab as the output of a collecting specimen with swab process. Chris Stoeckert OBIB/OBI swab specimen OBI:0002600 collecting specimen with swab A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick). Chris Stoeckert OBIB collecting specimen with swab OBI:0002627 ribosomal RNA-depleted RNA extract An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species). Dan Berrios https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1 ribosomal RNA-depleted RNA extract OBI:0002630 Illumina NovaSeq 6000 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. Dan Berrios http://www.illumina.com/systems/sequencing-platforms/novaseq.html Illumina NovaSeq 6000 OBI:0002632 PacBio Sequel A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation Bonita Lam Dan Berrios http://www.pacb.com/products-and-services/pacbio-systems/sequel/ PacBio Sequel OBI:0002633 PacBio Sequel II A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. Bonita Lam Dan Berrios http://www.pacb.com/products-and-services/pacbio-systems/sequel/ PacBio Sequel II OBI:0002650 biopsy A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. Damion Dooley Nicole Vasilevsky https://en.wikipedia.org/wiki/Biopsy biopsy OBI:0002651 image guided biopsy A biopsy which uses an imaging procedure to guide a needle biopsy. Damion Dooley https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 image guided biopsy OBI:0002654 needle biopsy A biopsy that uses a hollow needle to extract cells. Damion Dooley https://www.mayoclinic.org/tests-procedures/needle-biopsy/about/pac-20394749 needle biopsy OBI:0002692 polymerase chain reaction assay An assay that uses polymerase chain reaction technique to amplify DNA. VEuPathDB VEuPathDB polymerase chain reaction assay OBI:0002750 Oxford Nanopore MinION A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. PERSON: Bonita Lam https://nanoporetech.com/products/minion Oxford Nanopore MinION OBI:0002751 Oxford Nanopore GridION Mk1 A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individually. PERSON: Bonita Lam https://nanoporetech.com/products/gridion Oxford Nanopore GridION Mk1 OBI:0002752 Oxford Nanopore PromethION A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. PERSON: Bonita Lam https://nanoporetech.com/products/promethion Oxford Nanopore PromethION OBI:0002754 cDNA library A collection of DNA molecules with sequences complementary to a specified set of mRNA molecules and commonly developed by enzymatic reverse transcription. Dan Berrios modified from Wikipedia cDNA library OBI:0002778 tracheal aspirate specimen A specimen that is collected with a suctioning tube from the trachea. Asiyah Yu Lin ORCID:0000-0003-2620-0345 PMID:25338241 tracheal aspirate specimen OBI:0002786 personal protective device A device which is a wearable garment designed to protect the wearer's body from injury or infection. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Personal_protective_equipment personal protective device OBI:0002787 face mask A personal protective device worn over the nose and mouth as a respiratory filter to inhibit the flow of particles. https://orcid.org/0000-0002-8844-9165 Adapted from https://dictionary.cambridge.org/dictionary/english/face-mask face mask OBI:0002788 non-medical mask A face mask not manufactured according to medical equipment standards. https://orcid.org/0000-0002-8844-9165 https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/about-non-medical-masks-face-coverings.html non-medical mask OBI:0002789 medical mask A face mask manufactured according to a recognized medical equipment standard. https://orcid.org/0000-0002-9578-0788 https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/about-non-medical-masks-face-coverings.html medical mask OBI:0002790 N95 respirator A face mask that meets the U.S. National Institute for Occupational Safety and Health (NIOSH) N95 classification of air filtration, meaning that it filters at least 95% of incoming airborne particles. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/N95_mask N95 respirator OBI:0002791 face shield A personal protective device used to protect the wearer's entire face (or part of it) from hazards such as flying objects and road debris, chemical splashes, or alternately potentially infectious materials. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Face_shield face shield OBI:0002792 patient gown A personal protective clothing item which is a gown designed for use by a patient to facilitate caregiving by medical staff. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Patient_gown patient gown OBI:0002793 scrubs A personal protective clothing item which is sterilized and which is worn by a health care professional. It can reference a shirt and pants or dress, and depending on medical protocol, may include a medical cap. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Scrubs_(clothing) scrubs OBI:0002794 reusable patient gown A patient gown intended to be reused after being laundered. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Patient_gown reusable patient gown OBI:0002795 disposable patient gown A patient gown intended for a single period of continuous use and then disposed of. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Patient_gown disposable patient gown OBI:0002796 medical gown A personal protective clothing item which is a gown worn by a medical professional in order to provide a barrier between patient and professional. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Medical_gown medical gown OBI:0002798 surgical gown A medical gown which is subjected to a sterilization process and which is intended to be worn by a medical professional during surgical procedures. https://orcid.org/0000-0002-8844-9165 OBI surgical gown OBI:0002799 personal protective glove A personal protective device which is a glove. https://orcid.org/0000-0002-8844-9165 OBI personal protective glove OBI:0002800 personal protective clothing item A personal protective device which consists of a garment that serves in place of or in addition to regular body clothing. https://orcid.org/0000-0002-8844-9165 OBI personal protective clothing item OBI:0002802 laboratory coat A personal protective clothing item which is an overcoat worn by medical or laboratory professionals. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/White_coat laboratory coat OBI:0002803 medical glove A personal protective glove which is disposable and is used during medical examinations and procedures to help prevent cross-contamination between caregivers and patients. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Medical_glove medical glove OBI:0002804 nitrile glove A personal protective glove which is made out of nitrile rubber. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Medical_glove nitrile glove OBI:0002806 footwear cover A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants. https://orcid.org/0000-0002-8844-9165 https://en.wiktionary.org/wiki/shoecover footwear cover OBI:0002807 disposable footwear cover A footwear cover which is designed for a single period of continuous use and then disposed of. https://orcid.org/0000-0002-8844-9165 OBI disposable footwear cover OBI:0002808 reusable footwear cover A footwear cover which is designed for repeated use. https://orcid.org/0000-0002-8844-9165 OBI reusable footwear cover OBI:0002809 surgical N95 respirator A N95 respirator which has been approved by the FDA as a surgical mask. https://orcid.org/0000-0002-8844-9165 https://multimedia.3m.com/mws/media/1794572O/surgical-n95-vs-standard-n95-which-to-consider.pdf surgical N95 respirator OBI:0002810 protective coverall A personal protective clothing item which is a loose fitting coverall for ease of movement, with sleeves, full leggings and often a hood to cover the head. These can also include overshoe pieces to cover footwear and protect against contamination. https://orcid.org/0000-0002-8844-9165 https://www.safeopedia.com/definition/863/disposable-coveralls protective coverall OBI:0002811 protective sleeve A personal protective clothing item which is a protective cover worn over the arm. https://orcid.org/0000-0002-8844-9165 https://www.safeopedia.com/definition/974/protective-sleeves protective sleeve OBI:0002812 protective apron A personal protective clothing item which is an apron. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Apron protective apron OBI:0002813 medical cap A personal protective device which is worn on the head that helps prevent transmission of contaminants contained in hair and scalp. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Scrubs_(clothing) medical cap OBI:0002814 specimen collection device A container used to collect a specimen. https://orcid.org/0000-0002-8844-9165 specimen collection device OBI:0002819 specimen pad A sample collection device consisting of a soft flexible, absorbent pad usually made from natural material such as gauze or cotton, used to absorb specimen fluid or particulate matter. https://orcid.org/0000-0002-8844-9165 Derived from NCIT sponge definition. specimen pad OBI:0002820 specimen collection swab stick A specimen collection device which is a specimen pad attached to a long handle used to collect specimen material. https://orcid.org/0000-0002-8844-9165 https://medical-dictionary.thefreedictionary.com/swab specimen collection swab stick OBI:0002822 drag swab A specimen collection device consisting of a specimen pad made of sterile gauze which is aseptically attached to a pole by clips or to a string https://orcid.org/0000-0002-8844-9165 https://www.fda.gov/food/laboratory-methods-food/environmental-sampling-and-detection-salmonella-poultry-houses drag swab OBI:0002823 pre-moistened swab stick A specimen collection swab stick that is pre-moistened with liquid prior to sampling. https://orcid.org/0000-0002-8844-9165 pre-moistened swab stick OBI:0002824 surface wipe A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces. https://orcid.org/0000-0002-8844-9165 https://www.science.gov/topicpages/s/surface+wipe+sampling.html surface wipe OBI:0002825 OBI:0002826 OBI:0002827 OBI:0002831 OBI:0002858 OBI:0002859 OBI:0002860 OBI:0002861 OBI:0002862 OBI:0002866 OBI:0003114 Illumina MiniSeq A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. PERSON: Bonita Lam url:https://www.illumina.com/systems/sequencing-platforms/miniseq.html Illumina MiniSeq OBI:0003386 Illumina HiSeq 1500 A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. Jain Aluvathingal Michelle Giglio Suvarna Nadendla https://jp.support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseq1500/hiseq-1500-system-guide-15035788-03.pdf Illumina HiSeq 1500 OBI:0003387 NextSeq 550 A DNA sequencer manufactured by the Illumina corporation, which provides the increased flexibility of microarray scanning in addition to sequencing. Jain Aluvathingal Michelle Giglio Suvarna Nadendla https://www.illumina.com/systems/sequencing-platforms/nextseq.html NextSeq 550 OBI:0100026 organism A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism OBI:0100051 specimen A material entity that has the specimen role. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch sample specimen OBI:0100060 cultured cell population A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. PERSON:Matthew Brush cell culture sample PERSON:Matthew Brush The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. cultured cell population OBI:0200000 data transformation A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard Branch editors data transformation OBI:0302884 extraction A material separation in which a desired component of an input material is separated from the remainder Person:Bjoern Peters Philippe Rocca-Serra extraction OBI:0302885 filtration filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device Philippe Rocca-Serra OBI-Branch: adapted from wikipedia and wordnet filtration OBI:0400103 DNA sequencer A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. Trish Whetzel MO DNA sequencer OBI:0500000 study design A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. PERSON: Chris Stoeckert study design OBI:0600005 collecting specimen from organism a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation PERSON:Bjoern Peters IEDB collecting specimen from organism OBI:0600012 environmental material collection environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer. Bjoern Peters, Alan Ruttenberg IEDB environmental material collection process OBI:0600014 material component separation a material processing in which components of an input material become segregated in space Bjoern Peters IEDB material component separation OBI:0600016 pooling specimens physical combination of several instances of like material PlanAndPlannedProcess Branch OBI branch derived pooling specimens OBI:0600044 lavage A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid PlanAndPlannedProcess Branch OBI branch derived lavage OBI:0600047 sequencing assay An assay the uses chemical or biochemical means to infer the sequence of a biomaterial PlanAndPlannedProcess Branch OBI branch derived sequencing assay OBI:0666667 nucleic acid extraction a material separation to recover the nucleic acid fraction of an input material PlanAndPlannedProcess Branch OBI branch derived nucleic acid extraction OBI:1110034 antigen is a material entity that has the antigen role IEDB IEDB antigen OBI:1110040 infectious disease is a disease caused by an infectious agent IEDB IEDB infectious disease OBI:1110049 allergy is a disease in which an abnormally strong inflammatory immune response is triggered against non-self entities, and the immune response has no protective effect IEDB IEDB allergy OGMS:0000031 disease (OGMS) disease A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. disease OGMS:0000045 A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. disorder OGMS:0000063 The totality of all processes through which a given disease instance is realized. disease course OGMS:0000073 The representation of a conclusion of a diagnostic process. 2019-09-08T23:41:09Z diagnosis OGMS:0000087 An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. extended organism OGMS:0000090 treatment A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process treatment OGMS:0000104 A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output). Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e diagnostic process OMIABIS:0001008 A diagnosis that is the outcome of a diagnostic process targeting a second or additional health problem. Damion Dooley amended from http://en.wikipedia.org/wiki/Comorbidity NIAID: Comorbidity complications comorbidity Comorbidity OMIT:0001642 Acute Disease OMIT:0004227 Chronic Disease OMIT:0006951 Gastric Lavage OMIT:0012122 http://purl.obolibrary.org/obo/omit population density OMIT:0012935 Recurrence OMIT:0013001 Remission, Spontaneous OMIT:0017096 Vital signs are unstable and not within normal limits. Patient may be unconscious. Indicators are unfavorable. Damion Dooley grave Critical Illness OMIT:0019022 Bronchoalveolar Lavage OMIT:0020789 Disease Attributes OMIT:0020917 A type of Shiga toxin found in E. coli Damion Dooley Stx1 Shiga Toxin 1 Shiga toxin 1 OMIT:0020918 A type of Shiga toxin found in E. coli which is antigenically distinct from Shiga toxin 1 Damion Dooley Stx2 Shiga Toxin 2 Shiga toxin 2 OMIT:0021725 Escherichia coli Proteins OMIT:0027406 MLST typing Multilocus Sequence Typing OMIT:0027578 Urine Specimen Collection OMP:0000207 A microbial phenotype that is distinguished by the presence a specific surface antigen. serovar serotype phenotype OMRSE:00000001 A social role inhering in a human being. Mathias Brochhausen William R. Hogan human social role OMRSE:00000010 A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. Mathias Brochhausen William R. Hogan health care role human health care role OMRSE:00000011 A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter. Amanda Hicks Mathias Brochhausen patient CAFE domain expert working group. In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications. patient role OMRSE:00000012 A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism. Mathias Brochhausen William R. Hogan health care provider role OMRSE:00000013 A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments. physician role OMRSE:00000014 A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life. Mathias Brochhausen nurse based on: http://en.wikipedia.org/wiki/Nursing nurse role OMRSE:00000026 A role in human social processes that inheres in an organism. William R. Hogan Mathias Brochhausen Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants. Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc. Previous definition: A role in human social processes played by an organism. organism social role OMRSE:00000030 A patient role that inheres in a human being. human patient role OMRSE:00000048 material entity role OMRSE:00000049 organism role OMRSE:00000050 Homo sapiens role OMRSE:00000058 A human social role that, if realized, is realized by the process of formal education that the bearer undergoes. Mathias Brochhausen student role OMRSE:00002072 A role that inheres in some entity that is realized in a social act. Matthew Diller Previous definition: A role played by an entity in human social processes. role in human social processes PATO:0000001 A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATO:0000072 quality PATO:0000011 age A time quality inhering in a bearer by virtue of how long the bearer has existed. age PATO:0000047 An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. biological sex PATO:0000051 A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. morphology PATO:0000068 TODO: define this or obsolete it and move children somewhere else. qualitative PATO:0000069 A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. deviation (from_normal) PATO:0000070 The number of entities of this type that are part of the whole organism. PATO:0000053 PATO:0000071 PATO:0001169 PATO:0001226 presence or absence in organism quantitative This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. amount PATO:0000117 A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. size PATO:0000122 A 1-D extent quality which is equal to the distance between two points. Length often refers to the longer or longest dimension of an object, however, this is not always true. See https://github.com/pato-ontology/pato/issues/337 for full discussion. length PATO:0000146 A physical quality of the thermal energy of a system. Damion's Note: Future use might prefer: CMO_0000015 body temperature. temperature PATO:0000165 time A quality in which events occur in sequence. time PATO:0000383 A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. NCBI BioSample: female female PATO:0000384 A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. NCBI BioSample: male male PATO:0000462 A quality denoting the lack of an entity. PATO:0001996 absence absent from organism We recommend using the new absent terms (physical absence, absent anatomical entity, or absent process) instead of this class. This is a legacy term and will ultimately be obsoleted. See https://github.com/pato-ontology/pato/issues/331. absent PATO:0000467 A quality inhering in a bearer by virtue of the bearer's existence. present PATO:0001018 physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. A quality of a single physical entity that exists through action of continuants at the physical level of organisation. PATO:0002079 Wikipedia:Physical_property relational physical quality physical quality physical quality PATO:0001019 A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. mass density PATO:0001230 A quality inhering in a bearer by virtue of the bearer's power or force. strength PATO:0001237 quality of a single physical entity A physical object quality which inheres in a single-bearer. quality of a single physical entity PATO:0001241 physical object quality A quality which inheres in a continuant. A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality physical object quality PATO:0001323 A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent. area PATO:0001340 A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. NCBI BioSample: hermaphrodite hermaphroditic intersex hermaphrodite PATO:0001470 A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity. proportion proportionality quotient ratio Examples: height to weight; brain size to body size. These could all be children of proportionality. Proportions can be measured as ratios. Some measures may be dimensionless. Not all ratios measure proportionality, eg m/s measures velocity which is not a proportion in the sense defined above, it is a quality in its own right. proportionality to PATO:0001536 A molecular quality that inheres in a molecular entity by virtue of the bearer's disposition to dissolve in a liquid. solubility PATO:0001537 A solubility quality inhering in a substance by virtue of the bearer's disposition to dissolve in a liquid. soluble soluble in PATO:0001585 A physical quality inhering in a bearer by virtue of the bearer's disposition to transmit of an entity through a medium. Examples could be heat or electricity or sound. conductivity PATO:0001595 A 1-D extent quality inhering in a bearer by virtue of the bearer's downward or backward or inward dimension. depth PATO:0001708 A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. 1-D size 1-D extent PATO:0001709 A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions. 2-D size 2-D extent PATO:0001779 A strength which is relatively low. weak decreased strength PATO:0001827 A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of one sex and external sexual characteristics of the other sex. This value is not present in NCBI BioSample host sex. pseudohermaphrodite PATO:0001828 A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of male and external sexual characteristics of female. male pseudohermaphrodite PATO:0001829 A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of female and external sexual characteristics of male. female pseudohermaphrodite PATO:0001894 An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. Phenotypic sex refers to an individual's sex as determined by their internal and external genitalia, expression of secondary sex characteristics, and behavior. Note that NCBI Biosample has these values allowed: male | female | pooled male and female | neuter | hermaphrodite | intersex | not determined | missing | not applicable | not collected NCBI: http://www.ncbi.nlm.nih.gov/books/NBK10943/ phenotypic sex PATO:0001986 A quality inhering in a bearer by virtue of the bearer's passing into solution. dissolved PATO:0001995 A quality that inheres in an entire organism or part of an organism. organismal quality PATO:0002182 A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. PATO:0002061 relational molecular quality molecular quality PATO:0002301 A quality that has a value that is decreased compared to normal or average. decreased quality PATO:0002303 A quality of an object that has a value that is decreased compared to normal or average. decreased object quality PATO:0002365 Female quality of having complete, unaltered reproductive organs intact female PATO:0002366 Male quality of having complete, unaltered reproductive organs. intact male PATO:0002367 Male quality of being incapable to reproduce because of functional loss of the testicles from surgical removal or chemical means. castrated male PATO:0002390 A length quality which is equal to the length of any straight line segment that passes from the center of a circle to any endpoint on the circular boundary. The radius is half of the diameter. Damion Dooley's note: We can't say radius is a subclass of "linear coordinate" because length is considered a quality/specifically dependent continuant, which is disjoint with immaterial entity/independent continuant . I.e. "length" as quality unfortunately can't pertain to abstract entities, only "real" ones. radius PATO:0040020 Female quality of being incapable to reproduce because of functional loss of the ovaries and/or uterus from surgical removal. spayed female PATO:0040049 A biological sex quality inhering in an individual or a population who are otherwise male of a non-hermaphroditic species who has ambiguous or atypical congenital development of the reproductive system. intersex male with differences of sexual differentiation male with disorder of sexual development male, DSD The term intersex is popular in use, but may be considered offensive when applied to humans. DSD can be expanded multiple ways to 'disorders/differences of sexual development/differentiation'. male with DSD PATO:0040050 A phenotypic sex quality inhering in a plant organism or a population of plants in which the flowers have two stamens. diandrous PATO:0040051 A phenotypic sex quality inhering in a plant organism or a population of plants in which the flowers have only one stamen. monandrous PATO:0040052 A sequential hermaphroditic quality whereby organisms start out as female and change to male at a later life stage. protogyny protogynous PATO:0040053 A sequential hermaphroditic quality whereby organisms start out as male and change to female at a later life stage. protandry protandrous PATO:0040054 A protogynous quality whereby organisms start out as female and change to hermaphrodite at a later life stage. protogynous hermaphrodite protogynous hermaphroditic protogynous hermaphroditism PATO:0040055 A protandrous quality whereby organisms start out as male and change to hermaphrodite at a later life stage. protandrous hermaphrodite protandrous hermaphroditic protandrous hermaphroditism PATO:0040056 A biological sex quality inhering in an individual or a population who are otherwise female of a non-hermaphroditic species who has ambiguous or atypical congenital development of the reproductive system. intersex female with differences of sexual differentiation female with disorder of sexual development female, DSD The term intersex is popular in use, but may be considered offensive when applied to humans. DSD can be expanded multiple ways to 'disorders/differences of sexual development/differentiation'. female with DSD PATO:0070000 A hermaphroditic quality that inheres in a population or organism where an organism changes is a different sexes during different life stages. sequential hermaphroditic Sequential hermaphrodity is generally characterized by an organism producing female gametes and male gametes during different life stages. sequential hermaphrodite PCO:0000000 A material entity that consists of two or more organisms, viruses, or viroids. group of organism organism collection May be of the same or different species. collection of organisms PCO:0000001 A collection of organisms, all of the same species, that live in the same place. ISBN:0878932739 It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. population of organisms PCO:0000018 A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. collection of organisms of the same species single-species collection of organisms PCO:0000031 A material entity that is one or more organisms, viruses or viroids. organismal entity PCO:0000033 social gathering A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially. GenEpiO curators human social gathering activity PCO:0000034 A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area. GenEpio curators human community event PCO:0000035 A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose. GenEpiO curators party PCO:0000037 A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. GenEpio curators potluck PCO:0000038 A human social gathering at which two people are married. May include a legal or social ceremony. GenEpio curators wedding PCO:0000039 A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby. GenEpiO curators baby shower PECO:0007027 PO:0009011 PR:000000001 protein An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. protein RBO:00000016 Radiation classified by where the exposure to the radiation is occurring. radiation environment RBO:00000017 That part of the Earth exposed to the Earth atmosphere. Earth surface RO:0002310 A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. exposure event or process RO:0002577 A material entity consisting of multiple components that are causally integrated. Chris Mungall http://www.jbiomedsem.com/content/4/1/43 system SO:0000001 A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. sequence region SO:0000110 Any extent of continuous biological sequence. INSDC_feature:misc_feature INSDC_note:other INSDC_note:sequence_feature located_sequence_feature sequence feature sequence_feature SO:0000143 A region of known length which may be used to manufacture a longer region. assembly component assembly_component SO:0000149 A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. Damion Dooley http://en.wikipedia.org/wiki/Contig contig 1 SO:0000353 sequence assembly A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. http://en.wikipedia.org/wiki/Sequence_assembly http://edamontology.org/data_0925 http://purl.obolibrary.org/obo/OBI_0000973 - 'sequence data' sequence assembly sequence_assembly SO:0000700 A comment about the sequence. remark SO:0001026 A genome is the sum of genetic material within a cell or virion. Damion Dooley http://en.wikipedia.org/wiki/Genome genome SO:0001027 A genotype is a variant genome, complete or incomplete. http://en.wikipedia.org/wiki/Genotype genotype SO:0001082 Incompatibility in the sequence due to some experimental problem. BS:00125 sequencing_information Range. polypeptide_sequencing_information SO:0001085 Different sources report differing sequences. BS:00069 conflict Discrete. sequence_conflict SO:0001248 A region of the genome of known length that is composed by ordering and aligning two or more different regions. http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly assembly SO:0001260 A collection of discontinuous sequences. sequence collection sequence_collection SO:0001410 A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. experimental output artefact experimental_output_artefact experimental_feature SO:0001462 A collection of contigs. contig collection See tracker ID: 2138359. contig_collection SO:0001505 A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly. http://purl.obolibrary.org/obo/ERO_0002173 reference_genome SO:0001507 A collection of one or more sequences of an individual. variant_collection STATO:0000009 A Cartesian coordinate system is a coordinate system that specifies each point uniquely in a plane by a pair of numerical coordinates, which are the signed distances from the point to two fixed perpendicular directed lines, measured in the same unit of length. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra http://en.wikipedia.org/wiki/Cartesian_coordinate_system cartesian coordinate system STATO:0000010 n-dimensional coordinate system In geometry, a coordinate system is a system which uses one or more numbers, or coordinates, to uniquely determine the position of a point or other geometric element on a manifold such as Euclidean space. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra http://en.wikipedia.org/wiki/Coordinate_system Damion Dooley's note:Damion Dooley's note: Outstanding issue: How to attach units to each dimension? This depends on the instance of the problem involving a dimension? Linear offset can be decimal or integer or complex, or a count. - Can have a unit: meter, kilometer, foot, light-year, oranges, apples, fruit Angular offset can be radians or degrees. coordinate system STATO:0000013 a 2 dimensional cartesian coordinate system is a cartesian coordinate system which defines 2 orthogonal one dimensional axes and which may be used to describe a 2 dimensional spatial region. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra two dimensional cartesian coordinate system STATO:0000014 In mathematics, a spherical coordinate system is a coordinate system for three-dimensional space where the position of a point is specified by three numbers: the radial distance of that point from a fixed origin, its polar angle measured from a fixed zenith direction, and the azimuth angle of its orthogonal projection on a reference plane that passes through the origin and is orthogonal to the zenith, measured from a fixed reference direction on that plane. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra https://en.wikipedia.org/wiki/Spherical_coordinate_system spherical coordinate system STATO:0000015 A cylindrical coordinate system is a three-dimensional coordinate system that specifies point positions by the distance from a chosen reference axis, the direction from the axis relative to a chosen reference direction, and the distance from a chosen reference plane perpendicular to the axis. The latter distance is given as a positive or negative number depending on which side of the reference plane faces the point. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra https://en.wikipedia.org/wiki/Cylindrical_coordinate_system cylindrical coordinate system STATO:0000016 In mathematics, the polar coordinate system is a two-dimensional coordinate system in which each point on a plane is determined by a distance from a fixed point and an angle from a fixed direction. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra http://en.wikipedia.org/wiki/Polar_coordinate_system polar coordinate system STATO:0000022 A one dimensional cartesian coordinate system is a cartesian coordinate system which defines a one dimensional axis and which may be used to describe a one dimensional spatial region, i.e. a straight line. It is defined by a point O, the origin, a unit of length and the orientation for the one dimensional space. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra one dimensional cartesian coordinate system STATO:0000024 a three dimensional cartesian coordinate system is a cartesian coordinate system which defines 3 orthogonal one dimensional axes and which may be used to describe a 3 dimensional spatial region. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra three dimensional cartesian coordinate system STATO:0000047 a count is a data item denoted by an integer and represented the number of instances or occurences of an entity Damion Dooley's note: Unfortunately an IAO "count" cannot be a subclass of immaterial entity "linear coordinate" as this leads to disjoint conflict. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra STATO Damion Dooley's note: A count datum often implicity carries a date range for which the count is ascertained, or estimated, or simulated for. Damion Dooley's note: The result of the act of counting is a scalar number whose unit is a description of the thing being counted. One can count 10 oranges and compare that to a count of 5 oranges. One can generalize that a count of 5 oranges is a count of pieces of fruit. One can then compare 5 oranges and 5 apples, fruitfully! count STATO:0000050 signal to noise ratio is a measurement datum comparing the amount of meaningful, useful or interesting data (the signal) to the amount of irrelevant or false data (the noise). Depending on the field and domain of application, different variables will be used to determinate a 'signal to noise ratio'. In statistics, the definition of signal to noise ratio is the ratio of the mean of a measurement to its standard deviation. It thus corresponds to the inverse of the coefficient of variation Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra adapted from Wikipedia: http://en.wikipedia.org/wiki/Signal-to-noise_ratio#Alternative_definition last accessed: 2013-10-18 signal to noise ratio STATO:0000053 a false positive rate is a data item which accounts for the proportion of incorrect rejection of a true null hypothesis. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra PRS,AGB adapted from wikipedia and wolfram alpha false positive rate STATO:0000055 chromosome coordinate system is a genomic coordinate which uses chromosome of a particular assembly build process to define start and end positions. This coordinate system is unstable and will change with each new genome sequence assembly build. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra chromosome coordinate system STATO:0000064 sequence read count is a data item determining how many sequence reads generated by a DNA sequencing assay for a given stretch of DNA can counted Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra AGB-PRS, STATO sequence read count STATO:0000069 The number degree of freedom is a count evaluating the number of values in a calculation that can vary. In statistics, the number of degrees of freedom ν is equal to N-1 in the case of the direct measurement of a quantity estimated by the arithmetic mean of N independent observations. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra http://stats.stackexchange.com/questions/16921/how-to-understand-degrees-of-freedom http://www.optique-ingenieur.org/en/courses/OPI_ang_M07_C01/co/Contenu_07.html the rank of the quadratic form (mathematical definition) number of degrees of freedom STATO:0000071 reaction rate is a measurement datum which represents the speed of a chemical reaction turning reactive species into product species of event (i.e the number of such conversions)s occuring over a time interval Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra STATO reaction rate STATO:0000085 effect size estimate is a data item about the direction and strength of the consequences of a causative agent as explored by statistical methods. Those methods produce estimates of the effect size, e.g. confidence interval Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra AGB,PRS effect size estimate STATO:0000087 a polychotomous variable is a categorical variable which is defined to have minimally 2 categories or possible values Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra STATO http://udel.edu/~mcdonald/statvartypes.html polychotomous variable STATO:0000090 a dichotomous variable is a categorical variable which is defined to have only 2 categories or possible values Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra AGB-PRS http://udel.edu/~mcdonald/statvartypes.html 'has part' exactly 1 ('categorical measurement datum' and ('has category label' exactly 2 'categorical label')) dichotomous variable STATO:0000134 specificity is a measurement datum qualifying a binary classification test and is computed by substracting the false positive rate to the integral numeral 1 Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra specificity true negative rate STATO:0000169 Fold change is a number describing how much a quantity changes going from an initial to a final value or one condition to another condition Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra http://en.wikipedia.org/wiki/Fold_change fold change STATO:0000182 Odds ratio is a ratio that measures effect size, that is the strength of association between 2 dichotomous variables, one describing an exposure and one describing an outcome. It represents the odds that an outcome will occur given a particular exposure, compared to the odds of the outcome occurring in the absence of that exposure ( the probability of the event occuring divided by the probability of an event not occurring). The odds ratio is a ratio of describing the strength of association or non-independence between two binary data values by forming the ratio of the odds for the first group and the odds for the second group. Odds ratio are used when one wants to compare the odds of something occurring to two different groups. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938757/ http://www.stats.org/stories/2008/odds_ratios_april4_2008.html odds ratio STATO:0000184 A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra adapted from Wolfram Alpha: https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig76g7 ratio STATO:0000190 Threshold cycle (or Ct or Cq) is a count which is defined as the fractional PCR cycle number at which the reporter fluorescence is greater than the threshold in the context of the RT-qPCR assay. The Ct is a basic principle of real time PCR and is an essential component in producing accurate and reproducible data. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra Cq Ct http://www.ncbi.nlm.nih.gov/genome/probe/doc/TechQPCR.shtml threshold cycle STATO:0000197 a genomic coordinate system is a coordinate system to describe position of sequence on a genomic scaffold (assembly of chromosome, contig....) Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra ensembl, ucsc genomic coordinate system STATO:0000210 is a data item formed by dividing the fluorescence intensity obtained in one channel to that obtained in the other channel, typically the case when considering 2-color microarray data when imaging is done for Cy3 and Cy5 dyes. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra STATO channel1/channel2 fluorescence intensity ratio STATO:0000220 the false negative rate is a data item which denotes the proportion of missed detection of elements known to be meeting the detection criteria Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra STATO, adapted from false negative rate STATO:0000221 a random variable (or aleatory variable or stochastic variable) in probability and statistics, is a variable whose value is subject to variations due to chance (i.e. randomness, in a mathematical sense) Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra aleatory variable stochastic variable wikipedia: http://en.wikipedia.org/wiki/Random_variable random variable STATO:0000228 ordinal variable is a categorical variable where the discrete possible values are ordered or correspond to an implicit ranking Alejandra Gonzalez-Beltan Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra ranked variable http://udel.edu/~mcdonald/statvartypes.html ordinal variable STATO:0000232 number of PCR cycle is a count which enumerates how many iterations of 'annealing, renaturation, amplification,' rounds (or cycles) are performed during a polymerase chain reaction (PCR) or an assay relying on PCR. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra adapted from various sources including: http://www.ncbi.nlm.nih.gov/genome/probe/doc/TechQPCR.shtml number of PCR cycle STATO:0000233 sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1 Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra recall sensitivity adapted from: http://en.wikipedia.org/wiki/Sensitivity_and_specificity and http://mathworld.wolfram.com/Sensitivity.html true positive rate STATO:0000251 A continuous variable is one for which, within the limits the variable ranges, any value is possible. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra http://davidmlane.com/hyperstat/A97418.html http://udel.edu/~mcdonald/statvartypes.html continuous variable STATO:0000252 a categorical variable is a variable which that can only assume a finite number of value and cast observation in a small number of categories Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra discrete variable nominal variable qualitative factor http://udel.edu/~mcdonald/statvartypes.html categorical variable STATO:0000258 variable type a variable is a data item which can assume any of a set of values, either as determined by an agent or as randomly occuring through observation. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra STATO adapted from wolfram-alpha (http://www.wolframalpha.com/input/?i=variable) definition 2. and from Oxford English Dictionary: http://www.oed.com/view/Entry/221514?redirectedFrom=variable#eid, definition B,1 variable STATO:0000300 A ratio where the numerator and denominator are expressed in the same unit. Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra STATO dimensionless ratio STATO:0000409 the likelihood ratio is a ratio which is formed by dividing the post-test odds with the pre-test odds in the context of a Bayesian formulation Philippe Rocca-Serra likelihood ratio STATO:0000410 the likelihood ratio of negative results is a ratio which is formed by dividing the difference between 1 and sensitivity of the test by the specificity value of a test.. This can be expressed also as dividing the probability of a person who has the disease testing negative by the probability of a person who does not have the disease testing negative. Philippe Rocca-Serra likelihood ratio for negative results adapted from Wikipedia: https://en.wikipedia.org/wiki/Likelihood_ratios_in_diagnostic_testing last accessed: May 2016 negative likelihood ratio STATO:0000411 the likelihood ratio of positive results is a ratio which is form by dividing the sensitivity value of a test by the difference between 1 and specificity of the test. This can be expressed also as dividing the probability of the test giving a positive result when testing an affected subject versus the probability of the test giving a positive result when a subject is not affected. Philippe Rocca-Serra likelihood ratio for positive results adapted from Wikipedia: https://en.wikipedia.org/wiki/Likelihood_ratios_in_diagnostic_testing last accessed: May 2016 positive likelihood ratio STATO:0000412 prevalence is a ratio formed by the number of subjects diagnosed with a disease divided by the total population size. Philippe Rocca-Serra adapted from: https://www.health.ny.gov/diseases/chronic/basicstat.htm prevalence STATO:0000413 Incidence is the ratio of the number of new cases of a disease divided by the number of persons at risk for the disease. Philippe Rocca-Serra adapted from: https://www.health.ny.gov/diseases/chronic/basicstat.htm incidence STATO:0000414 mortality is a ratio formed by the number of deaths due to a disease divided by the total population size. Philippe Rocca-Serra adapted from: https://www.health.ny.gov/diseases/chronic/basicstat.htm mortality STATO:0000415 in the context of binary classification, accuracy is defined as the proportion of true results (both true positives and true negatives) to the total number of cases examined (the sum of true positive, true negative, false positive and false negative). It can be understood as a measure of the proximity of measurement results to the true value. Philippe Rocca-Serra Rand accuracy Rand index adapted from wikipedia: https://en.wikipedia.org/wiki/Accuracy_and_precision#In_binary_classification last accessed: May 2016 accuracy STATO:0000416 precision or positive predictive value is defined as the proportion of the true positives against all the positive results (both true positives and false positives) Philippe Rocca-Serra positive predictive value adapted from wikipedia: https://en.wikipedia.org/wiki/Accuracy_and_precision#In_binary_classification last accessed: May 2016 precision STATO:0000417 The probability of a patient having the target disorder before a diagnostic test result is known Philippe Rocca-Serra http://www.cebm.net/pre-test-probability/ pretest probability STATO:0000544 In a planned experiment where to covariance (genotype x environment) can be controlled and held at 0, the heritability is defined as the ratio of the variance of the genotypic variables to the variance of the phenotypic variables. H2 = Var(G)/Var(P) H2 is the broad-sense heritability. This reflects all the genetic contributions to a population's phenotypic variance including additive, dominant, and epistatic (multi-genic interactions), as well as maternal and paternal effects, where individuals are directly affected by their parents' phenotype, for example, milk production in mammals. Philippe Rocca-Serra https://en.wikipedia.org/wiki/Heritability heritability STATO:0000545 A particularly important component of the genetic variance is the additive variance, Var(A), which is the variance due to the average effects (additive effects) of the alleles. Since each parent passes a single allele per locus to each offspring, parent-offspring resemblance depends upon the average effect of single alleles. Additive variance represents, therefore, the genetic component of variance responsible for parent-offspring resemblance. The additive genetic portion of the phenotypic variance is known as Narrow-sense heritability and is defined as: h2 = Var(A)/Var(P) Philippe Rocca-Serra https://en.wikipedia.org/wiki/Heritability narrow sense heritability STATO:0000561 the frequency (i.e., the proportion) of possible confidence intervals that contain the true value of their corresponding parameter. In other words, if confidence intervals are constructed using a given confidence level in an infinite number of independent experiments, the proportion of those intervals that contain the true value of the parameter will match the confidence level. A probability measure of the reliability of an inferential statistical test that has been applied to sample data and which is provided along with the confidence interval for the output statistic. Philippe Rocca-Serra adapted from wikipedia: https://en.wikipedia.org/wiki/Confidence_interval and from: http://www.oxfordreference.com/view/10.1093/acref/9780191792236.001.0001/acref-9780191792236-e-103?rskey=tQCMI6&result=1 confidence level STATO:0000570 The selectivity ratio (SR) is defined as the ratio of explained vexpl,i to residual variance vres,i for the variable i on the target projection (TP) component in the context of Partial Least Squares Analysis. Philippe Rocca-Serra https://onlinelibrary.wiley.com/doi/pdf/10.1002/cem.1289 selectivity ratio STATO:0000587 the percentage of variance is an output of Principal Component Analysis which is obtained by forming the ratio of an eigenvalue divided by the sum of all eigenvalues. This produces a "percentage of variance" for each eigenvector. Philippe Rocca-Serra adapted from: https://stats.stackexchange.com/questions/31908/what-is-percentage-of-variance-in-pca percentage of variance SYMP:0000009 A skin and integumentary tissue symptom that is characterized by a fluid-filled elevation of the epidermis. blister SYMP:0000092 skin lesion SYMP:0000462 A symptom is a perceived change in function, sensation, loss, disturbance or appearance reported by a patient indicative of a disease. symptom SYMP:0000488 skin and integumentary tissue symptom TRANS:0000000 A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. https://www.ebi.ac.uk/ols/ontologies/trans TRANS follows the CDC Epidemiology model of transmission between two hosts, a reservoir and host or other non-host, non-reservoir entities (e.g), a needle and a host. transmission of infection transmission process TRANS:0000001 Direct and essentially immediate transfer of infectious agents to a receptive portal of entry through which human or animal infection may take place. This may be by direct contact such as touching, kissing, biting, or sexual intercourse or by the direct projection (droplet spread) of droplet spray onto the conjunctiva or the mucous membranes of the eyes, nose, or mouth. It may also be by direct exposure of susceptible tissue to an agent in soil, compost, or decaying vegetable matter or by the bite of a rabid animal. Transplacental transmission is another form of direct transmission. Direct transmission is a transmission process that is the means during which the pathogen is transmitted immediately from a reservoir, source or host to another host. https://www.ebi.ac.uk/ols/ontologies/trans direct transmission direct transmission TRANS:0000002 Indirect transmission is a transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by intermediary vehicles, vectors or as airborne dust particles. https://www.ebi.ac.uk/ols/ontologies/trans indirect transmission TRANS:0000006 Congenital transmission is a direct transmission process during which the pathogen is transmitted directly from mother to child at or around the time of birth. https://www.ebi.ac.uk/ols/ontologies/trans congenital TRANS:0000007 contact transmission Contact transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by kissing, skin-to-skin contact, sexual intercourse, or by contact with soil or vegetation containing the pathogen. https://www.ebi.ac.uk/ols/ontologies/trans contact TRANS:0000008 Droplet spread transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by spray of aerosols over a short distance, spray from sneezing, coughing or talking. https://www.ebi.ac.uk/ols/ontologies/trans droplet spread TRANS:0000012 Vehicle-borne ingestion transmission is an indirect vehicle-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by ingestion of fluids or foods or food products including: food, water, milk, or meat products. https://www.ebi.ac.uk/ols/ontologies/trans vehicle-born ingestion UBERON:0000000 An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. processual entity UBERON:0000002 Lower, narrow portion of the uterus where it joins with the top end of the vagina. cervix BTO:0001421 BTO:0002249 CALOHA:TS-0134 EFO:0000979 EMAPA:29927 EV:0100114 FMA:17740 GAID:376 MA:0000392 MAT:0000292 MESH:D002584 NCIT:C12311 OpenCyc:Mx4rvVipEJwpEbGdrcN5Y29ycA UMLS:C0007874 VHOG:0001359 galen:CervixUteri canalis cervicis uteri caudal segment of uterus cervical canal of uterus cervix uteri neck of uterus uterine cervix uterine cervix UBERON:0000003 Orifice of the olfactory system. The naris is the route by which odorants enter the olfactory system[MAH]. AAO:0000311 EHDAA2:0001225 EHDAA:9083 EMAPA:17847 MA:0000282 VHOG:0000663 galen:Naris naris UBERON:0000020 An organ that is capable of transducing sensory stimulus to the nervous system. AEO:0000094 BSA:0000121 BTO:0000202 CALOHA:TS-2043 EHDAA2:0001824 EHDAA:500 EMAPA:35955 FBbt:00005155 GAID:63 HAO:0000930 MA:0000017 MESH:D012679 NCIT:C33224 UMLS:C0935626 VHOG:0001407 WBbt:0006929 organ of sense organ system organ of sensory organ system organ of sensory system sense organ system organ sensory organ sensory organ system organ sensory system organ sensillum sense organ UBERON:0000021 Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales. CALOHA:TS-0051 FMA:71012 skin appendage epidermal appendage cutaneous appendage UBERON:0000022 One of the epidermal growths that form the distinctive outer covering, or plumage, on birds. Feathers are formed in tiny follicles in the epidermis, or outer skin layer, that produce keratin proteins. BTO:0000447 EFO:0000955 GAID:1214 MAT:0000156 MESH:D005241 OpenCyc:Mx4rvVjW-5wpEbGdrcN5Y29ycA feather UBERON:0000025 Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. galen:Tube anatomical tube duct tube UBERON:0000029 Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. BTO:0000784 CALOHA:TS-0579 EFO:0000872 EMAPA:35523 EV:0100050 FMA:5034 GAID:947 MA:0000139 MAT:0000442 MESH:D008198 NCIT:C12745 NCIT:C33027 OpenCyc:Mx4rwLPqLpwpEbGdrcN5Y29ycA TAO_RETIRED:0005318 UMLS:C0024204 VHOG:0001273 ZFA_RETIRED:0005318 galen:Lymphnode lymph node UBERON:0000057 The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening. BTO:0001426 CALOHA:TS-1132 EFO:0000931 EMAPA:30901 EV:0100099 FMA:19667 GAID:390 MA:0000379 MAT:0000121 MESH:D014521 MIAA:0000121 NCIT:C12417 OpenCyc:Mx4rvVjkypwpEbGdrcN5Y29ycA UMLS:C0041967 VHOG:0001264 XAO:0000153 galen:Urethra urethra UBERON:0000059 A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. AAO:0010396 BTO:0000706 CALOHA:TS-1306 EFO:0000840 EMAPA:19252 EV:0100077 FMA:7201 GAID:306 MA:0000333 MESH:D007420 MIAA:0000046 NCIT:C12379 OpenCyc:Mx4rvVkF5pwpEbGdrcN5Y29ycA UMLS:C0021851 VHOG:0000054 XAO:0000131 galen:LargeIntestine large intestine UBERON:0000061 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 biological structure connected biological structure anatomical structure UBERON:0000062 Anatomical structure that performs a specific function or group of functions [WP]. BIRNLEX:4 CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 NCIT:C13018 OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA UMLS:C0178784 WBbt:0003760 organ UBERON:0000064 A multicellular structure that is a part of an organ. AAO:0011124 BIRNLEX:16 EFO:0000635 FMA:82472 cardinal organ part organ part UBERON:0000065 Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts. EHDAA2:0001606 EHDAA:1568 EHDAA:2219 EMAPA:16737 FMA:265130 OpenCyc:Mx4rvvM--pwpEbGdrcN5Y29ycA VHOG:0000393 respiratory tract UBERON:0000068 A life cycle stage that starts with fertilization and ends with the fully formed embryo. BilaDO:0000002 EV:0300001 FBdv:00005289 FMA:72652 HsapDv:0000002 MmusDv:0000002 OGES:000000 OGES:000022 WBls:0000003 WBls:0000092 WBls:0000102 XAO:1000012 embryonic stage embryo stage UBERON:0000069 A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle. BTO:0000915 BTO:0000954 EFO:0001303 FBdv:00005336 MIAA:0000400 OGES:000008 ZFS:0000048 larva stage ammocoete ammocoete stage bipinnaria bipinnaria stage caterpillar caterpillar stage glochidium glochidium stage grub grub stage leptocephalus leptocephalus stage maggot maggot stage metacestode naiad, nymph naiad, nymph stage nauplius nauplius stage nymph nymph stage planula planula stage tornaria trochophore trochophore stage veliger veliger stage wriggler wriggler stage zoea zoea stage larval stage UBERON:0000071 End of the life of an organism. XAO:0000437 XtroDO:0000085 death stage UBERON:0000072 An section of a respiratory tract. EMAPA:16737 FMA:45660 MA:0000434 proximo-distal subdivision of respiratory tract UBERON:0000075 Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. UBERON:0010322 FMA:85544 NCIT:C34076 UMLS:C1519343 galen:ComplexSkeletalStructure skeletal system subdivision subdivision of skeletal system UBERON:0000105 A spatiotemporal region encompassing some part of the life cycle of an organism. BILS:0000105 EFO:0000399 FBdv:00007012 FMA:24120 HsapDv:0000000 MESH:D008018 MmusDv:0000000 OlatDv:0000010 PdumDv:0000090 WBls:0000002 XAO:1000000 ZFS:0000000 ZFS:0100000 ncithesaurus:Developmental_Stage developmental stage stage life cycle stage UBERON:0000115 The epithelial layer of the lung. BTO:0001653 EMAPA:32860 MA:0001783 epithelial tissue of lung epithelium of lung lung epithelial tissue lung epithelium UBERON:0000117 A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. EMAPA:37946 FMA:12224 segment of tracheobronchial tree respiratory conducting tube segment of tracheobronchial tree tracheobronchial tree segment respiratory tube UBERON:0000160 Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. AAO:0000246 ANISEED:1235303 BSA:0000093 BTO:0000648 CALOHA:TS-0490 EFO:0000834 EMAPA:32874 EV:0100071 FMA:7199 GAID:295 MA:0000328 MA:0001524 MESH:D007422 MIAA:0000043 NCIT:C12736 TAO:0001338 UMLS:C0021853 VHOG:0000056 WBbt:0005772 XAO:0000129 ZFA:0001338 galen:Intestine bowel intestine UBERON:0000161 Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. anatomical ostium ostium FMA:3724 anatomical orifice hilum orifice UBERON:0000162 Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures. AAO:0000095 GAID:1206 MESH:D002988 NCIT:C34127 UMLS:C0008987 VHOG:0001186 XAO:0000244 ZFA:0005781 cloaca UBERON:0000165 The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). AAO:0010355 BTO:0001090 BTO:0004698 CALOHA:TS-1315 EFO:0000825 EHDAA2:0001326 EHDAA:542 EMAPA:16262 FBbt:00003126 FMA:49184 GAID:75 MA:0000341 MA:0002474 MAT:0000038 MESH:D009055 MIAA:0000038 OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA TADS:0000040 TAO:0000547 TAO:0000590 TGMA:0000131 VHOG:0000280 VHOG:0000812 XAO:0003029 ZFA:0000547 ZFA:0000590 galen:Mouth regio oralis adult mouth mouth UBERON:0000168 A section dividing a colon along a proximal-distal axis. FMA:222905 proximal-distal subdivision of colon UBERON:0000171 Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. EMAPA:17607 SPD:0000428 TGMA:0001247 apparatus respiratorius organ breathing organ organ of apparatus respiratorius organ of respiratory system respiratory organ respiratory system organ respiration organ UBERON:0000173 Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid. BTO:0000068 CALOHA:TS-0034 EMAPA:36771 ENVO:02000021 EV:0100123 FMA:305905 GAID:1155 MA:0002893 MESH:D000653 NCIT:C13188 UMLS:C0002638 VHOG:0001267 amniotic fluid UBERON:0000174 A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity. UBERON:0000324 UBERON:0007550 AEO:0000184 BTO:0000491 EHDAA2_RETIRED:0003184 ENVO:02000022 FMA:9674 galen:Excretion excreted substance portion of excreted substance waste substance excreta UBERON:0000178 A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 BTO:0000089 CALOHA:TS-0079 EFO:0000296 EHDAA2:0000176 EHDAA:418 EMAPA:16332 ENVO:02000027 EV:0100047 FMA:9670 GAID:965 MA:0000059 MESH:D001769 MIAA:0000315 NCIT:C12434 OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA TAO:0000007 UMLS:C0005767 VHOG:0000224 XAO:0000124 ZFA:0000007 galen:Blood portion of blood vertebrate blood blood UBERON:0000179 Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. CARO:0000081 haemolymphatic fluid UBERON:0000344 A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]. AEO:0000199 BTO:0000886 CALOHA:TS-2031 EHDAA2_RETIRED:0003234 EV:0100382 FMA:85355 FMA:85358 GAID:297 MESH:D009092 NCIT:C13166 OpenCyc:Mx4rvmKNOpwpEbGdrcN5Y29ycA UMLS:C0026724 galen:Mucosa mucosa of organ mucosa of organ part mucosal region mucous membrane organ mucosa mucosa UBERON:0000456 A portion of organism substance that is produced by exocrine glands. UBERON:0006540 secretion AEO:0001005 BTO:0002977 BTO:0002979 EMAPA:36535 FMA:9675 MA:0002504 MESH:D012634 NCIT:C34062 UMLS:C1516992 galen:Secretion bodily secretion exocrine gland fluid/secretion secreted substance secretion of exocrine gland UBERON:0000463 organism body product Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. AAO:0010839 AEO:0000004 BILA:0000004 CALOHA:TS-2101 CARO:0000004 EHDAA2:0003004 EMAPA:35178 FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 NCIT:C13236 SPD:0000008 TAO:0001487 TGMA:0001824 VHOG:0001726 XAO:0004001 ZFA:0001487 galen:BodySubstance body fluid or substance body substance organism substance portion of body substance portion of organism substance organism substance UBERON:0000464 Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. lumen space AAO:0010110 AEO:0000005 BILA:0000005 CARO:0000005 EHDAA2:0003005 FBbt:00007017 FMA:5897 HAO:0000005 NCIT:C94478 TAO:0001668 TGMA:0001825 UMLS:C0524461 VHOG:0001728 XAO:0003190 ZFA:0001643 lumen space anatomical space UBERON:0000465 Anatomical entity that has mass. AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 material anatomical entity UBERON:0000466 Anatomical entity that has no mass. AAO:0010265 AEO:0000007 BILA:0000007 CARO:0000007 EHDAA2:0003007 FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 TGMA:0001827 VHOG:0001727 immaterial physical anatomical entity immaterial anatomical entity UBERON:0000467 Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. system AAO:0000007 AEO:0000011 BILA:0000011 BIRNLEX:14 BSA:0000049 CALOHA:TS-2088 CARO:0000011 EHDAA2:0003011 EHDAA:392 EMAPA:16103 EV:0100000 FBbt:00004856 FMA:7149 HAO:0000011 MA:0000003 NCIT:C12919 OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ TAO:0001439 TGMA:0001831 UMLS:C0460002 VHOG:0001725 WBbt:0005746 WBbt:0005763 XAO:0003002 ZFA:0001439 galen:AnatomicalSystem body system connected anatomical system organ system anatomical system UBERON:0000468 Anatomical structure that is an individual member of a species and consists of more than one cell. organism AAO:0010026 AEO:0000191 BILA:0000012 BIRNLEX:18 BSA:0000038 BTO:0000042 CARO:0000012 EFO:0002906 EHDAA2:0003103 EHDAA2:0003191 EHDAA:1 EMAPA:25765 EV:0100016 FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 TADS:0000001 TAO:0001094 TGMA:0001832 VHOG:0000671 WBbt:0007833 XAO:0003004 ZFA:0001094 galen:Organism ncithesaurus:Whole_Organism multi-cellular organism multicellular organism UBERON:0000475 Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. AAO:0010053 AEO:0000032 BILA:0000032 BIRNLEX:7 CALOHA:TS-2084 CARO:0000032 EFO:0000808 EHDAA2:0003032 EMAPA:36031 FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 MAT:0000293 MESH:D001829 MIAA:0000293 NCIT:C32221 OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA TAO:0001308 TGMA:0001840 UMLS:C0229962 VHOG:0001758 XAO:0003013 ZFA:0001308 galen:BodyPart anatomic region organism subdivision UBERON:0000476 Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. AAO:0010268 AEO:0000040 BILA:0000040 CARO:0000040 EHDAA2:0003040 FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 TGMA:0001841 XAO:0003162 ZFA:0000382 acellular anatomical structure UBERON:0000479 Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 BIRNLEX:19 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 EMAPA:35868 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:D014024 NCIT:C12801 TAO:0001477 TGMA:0001844 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 galen:Tissue portion of tissue tissue portion simple tissue tissue UBERON:0000483 Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. AAO:0000144 AAO:0010055 AEO:0000066 BILA:0000066 BTO:0000416 CALOHA:TS-0288 CARO:0000066 EHDAA2:0003066 EMAPA:32738 FBbt:00007005 FMA:9639 GAID:402 HAO:0000066 MA:0003060 MESH:D004848 NCIT:C12710 TAO:0001486 UMLS:C0014609 VHOG:0000387 XAO:0003045 ZFA:0001486 epithelial tissue portion of epithelium Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it? epithelium UBERON:0000485 Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]. columnar epithelium columnar epithlium AAO:0010063 AEO:0000068 BILA:0000068 CARO:0000068 EHDAA2_RETIRED:0003068 FBbt:00007027 FMA:45567 HAO:0000068 NCIT:C33552 TAO:0001496 UMLS:C0836135 XAO:0004008 ZFA:0001496 epithelium simplex columnare simple columnar epithelium simple columnar epithelium UBERON:0000489 Compound organ that contains one or more macroscopic anatomical spaces. AAO:0010016 AEO:0000072 BILA:0000072 CARO:0000072 EHDAA2:0003072 FMA:55671 HAO:0000072 TAO:0001490 TGMA:0001857 VHOG:0001730 XAO:0003165 ZFA:0001490 cavitated organ cavitated compound organ UBERON:0000490 Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]. AAO:0010062 AEO:0000073 BILA:0000073 BTO:0002073 CARO:0000073 EHDAA2:0003073 FMA:45561 HAO:0000073 NCIT:C33554 TAO:0001495 UMLS:C0682574 XAO:0004007 ZFA:0001495 simple epithelium unilaminar epithelium UBERON:0000569 The ileocecal valve is a sphincter muscle situated at the junction of the small intestine (ileum) and the large intestine. Its critical function is to limit the reflux of colonic contents into the ileum. FMA:15973 MESH:D007080 NCIT:C13066 UMLS:C0020880 galen:IleocecalValve valva ileocaecalis (valva ilealis) ileocecal valve UBERON:0000912 Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. CALOHA:TS-2144 ENVO:02000040 FMA:66938 GAID:1164 MESH:D009093 NCIT:C13259 OpenCyc:Mx4rvVjHq5wpEbGdrcN5Y29ycA UMLS:C0026727 galen:Mucus mucus UBERON:0000922 Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. AAO:0011035 AEO:0000169 BILA:0000056 BSA:0000039 BTO:0000379 CALOHA:TS-0229 EFO:0001367 EHDAA2:0000002 EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 FBbt:00000052 FMA:69068 GAID:963 MAT:0000226 MESH:D004622 MIAA:0000019 NCIT:C28147 OGEM:000001 OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA UMLS:C0013935 VHOG:0001766 XAO:0000113 ZFA:0000103 embryonic organism embryo UBERON:0000945 An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. AAO:0000579 ANISEED:1235297 BTO:0001307 CALOHA:TS-0980 EFO:0000837 EHDAA2:0001915 EHDAA:2993 EMAPA:17021 EV:0100070 FMA:7148 GAID:293 MA:0000353 MAT:0000051 MESH:D013270 MIAA:0000051 NCIT:C12391 OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA TAO:0002121 UMLS:C0038351 VHOG:0000408 XAO:0000128 galen:Stomach stomach chamber stomach UBERON:0000948 A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. AAO:0010210 BILA:0000020 BTO:0000562 CALOHA:TS-0445 EFO:0000815 EHDAA2:0000738 EHDAA:420 EMAPA:16105 EV:0100018 FMA:7088 GAID:174 MA:0000072 MAT:0000036 MESH:D006321 MIAA:0000036 NCIT:C12727 OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA TAO:0000114 UMLS:C0018787 VHOG:0000276 XAO:0000064 ZFA:0000114 galen:Heart chambered heart vertebrate heart branchial heart Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706 heart UBERON:0000970 An organ that detects light. BILA:0000017 BTO:0000439 CALOHA:TS-0309 EFO:0000827 EV:0100336 FBbt:00005162 GAID:69 MAT:0000140 MESH:D005123 MIAA:0000140 OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA eye UBERON:0000982 Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. articulation joint AEO:0000182 BTO:0001686 CALOHA:TS-2023 EFO:0000948 EMAPA:35456 FMA:7490 GAID:102 MA:0000319 MAT:0000188 MESH:D007596 MIAA:0000188 NCIT:C13044 OpenCyc:Mx4rvVjjdpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0003182 TAO:0000367 UMLS:C0022417 VHOG:0001276 VSAO:0000101 XAO:0000171 ZFA:0001596 galen:Joint skeletal joint UBERON:0000991 Reproductive organ that produces and releases eggs (ovary) or sperm (testis). AAO:0000213 BILA:0000123 BSA:0000079 BTO:0000534 EMAPA:17383 FBbt:00004858 FMA:18250 GAID:368 HAO:0000379 MA:0002420 MESH:D006066 NCIT:C12725 OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA TAO:0000413 UMLS:C0018067 VHOG:0000397 WBbt:0005175 XAO:0003146 ZFA:0000413 gonada gonad UBERON:0000992 The gonad of a female organism which contains germ cells. AAO:0000371 BILA:0000125 BSA:0000080 BTO:0000975 CALOHA:TS-0730 EFO:0000973 EHDAA2:0001360 EHDAA:8124 EMAPA:17962 EV:0100111 FBbt:00004865 FMA:7209 GAID:367 MA:0000384 MESH:D010053 MIAA:0000125 NCIT:C12404 OpenCyc:Mx4rvVi9QJwpEbGdrcN5Y29ycA TAO:0000403 UMLS:C0029939 VHOG:0000251 XAO:0000258 ZFA:0000403 animal ovary female gonad female organism genitalia gonad female organism genitalia gonada female organism reproductive system gonad female organism reproductive system gonada female reproductive system gonad female reproductive system gonada genitalia of female organism gonad genitalia of female organism gonada gonad of female organism genitalia gonad of female organism reproductive system gonad of female reproductive system gonad of genitalia of female organism gonad of reproductive system of female organism gonada of female organism genitalia gonada of female organism reproductive system gonada of female reproductive system gonada of genitalia of female organism gonada of reproductive system of female organism ovum-producing ovary reproductive system of female organism gonad reproductive system of female organism gonada ovary UBERON:0001003 The outer epithelial layer of the skin that is superficial to the dermis. epidermis skin AAO:0000143 BTO:0000404 CALOHA:TS-0283 EFO:0000954 EMAPA:17528 EV:0100153 FMA:70596 GAID:932 MA:0000153 MAT:0000154 MESH:D004817 MIAA:0000154 NCIT:C12708 TAO:0000105 UMLS:C0014520 VHOG:0000077 XAO:0000028 ZFA:0000105 vertebrate epidermis skin epidermis UBERON:0001004 Functional system which consists of structures involved in respiration. AAO:0000541 BTO:0000203 CALOHA:TS-1319 EFO:0000804 EHDAA2:0001604 EHDAA:2203 EMAPA:16727 EV:0100036 FMA:7158 GAID:78 MA:0000327 MAT:0000030 MESH:D012137 MIAA:0000030 NCIT:C12779 OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA TAO:0000272 UMLS:C0035237 VHOG:0000202 XAO:0000117 ZFA:0000272 apparatus respiratorius respiratory system respiratory system UBERON:0001005 An airway through which respiratory air passes in organisms. airway airways FMA:265130 respiratory airway UBERON:0001041 Anterior subdivision of a digestive tract. AAO:0011042 BILA:0000085 BTO:0000507 EHDAA2:0000557 EHDAA:520 EMAPA:16548 FBbt:00005379 FMA:45616 MA:0001526 NCIT:C34180 TGMA:0001014 UMLS:C0231051 VHOG:0000285 XAO:0000232 foregut UBERON:0001042 A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. pharynx AAO:0000967 BTO:0001049 CALOHA:TS-0785 EFO:0000836 EHDAA2:0001458 EHDAA:2947 EMAPA:16706 EV:0100065 FMA:46688 GAID:155 MA:0000432 MESH:D010614 NCIT:C12425 OpenCyc:Mx4rvViv7ZwpEbGdrcN5Y29ycA TAO:0000056 UMLS:C0031354 VHOG:0000462 XAO:0003227 ZFA:0000056 galen:Pharynx Consider generalizing to deuterostome pharynx chordate pharynx UBERON:0001043 Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993). AAO:0000145 ANISEED:1235301 BTO:0000959 CALOHA:TS-0700 EFO:0000835 EHDAA2:0001285 EHDAA:2937 EMAPA:16833 EV:0100069 FMA:7131 GAID:291 MA:0000352 MAT:0000048 MESH:D004947 MIAA:0000048 NCIT:C12389 OpenCyc:Mx4rvVj9Q5wpEbGdrcN5Y29ycA TAO:0000204 UMLS:C0014876 VHOG:0000450 XAO:0000127 ZFA:0000204 galen:Esophagus gullet oesophagus esophagus UBERON:0001045 Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. BILA:0000086 BTO:0000863 EFO:0001950 EHDAA2:0001185 EHDAA:983 EMAPA:16255 FBbt:00005383 FMA:45617 MA:0001564 NCIT:C34210 TGMA:0001036 UMLS:C0231052 VHOG:0000290 XAO:0000103 midgut UBERON:0001046 The caudalmost subdivision of a digestive tract. AAO:0011052 BILA:0000087 BTO:0000510 EHDAA2:0000779 EHDAA:975 EMAPA:16715 FBbt:00005384 FMA:45618 MA:0001527 NCIT:C34188 TGMA:0001020 UMLS:C0231053 VHOG:0000459 XAO:0000104 hindgut UBERON:0001052 The terminal portion of the intestinal tube, terminating with the anus. AAO:0010401 BTO:0001158 CALOHA:TS-1180 EFO:0000848 EHDAA2:0001592 EHDAA:5836 EMAPA:17896 EV:0100081 FMA:14544 GAID:311 MA:0000336 MAT:0000050 MESH:D012007 MIAA:0000050 NCIT:C12390 OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA UMLS:C0034896 VHOG:0001751 XAO:0000238 galen:Rectum terminal portion of intestine rectal rectum UBERON:0001062 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. AAO:0010841 AEO:0000000 BILA:0000000 BIRNLEX:6 CARO:0000000 EHDAA2:0002229 FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 NCIT:C12219 TAO:0100000 TGMA:0001822 UMLS:C1515976 WBbt:0000100 XAO:0000000 ZFA:0100000 anatomical entity UBERON:0001087 Transudate contained in the pleural cavity. BTO:0003080 FMA:12273 MA:0002532 MAT:0000500 ncithesaurus:Pleural_Fluid pleural fluid UBERON:0001088 Excretion that is the output of a kidney. BTO:0001419 CALOHA:TS-1092 EFO:0001939 EMAPA:36554 ENVO:00002047 FMA:12274 GAID:1189 MA:0002545 MAT:0000058 MESH:D014556 MIAA:0000058 NCIT:C13283 OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA UMLS:C0042036 galen:Urine urine UBERON:0001089 Secretion produced by a sweat gland. BTO:0001254 ENVO:02000025 FMA:12275 GAID:1172 MA:0002539 MESH:D013542 NCIT:C13280 OpenCyc:Mx4rvVjJtZwpEbGdrcN5Y29ycA UMLS:C0038984 sweat UBERON:0001090 Joint fluid is a transudate of plasma that is actively secreted by synovial cells. BTO:0001339 CALOHA:TS-0996 ENVO:02000039 FMA:12277 GAID:265 MA:0002544 MESH:D013582 NCIT:C33718 TAO:0005154 UMLS:C0039097 ZFA:0005154 galen:SynovialFluid joint fluid synovial fluid UBERON:0001097 The lymph nodes located around the axillary vein that receive lymphatic drainage from the upper or forelimb, scapular region and pectoral region. FMA:276805 MA:0000735 NCIT:C12904 UMLS:C0729594 axillary node axillary lymph node UBERON:0001130 Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO]. spine AAO:0000699 AAO:0000734 BTO:0000818 EFO:0001369 EHDA:10119 EMAPA:35919 FMA:13478 GAID:106 MA:0002416 MESH:D013131 NCIT:C12998 NCIT:C33588 NIF_Subcellular:sao1145756102 OpenCyc:Mx4rv2j-CpwpEbGdrcN5Y29ycA OpenCyc:Mx4rv6GF55wpEbGdrcN5Y29ycA OpenCyc:Mx4rvVkFEpwpEbGdrcN5Y29ycA TAO:0001559 UMLS:C0037949 UMLS:C1519455 VHOG:0001142 VSAO:0000185 XAO:0003074 ZFA:0001559 galen:SpinalColumn backbone vertebral column skeleton vertebral column http://purl.obolibrary.org/obo/BTO_0000818 UBERON:0001153 A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. BTO:0000166 CALOHA:TS-0122 EFO:0000850 EHDAA2:0000206 EHDAA:3913 EMAPA:35197 EV:0100397 FMA:14541 GAID:307 MA:0000334 MESH:D002432 MIAA:0000288 NCIT:C12381 OpenCyc:Mx4rve6u4JwpEbGdrcN5Y29ycA UMLS:C0007531 VHOG:0001559 galen:Cecum caecum cecum intestinum crassum caecum caeca ceca Taxon notes: in some herbivorous lizards, a cecum is present between small and large intestines[Kardong] caecum UBERON:0001155 A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. AAO:0010400 BTO:0000269 CALOHA:TS-0158 EFO:0000361 EMAPA:18939 EV:0100079 FMA:14543 GAID:309 MA:0000335 MAP:0000001 MAT:0000526 MESH:D003106 NCIT:C12382 OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA TAO:0000706 UMLS:C0009368 VHOG:0000648 XAO:0000243 ZFA:0000706 galen:Colon large bowel posterior intestine colon UBERON:0001156 Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified]. BTO:0000270 CALOHA:TS-0057 EFO:0000843 EMAPA:35151 FMA:14545 MA:0001541 MAT:0000311 MESH:D044682 MIAA:0000311 NCIT:C12265 OpenCyc:Mx4rv3H0FZwpEbGdrcN5Y29ycA UMLS:C0227375 galen:AscendingColon colon ascendens ascending colon UBERON:0001157 The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified]. BTO:0000272 CALOHA:TS-2052 EFO:0000844 EMAPA:35880 FMA:14546 MA:0001543 MAT:0000312 MESH:D044684 MIAA:0000312 NCIT:C12385 OpenCyc:Mx4rvg7qyJwpEbGdrcN5Y29ycA UMLS:C0227386 galen:TransverseColon colon transversum transverse colon UBERON:0001158 The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon. BTO:0000641 CALOHA:TS-2010 EFO:0000845 EMAPA:35285 FMA:14547 MA:0001542 MAT:0000313 MESH:D044683 MIAA:0000313 NCIT:C12268 OpenCyc:Mx4rwHsNhpwpEbGdrcN5Y29ycA UMLS:C0227389 galen:DescendingColon colon descendens descending colon UBERON:0001159 The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. BTO:0000645 CALOHA:TS-2044 EFO:0000846 EMAPA:36391 FMA:14548 MAT:0000314 MESH:D012809 MIAA:0000314 NCIT:C12384 NCIT:C33550 OpenCyc:Mx4rwHX_-5wpEbGdrcN5Y29ycA UMLS:C0227391 UMLS:C0682612 galen:SigmoidColon sigmoid colon UBERON:0001160 The fundus is the portion of the stomach that lies above the cardiac notch, and contains the fundic glands[GO, Kardong]. BTO:0000502 EFO:0002554 EHDAA2:0001919 EHDAA:4844 EMAPA:17886 FMA:14559 GAID:320 MA:0001612 MESH:D005748 NCIT:C12257 UMLS:C0017129 VHOG:0000421 galen:GastricFundus fundus gastricus (ventricularis) gastric fundus stomach fundus fundus of stomach UBERON:0001161 The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO]. BTO:0000505 EMAPA:35810 FMA:14560 MA:0002559 NCIT:C12258 UMLS:C0227230 galen:GastricCorpus corpus gastricum (ventriculare) gastric body stomach body body of stomach UBERON:0001162 The part of the stomach attached to the esophagus. The cardia begins immediately distal to the z-line of the gastroeosphageal junction, where the squamous epithelium of the esophagus gives way to the columnar epithelium of the gastrointestinal tract[WP]. UBERON:0004712 BTO:0000198 EMAPA:35811 FMA:14561 GAID:319 MA:0001609 MESH:D002299 NCIT:C12256 UMLS:C0007144 cardial part of stomach gastric cardia pars cardiaca (gaster) pars cardiaca gastricae stomach cardiac region cardia of stomach UBERON:0001163 The lesser curvature of the stomach, extending between the cardiac and pyloric orifices, forms the right or posterior border of the stomach. It descends as a continuation of the right margin of the esophagus in front of the fibers of the right crus of the diaphragm, and then, turning to the right, it crosses the first lumbar vertebra and ends at the pylorus. Nearer its pyloric than its cardiac end is a well-marked notch, the incisura angularis, which varies somewhat in position with the state of distension of the viscus; it serves to separate the stomach into a right and a left portion. The lesser curvature gives attachment to the two layers of the hepatogastric ligament, and between these two layers are the left gastric artery and the right gastric branch of the hepatic artery. [WP,unvetted]. EMAPA:37754 FMA:14572 MA:0001616 NCIT:C12261 UMLS:C0227221 galen:LesserCurvatureOfStomach stomach lesser curvature lesser curvature of stomach UBERON:0001164 The greater curvature of the stomach is directed mainly forward, and is four or five times as long as the lesser curvature. [WP,unvetted]. EMAPA:37753 FMA:14574 MA:0001615 NCIT:C12262 UMLS:C0227223 galen:GreaterCurvatureOfStomach stomach greater curvature greater curvature of stomach UBERON:0001165 The area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells. antrum BTO:0001732 EFO:0002555 EMAPA:17891 FMA:14579 GAID:332 MA:0001624 MESH:D011706 NCIT:C12259 UMLS:C0034193 galen:PyloricAntrum antrum of stomach stomach pyloric antrum pyloric antrum UBERON:0001166 The stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum. BTO:0001146 EHDAA2:0001580 EHDAA:4860 EMAPA:17631 FMA:14581 GAID:333 MA:0002560 MESH:D011708 NCIT:C12260 UMLS:C0034196 VHOG:0000420 galen:Pylorus pars pylorica pars pylorica gastricae pyloric part of stomach pyloric region stomach pyloric region pylorus UBERON:0001245 Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. BTO:0001680 CALOHA:TS-2005 EV:0100082 FBbt:00047153 FMA:15711 GAID:312 MA:0000331 NCIT:C43362 OpenCyc:Mx4rvVjaEZwpEbGdrcN5Y29ycA TADS:0000066 TGMA:0001279 UMLS:C0003461 WBbt:0005364 galen:Anus anal opening anal orifice opening of terminal part of digestive tract anus UBERON:0001255 Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. bladder AAO:0000623 BTO:0001418 CALOHA:TS-1090 EFO:0000290 EHDAA2:0000174 EHDAA:9328 EMAPA:18321 EV:0100098 FMA:15900 GAID:0000004 MA:0000380 MAT:0000122 MESH:D001743 MIAA:0000122 NCIT:C12414 OpenCyc:Mx4rvVjMmZwpEbGdrcN5Y29ycA UMLS:C0005682 VHOG:0000740 XAO:0000154 galen:UrinaryBladder vesica urinaria urinary bladder UBERON:0001268 Transudate contained in the peritoneal cavity. BTO:0001031 EMAPA:35683 FMA:16515 MA:0002531 ncithesaurus:Peritoneal_Fluid peritoneal fluid UBERON:0001359 cerebrospinal fluid (CSF) A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. BIRNLEX:1798 BTO:0000237 CALOHA:TS-0130 EFO:0000329 EHDAA2:0004441 ENVO:02000029 EV:0100311 FMA:20935 GAID:1181 MA:0002503 MAT:0000499 MESH:D002555 NCIT:C12692 TAO:0002184 UMLS:C0007806 VHOG:0001278 ZFA:0001626 CSF cerebral spinal fluid cerebrospinal fluid UBERON:0001474 Skeletal element that is composed of bone tissue. AAO:0000047 AEO:0000082 BTO:0000140 CALOHA:TS-0088 EFO:0000298 EHDAA2:0003082 EMAPA:32782 ENVO:00002039 EV:0100140 FMA:30317 FMA:5018 GAID:92 MA:0001459 MAT:0000299 MIAA:0000299 NCIT:C12366 OpenCyc:Mx4rvViDlpwpEbGdrcN5Y29ycA OpenCyc:Mx4rvVkCG5wpEbGdrcN5Y29ycA TAO:0001514 UMLS:C0262950 VHOG:0001190 VSAO:0000057 XAO:0000169 ZFA:0001514 galen:Bone bone organ bone element UBERON:0001488 A joint that connects the hindlimb autopod and zeugopod skeletons. BTO:0004706 EMAPA:35126 FMA:35195 GAID:257 MA:0000463 MESH:D000843 NCIT:C32078 OpenCyc:Mx4rvwiy35wpEbGdrcN5Y29ycA UMLS:C0003087 galen:AnkleJoint gambrel hock hock joint talotibial joint ankle joint UBERON:0001542 The lymph nodes located in the groin area. EMAPA:35431 FMA:44226 MA:0000737 NCIT:C32801 UMLS:C0729596 inguinal lymph node UBERON:0001543 The lymph nodes which drain the legs; contained in the popliteal fossa. FMA:44227 MA:0000738 NCIT:C53146 UMLS:C0588057 popliteal lymph node UBERON:0001555 A tube extending from the mouth to the anus. gut AAO:0010023 BILA:0000083 BTO:0000511 BTO:0000545 EHDAA2:0000726 EHDAA:518 EMAPA:16247 FBbt:00003125 FMA:45615 MA:0000917 NCIT:C34082 OpenCyc:Mx4rvVi0GpwpEbGdrcN5Y29ycA TAO:0000112 TGMA:0001819 UMLS:C0017189 VHOG:0000309 WBbt:0005743 ZFA:0000112 galen:AlimentaryTract digestive tube enteric tract alimentary canal alimentary tract digestive tract UBERON:0001557 The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. EHDAA2:0002136 EMAPA:17669 FMA:45661 MA:0000442 OpenCyc:Mx4rtT2HwgJMEdyAAADggVbxzQ VHOG:0000406 upper respiratory tract UBERON:0001558 The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]. EHDAA2:0001036 EMAPA:16738 FMA:45662 MA:0000435 OpenCyc:Mx4rQRqjUgAKEdyHxgDggVfs8g VHOG:0000382 lower respiratory system lower respiratory tract UBERON:0001560 FMA:45733 organ neck neck of organ UBERON:0001630 Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. muscle AAO:0011066 EMAPA:32715 EMAPA:37474 EV:0100146 FMA:5022 GAID:131 MA:0000015 OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA TAO:0005145 VHOG:0001245 XAO:0000172 ZFA:0005145 galen:Muscle muscle organ UBERON:0001707 An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. AAO:0000314 BTO:0002096 EHDAA2:0001226 EHDAA:6801 EMAPA:17604 FMA:54378 GAID:350 MA:0000284 MESH:D009296 NCIT:C12424 TAO:0000130 UMLS:C0027423 VHOG:0000271 ZFA:0000130 cavity of nose cavity of olfactory apparatus nasal canal nasal conduit space nasal fossa olfactory chamber cavity nasal cavity UBERON:0001728 The section of the pharynx that lies above the soft palate. BTO:0000662 CALOHA:TS-0663 EHDAA2:0001239 EHDAA:7086 EMAPA:17670 EV:0100066 FMA:54878 GAID:339 MA:0000443 MAT:0000447 MESH:D009305 NCIT:C12423 OpenCyc:Mx4rwUPoDJwpEbGdrcN5Y29ycA UMLS:C0027442 VHOG:0000375 nasal part of pharynx rhinopharynx nasopharynx UBERON:0001729 The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis. BTO:0005257 CALOHA:TS-0718 EFO:0001976 EHDAA2:0004082 EMAPA:25094 EV:0100067 FMA:54879 GAID:340 MA:0000351 MAT:0000446 MESH:D009960 NCIT:C12762 OpenCyc:Mx4rwACoxpwpEbGdrcN5Y29ycA UMLS:C0521367 VHOG:0000457 VSAO:0000034 XAO:0004048 oral part of pharynx oropharynx UBERON:0001762 The small curved bones that extends horizontally along the lateral wall of the nasal passage. EHDAA2:0004101 EMAPA:25093 GAID:224 MA:0000286 MESH:D014420 NCIT:C49594 OpenCyc:Mx4rv07bVJwpEbGdrcN5Y29ycA UMLS:C1266928 ossified nasal turbinal ossified nasal turbinate ossified turbinate turbinal bone turbinate bone turbinate bone UBERON:0001825 The paired air-filled cavities surrounded by the bones of the face that are lined by mucous membranes and are continuous with the nasal cavity. sinus CALOHA:TS-2082 EHDAA:6489 EMAPA:35662 EV:0100038 FMA:59679 GAID:355 MA:0000431 MESH:D010256 NCIT:C12763 UMLS:C0030471 paranasal sinus UBERON:0001827 Aqueous substance secreted by the lacrimal gland. BTO:0001499 CALOHA:TS-1016 EMAPA:36537 ENVO:02000034 FMA:59756 GAID:1173 MA:0002508 MESH:D013666 NCIT:C33739 UMLS:C0039409 galen:Tear galen:Tears lacrimal fluid lacrimal gland secretion lacrimal secretion tear tears secretion of lacrimal gland UBERON:0001836 A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. BTO:0001202 CALOHA:TS-0891 EMAPA:36536 ENVO:02000036 FMA:59862 GAID:1167 MA:0002507 MAT:0000444 MESH:D012463 NCIT:C13275 OpenCyc:Mx4rvVjJ95wpEbGdrcN5Y29ycA UMLS:C0036087 galen:Saliva salivary gland secretion saliva UBERON:0001913 An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. BTO:0000868 CALOHA:TS-0636 EMAPA:36540 ENVO:02000031 EV:0100126 FMA:62100 GAID:1230 MA:0002552 MAT:0000056 MESH:D008892 MIAA:0000056 NCIT:C13401 OpenCyc:Mx4rvVjGZJwpEbGdrcN5Y29ycA UMLS:C1511310 VHOG:0001263 galen:Milk mammary gland milk milk UBERON:0001914 The thin, yellow, serous fluid secreted by the mammary glands during pregnancy and immediately postpartum before lactation begins. It consists of immunologically active substances, white blood cells, water, protein, fat, and carbohydrates. BTO:0000276 CALOHA:TS-0167 FMA:62101 GAID:1159 MA:0002551 MESH:D003126 NCIT:C32348 UMLS:C0009413 colostrum UBERON:0001969 The liquid component of blood, in which erythrocytes are suspended. plasma portion of plasma BTO:0000131 CALOHA:TS-0800 EFO:0001905 EMAPA:35690 FMA:62970 GAID:1178 MA:0002501 MAT:0000052 MESH:D010949 MIAA:0000052 NCIT:C13356 OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw UMLS:C0032105 blood plasm portion of blood plasma blood plasma UBERON:0001977 The portion of blood plasma that excludes clotting factors. BTO:0000133 BTO:0001239 CALOHA:TS-0923 EHDAA2:0004728 EMAPA:35770 FMA:63083 MA:0002502 MESH:D044967 NCIT:C13325 UMLS:C0229671 serum blood serum UBERON:0001988 Portion of semisolid bodily waste discharged through the anus[MW,modified]. excreta BTO:0000440 CALOHA:TS-2345 ENVO:00002003 FMA:64183 GAID:1199 MA:0002509 MAT:0000053 MESH:D005243 MIAA:0000053 NCIT:C13234 OpenCyc:Mx4rvVjJMZwpEbGdrcN5Y29ycA UMLS:C0015733 galen:Feces faeces fecal material fecal matter piece of shit portion of excrement portion of faeces portion of fecal material portion of fecal matter portion of feces portionem cacas stool cow dung cow pat dung fewmet frass guano portion of dung portion of guano portion of scat scat spraint feces UBERON:0002048 Respiration organ that develops as an outpocketing of the esophagus. AAO:0000275 AAO:0010567 BTO:0000763 CALOHA:TS-0568 EFO:0000934 EHDAA2:0001042 EHDAA:1554 EHDAA:2205 EMAPA:16728 EV:0100042 FMA:7195 GAID:345 MA:0000415 MAT:0000135 MESH:D008168 MIAA:0000135 NCIT:C12468 OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA UMLS:C0024109 VHOG:0000310 XAO:0000119 galen:Lung pulmo Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP] lung UBERON:0002050 Anatomical structure that is part of an embryo. AAO:0000138 BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 NCIT:C13229 RETIRED_EHDAA2:0003169 TAO:0001105 UMLS:C0013948 VSAO:0000178 XAO:0003042 ZFA:0001105 developing embryonic structure embryonic anatomical structure embryonic structure UBERON:0002075 An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. AAO:0010386 BTO:0001491 EHDAA:512 EMAPA:16245 FMA:7085 MA:0000019 MESH:D014781 NCIT:C28287 RETIRED_EHDAA2:0002201 UMLS:C0042779 XAO:0003034 visceral organ visceral organ system viscus UBERON:0002106 The organ that functions to filter blood and to store red corpuscles and platelets. AAO:0010395 BTO:0001281 CALOHA:TS-0956 EFO:0000869 EMAPA:18767 EV:0100055 FMA:7196 GAID:1289 MA:0000141 MAT:0000085 MESH:D013154 MIAA:0000085 NCIT:C12432 OpenCyc:Mx4rvVjgw5wpEbGdrcN5Y29ycA TAO:0000436 UMLS:C0037993 VHOG:0000120 XAO:0000328 ZFA:0000436 galen:Spleen spleen UBERON:0002107 An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. AAO:0010111 BTO:0000759 CALOHA:TS-0564 EFO:0000887 EHDAA2:0000997 EHDAA:2197 EMAPA:16846 EV:0100089 FMA:7197 GAID:288 MA:0000358 MAT:0000097 MESH:D008099 MIAA:0000097 NCIT:C12392 OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA TAO:0000123 UMLS:C0023884 VHOG:0000257 XAO:0000133 ZFA:0000123 galen:Liver liver UBERON:0002108 Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong]. AAO:0010397 BTO:0000651 CALOHA:TS-0942 EFO:0000841 EMAPA:32834 EV:0100072 FMA:7200 GAID:313 MA:0000337 MAT:0000047 MESH:D007421 MIAA:0000047 NCIT:C12386 OpenCyc:Mx4rvVjlIJwpEbGdrcN5Y29ycA TAO:0001323 UMLS:C0021852 VHOG:0000055 XAO:0000130 ZFA:0001323 galen:SmallIntestine small bowel small intestine small intestine UBERON:0002109 Pair of nostrils. FMA:72005 OpenCyc:Mx4rvViCLpwpEbGdrcN5Y29ycA nares set nostrils pair of nostrils pair of nares UBERON:0002110 An organ that aids digestion and stores bile produced by the liver[WP]. AAO:0010114 BTO:0000493 CALOHA:TS-0394 EFO:0000853 EHDAA2:0000699 EHDAA:8062 EMAPA:17202 EV:0100090 FMA:7202 MA:0000356 MAT:0000072 MESH:D005704 MIAA:0000072 NCIT:C12377 OpenCyc:Mx4rvVkGr5wpEbGdrcN5Y29ycA TAO:0000208 UMLS:C0016976 VHOG:0000221 XAO:0000135 ZFA:0000208 galen:Gallbladder cholecyst gall bladder Rats do not have a gallbladder, but produce bile. The bile flows directly from the liver through the (hepatic) bile duct into the small intestine (Hebel and Stromberg, 1988) gallbladder UBERON:0002113 A paired organ of the urinary tract which has the production of urine as its primary function. AAO:0000250 BTO:0000671 CALOHA:TS-0510 EFO:0000929 EMAPA:17373 EV:0100096 FMA:7203 GAID:423 MA:0000368 MAT:0000119 MESH:D007668 MIAA:0000119 NCIT:C12415 OpenCyc:Mx4rvVjlYpwpEbGdrcN5Y29ycA UMLS:C0022646 XAO:0003267 galen:Kidney reniculate kidney kidney UBERON:0002114 The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). AAO:0010402 BTO:0000365 CALOHA:TS-0214 EFO:0000851 EMAPA:18852 EV:0100073 FMA:7206 GAID:284 MA:0000338 MAT:0000044 MESH:D004386 MIAA:0000044 NCIT:C12263 OpenCyc:Mx4rv4LJDpwpEbGdrcN5Y29ycA UMLS:C0013303 VHOG:0000052 XAO:0000236 galen:Duodenum duodenum UBERON:0002115 The portion of the small intestine that extends from the duodenum to the ileum. BTO:0000657 CALOHA:TS-0496 EFO:0001333 EMAPA:18666 EV:0100074 FMA:7207 GAID:318 MA:0000340 MAT:0000045 MESH:D007583 MIAA:0000045 NCIT:C12388 OpenCyc:Mx4rwATkPJwpEbGdrcN5Y29ycA UMLS:C0022378 VHOG:0000053 galen:Jejunum jejunum UBERON:0002116 The portion of the small intestine that extends from the jejunum to the colon. AAO:0010403 BTO:0000620 CALOHA:TS-0472 EFO:0001334 EMAPA:32764 EV:0100075 FMA:7208 GAID:315 MA:0000339 MAT:0000282 MESH:D007082 MIAA:0000282 NCIT:C12387 OpenCyc:Mx4rvdcLHZwpEbGdrcN5Y29ycA UMLS:C0020885 VHOG:0000647 XAO:0000237 galen:Ileum ileum UBERON:0002167 Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]. EHDAA2:0001730 EHDAA:4969 EMAPA:17661 FMA:7309 MA:0000426 NCIT:C33483 OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA UMLS:C0225706 VHOG:0000301 right lung UBERON:0002169 The small terminal dilation of the alveolar ducts around which the alveoli form pocket-like clusters. UBERON:0008871 BTO:0000061 EMAPA:35119 FMA:7317 MA:0000418 NCIT:C32057 OpenCyc:Mx4rwCvh75wpEbGdrcN5Y29ycA UMLS:C0225691 pulmonary alveolar sac sacculus alveolaris alveolar sac UBERON:0002185 The upper conducting airways of the lung; these airways arise from the terminus of the trachea. BTO:0001340 CALOHA:TS-1229 EFO:0000932 EMAPA:32689 EV:0100041 FMA:7409 GAID:346 MA:0000436 MAT:0000133 MESH:D001980 MIAA:0000133 NCIT:C12683 UMLS:C0006255 VHOG:0000262 XAO:0000121 bronchi bronchial trunk bronchus UBERON:0002186 The conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching. BTO:0002375 CALOHA:TS-2003 EHDAA:8171 EHDAA:8183 EHDAA:8199 EHDAA:8221 EMAPA:32697 FMA:7410 MA:0000422 MESH:D055745 NCIT:C12684 OpenCyc:Mx4rvl9iDpwpEbGdrcN5Y29ycA UMLS:C0006270 VHOG:0000675 lobular bronchiole bronchiole UBERON:0002217 Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]. AEO:0000183 CALOHA:TS-2138 EHDAA2:0003183 FMA:7501 MA:0000322 NCIT:C32461 OpenCyc:Mx4rv2bBV5wpEbGdrcN5Y29ycA TAO:0005153 ZFA:0005153 galen:SynovialJoint articulatio synoviale diarthroses diarthrosis diarthrosis joint synovial joint UBERON:0002355 The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. BTO:0001006 CALOHA:TS-2227 EFO:0002805 EMAPA:35931 EV:0100012 FMA:9578 GAID:87 MA:0000030 MESH:D010388 NCIT:C12767 OpenCyc:Mx4rvVjiTJwpEbGdrcN5Y29ycA UMLS:C0030797 galen:Pelvis lesser pelvis pelvic region pelvis pelvis region true pelvis pelvic region of trunk UBERON:0002365 A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas. AEO:0000097 BTO:0000765 CALOHA:TS-2012 EHDAA2:0003097 EMAPA:35327 FMA:9596 GAID:34 MA:0002564 MESH:D005088 NCIT:C12712 UMLS:C0015282 ducted gland glandula exocrina exocrine gland UBERON:0002368 Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. AEO:0000098 BTO:0001488 CALOHA:TS-1300 EHDAA2:0003098 EMAPA:35999 FMA:9602 GAID:335 MA:0002563 MESH:D004702 NCIT:C12704 OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA UMLS:C0014133 ductless gland glandula endocrina endocrine gland UBERON:0002371 The soft tissue that fills the cavities of bones. AAO:0011007 BTO:0000141 BTO:0000829 CALOHA:TS-0087 EFO:0000868 EMAPA:32760 EV:0100046 FMA:9608 GAID:1287 MA:0000134 MAT:0000084 MESH:D001853 MIAA:0000084 NCIT:C12431 OpenCyc:Mx4rvVm-FpwpEbGdrcN5Y29ycA UMLS:C0005953 VHOG:0001218 XAO:0000123 galen:BoneMarrow medulla ossea medulla ossium bone marrow UBERON:0002384 Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. AAO:0000098 BTO:0000421 CALOHA:TS-2009 EFO:0000952 EMAPA:35251 FMA:9640 GAID:100 MA:0000011 MAT:0000301 MESH:D003238 MIAA:0000301 NCIT:C12374 OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA TAO:0001641 UMLS:C0009780 VSAO:0000017 XAO:0001017 ZFA:0001632 galen:ConnectiveTissue portion of connective tissue textus connectivus connective tissue UBERON:0002385 Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. AAO:0000306 AEO:0000122 CALOHA:TS-0642 EHDAA2:0003122 EMAPA:32715 FMA:9641 MA:0002437 MESH:D009132 NCIT:C12435 UMLS:C2328219 galen:MuscleTissue muscular tissue portion of muscle tissue textus muscularis Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach. muscle tissue UBERON:0002391 Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]. BTO:0000855 CALOHA:TS-0580 EFO:0000871 ENVO:02000041 EV:0100049 FMA:9671 GAID:1186 MA:0002520 MAT:0000055 MESH:D008196 MIAA:0000055 NCIT:C13252 OpenCyc:Mx4rvpDOU5wpEbGdrcN5Y29ycA UMLS:C0024202 VHOG:0001590 ZFA:0005658 galen:Lymph lymph UBERON:0002398 Distal segment of the fore limb, including carpal region, metacarpal region and digits. AAO:0010803 BTO:0004668 CALOHA:TS-2213 EHDAA2:0000728 EMAPA:17428 FMA:9712 GAID:56 MA:0000037 MESH:D006225 NCIT:C32712 NLXANAT:20090603 OpenCyc:Mx4rvViGVZwpEbGdrcN5Y29ycA UMLS:C0018563 VHOG:0000344 galen:Hand forelimb autopod forelimb autopodium hand hand region terminal segment of free upper limb fore foot fore paw fore-paw forefeet forefoot forefoot of quadruped forepaw manus UBERON:0002399 The double layer of peritoneum that extends from the liver to the lesser curvature of the stomach and the start of the duodenum. [WP,unvetted]. EHDAA2:0000991 EHDAA:4858 EMAPA:17890 EV:0100086 FMA:9715 MA:0001623 NCIT:C32981 UMLS:C0230260 VHOG:0000357 lesser omentum UBERON:0002402 The fluid-filled cavity that lies between the visceral and parietal pleurae. BTO:0004422 EHDAA2:0001475 EMAPA:16773 EMAPA:16774 FMA:9740 GAID:95 MA:0000055 MESH:D035422 NCIT:C12840 OpenCyc:Mx4rwCKAppwpEbGdrcN5Y29ycA UMLS:C0178802 VHOG:0000581 cavitas pleuralis pleural cavity UBERON:0002409 Transudate contained in the pericardial cavity.[FMA]. BTO:0001016 FMA:9887 MA:0002530 MESH:D000069236 pericardial fluid UBERON:0002424 An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues. AAO:0010357 BTO:0001775 CALOHA:TS-0715 EHDAA2:0001325 EHDAA:2187 EMAPA:16839 EMAPA:26942 FMA:265152 MA:0000344 NCIT:C49595 TAO:0000816 UMLS:C1709332 VHOG:0000187 XAO:0003201 ZFA:0000816 epithelium of mucosa of mouth epithelium of oral mucosa oral epithelium UBERON:0002429 Cervical lymph nodes are lymph nodes found in the neck. [WP,unvetted]. FMA:61213 MA:0000736 NCIT:C32298 UMLS:C0588054 lymph node of neck cervical lymph node UBERON:0002453 The evaginations of the mucous membrane of the nasal cavity into the ethmoidal bony labyrinth, forming multiple small paranasal sinuses. FMA:84115 GAID:356 MA:0001792 MESH:D005005 NCIT:C12276 UMLS:C0015028 ethmoidal bone sinus ethmoidal sinus ethmoid sinus UBERON:0002470 Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot. autopod BTO:0004359 EFO:0000877 EMAPA:32722 FMA:83015 MA:0002714 MAT:0000091 MIAA:0000091 NCIT:C77660 UMLS:C0687080 autopodial limb segment autopodial segment autopodium autopodium region distal free limb segment distal segment of free limb autopod region UBERON:0002507 A lymph node that is part of an abdomen [Automatically generated definition]. EMAPA:35992 FMA:12787 MA:0002827 abdomen lymph node lymph node of abdomen abdominal lymph node UBERON:0002508 The visceral glands that are associated with the branches of the celiac artery, including the gastric, hepatic, and pancreaticolienal (splenic) lymph nodes. FMA:12792 MA:0002828 NCIT:C65166 UMLS:C0229766 celiac node coeliac node nodus lymphaticus coeliacus terminal ventral aortic node celiac lymph node UBERON:0002509 The lymph nodes located in the mesentery, of which there are 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group. BTO:0000767 EMAPA:35561 FMA:12795 MA:0002829 NCIT:C77641 UMLS:C0229792 mesenteric node mesenteric lymph node UBERON:0002513 Replacement bone that forms within cartilage. AAO:0010776 AEO:0000083 BTO:0002157 EHDAA2:0003083 FMA:24321 TAO:0001591 VSAO:0000145 XAO:0004018 ZFA:0001591 ossified chondrogenic bone endochondral bone UBERON:0002520 The submandibular lymph nodes (submaxillary glands in older texts), three to six in number, are placed beneath the body of the mandible in the submaxillary triangle, and rest on the superficial surface of the submaxillary salivary gland. One gland, the middle gland of Stahr, which lies on the external maxillary artery as it turns over the mandible, is the most constant of the series; small lymph glands are sometimes found on the deep surface of the submaxillary salivary glands. The afferents of the submaxillary glands drain the medial palpebral commissure, the cheek, the side of the nose, the upper lip, the lateral part of the lower lip, the gums, and the anterior part of the margin of the tongue. Efferent vessels from the facial and submental glands also enter the submaxillary glands. Their efferent vessels pass to the superior deep cervical glands. [WP,unvetted]. BTO:0000769 FMA:61224 MA:0002843 NCIT:C77650 UMLS:C0229722 submandibular node submandibular lymph node UBERON:0002524 A lymph node that is part of a mediastinum. Each consists of several lymph node groups, especially along the trachea (5 groups), along the esophagus and between the lung and the diaphragm. In the mediastinal lymph nodes arises lymphatic ducts, which draines the lymph to the left subclavian vein (to the venous angle in the confluence of the subclavian and deep jugular veins). The mediastinal lymph nodes along the esophagus are in tight connection with the abdominal lymph nodes along the esophagus and the stomach. That fact facilitates spreading of tumors cells through these lymphatics in cases of cancers of the stomach and particularly of the esophagus. Through the mediastinum, the main lymphatic drainage from the abdominal organs goes via the thoracic duct (ductus thoracicus), which drains majority of the lymph from the abdomen to the above mentioned left venous angle. EFO:0001670 EMAPA:35555 FMA:12774 MA:0002877 NCIT:C33073 UMLS:C0588055 mediastinal node mediastinal lymph node UBERON:0002525 The lymph nodes located along the brachial vein that receive drainage from most of the free upper limb and send efferent vessels to the central axillary lymph nodes. FMA:44314 MA:0002878 NCIT:C92221 UMLS:C0229840 brachial lymph node UBERON:0002526 The lumbar lymph nodes (paraaortic nodes) are a group of lymph nodes residing in the lumbar region. They consist of the following groups: right and left lateral aortic lymph nodes preaortic lymph nodes retroaortic lymph nodes (or 'postaortic'). FMA:84599 MA:0002879 NCIT:C118775 lumbar lymph node UBERON:0002527 A lymph node that is part of a pancreas [Automatically generated definition]. FMA:16626 MA:0002881 NCIT:C77642 UMLS:C0229783 lymph node of pancreas pancreas lymph node pancreatic node pancreatic lymph node UBERON:0002528 A lymph node located in the sacral region. FMA:16655 MA:0002883 NCIT:C77647 UMLS:C0229827 sacral node sacral lymph node UBERON:0002529 A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles. FMA:241863 MA:0002889 NCIT:C38630 UMLS:C1268195 free limb segment segment of limb subdivision of limb limb segment UBERON:0002530 An organ that functions as a secretory or excretory organ. AAO:0000212 AEO:0000096 BTO:0000522 EFO:0000797 EHDAA2:0003096 EHDAA:2161 EHDAA:4475 EHDAA:6522 EMAPA:18425 FBbt:00100317 FMA:7146 FMA:86294 HAO:0000375 MA:0003038 MAT:0000021 MIAA:0000021 NCIT:C13319 OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA UMLS:C1285092 WikipediaCategory:Glands galen:Gland glandular organ gland UBERON:0002553 Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. cavity BIRNLEX:1011 EMAPA:37442 FMA:67552 MA:0002447 NCIT:C34007 galen:Cavity anatomical cavity UBERON:0003102 Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. AAO:0010337 AEO_RETIRED:0000010 EHDAA2_RETIRED:0003010 TAO:0000292 VSAO:0000001 XAO:0003028 ZFA:0000292 galen:SurfaceRegion anatomical surface feature surface structure UBERON:0003103 Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. AAO:0010015 AEO:0000024 BILA:0000024 CARO:0000024 EHDAA2:0003024 HAO:0000024 TADS:0000598 TAO:0000496 TGMA:0001837 VHOG:0001723 XAO:0003041 ZFA:0000496 compound organ UBERON:0003126 The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. AAO:0010140 BTO:0001388 CALOHA:TS-1060 EFO:0000935 EHDAA2:0002066 EHDAA:3078 EMAPA:16853 EV:0100040 FMA:7394 GAID:361 MA:0000441 MAT:0000137 MESH:D014132 MIAA:0000137 NCIT:C12428 OpenCyc:Mx4rvViOX5wpEbGdrcN5Y29ycA UMLS:C0040578 VHOG:0000371 XAO:0000118 cartilaginous trachea vertebrate trachea windpipe trachea UBERON:0003133 An organ involved in reproduction. EMAPA:17381 EMAPA:37731 MA:0001752 MESH:D005835 NCIT:C25177 OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA TGMA:0000591 UMLS:C0017420 WBbt:0008422 genital organ reproductive system organ sex organ reproductive organ UBERON:0003134 A female organ involved in reproduction. EMAPA:28540 MA:0000544 female organism reproductive organ female organism reproductive structure female organism reproductive system organ female organism sex organ female reproductive gland/organ female reproductive system organ female sex organ reproductive organ of female organism reproductive structure of female organism reproductive system organ of female organism sex organ of female organism female reproductive organ UBERON:0003135 A male organ involved in reproduction. MA:0000545 WBbt:0008423 male organism reproductive organ male organism reproductive structure male organism reproductive system organ male organism sex organ male reproductive gland/organ male reproductive system organ male sex organ reproductive organ of male organism reproductive structure of male organism reproductive system organ of male organism sex organ of male organism male reproductive organ UBERON:0003286 EHDAA2:0000560 EHDAA:3830 EMAPA:17178 foregut duodenum foregut region of duodenum UBERON:0003287 EHDAA2:0001189 EHDAA:3937 EMAPA:17193 midgut duodenum midgut region of duodenum UBERON:0003350 A layer of epithelial cells on the surface of the mucosa. BTO:0003752 lies on top of lamina propria epithelium of mucosa UBERON:0003425 A lymph node that is located in a kidney [Automatically generated definition]. FMA:276799 MA:0002882 NCIT:C77646 UMLS:C2699031 kidney lymph node lymph node of kidney renal lymph node UBERON:0003457 A bone that is part of a head [Automatically generated definition]. EMAPA:35996 MA:0000576 adult head bone adult head bone organ bone of adult head bone of head bone organ of adult head bone organ of head head bone organ Different sources vary regarding which bones are craniofacial; e.g. hyoid bone head bone UBERON:0003462 A bone that is part of a facial skeleton [Automatically generated definition]. EMAPA:19019 EMAPA:35924 MA:0001482 MA:0003159 MESH:D005147 NCIT:C63706 UMLS:C0015455 bone of facial skeleton facial bone facial skeleton bone facial bone UBERON:0003657 Any joint that is part of a (free) limb. EMAPA:36501 FMA:321558 MA:0000691 galen:LimbJoint joint of limb joint of limb skeletal system skeletal limb joint Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses limb joint UBERON:0003668 A small fluid-filled sac lined by synovial membrane with an inner capillary layer of slimy fluid. It provides a cushion between bones and tendons and/or muscles around a joint. This helps to reduce friction between the bones and allows free movement. Bursae are filled with synovial fluid and are found around most major joints of the body. bursa FMA:9692 GAID:252 MESH:D002061 NCIT:C33717 UMLS:C0006441 galen:Bursa synovial bursa UBERON:0003672 A collection of teeth arranged in some pattern in the mouth or other part of the body. The arrangement may be a simple row, a collection of rows, or a more elaborate structure, such as a toooth whorl. AAO:0000126 FMA:75150 GAID:1249 MESH:D003817 NCIT:C13072 OpenCyc:Mx4rvVi65JwpEbGdrcN5Y29ycA UMLS:C0011443 dentes set of teeth teeth teeth set dentition UBERON:0003688 A fold of peritoneum originating at the stomach and supporting the viscera. CALOHA:TS-2004 EV:0100084 FMA:14650 GAID:23 MESH:D009852 NCIT:C33209 UMLS:C0028977 galen:Omentum omentum UBERON:0003729 A mucous membrane that lines the mouth. BTO:0002860 CALOHA:TS-0716 EMAPA:26937 FMA:59660 GAID:951 MA:0002794 MESH:D009061 NCIT:C77637 UMLS:C0026639 mouth mucosa mouth mucous membrane mouth organ mucosa mucosa of mouth mucous membrane of mouth oral mucous membrane oral part of viscerocranial mucosa tunica mucosa oris mouth mucosa UBERON:0003840 A limb joint that is part of a hindlimb [Automatically generated definition]. EMAPA:32635 MA:0000662 hind limb joint of limb hind limb limb joint hindlimb joint of limb hindlimb limb joint inferior member joint of limb inferior member limb joint joint of free lower limb joint of limb of hind limb joint of limb of hindlimb joint of limb of inferior member joint of limb of lower extremity joint of lower limb limb joint of hind limb limb joint of hindlimb limb joint of inferior member limb joint of lower extremity lower extremity joint of limb lower extremity limb joint hindlimb joint UBERON:0003914 Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. AEO:0000114 EHDAA2:0003114 FBbt:00007474 epithelial or endothelial tube epithelial tube UBERON:0003929 An epithelium that lines the lumen of the digestive tract. BTO:0000956 EHDAA2:0004567 EMAPA:32928 MA:0003201 NCIT:C12963 TAO:0005123 UMLS:C0836205 XAO:0003200 ZFA:0005123 digestive tract epithelial tissue epithelial tissue of digestive tract epithelial tissue of gut epithelium of digestive tract epithelium of gut gastrodermis gut epithelial tissue gut epithelium digestive tract epithelium UBERON:0003968 The lymph nodes located outside the thoracic and abdominal cavities, such as the submandibular, prescapular, axillary, inguinal and popliteal lymph nodes. EMAPA:37938 peripheral lymph node UBERON:0003973 One of the conchae of the ethmoid bone, which occupy the caudal part of the nasal fossae and form the lateral and superior portions of the turbinate bones in mammals[MP]. The ethmoturbinals are associated with the cribiform plate. They are covered with olfactory epithelium. Primarily, they serve to increase the surface area over which olfactory receptor neurons can come in contact with respiratory air. These olfactory receptor nerves then synapse with the mitral cells of the olfactory lobes through the cribiform plate in the manner described above[Palaeos]. EMAPA:37914 FMA:57456 ethmo-turbinate ethmoturbinal ethmoturbinate nasal turbinate of ethmoid bone turbinate of ethmoid bone nasal concha of ethmoid bone UBERON:0003978 EHDAA2:0004046 EHDAA:1892 EHDAA:4406 FMA:67611 OpenCyc:Mx4rvqiwE5wpEbGdrcN5Y29ycA galen:Valve anatomical valve valve UBERON:0004045 The extension of the hindgut of the primitive digestive tube of the embryo, caudal to the location of the anal opening. EMAPA:36331 tailgut UBERON:0004111 Any tube, opening or passage that connects two distinct anatomical spaces. AEO:0000080 EHDAA2:0003080 FMA:242873 foramen foramina anatomical conduit UBERON:0004119 An anatomical structure that develops (entirely or partially) from the endoderm. endoderm-derived structure UBERON:0004120 An anatomical structure that develops (entirely or partially) from the mesoderm. mesodermal derivative mesoderm-derived structure UBERON:0004121 An anatomical structure that develops (entirely or partially) from the ectoderm. ectodermal deriviative ectoderm-derived structure UBERON:0004175 The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals. FMA:45652 internal genitalia internal genitals TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 internal genitalia UBERON:0004176 The external genitalia are the outer sex organs, such as the penis or vulva in mammals. FMA:45643 external genitalia TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 external genitalia UBERON:0004177 Organ that is part of the hematopoietic system. BTO:0004605 EMAPA:37665 FMA:7143 MA:0000747 haematological system organ haemopoietic system organ hematopoeitic organ hematopoietic system organ organ of haematological system organ of haemopoietic system organ of hematopoietic system organ of organa haemopoietica organa haemopoietica organ hematopoeitic or lymphoid organ lymph organ lymphoid organ hemopoietic organ UBERON:0004185 A portions of the gut that is derived from endoderm. EMAPA:32930 endodermal gut gut endoderm endodermal part of digestive tract UBERON:0004529 A projection or outgrowth of tissue from a larger body or organ. anatomical process process AAO:0010278 FMA:67601 HAO:0000822 NCIT:C61549 TAO:0001834 VSAO:0000180 XAO:0004020 galen:Ridge processus projection flange flanges lamella lamellae lamina laminae organ process papilla process of organ processes projection projections ridge ridges shelf shelves anatomical projection UBERON:0004538 A kidney that is part of a left side of organism [Automatically generated definition]. EMAPA:36589 FMA:7205 MA:0001655 NCIT:C34006 UMLS:C0227614 left kidney UBERON:0004539 A kidney that is part of a right side of organism [Automatically generated definition]. EMAPA:36590 FMA:7204 MA:0001683 NCIT:C34005 UMLS:C0227613 right kidney UBERON:0004590 A structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. FMA:75004 NCIT:C28381 UMLS:C1409894 sphincter sphincter muscle UBERON:0004722 The deep cervical lymph nodes are a group of cervical lymph nodes found near the internal jugular vein. They can be divided into upper and lower groups, or superior and inferior groups. Alternatively, they can be divided into deep anterior cervical lymph nodes and deep lateral cervical lymph nodes. They can also be divided into three groups: superior deep jugular, middle deep jugular, and 'inferior deep jugular'. EMAPA:37510 MA:0002885 NCIT:C32431 UMLS:C0458298 deep cervical lymph node UBERON:0004765 Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 VSAO:0000128 XAO:0004012 ZFA:0005494 galen:SkeletalStructure skeletal element UBERON:0004766 A bone that is part of a cranium. cranium bone cranial bone UBERON:0004802 The pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi. BTO:0000419 CALOHA:TS-0023 EMAPA:32827 MA:0001480 VHOG:0000981 epithelial tissue of respiratory tract epithelium of respiratory tract respiratory tract epithelial tissue respiratory tract epithelium UBERON:0004807 An epithelium that is part of a respiratory system [Automatically generated definition]. CALOHA:TS-0023 EMAPA:32826 MA:0001823 VHOG:0000981 apparatus respiratorius epithelial tissue apparatus respiratorius epithelium epithelial tissue of apparatus respiratorius epithelial tissue of respiratory system epithelium of apparatus respiratorius epithelium of respiratory system respiratory system epithelial tissue respiratory system epithelium UBERON:0004815 An epithelium that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:37549 MA:0001481 epithelial tissue of lower respiratory tract epithelium of lower respiratory tract lower respiratory tract epithelial tissue lower respiratory tract epithelium UBERON:0004870 A group of nodes lying along the external jugular vein; they drain the skin and superficial structures over the region of the sternocleidomastoid muscle and anterior cervical regions. Efferent vessels drain to the deep cervical lymph nodes. Lymph nodes can be further subdivided into anterior and lateral groupings. EMAPA:37725 MA:0002886 NCIT:C33659 UMLS:C0458297 superficial cervical lymph node UBERON:0004905 Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. FBbt:00005811 joint articulation UBERON:0004906 A portion of the gut that is derived from ectoderm. ectodermal gut gut ectoderm ectodermal part of digestive tract UBERON:0004907 The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition]. gut FMA:49179 NCIT:C33010 UMLS:C0226875 galen:LowerGastrointestinalTract lower GI tract lower gastrointestinal tract lower digestive tract UBERON:0004908 The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum. FMA:49177 NCIT:C33837 UMLS:C0226874 galen:UpperGastrointestinalTract upper GI tract upper gastrointestinal tract upper digestive tract UBERON:0004912 EHDAA2:0000171 EMAPA:16561 EMAPA_RETIRED:16565 VHOG:0001351 biliary bud UBERON:0004921 A proximal-distal subdivision of the digestive tract. FBbt:00100315 FMA:71131 subdivision of digestive tract UBERON:0004923 A part of a wall of an organ that forms a layer. FMA:82485 organ component layer UBERON:0005052 The muscular enlargement of the alimentary canal that has usually thick muscular walls and a tough horny lining for grinding the food and when the crop is present follows it and the proventriculus. BTO:0000520 GAID:1238 MESH:D005895 NCIT:C77615 UMLS:C1510668 gastric mill gigerium gizzard UBERON:0005057 An organ that is part of a immune system [Automatically generated definition]. immune system organ immune organ UBERON:0005079 A product of the somatic follicle cell epithelium and a structure that supports the egg in a hostile environment, minimizing water loss whilst allowing gas exchanges essential for embryonic respiration[GO]. BTO:0001716 MESH:D004528 WBbt:0005843 egg shell eggshell UBERON:0005090 Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. EMAPA:32715 FMA:30316 musculus muscle structure UBERON:0005156 Any anatomical structure that is part of the reproductive system. reproductive system element reproductive system structure reproductive structure UBERON:0005172 An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. MA:0000522 abdomen organ abdomen element UBERON:0005173 An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. EMAPA:37062 MA:0000529 abdominal segment organ abdominal segment element UBERON:0005177 An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. EMAPA:37270 MA:0000516 trunk organ trunk region element UBERON:0005178 An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. EMAPA:37273 MA:0000557 thoracic cavity organ thoracic cavity element UBERON:0005179 An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis. EMAPA:37275 MA:0000543 pelvic element pelvis organ pelvis region organ pelvic region element UBERON:0005181 An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. EMAPA:37271 MA:0000563 thoracic segment organ UBERON:0005291 A portion of tissue that is part of an embryo. CALOHA:TS-2100 portion of embryonic tissue embryonic tissue UBERON:0005423 AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 FBbt:00007006 FMA:292313 MIAA:0000019 developing anatomical structure UBERON:0005906 Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]. EMAPA:16060 FMA:9689 MA:0000005 See notes for serous membrane serous sac UBERON:0005911 Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]. FMA:69065 endoderm-derived epithelium endoepithelium endo-epithelium UBERON:0005913 FMA:10483 bone organ zone zone of bone organ UBERON:0005921 The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha. FMA:57459 middle nasal turbinate middle turbinate middle nasal concha UBERON:0005922 A turbinal located on the maxilla bone. FMA:54736 NCIT:C32794 UMLS:C0225434 inferior nasal turbinate inferior nasal turbinate bone inferior turbinate inferior nasal concha UBERON:0005928 A naris that provides one of the small external openings of the head that give passage to air for breathing. naris AAO:0000024 AAO:0000983 AAO:0010358 EHDAA2:0001275 EHDAA:9085 EMAPA:17848 FMA:59645 MA:0001320 NCIT:C33178 OpenCyc:Mx4rvViCLpwpEbGdrcN5Y29ycA TAO:0000550 UMLS:C0595944 VHOG:0000544 XAO:0003033 ZFA:0000550 external nares nostril blowhole external naris UBERON:0006003 Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. EMAPA:37883 body hair or bristle integumentary adnexa UBERON:0006314 Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. fluid BIRNLEX:20 EMAPA:37441 FMA:280556 GAID:266 MESH:D001826 galen:BodyFluid body fluid bodily fluid UBERON:0006530 A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended. BTO:0001232 CALOHA:TS-0918 EMAPA:36543 FMA:62967 MA:0002523 MAT:0000057 MIAA:0000057 seminal plasma seminal fluid UBERON:0006536 A portion of organism substance that is secreted by a male reproductive gland. EMAPA:36541 MA:0002521 male reproductive system fluid/secretion male reproductive gland secretion UBERON:0006538 A portion of organism substance that secreted_by a respiratory system. EMAPA:36550 MA:0002533 NCIT:C13722 UMLS:C1514899 respiratory system fluid/secretion UBERON:0006539 A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards. EMAPA:36538 MA:0002505 mammary gland fluid/secretion UBERON:0006562 The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. FBbt:00005380 MAT:0000049 MESH:D010614 MIAA:0000049 pharynx UBERON:0006866 The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. FBbt:00005756 WBbt:0005773 rectum terminal part of digestive tract UBERON:0006925 Any gland that is part of the digestive system. AAO:0000130 BTO:0000345 digestive system gland UBERON:0006956 The inner lining of the cheeks and lips. BTO:0003833 CALOHA:TS-2349 FMA:59785 NCIT:C12505 UMLS:C1578559 buccal mucosa UBERON:0007023 A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage. adult BILA:0000078 FBbt:00003004 HAO:0000087 NCIT:C17600 TAO:0002046 UMLS:C0001675 galen:Adult adults adult organism UBERON:0007100 A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. SPD:0000130 TADS:0000147 dorsal tube heart Gene notes: Bmp, Nkx, Gata primary circulatory organ UBERON:0007109 A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth. BTO:0000838 MESH:D008470 ncithesaurus:Meconium meconium UBERON:0007221 Of or pertaining to the period of time immediately following birth, or to the newborn. BTO:0001762 EV:0300037 HsapDv:0000082 MmusDv:0000096 NIF_Organism:birnlex_695 OGES:000025 neonatal stage fledgling stage hatchling hatchling stage infant stage nestling stage pouch stage puggle puggle stage neonate stage UBERON:0007222 EV:0300123 HsapDv:0000093 NCIT:C16268 NIF_Organism:birnlex_691 UMLS:C0001792 late adult stage UBERON:0007311 Matter ejected from the lungs, bronchi, and trachea, through the mouth. BTO:0001297 CALOHA:TS-0963 EMAPA:36553 FMA:312401 GAID:1171 MA:0002536 MESH:D013183 NCIT:C13278 UMLS:C0038056 sputum UBERON:0007357 The glandular or true stomach of a bird that is situated between the crop and gizzard. BTO:0001136 GAID:1239 MESH:D011531 NCIT:C111301 proventriculus UBERON:0007358 The fourth stomach of ruminating animals, which is an elongated pear-shaped sac lying on the floor of the abdomen, on the right-hand side, and roughly between the seventh and twelfth ribs. It leads to the beginning of the small intestine. (Adapted From Black's Veterinary Dictionary, 17th ed). BTO:0000024 GAID:1241 MESH:D000018 NCIT:C98702 UMLS:C0000780 abomasum UBERON:0007359 Any of the first three stomachs of a ruminant, i.e., the rumen, reticulum, or omasum. forestomach BTO:0000480 ruminant forestomach UBERON:0007361 The second stomach of ruminants. It lies almost in the midline in the front of the abdomen, in contact with the liver and diaphragm and communicates freely with the RUMEN via the ruminoreticular orifice. The lining of the reticulum is raised into folds forming a honeycomb pattern over the surface. (From Concise Veterinary Dictionary, 1988). reticulum BTO:0000347 MESH:D012159 NCIT:C98777 UMLS:C0035295 ruminant reticulum UBERON:0007362 The third stomach of ruminants, situated on the right side of the abdomen at a higher level than the fourth stomach and between this latter and the second stomach, with both of which it communicates. From its inner surface project large numbers of leaves or folia, each of which possesses roughened surfaces. In the center of each folium is a band of muscle fibers which produces a rasping movement of the leaf when it contracts. One leaf rubs against those on either side of it, and large particles of food material are ground down between the rough surfaces, preparatory to further digestion in the succeeeding parts of the alimentary canal. (Black's Veterinary Dictionary, 17th ed). BTO:0000348 GAID:1242 MESH:D009851 NCIT:C98766 UMLS:C0028972 omasum UBERON:0007364 The first chamber in the alimentary canal of a ruminant stomach, composed of the rumen and reticulum. retriculo-rumen reticulorumen UBERON:0007365 The first compartment of the ruminant stomach. It lies on the left side of the body, occupying the whole of the left side of the abdomen and even stretching across the median plane of the body to the right side. It is capacious, divided into an upper and a lower sac, each of which has a blind sac at its posterior extremity. BTO:0001194 GAID:1244 MESH:D012417 NCIT:C98778 UMLS:C0035946 rumen UBERON:0007366 The ruminants' stomach consists of four compartments: rumen, reticulum, omasum and abomasum. The first three compartments comprise the forestomach (proventriculus). They are lined with nonglandular membrane. The fourth compartment, the abomasum comprises the true stomach of the ruminants. It is lined with glandular mucous membrane. The rumen lies on the left of the abdominal cavity, the reticulum cranially and the omasum on the right. The abomasum lies ventrally, its proximal end lies ventral to the rumen, reticulum and omasum. GAID:1240 MESH:D013279 ruminant stomach UBERON:0007376 The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. BSA:0000073 BTO:0000313 FBbt:00004993 HAO:0000298 TADS:0000109 WBbt:0005733 epidermis epidermis (sensu Metazoa) outer epidermal layer outer epithelial layer outer epithelium UBERON:0007378 The yellow spheroidal mass of stored food that forms the inner portion of the egg of a bird or reptile and is surrounded by the white. AAO:0010579 BTO:0000371 MESH:D004530 VHOG:0001742 ncithesaurus:Egg_Yolk egg yolk UBERON:0007379 The hard-shelled reproductive body produced by a bird (especially by the common domestic chicken) or a reptile; also: its contents used as food. BSA:0000081 BTO:0000369 shelled egg UBERON:0007499 An epithelial tube that is open at one end only. AEO:0000115 EHDAA2:0003115 epithelial sac UBERON:0007592 Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]. FMA:64798 ciliated columnar epithelium UBERON:0007601 Epithelium bearing vibratile cilia on the free surface. ciliated epithelium UBERON:0007643 An inconstant lymph node of the anterior mediastinal group located adjacent to the ligamentum arteriosum. FMA:74033 Botallo's node ligamentum arteriosum node lymph node of ligamentum arteriosum nodus ligamenti arteriosi node of ligamentum arteriosum UBERON:0007644 A lymph node that is part of a thorax. Includes lymph nodes of the lungs and mediastinal lymph nodes. FMA:12772 NCIT:C33769 UMLS:C0229745 lymph node of thorax thoracic lymph node UBERON:0007779 Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces. FMA:12276 GAID:1195 MESH:D005122 ncithesaurus:Transudate transudate UBERON:0007794 Any fluid produced by a serous gland. serous fluid serosal fluid serous gland fluid secretion of serous gland UBERON:0007914 A bone that is part of a craniocervical region. EMAPA:37245 MA:0000569 head or neck bone bone of craniocervical region UBERON:0008001 The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid. FMA:7477 NCIT:C32881 UMLS:C0502414 os irregulare irregular bone UBERON:0008246 The mouth of a starfish is located on the underside of the body, and opens through a short esophagus into firstly a cardiac stomach, and then, a second, pyloric stomach. Each arm also contains two pyloric caeca, long hollow tubes branching outwards from the pyloric stomach. Each pyloric caecum is lined by a series of digestive glands, which secrete digestive enzymes and absorb nutrients from the food. A short intestine runs from the upper surface of the pyloric stomach to open at an anus in the center of the upper body. BTO:0002121 pyloric stomach UBERON:0008248 The pyloric ceca (or digestive glands) and the cardiac stomach produce digestive enzymes in starfishes. Digested material is absorbed through the pyloric ceca for transport to the rest of the body. Each pyloric cecum extends the length of each arm. pyloric caecum pyloric cecum BTO:0002120 echinoderm pyloric cecum UBERON:0008250 In starfishes the cardiac stomach is connected to a pyloric stomach which is located above it. Food can be brought into the stomach through the mouth or, in many species, the cardiac stomach can be extended out through the mouth to digest food outside the body. Suspension-feeding starfish use their tube feet to pass food to the mouth. BTO:0002122 cardiac stomach UBERON:0008291 poultry fluff A feather lacking a vane and having a rudimentary rachis and a tuft of non-interlocked barbs with elongated barbules extending from the calamus. Damion Dooley's note: Poultry fluff is both an 'anatomical structure' and a body product when it is shed. downy feather plumaceous feather plumulaceous feather body down feather natal down feather powder down feather down feather UBERON:0008785 A limb segment that is part of a forelimb. FMA:24876 free upper limb segment free upper limb subdivision segment of free upper limb subdivision of free upper limb upper limb segment UBERON:0008827 A distinct rodent non-glandular region of the stomach which is demarcated from the glandular stomach by the limiting ridge (margo plicatus). forestomach stomach non-glandular region EMAPA:17627 MA:0001606 NCIT:C77956 UMLS:C0033745 murine forestomach UBERON:0008835 An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts. AAO:0011057 EHDAA2:0000740 EHDAA:1530 NCIT:C34187 UMLS:C1512407 XAO:0000101 liver diverticulum hepatic diverticulum UBERON:0008836 BTO:0001642 liver bud UBERON:0008858 The short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter. EMAPA:37944 FMA:14580 canalis pyloricus pyloric canal UBERON:0008944 Albumen is the clear liquid contained within an egg and consists of water and proteins, among which are ovomucin and ovomucoid. It protects the egg yolk and provides additional nutrition for the growth of the embryo. BTO:0000370 GO:0097099 ncithesaurus:Egg_White egg white albumen UBERON:0008994 Stomach found in horses; includes cardiac, proper gastric and pyloric glandular zones. BTO:0003791 equine glandular stomach UBERON:0009006 One of several small inconstant lymph nodes, proximal, intermediate and distal deep to the fascia lata and medial to the femoral vein; they receive lymph from the deep structures of the lower limb, from the glans penis and from superficial inguinal nodes; efferents pass to the external iliac nodes. BTO:0004548 FMA:44225 deep inguinal node nodus lymphaticus inguinalis profundus deep inguinal lymph node UBERON:0009007 A group of 12-20 lymph nodes that lie in the subcutaneous tissue below the inguinal ligament and along the terminal part of the great saphenous vein; they drain the skin and subcutaneous tissue of the lower abdominal wall, perineum, buttocks, external genitalia, and lower limbs. BTO:0004549 FMA:5036 lymph node of Cloquet lymph node of Rosenmuller nodus lymphaticus inguinalis superficialis superficial inguinal node superficial inguinal lymph node UBERON:0009060 Any of the membranous air-filled extensions of the lungs of birds, which increase the efficiency of gaseous exchange in the lungs. MESH:D000400 NCIT:C120926 sacci pneumatici Three distinct sets of organs perform respiration-the anterior air sacs (interclavicular, cervicals, and anterior thoracics), the lungs, and the posterior air sacs (posterior thoracics and abdominals). The posterior and anterior air sacs, typically nine, expand during inhalation. Air enters the bird via the trachea. Half of the inhaled air enters the posterior air sacs, the other half passes through the lungs and into the anterior air sacs. Air from the anterior air sacs empties directly into the trachea and out the bird's mouth or nares. The posterior air sacs empty their air into the lungs. Air passing through the lungs as the bird exhales is expelled via the trachea. Some taxonomic groups (Passeriformes) possess 7 air sacs, as the clavicular air sacs may interconnect or be fused with the cranial thoracic air sacs[WP] air sac UBERON:0009097 An organism containing a developing embryo, fetus, or unborn offspring within the body. BTO:0004733 gravid organism UBERON:0009472 The axilla is the area directly under the joint where the forelimb connects to the shoulder. CALOHA:TS-2208 EFO:0001395 FMA:24864 MESH:D001365 NCIT:C12674 UMLS:C0004454 galen:Axilla arm pit armpit axillary region regio axillaris axilla UBERON:0009497 An epithelium that is part of a foregut-midgut junction. EHDAA2:0000573 EMAPA:16564 epithelium of foregut-midgut junction UBERON:0009778 A serous sac that has the pleura and the pleural cavity as parts. EHDAA2:0004737 FMA:9690 pleural sac UBERON:0009854 Branch or outpocketing of the digestive tract. FBbt:00100316 digestive tract diverticulum UBERON:0009855 Non-contractile pouch that is connected to the anterior stomach through a slit-like opening. This pouch is also well-connected to the haemal system through numerous haemal ducts within its connective tissue layer. The digestive tract of many metazoan invertebrates is characterized by the presence of caeca or diverticula that serve secretory and/or absorptive functions. With the development of various feeding habits, distinctive digestive organs may be present in certain taxa. This also holds true for sea urchins (Echinodermata: Echinoidea), in which a highly specialized gastric caecum can be found in members of a derived subgroup, the Irregularia (cake urchins, sea biscuits, sand dollars, heart urchins, and related forms)... Homologous with the more or less pronounced dilation of the anterior stomach that is observed in most "regular" sea urchin taxa[PMID:20955602] echinoderm gastric caecum UBERON:0009856 galen:Diverticulum pouch sac UBERON:0009870 A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland. UBERON:0009034 EMAPA:35821 FMA:14558 MA:0002561 gastric zone region of stomach section of stomach zone of stomach UBERON:0009878 The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton. VSAO:0005022 basipodium skeleton carpal/tarsal skeleton mesopodial skeleton mesopodium skeleton skeletal parts of mesopodium mesopodial skeleton UBERON:0009880 Subdivision of skeleton that consists of the endochondral elements distal to the anterior limb/fin zeugopodial skeletal elements which constitute the proximal region of the anterior autopod skeleton[PHENOSCAPE:ad]. AAO:0000201 FMA:71335 MA:0000040 VHOG:0001161 VSAO:0005023 XAO:0003207 carpal bones carpal bones set fore mesopodial skeleton fore mesopodium skeleton ossa carpi skeletal parts of fore mesopodium skeleton of carpus carpal skeleton UBERON:0010000 An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure multicellular anatomical structure UBERON:0010039 An organ of the digestive tract that is capable of retaining and storing food. BSA:0000123 TADS:0000172 TGMA:0001041 food storage organ UBERON:0010239 A variant of the ascending colon in ruminants and pigs. NCIT:C92438 UMLS:C0227374 coiled colon spiral colon UBERON:0010313 An anatomical structure that develops from the neural crest. neural crest-derived structure UBERON:0010314 An anatomical structure that has some part that develops from the neural crest. structure with developmental contribution from neural crest UBERON:0010363 A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. VSAO:0000139 XAO:0004017 ZFA:0005620 endochondral replacement element endochondral element UBERON:0010371 Epithelium composed of cells that develops from the ectoderm[FMA,modified]. FMA:69064 ectoderm-derived epithelium ecto-epithelium UBERON:0010498 A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. FMA:45572 NCIT:C33419 NCIT:C49316 UMLS:C0836138 UMLS:C1514590 pseudostratified columnar epithelium UBERON:0010499 Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. FMA:13146 NCIT:C13181 UMLS:C0506992 epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) pseudostratified ciliated columnar epithelium UBERON:0010538 An appendage segment that is part of a limb/fin. limb/fin segment paired limb/fin segment UBERON:0010712 Skeletal subdivision that is a segment of the limb skeleton. VSAO:0005018 limb skeleton subdivision UBERON:0010758 A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg. FBbt:00007018 appendage segment appendicular segment subdivision of organism along appendicular axis UBERON:0010912 Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 VSAO:0000042 skeletal subdivision subdivision of skeleton UBERON:0011139 Any synovial joint that is part of a (free) limb. FMA:258776 synovial joint of free limb segment Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses. synovial limb joint UBERON:0011164 A bone that is part of a neurocranium [Automatically generated definition]. EMAPA:35238 MA:0001478 chondrocranium bone neurocranium bone UBERON:0011185 A sphincter muscle that is part of the gastrointestinal system. NCIT:C32669 UMLS:C1517464 gastrointestinal sphincter UBERON:0011216 A subdivision of an anatomical system. FBbt:00007330 FMA:67509 organ system subdivision UBERON:0011374 A retractable double-layered fold of skin and mucous membrane that covers the glans penis or clitoris. Glands may also be present. NCIT:C12323 prepuce UBERON:0011642 An epithelium that develops_from a ectoderm and is part of a oral epithelium. EHDAA2:0004137 oral epithelium from ectoderm UBERON:0011698 Portion of midgut after it bends around the superior mesenteric artery. EMAPA:17036 NCIT:C34211 UMLS:C1513298 VHOG:0000673 midgut loop UBERON:0011953 A region of the stomach that is lined with glandular epithelium. EMAPA:17623 MA:0001613 NCIT:C77661 UMLS:C0227197 stomach glandular region UBERON:0011954 A region of the stomach is lined with non-glandular epithelium. Examples of a stomach non-glandular region are found in rodents. EMAPA:17627 MA:0001625 NCIT:C77662 stomach non-glandular region UBERON:0012168 Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. BTO:0004053 CALOHA:TS-1079 EFO:0001942 MESH:D005312 Cord blood is collected because it contains stem cells, which can be used to treat hematopoietic and genetic disorders.[WP] umbilical cord blood UBERON:0012236 The intercostal lymph nodes (intercostal glands ) occupy the posterior parts of the intercostal spaces, in relation to the intercostal vessels. They receive the deep lymphatics from the postero-lateral aspect of the chest; some of these vessels are interrupted by small lateral intercostal glands. FMA:5932 NCIT:C77652 UMLS:C0229761 intercostal node nodi lymphoidei intercostales nodus intercostale intercostal lymph node UBERON:0012273 NCIT:C60699 UMLS:C1882332 periampullary region periampullary region of duodenum UBERON:0012274 An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]. columnar epithelium UBERON:0012287 An epithelial sac that is part of a Rathke's pouch. EHDAA2:0001473 EMAPA:25036 Rathkes pouch epithelium UBERON:0012306 A cervical lymph nodes are found in proximity to an internal or external jugular vein. FMA:61232 lateral cervical node lateral cervical lymph node UBERON:0012307 The anterior cervical lymph nodes are a group of nodes found on the anterior part of the neck. FMA:61230 anterior cervical node anterior cervical lymph node UBERON:0012308 The superficial lateral cervical lymph nodes are found in proximity to the external jugular vein. FMA:12769 superficial lateral cervical node superficial lateral cervical lymph node UBERON:0012309 The superficial anterior cervical lymph nodes are found in proximity to the anterior jugular vein. FMA:12776 anterior jugular lymph node superficial anterior cervical lymph node UBERON:0012310 The deep lateral cervical lymph nodes are found near the upper part of the internal jugular vein in the neck, lateral or posterior to the carotid sheath. FMA:12770 deep lateral cervical node deep lateral cervical lymph node UBERON:0012311 The deep anterior cervical lymph nodes are found near the middle cricothyroid ligament and the trachea. FMA:12779 deep anterior cervical lymph node UBERON:0012474 A ventral evagination extending anteriorly in the mid-portion of the intestine in Amphioxi. BTO:0002855 hepatic caecum hepatic cecum UBERON:0012652 The subdivision of the digestive tract that consists of the colon and the rectum. BTO:0001613 CALOHA:TS-1298 NCIT:C54189 UMLS:C1711309 colorectum UBERON:0013472 The upper one third of esophagus in which the muscle layer is composed of muscle cells of the striated type. NCIT:C12253 UMLS:C0227187 upper esophagus UBERON:0013473 The lower one third of the esophagus in which the muscle layer is composed of muscle cells predominantly of the smooth type. NCIT:C12255 UMLS:C0227191 lower esophagus UBERON:0013474 The middle one third of the esophagus in which the muscle layer is composed of muscle cells of the striated and smooth types. NCIT:C12254 UMLS:C0227189 middle part of esophagus UBERON:0013522 subdivision of tube UBERON:0013644 The very first part of the duodenum which is slightly dilated. FMA:14927 ampulla (duodenum) ampulla duodeni ampulla of duodenum bulbus (duodenum) bulbus duodeni duodenal cap duodenal cap viewed radiologically duodenal ampulla UBERON:0013703 Anatomical projection that is part of the integumentl system. skin projection integumentary projection UBERON:0013755 A blood that is part of a artery. FMA:83066 arterial blood blood in artery portion of arterial blood arterial blood UBERON:0013756 A blood that is part of a vein. FMA:83067 blood in vein portion of venous blood venous blood venous blood UBERON:0013757 A blood that is part of a capillary. FMA:263901 NCIT:C32212 blood in capillary portion of blood in capillary portion of capillary blood capillary blood UBERON:0013765 Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. EMAPA:37843 digestive organ digestive system organ digestive system element UBERON:0015212 Any structure that is placed on one side of the left-right axis of a bilaterian. lateral structure UBERON:0015228 A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. heart SPD:0000130 cardiac pump heart or heart like organ circulatory vessel circulatory organ UBERON:0015232 The feeding organ, a neuro-muscular pump in the head of the animal, used to ingest food, bacteria suspended in liquid, filter them out, grind them up and transport posteriorly into the instestine. WBbt:0003681 nematode pharynx UBERON:0015453 A lymph node that is part of a hypodermis. MA:0003028 subcutaneous lymph node UBERON:0015469 The splenic lymph nodes (or pancreaticolienal) accompany the lienal (splenic) artery, and are situated in relation to the posterior surface and upper border of the pancreas; one or two members of this group are found in the gastrolienal ligament. Their afferents are derived from the stomach, spleen, and pancreas, their efferents join the celiac group of preaortic glands. FMA:66187 MA:0003074 splenic lymph node UBERON:0015472 A lymph node located near the bifurcation of the trachea. UBERON:0016381 FMA:5950 MA:0003068 NCIT:C77651 nodus tracheobronchiale lymphaticus tracheobronchal lymph node tracheobronchal node tracheobronchial node bronchial lymph node tracheobronchial lymph node UBERON:0015757 FMA:62798 portion of heterogeneous tissue heterogeneous tissue UBERON:0015833 An epithelium that is part of a foregut. EMAPA:32922 MA:0003204 foregut epithelium UBERON:0015857 A lymph node found near the parotid gland. FMA:61216 MA:0003088 parotid node parotid lymph node UBERON:0015859 Any of the lymph nodes adjacent to the stomach and duodenum. FMA:12798 MA:0003072 NCIT:C77640 hepatic node lymphoglandulae hepaticae lymphoglandulæ hepaticæ nodi lymphoidei hepatici portal lymph node hepatic lymph node UBERON:0015860 FMA:66178 visceral abdominal lymph node UBERON:0015863 A lymph node along the left gastric artery or greater omentum. FMA:12796 MA:0003071 NCIT:C92222 gastric node nodi lymphoidei gastrici gastric lymph node UBERON:0015865 Lymph nodes of the pancreatic tail and spleen, receiving afferents from both organs plus the greater curvature of the stomach; they drain to the celiac lymph nodes. FMA:12799 pancreaticosplenic node pancreaticosplenic lymph node UBERON:0015866 FMA:12802 pyloric node pyloric lymph node UBERON:0015867 FMA:12804 cystic node cystic lymph node UBERON:0015868 FMA:12805 lymph node of anterior border of epiploic foramen lymph node of anterior border of omental foramen node of anterior border of epiploic foramen node of anterior border of omental foramen nodus foraminalis nodus lymphoideus foraminalis lymph node of epiploic foramen UBERON:0015869 The retropharyngeal lymph nodes, from one to three in number, lie in the buccopharyngeal fascia, behind the upper part of the pharynx and in front of the arch of the atlas, being separated, however, from the latter by the Longus capitis. Their afferents drain the nasal cavities, the nasal part of the pharynx, and the auditory tubes. Their efferents pass to the superior deep cervical glands. They are in the retropharyngeal space. EMAPA:37724 FMA:61237 MA:0003070 NCIT:C77649 retropharyngeal node retropharyngeal lymph node UBERON:0015870 A lymph node that is part of a head. FMA:61212 lymph node of head UBERON:0015871 Any of the lymph nodes that are part of a face. FMA:61222 buccal lymph node facial lymph node UBERON:0015872 The mandibular lymph node is a lymph node found near the jaw. FMA:61227 MA:0003067 mandibular node nodus mandibularis Editor nodes: consider merging with submandibular, at least for mouse, see http://www.ncbi.nlm.nih.gov/pubmed/16624319 mandibular lymph node UBERON:0015876 Any lymph node within the abdominal pelvic region. FMA:12800 NCIT:C12363 lymph node of pelvis pelvic lymph node UBERON:0015877 FMA:66193 parietal pelvic lymph node UBERON:0015878 The external iliac lymph nodes, from eight to ten in number, lie along the external iliac vessels. They are arranged in three groups, one on the lateral, another on the medial, and a third on the anterior aspect of the vessels; the third group is, however, sometimes absent. Their principal afferents are derived from the inguinal lymph nodes, the deep lymphatics of the abdominal wall below the umbilicus and of the adductor region of the thigh, and the lymphatics from the glans penis vel clitoridis, the membranous urethra, the prostate, the fundus of the urinary bladder, the cervix uteri, and upper part of the vagina. FMA:12806 MA:0003066 NCIT:C32761 common iliac node iliac lymph node common iliac lymph node UBERON:0015880 FMA:16646 NCIT:C88143 external iliac node external iliac lymph node UBERON:0015881 The internal iliac lymph nodes (or hypogastric) surround the internal iliac artery and its branches (the hypogastric vessels), and receive the lymphatics corresponding to the distribution of the branches of it, i. e. , they receive lymphatics from all the pelvic viscera, from the deeper parts of the perineum, including the membranous and cavernous portions of the urethra, and from the buttock and back of the thigh. It does not receive lymph from the ovary, testis, or superior half of the rectum; the gonads drain to the paraaortic lymph nodes, while the superior half of the rectum drains to the pararectal lymph nodes. FMA:16654 NCIT:C88142 internal iliac node internal iliac lymph node UBERON:0015883 FMA:16657 gluteal node gluteal lymph node UBERON:0015884 FMA:16667 presymphysial node presymphysial lymph node UBERON:0015895 One of the deep inguinal lymph nodes located in or adjacent to the femoral canal; sometimes mistaken for a femoral hernia when enlarged. BTO:0004550 FMA:44303 nodus inguinales profundi proximalis nodus lymphoideus inguinales profundi proximalis proximal deep inguinal node proximal inguinal lymph node rosenmuller's gland rosenmuller's node proximal deep inguinal lymph node UBERON:0015917 A lymph node that is located close to the surface. FMA:12767 NCIT:C102716 superficial lymph node UBERON:0015918 A lymph node that is located deeper within the organism, further from the surface. FMA:12768 deep lymph node UBERON:0015922 accessory mandibular lymph node UBERON:0015923 A parotid lymph node that is located superficially. FMA:61217 superficial parotid node superficial parotid lymph node UBERON:0015925 superficial intraparotid node superficial intraparotid lymph node UBERON:0015926 cranial deep node cranial deep lymph node UBERON:0016374 A lymph node that is medial to the gluteus superficialis m., caudal to gluteus medius m. and sciatic nerve lymph node. MA:0002884 sciatic lymph node UBERON:0016378 One of the lymph nodes that form a chain around the ileocolic artery. FMA:16611 MA:0003065 NCIT:C77653 nodi lymphoidei ileocolici ileocecocolic lymph node ileocolic lymph node UBERON:0016382 EMAPA:37723 MA:0003069 NCIT:C77654 prescapular lymph node UBERON:0016386 The paraaortic lymph nodes (also known as para-aortic, periaortic, and peri-aortic) are a group of lymph nodes that lie in front of the lumbar vertebral bodies near the aorta. These lymph nodes receive drainage from the lower gastrointestinal tract and the pelvic organs. FMA:16604 MA:0003073 NCIT:C77643 lateral aortic lymph node lateral aortic node para-aortic lymph node paraaortic lymph node UBERON:0016390 MA:0003092 auricular lymph node UBERON:0016391 MA:0003118 thymic lymph node UBERON:0016392 The mastoid lymph nodes (retroauricular lymph nodes, posterior auricular glands), usually two in number, are situated on the mastoid insertion of the Sternocleidomastoideus, beneath the Auricularis posterior. Their afferent vessels drain the posterior part of the temporoparietal region, the upper part of the cranial surface of the auricula or pinna, and the back of the external acoustic meatus; their efferents pass to the superior deep cervical glands. FMA:61215 mastoid node postauricular lymph node retro-auricular lymph node retro-auricular node mastoid lymph node UBERON:0016393 The deep parotid lymph nodes are lymph nodes found below the parotid gland. The afferents of the subparotid glands drain the nasal part of the pharynx and the posterior parts of the nasal cavities. Their efferents pass to the superior deep cervical glands. FMA:61218 deep parotid node deep parotid lymph node UBERON:0016394 The preauricular deep parotid lymph nodes (anterior auricular glands or preauricular glands), from one to three in number, lie immediately in front of the tragus. Their afferents drain the lateral surface of the auricula and the skin of the adjacent part of the temporal region; their efferents pass to the superior deep cervical glands. FMA:61219 NCIT:C103429 pre-auricular lymph node pre-auricular node preauricular lymph node preauricular node anterior auricular lymph node UBERON:0016395 The infra-auricular deep parotid lymph nodes are a group of lymph nodes found underneath the ear. FMA:61220 infra-auricular deep node infra-auricular deep parotid lymph node infra-auricular deep parotid node infra-auricular node infra-auricular lymph node UBERON:0016396 FMA:61221 intraglandular node intraglandular lymph node UBERON:0016397 The submental lymph nodes (or suprahyoid) are situated between the anterior bellies of the Digastrici. Their afferents drain the central portions of the lower lip and floor of the mouth and the apex of the tongue. Their efferents pass partly to the submandibular lymph nodes and partly to a gland of the deep cervical group situated on the internal jugular vein at the level of the cricoid cartilage. FMA:61229 level Ia neck node submental node submental lymph node UBERON:0016398 A lymph node that is part of a hindlimb. FMA:44310 lymph node of lower limb UBERON:0016399 A lymph node that is part of a forelimb. FMA:44311 lymph node of upper limb UBERON:0016401 FMA:16623 pancreaticoduodenal node pancreaticoduodenal lymph node UBERON:0016402 FMA:300965 mesocolic lymph node UBERON:0016481 A lymph node that is part of a bronchus. MA:0003078 NCIT:C32232 bronchial lymph node UBERON:0017672 A viscus that is part of a abdomen. FMA:32413 FMA:67355 abdominal viscera abdominal viscera set set of abdominal viscera abdominal viscera UBERON:0018241 A life cycle stage that starts at completion of development and growth of the sexually mature adult animal, and ends before senescence. prime adult stage UBERON:0018707 A membranous sac in animals that serves as the receptacle of a liquid or contains gas. BTO:0000123 bladder bladder organ UBERON:0022293 A portion of organism substance that is secreted by a reproductive gland. reproductive gland secretion UBERON:0034768 A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology. morphological feature UBERON:0034873 Any substance in the body or expelled from the body that is in a gaseous state. FMA:84580 gas in anatomical space portion of gas in anatomical space bodily gas UBERON:0034919 The stage of being no more dependent of the nest and/or from caregivers for subsistence while having not reach sexual maturity. juvenile stage UBERON:0034920 Nursing stage that follows the neonate stage in mammals and ends at weaning. infant stage UBERON:0034921 An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 multi organ part structure UBERON:0034925 A collection of anatomical structures that are alike in terms of their morphology or developmental origin. anatomical collection UBERON:0034929 A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures. external soft tissue zone UBERON:0034944 FMA:55268 organ sector organ zonal region organ zone zone of organ UBERON:0034945 Any gaseous product of an excretory process. excreted gas UBERON:0034946 Any excreted gas that is produced by the digestive tract. FMA:78440 flatulence flatus intestinal gas In mammals, mostly produced as a byproduct of bacterial fermentation in the gastrointestinal (GI) tract, especially the colon, and excreted through the rectum gas excreted from digestive tract UBERON:0035079 The intraglandular deep parotid lymph nodes are a group of lymph nodes found inside the parotid gland. deep intraparotid node intraglandular deep parotid lymph nodes deep intraparotid lymph node UBERON:0035080 intraparotid node intraparotid lymph node UBERON:0035162 A lymph node located in the area below the clavicle. FMA:14193 NCIT:C63705 deltopectoral lymph node deltopectoral node infraclavicular node nodus lymphaticus infraclavicularis axillae infraclavicular lymph node UBERON:0035171 FMA:16656 NCIT:C88141 obturator node obturator lymph node UBERON:0035204 A lymph node located in the back of the head adjacent to the trapezius muscle. FMA:61214 NCIT:C98188 occipital node occipital lymph node UBERON:0035219 Any of the lymph nodes of the breast located under the ribcage, near the sternum. FMA:5849 NCIT:C32853 internal mammary lymph node nodus parasternale parasternal node parasternal lymph node UBERON:0035279 A lymph node which is located above the clavicle. FMA:14192 NCIT:C12903 nodus lymphaticus supraclavicularis axillae supraclavicular node supraclavicular lymph node UBERON:0035371 A lymph node located in the retroperitoneal space. FMA:16694 NCIT:C98189 retroperitoneal node retroperitoneal lymph node UBERON:0035520 A lymph node located in the superior mediastinum that collects lymph from the thymus, the pericardium, and the right side of the heart. FMA:12775 NCIT:C32097 anterior mediastinal node anterior mediastinal lymph node UBERON:0035612 A skeletal element of the ethmoid region with complex morphology that are lined with mucuous membranes involved in either olfaction or air conditioning. nasal turbinal nasal turbinal element nasal turbinate turbinal turbinate nasal turbinal UBERON:0035764 FMA:5968 intrapulmonary lymph node pulmonary node pulmonary lymph node UBERON:0035765 The lymph nodes around the subsegmental bronchi. FMA:276861 NCIT:C28745 subsegmental lymph node UBERON:0035809 FMA:12241 serous cavity UBERON:0036072 EHDAA2:0004070 respiratory primordium epithelium UBERON:0036217 A bodily fluid that is located in the coelom. BTO:0001708 coelomic fluid UBERON:0036243 Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands. vaginal fluid UBERON:0036244 A transudate found in the serous sac. serous fluid FMA:20932 serous sac fluid secretion of serous membrane UBERON:0037480 FMA:12785 supramammary node supramammary lymph node UBERON:0037494 Gastric lymph node located around the cardia of stomach. FMA:12803 aJCC level 16 lymph node ring of cardia of stomach paracardial gastric node paracardial lymph node paracardial gastric lymph node UBERON:0037500 An axillary lymph node that is placed along the lower margin of the posterior wall of the axilla in the course of the subscapular artery. FMA:14187 nodus lymphaticus subscapularis axillae posterior axillary node subcapsular node subscapular axillary lymph node UBERON:0037501 An axiallary lymph node along the lower border of the Pectoralis minor, in relation with the lateral thoracic artery. Their afferents drain the skin and muscles of the anterior and lateral thoracic walls, and the central and lateral parts of the mamma; their efferents pass partly to the central and partly to the subclavicular groups of axillary glands. FMA:14188 anterior axillary lymph node nodus lymphaticus pectoralis axillae pectoral lymph node pectoral axillary lymph node UBERON:0037502 An axillary lymph node that is imbedded in the adipose tissue near the base of the axilla. FMA:14189 central node nodus lymphaticus centralis axillae central axillary lymph node UBERON:0037503 An axillary lymph node that is situated partly posterior to the upper portion of the Pectoralis minor and partly above the upper border of this muscle. FMA:14190 nodus lymphaticus apicalis axillae apical axillary lymph node UBERON:0037514 FMA:16609 central mesenteric lymph node central superior mesenteric lymph node intermediate lymph node of small intestine intermediate mesenteric node intermediate mesenteric lymph node UBERON:0037515 FMA:16610 juxta-arterial mesenteric node juxta-arterial mesenteric lymph node UBERON:0037518 FMA:16613 epicolic node epicolic lymph node UBERON:0037521 FMA:16616 preterminal colic node preterminal colic lymph node UBERON:0037522 FMA:16617 ileal mesentary lymph node ileal node ileal lymph node UBERON:0037527 FMA:16624 superior pancreaticoduodenal node superior pancreaticoduodenal lymph node UBERON:0037528 FMA:16625 inferior pancreaticoduodenal node inferior pancreaticoduodenal lymph node UBERON:0037530 Pancreaticosplenioc lymph node located along the inferior margin of pancreas. FMA:16628 inferior pancreatic node inferior pancreatiosplenic lymph node jPS 18 node jPS no. 18 node no. 18 pancreatic lymph node no. 18 pancreaticoduodenal lymph node inferior pancreatic lymph node UBERON:0037531 FMA:16629 intestinal node visceral lumbar lymph node intestinal lymph node UBERON:0037532 FMA:16641 medial common iliac node medial common iliac lymph node UBERON:0037533 FMA:16642 intermediate common iliac node intermediate common iliac lymph node UBERON:0037534 FMA:16643 lateral common iliac node lateral common iliac lymph node UBERON:0037535 FMA:16644 subaortic common iliac node subaortic lymph node subaortic common iliac lymph node UBERON:0037536 FMA:16645 promontory node promontory lymph node UBERON:0037538 FMA:16647 medial external iliac node medial external iliac lymph node UBERON:0037539 FMA:16648 intermediate external iliac node intermediate external iliac lymph node UBERON:0037540 FMA:16649 lateral external iliac node lateral external iliac lymph node UBERON:0037541 FMA:16651 interiliac node interiliac lymph node UBERON:0037548 FMA:16658 superior gluteal node superior gluteal lymph node UBERON:0037549 FMA:16659 inferior gluteal node inferior gluteal lymph node UBERON:0037559 FMA:16669 anorectal lymph node UBERON:0037560 axillary node FMA:12771 superficial axillary lymph node UBERON:0037566 FMA:12773 diaphragmatic node diaphragmatic lymph node UBERON:0037580 Gastric lymph node located along the lesser curvature of stomach. FMA:12797 aJCC level 17L node left gastric node left gastric lymph node UBERON:0037590 FMA:14186 brachial axillary node humeral node nodus lymphaticus brachialis axillae lateral axillary lymph node UBERON:0037601 FMA:16602 left parietal lumbar node left parietal lumbar lymph node UBERON:0037614 FMA:16620 appendicular node appendicular lymph node UBERON:0037615 FMA:16621 pararectal node perirectal lymph node rectal lymph node pararectal lymph node UBERON:0037722 FMA:224626 right retropharyngeal lymph node UBERON:0037723 FMA:224628 left retropharyngeal lymph node UBERON:0037763 FMA:232351 lateral superior deep cervical lymph node UBERON:0037764 FMA:232355 anterior superior deep cervical lymph node UBERON:0037765 FMA:232358 lateral inferior deep cervical lymph node UBERON:0037766 FMA:232361 anterior inferior deep cervical lymph node UBERON:0037787 FMA:232552 right occipital lymph node UBERON:0037788 FMA:232554 left occipital lymph node UBERON:0037789 FMA:232558 right apical axillary lymph node UBERON:0037790 FMA:232560 left apical axillary lymph node UBERON:0037793 FMA:232566 right subscapular axillary lymph node UBERON:0037794 FMA:232568 left subscapular axillary lymph node UBERON:0037795 FMA:232570 right pectoral axillary lymph node UBERON:0037796 FMA:232572 left pectoral axillary lymph node UBERON:0037797 FMA:232574 right central axillary lymph node UBERON:0037798 FMA:232576 left central axillary lymph node UBERON:0037865 FMA:232854 jugular lymph node UBERON:0037995 FMA:234376 supramandibular lymph node UBERON:0037998 FMA:234382 external jugular lymph node UBERON:0038001 FMA:234388 sternal lymph node UBERON:0038002 FMA:234390 upper intercostal lymph node UBERON:0038003 FMA:234392 lower intercostal lymph node UBERON:0038037 FMA:234498 subclavian lymph node UBERON:0038048 FMA:234527 antebrachial lymph node UBERON:0038053 FMA:265353 cardiophrenic angle node cardiophrenic angle lymph node UBERON:0038054 FMA:265356 retrocrural node retrocrural lymph node UBERON:0038093 FMA:276784 jejunal mesentary lymph node jejunal lymph node UBERON:0038094 FMA:276796 inferior rectal lymph node UBERON:0038124 FMA:12807 medial diaphragmatic node middle diaphragmatic lymph node medial diaphragmatic lymph node UBERON:0038137 FMA:16603 parietal pre-aortic node parietal preaortic node parietal pre-aortic lymph node UBERON:0038139 FMA:16607 post-aortic lymph node postaortic lymph node retro-aortic node retroaortic lymph node retro-aortic lymph node UBERON:0038587 FMA:265350 paracardiac node paracardiac lymph node UBERON:0038632 FMA:276807 pericardial lymph node UBERON:0038633 FMA:276813 5 thoracic lymph node aortopulmonary window lymph node mediastinal lymph node station # 5 station 5 N2 lymph node station 5 lymph node aortopulmonary lymph node UBERON:0038634 FMA:276820 6 thoracic lymph node pre-aortic No. 6 lymph node station 6 N2 lymph node station 6 lymph node para-aortic thoracic lymph node UBERON:0038635 FMA:276828 11 R+L thoracic 11 thoracic lymph node station 11 N1 lymph node station 11 lymph node interlobar lymph node UBERON:0038638 FMA:276849 12R+L thoracic lymph node station 12 N1 lymph node station 12 lymph node lobar lymph node UBERON:0038641 FMA:276855 13R+L thoracic lymph node station 13 N1 lymph node station 13 lymph node segmental lymph node UBERON:0038647 FMA:276867 9R+L thoracic lymph node inferior pulmonary ligament lymph node node of inferior pulmonary ligament pulmonary ligament lymph node station 9 N2 lymph node station 9 lymph node lymph node of inferior pulmonary ligament UBERON:0038651 FMA:276903 superior mediastinal lymph node UBERON:0038684 Left gastric lymph node located along the left gastric artery. FMA:277061 jPS 7 node jPS no. 7 node no. 7 left gastric lymph node superior left gastric node superior left gastric lymph node UBERON:0038685 Left gastric lymph node located along the cardiac half of the lesser curvature of stomach in the lesser omentum. FMA:277064 inferior left gastric node jPS 3 node jPS No. 3 node inferior left gastric lymph node UBERON:0038687 FMA:277227 visceral lymph node of abdomen UBERON:0038691 Hepatic lymph node located along the common hepatic artery. FMA:277259 common hepatic lymph node UBERON:0038694 Hepatic lymph node located along the portal vein. portal lymph node FMA:277271 jPS 12p node jPS No. 12p node no. 12p hepatic lymph node periportal lymph node porta hepatis lymph node portahepatic lymph node hepatoportal lymph node UBERON:0038695 Superior pancreatic lymph node located along the proximal segment of splenic artery. FMA:277295 jPS 11p node jPS no. 11p node no. 11p superior pancreatic lymph node proximal superior pancreaticosplenic lymph node proximal superior pancreatic lymph node UBERON:0038696 Superior pancreatic lymph node located along the distal segment of splenic artery. FMA:277298 distal superior pancreaticosplenic lymph node jPS 11d node jPS no. 11d node no. 11d superior pancreatic lymph node distal superior pancreatic lymph node UBERON:0038697 Superior pancreaticoduodenal lymph node located on the anterior anterior of superior region of head of pancreas. FMA:277305 anterosuperior pancreaticoduodenal lymph node jPS 17a node jPS no. 17a node no. 17a pancreaticoduodenal lymph node anterior superior pancreaticoduodenal lymph node UBERON:0038698 Superior pancreaticoduodenal lymph node located on the posterior aspect of superior portion of head of pancreas. FMA:277310 jPS 13a node jPS no. 13a node no. 13a pancreaticoduodenal lymph node posterosuperior pancreaticoduodenal lymph node posterior superior pancreaticoduodenal lymph node UBERON:0038699 Inferior pancreaticoduodenal lymph node located on the anterior aspect of inferior region of head of pancreas. FMA:277315 anteroinferior pancreaticoduodenal lymph node jPS 17b node jPS no. 17b node no. 17b pancreaticoduodenal lymph node anterior inferior pancreaticoduodenal lymph node UBERON:0038700 Inferior pancreaticoduodenal lymph node located on the posterior aspect of inferior region of head of pancreas. FMA:277317 jPS 13b node jPS no. 13b node no. 13b pancreaticoduodenal lymph node posteroinferior pancreaticoduodenal lymph node posterior inferior pancreaticoduodenal lymph node UBERON:0038707 FMA:277368 jPS 17 node no. 17 pancreaticoduodenal lymph node anterior pancreaticoduodenal lymph node UBERON:0038727 FMA:277581 mural mesenteric lymph node para-intestinal mesenteric lymph node juxta-intestinal mesenteric lymph node UBERON:0038734 Intestinal lymph node located anterior to aorta. FMA:277610 visceral para-aortic lymph node visceral pre-aortic node visceral preaortic lymph node visceral pre-aortic lymph node UBERON:0038735 FMA:277614 juxta-arterial jejunal lymph node UBERON:0038736 FMA:277616 juxta-arterial ileal lymph node UBERON:0038737 FMA:277618 intermediate jejunal lymph node UBERON:0038738 FMA:277620 intermediate ileal lymph node UBERON:0038746 Gastric lymph node located along the greater curvature of stomach. FMA:277652 gastro-epiploic node gastro-omental lymph node gastro-omental node jPS 4 node jPS No. 4 node lymph node of greater curvature of stomach gastro-epiploic lymph node UBERON:0038784 FMA:278181 pararectal lymph node of pelvis UBERON:0038787 FMA:278188 superior ileocolic lymph node UBERON:0038796 FMA:281309 biliary lymph node jPS 12b node jPS No. 12b node no. 12b hepatic lymph node lymph node along bile duct UBERON:0038818 FMA:304577 jPS 13 node no. 13 pancreaticoduodenal lymph node posterior ancreaticoduodenal lymph node UBERON:0038849 Lymph node located in either head and neck region. FMA:321555 head and neck lymph node lymph node of head and neck craniocervical lymph node UBERON:0038853 FMA:44231 superficial popliteal lymph node UBERON:0038854 FMA:44232 deep popliteal lymph node UBERON:0038855 FMA:44297 superomedial node superior medial inguinal lymph node UBERON:0038856 FMA:44301 superolateral node superior lateral inguinal lymph node UBERON:0038857 FMA:44302 inferior inguinal node subinguinal lymph node inferior inguinal lymph node UBERON:0038859 FMA:44304 cloquet's gland cloquet's node intermediate deep inguinal node intermediate inguinal lymph node middle inguinal node nodus inguinales profundi intermedius nodus lymphoideus inguinales profundi intermedius intermediate deep inguinal lymph node UBERON:0038860 FMA:44305 distal deep inguinal node distal inguinal lymph node nodus inguinales profundi distalis nodus lymphoideus inguinales profundi distalis distal deep inguinal lymph node UBERON:0038861 FMA:44306 tIbial node tibial lymph node UBERON:0038864 FMA:44309 fibular node nodus fibularis nodus lymphoideus fibularis peroneal lymph node peroneal node fibular lymph node UBERON:0038867 FMA:44312 interpectoral node interpectoral lymph node UBERON:0038868 FMA:44313 paramammary node paramammary lymph node UBERON:0038870 FMA:44315 cubital node cubital lymph node UBERON:0038871 FMA:44316 supra-epicondylar lymph node supratrochlear node supratrochlear lymph node UBERON:0038878 FMA:5935 lateral diaphragmatic node lateral diaphragmatic lymph node UBERON:0038879 FMA:5936 anterior diaphragmatic node anterior diaphragmatic lymph node UBERON:0038882 FMA:5941 posterior diaphragmatic node posterior diaphragmatic lymph node UBERON:0038885 FMA:5944 brachiocephalic node innominate lymph node brachiocephalic lymph node UBERON:0038888 FMA:5947 nodus mediastinale posteriore lymphaticus posterior mediastinal node posterior mediastinal lymph node UBERON:0038894 FMA:5953 cervical paratracheal lymph node nodus paratracheale lymphaticus paratracheal node tracheal lymph node paratracheal lymph node UBERON:0038897 FMA:5959 4 thoracic lymph node 4R+L thoracic lymph node lower paratracheal lymph node nodus tracheobronchiale superiore lymphaticus station 4 N2 lymph node station 4 lymph node superior tracheobronchial lymph node UBERON:0038900 FMA:5962 carinate lymph node nodus tracheobronchialis inferioris lymphaticus inferior tracheobronchial lymph node UBERON:0038920 FMA:61223 buccinator node nodus buccinatorius nodus lymphoideus buccinatorius buccinator lymph node UBERON:0038922 FMA:61225 nasolabial node nodus lymphoideus nasolabialis nodus nasolabialis nasolabial lymph node UBERON:0038923 FMA:61226 malar node nodus lymphoideus malaris nodus malaris malar lymph node UBERON:0038925 FMA:61228 lingual lymph node UBERON:0038929 FMA:61233 infrahyoid node infrahyoid lymph node UBERON:0038930 FMA:61234 prelaryngeal node prelaryngeal lymph node UBERON:0038931 FMA:61235 thyroid node thyroid lymph node UBERON:0038932 FMA:61236 pretracheal node pretracheal lymph node UBERON:0038934 FMA:61238 superior deep lateral cervical lymph node UBERON:0038935 FMA:61239 inferior deep lateral cervical lymph node UBERON:0038936 FMA:61240 jugulodigastric node nodus jugulodigastricus nodus lymphoideus jugulodigastricus jugulodigastric lymph node UBERON:0038938 FMA:61242 accessory cervical lymph node UBERON:0038943 FMA:66167 superior diaphragmatic node superior diaphragmatic lymph node UBERON:0038951 Pylorioc lymph node located near the bifurcation of gastroduodenal artery and superior to the pylorus. FMA:66183 jPS 5 node jPS no.5 node no. 5 station pyloric lymph node nodus lymphoideus suprapyloricus nodus suprapyloricus suprapyloric node suprapyloric lymph node UBERON:0038952 Pylorioc lymph node located in the angle between the superior and descending parts of duodenum. FMA:66184 infrapyloric lymph node infrapyloric node jPS 6 node jPS no. 6 node no. 6 station pyloric lymph node subpyloric node subpyloric lymph node UBERON:0038953 FMA:66185 retropyloric node retropyloric lymph node UBERON:0039162 FMA:78731 inferior ileocolic lymph node UBERON:0039163 FMA:84597 lateral sacral lymph node UBERON:0039164 FMA:84598 medial sacral lymph node UBERON:0039167 A tracheobronchial lymph node situated in the hilum of a lung. FMA:5965 10 R+L thoracic bronchopulmonary node hilar lymph node station 10 N1 lymph node station 10 lymph node bronchopulmonary lymph node UBERON:0039168 FMA:16612 colic node pericolic lymph node pericolonic lymph node colic lymph node UBERON:2001427 ZFA:0001427 anterior nostril anterior naris UBERON:3000961 Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305 external integument structure UBERON:4300174 A finger-like out-pocketing of the intestine where it meets the end of the stomach (pylorus). Also spelled cecum (ceca). Serves to aid digestion. TAO:0002253 pyloric appendage pyloric caeca pyloric caecum actinopterygian pyloric caecum UBERON:8410050 A subdivision of the digestive tract in humans that includes the rectum, the anal canal and the anus. anorectal canal anorectum UBERON:8470000 Blood located in the placenta. placental blood UBERON:8470001 A lymph node with a lymph center located within the caudal abdomen and pelvis, on the ventral side of the lumbar region. Includes the medial iliac, internal iliac (previously termed hypogastric) and sacral lymph nodes. sublumbar lymph node UO:0000000 "A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia] Damion Dooley's note: Need to build this out further with reference to http://unitsofmeasure.org/trac and other unit ontologies: [1] R. Hodgson and P. J. Keller, "QUDT-quantities, units, dimensions and data types in OWL and XML." Online (September 2011) http://www. qudt.org [2] M. van Assem, H. Rijgersberg, and J. Top, "Ontology of units of measure and related concepts." Semantic Web 4, no. 1 (2013): 3-13. [3] G. V. Gkoutos, P. N. Schofield, and R. Hoehndorf, "The Units Ontology: a tool for integrating units of measurement in science." Database2012 (2012): bas033. unit UO:0000001 "A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia] length unit UO:0000003 time derived unit "A unit which is a standard measure of the dimension in which events occur in sequence." [Wikipedia:Wikipedia] time unit UO:0000005 temperature derived unit "A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter." [Wikipedia:Wikipedia] temperature unit UO:0000006 "A unit which is a standardised quantity of an element or compound with uniform composition." [Wikipedia:Wikipedia] substance unit UO:0000045 "A unit which is one of a particular measure to which all measures of that type can be related." [NIST:NIST] base unit UO:0000051 "A unit which represents a standard measurement of how much of a given substance there is mixed with another substance." [UOC:GVG] concentration unit UO:0000052 mass per unit volume "A density unit which is a standard measure of the mass of a substance in a given volume." [UOC:GVG] mass density unit UO:0000056 "A unit which is a standard measure of the volume of a homogeneous substance containing 6.02 x 1023 atoms or molecules." [Wikipedia:Wikipedia] molar volume unit UO:0000059 "A unit which is a standard measure of the volume of a given mass of substance (the reciprocal of density)." [Wikipedia:Wikipedia] specific volume unit UO:0000060 "A unit which is a standard measure of the rate of movement. Speed is measured in the same physical units of measurement as velocity, but does not contain the element of direction that velocity has. Speed is thus the magnitude component of velocity." [Wikipedia:Wikipedia] speed/velocity unit UO:0000067 "A concentration unit which is a standard measure of the number of moles of a given substance per kilogram of solvent." [UOC:GVG] unit of molality UO:0000095 "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [NIST:NIST] volume unit UO:0000121 "A unit which is a standard measure of the figure or space formed by the junction of two lines or planes." [Wikipedia:Wikipedia] angle unit UO:0000122 "A unit which is a standard measure of the angle formed by two straight lines in the same plane." [Wikipedia:Wikipedia] plane angle unit UO:0000182 "A unit which is a standard measure of the influence exerted by some mass." [Wikipedia:Wikipedia] density unit UO:0000186 "A unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [Wikipedia:Wikipedia] dimensionless unit UO:0000187 % "A dimensionless ratio unit which denotes numbers as fractions of 100." [Wikipedia:Wikipedia] percent UO:0000189 count "A dimensionless unit which denotes a simple count of things." [MGED:MGED] count unit UO:0000190 "A dimensionless unit which denotes an amount or magnitude of one quantity relative to another." [Wikipedia:Wikipedia] ratio unit UO:0000191 "A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator)." [Wikipedia:Wikipedia] fraction UO:0000205 "A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution." [NIST:NIST] volume per unit volume UO:0000212 "A concentration unit which a measure of viable bacterial numbers in a given volume." [Wikipedia:Wikipedia] colony forming unit per volume UO:0000217 "A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field." [Wikipedia:Wikipedia] electric potential difference unit UO:0000261 "A unit which represents a standard measurement of the transmission of an entity through a medium." [UOC:GVG] conduction unit UO:0000262 "A unit which represents a standard measurement of the movement of electrically charged particles through a transmission medium (electrical conductor)." [UOC:GVG] electrical conduction unit UO:0000315 "A unit used to indicate the clarity of water or other solutions or suspensions, as measured by the ability of the solution or suspension to scatter light of a defined wavelength range." [UO:PC] turbidity unit UO:0000318 FNU "1000 formazin turbidity units (FNU) on the empirical formazin turbidity scale represents reflectance of insol. reaction products of 0.0725 g hydrazine sulfate with 0.7250 g hexamethylenetetramine diluted to 1 L." [AOAC:192] formazin nephelometric unit UO:0000328 kbp kilobasepair "A unit equal to one thousand base pairs." [UOC:GVG] kilo base pair UO:0010041 us customary teaspoon "A United States customary units teaspoon is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions in America. It equals a 4.93 mL volume." [Wikipedia:https://en.wikipedia.org/wiki/United_States_customary_units#Cooking_measures] united states customary teaspoon UO:0010042 metric tablespoon tbsp "A metric tablespoon is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions. It equals a 15mL volume." [Wikipedia:https://en.wikipedia.org/wiki/Tablespoon] tablespoon UO:0010043 "An Australian metric tablespoon is a unit of measurement of volume used in Australia for cooking recipes and pharmaceutic prescriptions. It equals a 20mL volume." [Wikipedia:https://en.wikipedia.org/wiki/Tablespoon] australian metric tablespoon UO:0010044 us customary tablespoon "A United States customary units tablespoon is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions in America. It equals a 14.79 mL volume." [Wikipedia:https://en.wikipedia.org/wiki/United_States_customary_units#Cooking_measures] united states customary tablespoon UO:0010045 C "A metric cup is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions. It equals a 250mL volume." [Wikipedia:https://en.wikipedia.org/wiki/Cooking_weights_and_measures] metric cup UO:0010046 us customary cup "A United States customary units cup is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions in America. It equals a 236.59 mL volume." [Wikipedia:https://en.wikipedia.org/wiki/United_States_customary_units#Cooking_measures] united states customary cup UO:0010047 us fda cup "A United States FDA cup is a unit of measurement of volume used by the US Federal Department of Agriculture as a nutritional serving measure. It equals a 240 mL volume." [Wikipedia:https://en.wikipedia.org/wiki/United_States_customary_units#Cooking_measures] united states fda cup UO:0010070 pg/mL A gram per milliliter unit which is equal to one picogram per one milliliter. picogram per milliliter UO:0010072 mcg/mcL ug/uL µg/µL "A mass unit density which is equal to mass of an object in nanograms divided by the volume in microliters." [UOB:LTS] microgram per microliter UO:1000008 meter based unit UO:1000010 second based unit UO:1000012 kelvin based unit UO:1000013 mole based unit UO:1000019 angstrom based unit UO:1000027 degree Celsius based unit UO:1000031 minute based unit UO:1000032 hour based unit UO:1000033 day based unit UO:1000034 week based unit UO:1000035 month based unit UO:1000036 year based unit UO:1000076 mole fraction based unit UO:1000084 gram per cubic centimeter based unit UO:1000089 cubic meter per mole based unit UO:1000090 cubic centimeter per mole based unit UO:1000093 cubic meter per kilogram based unit UO:1000094 meter per second based unit UO:1000096 cubic meter based unit UO:1000097 cubic centimeter based unit UO:1000099 liter based unit UO:1000100 cubic decimeter based unit UO:1000123 radian based unit UO:1000151 century based unit UO:1000152 half life based unit UO:1000163 mass percentage based unit UO:1000164 mass volume percentage based unit UO:1000165 volume percentage based unit UO:1000173 gram per milliliter based unit UO:1000175 gram per liter based unit UO:1000185 degree based unit UO:1000193 purity percentage based unit UO:1000194 confluence percentage based unit UO:1000195 degree Fahrenheit based unit UO:1000196 pH based unit UO:1000197 liter per kilogram based unit UO:1000208 gram per deciliter based unit UO:1000210 colony forming unit based unit UO:1000213 colony forming unit per milliliter based unit UO:1000218 volt based unit UO:1000244 base pair based unit UO:1000264 siemens based unit UO:1010011 inch based unit UO:1010012 thou based unit UO:1010013 foot based unit UO:1010014 yard based unit UO:1010015 chain based unit UO:1010016 furlong based unit UO:1010017 mile based unit UO:1010018 league based unit UO:1010019 maritime length unit based unit UO:1010020 fathom based unit UO:1010021 cable based unit UO:1010022 nautical mile based unit UO:1010026 fluid ounce based unit UO:1010027 gill based unit UO:1010028 pint based unit UO:1010029 quart based unit UO:1010030 gallon based unit UO:1010040 teaspoon based unit VO:0004921 Anna Maria Masci, Anthony Huffman, Oliver He The human age is classified into four categories as Child (0-12 years), Adolescence (13-18 years), Adult (19-59 years) and Senior Adult (60 years and above) which is discussed in the paper. Reference: https://ieeexplore.ieee.org/abstract/document/6416855. human age VO:0004925 Anna Maria Masci, Anthony Huffman, Oliver He The human age is classified into four categories as Child (0-12 years), Adolescence (13-18 years), Adult (19-59 years) and Senior Adult (60 years and above) which is discussed in the paper. Reference: https://ieeexplore.ieee.org/abstract/document/6416855. senior age VT:0000001 Any measurable or observable characteristic of a vertebrate organism. vertebrate trait VT:0002292 The length of time between when a fertilized egg implants in the wall of the uterus and the birth of offspring. The length of time between when a fertilized egg implants in the wall of the uterus and the birth of offspring. ATOL:0002292 gestation length gestational length gestation period duration XCO:0000412 ongoing pregnancy The state of a female and/or her offspring, and the processes which occur, during the period from conception to birth or termination of the pregnancy. gestation hancestro:0004 ancestral group sep:00196 A description of the biological sample analysed. Damion Dooley specimen description A personal health datum which specifies host role at time of specimen collection. 0000-0002-9578-0788 2022-01-31T23:53:59Z host role at time of specimen collection NCBITaxon:_taxonomic_rank taxonomic rank taxonomic rank MLVA typing MLVA stands for Multilocus Variable Number of Tandem Repeats Analysis. This method can be performed by three distinct methodologies: by running the amplified locus in a gel , using a capilary electrophoresis apparatus or sequencing the resulting amplified fragment. The first two infer the number of repeats on each locus indirectly by the fragment size. Multilocus Variable Number of Tandem Repeats Analysis typing resource:SIO_000136 A description is language entity in which elements of a language (formal or natural) are used to characterize an entity. description resource:SIO_000415 a geopolitical region is a geographic region recognized by social or legal convention. geopolitical region A polygon edge is a line segment joining two polygon vertices. http://semanticscience.org/resource/SIO_000501 A polygon edge must exist in the same 2 dimensional space (plane or quadratic surface) as the polygon's other edges. Each polygon edge vertex must join to exactly 1 other polygon edge. A polygon's edges exist in exactly 1 circuit. polygon edge resource:SIO_000503 A polygon serves as a boundary for an area of interest that exists within a larger area. Damion Dooley's comment: On spheroids a polygon can be minimally defined by latitude and longitude coordinates, however technically this is ambiguous whether the larger or smaller area is being referred to. Unambiguously, such a polygon could be defined by an epicenter, and a latitude width and longitude height. polygonal face 3 resource:SIO_000505 In elementary geometry, a polygon is a plane figure that is bounded by a finite chain of straight line segments closing in a loop to form a closed chain or circuit. Damion Dooley https://en.wikipedia.org/wiki/Polygon polygon resource:SIO_000507 A point is a geometric entity that is located in a zero-dimensional spatial region and whose position is defined by its coordinates in some coordinate system. point A line is curve that extends in a single dimension (e.g. straight line; exhibits no curvature), and is composed of at least two fully connected points. http://semanticscience.org/resource/SIO_000511 line A line segment is a line and a part of a curve that is (inclusively) bounded by two terminal points. http://semanticscience.org/resource/SIO_000512 line segment Damion Dooley http://semanticscience.org/resource/SIO_000546 collection of points resource:SIO_000608 A curve is a geometric entity that may be located in n-dimensional spatial region whose extension may be n-dimensional, is composed of at least two fully connected points and does not intersect itself. http://semanticscience.org/resource/SIO_000608 curve resource:SIO_000666 resource:SIO_000729 A record identifier is an identifier for a database entry. PulseNet: Key record identifier resource:SIO_000811 A Uniform Resource Locator or Universal Resource Locator (URL) is a specific character string that constitutes a reference to an Internet resource. URL resource:SIO_000964 resource:SIO_001027 A medical health record is a record of a single patient's medical history. Damion Dooley medical health record medical health record (history / timeline) resource:SIO_001322 an IP number is an number to connect to a device on the internet. IP number resource:SIO_010057 depth:1 lookup life status is the quality of whether something is alive or dead. life status An assay for detecting bacteria by subjecting them to strain-specific bacteriophages. Damion Dooley Bacterial bacteriophage typing http://phinvads.cdc.gov/vads/http:/phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.6.96&code=22642004 A microplate having 96 wells. Damion Dooley 96 well plate http://purl.obolibrary.org/obo/hancestro_0004 obsolete: ancestral group true efo:EFO_0000246 A temporal measurement of the time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting). James Malone Jie Zheng Tomasz Adamusiak MO:467 NCIt:C25150 SNOMEDCT:397669002 http://purl.obolibrary.org/obo/PATO_0000011 age efo:EFO_0000408 A disease is a disposition that describes states of disease associated with a particular sample and/or organism. A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. James Malone DOID:4 ICD10:R69 ICD9:799.9 MESH:D004194 MONDO:0000001 MeSH:D004194 NCIT:C2991 OGMS:0000031 Orphanet:377788 SCTID:64572001 SNOMEDCT:64572001 UMLS:C0012634 Homo sapiens disease condition disease disease or disorder disease or disorder, non-neoplastic diseases diseases and disorders disorder disorders human disease medical condition other disease disease efo:EFO_0000409 A temporal measurement of the period after successful treatment in which there is no appearance of the symptoms or effects of the disease. James Malone MeSH:D018572 Disease-Free Survival morbidity-free survival disease free survival efo:EFO_0000412 Is a temporal measure from a defined start point e.g. diagnosis, or treatment of the period to appearance of a distant metastasis. A distant metastasis refers to cancer that has spread from the original (primary) tumor to distant organs or distant lymph nodes. Also known as distant cancer. Helen Parkinson http://www.cancer.gov/dictionary?cdrid=415317 event distant metastases time to development of distant metastases distant metastasis free survival efo:EFO_0000433 A temporal measurement of the time between two specified points. James Malone Tomasz Adamusiak NCIt:C25330 NIFSTD:birnlex_2052 SNOMEDCT:103335007 duration efo:EFO_0000482 Is the survival of a subject (or group of subjects) measured from the date of diagnosis until locoregional or systemic recurrence, second malignancy, or death from any cause or disease progression or relapse, institution of new unplanned anticancer treatment, or death from any cause. James Malone http://en.wikibooks.org/wiki/Radiation_Oncology/Survival_curve_terminology event free survival time efo:EFO_0000512 A disease involving the reproductive system. Any disease of the reproductive system. James Malone Sirarat Sarntivijai Tomasz Adamusiak DOID:15 MONDO:0005039 NCIT:C4875 SCTID:362968007 SNOMEDCT:362968007 UMLS:C0178829 Wikipedia:Reproductive_system_disease Disorder of reproductive system Disorder of reproductive system (disorder) Non-neoplastic Reproductive system disease disease of reproductive system disease or disorder of reproductive system disorder of reproductive system genital disorders genital system disease reproductive disease reproductive system disease reproductive system disease or disorder reproductive system disorder reproductive system disease efo:EFO_0000638 A measurement of the survival rate for a group of individuals suffering from a disease. James Malone overall survival efo:EFO_0000648 James Malone period of infection efo:EFO_0000683 A role played by a a biological sample in the context of an experiment where the intent is that biological or technical variation is measured. James Malone NCIt:C28038 replicate efo:EFO_0000689 James Malone Jie Zheng Tomasz Adamusiak MO:866 sampling_time_point sampling time efo:EFO_0000714 Time of survival is an information entity which is about the length of time a material entity has survived after some adverse event, such as infection from a disease. James Malone MeSH:D013534 NCIt:C17177 PERSON: James Malone SNOMEDCT:445320007 survival time of survival survival time efo:EFO_0000719 A temporal entity is an entity that has temporal parts and that happens, unfolds or develops through time. An occurrent is something which exists over time, rather than existing completely at many times James Malone temporal measurement efo:EFO_0000724 Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point. James Malone Jie Zheng Tomasz Adamusiak MO:738 NCIt:C68568 timepoint efo:EFO_0001444 A measurement is an information entity that is a recording of the output of a measurement such as produced by an instrument. James Malone Jie Zheng Tomasz Adamusiak MO:144 NCIt:C25209 NIFSTD:sao279801585 SNOMEDCT:122869004 measurement efo:EFO_0001799 A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP) efo:EFO_0002090 A technical replicate is a replicate role where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment. James Malone MO:641 technical_replicate technical replicate efo:EFO_0002091 A biological replicate is a replicate role that consists of independent biological replicates made from different individual biosamples. James Malone MO:952 biological_replicate biological replicate efo:EFO_0002571 An activity that produces an effect, or that is intended to alter the course of a disease in a patient or population. This is a general term that encompasses the medical, social, behavioral, and environmental acts that can have preventive, therapeutic, or palliative effects. Jie Zheng Tomasz Adamusiak ICD10:Z41 NCIt:C25218 NCIt:C79751 SNOMEDCT:50731006 Intervention Intervention Strategies Intervention or Procedure Interventional Procedure SURGICAL AND MEDICAL PROCEDURES interventionDescription medical procedure efo:EFO_0002694 A process performed as part of an experiment or wider study, i.e. intentionally designed. NCIt:C42790 NIFSTD:birnlex_2117 Experiment experimental process efo:EFO_0002950 The state or condition of having a developing embryo or fetus in the body (uterus), after union of an ovum and spermatozoon, during the period from conception to birth. The status during which female mammals carry their developing young (EMBRYOS or FETUSES) in utero before birth, beginning from FERTILIZATION to BIRTH. Tomasz Adamusiak ICD10:Z34 MeSH:D011247 MedDRA:10036556 NCIt:C25742 SNOMEDCT:289908002 Gestation PREGN Pregnancies pregnancy efo:EFO_0004302 Anthropometry is a measurement of the size, weight, and proportions of the human or other primate body. Dani Welter MeSH:D000886 anthropometric traits anthropometry anthropometric measurement efo:EFO_0004318 Inhaling and exhaling the smoke of tobacco or something similar to tobacco. Dani Welter MeSH:D012907 NCIt:C20134 smoking smoking behavior efo:EFO_0004324 Measurements of the height, weight, length, area, etc., of the human and animal body or its parts. Dani Welter MeSH:D001837 body measures body weights and measures efo:EFO_0004340 An indicator of body density as determined by the relationship of BODY WEIGHT to BODY HEIGHT. BMI=weight (kg)/height squared (m2). BMI correlates with body fat (ADIPOSE TISSUE). Their relationship varies with age and gender. For adults, BMI falls into these categories: below 18.5 (underweight); 18.5-24.9 (normal); 25.0-29.9 (overweight); 30.0 and above (obese). (National Center for Health Statistics, Centers for Disease Control and Prevention) Dani Welter https://en.wikipedia.org/wiki/Body_mass_index ICD9:V85-V85.99 MeSH:D015992 MedDRA:10005894 NCIt:C16358 SNOMEDCT:60621009 BMI Quetelet's Index body mass index efo:EFO_0004352 Quantification of the number of deaths in a population. Dani Welter MeSH:D009026 MeSH:Q000401 NCIt:C16880 SNOMEDCT:409651001 mortality measurement mortality rate mortality efo:EFO_0004425 The first time point measured at the start of some process. James Malone initial timepoint initial time point efo:EFO_0004542 A processual entity that realizes a plan which is the concretization of a plan specification. OBI_0000011 planned process efo:EFO_0004557 Is the quantification of some measureable quality of a population e.g. birth rate. Helen Parkinson population measurement efo:EFO_0004703 The age of onset of (human) menarche, the beginning of the first menstrual cycle in an individual Helen Parkinson NCIt:C19666 SNOMEDCT:398700009 age at menarche efo:EFO_0004704 The age of onset of (human) menopause, the beginning of the first menstrual cycle in an individual Helen Parkinson NCIt:C106497 age at menopause efo:EFO_0004847 The age at which some process, or disease started in a human individual. Helen Parkinson age at onset efo:EFO_0004918 The age, measured from some defined time point e.g. birth at which a subject (e.g. a human patient) is diagnosed with some disease e.g. breast cancer. Helen Parkinson http://purl.bioontology.org/ontology/SNOMEDCT/423493009 SNOMEDCT:423493009 age at diagnosis efo:EFO_0004919 The percentage of subjects in a study who have survived without cancer spread for a defined period of time. Usually reported as time since diagnosis or treatment. Can be reported for an individual or a study population. Helen Parkinson www.oncura.net/glossary.php metastasis free survival time metastasis free survival efo:EFO_0004920 Progression free survival is a measurement from a defined time point e.g. diagnosis and indicates that the disease did not progress i.e. tumours did not increase in size and new incidences did not occur. PFS is usually used in analyzing results of treatment for advanced disease. Helen Parkinson http://cancerguide.org/scurve_basic.html time before disease progression progression free survival efo:EFO_0004949 A temporal measurement related to disease progression Helen Parkinson clinical event clinical temporal measurement efo:EFO_0004950 The point in time at which an individual was born. Helen Parkinson SNOMEDCT:184099003 date of birth efo:EFO_0004951 A clinical temporal measurement indicating that the subject is alive at the end of the clinical investigation. Helen Parkinson alive at endpoint efo:EFO_0004952 The recurrence of a disease after treatment Helen Parkinson MedDRA:10061819 relapse disease recurrence efo:EFO_0004953 The point at which a clinical diagnosis is made. Helen Parkinson SNOMEDCT:432213005 date of diagnosis efo:EFO_0005056 The age at which death occurs. Dani Welter age at death efo:EFO_0005112 The age of the conceptus, beginning from the time of FERTILIZATION. In clinical obstetrics, the gestational age is often estimated as the time from the last day of the last MENSTRUATION which is about 2 weeks before OVULATION and fertilization. Dani Welter MeSH:D005865 gestational age efo:EFO_0005602 Helen Parkinson The age at which an alcohol diagnosis was made in a human patient age at alcohol diagnosis efo:EFO_0005603 Helen Parkinson The age at which a breast cancer diagnosis was made in a human patient age at breast cancer diagnosis efo:EFO_0007058 The date or time of the last check of a patient by a medical professional. Catherine Leroy last follow up efo:EFO_0007888 The age of onset of (human) voice drop, the deepening of the voice of adolescents as they reach puberty Dani Welter age at voice drop efo:EFO_0008007 The age of an individual at the time an assessment takes place Dani Welter PMID:20634892 age at assessment efo:EFO_0008336 quantification of some aspect of disease progression such as speed or symptom variability. Disease progression can be quantified in a number of ways, for example as a correlated measure of progression scores from different symptom areas Dani Welter PMID:28642124 disease progression measurement efo:EFO_0009549 A disease involving the female reproductive system. SCTID:310789003 DOID:229 ICD10:N85 ICD10:N88 ICD10:N89 ICD10:N90 ICD10:N94 ICD9:629.9 MESH:D005831 MONDO:0002263 MeSH:D005831 NCIT:C27020 NCIt:C27020 SCTID:310789003 disease of female reproductive system disease or disorder of female reproductive system disorder of female genital system disorder of female reproductive system female reproductive disease female reproductive system disease female reproductive system disease or disorder female reproductive system disorder female reproductive system disease efo:EFO_0009642 The process by which information about the health status of an individual is obtained after a study has officially closed; an activity that continues something that has already begun or that repeats something that has already been done. [def-source: NCI] ICD10:Z08 ICD10:Z09 ICD10:Z42 ICD10:Z48 NCIt:C16033 follow up EFO:0009642 'follow-up' refers to the medical procedure process of running follow-ups; EFO:0030038 'follow up status' refers to an observed quality. follow-up efo:EFO_0009712 The age of a person's father at which father's death occurred. father's age at death efo:EFO_0009716 The age of onset of first facial hair. age at first facial hair efo:EFO_0009721 The age of a person's mother at which mother's death occurred. mother's age at death efo:EFO_0010162 Death in during childhood, defined here as between the ages of 2 and 10 years. Baron Koylass UMLS:C1843392 death in childhood efo:EFO_0020044 The determination of the amount of eicosanoids present in a sample, typically blood PMID:34503513 ecosanoids measurement efo:EFO_0020045 The determination of the amount of prostaglandins present in a sample, typically blood PMID:34503513 prostaglandins measurement efo:EFO_0021779 Age at initiation of a medical treatment, such as a drug, therapy or medical device. NCIT:C124440 age at first treatment age at initiation of medical treatment age at initiation of treatment efo:EFO_0021780 Age at initiation of hormone replacement therapy, the therapeutic use of hormones to alleviate the effects of hormone deficiency. age at initiation of hormone replacement therapy efo:EFO_0021781 Age at initiation of the use of corrective lenses, such as glasses or contact lenses, to treat an abnormality of the eye. age at initiation of corrective lens use efo:EFO_0021782 Age at initiation of the use of an oral contraceptive pill. age at initiation of oral contraceptive pill use efo:EFO_0021783 Age at the time of a specific medical procedure or intervention intended to alter the course of a disease. age at intervention age at medical intervention age at procedure age at medical procedure efo:EFO_0021784 Age of initation of the habit of smoking, the inhaling and exhaling of tobacco smoke. age at initiation of smoking efo:EFO_0021785 Age of initiation of the consumption of the drug cannabis. age at initiation of cannabis consumption age at initiation of cannabis use efo:EFO_1001491 the ending of pregnancy by removing a fetus or embryo before it can survive outside the uterus. Sirarat Sarntivijai ICD10:O04 ICD10:O06 MESH:D000028 MedDRA:10000210 Wikipedia:Abortion loss of pregnancy abortion owl:Thing Welcome to the GenEpiO ontology! The "information content entity" class has many GenEpiO terms. "data item > measurement data item" has many datum terms; see "data representational model" for collections of terms set up for compatibility with 3rd party sources. Note that this file contains examples of cities, provinces, states, territories, and soverign nations from around the world; customization of this geographical content would be expected for particular regional use. acquaintance address linkml:Definition Base class for definitions. linkml:Element A named element in the model. linkml:Example Usage example and description. linkml:LocalName An attributed label. linkml:PermissibleValue A permissible value, accompanied by intended text and an optional mapping to a concept URI. linkml:SchemaDefinition A collection of subset, type, slot and class definitions. linkml:SlotDefinition The definition of a property or a slot. Marianas Islands INSDC:country:arctic ocean Arctic Ocean INSDC:country:atlantic ocean Atlantic Ocean INSDC:country:pacific ocean Pacific Ocean INSDC:country:indian ocean Indian Ocean INSDC:country:southern ocean North Atlantic Ocean South Atlantic Ocean INSDC:country:australia Australia Europe Asia Indian subcontinent INSDC:country:new zealand New Zealand INSDC:country:south africa South Africa West Africa North Africa East Africa Anatolia INSDC:country:turkey Turkey Southeast Asia INSDC:country:sudan Sudan INSDC:country:tunisia Tunisia INSDC:country:algeria Algeria INSDC:country:western sahara Western Sahara INSDC:country:morocco Morocco INSDC:country:libya Libya INSDC:country:ethiopia Ethiopia INSDC:country:eritrea Eritrea INSDC:country:djibouti Djibouti INSDC:country:mauritania Mauritania INSDC:country:mali Mali INSDC:country:niger Niger INSDC:country:chad Chad Sub-Saharan Africa Central Africa Cape Verde Islands INSDC:country:iceland Iceland INSDC:country:saint helena Saint Helena INSDC:country:benin Benin INSDC:country:burkina faso Burkina Faso INSDC:country:cote d'ivoire Cote d'Ivoire INSDC:country:gambia Gambia INSDC:country:ghana Ghana INSDC:country:guinea Guinea INSDC:country:guinea-bissau Guinea-Bissau INSDC:country:liberia Liberia INSDC:country:nigeria Nigeria INSDC:country:senegal Senegal INSDC:country:sierra leone Sierra Leone INSDC:country:togo Togo INSDC:country:belgian congo INSDC:country:democratic republic of the congo Democratic Republic of the Congo INSDC:country:rwanda Rwanda INSDC:country:republic of the congo Republic of Congo INSDC:country:central african republic Central African Republic INSDC:country:burundi Burundi INSDC:country:equatorial guinea Equatorial Guinea INSDC:country:gabon Gabon INSDC:country:cameroon Cameroon Republic of South Africa INSDC:country:angola Angola INSDC:country:namibia Namibia INSDC:country:botswana Botswana INSDC:country:lesotho Lesotho INSDC:country:swaziland Swaziland INSDC:country:mozambique Mozambique INSDC:country:kenya Kenya INSDC:country:uganda Uganda INSDC:country:tanzania Tanzania INSDC:country:somalia Somalia INSDC:country:malawi Malawi INSDC:country:zimbabwe Zimbabwe INSDC:country:zambia Zambia INSDC:country:madagascar Madagascar Canary Islands Macaronesian Islands INSDC:country:cape verde Cape Verde Bouvet Islands INSDC:country:barbados Barbados INSDC:country:bouvet island Bouvet Island Faroes British Isles INSDC:country:greenland Greenland Channel Islands Isles of Man INSDC:country:guernsey Guernsey INSDC:country:jersey Jersey Equatorial Pacific Ocean North Pacific Ocean South Pacific Ocean State of California Central Asia Southwest Asia Levant Arabian Peninsula Kurdistan Caucasus Iranian Plateau East Asia South Asia Jordan INSDC:country:switzerland Syria Palestinian Territories INSDC:country:israel Israel INSDC:country:lebanon Lebanon Hawaiian Islands INSDC:country:bolivia Bolivia State of New York State of Oregon Guyane State of Arizona State of Maryland State of North Carolina State of Alaska INSDC:country:british guiana INSDC:country:guyana Guyana State of South Carolina INSDC:country:suriname Suriname State of Rhode Island State of Wyoming Mediterranean Sea, Eastern Basin Commonwealth of Massachusetts State of Minnesota Commonwealth of Pennsylvania State of Oklahoma State of Washington State of New Jersey INSDC:country:canada Canada State of Texas State of Wisconsin State of Connecticut State of Maine State of Montana State of Georgia INSDC:country:united kingdom United Kingdom Northern Ireland Scotland Wales England INSDC:country:germany begin_date: 1990-10-03. Germany INSDC:country:italy Italy INSDC:country:croatia Croatia INSDC:country:russia begin_date: 1991-12. Russia INSDC:country:ukraine Ukraine INSDC:country:sweden Sweden INSDC:country:bahamas The Bahamas INSDC:country:japan Japan Korean Peninsula INSDC:country:north korea North Korea INSDC:country:south korea South Korea Hispaniola INSDC:country:chile Chile INSDC:country:brazil Brazil INSDC:country:india India populated place, Mozambique INSDC:country:china China Northeast Asia INSDC:country:mexico Mexico State of Delaware State of Florida Central America INSDC:country:panama Panama INSDC:country:honduras Honduras INSDC:country:costa rica Costa Rica Cocos Island INSDC:country:ecuador Ecuador INSDC:country:argentina Argentina INSDC:country:colombia Colombia INSDC:country:uruguay Uruguay INSDC:country:venezuela Venezuela INSDC:country:peru Peru INSDC:country:paraguay Paraguay INSDC:country:belize Belize INSDC:country:el salvador El Salvador INSDC:country:guatemala Guatemala INSDC:country:finland Finland INSDC:country:belgium Belgium INSDC:country:poland Poland INSDC:country:switzerland Switzerland INSDC:country:austria Austria Republic of Ireland INSDC:country:greece Greece The Netherlands INSDC:country:luxembourg Luxembourg INSDC:country:andorra Andorra Iberian Peninsula INSDC:country:bulgaria Bulgaria INSDC:country:romania Romania INSDC:country:hungary Hungary INSDC:country:albania Albania INSDC:country:czech republic INSDC:country:czechoslovakia Czech Republic INSDC:country:slovenia Slovenia INSDC:country:slovakia Slovak Republic INSDC:country:serbia Serbia INSDC:country:latvia ISO3166-2 codes for 2009 revision of admin. units seem not to have been assigned. Latvia INSDC:country:estonia Estonia INSDC:country:lithuania Lithuania INSDC:country:nicaragua Nicaragua Middle Atlantic Division Italian Peninsula INSDC:country:san marino San Marino Vatican City East North Central Division State of Illinois State of Michigan Commonwealth of Virginia Pacific Division District of Columbia West North Central Division Scandinavian Peninsula INSDC:country:indonesia Indonesia Bali INSDC:country:siam INSDC:country:thailand Thailand INSDC:country:mauritius Mauritius INSDC:country:bangladesh Bangladesh INSDC:country:french southern and antarctic lands Territoire des Terres australes et antarctiques francaises INSDC:country:viet nam Viet Nam INSDC:country:cuba Cuba INSDC:country:trinidad and tobago Trinidad and Tobago West Indies Greater Antilles West South Central Division INSDC:country:jamaica Jamaica INSDC:country:monaco Monaco INSDC:country:liechtenstein Liechtenstein East South Central Division South Atlantic Division Mountain Division Moldova INSDC:country:brunei Brunei Darussalam INSDC:country:malaysia Malaysia INSDC:country:bhutan Bhutan INSDC:country:papua new guinea Papua New Guinea INSDC:country:singapore Singapore INSDC:country:sri lanka Sri Lanka Timor Metropolitan Spain contiguous United States of America State of Hawaii Metropolitan France Reunion Island INSDC:country:guadeloupe Guadeloupe Archipelago Lesser Antilles Leeward Islands Leeward Antilles Windward islands INSDC:country:dominican republic Dominican Republic INSDC:country:haiti Haiti Lucayan Archipelago INSDC:country:northern mariana islands Northern Mariana Islands INSDC:country:virgin islands Virgin Islands Archipelago Island of Cyprus INSDC:country:malta Malta INSDC:country:ireland Ireland INSDC:country:netherlands antilles Netherlands Antilles Curacao Island INSDC:country:aruba Aruba INSDC:country:armenia Armenia Metropolitan Portugal INSDC:country:nepal Nepal State of Tennessee State of Utah State of West Virginia State of Ohio State of New Mexico State of New Hampshire State of Vermont State of Mississippi State of Missouri State of Louisiana State of Kansas State of Iowa State of Indiana Commonwealth of Kentucky State of Arkansas State of North Dakota State of South Dakota State of Nevada INSDC:country:iran Iran INSDC:country:iraq Iraq INSDC:country:philippines The Philippines Great Britain South Caucasus INSDC:country:azerbaijan Azerbaijan INSDC:country:georgia begin_date: 1936-12-05. end_date: 1990-10-20. Georgia INSDC:country:uzbekistan begin_date: 1991-12-31. Uzbekistan INSDC:country:kazakhstan Geographically the western regions of Kazakhstan may be in Europe. Kazakhstan INSDC:country:turkmenistan Turkmenistan State of Nebraska New Guinea INSDC:country:pakistan Pakistan INSDC:country:solomon islands Solomon Islands INSDC:country:saudi arabia Saudi Arabia INSDC:country:bahrain Bahrain INSDC:country:united arab emirates United Arab Emirates INSDC:country:oman Oman INSDC:country:yemen Yemen INSDC:country:kuwait Kuwait INSDC:country:qatar Qatar Persian Gulf Society Islands Windward Islands Tahiti INSDC:country:taiwan Republic of China INSDC:country:svalbard Svalbard Archipelago Manchuria INSDC:country:kerguelen archipelago Kerguelen Archipelago INSDC:country:glorioso islands Glorioso Islands INSDC:country:juan de nova island JIle uan de Nova INSDC:country:bassas da india Ile Bassas da India INSDC:country:europa island Ile Europa INSDC:country:tromelin island Ile Tromelin INSDC:country:comoros Comoros Caucasian Russia INSDC:country:clipperton island Clipperton Island Metropolitan Norway Metropolitan Denmark INSDC:country:jan mayen Jan Mayen Melanesia Polynesia INSDC:country:micronesia Micronesia Australasia Christmas Island State of Colorado State of Idaho New England Division Borneo group State of Alabama INSDC:country:afghanistan Afghanistan INSDC:country:antigua and barbuda Antigua and Barbuda INSDC:country:belarus begin_date: 1990-07-27. Belarus INSDC:country:bosnia and herzegovina Bosnia and Herzegovina INSDC:country:cambodia Cambodia INSDC:country:laos Laos INSDC:country:dominica Dominica Fiji Fiji islands INSDC:country:kyrgyzstan Kyrgyzstan INSDC:country:kiribati Kiribati INSDC:country:former yugoslav republic of macedonia Macedonia INSDC:country:montenegro Montenegro INSDC:country:burma INSDC:country:myanmar Myanmar INSDC:country:nauru Nauru Nauru Island Niue Fekai Niue Islands INSDC:country:palau Palau INSDC:country:saint kitts and nevis Saint Kitts-Nevis INSDC:country:saint lucia Saint Lucia INSDC:country:samoa Samoa Samoan Archipelago INSDC:country:tajikistan Tajikistan INSDC:country:east timor Timor-Leste Tuvalu Islands Tonga Tonga Archipelago INSDC:country:vanuatu Vanuatu Vanuatu Islands Islands of Mauritius The Seychelles Comoro Islands Maldives Archipelago INSDC:country:sao tome and principe Sao Tome and Principe Madagascar Island Bahrain Archipelago Solomon Archipelago Cook Archipelago Kiribati islands Greater Sunda Islands Sunda Islands Lesser Sunda Islands INSDC:country:wake island Wake Island INSDC:country:midway islands Midway Atoll INSDC:country:johnston atoll Johnston Atoll INSDC:country:kingman reef Kingman Reef Baker Island INSDC:country:jarvis island Jarvis Island INSDC:country:navassa island Navassa Island Howland Island Caroline Islands INSDC:country:line islands Line Islands INSDC:country:marshall islands Marshall Islands INSDC:country:pitcairn islands Pitcairn Island Wallis and Futuna islands Island of Sri Lanka Federal District (Mexico) Cuban Archipelago Province (Turkmenistan) Barents Sea INSDC:country:mongolia Mongolia Gulf of Saint Lawrence Gulf of Guinea Laccadive Sea Mozambique Channel Bali Sea South China Sea Coral Sea INSDC:country:heard island and mcdonald islands Heard and McDonald islands INSDC:country:cocos islands Cocos Islands Delmarva Peninsula INSDC:country:spratly islands Spratly Islands INSDC:country:paracel islands Paracel Islands INSDC:country:kosovo Kosovo INSDC:country:sint maarten Sint Maarten Country of Curacao Northeast Atlantic Ocean Northwest Atlantic Ocean Southwest Pacific Ocean North East Pacific Ocean North West Pacific Ocean Nanumanga Atoll Bjornoya [Svalbard] INSDC:country:ross sea Ross Sea Java Sumatra Sulawesi INSDC:country:borneo Borneo Caucasus Mountains Saint-Martin Island Singapore Island Puntarenas Canton Prince Edward Island Island of Dominica Western Indian Ocean Eastern Indian Ocean Malacca and Singapore Straits Southeast Atlantic Ocean Southwest Atlantic Ocean Southeast Pacific Ocean North East Pacific Ocean coastal waters of Central America and Columbia Northwest Atlantic Ocean coastal waters of Canada Isle of Man INSDC:country:yugoslavia begin_date: 1943-11-29. end_date: 1991-06-25. Previous to 1943: Kingdom of Yugoslavia, begins_in: 1918-12-01; end_date: 1941-04_17. [Former] Yugoslavia INSDC:country:cook islands Cook Islands Southern Marianas Islands Paulu Archipelago Malay Peninsula Qatari Peninsula INSDC:country:faroe islands Faroe Islands Island of Cuba Department of Guadeloupe Mascarene Islands Bahama Banks Sumatra group Sulawesi group Java group Northeast Atlantic Ocean coastal waters of Africa Northwest Atlantic Ocean coastal waters of Barbados Northwest Atlantic Ocean coastal waters of Bermuda Western Indian Ocean coastal waters of Southern Africa and Madagascar Nanumanga Island Northwest Atlantic Ocean coastal waters of Greenland INSDC:country:south sudan South Sudan INSDC:country:tokelau Tokelau British Isles Caribbean Region Grenadines INSDC:country:saint vincent and the grenadines Saint Vincent and the Grenadines INSDC:country:grenada Grenada Ulster Damion Dooley Damion Dooley's note: Here we are exploring the use of individuals/instances to describe local picklists for GenEpiO driven software. E gene (orf4) [GENEPIO:0100151] A data field which describes the name and version number of the protocol used for diagnostic marker amplification. gene name 1 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z gene name 1 field gene name 1 slot gene name one Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select a gene from the pick list. If the gene of interest is not in the list, provide the full name of the gene or the gene symbol (short form of gene name). Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gene name 1 field EGenePCRTest 2 A data field which describes the name and version number of the protocol used for diagnostic marker amplification. diagnostic pcr protocol 1 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr protocol 1 field diagnostic pcr protocol 1 slot diagnostic pcr protocol one Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. diagnostic pcr protocol 1 field 21 A data field which describes the Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. diagnostic pcr Ct value 1 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr Ct value 1 field diagnostic pcr Ct value 1 slot diagnostic pcr Ct value one Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the cycle threshold (Ct) value of the sample from the diagnostic RT-PCR test. diagnostic pcr Ct value 1 field RdRp gene (nsp12) [GENEPIO:0100168] A data field which describes the name and version number of the protocol used for diagnostic marker amplification. gene name 2 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z gene name 2 field gene name 2 slot gene name two Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select a gene from the pick list. If the gene of interest is not in the list, provide the full name of the gene or the gene symbol (short form of gene name). Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gene name 2 field RdRpGenePCRTest 3 A data field which describes the name and version number of the protocol used for diagnostic marker amplification. diagnostic pcr protocol 2 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr protocol 2 field diagnostic pcr protocol 2 slot diagnostic pcr protocol two Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. diagnostic pcr protocol 2 field 36 A data field which describes the Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. diagnostic pcr Ct value 2 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr Ct value 2 field diagnostic pcr Ct value 2 slot diagnostic pcr Ct value two Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the cycle threshold (Ct) value of the sample from the second diagnostic RT-PCR test. diagnostic pcr Ct value 2 field RdRp gene (nsp12) [GENEPIO:0100168] A data field which describes the name of the gene used in the diagnostic RT-PCR test. gene name 3 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z gene name 3 field gene name 3 slot gene name three Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gene name 3 field RdRpGenePCRTest 3 A data field which describes the name and version number of the protocol used for diagnostic marker amplification. diagnostic pcr protocol 3 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr protocol 3 field diagnostic pcr protocol 3 slot diagnostic pcr protocol three Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. diagnostic pcr protocol 3 field 30 A data field which describes the Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. diagnostic pcr Ct value 3 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr Ct value 3 field diagnostic pcr Ct value 3 slot diagnostic pcr Ct value three Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the CT value of the sample from the second diagnostic RT-PCR test. diagnostic pcr Ct value 3 field United Nations MSH NCI_Thesaurus NIFSTD _test_individual LabID assigned by NLEP Damion Dooley 2019-04-17T23:31:44Z PulseNet:LabID Country where isolate was collected Damion Dooley 2019-04-17T23:32:45Z SourceCountry Country where isolate was collected Currently not used for PulseNet Canada Damion Dooley 2019-04-17T23:37:19Z PulseNet:SourceCountry (Province for PNC) where isolate was collected. Damion Dooley 2019-04-17T23:38:09Z PulseNet:SourceState Damion Dooley 2019-04-17T23:40:57Z PulseNet:SourceCity Site of the source type where isolate was collected, e.g. blood, CSF, etc. Damion Dooley 2019-04-17T23:47:10Z PulseNet:SourceSite The source type of the isolate, e.g. human, environmental, etc. Damion Dooley 2019-04-17T23:48:49Z PulseNet:SourceType Other countries where the patient traveled Damion Dooley 2019-04-17T23:49:47Z PulseNet:Traveled_To Further description of the source type, e.g. bovine, chicken Damion Dooley 2019-04-17T23:51:02Z PulseNet:TypeDetails Submitted isolate # (if diff. From Key #), NLEP will enter Prov. Submitted # if sample was sent to NLEP for PFGE Damion Dooley 2019-04-17T23:52:01Z PulseNet:SubmittedNumber (Province for PNC) additional number used to identify the isolate Damion Dooley 2019-04-17T23:53:47Z PulseNet:OtherStateIsolate Age of patient when isolate was collected Damion Dooley 2019-04-17T23:54:24Z PulseNet:PatientAge Sex of patient when isolate was collected Damion Dooley 2019-04-17T23:55:04Z PulseNet:PatientSex Date of collection Damion Dooley 2019-04-17T23:56:33Z PulseNet:IsolatDate Date the isolate is uploaded to the national database after initial upload Damion Dooley 2019-04-18T00:21:46Z PulseNet:UploadModifiedDate Antigenic Formula Damion Dooley 2019-04-18T00:23:18Z PulseNet:AntigenForm Subspecies, I - VI (roman numerals) Damion Dooley 2019-04-18T00:24:11Z PulseNet:Subspecies O polysaccharide (LPS) Group Damion Dooley 2019-04-18T00:24:53Z PulseNet:OGroup Serotype of isolate Damion Dooley 2019-04-18T00:25:22Z PulseNet:Serotype Code issued by CDC; see: 'Naming of outbreaks…' on WebBoard. (format YYMMLabIDLITScode-#) Currently not used for PulseNet Canada Damion Dooley 2019-04-18T00:27:08Z PulseNet:Outbreak Number issued by CDC if isolate is run at CDC (Key will be # issued by NLEP if isolate run at NLEP) Damion Dooley 2019-04-18T00:28:01Z PulseNet:cdc_id Enzyme name present if part of that national list. Damion Dooley 2019-04-18T00:28:35Z PulseNet:ListMember Phage type Damion Dooley 2019-04-18T00:29:20Z PulseNet:Phagetype Provides LabID, gel and lane information Damion Dooley 2019-04-18T00:29:58Z PulseNet:TEMP Status of the isolate; this is only confirmed once CDC runs it. Currently not used for PulseNet Canada Damion Dooley 2019-04-18T00:30:44Z PulseNet:Status Currently not used for PulseNet Canada checked if the isolate is part of NARMS. Damion Dooley 2019-04-18T00:35:55Z PulseNet:NARMS-EB Checked if the isolate is part of FoodNet. Currently not used for PulseNet Canada Damion Dooley 2019-04-18T00:36:39Z PulseNet:FoodNet XbaI gel where the isolate is located, lane of gel Damion Dooley 2019-04-18T00:38:57Z PulseNet:PFGE-XbaI-file XbaI pattern assigned by CDC (format XXXXXX.####) Damion Dooley 2019-04-18T00:39:23Z PulseNet:PFGE-XbaI-pattern The date the XbaI gel is run Damion Dooley 2019-04-18T00:40:05Z PulseNet:PFGE-XbaI-rundate Once the XbaI pattern is named, the status is confirmed by CDC Damion Dooley 2019-04-18T00:41:39Z PulseNet:PFGE-XbaI-status BlnI gel where the isolate is located, lane of gel Damion Dooley 2019-04-18T00:42:11Z PulseNet:PFGE-BlnI-file BlnI pattern assigned by CDC (format XXXXXX.####). Damion Dooley 2019-04-18T00:42:42Z PulseNet:PFGE-BlnI-pattern The date the BlnI gel is run Damion Dooley 2019-04-18T00:43:50Z PulseNet:PFGE-BlnI-rundate Once the BlnI pattern is named, the status is confirmed by CDC Damion Dooley 2019-04-18T00:44:44Z PulseNet:PFGE-BlnI-status SpeI gel where the isolate is located, lane of gel. Damion Dooley 2019-04-18T00:45:15Z PulseNet:PFGE-SpeI-file SpeI pattern assigned by CDC (format XXXXXX.####). Damion Dooley 2019-04-18T00:45:41Z PulseNet:PFGE-SpeI-pattern The date the SpeI gel is run. Damion Dooley 2019-04-18T00:46:21Z PulseNet:PFGE-SpeI-rundate Once the SpeI pattern is named, the status is confirmed by CDC. Damion Dooley 2019-04-18T00:47:00Z PulseNet:PFGE-SpeI-status Date WHICH (PH?) lab received isolate. Damion Dooley 2019-04-18T00:57:28Z PulseNet:ReceivedDate 2019-11-17T00:54:44Z ISO_23418.organization_contact.service Date the isolate uploaded to the national database. Damion Dooley 2019-04-17T22:47:51Z PulseNet:UploadDate A Canadian public research university in the province of Manitoba. 2023-06-21T14:22:42Z University of Manitoba (UM) The Public Health Agency of Canada is an agency of the Government of Canada that is responsible for public health, emergency preparedness and response, and infectious and chronic disease control and prevention. https://en.wikipedia.org/wiki/Public_Health_Agency_of_Canada 2022-09-23T10:10:13Z PHAC Public Health Agency of Canada (PHAC) The Canadian Food Inspection Agency is a regulatory agency that is dedicated to the safeguarding of food, plants, and animals in Canada https://en.wikipedia.org/wiki/Canadian_Food_Inspection_Agency 2022-09-23T10:23:42Z CFIA Canadian Food Inspection Agency (CFIA) Agriculture and Agri-Food Canada is the department of the Government of Canada responsible for the federal regulation of agriculture, including policies governing the production, processing, and marketing of all farm, food, and agri-based products. https://en.wikipedia.org/wiki/Agriculture_and_Agri-Food_Canada 2022-09-23T10:29:32Z AAFC Agriculture and Agri-Food Canada (AAFC) Health Canada is the department of the Government of Canada responsible for national health policy. https://en.wikipedia.org/wiki/Health_Canada 2022-09-23T10:33:24Z HC Health Canada Environment and Climate Change Canada, is the department of the Government of Canada, that is responsible for coordinating environmental policies and programs, as well as preserving and enhancing the natural environment and renewable resources. It is also colloquially known by its former name, Environment Canada. https://en.wikipedia.org/wiki/Environment_and_Climate_Change_Canada 2022-09-23T10:38:21Z ECCC Environment Canada Environment and Climate Change Canada (ECCC) Fisheries and Oceans Canada, is a department of the Government of Canada that is responsible for developing and implementing policies and programs in support of Canada's economic, ecological and scientific interests in oceans and inland waters. https://en.wikipedia.org/wiki/Fisheries_and_Oceans_Canada 2022-09-23T10:42:12Z DFO Fisheries and Oceans Canada (DFO) G2R_G (TNFR) [GENEPIO:0100510] A data field which describes the name of the gene used in the diagnostic RT-PCR test. gene name 4 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z gene name 4 field gene name 4 slot gene name four Monkeypox Example Guidance: Select the name of the gene used for the diagnostic PCR from the standardized pick list. gene name 4 field 27 A data field which describes the Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. diagnostic pcr Ct value 4 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z Monkeypox Example Guidance: Provide the CT value of the sample from the second diagnostic RT-PCR test. diagnostic pcr Ct value 4 field RNAse P [GENEPIO:0100508] A data field which describes the name of the gene used in the diagnostic RT-PCR test. gene name 5 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z gene name 5 slot gene name five gene name5 field Monkeypox Example Guidance: Select the name of the gene used for the diagnostic PCR from the standardized pick list. gene name 5 field 30 A data field which describes the Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. diagnostic pcr Ct value 5 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z Monkeypox Example Guidance: Provide the CT value of the sample from the second diagnostic RT-PCR test. diagnostic pcr Ct value 5 field example to be eventually removed example to be eventually removed metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion Thermo Philippe Rocca-Serra Thermo Helicos Philippe Rocca-Serra Helicos Roche Philippe Rocca-Serra Roche Illumina Philippe Rocca-Serra Illumina Applied Biosystems Philippe Rocca-Serra Applied Biosystems Pacific Biosciences An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. Person: Jie Zheng Pacific Biosciences 2 2 Person:Alan Ruttenberg has part a core relation that holds between a whole and its part Damion comments: In GenEpiO, If an entity has more than one value specification (in a conjunction), then it means the entitiy is a complex entity that can have a value for each specification. Minimum data requirements can be spelled out using some, min 1, max 10 etc. restrictions. has part preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) NCBI SRA: ION_TORRENT asian tiger shrimp black tiger shrimp GAZ:00000013 continent GAZ:00000106 populated place, Haiti GAZ:00000448 geographic location GAZ:00000457 Africa GAZ:00000458 North America GAZ:00000459 South America GAZ:00000460 Eurasia GAZ:00000462 INSDC:country:antarctica Antarctica GAZ:00000468 Oceania GAZ:00000590 [Oceans and Seas] Oceans and Seas GAZ:00000591 INSDC:country:spain Kingdom of Spain GAZ:00000641 Province (Algeria) GAZ:00000847 Azores GAZ:00001016 Capital Territory (Nigeria) GAZ:00001018 State (Nigeria) GAZ:00001066 Province (Sierra Leone) GAZ:00001264 INSDC:country:bermuda Bermuda GAZ:00001412 INSDC:country:falkland islands (islas malvinas) Falkland Islands GAZ:00001508 Province (Greenland) GAZ:00001549 INSDC:country:netherlands Kingdom of the Netherlands INSDC:country:baltic sea GAZ:00002284 INSDC:country:north sea North Sea GAZ:00002285 Irish Sea GAZ:00002286 English Channel GAZ:00002287 INSDC:country:mediterranean sea Mediterranean Sea GAZ:00002459 INSDC:country:usa United States of America GAZ:00002547 Province (Argentina) GAZ:00002561 Province (Canada) GAZ:00002562 Province of British Columbia GAZ:00002563 Province of Ontario GAZ:00002564 Province of Saskatchewan GAZ:00002565 Province of Nova Scotia GAZ:00002566 Province of Alberta GAZ:00002567 Province of Newfoundland and Labrador GAZ:00002569 Province of Quebec GAZ:00002570 Province of New Brunswick GAZ:00002571 Province of Manitoba GAZ:00002572 Province of Prince Edward Island GAZ:00002573 Territory (Canada) GAZ:00002574 Nunavut GAZ:00002575 Northwest Territories GAZ:00002576 Yukon GAZ:00002616 populated place, Argentina GAZ:00002635 INSDC:country:denmark Kingdom of Denmark populated place, Scotland populated place, England GAZ:00002648 populated place, Metropolitan Spain GAZ:00002651 populated place, Italy populated place, Germany GAZ:00002699 Kingdom of Norway GAZ:00002705 populated place, Israel GAZ:00002718 populated place, Norway populated place, Russia GAZ:00002734 populated place, Bahamas GAZ:00002756 populated place, Japan GAZ:00002784 Territory (Australia) GAZ:00002785 State (Australia) GAZ:00002787 Northern Territory GAZ:00002788 Australian Capital Territory GAZ:00002794 Jervis Bay Territory GAZ:00002805 Province (Republic of Korea) GAZ:00002810 Province (Republic of South Africa) GAZ:00002820 Caribbean Sea INSDC:country:puerto rico GAZ:00002826 populated place, Chile GAZ:00002831 populated place, Brazil GAZ:00002840 State (India) GAZ:00002844 populated place, Canada GAZ:00002848 Autonomous Region (China) GAZ:00002855 populated place, Mexico GAZ:00002857 State (United States of Mexico) GAZ:00002896 populated place, Panama GAZ:00002918 INSDC:country:french polynesia French Polynesia GAZ:00002940 INSDC:country:france French Republic GAZ:00002944 INSDC:country:portugal Portuguese Republic GAZ:00003034 populated place, Republic of South Africa GAZ:00003092 Census Regions and Divisions are groupings of States that subdivide the United States. Damion Dooley United States Census Bureau Region (contiguous United States of America) http://www.census.gov/econ/census/help/geography/regions_and_divisions.html GAZ:00003093 A census region in the United States of America Damion Dooley Midwest Region GAZ:00003094 A census region in the United States of America Damion Dooley South Region GAZ:00003095 A census region in the United States of America Damion Dooley Northeast Region GAZ:00003096 A census region in the United States of America Damion Dooley West Region GAZ:00003108 populated place, Sweden GAZ:00003138 populated place, contiguous United States of America GAZ:00003176 populated place, Uruguay GAZ:00003192 populated place, Hawaii GAZ:00003194 populated place, Chad GAZ:00003198 Province (China) GAZ:00003199 Municipality (China) GAZ:00003201 Special Adminstrative Region (China) GAZ:00003202 INSDC:country:macau Macau GAZ:00003203 INSDC:country:hong kong Hong Kong GAZ:00003204 Province (Costa Rica) GAZ:00003209 Puntarenas Province GAZ:00003214 Province (Panama) populated place, Czech Republic GAZ:00003269 populated place, Slovakia GAZ:00003287 populated place, Denmark GAZ:00003382 populated place, Metropolitan France populated place, Austria populated place, Belgium GAZ:00003603 populated place, Hungary Province (Finland) populated place, Finland Province (Republic of Ireland) populated place, Republic of Ireland GAZ:00003626 Province (The Netherlands) GAZ:00003628 populated place, The Netherlands GAZ:00003651 populated place, Switzerland populated place, Wales GAZ:00003670 South West Region GAZ:00003671 Greater London Region GAZ:00003687 North West Region GAZ:00003688 Yorkshire and the Humber GAZ:00003689 North East Region GAZ:00003690 West Midlands Region GAZ:00003691 East Midlands Region GAZ:00003692 East Region GAZ:00003693 South East Region GAZ:00003706 lat_lon: 13deg27minN, 144deg47minE. Territory of Guam GAZ:00003708 populated place, Australia GAZ:00003717 Province (Rwanda) GAZ:00003724 populated place, Rwanda GAZ:00003728 populated place, Indonesia GAZ:00003730 Province (Indonesia) GAZ:00003731 Bali Province GAZ:00003740 populated place, Tanzania GAZ:00003742 populated place, Tunisia GAZ:00003746 populated place, Thailand GAZ:00003751 populated place, Bangladesh GAZ:00003757 populated place, Viet Nam GAZ:00003763 populated place, Cuba GAZ:00003765 Province (Cuba) GAZ:00003775 populated place, India GAZ:00003934 INSDC:country:egypt The 2nd level administrative regions of Egypt are very confusuing and different sources conflicting. Those in gaz.obo are from GeoHive (http://www.xist.org/default1.aspx) and are not fully in agreement with those from the WHO (the file EGY_SALB_table.xls downloaded from http://www.who.int/whosis/database/gis/salb/salb_coding.aspx#DATA). Egypt GAZ:00003941 Collectivite d'outre-mer GAZ:00003942 INSDC:country:saint pierre and miquelon Saint-Pierre and Miquelon GAZ:00003943 INSDC:country:mayotte Mayotte GAZ:00003944 Region d'outre-mer GAZ:00003955 INSDC:country:turks and caicos islands Turks and Caicos Islands GAZ:00003956 Unincorporated Territory (USA) GAZ:00003957 INSDC:country:american samoa American Samoa GAZ:00003959 United States Virgin Islands GAZ:00003961 INSDC:country:british virgin islands British Virgin Islands GAZ:00003981 British Overseas Territory GAZ:00003985 British Indian Ocean Territory GAZ:00003986 INSDC:country:cayman islands Cayman Islands GAZ:00003987 Gibraltar GAZ:00003988 Montserrat GAZ:00003990 INSDC:country:south georgia and the south sandwich islands South Georgia and South Sandwich Islands GAZ:00004026 Province (Burundi) GAZ:00004028 populated place, Burundi GAZ:00004031 populated place, Mauritania GAZ:00004040 populated place, Alaska GAZ:00004095 Villages and Cities from SALB; divided into communities from http://www.armstat.am/en/?nid=52. Province (Armenia) GAZ:00004098 populated place, Armenia GAZ:00004125 Autonomous Region (Portugal) GAZ:00004135 populated place, mainland Portugal GAZ:00004187 Union Territory (India) INSDC:country:fiji GAZ:00004373 populated place, Ghana GAZ:00004477 Province (Iran) GAZ:00004480 populated place, Iran GAZ:00004495 populated place, Iraq GAZ:00004517 populated place, Canary Islands GAZ:00004529 populated place, Philippines GAZ:00004665 Province (Sri Lanka) GAZ:00004676 populated place, Sri Lanka GAZ:00004682 populated place, Slovenia populated place, Republic of Korea GAZ:00004699 Metropolitan City (Republic of Korea) GAZ:00004704 populated place, Kenya GAZ:00004706 When an authorative list of Divisions of the new (2007) Districts is available this needs revision. Province (Kenya) GAZ:00004759 Region (New Zealand) GAZ:00004762 populated place, New Zealand populated place, Northern Ireland GAZ:00004944 Region (Azerbaijan) GAZ:00004980 Province (Uzbekistan) GAZ:00004983 populated place, Uzbekistan populated place, Estonia GAZ:00005000 Province (Kazakhstan) GAZ:00005004 populated place, Kazakhstan GAZ:00005015 populated place, Ukraine GAZ:00005033 populated place, Guadeloupe GAZ:00005040 Province (Poland) GAZ:00005042 populated place, Poland GAZ:00005074 The provinces are under reorganization, this list is part new part old. See: http://www.statoids.com/ucd.html Province (Democratic Republic of Congo) GAZ:00005075 populated place, Democratic Republic of Congo GAZ:00005100 populated place, Republic of Congo GAZ:00005109 Province (Zimbabwe) GAZ:00005121 populated place, Zimbabwe GAZ:00005137 populated place, Serbia GAZ:00005139 Autonomous Province (Serbia) populated place, Croatia GAZ:00005151 populated place, Greece GAZ:00005153 populated place, Guatemala GAZ:00005160 INSDC:country:french guiana populated place, French Guiana GAZ:00005165 populated place, Honduras Province (Papua New Guinea) GAZ:00005196 populated place, Papua New Guinea GAZ:00005206 INSDC:country:new caledonia New Caledonia GAZ:00005210 Province (New Caledonia) GAZ:00005221 populated place, Nicaragua GAZ:00005223 populated place, Nigeria GAZ:00005247 Province (Pakistan) GAZ:00005252 Territory (Pakistan) GAZ:00005258 populated place, Pakistan GAZ:00005277 populated place, Dominican Republic GAZ:00005299 populated place, Sierra Leone GAZ:00005322 populated place, Surinam GAZ:00005343 Province (Republic of China) populated place, Turkey GAZ:00005382 populated place, Uganda populated place, Svalbard populated place, Luxembourg GAZ:00005421 Province (Madagascar) GAZ:00005432 populated place, Madagascar GAZ:00005448 populated place, Malawi GAZ:00005453 populated place, Malaysia GAZ:00005458 populated place, Mali GAZ:00005464 populated place, Mauritius GAZ:00005469 populated place, Morocco GAZ:00005491 populated place, Nepal populated place, Aruba populated place, Bulgaria GAZ:00005621 populated place, Colombia GAZ:00005631 populated place, Central African Republic GAZ:00005643 Province (Ecuador) GAZ:00005649 populated place, Egypt GAZ:00005660 Province (Dominican Republic) GAZ:00005666 Province (Gabon) GAZ:00005669 populated place, Gabon GAZ:00005680 populated place, Cote d'Ivoire INSDC:country:seychelles GAZ:00005841 Saint Martin GAZ:00005867 Pitcairn, Henderson, Ducie and Oeno Islands GAZ:00005901 INSDC:country:ashmore and cartier islands Territory of Ashmore and Cartier Islands GAZ:00005908 Territory of Norfolk Island GAZ:00005909 Australian Antarctic Territory GAZ:00005910 Territory, Antarctica INSDC:country:norfolk island GAZ:00005914 Territory of Christmas Island GAZ:00005916 Territory of the Cocos (Keeling) Islands GAZ:00005917 INSDC:country:coral sea islands Coral Sea Islands Territory GAZ:00005918 Heard Island and McDonald Islands Territory INSDC:country:maldives INSDC:country:guam GAZ:00006935 Commonwealth of Puerto Rico GAZ:00007113 United States Minor Outlying Islands INSDC:country:palmyra atoll GAZ:00007191 INSDC:country:wallis and futuna Wallis and Futuna Islands GAZ:00007292 populated place, Bhutan Province (Bulgaria) GAZ:00007370 populated place, Costa Rica GAZ:00007508 populated place, Saudi Arabia GAZ:00007509 Province (Saudi Arabia) GAZ:00007610 populated place, Algeria GAZ:00007642 populated place, Romania GAZ:00007644 populated place, Trinidad and Tobago GAZ:00007698 populated place, Iceland GAZ:00007859 populated place, Sudan GAZ:00008372 Province (Tajikistan) GAZ:00008375 populated place, Tajikistan populated place, Turkmenistan GAZ:00008386 populated place, Georgia GAZ:00008577 populated place, Dijubti GAZ:00008583 populated place, Azores GAZ:00008595 populated place, Senegal GAZ:00008622 populated place, Jamaica GAZ:00008678 populated place, Lebanon GAZ:00008796 Province (Cambodia) GAZ:00008835 populated place, Netherlands Antiles INSDC:country:tasman sea GAZ:00009150 State (Venezuela) GAZ:00009152 populated place, Venezuala GAZ:00009159 INSDC:country:anguilla Anguilla GAZ:00009238 Province (North Korea) GAZ:00009419 Province (Zambia) GAZ:00009431 Province (Angola) GAZ:00009433 Province (Mozambique) GAZ:00009461 Province (Afghanistan) GAZ:00009465 Province (Mongolia) GAZ:00009509 Province (Laos) GAZ:00009554 Province (Solomon Islands) GAZ:00009571 INSDC:country:gaza strip Gaza Strip GAZ:00009572 INSDC:country:west bank West Bank GAZ:00009573 District (Palestinian Territories) Province (Belarus) GAZ:00009715 INSDC:country:tuvalu Tuvalu GAZ:00009905 populated place, Somalia GAZ:00009998 populated place, Angola GAZ:00010010 populated place, Zambia GAZ:00010069 populated place, Antigua and Barbuda populated place, Belarus GAZ:00010088 populated place, North Korea GAZ:00010090 directly governed city (North Korea) Directly Governed City GAZ:00010130 populated place, Cambodia GAZ:00010365 populated place, Yemen GAZ:00010408 populated place, Peru GAZ:00010410 populated place, Paraguay populated place, Lithuania populated place, Bosnia and Herzogovina GAZ:00011335 populated place, Montenegro GAZ:00012231 populated place, Bolivia populated place, Albania GAZ:00013569 populated place, American Samoa GAZ:00013579 populated place, Andorra INSDC:country:zaire populated place, Brunei Darussalam GAZ:00013726 populated place, Azerbaijan GAZ:00013817 populated place, Liechtenstein GAZ:00013864 populated place, Burkina Faso GAZ:00013888 populated place, Benin GAZ:00013955 populated place, Botswana GAZ:00014424 Nanumanga District GAZ:00014914 Province (Oman) GAZ:00016203 populated place, Palestinian Territories INSDC:country:korea INSDC:country:ussr INSDC:country:baker island INSDC:country:isle of man GAZ:00049570 Dependancy (Grenada) GAZ:00051031 Australasian Mediterranean Sea GAZ:00051067 Arctic Ocean region GAZ:00051071 Atlantic Ocean region GAZ:00051073 Pacific Ocean region GAZ:00051074 European Seas GAZ:00051084 Indian Ocean region GAZ:00051448 populated place, Cameroon INSDC:country:serbia and montenegro INSDC:country:the former yugoslav republic of macedonia GAZ:00067142 Guadeloupe Region GAZ:00067143 Martinique Region GAZ:00067144 French Guiana Region GAZ:00067145 Reunion Region INSDC:country:reunion INSDC:country:norway INSDC:country:howland island INSDC:country:christmas island INSDC:country:niue INSDC:country:tonga INSDC:country:curacao INSDC:country:gibraltar INSDC:country:moldova INSDC:country:cyprus INSDC:country:jordan GAZ:01000020 biogeographic location GAZ:01000021 floristic kingdom GAZ:01000022 Takhtajan's floristic provinces GAZ:01000047 Neotropical Kingdom GAZ:02000609 Special Territory (Indonesia) GAZ:02000610 Papua Province INSDC:country:martinique INSDC:country:montserrat GAZ:02000896 State (Myanmar) GAZ:03000061 populated place, Macedonia GAZ:04000000 Province (Vanuatu) GAZ:07000033 populated place, Moldova GAZ:07000054 populated place, Syria populated place, State of Alabama populated place, Rhode Island INSDC:country:state of palestine populated place, Utah populated place, Washington populated place, South Carolina Damion Dooley This is a catch-all category for Gazetteer items that have "located in" relations but not an imported GAZETTEER class parent in GenEpiO. Damion Dooley T1 after t2 iff:= t2 before_or_simulataneous_with t1 and not (t1 simultaeous_with t2) Damion Dooley Damion Dooley's note: Intention is to have it be the inverse of "before". This allows axioms like "B after A" to be placed in class B, rather than having to phrase them as "A before B" in class A. I believe time dependency relations (conditions) don't imply existence by themselves. If B after A, and B exists, this doesn't necessarily mean that A exists, only that if A does exist, it must be before B. To add that extra existence implication probably requires the "causally downstream of" and "immediately causally downstream of" RO relations, in a closed system where B cannot exist any other way. after GENEPIO:0001897 home phone type - home GSSO:000096 Having a gender (identity) which is different from the sex one was assigned at birth: being assigned male at birth but having a female gender or vice versa; or, pertaining to such people. Not identifying with culturally conventional gender roles and categories of male or female; having changed gender identity from male to female or female to male, or identifying with elements of both, or having some other gender identity; or, pertaining to such people. Transgender people have a gender identity or gender expression that differs from their assigned sex. In some select cases, transgender people are sometimes called transsexual if they desire medical assistance to transition from one sex to another. "Transgender" is also an umbrella term: in addition to including people whose gender identity is the opposite of their assigned sex (trans men and trans women), it may include people who are not exclusively masculine or feminine (people who are genderqueer or non-binary, including bigender, pangender, genderfluid, or agender). Other definitions of transgender also include people who belong to a third gender, or else conceptualize transgender people as a third gender. transgender and nonbinary https://data.nonbinary.wiki/wiki/Item:Q9 https://en.wikipedia.org/wiki/Category:Transgender https://en.wikipedia.org/wiki/Transgender https://lgbt-plus.fandom.com/wiki/Transgender https://lgbt.wikia.org/wiki/Transgender https://lgbta.fandom.com/wiki/Transgender https://lgbtq-wiki.fandom.com/wiki/Transgender https://lgbtqia.fandom.com/wiki/Transgender https://mogai-genders.fandom.com/wiki/Transgender "Transgender" and its derivatives ("transgender male", "transgender female", "transgender woman", "transgender man", etc.) are generally not considered genders and/or gender identities. Listing "male" separate from "transgender male" or listing "transgender" separate from "male"/"female" is transphobic in the sense that it denies a transgender person's gender, forcing them to choose in an unclear situation, and implies that they are somehow deviant from "normal" maleness/femaleness. A few transgender persons still utilize these terms in identifying, however, but an "other (please specify)" option is much more functional in this regard (as well as a "select all that apply" for gender/gender identity). "Transgender" is an adjective and should not be formed into a collective noun. This terminology is often used by anti-transgender activists aiming to dehumanize transgender people. The adjective "transgender" should never have an extraneous "-ed" attached to it. This is confusing and grammatically unnecessary. transcinsiyet transgender transgender transgenre transgjinor transgénero transgênero transkjønnet transkønnet տրանսգենդեր ट्रांसजेंडर ট্রান্সজেন্ডার GSSO:002294 Gender variance, or, sometimes, gender nonconformity, is behavior or gender expression exhibited by an individual that does not match cultural/social masculine and feminine gender norms and/or expectations. https://en.wikipedia.org/wiki/Gender_variance https://www.wikidata.org/wiki/Q4135211 gender variance among youth "Gender non-conforming" and "gender diverse" are often preferred to "gender variant" because "gender variant" (and, by extension, "gender variance") implies a standard normative for gender (i.e. a way gender is "supposed to be"). However, many resources emply the term as a helpful "catch-all" for various transgender and cultural gender roles and identities. gender variance kønsvarians GSSO:009468 The correspondence (or lack thereof) between one's assigned gender at birth and one's actual gender and/or gender presentation. The two primary, and most well known gender modalities are cisgender and transgender. However those are not the only possible relations for one to have. Gender modality is an open-ended category which welcomes the elaboration of further terms. https://mogai-genders.fandom.com/wiki/Gender_Modality https://nonbinary.wiki/wiki/Gender_modality https://www.wikidata.org/wiki/Q106647285 gender modality has unit has measurement unit label A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about An information artifact IA mentions an entity E exactly when it has a component/part that denotes E 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition PERSON: Jonathan Rees Person: Alan Ruttenberg mentions A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes NCBI SRA: HELICOS NCBI SRA: ABI_SOLID specifies specifies value of A relation between a value specification and an entity which the specification is about. specifies value of inheres in a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence inheres in this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in located in located_in located_in (type level) aligned with T1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) David Osumi-Sutherland t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) before David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. Chris Mungall produces has output has output An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of member of has member is a mereological relation between a collection and an item. SIO has member has member output of a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel produced by UO:0000008 m metre "A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second." [BIPM:BIPM, NIST:NIST] meter UO:0000010 s "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom." [BIPM:BIPM, NIST:NIST] second UO:0000012 K "A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water." [BIPM:BIPM, NIST:NIST] kelvin UO:0000015 centimetre cm "A length unit which is equal to one hundredth of a meter or 10^[-2] m." [NIST:NIST] centimeter UO:0000016 mm millimetre mm "A length unit which is equal to one thousandth of a meter or 10^[-3] m." [NIST:NIST] millimeter UO:0000017 micrometre micron um "A length unit which is equal to one millionth of a meter or 10^[-6] m." [NIST:NIST] micrometer UO:0000018 nanometre nm "A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m." [NIST:NIST] nanometer UO:0000019 Å "A length unit which is equal to 10 [-10] m." [NIST:NIST] angstrom UO:0000020 picometre pm "A length unit which is equal to 10^[-12] m." [NIST:NIST] picometer UO:0000027 C "A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K." [NIST:NIST] degree Celsius UO:0000028 ms "A time unit which is equal to one thousandth of a second or 10^[-3] s." [NIST:NIST] millisecond UO:0000029 us "A time unit which is equal to one millionth of a second or 10^[-6] s." [NIST:NIST] microsecond UO:0000030 ps "A time unit which is equal to 10^[-12] s." [NIST:NIST] picosecond UO:0000031 min "A time unit which is equal to 60 seconds." [Wikipedia:Wikipedia] minute UO:0000032 h "A time unit which is equal to 3600 seconds or 60 minutes." [Wikipedia:Wikipedia] hour UO:0000033 "A time unit which is equal to 24 hours." [Wikipedia:Wikipedia] day UO:0000034 "A time unit which is equal to 7 days." [Wikipedia:Wikipedia] week UO:0000035 "A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days." [Wikipedia:Wikipedia] month UO:0000036 "A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days." [Wikipedia:Wikipedia] year UO:0000039 umol "A substance unit equal to a millionth of a mol or 10^[-6] mol." [NIST:NIST] micromole UO:0000076 (x) chi "A concentration unit which denotes the number of moles of solute as a proportion of the total number of moles in a solution." [Wikipedia:Wikipedia] mole fraction UO:0000083 kg/m^[3] kilogram per cubic metre "A mass unit density which is equal to mass of an object in kilograms divided by the volume in cubic meters." [UOC:GVG] kilogram per cubic meter UO:0000084 g/cm^[3] gram per cubic centimetre "A mass unit density which is equal to mass of an object in grams divided by the volume in cubic centimeters." [UOC:GVG] gram per cubic centimeter UO:0000089 cubic metre per mole m^[3]/mol "A molar volume unit which is equal to 1 cubic meter occupied by one mole of a substance in the form of a solid, liquid, or gas." [NIST:NIST] cubic meter per mole UO:0000090 cm^[3]/mol cubic centimetre per mole "A molar volume unit which is equal to 1 cubic centimeter occupied by one mole of a substance in the form of a solid, liquid, or gas." [NIST:NIST] cubic centimeter per mole UO:0000093 cubic metre per kilogram m^[3]/kg "A specific volume unit which is equal to one cubic meter volume occupied by one kilogram of a particular substance." [NIST:NIST] cubic meter per kilogram UO:0000094 m/s metre per second "A speed/velocity unit which is equal to the speed of an object traveling 1 meter distance in one second." [NIST:NIST] meter per second UO:0000096 cubic metre m^[3] "A volume unit which is equal to the volume of a cube with edges one meter in length. One cubic meter equals to 1000 liters." [NIST:NIST] cubic meter UO:0000097 cc cm^3 cubic centimetre "A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml." [NIST:NIST] cubic centimeter UO:0000098 millilitre ml "A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter." [NIST:NIST] milliliter UO:0000099 L l litre "A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter." [NIST:NIST] liter UO:0000100 cubic decimetre dm^[3] "A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L." [NIST:NIST] cubic decimeter UO:0000101 microlitre ul "A volume unit which is equal to one millionth of a liter or 10^[-6] L." [NIST:NIST] microliter UO:0000102 nanolitre nl "A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L." [NIST:NIST] nanoliter UO:0000103 picolitre pl "A volume unit which is equal to 10^[-12] L." [NIST:NIST] picoliter UO:0000104 femtolitre fl "A volume unit which is equal to 10^[-15] L." [NIST:NIST] femtoliter UO:0000123 rad "A plane angle unit which is equal to the angle subtended at the center of a circle by an arc equal in length to the radius of the circle, approximately 57 degrees 17 minutes and 44.6 seconds." [NIST:NIST] radian UO:0000150 ns "A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s." [NIST:NIST] nanosecond UO:0000151 "A time unit which is equal to 100 years." [Wikipedia:Wikipedia] century UO:0000152 "A time unit which represents the period over which the activity or concentration of a specified chemical or element falls to half its original activity or concentration." [MGED:MGED] half life UO:0000163 w/w weight-weight percentage "A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture." [Wikipedia:Wikipedia] mass percentage UO:0000164 (w/v) weight-volume percentage "A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture." [UOC:GVG] mass volume percentage UO:0000165 % (v/v) "A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution." [UOC:GVG] volume percentage UO:0000173 g/ml gram per millilitre "A mass unit density which is equal to mass of an object in grams divided by the volume in milliliter." [UOC:GVG] gram per milliliter UO:0000174 kg/L kilogram per litre "A mass unit density which is equal to mass of an object in kilograms divided by the volume in liters." [UOC:GVG] kilogram per liter UO:0000175 g/L gram per litre "A mass unit density which is equal to mass of an object in grams divided by the volume in liters." [UOC:GVG] gram per liter UO:0000176 mg/ml milligram per millilitre "A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters." [UOC:GVG] milligram per milliliter UO:0000185 "A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad." [Wikipedia:Wikipedia] degree UO:0000193 "A dimensionless percent unit which denotes the homogeneity of a biomaterial." [MGED:MGED] purity percentage UO:0000194 "A dimensionless percent unit which denotes the density of an attached or monolayer culture (e.g., cell culture)." [MGED:MGED] confluence percentage UO:0000195 F "A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius." [Wikipedia:Wikipedia] degree Fahrenheit UO:0000196 "A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+)." [Wikipedia:Wikipedia] pH UO:0000197 l/kg litre per kilogram "A specific volume unit which is equal to one liter volume occupied by one kilogram of a particular substance." [NIST:NIST] liter per kilogram UO:0000198 millilitre per kilogram ml/kg "A specific volume unit which is equal to a thousandth of a liter per kilogram or 10^[-3] l/kg." [NIST:NIST] milliliter per kilogram UO:0000199 microlitre per kilogram ul/kg "A specific volume unit which is equal to one millionth of a liter per kilogram or 10^[-6] l/kg." [NIST:NIST] microliter per kilogram UO:0000208 g/dl gram per decilitre "A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters." [UOC:GVG] gram per deciliter UO:0000209 decilitre dl "A volume unit which is equal to one tenth of a liter or 10^[-1] L." [NIST:NIST] deciliter UO:0000210 cfu "A dimensionless count unit which a measure of viable bacterial numbers." [Wikipedia:Wikipedia] colony forming unit UO:0000213 cfu/mL Damion Dooley cfu/ml colony forming unit per millilitre "A colony forming unit which a measure of viable bacterial numbers in one milliliter." [Wikipedia:Wikipedia] colony forming unit per milliliter UO:0000244 A count unit which contains one nucleotide. basepair bp "A count unit which contains one nucleotide." [UO:GVG] base pair UO:0000247 mV "An electric potential difference unit which is equal to one thousandth of a volt or 10^[-3] V." [UOC:GVG] millivolt UO:0000264 A V^-1 mho "An electrical conduction unit which is equal to A/V." [NIST:NIST] siemens UO:0000273 mg/L milligram per litre "A mass unit density which is equal to mass of an object in milligrams divided by the volume in liters." [UOC:GVG] milligram per liter UO:0000274 µg/ml mcg/mL microgram per millilitre ug/ml µg/mL "A mass unit density which is equal to mass of an object in micrograms divided by the volume in millliters." [UOC:GVG] microgram per milliliter UO:0000275 nanogram per millilitre ng/ml "A mass unit density which is equal to mass of an object in nanograms divided by the volume in milliliters." [UOC:GVG] nanogram per milliliter UO:0000301 microgram per litre ug/L "A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters." [UOC:GVG] microgram per liter UO:0000326 cM "A unit used to express distances on a genetic map. In genetic mapping, distances between markers are determined by measuring the rate of meoitic recombination between them, which increases proportionately with the distance separating them. A cM is defined as the length of an interval in which there is a 1% probability of recombination. On the average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA, although this can vary widely due to hot and cold spots of recombination." [NCBI:http\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html] centiMorgan UO:0000327 cR "A unit of genetic map distance defined corresponding to an interval in which there is a 1% probability of X-irradiation induced breakage. To be completely specified, the unit must be qualified by the radiation in dosage in rads (e.g. cR8000), because this determines the actual breakage probability." [NCBI:http\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html] centiRay UO:0000329 Mb megabasepair "A unit equal to one million base pairs" [UOC:GVG] mega base pair UO:0000330 Gb gigabasepair "A unit equal to one billion base pairs." [UOC:GVG] giga base pair UO:0010002 "An electrical conduction unit which is equal to one thousandth of a siemen or 10^[-3] siemens." [NIST:NIST] millisiemens UO:0010003 "A specific concentration unit which is equal to 1 micromole in a given volume of one thousandth of a cubic meter." [NIST:NIST] micromole per litre UO:0010004 "A specific concentration unit which is equal to 1 micromole of a given substance per kilogram of solvent." [UOB:LKSR] micromole per kilogram UO:0010011 in "A length unit which is equal to 0.0254 metres." [Wikipedia:Wikpiedia] inch UO:0010012 mil th "A length unit which is equal to 0.0254 millimetres." [Wikipedia:Wikpiedia] thou UO:0010013 ft "A length unit which is equal to 0.3048 metres, or 12 inches." [Wikipedia:Wikpiedia] foot UO:0010014 yd "A length unit which is equal to 0.9144 metres, or 3 feet." [Wikipedia:Wikpiedia] yard UO:0010015 ch "A length unit which is equal to 20.1168 metres, 66 feet, or 22 yards." [Wikipedia:Wikpiedia] chain UO:0010016 fur "A length unit which is equal to 20,116.8 metres, 660 feet, or 10 chains." [Wikipedia:Wikpiedia] furlong UO:0010017 mi "A length unit which is equal to 1,609.344 metres, or 8 furlongs." [Wikipedia:Wikpiedia] mile UO:0010018 lea "A length unit which is equal to 3 miles, or 4,828.032 metres" [Wikipedia:Wikpiedia] league UO:0010019 "A maritime length unit is one used primarily at sea." [Wikipedia:Wikpiedia] maritime length unit UO:0010020 ftm "A maritime length unit which is equal to 6.08 feet, or 1.853184 metres" [Wikipedia:Wikpiedia] fathom UO:0010021 "A maritime length unit which is equal to 608 feet, 100 fathoms, or 185.3184 metres" [Wikipedia:Wikpiedia] cable UO:0010022 "A maritime length unit which is equal to 6,080 feet, 10 cables, or 1,853.184 metres" [Wikipedia:Wikpiedia] nautical mile UO:0010026 fl oz "An imperial volume unit which is equivalent to 28.413,0625 millilitres." [Wikipedia:Wikipedia] fluid ounce UO:0010027 gi "An imperial volume unit which is equivalent to 142.065,3125 millilitres." [Wikipedia:Wikipedia] gill UO:0010028 pt "An imperial volume unit which is equivalent to 568.261,25 millilitres." [Wikipedia:Wikipedia] pint UO:0010029 qt "An imperial volume unit which is equivalent to 1,136.5225 millilitres, or two pints." [Wikipedia:Wikipedia] quart UO:0010030 gal "An imperial volume unit which is equivalent to 4,546.09 millilitres, or 8 pints." [Wikipedia:Wikipedia] gallon UO:0010040 metric teaspoon tsp "A metric teaspoon is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions. It equals a 5mL volume." [Wikipedia:https://en.wikipedia.org/wiki/Teaspoon] teaspoon UO:0010050 nanogram per microlitre ng/ul "A mass unit density which is equal to mass of an object in nanograms divided by the volume in microliters." [UOB:LTS] nanogram per microliter UO:0010053 micrograms per bottle "A unit of mass concentration defined as the number of micrograms of a substance per 250 ml Wheaton bottle." [UOB:LTS] micrograms per wheaton bottle UO:0010066 kilometre km "A length unit which is equal to one thousand meters." [UOB:LKSR] kilometer UO:0010067 mg/dl milligram per decilitre "A mass unit density which is equal to mass of an object in milligrams divided by the volume in deciliters." [UOB:LKSR] milligram per deciliter UO:0010068 microgram per decilitre ug/dl "A mass unit density which is equal to mass of an object in micrograms divided by the volume in deciliters." [UOB:LKSR] microgram per deciliter BFO 2 Reference: BFO does not claim to be a complete coverage of all entities. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning – coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation [17 BFO 2 Reference: BFO’s treatment of continuants and occurrents – as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality – earlier called the ‘SNAP’ and ‘SPAN’ perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science [30 BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. ‘Entity’ is an example of one such primitive term. Primitive terms in a highest-level ontology such as BFO are terms that are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms. Alan Ruttenberg Albert Goldfain Barry Smith Bill Duncan Bjoern Peters Chris Mungall David Osumi-Sutherland Fabian Neuhaus James A. Overton Janna Hastings Jie Zheng Jonathan Bona Larry Hunter Leonard Jacuzzo Ludger Jansen Mark Ressler Mathias Brochhausen Mauricio Almeida Melanie Courtot Pierre Grenon Randall Dipert Robert Rovetto Ron Rudnicki Stefan Schulz Thomas Bittner Werner Ceusters Yongqun "Oliver" He The http://purl.obolibary.org/obo/bfo/classes-only.owl variant of BFO ("bfo_classes_only.owl") includes only the class hierarchy and annotations from the full OWL version of BFO 2: http://purl.obolibary.org/obo/bfo.owl ("bfo.owl"). There are no object properties or logical axioms that use the object properties in bfo_classes_only.owl. As the logical axioms in the bfo_classes_only.owl variant are limited to subclass and disjoint assertions they are much weaker than the logical axioms in bfo.owl. If you plan to use the relations that define BFO 2, you should import bfo.owl instead of bfo_classes_only.owl. To the extent that the relations are used without importing bfo.owl, be mindful that they should be used in a manner consistent with their use in bfo.owl. Otherwise if your ontology is imported by a another ontology that imports bfo.owl there may be inconsistencies. See the BFO 2 release notes for further information about BFO 2. Please note that the current release of bfo.owl uses temporal relations when the subject or object is a continuant, a major change from BFO 1. This is an early version of BFO version 2 and has not yet been extensively reviewed by the project team members. Please see the project site http://code.google.com/p/bfo/ , the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel , the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx . This ontology is generated from a specification at http://bfo.googlecode.com/svn/trunk/src/ontology/owl-group/specification/ and with the code that generates the OWL version in http://bfo.googlecode.com/svn/trunk/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif 2023-08-19 The Genomic Epidemiology Ontology aims to provide a comprehensive controlled vocabulary for infectious disease surveillance and outbreak investigations. It is an application ontology that draws on many other ontologies including anatomy, taxonomy, disease, symptoms, environment and food types for foodborn pathogen metadata. Genomic Epidemiology Ontology GENEPIO