Amanda Hicks Chris Stoeckert Danielle Mowery Mark A. Miller Hypertension Ontology For Clinical Data 2019-05-20 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 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 example of usage A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not 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> example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch 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. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. 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.obfoundry.org/obo/obi> editor note 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 http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor definition editor term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source 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 curator note term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ 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 The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester is denotator type relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg is denotator type imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand expression to expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to first order logic expression An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. PERSON:Alan Ruttenberg first order logic expression antisymmetric property part_of antisymmetric property xsd:true use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label obo foundry unique label Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" 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 Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] 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 to Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. Person:Alan Ruttenberg has ID prefix elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which 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 elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) is allocated id range Add as annotation triples in the granting ontology Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg is allocated id range retired from use as of relates a class of CRID to the date after which further instances should not be made, according to the central authority In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp Alan Ruttenberg retired from use as of has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI 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 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 https://github.com/oborel/obo-relations/wiki/ROAndTime tooth SubClassOf 'never in taxon' value 'Aves' x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. Chris Mungall ?X DisjointWith RO_0002162 some ?Y never in taxon A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. non-overlapping with shares no parts with Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) mutually spatially disjoint with https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. taxonomic class assertion S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] ambiguous for taxon S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. https://orcid.org/0000-0002-6601-2165 This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost dubious for taxon S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S https://orcid.org/0000-0002-6601-2165 present in taxon defined by inverse An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion https://github.com/oborel/obo-relations/wiki/ShortcutRelations An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. annotation property cardinality A logical macro assertion whose domain is an IRI for a class The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL logical macro assertion on a class A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property logical macro assertion on an object property logical macro assertion on an annotation property An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. dispositional interpretation 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. shares no connection with Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) has no connections with inherited annotation property Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) curator guidance link brain always_present_in_taxon 'Vertebrata' forelimb always_present_in_taxon Euarchontoglires S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. never lost in always present in taxon This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. temporal logical macro assertion on a class measurement property has unit has start time value has end time value Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. start, days post fertilization Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. end, days post fertilization Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. start, years post birth Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 end, years post birth Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. start, months post birth Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 end, months post birth Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. month of gestation A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process has developmental stage marker Count of number of days intervening between the start of the stage and the time of coitum. For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) start, days post coitum Count of number of days intervening between the end of the stage and the time of coitum. end, days post coitum start, weeks post birth end, weeks post birth If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p is asymmetric relational form of process class https://github.com/oborel/obo-relations/wiki/InteractionRelations If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p is symmetric relational form of process class https://github.com/oborel/obo-relations/wiki/InteractionRelations R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process is relational form of process class https://github.com/oborel/obo-relations/wiki/InteractionRelations 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 The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' Chris Mungall is direct form of relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y Chris Mungall is indirect form of logical macro assertion on an axiom If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. is relational form of a class A shortcut relationship that holds between two entities based on their identity criteria logical macro assertion involving identity A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. in approximate one to one relationship with x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" is approximately equivalent to 'anterior end of organism' is-opposite-of 'posterior end of organism' 'increase in temperature' is-opposite-of 'decrease in temperature' x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). is opposite of x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). is indistinguishable from evidential logical macro assertion on an axiom A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. axiom has evidence A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. axiom contradicted by evidence In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context. this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent. If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion is representative IRI for equivalence set OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member A metadata relation between a class and its taxonomic rank (eg species, family) A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored has_rank eco subset Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. An entity responsible for making contributions to the content of the resource. Contributor Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges. The extent or scope of the content of the resource. Coverage Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. An entity primarily responsible for making the content of the resource. Creator Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). The physical or digital manifestation of the resource. Format Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN). An unambiguous reference to the resource within a given context. Resource Identifier Recommended best practice is to use RFC 3066 [RFC3066], which, in conjunction with ISO 639 [ISO639], defines two- and three-letter primary language tags with optional subtags. Examples include "en" or "eng" for English, "akk" for Akkadian, and "en-GB" for English used in the United Kingdom. A language of the intellectual content of the resource. Language Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity. An entity responsible for making the resource available Publisher Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a related resource. Relation Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource. Information about rights held in and over the resource. Rights Management The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. The topic of the content of the resource. Subject and Keywords Typically, a Title will be a name by which the resource is formally known. A name given to the resource. Title Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element. The nature or genre of the content of the resource. Resource Type subset_property has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym in_subset shorthand is defined by is defined by This is an experimental annotation label label is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 human_stages_ontology part_of part_of part of part of http://www.obofoundry.org/ro/#OBO_REL:part_of inheres in at all times realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes 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 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 occurs_in unfolds in unfolds_in BFO:0000066 occurs_in occurs_in 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 occurs in 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 feature gives rise to disease relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point has coordinate unit label relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of inverse of the relation of is quality measurement of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg is quality measured as a relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. Person:Alan Ruttenberg Person:Bjoern Peters is quality specification of inverse of the relation of is quality specification of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg Person:Bjoern Peters quality is specified as relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken Alan Ruttenberg has time stamp relates a time stamped measurement datum to the measurement datum that was measured Alan Ruttenberg has measurement datum participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function 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 a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition 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 contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained_in contained in contains contains penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. is allergic trigger for A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. is autoimmune trigger for penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. has allergic trigger A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. has autoimmune trigger 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 the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of 2D boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. David Osumi-Sutherland has boundary has_2D_boundary has 2D boundary The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). David Osumi-Sutherland tracheates David Osumi-Sutherland has synaptic terminal of X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 David Osumi-Sutherland A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label David Osumi-Sutherland Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. coincident with x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). David Osumi-Sutherland regulates in other organism A part of relation that applies only between occurents. occurent part 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 t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) before David Osumi-Sutherland Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which ends David Osumi-Sutherland di Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. encompasses David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which starts David Osumi-Sutherland starts before David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes David Osumi-Sutherland io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during David Osumi-Sutherland d during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during David Osumi-Sutherland o overlaps X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) has soma location relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. David Osumi-Sutherland fasciculates with (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) (and ("neuron ; CL_0000540" ?x) ("neuron projection bundle ; CARO_0001001" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500' " ?npbs) (part_of ?npbs ?y) (part_of ?nps ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) )))))) fasciculates with Relation between a neuron and some structure its axon forms (chemical) synapses in. Chris Mungall David Osumi-Sutherland David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) axon synapses in Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. Alexander Diehl Chris Mungall Lindsay Cowell <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) has plasma membrane part Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. Chris Mungall David Osumi-Sutherland synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) has postsynaptic terminal in Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. synapses in <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) has presynaptic terminal in Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. Chris Mungall David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) dendrite synapsed in A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. David Osumi-Sutherland has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) has synaptic terminal in x overlaps y if and only if there exists some z such that x has part z and z part of y x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps true The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. David Osumi-Sutherland has fasciculating component (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and ("neuron projection bundle ; CARO_0001001" ?x) ("neuron projection ; GO0043005" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) )))))) has fasciculating neuron projection X continuous_with Y if and only if X and Y share a fiat boundary. David Osumi-Sutherland connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) continuous with FMA:85972 x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom proper overlaps (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x))))) partially overlaps A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern The M8 connects Glasgow and Edinburgh a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure supplies Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure drains 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 inverse of has phenotype Chris Mungall phenotype of x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y Chris Mungall negatively regulates (process to process) negatively regulates x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y Chris Mungall positively regulates (process to process) positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO_0000053 some (RO_0000054 only ?Y) capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of true x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in actively participates in 'heart development' has active participant some Shh protein x has participant y if and only if x realizes some active role that inheres in y This may be obsoleted and replaced by the original 'has agent' relation Chris Mungall has agent has active participant x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x Chris Mungall surrounded by 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 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. inverse of surrounded by Chris Mungall surrounds Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to inverse of starts with Chris Mungall Allen starts Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(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. Chris Mungall started by starts with inverse of ends with Chris Mungall ends x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(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. Chris Mungall finished by ends with x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y Chris Mungall starts with process that occurs in has start location x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y Chris Mungall ends with process that occurs in has end location p has direct input c iff 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 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 A broad relationship between an exposure event or process and any entity (e.g., a human, human population, or a human organ) that interacts with an exposure stressor during the exposure event ExO:0000001 has exposure receptor A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. ExO:0000000 has exposure stressor A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor ExO:0000055 has exposure route A broad relationship between an exposure event or process and a the material an agent takes from the source to the target. has exposure transport path related via exposure to Any portion of roundup 'has active ingredient' some glyphosate A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. has active substance has active pharmaceutical ingredient has active ingredient inverse of has active ingredient active ingredient in' b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. connecting branch of inverse of connecting branch of has connecting branch c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) has biological role c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) has application role c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) has chemical role c involved in regulation of p if c enables 'p' and p' causally upstream of p acts upstream of c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p affects acts upstream of or within Inverse of 'is substance that treats' cjm is treated by substance cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of inheres in part of Chris Mungall RO:0002314 inheres_in_part_of inheres_in_part_of inheres in part of inheres in part of true A mereological relationship or a topological relationship A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. Chris Mungall http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium colocalizes with ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. Chris Mungall http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. contributes to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of involved in every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c Chris Mungall regulates levels of (process to entity) regulates levels of inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by 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 has member is a mereological relation between a collection and an item. SIO has member inverse of has input Chris Mungall input of inverse of has output Chris Mungall output of Chris Mungall formed as result of Chris Mungall http://neurolex.org/wiki/Property:DendriteLocation has dendrite location A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) in branching relationship with https://github.com/obophenotype/uberon/issues/170 Deschutes River tributary_of Columbia River inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. Chris Mungall drains into drains to tributary channel of http://en.wikipedia.org/wiki/Tributary http://www.medindia.net/glossary/venous_tributary.htm This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) tributary of http://en.wikipedia.org/wiki/Tributary Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x Chris Mungall branch of distributary channel of http://en.wikipedia.org/wiki/Distributary This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes distributary of x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. Chris Mungall anastomoses with anabranch of A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location Chris Mungall This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y Chris Mungall branching part of FMA:85994 x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. Chris Mungall main stem of x proper_distributary_of y iff x distributary_of y and x does not flow back into y Chris Mungall proper distributary of x proper_tributary_of y iff x tributary_of y and x does not originate from y Chris Mungall proper tributary of 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff 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 directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' has direct input Chris Mungall Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit obsolete has indirect output true inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q Chris Mungall directly positively regulates directly activates (process to process) directly activates p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q Chris Mungall indirectly positively regulates indirectly activates Chris Mungall directly negatively regulates directly inhibits (process to process) directly inhibits Chris Mungall indirectly negatively regulates indirectly inhibits This relation groups causal relations between material entities and causal relations between processes This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to 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 p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall directly provides input for (process to process) directly provides input for transitive form of directly_provides_input_for Chris Mungall This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for') transitively provides input for (process to process) transitively provides input for p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some 'p' and p' regulates some p Chris Mungall involved in regulation of Chris Mungall involved in positive regulation of Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d Chris Mungall executes activity in enables activity in true p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. Chris Mungall contributes to morphology of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b Chris Mungall molecularly controls Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b. Chris Mungall inhibits molecularly decreases activity of Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b. Chris Mungall activates molecularly increases activity of A relation that holds between a disease or an organism and a phenotype Chris Mungall has symptom Chris Mungall Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target partner in Chris Mungall Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. subject participant in Chris Mungall Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. target participant in A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b. Chris Mungall is evidence for 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. Chris Mungall composed primarily of p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true See notes for inverse relation Chris Mungall receives input from This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. Chris Mungall sends output to A relationship between a material entity and a process where the material entity has some causal role that influences the process A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall depends on depends_on q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. Chris Mungall towards 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c Chris Mungall has intermediate product has intermediate The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entities A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future Chris Mungall determined by (system to material entity) Chris Mungall Pier Buttigieg determined by inverse of determined by Chris Mungall determines (material entity to system) determines s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. Chris Mungall determined by part of true A relation that holds between two entities that have the property of being sequences or having sequences. Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. sequentially related to Every UTR is adjacent to a CDS of the same transcript Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 sequentially adjacent to Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence Chris Mungall started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 has start sequence inverse of has start sequence Chris Mungall starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 is start sequence of Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence Chris Mungall ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 has end sequence inverse of has end sequence Chris Mungall ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 is end sequence of x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 is consecutive sequence of Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering Chris Mungall is sequentially aligned with The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y Chris Mungall bounds sequence of inverse of bounds sequence of Chris Mungall is bound by sequence of x has subsequence y iff all of the sequence parts of x are sequence parts of y Chris Mungall contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 has subsequence inverse of has subsequence Chris Mungall contained by is subsequence of x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. Chris Mungall overlaps sequence of x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. Chris Mungall disconnected from does not overlap sequence of inverse of downstream of sequence of Chris Mungall is upstream of sequence of x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. Chris Mungall is downstream of sequence of A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y Chris Mungall is immediately downstream of sequence of A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of Chris Mungall is immediately upstream of sequence of Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. Chris Mungall has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). has skeleton inverse of is evidence for Chris Mungall x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. has evidence Chris Mungall causally influenced by (material entity to material entity) causally influenced by Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall results in movement of Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b Chris Mungall causally influences (material entity to material entity) causally influences inverse of branching part of Chris Mungall has branching part x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. Chris Mungall UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. conduit for x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. Chris Mungall GOC:cjm lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity Chris Mungall luminal space of A relation that holds between an attribute or a qualifier and another attribute. Chris Mungall This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. RO:0002180 qualifier qualifier placeholder relation to indicate normality/abnormality. has modifier inverse of has skeleton Chris Mungall skeleton of p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p Chris Mungall directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall has part structure that is capable of p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p results in breakdown of p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. results in catabolism of results in disassembly of results in remodeling of p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c results in organization of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating pazopanib -> pathological angiogenesis Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. treats The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. capable of inhibiting or preventing pathological process treats Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship benzene -> cancer [CHEBI] Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. causes disease capable of upregulating or causing pathological process c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. treats is substance that treats c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. May be ceded to OBI is marker for Inverse of 'causal agent in' has causal agent A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. related via dependence to An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. A relationship between a piece of evidence and an entity that plays a role in supporting that evidence. In the Gene Ontology association model, this corresponds to the With/From field is evidence with support from related via evidence or inference to p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p directly positively regulates (process to process) directly positively regulates p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p directly negatively regulates (process to process) directly negatively regulates Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b. Logical axioms to be added after the relevant branch of GO is MIREOTed in represses expression of Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b. Logical axioms to be added after the relevant branch of GO is MIREOTed in increases expression of The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition. Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions. causes or contributes to condition A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition. causes condition A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition. contributes to condition A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual. contributes to expressivity of condition contributes to severity of condition A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population. contributes to penetrance of condition contributes to frequency of condition A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition. Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions. is preventative for condition A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. correlated with condition has phenotype affecting AG: Currently the only way to handle relational quality? relation binding a relational quality or disposition to the relevant type of entity towards has measurement value has x coordinate value has z coordinate value has y coordinate value BFO:0000001 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 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 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 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 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 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 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. 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]) 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 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] 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 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. 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]) 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) (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] 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 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. 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] 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] 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 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] bfo BFO:0000019 quality quality BFO:0000019 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] BFO:0000020 sdc SpecificallyDependentContinuant 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. 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. (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (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] 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. 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. 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] 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] 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] bfo BFO:0000024 fiat object part fiat object part BFO:0000024 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) 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] 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] 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]) bfo BFO:0000030 object object BFO:0000030 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] material MaterialEntity 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 An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. 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. 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 BFO:0000040 material entity material entity BFO:0000040 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]) CARO:0000007 immaterial anatomical entity CARO:0030000 biological entity A disease that involving errors in metabolic processes of building or degradation of molecules. ICD10CM:E88.9 ICD9CM:277.9 MESH:D008659 NCI:C3235 SNOMEDCT_US_2016_03_01:154733004 SNOMEDCT_US_2016_03_01:190961002 SNOMEDCT_US_2016_03_01:267456000 SNOMEDCT_US_2016_03_01:30390004 SNOMEDCT_US_2016_03_01:75934005 UMLS_CUI:C0025517 metabolic disease disease_ontology DOID:0014667 disease of metabolism DOID:0014667 An acquired metabolic disease that is characterized by abnormal carbohydrate metabolism. disease_ontology DOID:0050013 carbohydrate metabolism disease DOID:0050013 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. DOID:10115 DOID:11078 DOID:1304 DOID:1321 DOID:2040 DOID:2288 DOID:3099 DOID:4120 DOID:4620 DOID:5256 DOID:945 DOID:95 DOID:9532 DOID:9696 ICD9CM:079.0 UMLS_CUI:C0001485 infectious disease disease_ontology DOID:0050117 disease by infectious agent DOID:0050117 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. ICD10CM:J69.0 MESH:D011015 SNOMEDCT_US_2016_03_01:422588002 SNOMEDCT_US_2016_03_01:47839005 UMLS_CUI:C0032290 disease_ontology DOID:0050152 aspiration pneumonia DOID:0050152 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). disease_ontology DOID:0050155 sensory system disease DOID:0050155 A respiratory system disease which involves the lower respiratory tract. ICD9CM:478.1 ICD9CM:478.19 SNOMEDCT_US_2016_03_01:195823002 SNOMEDCT_US_2016_03_01:266346007 UMLS_CUI:C0029581 disease_ontology DOID:0050161 lower respiratory tract disease DOID:0050161 A genetic disease that is the result of one or more abnormal alleles and may be dominant (a single copy of the abnormal allele is sufficient to give rise to the disease), semi-dominant, or recessive (requiring both copies of the gene to have an abnormal allele). disease_ontology DOID:0050177 monogenic disease DOID:0050177 An organ system cancer located_in the respiratory system that is characterized by uncontrolled cellular proliferation in the respiratory tract. disease_ontology DOID:0050615 respiratory system cancer DOID:0050615 An organ system benign neoplasm that is located_in reproductive system organs. disease_ontology DOID:0050622 reproductive organ benign neoplasm DOID:0050622 A cancer that is classified based on the organ it starts in. snadendla 2011-06-13T03:28:33Z MESH:D009371 disease_ontology DOID:0050686 organ system cancer DOID:0050686 A cancer that is classified by the type of cell from which it is derived. snadendla 2011-06-13T03:28:50Z disease_ontology DOID:0050687 cell type cancer DOID:0050687 A heart disease and a myopathy that is characterized by deterioration of the function of the heart muscle. lschriml 2012-01-03T02:54:11Z ICD10CM:I42 ICD10CM:I42.9 ICD10CM:I51.5 ICD9CM:425 ICD9CM:425.9 MESH:D009202 NCI:C34830 NCI:C53654 SNOMEDCT_US_2016_03_01:155351008 SNOMEDCT_US_2016_03_01:155353006 SNOMEDCT_US_2016_03_01:195035002 SNOMEDCT_US_2016_03_01:195037005 SNOMEDCT_US_2016_03_01:20072003 SNOMEDCT_US_2016_03_01:266244008 SNOMEDCT_US_2016_03_01:266301006 SNOMEDCT_US_2016_03_01:57809008 SNOMEDCT_US_2016_03_01:85898001 SNOMEDCT_US_2016_03_01:89461002 SNOMEDCT_US_2016_03_01:89600009 UMLS_CUI:C0033141 UMLS_CUI:C0036529 UMLS_CUI:C0878544 Cardiomyopathies disease_ontology DOID:0050700 MESH:D009202 added from NeuroDevNet [WAK]. cardiomyopathy DOID:0050700 An autosomal genetic disease that is characterized by the presence of one disease-associated mutation of a gene which is sufficient to cause the disease. lschriml 2012-07-24T12:51:47Z disease_ontology DOID:0050736 autosomal dominant disease DOID:0050736 A monogenic disease that is has material basis in a mutation in a single gene on one of the non-sex chromosomes. lschriml 2012-07-24T04:45:53Z disease_ontology DOID:0050739 autosomal genetic disease DOID:0050739 An acquired metabolic disease that characterized by excessive production of acid. lschriml 2013-01-16T01:23:37Z disease_ontology DOID:0050758 metabolic acidosis DOID:0050758 A vascular disease that is located_in an artery. lschriml 2014-02-12T03:08:35Z disease_ontology DOID:0050828 artery disease DOID:0050828 A glomerulonephritis that is characterized by hardening of the glomerulus in the kidney. lschriml 2014-04-15T03:40:31Z disease_ontology DOID:0050851 glomerulosclerosis DOID:0050851 lschriml 2014-06-25T05:14:03Z disease_ontology DOID:0050871 fibroma DOID:0050871 A cardiomyopathy that is characterized as weakness in the muscle of the heart that is not due to an identifiable external cause. disease_ontology DOID:0060036 intrinsic cardiomyopathy DOID:0060036 A disease of mental health that involves the impairment in normal sexual functioning. disease_ontology DOID:0060043 sexual disorder DOID:0060043 A disease of cellular proliferation that results in abnormal growths in the body which lack the ability to metastasize. lschriml 2011-05-11T12:18:41Z disease_ontology DOID:0060072 benign neoplasm DOID:0060072 A benign neoplasm that is classified by the type of cell or tissue from which it is derived. lschriml 2011-07-14T11:59:48Z disease_ontology DOID:0060084 cell type benign neoplasm DOID:0060084 A benign neoplasm that is classified by the organ system from which it is arising from. lschriml 2011-07-14T12:12:23Z disease_ontology DOID:0060085 organ system benign neoplasm DOID:0060085 lschriml 2011-07-14T12:20:52Z disease_ontology DOID:0060086 female reproductive organ benign neoplasm DOID:0060086 lschriml 2011-07-15T01:42:11Z DOID:0060113 disease_ontology DOID:0060095 uterine benign neoplasm DOID:0060095 A disease of metabolism that has _material_basis_in enzyme deficiency or accumulation of enzymes or toxins which interfere with normal function due to an endocrine organ disease, organ malfunction, inadequate intake, dietary deficiency, or malabsorption. lschriml 2011-08-24T02:53:03Z disease_ontology DOID:0060158 acquired metabolic disease DOID:0060158 A congestive heart failure characterized by a sudden stop in effective blood circulation due to the failure of the heart to contract effectively or at all. emitraka 2015-02-25T15:12:30Z ICD10CM:I46 ICD9CM:427.5 MESH:D006323 NCI:C50479 NCI:C50483 SNOMEDCT_US_2016_03_01:155372006 SNOMEDCT_US_2016_03_01:195085006 SNOMEDCT_US_2016_03_01:195090009 SNOMEDCT_US_2016_03_01:233926006 SNOMEDCT_US_2016_03_01:251189000 SNOMEDCT_US_2016_03_01:30298009 SNOMEDCT_US_2016_03_01:309810002 SNOMEDCT_US_2016_03_01:397829000 SNOMEDCT_US_2016_03_01:397912004 SNOMEDCT_US_2016_03_01:410429000 SNOMEDCT_US_2016_03_01:410430005 UMLS_CUI:C0018790 UMLS_CUI:C0600228 cardiopulmonary arrest circulatory arrest disease_ontology DOID:0060319 cardiac arrest DOID:0060319 ICD10CM:I44.60 ICD9CM:426.2 SNOMEDCT_US_2016_03_01:195044001 SNOMEDCT_US_2016_03_01:195045000 SNOMEDCT_US_2016_03_01:266245009 SNOMEDCT_US_2016_03_01:4973001 UMLS_CUI:C0155702 Left bundle branch [block] or [hemiblock] Left bundle branch hemiblock (disorder) Left bundle branch hemiblock NOS (disorder) disease_ontology DOID:10272 left bundle branch hemiblock DOID:10272 A cardiovascular system disease that involves the heart's electrical conduction system. ICD9CM:426.6 SNOMEDCT_US_2016_03_01:195053008 SNOMEDCT_US_2016_03_01:195056000 UMLS_CUI:C0029630 heart rhythm disease disease_ontology DOID:10273 heart conduction disease DOID:10273 A disease by infectious agent that results_in infection, has_material_basis_in Bacteria. ICD10CM:A49 ICD10CM:A49.9 MESH:D001424 MESH:D016905 MESH:D016908 NCI:C2890 SNOMEDCT_US_2016_03_01:154318005 SNOMEDCT_US_2016_03_01:186470002 SNOMEDCT_US_2016_03_01:187347000 SNOMEDCT_US_2016_03_01:266182006 SNOMEDCT_US_2016_03_01:266187000 SNOMEDCT_US_2016_03_01:301811001 SNOMEDCT_US_2016_03_01:87628006 UMLS_CUI:C0004623 disease_ontology DOID:104 bacterial infectious disease DOID:104 A hypertension occurring during pregnancy characterized by large amounts of protein in the urine (proteinuria) and edema, usually by the last trimester of pregnancy. DOID:12684 ICD10CM:O14 ICD10CM:O14.9 ICD10CM:O14.90 MESH:D011225 NCI:C34943 NCI:C85021 OMIM:189800 OMIM:609402 OMIM:609403 OMIM:609404 OMIM:614592 ORDO:275555 SNOMEDCT_US_2016_03_01:15394000 SNOMEDCT_US_2016_03_01:156106005 SNOMEDCT_US_2016_03_01:156109003 SNOMEDCT_US_2016_03_01:198972006 SNOMEDCT_US_2016_03_01:198979002 SNOMEDCT_US_2016_03_01:199011002 SNOMEDCT_US_2016_03_01:237280005 SNOMEDCT_US_2016_03_01:267306006 SNOMEDCT_US_2016_03_01:288201007 SNOMEDCT_US_2016_03_01:398254007 SNOMEDCT_US_2016_03_01:46764007 SNOMEDCT_US_2016_03_01:6758009 UMLS_CUI:C0032914 gestational hypertension hypertension induced by pregnancy pre-eclamptic toxaemia preeclampsia preeclampsia/eclampsia pregnancy associated hypertension pregnancy toxemia proteinuric hypertension of pregnancy toxaemia of pregnancy disease_ontology DOID:10591 Xref MGI. OMIM mapping confirmed by DO. [SN]. pre-eclampsia DOID:10591 MESH:D006977 NCI:C3121 SNOMEDCT_US_2016_03_01:194775007 SNOMEDCT_US_2016_03_01:28119000 UMLS_CUI:C0020544 disease_ontology DOID:1073 renal hypertension DOID:1073 A kidney disease characterized by the failure of the kidneys to adequately filter waste products from the blood. ICD10CM:N19 ICD9CM:586 MESH:D051437 NCI:C4376 SNOMEDCT_US_2016_03_01:156092003 SNOMEDCT_US_2016_03_01:197656003 SNOMEDCT_US_2016_03_01:198524000 SNOMEDCT_US_2016_03_01:266553002 SNOMEDCT_US_2016_03_01:266616000 SNOMEDCT_US_2016_03_01:42399005 UMLS_CUI:C0035078 renal failure disease_ontology DOID:1074 PRISM. kidney failure DOID:1074 ICD10CM:N11 ICD10CM:N11.9 ICD9CM:590.0 NCI:C123216 SNOMEDCT_US_2016_03_01:123293005 SNOMEDCT_US_2016_03_01:155861006 SNOMEDCT_US_2016_03_01:197767009 SNOMEDCT_US_2016_03_01:266619007 SNOMEDCT_US_2016_03_01:63302006 UMLS_CUI:C0085697 disease_ontology DOID:1076 chronic pyelonephritis DOID:1076 An artery disease characterized by chronic elevated blood pressure in the arteries. EFO:0000537 ICD10CM:I10 ICD10CM:I10-I15 ICD9CM:401-405.99 ICD9CM:997.91 MESH:D006973 NCI:C3117 SNOMEDCT_US_2016_03_01:155295004 SNOMEDCT_US_2016_03_01:155302005 SNOMEDCT_US_2016_03_01:194756002 SNOMEDCT_US_2016_03_01:194757006 SNOMEDCT_US_2016_03_01:194760004 SNOMEDCT_US_2016_03_01:194794002 SNOMEDCT_US_2016_03_01:195537001 SNOMEDCT_US_2016_03_01:266287006 SNOMEDCT_US_2016_03_01:38341003 UMLS_CUI:C0020538 HTN High blood pressure (& [essential hypertension]) hyperpiesia vascular hypertensive disorder disease_ontology hypertensive disease DOID:10763 hypertension DOID:10763 ICD10CM:M31.1 MESH:D011697 NCI:C78797 SNOMEDCT_US_2016_03_01:155443009 SNOMEDCT_US_2016_03_01:195358008 SNOMEDCT_US_2016_03_01:195359000 SNOMEDCT_US_2016_03_01:360402008 SNOMEDCT_US_2016_03_01:78129009 UMLS_CUI:C0034155 Moschcowitz's syndrome disease_ontology DOID:10772 thrombotic thrombocytopenic purpura DOID:10772 A hypertension with no known cause. It is the most common type of hypertension. ICD10CM:I10 ICD9CM:401 ICD9CM:401.9 MESH:C562386 NCI:C3478 OMIM:145500 OMIM:603918 OMIM:604329 OMIM:607329 OMIM:608742 OMIM:610261 OMIM:610262 OMIM:610948 OMIM:611014 ORDO:243761 SNOMEDCT_US_2016_03_01:155296003 SNOMEDCT_US_2016_03_01:194757006 SNOMEDCT_US_2016_03_01:194760004 SNOMEDCT_US_2016_03_01:266228004 SNOMEDCT_US_2016_03_01:59621000 UMLS_CUI:C0085580 idiopathic hypertension primary hypertension disease_ontology DOID:10825 Xref MGI. OMIM mapping confirmed by DO. [SN]. essential hypertension DOID:10825 ICD10CM:H49.2 ICD9CM:378.54 MESH:D020434 NCI:C27592 NCI:C27593 OMIM:100200 SNOMEDCT_US_2016_03_01:14720007 SNOMEDCT_US_2016_03_01:230533001 SNOMEDCT_US_2016_03_01:398760006 SNOMEDCT_US_2016_03_01:398925009 SNOMEDCT_US_2016_03_01:398963001 SNOMEDCT_US_2016_03_01:46587002 SNOMEDCT_US_2016_03_01:4892003 SNOMEDCT_US_2016_03_01:82373004 UMLS_CUI:C0271355 Abducens nerve disorder Abducens nerve weakness Lateral rectus muscle denervation paresis Lateral rectus muscle innervation disorder Sixth cranial nerve disorder, NOS Sixth nerve palsy (disorder) Sixth or abducens nerve palsy VIth nerve Paralysis VIth nerve disorder disorder of abducent nerve disease_ontology DOID:10865 abducens nerve disease DOID:10865 A cerebral degeneration characterized by an abnormal accumulation of cerebrospinal fluid in the ventricles of the brain, leading to progressive enlargement of the head. ICD10CM:G91 ICD10CM:G91.9 MESH:D006849 NCI:C3111 OMIM:123155 OMIM:236600 OMIM:236635 OMIM:307000 OMIM:615219 ORDO:2182 ORDO:2185 SNOMEDCT_US_2016_03_01:154995000 SNOMEDCT_US_2016_03_01:154997008 SNOMEDCT_US_2016_03_01:192807008 SNOMEDCT_US_2016_03_01:230745008 SNOMEDCT_US_2016_03_01:267687006 UMLS_CUI:C0020255 hydrocephalus, X-linked hydrocephalus, nonsyndromic, autosomal recessive disease_ontology DOID:10908 Xref MGI. OMIM mapping confirmed by DO. [SN]. hydrocephalus DOID:10908 ICD10CM:K14 ICD10CM:K14.9 ICD9CM:529.9 MESH:D014060 SNOMEDCT_US_2016_03_01:155533008 SNOMEDCT_US_2016_03_01:155665004 SNOMEDCT_US_2016_03_01:155667007 SNOMEDCT_US_2016_03_01:196595001 SNOMEDCT_US_2016_03_01:266496009 SNOMEDCT_US_2016_03_01:69244009 UMLS_CUI:C0040409 disease_ontology DOID:10944 tongue disease DOID:10944 A kidney disease that is characterized by an inflammation of the kidneys. ICD10CM:N05 ICD10CM:N08 MESH:D009393 NCI:C26833 SNOMEDCT_US_2016_03_01:155853001 SNOMEDCT_US_2016_03_01:266615001 SNOMEDCT_US_2016_03_01:274107001 SNOMEDCT_US_2016_03_01:52845002 UMLS_CUI:C0027697 disease_ontology DOID:10952 nephritis DOID:10952 ICD10CM:I15 ICD10CM:I15.9 ICD9CM:405 ICD9CM:405.9 NCI:C3657 SNOMEDCT_US_2016_03_01:155300002 SNOMEDCT_US_2016_03_01:194789002 SNOMEDCT_US_2016_03_01:194792003 SNOMEDCT_US_2016_03_01:31992008 UMLS_CUI:C0155616 disease_ontology DOID:11130 secondary hypertension DOID:11130 A lung disease characterized by inadequate gas exchange by the respiratory system. DOID:11391 DOID:11392 DOID:11393 ICD10CM:J96.0 ICD9CM:518.81 NCI:C27043 SNOMEDCT_US_2016_03_01:65710008 UMLS_CUI:C0264490 acute and chronic respiratory failure acute respiratory Failure acute-on-chronic respiratory failure chronic respiratory failure respiratory insufficiency/failure disease_ontology DOID:11162 respiratory failure DOID:11162 ICD10CM:D65 ICD9CM:286.6 MESH:D004211 NCI:C2992 SNOMEDCT_US_2016_03_01:267563002 SNOMEDCT_US_2016_03_01:67406007 UMLS_CUI:C0012739 DIC Defibrination syndrome Diffuse or disseminated intravascular coagulation disease_ontology DOID:11247 disseminated intravascular coagulation DOID:11247 DOID:13472 ICD10CM:J81 ICD10CM:J81.1 MESH:D011654 NCI:C26868 SNOMEDCT_US_2016_03_01:19242006 SNOMEDCT_US_2016_03_01:196119001 SNOMEDCT_US_2016_03_01:266408001 UMLS_CUI:C0034063 disease_ontology DOID:11396 pulmonary edema DOID:11396 A cardiovascular system disease that involves the heart. ICD10CM:I51.9 ICD9CM:429.9 MESH:D006331 NCI:C3079 SNOMEDCT_US_2016_03_01:155263000 SNOMEDCT_US_2016_03_01:194707003 SNOMEDCT_US_2016_03_01:195152001 SNOMEDCT_US_2016_03_01:266275004 SNOMEDCT_US_2016_03_01:266311004 SNOMEDCT_US_2016_03_01:56265001 UMLS_CUI:C0018799 disease_ontology DOID:114 heart disease DOID:114 ICD10CM:N10-N16 ICD10CM:N12 ICD10CM:N16 ICD9CM:590.80 MESH:D011704 NCI:C34965 SNOMEDCT_US_2016_03_01:197779009 SNOMEDCT_US_2016_03_01:197784003 SNOMEDCT_US_2016_03_01:45816000 UMLS_CUI:C0034186 disease_ontology DOID:11400 pyelonephritis DOID:11400 ICD10CM:G93.2 ICD9CM:348.2 MESH:D011559 NCI:C85035 OMIM:243200 SNOMEDCT_US_2016_03_01:155052007 SNOMEDCT_US_2016_03_01:267701004 SNOMEDCT_US_2016_03_01:68267002 UMLS_CUI:C0033845 Pseudotumor cerebri benign intracran. hypt. benign intracranial hypertension benign intracranial hypertension (disorder) idiopathic intracranial hypertension disease_ontology DOID:11459 OMIM mapping confirmed by DO. [SN]. pseudotumor cerebri DOID:11459 ICD9CM:337.1 UMLS_CUI:C0154691 autonomic nervous system disorder disease_ontology DOID:11465 autonomic nervous system disease DOID:11465 DOID:11737 DOID:13947 ICD10CM:Q23.3 ICD9CM:396.3 ICD9CM:746.6 MESH:D008944 NCI:C50852 NCI:C50888 SNOMEDCT_US_2016_03_01:194736003 SNOMEDCT_US_2016_03_01:194977007 SNOMEDCT_US_2016_03_01:233857005 SNOMEDCT_US_2016_03_01:29928006 SNOMEDCT_US_2016_03_01:48724000 UMLS_CUI:C0026266 UMLS_CUI:C0158619 UMLS_CUI:C0264774 Congenital insufficiency of mitral valve (disorder) Mitral valve incompetence congenital mitral insufficiency congenital mitral regurgitation mitral regurgitation disease_ontology DOID:11502 mitral valve insufficiency DOID:11502 A heart disease that is caused by high blood pressure. ICD10CM:I11 ICD10CM:I11.9 ICD9CM:402 ICD9CM:402.9 SNOMEDCT_US_2016_03_01:155297007 SNOMEDCT_US_2016_03_01:194769003 SNOMEDCT_US_2016_03_01:194772005 SNOMEDCT_US_2016_03_01:64715009 UMLS_CUI:C0152105 disease_ontology DOID:11516 hypertensive heart disease DOID:11516 ICD10CM:H35.03 ICD9CM:362.11 MESH:D058437 NCI:C3514 SNOMEDCT_US_2016_03_01:155108001 SNOMEDCT_US_2016_03_01:193356005 SNOMEDCT_US_2016_03_01:193358006 SNOMEDCT_US_2016_03_01:421731000 SNOMEDCT_US_2016_03_01:422001004 SNOMEDCT_US_2016_03_01:6962006 UMLS_CUI:C0152132 disease_ontology DOID:11561 hypertensive retinopathy DOID:11561 ICD10CM:I12 ICD10CM:N26.9 ICD9CM:587 MESH:D009400 SNOMEDCT_US_2016_03_01:194773000 SNOMEDCT_US_2016_03_01:197658002 SNOMEDCT_US_2016_03_01:197662008 SNOMEDCT_US_2016_03_01:32916005 UMLS_CUI:C0027719 renal sclerosis disease_ontology DOID:11664 nephrosclerosis DOID:11664 DOID:3147 ICD10CM:E78.5 MESH:D006949 MESH:D006951 NCI:C34707 NCI:C34709 SNOMEDCT_US_2016_03_01:154739000 SNOMEDCT_US_2016_03_01:154743001 SNOMEDCT_US_2016_03_01:190782002 SNOMEDCT_US_2016_03_01:267499005 SNOMEDCT_US_2016_03_01:3744001 SNOMEDCT_US_2016_03_01:55822004 UMLS_CUI:C0020473 UMLS_CUI:C0020476 familial hyperlipoproteinemia hyperlipemia disease_ontology hyperlipidaemia DOID:1168 familial hyperlipidemia DOID:1168 A nervous system cancer that is located_in the peripheral nervous system. DOID:3194 MESH:D010524 MESH:D018317 NCI:C3321 NCI:C4972 SNOMEDCT_US_2016_03_01:115242003 SNOMEDCT_US_2016_03_01:126980002 SNOMEDCT_US_2016_03_01:134214003 SNOMEDCT_US_2016_03_01:189946005 SNOMEDCT_US_2016_03_01:189953001 UMLS_CUI:C0031118 UMLS_CUI:C0206727 neoplasm of peripheral nerve (disorder) nerve sheath neoplasm nerve sheath tumors tumor of PNS disease_ontology DOID:1192 peripheral nervous system neoplasm DOID:1192 A placenta disease that is characterized by a deficiency of amniotic fluid sometimes resulting in an embryonic defect through adherence between embryo and amnion. DOID:12595 DOID:12596 ICD10CM:O41.0 ICD10CM:O41.00 ICD9CM:658.0 MESH:D016104 NCI:C92839 SNOMEDCT_US_2016_03_01:156190009 SNOMEDCT_US_2016_03_01:157051001 SNOMEDCT_US_2016_03_01:199652007 SNOMEDCT_US_2016_03_01:199656005 SNOMEDCT_US_2016_03_01:59566000 UMLS_CUI:C0079924 Oligohydramnios - delivered antepartum oligohydramnios delivered oligohydramnios disease_ontology DOID:12215 oligohydramnios DOID:12215 A pneumonia involving inflammation of lungs that begins in the terminal bronchioles, which become clogged with thick mucus that forms consolidated patches in adjacent lobules. It is caused by bacteria and viruses. ICD10CM:J18.0 ICD9CM:485 MESH:D001996 NCI:C26710 SNOMEDCT_US_2016_03_01:155551009 SNOMEDCT_US_2016_03_01:195914001 SNOMEDCT_US_2016_03_01:266352008 SNOMEDCT_US_2016_03_01:396285007 SNOMEDCT_US_2016_03_01:67814005 UMLS_CUI:C0006285 Chest infection - unspecified bronchopneumonia bronchial pneumonia lobular pneumonia disease_ontology DOID:12375 bronchopneumonia DOID:12375 DOID:13997 DOID:9474 ICD10CM:D68.9 ICD9CM:286 MESH:D001778 NCI:C2902 SNOMEDCT_US_2016_03_01:127073005 SNOMEDCT_US_2016_03_01:154815003 SNOMEDCT_US_2016_03_01:191303002 SNOMEDCT_US_2016_03_01:267562007 SNOMEDCT_US_2016_03_01:362970003 SNOMEDCT_US_2016_03_01:64779008 UMLS_CUI:C0005779 postpartum coagulation defect postpartum coagulation defect with delivery disease_ontology DOID:1247 blood coagulation disease DOID:1247 ICD10CM:H35.82 ICD9CM:362.84 SNOMEDCT_US_2016_03_01:193427006 SNOMEDCT_US_2016_03_01:26468004 UMLS_CUI:C0162291 disease_ontology DOID:12510 retinal ischemia DOID:12510 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. DOID:73 ICD9CM:429.2 MESH:D002318 NCI:C2931 SNOMEDCT_US_2016_03_01:155263000 SNOMEDCT_US_2016_03_01:194707003 SNOMEDCT_US_2016_03_01:195139006 SNOMEDCT_US_2016_03_01:195594006 SNOMEDCT_US_2016_03_01:266275004 SNOMEDCT_US_2016_03_01:266336005 SNOMEDCT_US_2016_03_01:49601007 UMLS_CUI:C0007222 disease of subdivision of hemolymphoid system disease_ontology DOID:1287 cardiovascular system disease DOID:1287 An intrinsic cardiomyopathy that is characterized by an an enlarged heart and damage to the myocardium causing the heart to pump blood inefficiently. EFO:0000407 ICD10CM:I42.0 KEGG:05414 MESH:D002311 NCI:C84673 OMIM:PS115200 ORDO:217604 SNOMEDCT_US_2016_03_01:195018001 SNOMEDCT_US_2016_03_01:195021004 SNOMEDCT_US_2016_03_01:389995008 SNOMEDCT_US_2016_03_01:399020009 SNOMEDCT_US_2016_03_01:74368002 UMLS_CUI:C0007193 primary dilated cardiomyopathy disease_ontology Congestive cardiomyopathy Familial dilated cardiomyopathy Idiopathic dilation cardiomyopathy DOID:12930 Xref MGI. OMIM mapping confirmed by DO. [LS]. dilated cardiomyopathy DOID:12930 ICD10CM:H34.23 ICD9CM:362.32 MESH:D015356 NCI:C34436 SNOMEDCT_US_2016_03_01:50821009 UMLS_CUI:C0006123 Arterial retinal branch occlusion (disorder) Retinal Arterial Branch Occlusion Retinal arterial branch occlusion disease_ontology DOID:13094 branch retinal artery occlusion DOID:13094 DOID:3945 EFO:0004236 MESH:D005923 NCI:C37308 OMIM:PS603278 SNOMEDCT_US_2016_03_01:236403004 SNOMEDCT_US_2016_03_01:25821008 UMLS_CUI:C0017668 FGS (focal glomerular sclerosis) FSGS focal glomerular sclerosis focal glomerulosclerosis disease_ontology DOID:1312 Xref MGI. OMIM mapping confirmed by DO. [SN]. focal segmental glomerulosclerosis DOID:1312 A cystitis characterized by a sudden onset or severe symptoms. ICD10CM:N30.0 ICD9CM:595.0 NCI:C26934 SNOMEDCT_US_2016_03_01:155883005 SNOMEDCT_US_2016_03_01:197833009 SNOMEDCT_US_2016_03_01:266628008 SNOMEDCT_US_2016_03_01:68226007 UMLS_CUI:C0149523 urinary tract infection disease_ontology DOID:13148 acute cystitis DOID:13148 A uterine benign neoplasm derived from the smooth muscle layer of the uterus. EFO:0000731 ICD10CM:D25 ICD10CM:D25.9 ICD9CM:218 ICD9CM:218.9 MESH:D007889 NCI:C3434 OMIM:150699 SNOMEDCT_US_2016_03_01:146801000119103 SNOMEDCT_US_2016_03_01:154616000 SNOMEDCT_US_2016_03_01:189106003 SNOMEDCT_US_2016_03_01:44598004 SNOMEDCT_US_2016_03_01:95315005 UMLS_CUI:C0042133 Plexiform leiomyoma UTERUS FIBROMA leiomyoma of Corpus Uteri uterine leiomyoma disease_ontology DOID:13223 OMIM mapping confirmed by DO. [LS]. uterine fibroid DOID:13223 A respiratory system cancer that is located_in the lung. DOID:13075 DOID:1322 DOID:9881 ICD10CM:C34.1 ICD10CM:C34.2 ICD10CM:C34.3 ICD9CM:162.3 ICD9CM:162.4 ICD9CM:162.5 ICD9CM:162.8 OMIM:211980 OMIM:608935 OMIM:612571 OMIM:612593 OMIM:614210 SNOMEDCT_US_2016_03_01:187860004 SNOMEDCT_US_2016_03_01:187863002 SNOMEDCT_US_2016_03_01:187864008 SNOMEDCT_US_2016_03_01:187867001 SNOMEDCT_US_2016_03_01:187868006 SNOMEDCT_US_2016_03_01:187871003 SNOMEDCT_US_2016_03_01:187874006 SNOMEDCT_US_2016_03_01:269464000 UMLS_CUI:C0024624 UMLS_CUI:C0153491 UMLS_CUI:C0153492 UMLS_CUI:C0153493 disease_ontology lung neoplasm DOID:1324 lung cancer DOID:1324 ICD10CM:G91.1 ICD9CM:331.4 MESH:D006849 NCI:C116347 SNOMEDCT_US_2016_03_01:230746009 SNOMEDCT_US_2016_03_01:82346000 UMLS_CUI:C0549423 disease_ontology DOID:14159 obstructive hydrocephalus DOID:14159 ICD9CM:331.9 SNOMEDCT_US_2016_03_01:154994001 SNOMEDCT_US_2016_03_01:154998003 SNOMEDCT_US_2016_03_01:192824002 SNOMEDCT_US_2016_03_01:267579001 SNOMEDCT_US_2016_03_01:267686002 SNOMEDCT_US_2016_03_01:267688001 SNOMEDCT_US_2016_03_01:418143002 SNOMEDCT_US_2016_03_01:52522001 SNOMEDCT_US_2016_03_01:73768007 UMLS_CUI:C0154671 Brain degeneration disease_ontology DOID:1443 cerebral degeneration DOID:1443 A disease that is characterized by abnormally rapid cell division. DOID:0000818 cell process disease neoplasm disease_ontology DOID:14566 disease of cellular proliferation DOID:14566 A sensory system disease that is located_in the eye or the adnexa of the eye. ICD10CM:H35.00 ICD9CM:362.10 SNOMEDCT_US_2016_03_01:193355009 SNOMEDCT_US_2016_03_01:31411005 SNOMEDCT_US_2016_03_01:42873008 UMLS_CUI:C0004608 disease_ontology DOID:1492 eye and adnexa disease DOID:1492 A disease of anatomical entity that is located_in reproductive system organs. DOID:6309 NCI:C27613 UMLS_CUI:C1335037 genital system disease disease_ontology DOID:15 reproductive system disease DOID:15 A disease that involves a psychological or behavioral pattern generally associated with subjective distress or disability that occurs in an individual, and which are not a part of normal development or culture. ICD10CM:F99 ICD10CM:F99-F99 MESH:D001523 NCI:C2893 SNOMEDCT_US_2016_03_01:154843007 SNOMEDCT_US_2016_03_01:154971002 SNOMEDCT_US_2016_03_01:154972009 SNOMEDCT_US_2016_03_01:154980002 SNOMEDCT_US_2016_03_01:192637001 SNOMEDCT_US_2016_03_01:192639003 SNOMEDCT_US_2016_03_01:74732009 UMLS_CUI:C0004936 disease_ontology DOID:150 disease of mental health DOID:150 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. DOID:1531 MESH:D010995 NCI:C26859 SNOMEDCT_US_2016_03_01:88075009 UMLS_CUI:C0032226 disorder of pleura non-neoplastic pleural disease disease_ontology DOID:1532 pleural disease DOID:1532 A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm. DOID:3226 ICD10CM:J96-J99 ICD10CM:J98 ICD9CM:510-519.99 ICD9CM:519 SNOMEDCT_US_2016_03_01:155603009 SNOMEDCT_US_2016_03_01:196057004 SNOMEDCT_US_2016_03_01:196184000 SNOMEDCT_US_2016_03_01:196255004 SNOMEDCT_US_2016_03_01:266373008 UMLS_CUI:C0029582 disease_ontology DOID:1579 respiratory system disease DOID:1579 A blood platelet disease characterized by low a platelet count in the blood. ICD10CM:D69.6 ICD9CM:287.5 MESH:D013921 NCI:C3408 OMIM:188000 OMIM:273900 OMIM:300367 OMIM:313900 OMIM:612004 ORDO:852 SNOMEDCT_US_2016_03_01:142969008 SNOMEDCT_US_2016_03_01:154827000 SNOMEDCT_US_2016_03_01:165556002 SNOMEDCT_US_2016_03_01:191326009 SNOMEDCT_US_2016_03_01:302215000 SNOMEDCT_US_2016_03_01:415116008 SNOMEDCT_US_2016_03_01:70786006 UMLS_CUI:C0040034 disease_ontology DOID:1588 Xref MGI. thrombocytopenia DOID:1588 ICD10CM:I15.0 MESH:D006978 NCI:C85044 SNOMEDCT_US_2016_03_01:123799005 SNOMEDCT_US_2016_03_01:194790006 UMLS_CUI:C0020545 Renovascular hypertension (disorder) disease_ontology DOID:1591 renovascular hypertension DOID:1591 A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. ICD10CM:C80 ICD10CM:C80.1 ICD9CM:199 MESH:D009369 NCI:C9305 SNOMEDCT_US_2016_03_01:154432008 SNOMEDCT_US_2016_03_01:154433003 SNOMEDCT_US_2016_03_01:154577008 SNOMEDCT_US_2016_03_01:187597000 SNOMEDCT_US_2016_03_01:188475001 SNOMEDCT_US_2016_03_01:188482002 SNOMEDCT_US_2016_03_01:190150006 SNOMEDCT_US_2016_03_01:269513004 SNOMEDCT_US_2016_03_01:269623003 SNOMEDCT_US_2016_03_01:269626006 SNOMEDCT_US_2016_03_01:269634000 SNOMEDCT_US_2016_03_01:363346000 SNOMEDCT_US_2016_03_01:38807002 UMLS_CUI:C0006826 malignant neoplasm malignant tumor primary cancer disease_ontology DOID:162 Updating out dated UMLS CUI. cancer DOID:162 ICD10CM:J93.1 SNOMEDCT_US_2016_03_01:196103008 SNOMEDCT_US_2016_03_01:196105001 SNOMEDCT_US_2016_03_01:196251008 SNOMEDCT_US_2016_03_01:266367007 UMLS_CUI:C0029850 disease_ontology DOID:1673 pneumothorax DOID:1673 ICD10CM:N30 ICD10CM:N30.9 ICD9CM:595 ICD9CM:595.9 MESH:D003556 NCI:C26738 SNOMEDCT_US_2016_03_01:155882000 SNOMEDCT_US_2016_03_01:155885003 SNOMEDCT_US_2016_03_01:197857009 SNOMEDCT_US_2016_03_01:266629000 SNOMEDCT_US_2016_03_01:38822007 UMLS_CUI:C0010692 disease_ontology DOID:1679 cystitis DOID:1679 ICD10CM:H34 ICD10CM:H34.9 ICD9CM:362.3 ICD9CM:362.30 NCI:C34980 SNOMEDCT_US_2016_03_01:155111000 SNOMEDCT_US_2016_03_01:193373007 SNOMEDCT_US_2016_03_01:193380009 SNOMEDCT_US_2016_03_01:267717005 SNOMEDCT_US_2016_03_01:73757007 UMLS_CUI:C0035326 Retinal vasc. occlusion Retinal vascular Occlusion Retinal vascular occlusion (disorder) Retinal vascular occlusion NOS (disorder) Retinal vascular occlusion, unspecified Unspecified retinal vascular occlusion (disorder) disease_ontology DOID:1729 retinal vascular occlusion DOID:1729 A cardiovascular system disease that primarily affects the blood vessels which includes the arteries, veins and capillaries that carry blood to and from the heart. DOID:0000405 DOID:2403 DOID:2869 DOID:324 DOID:325 DOID:45 ICD10CM:I72.9 ICD9CM:442.9 MESH:D000783 MESH:D014652 MESH:D020758 MESH:D020760 NCI:C26693 NCI:C35117 SNOMEDCT_US_2016_03_01:134342004 SNOMEDCT_US_2016_03_01:155425005 SNOMEDCT_US_2016_03_01:155428007 SNOMEDCT_US_2016_03_01:195292009 SNOMEDCT_US_2016_03_01:27550009 SNOMEDCT_US_2016_03_01:362727005 SNOMEDCT_US_2016_03_01:371029002 SNOMEDCT_US_2016_03_01:432119003 SNOMEDCT_US_2016_03_01:85659009 UMLS_CUI:C0002940 UMLS_CUI:C0042373 UMLS_CUI:C0752127 UMLS_CUI:C0752130 vascular tissue disease disease_ontology DOID:178 vascular disease DOID:178 A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra. DOID:579 NCI:C27599 UMLS_CUI:C1335051 Non-neoplastic urinary tract disease urinary tract disease disease_ontology DOID:18 urinary system disease DOID:18 EFO:0004234 Sexual impotence (finding) erectile dysfunction disease_ontology DOID:1875 impotence DOID:1875 ICD10CM:F52.9 ICD10CM:R37 MESH:D012735 NCI:C3347 SNOMEDCT_US_2016_03_01:225723003 SNOMEDCT_US_2016_03_01:231532002 SNOMEDCT_US_2016_03_01:39894007 SNOMEDCT_US_2016_03_01:56925008 SNOMEDCT_US_2016_03_01:65655009 UMLS_CUI:C0549622 disease_ontology DOID:1876 sexual dysfunction DOID:1876 An acquired metabolic disease that has_material_basis_in an abnormally high level of uric acid in the blood. MESH:D033461 NCI:C3961 SNOMEDCT_US_2016_03_01:144021008 SNOMEDCT_US_2016_03_01:166733000 SNOMEDCT_US_2016_03_01:237857006 SNOMEDCT_US_2016_03_01:271198001 SNOMEDCT_US_2016_03_01:35885006 UMLS_CUI:C0740394 (Blood urate raized) or (hyperuricemia) uricacidemia disease_ontology DOID:1920 hyperuricemia DOID:1920 EFO:0003914 ICD10CM:I25.1 ICD10CM:I70 ICD9CM:440 MESH:D050197 NCI:C35768 NCI:C35771 SNOMEDCT_US_2016_03_01:155382007 SNOMEDCT_US_2016_03_01:155414001 SNOMEDCT_US_2016_03_01:194848007 SNOMEDCT_US_2016_03_01:195251000 SNOMEDCT_US_2016_03_01:266318005 SNOMEDCT_US_2016_03_01:38716007 UMLS_CUI:C0004153 disease_ontology DOID:1936 atherosclerosis DOID:1936 ICD10CM:D69.9 ICD9CM:287.9 MESH:D006474 SNOMEDCT_US_2016_03_01:191327000 SNOMEDCT_US_2016_03_01:191331006 SNOMEDCT_US_2016_03_01:191437009 SNOMEDCT_US_2016_03_01:268884000 UMLS_CUI:C0019087 Hemorrhagic diathesis Hemorrhagic disease disease_ontology DOID:2213 hemorrhagic disease DOID:2213 MESH:D001791 SNOMEDCT_US_2016_03_01:22716005 UMLS_CUI:C0005818 Thrombocytopathy platelet disorder disease_ontology DOID:2218 blood platelet disease DOID:2218 DOID:2315 ICD10CM:G45.9 ICD9CM:435.8 MESH:D002546 NCI:C50781 SNOMEDCT_US_2016_03_01:155404005 SNOMEDCT_US_2016_03_01:195196001 SNOMEDCT_US_2016_03_01:195207009 SNOMEDCT_US_2016_03_01:266257000 SNOMEDCT_US_2016_03_01:266314007 SNOMEDCT_US_2016_03_01:313242003 SNOMEDCT_US_2016_03_01:38609002 UMLS_CUI:C0007787 UMLS_CUI:C0155728 TIA TIA - Transient ischaemic attack TRANSIENT ISCHEMIC ATTACK Transient cerebral ischaemia Transient cerebral ischaemia NOS Transient cerebral ischemia (disorder) [Ambiguous] Transient ischemic attacks (disorder) transient ischemic attack disease_ontology DOID:224 transient cerebral ischemia DOID:224 A reproductive system disease that impairs the ability to reproduce and is located in the uterus, vagina, cervix, ovaries or fallopian tubes. ICD9CM:629.9 MESH:D005831 SNOMEDCT_US_2016_03_01:156032001 SNOMEDCT_US_2016_03_01:156066005 SNOMEDCT_US_2016_03_01:198486002 SNOMEDCT_US_2016_03_01:244938009 SNOMEDCT_US_2016_03_01:266680004 SNOMEDCT_US_2016_03_01:310789003 SNOMEDCT_US_2016_03_01:38233001 UMLS_CUI:C0017411 disease_ontology DOID:229 female reproductive system disease DOID:229 MESH:D002545 SNOMEDCT_US_2016_03_01:11890005 SNOMEDCT_US_2016_03_01:193049009 SNOMEDCT_US_2016_03_01:389100007 UMLS_CUI:C0007786 Ischaemic encephalopathy Ischemic encephalopathy (disorder) disease_ontology DOID:2316 brain ischemia DOID:2316 ICD10CM:I25.1 ICD10CM:I70 ICD9CM:440 MESH:D050197 NCI:C34403 NCI:C35768 NCI:C35771 SNOMEDCT_US_2016_03_01:155382007 SNOMEDCT_US_2016_03_01:155414001 SNOMEDCT_US_2016_03_01:194848007 SNOMEDCT_US_2016_03_01:195121002 SNOMEDCT_US_2016_03_01:195251000 SNOMEDCT_US_2016_03_01:266318005 SNOMEDCT_US_2016_03_01:38716007 SNOMEDCT_US_2016_03_01:39468009 UMLS_CUI:C0004153 UMLS_CUI:C3665365 Arteriosclerotic Cardiovascular disease Arteriosclerotic cardiovascular disease Arteriosclerotic cardiovascular disease, NOS Atherosclerotic Cardiovascular disease Atherosclerotic cardiovascular disease Cardiovascular arteriosclerosis unspecified (disorder) disease_ontology DOID:2348 arteriosclerotic cardiovascular disease DOID:2348 An artery disease that is characterized by a thickening and hardening of arterial walls in the arteries. CSP:0571-2299 ICD10CM:I70 MESH:D001161 NCI:C34398 SNOMEDCT_US_2016_03_01:107671003 SNOMEDCT_US_2016_03_01:155414001 SNOMEDCT_US_2016_03_01:155418003 SNOMEDCT_US_2016_03_01:195251000 SNOMEDCT_US_2016_03_01:195257001 SNOMEDCT_US_2016_03_01:266318005 SNOMEDCT_US_2016_03_01:28960008 SNOMEDCT_US_2016_03_01:72092001 UMLS_CUI:C0003850 Arteriosclerosis (morphologic abnormality) Arteriosclerosis NOS Arteriosclerotic vascular disease (disorder) Arteriosclerotic vascular disease NOS disease_ontology DOID:2349 arteriosclerosis DOID:2349 A hematopoietic system disease that is characterized by a decrease in the normal number of red blood cells. EFO:0004272 ICD10CM:D64.9 ICD9CM:285.9 MESH:D000740 NCI:C2869 SNOMEDCT_US_2016_03_01:154786001 SNOMEDCT_US_2016_03_01:154812000 SNOMEDCT_US_2016_03_01:191277004 SNOMEDCT_US_2016_03_01:267531008 SNOMEDCT_US_2016_03_01:271737000 SNOMEDCT_US_2016_03_01:64593003 UMLS_CUI:C0002871 anaemia disease_ontology DOID:2355 PRISM. anemia DOID:2355 ICD9CM:593.81 NCI:C35338 SNOMEDCT_US_2016_03_01:16934004 SNOMEDCT_US_2016_03_01:197814004 SNOMEDCT_US_2016_03_01:266559003 UMLS_CUI:C0268790 renal vascular disease vascular disorder of kidney disease_ontology DOID:2388 renal artery disease DOID:2388 ICD10CM:D68.59 MESH:D018455 NCI:C99026 SNOMEDCT_US_2016_03_01:1563006 UMLS_CUI:C0242666 Protein S deficiency Protein S deficiency disease (disorder) disease_ontology DOID:2451 protein S deficiency DOID:2451 ICD10CM:D68.59 MESH:D019851 NCI:C84479 OMIM:188050 OMIM:614486 SNOMEDCT_US_2016_03_01:191302007 SNOMEDCT_US_2016_03_01:234467004 SNOMEDCT_US_2016_03_01:76612001 UMLS_CUI:C0398623 hypercoagulability state disease_ontology DOID:2452 OMIM mapping confirmed by DO. [LS]. thrombophilia DOID:2452 MESH:D009401 SNOMEDCT_US_2016_03_01:90708001 UMLS_CUI:C0027720 disease_ontology DOID:2527 nephrosis DOID:2527 An inherited metabolic disorder that involves elevated levels of bilirubin resulting from disruption of bilirubin metabolism. DOID:2740 MESH:D006932 MESH:D006933 NCI:C84761 SNOMEDCT_US_2016_03_01:143932000 SNOMEDCT_US_2016_03_01:14783006 SNOMEDCT_US_2016_03_01:154770008 SNOMEDCT_US_2016_03_01:166612004 SNOMEDCT_US_2016_03_01:20505009 SNOMEDCT_US_2016_03_01:235904007 SNOMEDCT_US_2016_03_01:267509000 UMLS_CUI:C0020433 UMLS_CUI:C0020435 hereditary hyperbilirubinemia hyperbilirubinemia disease_ontology hyperbilirubinaemia DOID:2741 bilirubin metabolic disorder DOID:2741 ICD10CM:N12 MESH:D011702 NCI:C34964 SNOMEDCT_US_2016_03_01:197780007 SNOMEDCT_US_2016_03_01:27174002 UMLS_CUI:C0034183 disease_ontology DOID:2744 pyelitis DOID:2744 MESH:D002526 SNOMEDCT_US_2016_03_01:155010002 SNOMEDCT_US_2016_03_01:192867005 SNOMEDCT_US_2016_03_01:223176004 SNOMEDCT_US_2016_03_01:224186005 SNOMEDCT_US_2016_03_01:267691001 SNOMEDCT_US_2016_03_01:307361005 SNOMEDCT_US_2016_03_01:49784007 UMLS_CUI:C0007760 disease_ontology DOID:2786 cerebellar disease DOID:2786 A nephritis that causes inflammation of the glomeruli located_in kidney. ICD10CM:N05 ICD10CM:N08 MESH:D005921 NCI:C26784 SNOMEDCT_US_2016_03_01:197648001 SNOMEDCT_US_2016_03_01:36171008 UMLS_CUI:C0017658 disease_ontology DOID:2921 glomerulonephritis DOID:2921 MESH:D001002 NCI:C114699 SNOMEDCT_US_2016_03_01:139460001 SNOMEDCT_US_2016_03_01:158479000 SNOMEDCT_US_2016_03_01:207182009 SNOMEDCT_US_2016_03_01:2472002 UMLS_CUI:C0003460 Suppression of urinary secretion disease_ontology DOID:2983 anuria DOID:2983 A glomerulonephritis characterized by build up of IgA antibody in the glomerulus. EFO:0004194 MESH:D005922 NCI:C34643 NCI:C35280 OMIM:161950 SNOMEDCT_US_2016_03_01:236407003 SNOMEDCT_US_2016_03_01:68779003 UMLS_CUI:C0017661 Berger's IgA or IgG nephropathy Focal Glomerulonephritis IGA glomerulonephritis IgA nephropathy primary IgA nephropathy segmental glomerulonephritis disease_ontology DOID:2986 OMIM mapping confirmed by DO. [SN]. IgA glomerulonephritis DOID:2986 A substance-related disorder that involves a maladaptive pattern of substance use leading to significant impairment in functioning. MESH:D019966 NCI:C16522 SNOMEDCT_US_2016_03_01:26416006 UMLS_CUI:C0013146 disease_ontology DOID:302 substance abuse DOID:302 disease_ontology DOID:3021 acute kidney failure DOID:3021 A disease of mental health involving the abuse or dependence on a substance that is ingested in order to produce a high, alter one's senses, or otherwise affect functioning. MESH:D019966 NCI:C92203 UMLS_CUI:C0236969 disease_ontology DOID:303 substance-related disorder DOID:303 A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells. DOID:2428 DOID:6570 CSP:2000-1867 MESH:D002277 MESH:D009375 NCI:C2916 NCI:C3709 SNOMEDCT_US_2016_03_01:118285006 SNOMEDCT_US_2016_03_01:134207000 SNOMEDCT_US_2016_03_01:154433003 SNOMEDCT_US_2016_03_01:188083002 SNOMEDCT_US_2016_03_01:189546004 SNOMEDCT_US_2016_03_01:189549006 SNOMEDCT_US_2016_03_01:189559007 SNOMEDCT_US_2016_03_01:269513004 SNOMEDCT_US_2016_03_01:68453008 SNOMEDCT_US_2016_03_01:71298006 UMLS_CUI:C0007097 UMLS_CUI:C0553707 UMLS_CUI:C1368683 epithelioma malignant Epithelioma disease_ontology DOID:305 carcinoma DOID:305 An organ system cancer located_in the nervous system that affects the central or peripheral nervous system. DOID:1193 DOID:3195 DOID:4695 ICD9CM:192 ICD9CM:192.9 MESH:D009380 NCI:C35562 SNOMEDCT_US_2016_03_01:188306000 UMLS_CUI:C0027665 UMLS_CUI:C0153643 UMLS_CUI:C1334956 malignant neoplasm of nervous system neoplasm of nervous system (disorder) nervous system neoplasm neural neoplasm neural tumor tumor of the nervous system disease_ontology DOID:3093 nervous system cancer DOID:3093 An organ system cancer located_in gastrointestinal tract that is manifested in organs of the gastrointestinal system. DOID:4945 DOID:8377 ICD10CM:C26.9 ICD9CM:239.0 MESH:D004067 MESH:D005770 NCI:C3052 NCI:C4890 SNOMEDCT_US_2016_03_01:126768004 SNOMEDCT_US_2016_03_01:128348002 SNOMEDCT_US_2016_03_01:128415001 SNOMEDCT_US_2016_03_01:189527000 SNOMEDCT_US_2016_03_01:276806006 SNOMEDCT_US_2016_03_01:367543008 SNOMEDCT_US_2016_03_01:428905002 SNOMEDCT_US_2016_03_01:93811007 UMLS_CUI:C0012243 UMLS_CUI:C0017185 UMLS_CUI:C0685938 GI tumor digestive system cancer gastrointestinal tract cancer disease_ontology DOID:3119 gastrointestinal system cancer DOID:3119 An inherited metabolic disorder that involves the creation and degradation of lipids. MESH:D008052 UMLS_CUI:C0023772 dyslipidemia fatty acid metabolism disorder disease_ontology DOID:3146 lipid metabolism disorder DOID:3146 A peripheral nervous system neoplasm that is located_in the connective tissue surrounding nerves. MESH:D018317 UMLS_CUI:C0751689 neoplasm of the nerve Sheath nerve sheath tumour disease_ontology DOID:3193 peripheral nerve sheath neoplasm DOID:3193 A vascular disease that is characterized by a restriction in blood supply to tissues. MESH:D007511 MESH:D054058 NCI:C34738 SNOMEDCT_US_2016_03_01:52674009 UMLS_CUI:C0022116 disease_ontology DOID:326 ischemia DOID:326 A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system. ICD10CM:G96.9 MESH:D002493 NCI:C2934 SNOMEDCT_US_2016_03_01:138748005 SNOMEDCT_US_2016_03_01:154981003 SNOMEDCT_US_2016_03_01:155049004 SNOMEDCT_US_2016_03_01:155059003 SNOMEDCT_US_2016_03_01:192641002 SNOMEDCT_US_2016_03_01:193076009 SNOMEDCT_US_2016_03_01:194566008 SNOMEDCT_US_2016_03_01:23853001 SNOMEDCT_US_2016_03_01:267144009 SNOMEDCT_US_2016_03_01:267679005 SNOMEDCT_US_2016_03_01:267700003 SNOMEDCT_US_2016_03_01:267702006 SNOMEDCT_US_2016_03_01:275539005 UMLS_CUI:C0007682 disease_ontology DOID:331 central nervous system disease DOID:331 An artery disease that is characterized by plaque building up along the inner walls of the arteries of the heart resulting in a narrowing of the arteries and a reduced blood supply to the cardiac muscles. DOID:10506 DOID:3363 DOID:3394 DOID:9420 EFO:0001645 ICD10CM:I20-I25 ICD10CM:I25 ICD10CM:I25.1 ICD10CM:I25.10 ICD10CM:I25.9 ICD10CM:K76.1 ICD9CM:410-414.99 ICD9CM:414.0 ICD9CM:414.9 MESH:D003324 MESH:D003327 MESH:D017202 NCI:C35505 NCI:C50625 OMIM:300464 OMIM:607339 OMIM:608316 OMIM:608318 OMIM:608320 OMIM:610947 OMIM:611139 OMIM:612030 OMIM:614293 SNOMEDCT_US_2016_03_01:155303000 SNOMEDCT_US_2016_03_01:155315001 SNOMEDCT_US_2016_03_01:155316000 SNOMEDCT_US_2016_03_01:155318004 SNOMEDCT_US_2016_03_01:155322009 SNOMEDCT_US_2016_03_01:194795001 SNOMEDCT_US_2016_03_01:194841001 SNOMEDCT_US_2016_03_01:194852007 SNOMEDCT_US_2016_03_01:194878003 SNOMEDCT_US_2016_03_01:195540001 SNOMEDCT_US_2016_03_01:233822007 SNOMEDCT_US_2016_03_01:2610009 SNOMEDCT_US_2016_03_01:266231003 SNOMEDCT_US_2016_03_01:266290000 SNOMEDCT_US_2016_03_01:266291001 SNOMEDCT_US_2016_03_01:271430002 SNOMEDCT_US_2016_03_01:32598000 SNOMEDCT_US_2016_03_01:413838009 SNOMEDCT_US_2016_03_01:413844008 SNOMEDCT_US_2016_03_01:414545008 SNOMEDCT_US_2016_03_01:414795007 SNOMEDCT_US_2016_03_01:41702007 SNOMEDCT_US_2016_03_01:443502000 SNOMEDCT_US_2016_03_01:53741008 SNOMEDCT_US_2016_03_01:84537008 UMLS_CUI:C0010054 UMLS_CUI:C0010068 UMLS_CUI:C0151744 UMLS_CUI:C0264694 CHD (coronary heart disease) Coronary disease coronary arteriosclerosis coronary heart disease disease_ontology DOID:3393 Xref MGI. coronary artery disease DOID:3393 A vascular disease that is characterized by obstruction of larger arteries not within the coronary, aortic arch vasculature, or brain. DOID:2868 ICD9CM:443.81 MESH:D001157 MESH:D016481 SNOMEDCT_US_2016_03_01:195624006 SNOMEDCT_US_2016_03_01:2929001 UMLS_CUI:C0003838 UMLS_CUI:C0031115 arterial occlusive disease disease_ontology DOID:341 peripheral vascular disease DOID:341 A female reproductive system disease that is located_in the uterus. ICD10CM:N85.9 ICD9CM:621.9 MESH:D014591 NCI:C26907 SNOMEDCT_US_2016_03_01:12337004 SNOMEDCT_US_2016_03_01:156004005 SNOMEDCT_US_2016_03_01:156009000 SNOMEDCT_US_2016_03_01:198335006 SNOMEDCT_US_2016_03_01:237068005 UMLS_CUI:C0042131 disease_ontology DOID:345 uterine disease DOID:345 A urinary system disease that is located_in the bladder. ICD10CM:N32.9 ICD9CM:596.9 MESH:D001745 NCI:C2900 SNOMEDCT_US_2016_03_01:155886002 SNOMEDCT_US_2016_03_01:155890000 SNOMEDCT_US_2016_03_01:197897007 SNOMEDCT_US_2016_03_01:266630005 SNOMEDCT_US_2016_03_01:42643001 UMLS_CUI:C0005686 Urinary Bladder Disease disease_ontology DOID:365 bladder disease DOID:365 MESH:D003389 NCI:C26941 SNOMEDCT_US_2016_03_01:73013002 UMLS_CUI:C0151311 Cranial nerve Paralysis Cranial nerve palsy disease_ontology DOID:3817 cranial nerve palsy DOID:3817 A lung cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells and is located_in the lungs and has_symptom cough and has_symptom chest discomfort or pain and has_symptom weight loss and has_symptom hemoptysis. EFO:0001071 ICD10CM:C34.90 NCI:C4878 SNOMEDCT_US_2016_03_01:154485001 SNOMEDCT_US_2016_03_01:187875007 SNOMEDCT_US_2016_03_01:269561006 UMLS_CUI:C0684249 cancer of lung disease_ontology carcinoma of lung DOID:3905 OMIM mapping confirmed by DO. [SN]. lung carcinoma DOID:3905 A lung carcinoma that is characterized as any type of epithelial lung cancer other than small cell lung carcinoma. EFO:0003060 ICD10CM:C34 KEGG:05223 MESH:D002289 NCI:C2926 SNOMEDCT_US_2016_03_01:254637007 UMLS_CUI:C0007131 NSCLC Non-small cell lung cancer disease_ontology DOID:3908 non-small cell lung carcinoma DOID:3908 A gastrointestinal system disease that is located_in the mouth. MESH:D009059 NCI:C27641 NCI:C3240 SNOMEDCT_US_2016_03_01:118938008 SNOMEDCT_US_2016_03_01:155630004 SNOMEDCT_US_2016_03_01:266484002 UMLS_CUI:C0026636 disease_ontology DOID:403 mouth disease DOID:403 A heart disease involving one or more of the four valves of the heart (the aortic and mitral valves on the left and the pulmonary and tricuspid valves on the right). DOID:989 MESH:D006349 MESH:D016127 NCI:C45525 SNOMEDCT_US_2016_03_01:195013005 SNOMEDCT_US_2016_03_01:368009 SNOMEDCT_US_2016_03_01:398995000 UMLS_CUI:C0018824 UMLS_CUI:C0079485 Valvular heart disease disease_ontology DOID:4079 heart valve disease DOID:4079 MESH:D044882 NCI:C53655 SNOMEDCT_US_2016_03_01:126877002 UMLS_CUI:C1257958 disorder of glucose metabolism (disorder) disease_ontology DOID:4194 glucose metabolism disease DOID:4194 A carcinoma that is composed of large, monotonous rounded or overtly polygonal-shaped cells with abundant cytoplasm. MESH:D018287 NCI:C3780 SNOMEDCT_US_2016_03_01:189551005 SNOMEDCT_US_2016_03_01:22687000 UMLS_CUI:C0206704 disease_ontology DOID:4552 large cell carcinoma DOID:4552 NCI:C4450 SNOMEDCT_US_2016_03_01:254629004 UMLS_CUI:C0345958 large cell carcinoma of lung (disorder) large cell lung carcinoma disease_ontology DOID:4556 lung large cell carcinoma DOID:4556 An artery disease that is characterized by degeneration of the cells composing the aortic wall. MESH:D001018 NCI:C101253 SNOMEDCT_US_2016_03_01:47040006 UMLS_CUI:C0003493 aortic disorder disorder of the aorta (disorder) disease_ontology DOID:520 aortic disease DOID:520 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. DOID:10509 DOID:11742 DOID:5871 MESH:D011014 NCI:C3333 SNOMEDCT_US_2016_03_01:155548002 SNOMEDCT_US_2016_03_01:155552002 SNOMEDCT_US_2016_03_01:155558003 SNOMEDCT_US_2016_03_01:233604007 SNOMEDCT_US_2016_03_01:266391003 SNOMEDCT_US_2016_03_01:274103002 SNOMEDCT_US_2016_03_01:60363000 UMLS_CUI:C0032285 acute pneumonia disease_ontology DOID:552 pneumonia DOID:552 A urinary system disease that is located_in the kidney. EFO:0003086 ICD10CM:N08 ICD10CM:N28.9 MESH:D007674 NCI:C3149 NCI:C34843 SNOMEDCT_US_2016_03_01:155871008 SNOMEDCT_US_2016_03_01:266612003 SNOMEDCT_US_2016_03_01:266624005 SNOMEDCT_US_2016_03_01:266627003 SNOMEDCT_US_2016_03_01:274108006 SNOMEDCT_US_2016_03_01:90708001 UMLS_CUI:C0022658 nephropathy disease_ontology DOID:557 kidney disease DOID:557 An eye and adnexa disease that is located_in the eye. DOID:2933 ICD10CM:H44 ICD10CM:H44.9 ICD9CM:360 ICD9CM:360.9 ICD9CM:379.90 MESH:D005128 NCI:C26767 SNOMEDCT_US_2016_03_01:111509007 SNOMEDCT_US_2016_03_01:155101007 SNOMEDCT_US_2016_03_01:155198005 SNOMEDCT_US_2016_03_01:193265001 SNOMEDCT_US_2016_03_01:193266000 SNOMEDCT_US_2016_03_01:193316008 SNOMEDCT_US_2016_03_01:194183009 SNOMEDCT_US_2016_03_01:264555006 SNOMEDCT_US_2016_03_01:366261005 SNOMEDCT_US_2016_03_01:371405004 SNOMEDCT_US_2016_03_01:371409005 SNOMEDCT_US_2016_03_01:79517001 UMLS_CUI:C0015397 disease_ontology DOID:5614 eye disease DOID:5614 A neuropathy that is located_in one of the twelve cranial nerves. ICD10CM:G52.9 ICD9CM:352.9 MESH:D003389 NCI:C26733 SNOMEDCT_US_2016_03_01:193104009 SNOMEDCT_US_2016_03_01:267598004 SNOMEDCT_US_2016_03_01:267709002 SNOMEDCT_US_2016_03_01:276379008 SNOMEDCT_US_2016_03_01:73013002 UMLS_CUI:C0010266 Cranial nerve disorder disorder of cranial nerve disease_ontology DOID:5656 cranial nerve disease DOID:5656 An eye disease that is located_in the retina. ICD10CM:H35.9 ICD9CM:362.9 MESH:D012164 NCI:C26875 NCI:C62601 SNOMEDCT_US_2016_03_01:193430004 SNOMEDCT_US_2016_03_01:267715002 SNOMEDCT_US_2016_03_01:29555009 SNOMEDCT_US_2016_03_01:35426003 SNOMEDCT_US_2016_03_01:399625000 UMLS_CUI:C0035309 disease_ontology DOID:5679 retinal disease DOID:5679 A nervous system disease that affects the peripheral nervous system. DOID:13069 ICD10CM:G64 ICD9CM:350-359.99 MESH:D010523 NCI:C119734 NCI:C27580 NCI:C27587 SNOMEDCT_US_2016_03_01:155064004 SNOMEDCT_US_2016_03_01:155080009 SNOMEDCT_US_2016_03_01:155100008 SNOMEDCT_US_2016_03_01:193088006 SNOMEDCT_US_2016_03_01:193264002 SNOMEDCT_US_2016_03_01:264554005 SNOMEDCT_US_2016_03_01:267706009 SNOMEDCT_US_2016_03_01:302226006 SNOMEDCT_US_2016_03_01:42658009 UMLS_CUI:C0031117 UMLS_CUI:C1335029 disease_ontology peripheral nerve disease peripheral neuropathy DOID:574 peripheral nervous system disease DOID:574 ICD10CM:R80 ICD10CM:R80.9 ICD9CM:791.0 MESH:D011507 NCI:C38012 SNOMEDCT_US_2016_03_01:144515004 SNOMEDCT_US_2016_03_01:158565005 SNOMEDCT_US_2016_03_01:158568007 SNOMEDCT_US_2016_03_01:167279003 SNOMEDCT_US_2016_03_01:207310001 SNOMEDCT_US_2016_03_01:207315006 SNOMEDCT_US_2016_03_01:232691000 SNOMEDCT_US_2016_03_01:236719005 SNOMEDCT_US_2016_03_01:29738008 UMLS_CUI:C0033687 disease_ontology DOID:576 proteinuria DOID:576 ICD10CM:D55-D59 MESH:D000743 NCI:C34376 OMIM:266120 OMIM:612631 SNOMEDCT_US_2016_03_01:191231008 SNOMEDCT_US_2016_03_01:191416001 SNOMEDCT_US_2016_03_01:61261009 UMLS_CUI:C0002878 ANEMIA HEMOLYTIC disease_ontology DOID:583 OMIM mapping confirmed by DO. [SN]. OMIM mapping by NeuroDevNet. [LS]. hemolytic anemia DOID:583 A coronary artery disease characterized by myocardial cell death (myocardial necrosis) due to prolonged ischaemia. EFO:0000612 ICD10CM:I21 ICD10CM:I22 MESH:D009203 NCI:C27996 OMIM:608557 SNOMEDCT_US_2016_03_01:155304006 SNOMEDCT_US_2016_03_01:194796000 SNOMEDCT_US_2016_03_01:22298006 SNOMEDCT_US_2016_03_01:233824008 SNOMEDCT_US_2016_03_01:266288001 SNOMEDCT_US_2016_03_01:66514008 UMLS_CUI:C0027051 Myocardial infarct heart attack disease_ontology DOID:5844 Xref MGI. myocardial infarction DOID:5844 A heart disease that is characterized by any structural or functional cardiac disorder that impairs the ability of the heart to fill with or pump a sufficient amount of blood throughout the body. DOID:395 ICD10CM:I50 ICD10CM:I50.9 ICD9CM:428 ICD9CM:428.0 ICD9CM:428.9 MESH:D006333 NCI:C3080 NCI:C50577 SNOMEDCT_US_2016_03_01:155374007 SNOMEDCT_US_2016_03_01:155375008 SNOMEDCT_US_2016_03_01:155377000 SNOMEDCT_US_2016_03_01:195108009 SNOMEDCT_US_2016_03_01:195117009 SNOMEDCT_US_2016_03_01:266248006 SNOMEDCT_US_2016_03_01:266308000 SNOMEDCT_US_2016_03_01:42343007 SNOMEDCT_US_2016_03_01:84114007 UMLS_CUI:C0018801 UMLS_CUI:C0018802 CHF Cardiac Failure Congestive Congestive heart disease Weak heart disease_ontology DOID:6000 congestive heart failure DOID:6000 DOID:11505 DOID:58 DOID:59 ICD10CM:I05 ICD10CM:I05.1 ICD10CM:I05.9 ICD9CM:394 ICD9CM:394.1 ICD9CM:424.0 NCI:C78446 SNOMEDCT_US_2016_03_01:11851006 SNOMEDCT_US_2016_03_01:155276006 SNOMEDCT_US_2016_03_01:155278007 SNOMEDCT_US_2016_03_01:155279004 SNOMEDCT_US_2016_03_01:194724009 SNOMEDCT_US_2016_03_01:194729004 SNOMEDCT_US_2016_03_01:194982000 SNOMEDCT_US_2016_03_01:250998008 SNOMEDCT_US_2016_03_01:266278002 SNOMEDCT_US_2016_03_01:266279005 SNOMEDCT_US_2016_03_01:31085000 SNOMEDCT_US_2016_03_01:83898004 UMLS_CUI:C0026265 UMLS_CUI:C0155563 UMLS_CUI:C0264765 Mitral RH valve dis. Rheumatic disease of mitral valve (disorder) Rheumatic mitral insufficiency Rheumatic mitral valve changes Rheumatic mitral valve regurgitation chronic rheumatic mitral valve (disorder) disease of mitral valve rheumatic disease of mitral valve rheumatic mitral valve incompetence disease_ontology DOID:61 mitral valve disease DOID:61 MESH:D001796 UMLS_CUI:C0005830 blood protein disorder disease_ontology DOID:620 blood protein disease DOID:620 A disease that has_material_basis_in genetic variations in the human genome. MESH:D030342 NCI:C3101 SNOMEDCT_US_2016_03_01:264530000 SNOMEDCT_US_2016_03_01:32895009 UMLS_CUI:C0019247 disease_ontology DOID:630 genetic disease DOID:630 A disease of metabolism that is characterized by enzyme deficiency or accumulation of enzymes or toxins which interfere with normal function due to inherited enzyme abnormality. MESH:D008661 NCI:C34816 SNOMEDCT_US_2016_03_01:363205007 SNOMEDCT_US_2016_03_01:86095007 UMLS_CUI:C0025521 Inborn Errors of Metabolism Metabolic hereditary disorder inborn metabolism disorder disease_ontology DOID:655 inherited metabolic disorder DOID:655 An artery disease that is characterized by dysfunction of the blood vessels supplying the brain. DOID:12214 DOID:3455 DOID:8231 EFO:0000712 ICD10CM:I60-I69 ICD10CM:I63.9 ICD10CM:I67.9 ICD9CM:430-438.99 ICD9CM:437.9 MESH:D002561 MESH:D020521 NCI:C2938 NCI:C3390 OMIM:601367 SNOMEDCT_US_2016_03_01:155388006 SNOMEDCT_US_2016_03_01:155405006 SNOMEDCT_US_2016_03_01:155412002 SNOMEDCT_US_2016_03_01:195208004 SNOMEDCT_US_2016_03_01:195249004 SNOMEDCT_US_2016_03_01:195595007 SNOMEDCT_US_2016_03_01:230690007 SNOMEDCT_US_2016_03_01:266312006 SNOMEDCT_US_2016_03_01:266315008 SNOMEDCT_US_2016_03_01:270883006 SNOMEDCT_US_2016_03_01:313267000 SNOMEDCT_US_2016_03_01:62914000 SNOMEDCT_US_2016_03_01:82797006 UMLS_CUI:C0007820 UMLS_CUI:C0038454 CVA (cerebral vascular accident) Cerebrovascular accident (disorder) cerebrovascular accident cerebrovascular disorder stroke disease_ontology DOID:6713 OMIM mapping confirmed by DO. [SN]. cerebrovascular disease DOID:6713 ICD10CM:H35.81 ICD9CM:362.83 MESH:D010211 SNOMEDCT_US_2016_03_01:193426002 SNOMEDCT_US_2016_03_01:6141006 UMLS_CUI:C0242420 disease_ontology DOID:6929 retinal edema DOID:6929 A disease that manifests in a defined anatomical structure. DOID:1 DOID:2 DOID:5 DOID:71 DOID:72 DOID:8 disease_ontology DOID:7 disease of anatomical entity DOID:7 NCI:C35142 SNOMEDCT_US_2016_03_01:300980002 UMLS_CUI:C0085577 ANEMIA NORMOCYTIC Normocytic anemia (disorder) disease_ontology DOID:720 normocytic anemia DOID:720 An immune system disease that has_material_basis_in hematopoietic cells. ICD10CM:D75.9 ICD9CM:280-289.99 ICD9CM:289.9 MESH:D006402 NCI:C26323 SNOMEDCT_US_2016_03_01:154785002 SNOMEDCT_US_2016_03_01:154842002 SNOMEDCT_US_2016_03_01:191124002 SNOMEDCT_US_2016_03_01:191402006 SNOMEDCT_US_2016_03_01:191446003 SNOMEDCT_US_2016_03_01:267552000 SNOMEDCT_US_2016_03_01:267573000 SNOMEDCT_US_2016_03_01:34093004 UMLS_CUI:C0018939 Blood disease Blood dyscrasia NOS DISEASE OF THE BLOOD AND BLOOD-FORMING ORGANS Hematological disease blood disorder disease of hematopoietic system disease_ontology DOID:74 hematopoietic system disease DOID:74 A disease of anatomical entity that is located_in the gastrointestinal tract. DOID:27 DOID:944 ICD10CM:K92.9 ICD9CM:520-579.99 MESH:D004066 SNOMEDCT_US_2016_03_01:155629009 SNOMEDCT_US_2016_03_01:155847001 SNOMEDCT_US_2016_03_01:197575000 SNOMEDCT_US_2016_03_01:266483008 SNOMEDCT_US_2016_03_01:53619000 UMLS_CUI:C0012242 GIT disease Gastroenteropathy alimentary system disease digestive system disorder gastrointestinal disease gastrointestinal disorder disease_ontology DOID:77 gastrointestinal system disease DOID:77 A uterine disease that is located_in the placenta. DOID:1815 DOID:5366 DOID:9219 ICD10CM:O43 ICD10CM:O43.9 ICD10CM:O43.90 ICD9CM:646.9 MESH:D010922 MESH:D011248 NCI:C26857 NCI:C27619 NCI:C34941 NCI:C35169 SNOMEDCT_US_2016_03_01:125586008 SNOMEDCT_US_2016_03_01:156069003 SNOMEDCT_US_2016_03_01:156097009 SNOMEDCT_US_2016_03_01:156123001 SNOMEDCT_US_2016_03_01:156131006 SNOMEDCT_US_2016_03_01:172422001 SNOMEDCT_US_2016_03_01:173300003 SNOMEDCT_US_2016_03_01:198881004 SNOMEDCT_US_2016_03_01:199152008 SNOMEDCT_US_2016_03_01:23288008 SNOMEDCT_US_2016_03_01:267293009 SNOMEDCT_US_2016_03_01:267311008 SNOMEDCT_US_2016_03_01:267314000 SNOMEDCT_US_2016_03_01:90821003 UMLS_CUI:C0032045 UMLS_CUI:C0032962 UMLS_CUI:C0151864 UMLS_CUI:C1335423 disease_ontology DOID:780 placenta disease DOID:780 end stage renal disease disease_ontology DOID:783 end stage renal failure DOID:783 EFO:0003884 ICD10CM:N18.9 ICD9CM:585.6 MESH:D007676 NCI:C9438 SNOMEDCT_US_2016_03_01:155856009 SNOMEDCT_US_2016_03_01:197654000 SNOMEDCT_US_2016_03_01:197655004 SNOMEDCT_US_2016_03_01:197755007 SNOMEDCT_US_2016_03_01:46177005 SNOMEDCT_US_2016_03_01:90688005 UMLS_CUI:C0022661 CKD CRF chronic kidney failure chronic renal disease chronic renal failure syndrome renal failure - chronic disease_ontology DOID:784 chronic kidney disease DOID:784 A substance abuse that involves the recurring use of cocaine despite negative consequences. ICD10CM:F14.1 ICD9CM:305.6 ICD9CM:305.60 MESH:D019970 SNOMEDCT_US_2016_03_01:78267003 UMLS_CUI:C0009171 disease_ontology DOID:809 cocaine abuse DOID:809 MESH:D015356 NCI:C34978 SNOMEDCT_US_2016_03_01:232035005 UMLS_CUI:C0035302 Retinal artery occlusion (disorder) disease_ontology DOID:8483 retinal artery occlusion DOID:8483 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. DOID:11894 DOID:11895 DOID:29 DOID:766 ICD10CM:J98.4 MESH:D008171 NCI:C3198 SNOMEDCT_US_2016_03_01:196164004 SNOMEDCT_US_2016_03_01:19829001 SNOMEDCT_US_2016_03_01:266374002 UMLS_CUI:C0024115 disease_ontology DOID:850 Updating out dated CUI and removing lung abscess as a synonym. lung disease DOID:850 A gastrointestinal system cancer that is located_in the oral cavity. DOID:0050627 DOID:8617 DOID:9049 DOID:9055 ICD10CM:C04 ICD10CM:C04.0 ICD10CM:C04.1 ICD10CM:C04.9 ICD9CM:144 ICD9CM:144.0 ICD9CM:144.1 ICD9CM:144.9 NCI:C9318 SNOMEDCT_US_2016_03_01:187652003 SNOMEDCT_US_2016_03_01:187653008 SNOMEDCT_US_2016_03_01:187656000 SNOMEDCT_US_2016_03_01:363385007 SNOMEDCT_US_2016_03_01:93672006 SNOMEDCT_US_2016_03_01:93802007 SNOMEDCT_US_2016_03_01:93860002 UMLS_CUI:C0153368 UMLS_CUI:C0153369 UMLS_CUI:C0496758 malignant neoplasm of anterior portion of floor of mouth malignant neoplasm of floor of mouth malignant neoplasm of lateral floor of mouth malignant neoplasm of lateral portion of floor of mouth malignant tumor of anterior floor of mouth (disorder) malignant tumor of lateral floor of mouth (disorder) malignant tumor of the Floor of the Mouth disease_ontology DOID:8618 oral cavity cancer DOID:8618 A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system. ICD10CM:G00-G99 ICD10CM:G98 ICD10CM:G98.8 ICD9CM:349.9 MESH:D009422 NCI:C26835 SNOMEDCT_US_2016_03_01:118940003 SNOMEDCT_US_2016_03_01:154981003 SNOMEDCT_US_2016_03_01:155262005 SNOMEDCT_US_2016_03_01:192641002 SNOMEDCT_US_2016_03_01:267679005 SNOMEDCT_US_2016_03_01:286946008 UMLS_CUI:C0027765 disease_ontology DOID:863 nervous system disease DOID:863 DOID:8648 DOID:8779 DOID:8900 DOID:8940 DOID:8999 DOID:9058 DOID:9068 DOID:9196 ICD10CM:C01 ICD10CM:C02.0 ICD10CM:C02.1 ICD10CM:C02.2 ICD10CM:C02.4 ICD10CM:C02.9 ICD9CM:141 ICD9CM:141.0 ICD9CM:141.1 ICD9CM:141.2 ICD9CM:141.3 ICD9CM:141.5 ICD9CM:141.6 ICD9CM:141.9 MESH:D014062 NCI:C3524 NCI:C9345 SNOMEDCT_US_2016_03_01:187632004 SNOMEDCT_US_2016_03_01:187633009 SNOMEDCT_US_2016_03_01:187636001 SNOMEDCT_US_2016_03_01:187637005 SNOMEDCT_US_2016_03_01:187638000 SNOMEDCT_US_2016_03_01:187642002 SNOMEDCT_US_2016_03_01:187644001 SNOMEDCT_US_2016_03_01:187646004 SNOMEDCT_US_2016_03_01:363375006 SNOMEDCT_US_2016_03_01:363376007 SNOMEDCT_US_2016_03_01:363377003 SNOMEDCT_US_2016_03_01:371974006 SNOMEDCT_US_2016_03_01:93687001 SNOMEDCT_US_2016_03_01:93773005 SNOMEDCT_US_2016_03_01:93848003 SNOMEDCT_US_2016_03_01:93868009 SNOMEDCT_US_2016_03_01:94100005 SNOMEDCT_US_2016_03_01:94101009 SNOMEDCT_US_2016_03_01:94134006 UMLS_CUI:C0153349 UMLS_CUI:C0153350 UMLS_CUI:C0153351 UMLS_CUI:C0153356 UMLS_CUI:C0474963 UMLS_CUI:C0496755 UMLS_CUI:C0684333 Tongue neoplasm malignant stage Unspecified malignant neoplasm of anterior 2/3 of tongue unspecified (disorder) malignant neoplasm of anterior two-thirds of tongue, part unspecified malignant neoplasm of base of tongue malignant neoplasm of border of tongue malignant neoplasm of dorsal surface of tongue malignant neoplasm of dorsal tongue NOS malignant neoplasm of dorsum of tongue NOS (disorder) malignant neoplasm of fixed part of tongue NOS malignant neoplasm of fixed part of tongue NOS (disorder) malignant neoplasm of junctional zone of tongue malignant neoplasm of lingual tonsil malignant neoplasm of mobile part of tongue NOS malignant neoplasm of other sites of tongue malignant neoplasm of other sites of tongue (disorder) malignant neoplasm of tip and lateral border of tongue malignant neoplasm of tip and/or lateral border of tongue malignant neoplasm of tongue malignant neoplasm of tongue NOS malignant neoplasm of tongue NOS (disorder) malignant neoplasm of tongue, NOS malignant neoplasm of tongue, tip and lateral border (disorder) malignant neoplasm of ventral surface of tongue malignant neoplasm of ventral tongue surface NOS (disorder) malignant tumor of Posterior Tongue malignant tumor of anterior two-thirds of tongue (disorder) malignant tumor of base of tongue (disorder) malignant tumor of lingual tonsil malignant tumor of lingual tonsil (disorder) malignant tumor of mobile part of tongue malignant tumor of tongue (disorder) disease_ontology DOID:8649 tongue cancer DOID:8649 A vascular disease that is located_in a vein. ICD10CM:I82 ICD9CM:453 SNOMEDCT_US_2016_03_01:195435006 UMLS_CUI:C0155774 disease_ontology DOID:866 vein disease DOID:866 A nervous system disease that is located_in nerves or nerve cells. ICD10CM:G62.9 NCI:C4731 SNOMEDCT_US_2016_03_01:193167000 SNOMEDCT_US_2016_03_01:264554005 SNOMEDCT_US_2016_03_01:277317008 SNOMEDCT_US_2016_03_01:277878001 SNOMEDCT_US_2016_03_01:386033004 SNOMEDCT_US_2016_03_01:42658009 UMLS_CUI:C0442874 peripheral neuropathy disease_ontology DOID:870 neuropathy DOID:870 DOID:14750 DOID:8711 DOID:9137 ICD10CM:Q85.00 ICD10CM:Q85.01 ICD10CM:Q85.02 ICD9CM:237.7 ICD9CM:237.70 ICD9CM:237.71 ICD9CM:237.72 MESH:C537392 MESH:D009456 MESH:D016518 MESH:D017253 NCI:C3273 NCI:C3274 NCI:C6727 OMIM:101000 OMIM:162200 OMIM:162210 OMIM:162260 OMIM:162270 ORDO:636 ORDO:637 ORDO:93921 SNOMEDCT_US_2016_03_01:154642000 SNOMEDCT_US_2016_03_01:19133005 SNOMEDCT_US_2016_03_01:700060008 SNOMEDCT_US_2016_03_01:700061007 SNOMEDCT_US_2016_03_01:81669005 SNOMEDCT_US_2016_03_01:92503002 SNOMEDCT_US_2016_03_01:92824003 UMLS_CUI:C0027831 UMLS_CUI:C0027832 UMLS_CUI:C0162678 UMLS_CUI:C0220695 Acoustic neurofibromatosis Neurofibromatosis 1 Recklinghausen's neurofibromatosis central Neurofibromatosis neurofibromatosis type 1 neurofibromatosis type 2 neurofibromatosis type 4 neurofibromatosis type IV peripheral Neurofibromatosis type IV neurofibromatosis of riccardi von Reklinghausen disease disease_ontology DOID:8712 Xref MGI. OMIM mapping confirmed by DO. [SN]. neurofibromatosis DOID:8712 A pneumonia involving inflammation of the lungs caused by bacteria. DOID:13815 ICD10CM:J15.9 ICD9CM:482.9 MESH:D018410 NCI:C26704 SNOMEDCT_US_2016_03_01:155553007 SNOMEDCT_US_2016_03_01:195891009 SNOMEDCT_US_2016_03_01:195892002 SNOMEDCT_US_2016_03_01:53084003 UMLS_CUI:C0004626 Pneumonia due to other gram-negative bacteria gram-negative pneumonia disease_ontology DOID:874 bacterial pneumonia DOID:874 ICD10CM:N84.0 ICD9CM:621.0 NCI:C3662 SNOMEDCT_US_2016_03_01:11314008 SNOMEDCT_US_2016_03_01:266659005 UMLS_CUI:C0156369 endometrial/uterine polyp polyp of Endometrium polyp of corpus uteri polyp of the Uterus polyp, uterus disease_ontology DOID:9042 polyp of corpus uteri DOID:9042 A glucose metabolism disease characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both. ICD10CM:E08-E13 ICD10CM:E11 ICD9CM:250 MESH:D003920 NCI:C2985 SNOMEDCT_US_2016_03_01:154671004 SNOMEDCT_US_2016_03_01:191044006 SNOMEDCT_US_2016_03_01:267467004 SNOMEDCT_US_2016_03_01:73211009 UMLS_CUI:C0011849 disease_ontology DOID:9351 diabetes mellitus DOID:9351 A diabetes mellitus that involves high blood glucose resulting from cells fail to use insulin properly. EFO:0001360 ICD10CM:E11 KEGG:04930 MESH:D003924 NCI:C26747 OMIM:125853 OMIM:601283 OMIM:601407 OMIM:603694 OMIM:608036 SNOMEDCT_US_2016_03_01:154672006 SNOMEDCT_US_2016_03_01:190323008 SNOMEDCT_US_2016_03_01:190384004 SNOMEDCT_US_2016_03_01:267468009 SNOMEDCT_US_2016_03_01:44054006 UMLS_CUI:C0011860 NIDDM non-insulin-dependent diabetes mellitus type II diabetes mellitus disease_ontology DOID:9352 Xref MGI. OMIM mapping confirmed by DO. [SN]. type 2 diabetes mellitus DOID:9352 A central nervous system disease that is located_in the brain. DOID:8510 ICD10CM:G93.40 ICD10CM:G93.9 ICD9CM:348.3 ICD9CM:348.30 ICD9CM:348.9 MESH:D001927 NCI:C26920 NCI:C96413 SNOMEDCT_US_2016_03_01:155053002 SNOMEDCT_US_2016_03_01:193051008 SNOMEDCT_US_2016_03_01:193059005 SNOMEDCT_US_2016_03_01:76011009 SNOMEDCT_US_2016_03_01:81308009 UMLS_CUI:C0006111 UMLS_CUI:C0085584 encephalopathy disease_ontology DOID:936 brain disease DOID:936 MESH:D019586 NCI:C84791 SNOMEDCT_US_2016_03_01:155052007 SNOMEDCT_US_2016_03_01:267701004 SNOMEDCT_US_2016_03_01:271719001 SNOMEDCT_US_2016_03_01:28073009 UMLS_CUI:C0151740 Raised intracranial pressure disease_ontology DOID:9428 intracranial hypertension DOID:9428 MESH:D009455 NCI:C3272 SNOMEDCT_US_2016_03_01:115242003 SNOMEDCT_US_2016_03_01:134214003 SNOMEDCT_US_2016_03_01:189947001 SNOMEDCT_US_2016_03_01:404029005 SNOMEDCT_US_2016_03_01:89084002 UMLS_CUI:C0027830 disease_ontology DOID:962 neurofibroma DOID:962 ENVO:00000428 biome ENVO:01000254 environmental system GAZ:00000448 geographic location A reference to a place on the Earth, by its name or by its geographical location. geographic location GO:0003008 system process GO:0003013 circulatory system process GO:0006950 response to stress GO:0006952 defense response GO:0006954 inflammatory response GO:0007585 respiratory gaseous exchange GO:0007596 blood coagulation GO:0007599 hemostasis GO:0007610 behavior GO:0007631 feeding behavior GO:0008015 blood circulation GO:0008150 biological_process GO:0032501 multicellular organismal process GO:0032502 developmental process GO:0040007 growth GO:0040011 locomotion GO:0044403 symbiosis, encompassing mutualism through parasitism GO:0044419 interspecies interaction between organisms GO:0050817 coagulation GO:0050878 regulation of body fluid levels GO:0050896 response to stimulus GO:0051702 interaction with symbiont GO:0051704 multi-organism process GO:0051705 multi-organism behavior GO:0051816 acquisition of nutrients from other organism during symbiotic interaction GO:0051850 acquisition of nutrients from symbiont GO:0065007 biological regulation GO:0065008 regulation of biological quality GO:0072519 parasitism GO:0085030 mutualism GO:0085031 commensalism HP:0000822 hypertensive phenotype The presence of chronic increased pressure in the systemic arterial system. Hypertension HTN:00000000 Amanda Hicks A blood pressure measurement datum that is a quality measure of some diastolic blood pressure diastolic blood pressure measurement datum HTN:00000001 A blood pressure measurement datum that is a quality measure of some systolic blood pressure Amanda Hicks systolic blood pressure measurement datum 120.0 HTN:00000003 A systolic blood pressure measurement datum that is about a blood pressure that inheres in an adult with a measurement value that is equal to or above some specified threshold for adults elevated adult systolic blood pressure measurement datum 2 HTN:00000004 A phenotype of hypertension that has been documented Amanda Hicks documented hypertensive phenotype HTN:00000005 Amanda Hicks A human who is equal to or older than 18 years old adult over 18 years of age HTN:00000006 An elevated blood pressure phenotype of systolic blood pressure that is above some specifed threshold Amanda Hicks elevated systolic phenotype HTN:00000009 Amanda Hicks A systolic blood pressure measurement datum with a measurement value that is equal to or above some specified threshold elevated systolic blood pressure measurement datum HTN:00000014 A phenotype of blood pressure that is above some specified threshold Amanda Hicks elevated blood pressure phenotype HTN:00000015 A blood pressure measurement datum with a measurement value that is equal to or above some specified threshold elevated blood pressure measurement datum HTN:00000016 An elevated blood pressure phenotype of diastolic blood pressure that is above some specifed threshold Amanda Hicks elevated diastolic phenotype HTN:00000035 A diagnosis that asserts of some patient that they have a disposition to chronically elevated blood pressure diagnosis of hypertension 130.0 139.0 HTN:00000040 2017 Guideline for High Blood Pressure in Adults http://www.onlinejacc.org/content/71/19/e127?_ga=2.55616109.754894593.1553089039-383350264.1553089039 An elevated adult diastolic blood pressure measurement datum that is quality measurement of a diastolic blood pressure is equal to above 120 mm Hg and equal to or less than 139 mm Hg Amanda Hicks stage 1 elevated adult systolic blood pressure meaurement datum per ACC 2017 guidelines HTN:00000043 A diastolic blood pressure measurement datum with a measurement value that is equal to or above some specified threshold elevated diastolic blood pressure measurement datum 80.0 HTN:00000044 Amanda Hicks An elevated diastolic blood pressure measurement datum that is quality measurement of a diastolic blood pressure that inheres in an adult with a measurement value that is equal to or above some specified threshold for adults elevated adult diastolic blood pressure measurement datum 80.0 89.0 HTN:00000045 2017 Guideline for High Blood Pressure in Adults http://www.onlinejacc.org/content/71/19/e127?_ga=2.55616109.754894593.1553089039-383350264.1553089039 An elevated adult diastolic blood pressure measurement datum that is quality measurement of a diastolic blood pressure is equal to above 80 mm Hg and equal to or less than 89 mm Hg stage 1 elevated adult diastolic blood pressure measurement datum per 2017 guidelines 90.0 HTN:00000046 stage 2 elevated adult diastolic blood pressure measurement datum per 2017 guidelines 140.0 HTN:00000047 stage 2 elevated adult systolic blood pressure meaurement datum per ACC 2017 guidelines 80.0 129.0 HTN:00000048 120–129 mm Hg and <80 mm Hg elevated adult blood pressure measurement datum per 2017 guidelines HTN:00000049 130–139 mm Hg or 80–89 mm Hg stage 1 adult blood pressure measurement datum per 2017 guidelines HTN:00000050 stage 2 adult blood pressure measurement datum per 2017 guidelines 18.0 HTN:00000051 An age measurement datum that is about a human being has a measurement value equal to or greater than 18 years Amanda Hicks adult over 18 years of age measurement datum IAO:0000001 conditional specification a directive information entity that specifies what should happen if the trigger condition is fulfilled PlanAndPlannedProcess Branch OBI branch derived OBI_0000349 conditional specification IAO:0000003 measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label IAO:0000005 objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. 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. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification IAO:0000006 narrative object Examples of narrative objects are reports, journal articles, and patents submission. A narrative object is an information content entity that is a set of propositions. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions person:Chris Stoeckert OBI_0000013 group:OBI narrative object IAO:0000007 Pour the contents of flask 1 into flask 2 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 http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. 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:0000013 journal article Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. a report that is published in a journal person:Alan Ruttenberg person:Chris Stoeckert OBI_0000159 group:OBI journal article IAO:0000015 information carrier In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. A quality of an information bearer that imparts the information content 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. PERSON: Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy information carrier IAO:0000017 model number A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers Person: Alan Ruttenberg model number IAO:0000025 programming language R, Perl, Java A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. person:Alan Ruttenberg person:Chris Stoeckert OBI_0000058 group:OBI programming language IAO:0000027 data item data item Data items include counts of things, analyte concentrations, and statistical summaries. 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: Chris Stoeckert PERSON: Jonathan Rees data data item IAO:0000028 symbol a serial number such as "12324X" a stop sign a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). 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 Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 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. PERSON: Chris Stoeckert OBI_0000142 information content entity IAO:0000031 integer numeral a numeral that denotes an integer PERSON: Jonathan Rees integer numeral 1 1 IAO:0000032 10 feet. 3 ml. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. 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 content entity directive information entity IAO:0000034 time trigger revisit? PlanAndPlannedProcess Branch OBI branch derived OBI_0000331 time trigger IAO:0000037 dot plot Dot plot of SSC-H and FSC-H. A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. person:Allyson Lister person:Chris Stoeckert OBI_0000123 group:OBI dot plot IAO:0000038 graph A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. PERSON: Lawrence Hunter person:Alan Ruttenberg person:Allyson Lister OBI_0000240 group:OBI graph IAO:0000055 rule example to be added a rule is an executable which guides, defines, restricts actions MSI PRS OBI_0500021 PRS rule IAO:0000057 contour plot Contour plot of SSC-H, FSC-H, and FL1-H. generically_dependent_continuants person:Allyson Lister person:Chris Stoeckert OBI_0000246 group:Flow Cytometry community contour plot IAO:0000064 algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. Philippe Rocca-Serra PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm IAO:0000065 software interpreter R program, Perl interpreter, Java virtual machine A software interpreter is a software application that executes some specified input software. Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter person:Alan Ruttenberg person:Chris Stoeckert OBI_0000199 group:OBI software interpreter 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:0000079 density plot Density plot of SSC-H and FSC-H. A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. person:Allyson Lister person:Chris Stoeckert OBI_0000179 group:Flow Cytometry community density plot IAO:0000088 report Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record) 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted. 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification PERSON: Alan Ruttenberg PERSON: Melanie Courtot PERSON:Chris Stoeckert GROUP: OBI OBI_0000099 report IAO:0000096 source code module The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. A source code module is a directive information entity that specifies, using a programming language, some algorithm. person:Alan Ruttenberg person:Chris Stoeckert OBI_0000039 group:OBI source code module IAO:0000098 data format specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" PERSON: Alan Ruttenberg PlanAndPlannedProcess Branch OBI branch derived OBI_0000187 data format specification IAO:0000100 data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). 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. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set IAO:0000101 image An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. person:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI image IAO:0000102 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 PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. 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. 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. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg 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 measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum IAO:0000129 version number A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version GROUP: IAO version number IAO:0000131 serial number A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-) GROUP: IAO serial number IAO:0000132 lot number A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. GROUP: IAO batch number lot number IAO:0000140 A settings datum is a datum that denotes some configuration of an instrument. 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable. Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. setting datum IAO:0000144 conclusion textual entity that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/23 Alan Ruttenberg: We need to work on the definition still Person:Alan Ruttenberg conclusion textual entity IAO:0000178 material information bearer A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. a brain a hard drive A material entity in which a concretization of an information content entity inheres. GROUP: IAO material information bearer IAO:0000179 histogram A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI histogram IAO:0000180 heatmap A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI heatmap IAO:0000181 Venn diagram A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Venn_diagram Venn diagram IAO:0000183 dendrogram Dendrograms are often used in computational biology to illustrate the clustering of genes. A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Dendrogram dendrogram IAO:0000184 scatter plot Comparison of gene expression values in two samples can be displayed in a scatter plot A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot scattergraph WEB: http://en.wikipedia.org/wiki/Scatterplot scatter plot IAO:0000185 A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. PERSON:Alan Ruttenberg PERSON:Joanne Luciano PERSON:Melanie Courtot WEB: http://en.wiktionary.org/wiki/photograph photograph IAO:0000186 photographic print A photographic print is a material entity upon which a photograph generically depends. PERSON:Alan Ruttenberg PERSON:Melanie Courtot photographic print IAO:0000225 obsolescence reason specification The reason for which a term has been deprecated. 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. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification IAO:0000300 textual entity Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities 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. AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. PERSON: Lawrence Hunter text textual entity IAO:0000301 citation Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183. a textual entity intended to identify a particular publication PERSON: Lawrence Hunter citation IAO:0000302 author identification L. Hunter A textual entity intended to identify a particular author PERSON: Lawrence Hunter author identification IAO:0000303 institutional identification University of Colorado Denver School of Medicine A textual entity intended to identify a particular institution PERSON: Lawrence Hunter institutional identification IAO:0000304 caption Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool. A textual entity that describes a figure PERSON: Lawrence Hunter caption IAO:0000305 document title Textual characteristics of traditional and Open Access scientific journals are similar A textual entity that names a document PERSON: Lawrence Hunter document title IAO:0000306 table | T F --+----- T | T F F | F F A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions PERSON: Lawrence Hunter table IAO:0000307 table of abbreviations IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology A table where the constituent texts are abbreviations and their expansions PERSON: Lawrence Hunter table of abbreviations IAO:0000308 figure Any picture, diagram or table An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. PERSON: Lawrence Hunter figure IAO:0000309 diagram A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. A figure that expresses one or more propositions PERSON: Lawrence Hunter diagram IAO:0000310 document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document IAO:0000311 publication A journal article or book A document that has been accepted by a publisher PERSON: Lawrence Hunter publication IAO:0000312 publication about an investigation Most scientific journal articles A publication that is about an investigation PERSON: Lawrence Hunter scientific publication publication about an investigation IAO:0000313 patent US Patent 6,449,603 A document that has been accepted by a patent authority PERSON: Lawrence Hunter patent IAO:0000314 document part An abstract, introduction, method or results section. an information content entity that is part of a document PERSON: Lawrence Hunter document part IAO:0000315 abstract The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes. PERSON: Lawrence Hunter abstract IAO:0000316 introduction to a publication about an investigation Section labelled 'introduction' of a typical scientific journal article A part of a publication about an investigation that is about the objective specification (why the investigation is being done) PERSON: Lawrence Hunter background introduction introduction to a publication about an investigation IAO:0000317 methods section The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article. A part of a publication about an investigation that is about the study design of the investigation PERSON: Lawrence Hunter experimental experimental procedures experimental section methods methods section IAO:0000318 results section The section labelled 'results' in a typical scientific journal article A part of a publication about an investigation that is about a study design execution PERSON: Lawrence Hunter results results section IAO:0000319 discussion section of a publication about an investigation A part of a publication about an investigation that is about the study interpretation of the investigation PERSON: Lawrence Hunter discussion discussion section discussion section of a publication about an investigation IAO:0000320 references section The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography" A part of a document that has citations as parts PERSON: Lawrence Hunter references section IAO:0000321 author list Lawrence Hunter and Kevin Brettonel Cohen part of a document that enumerates the authors of the document PERSON: Lawrence Hunter author list IAO:0000322 institution list The University of Colorado Denver School of Medicine and the University of Colorado Boulder. part of a document that has parts that are institution identifications associated with the authors of the document PERSON: Lawrence Hunter institution list IAO:0000323 author contributions section LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript. A part of a publication that is about the specific contributions of each author PERSON: Lawrence Hunter author contributions contributions by the authors author contributions section IAO:0000324 acknowledgements section The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript Part of a publication that is about the contributions of people or institutions other than the authors. PERSON: Lawrence Hunter acknowledgements acknowledgments acknowledgements section IAO:0000325 footnote The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text. A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document. PERSON: Lawrence Hunter endnote footnote IAO:0000326 supplementary material to a document part of a document that is segregated from the rest of the document due to its size PERSON: Lawrence Hunter additional information appendix supplemental information supplementary material supporting information supplementary material to a document IAO:0000327 table of contents A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred). PERSON: Lawrence Hunter table of contents IAO:0000328 table of figures A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred). PERSON: Lawrence Hunter table of figures IAO:0000329 running title A shorter version of a document title PERSON: Lawrence Hunter running title IAO:0000330 copyright section This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License. A document part that describes legal restrictions on making or distributing copies of the document PERSON: Lawrence Hunter copyright section 1 IAO:0000400 A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 Alan Ruttenberg AR notes: We need to discuss whether it should include site. cartesian spatial coordinate datum http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 1 IAO:0000401 A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region Alan Ruttenberg one dimensional cartesian spatial coordinate datum 1 1 IAO:0000402 A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region Alan Ruttenberg two dimensional cartesian spatial coordinate datum 1 1 1 IAO:0000403 A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region Alan Ruttenberg three dimensional cartesian spatial coordinate datum IAO:0000408 A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg length measurement datum IAO:0000409 The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type IAO:0000414 A scalar measurement datum that is the result of measurement of mass quality 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg mass measurement datum IAO:0000415 hypothesis textual entity that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 A textual entity that expresses an assertion that is intended to be tested. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg hypothesis textual entity IAO:0000416 A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg time measurement datum IAO:0000422 A textual entity that is used as directive to deliver something to a person, or organization 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59 postal address IAO:0000429 email address Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583 Person:Alan Ruttenberg Person:Chris Stoeckart email address IAO:0000442 author role A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. PERSON: Alan Ruttenberg PERSON: Melanie Courtot author role IAO:0000443 a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing Person:Alan Ruttenberg data item extraction from journal article IAO:0000572 Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. a planned process in which a document is created or added to by including the specified input in it. 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape Bjoern Peters wikipedia http://en.wikipedia.org/wiki/Documenting documenting IAO:0000573 line graph A line graph is a type of graph created by connecting a series of data points together with a line. PERSON:Chris Stoeckert PERSON:Melanie Courtot line chart GROUP:OBI WEB: http://en.wikipedia.org/wiki/Line_chart line graph IAO:0000574 A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry. Person:Alan Ruttenberg Person:Bjoern Peters Person:Melanie Courtot assigning a CRID assigning a centrally registered identifier IAO:0000575 Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. A planned process in which a CRID registry associates an information content entity with a CRID symbol PERSON:Alan Ruttenberg associating information with a CRID in the CRID registry associating information with a centrally registered identifier in its registry IAO:0000577 The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. 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 CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol IAO:0000578 The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Original proposal from Bjoern, discussions at IAO calls centrally registered identifier IAO:0000579 PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls centrally registered identifier registry IAO:0000580 Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot looking up a CRID looking up a centrally registered identifier IAO:0000582 time stamped measurement datum IAO:0000584 pmid:20604925 - time-lapse live cell microscopy A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. Alan Ruttenberg experimental time series time sampled measurement data set IAO:0000590 written name "Bill Clinton" "The Eiffel Tower" "United States of America" A textual entity that denotes a particular in reality. PERSON: Bill Hogan https://github.com/information-artifact-ontology/IAO/issues/114 The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. written name IAO:0000591 A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software method IAO:0000592 A software module is software composed of a collection of software methods. PERSON: Melanei Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software module IAO:0000593 A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software library 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:0000595 A software script is software whose instructions can be executed using a software interpreter. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software script IAO:0000605 abbreviation textual entity From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect. A textual entity listing abbreviations and their expansions that are used in a document. PERSON: Bill Baumgartner abbreviation textual entity IAO:0000606 abbreviations section The section labelled 'abbreviations' in a typical scientific journal article. A part of a document where abbreviations and their long-forms used within the document are listed. PERSON: Bill Baumgartner abbreviations abbreviations list abbreviations used list of abbreviations list of abbreviations used abbreviations section IAO:0000607 author information section The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/) A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. PERSON: Bill Baumgartner author information authors’ information author information section IAO:0000608 author information textual entity From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD. A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. PERSON: Bill Baumgartner author information textual entity IAO:0000609 author summary section The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/) A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers. PERSON: Bill Baumgartner author summary summary synopsis Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines) author summary section IAO:0000610 author summary textual entity From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX. A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). PERSON: Bill Baumgartner Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). author summary textual entity IAO:0000611 availability section The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained. PERSON: Bill Baumgartner availability availability section IAO:0000612 availability textual entity From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): Project home page:http://krux.googlecode.com A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained. PERSON: Bill Baumgartner availability textual entity IAO:0000613 case report section The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/) A part of a document about the medical history of a specific patient as it relates to the topic of the document. PERSON: Bill Baumgartner case presentation case report case report section IAO:0000614 case report textual entity Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension. A textual entity that expresses a detailed account of a portion of the medical history for a specific patient. PERSON: Bill Baumgartner case report textual entity IAO:0000615 conclusion section The section labelled 'conclusion' in a typical scientific journal article. A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document. PERSON: Bill Baumgartner concluding remarks conclusion conclusions findings summary conclusion section IAO:0000616 conflict of interest section The section labelled 'conflict of interest statement' in a typical scientific journal article. A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document. PERSON: Bill Baumgartner competing interests conflict of interest conflict of interest statement declaration of competing interests disclosure of potential conflicts of interest conflict of interest section IAO:0000617 conflict of interest statement SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document. PERSON: Bill Baumgartner conflict of interest textual entity IAO:0000618 consent section The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/) A part of a document about the consent process that was used to enroll patients in a study. PERSON: Bill Baumgartner consent consent section IAO:0000619 consent textual entity From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal. A textual entity that documents the consenting process used to enroll patients in a study. PERSON: Bill Baumgartner consent textual entity IAO:0000620 ethical approval section The section labelled 'ethical approval' in a typical scientific journal article. A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis. PERSON: Bill Baumgartner ethical approval ethical approval section IAO:0000621 ethical approval textual entity From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review. A textual entity that documents the ethical approval of some study design. PERSON: Bill Baumgartner ethical approval textual entity IAO:0000622 figures section The section labelled 'figures' in a typical scientific journal article. A part of a document that contains one or more figures. PERSON: Bill Baumgartner figures figures section IAO:0000623 funding source declaration section The section labelled 'funding' in a typical scientific journal article. A part of a document used to detail information regarding the source of funding used in support of the generation of the document content. PERSON: Bill Baumgartner funding funding information funding sources funding statement funding/support source of funding sources of funding funding source declaration section IAO:0000624 funding souce declaration textual entity From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication. A textual entity documenting the source of funding that supported some study. PERSON: Bill Baumgartner funding source declaration textual entity IAO:0000625 future directions section The section labelled 'future directions' in a typical scientific journal article. A part of a document detailing extensions of the described work that may be implemented at some future point in time. PERSON: Bill Baumgartner future challenges future considerations future developments future directions future outlook future perspectives future plans future prospects future research future research directions future studies future work future directions section IAO:0000626 future directions textual entity Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members. A textual entity expressing ideas regarding future work relevant to work described in a document that could be done. PERSON: Bill Baumgartner future directions textual entity IAO:0000627 genome announcement section The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/) A document part announcing the publication of a novel draft genome sequence. PERSON: Bill Baumgartner genome announcement genome announcement section IAO:0000628 genome announcement textual entity Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB). A textual entity that describes the generation and public release of a novel, draft genome sequence. PERSON: Bill Baumgartner genome announcement textual entity IAO:0000629 keyword textual entity From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): Exon orthology; alternative splicing; exon duplication; intron-exon structure. A textual entity listing keywords indicating the major theme(s) of a document. PERSON: Bill Baumgartner keyword textual entity IAO:0000630 keywords section The section labelled 'keywords' in a typical scientific journal article. A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed. PERSON: Bill Baumgartner keywords keywords section IAO:0000631 study limitations section The section labelled 'limitations' in a typical scientific journal article. A part of a document about biases or short comings related to the study design and execution. PERSON: Bill Baumgartner limitations study limitations Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) study limitations section IAO:0000632 study limitations textual entity Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out. A textual entity addressing a shortcoming or bias of a study design or execution. PERSON: Bill Baumgartner Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) study limitations textual entity IAO:0000633 materials section The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/) A part of a document about the materials required to reproduce the content of the document. PERSON: Bill Baumgartner materials materials section IAO:0000634 notes section The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): 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 footnotes notes notes section IAO:0000635 patients section The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/) A part of a document about the patients that participated in a study. PERSON: Bill Baumgartner patients section IAO:0000636 patients textual entity Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred. A textual entity expressing information regarding the patients used in a study. PERSON: Bill Baumgartner patients textual entity IAO:0000637 pre-publication history section The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/) A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors. PERSON: Bill Baumgartner notice of republication pre-publication history pre-publication history section IAO:0000638 pre-publication history textual entity From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): The pre-publication history for this paper can be accessed here: http://www.biomedcentral.com/1471-2253/13/33/prepub A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information. PERSON: Bill Baumgartner pre-publication history textual entity IAO:0000639 related work section The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/) A part of a document about work in other publications that is relevant to the content of the document. PERSON: Bill Baumgartner related literature related work related work section IAO:0000640 related work textual entity Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015). A textual entity that discusses work from other publications and expresses their relevancy to the content of a document. PERSON: Bill Baumgartner related work textual entity IAO:0000641 requirements section The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource. PERSON: Bill Baumgartner requirements requirements section IAO:0000642 requirements textual entity From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): • Operating systems: Platform independent • Programming language: Matlab, R, Python • Other requirements: None • License: GNU GPL v3 • Any restrictions to use by non-academics: None A textual entity that expresses the requirements necessary to use a resource, e.g. software. PERSON: Bill Baumgartner requirements textual entity IAO:0000643 statistical analysis textual entity From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant. A textual entity documenting statistical analysis tools and techniques employed. PERSON: Bill Baumgartner statistical analysis textual entity IAO:0000644 statistical analysis section The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/) A part of the document used to describe the statistical methodologies employed in the work presented in the document. PERSON: Bill Baumgartner statistical analysis statistical analysis section IAO:0000645 tables section The section labelled 'tables' in a typical scientific journal article. A part of a document that contains one or more tables. PERSON: Bill Baumgartner tables tables section IAO:0000650 database extract, transform, and load process A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second. Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output. PERSON:Alan Ruttenberg ETL WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load database extract, transform, and load process NCBITaxon:131567 GC_ID:1 ncbi_taxonomy biota cellular organisms NCBITaxon:2 GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11542017 PMID:11542087 PMID:11760965 PMID:12054223 PMID:2112744 PMID:270744 PMID:8123559 PMID:8590690 PMID:9103655 PMID:9336922 eubacteria ncbi_taxonomy Monera Procaryotae Prokaryota Prokaryotae bacteria not Bacteria Haeckel 1894 prokaryote prokaryotes Bacteria Bacteria <prokaryote> NCBITaxon:9606 GC_ID:1 human man ncbi_taxonomy Home sapiens Homo sampiens Homo sapeins Homo sapian Homo sapians Homo sapien Homo sapience Homo sapiense Homo sapients Homo sapines Homo spaiens Homo spiens Humo sapiens Homo sapiens OBI:0000011 planned process planned process A processual entity that realizes a plan which is the concretization of a plan specification. planned process OBI:0000066 investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). investigation OBI:0000245 organization OBI:0000471 study design execution a planned process that carries out a study design study design execution OBI:0001167 age measurement datum A time measurement datum that is the result of measurement of age of an organism note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng MO_178 Age In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class discussed on Nov 15, dev call All subtype will be defined by textual definition now. age measurement datum OBI:0001931 scalar value specification OBI:0001933 value specification OBI:0100026 organism 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. study design OGMS:0000014 A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T10:18:02Z clinical finding OGMS:0000015 A series of statements representing health-relevant qualities of a patient and of a patient's family. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T10:18:59Z clinical history OGMS:0000016 A representation of clinically significant bodily components, dispositions, and/or bodily processes of a human being that is inferred from relevant clinical findings. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T10:20:20Z clinical picture OGMS:0000017 A representation of an image that supports an inference to an assertion about some quality of a patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:21:10Z image finding OGMS:0000018 A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:21:58Z laboratory finding OGMS:0000019 A representation of a quality of a patient that is (1) recorded by a clinician because the quality is hypothesized to be of clinical significance and (2) refers to qualities obtaining in the patient prior to their becoming detectable in a clinical history taking or physical examination. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:22:44Z preclinical finding OGMS:0000020 A quality of a patient that is observed by the patient or a processual entity experienced by the patient, either of which is hypothesized by the patient to be a realization of a disease. note: defined class http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-11-18T11:02:10Z symptom OGMS:0000022 A quality of a patient that is (a) a deviation from clinical normality that exists in virtue of the realization of a disease and (b) is observable. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:12:33Z manifestation of a disease OGMS:0000023 A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T11:13:49Z phenotype OGMS:0000024 sign A quality of a patient, a material entity that is part of a patient, or a processual entity that a patient participates in that is observed in a physical examination and is deemed by the clinician to be of clinical significance. A quality of a patient, a material entity that is part of a patient, or a processual entity that a patient participates in, any one of which is observed in a physical examination and is deemed by the clinician to be of clinical significance. note: defined class Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-11-18T11:14:36Z sign sign OGMS:0000025 A manifestation of a disease that is detectable in a clinical history taking or physical examination. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:15:43Z clinical manifestation of a disease OGMS:0000026 A manifestation of a disease that exists prior to the time at which it would be detected in a clinical history taking or physical examination, if the patient were to present to a clinician. A realization of a disease that exists prior to its becoming detectable in a clinical history taking or physical examination. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:16:50Z preclinical manifestation of a disease OGMS:0000029 vital sign A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:19:17Z vital sign vital sign OGMS:0000030 A disposition in an organism that constitutes an increased risk of the organism's subsequently developing the disease X. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:20:25Z predisposition to disease of type X OGMS:0000031 A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:21:20Z disease OGMS:0000032 Albert Goldfain creation date: 2009-06-23T11:22:01Z homeostasis OGMS:0000033 A predisposition to disease of type X whose physical basis is a constitutional abnormality in an organism's genome. This abnormality is the physical basis for the increased risk of acquiring the disease X. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:23:07Z genetic predisposition to disease of type X OGMS:0000034 A disease whose physical basis is an acquired genetic disorder. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:24:05Z acquired genetic disease OGMS:0000035 A disease whose physical basis is a constitutional genetic disorder. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:24:59Z constitutional genetic disease OGMS:0000037 Homeostasis that is clinically abnormal for an organism of a given type and age in a given environment. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:26:44Z abnormal homeostasis OGMS:0000038 Homeostasis of a type that is not clinically abnormal. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:27:28Z normal homeostasis OGMS:0000039 A quality which is an spatial arrangement or distribution of a(n) independent continuant(s) across a Three Dimensional Region. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:36:24Z configuration OGMS:0000040 A configuration which deviates in some way from a canonical configuration for a particular organism. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:36:58Z pathological physical configuration OGMS:0000045 A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:39:44Z disorder OGMS:0000046 A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:40:27Z epigenetic disorder OGMS:0000047 A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:41:14Z genetic disorder OGMS:0000050 A genetic disorder acquired by a single cell in an organism that leads to a population of cells within the organism bearing the disorder. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:43:09Z acquired genetic disorder OGMS:0000051 A genetic disorder inherited during conception that is part of all cells in the organism. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:43:44Z constitutional genetic disorder OGMS:0000055 A health care process in which a clinician elicits a description of previous sign and symptoms of disease from a patient or from a third party who is reporting on behalf of the patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:49:16Z clinical history taking OGMS:0000056 A measurement assay that has as input a patient-derived specimen and as output a data itme that is about a quality of the specimen. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:49:49Z laboratory test OGMS:0000057 A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T11:50:18Z physical examination OGMS:0000059 A process in an organism that leads to a subsequent disorder. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:53:07Z etiological process OGMS:0000060 Albert Goldfain creation date: 2009-06-23T11:53:49Z bodily process OGMS:0000061 A bodily process that is clinically abnormal. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:54:29Z pathological bodily process OGMS:0000063 The totality of all processes through which a given disease instance is realized. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:55:44Z disease course OGMS:0000064 A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:56:26Z chronic disease course OGMS:0000065 A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, involve an increasing deviation from homeostasis. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:57:09Z progressive disease course OGMS:0000066 A disease course that terminates in a return to normal homeostasis. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:57:44Z transient disease course OGMS:0000073 The representation of a conclusion of a diagnostic process. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T12:42:23Z diagnosis OGMS:0000074 A value for a quality reported in a lab report and asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-26T10:31:34Z normal value OGMS:0000077 TODO: Define, relate to disorder, and place in the OGMS hierarchy. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:14:59Z pathological formation OGMS:0000078 An anatomical structure (FMA) is pathological whenever (1) it has come into being as a result of changes in some pre-existing canonical anatomical structure, (2) through processes other than the expression of the normal complement of genes of an organism of the given type, and (3) is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:14:05Z pathological anatomical structure OGMS:0000079 TODO: Define, relate to disorder, and place in the OGMS hierarchy. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:15:17Z portion of pathological body substance OGMS:0000080 A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:17:07Z pathological transformation OGMS:0000081 A pathological bodily process in which matter is reorganized in such a way as to give rise to new pathological formations which take the place of entities existing earlier. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:17:24Z pathological derivation OGMS:0000082 TODO: Define. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:17:47Z pathological invasion OGMS:0000083 TODO: Define. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=26 creation date: 2009-11-24T04:51:11Z physical examination finding OGMS:0000084 An aggregate of organisms of the same type. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=33 creation date: 2009-11-24T04:51:11Z organism population OGMS:0000085 A bodily process in an organism S involving two integrated levels: (a) activation of the nociceptive system and associated emotion generating brain components of S, and (b) a simultaneous aversive sensory and emotional experience on the part of S, where (b) is phenomenologically similar to the sort of aversive experience involved in pain with concordant tissue damage. Albert Goldfain http://www.referent-tracking.com/RTU/sendfile/?file=painTokyo1_27_2011.pdf creation date: 2009-11-24T04:51:11Z pain OGMS:0000086 A pattern of signs and symptoms that typically co-occur. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=32 creation date: 2009-11-24T04:51:11Z syndrome 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. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=3 creation date: 2010-01-25T04:51:11Z extended organism OGMS:0000088 A communication from a patient about something they perceive as being abnormal about their body or life. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=12 creation date: 2010-01-25T04:51:11Z patient symptom report OGMS:0000089 A structurally anomalous part of an organism acquired during fetal development and present at birth (but not necessarily hereditary) which is hypothesized to be harmful for the organism. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=28 creation date: 2010-03-31T04:51:11Z congenital malformation OGMS:0000090 A planned process whose completion is hypothesized by a health care provider to eliminate a disorder or to alleviate the signs and symptoms of a disorder. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T04:51:11Z treatment OGMS:0000091 A processual entity during which a patient participating in a disease course gradually returns to participating in a canonical life course. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T04:51:11Z convalescence OGMS:0000092 A process which has as parts all the processes in which a given organism is participant. Albert Goldfain Richard Scheuermann Sagar Jain http://code.google.com/p/ogms/issues/detail?id=38 creation date: 2010-03-31T04:51:11Z EDIT: 10 NOV 2015 life course OGMS:0000093 A hypothesis about some future part of a disease course. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T12:42:23Z prognosis OGMS:0000094 a disease course with a rapid onset but typical unfolding of signs and symptoms after this rapid onset. Albert Goldfain http://code.google.com/p/ogms/wiki/Meeting_notes_20100513 creation date: 2010-07-19T11:57:44Z acute disease course OGMS:0000095 A bodily process caused by some disorder that results in recruitment of leukocytes into a localized tissue site, typically causing localized pain and swelling. Albert Goldfain Richard Scheuermann Sagar Jain http://code.google.com/p/ogms/wiki/Meeting_notes_20100513 creation date: 2010-07-19T11:57:44Z Updated: 10 NOV 2015 inflammatory process OGMS:0000096 A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient Albert Goldfain Sagar Jain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z editor date: 2017-04-18 health care process OGMS:0000097 A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z health care encounter OGMS:0000098 TODO Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z hospitalization OGMS:0000099 TODO Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z outpatient encounter OGMS:0000100 TODO Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z inpatient encounter OGMS:0000101 TODO Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z ED encounter OGMS:0000102 A disorder that involves some structural damage that is immediately caused by a catastrophic external force. At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level. Albert Goldfain Sagar Jain http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5 OGMS call adoption- 16 SEPT 2015 https://docs.google.com/document/d/1iiV1-fTS7BUUSzDw3N_Afx42698YWf54-FOTY2NkAxo/edit creation date: 2011-09-20T09:57:44Z edited date: 30 SEPT 2015 injury OGMS:0000103 A planned process whose completion is hypothesized by a health care provider to reduce the risk of developing a disorder or the signs and symptoms of a disorder. Whether or not 'prophylaxis' and 'treatment' classes are disjoint is an open question. Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/e42bde79218ee34e creation date: 2011-09-20T09:57:44Z disease prophylaxis 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 creation date: 2011-09-20T09:57:44Z diagnostic process OGMS:0000105 a disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease. A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course. Albert Goldfain Richard Scheuermann Sagar Jain http://code.google.com/p/ogms/issues/detail?id=73 10 NOV 2015 relapse OGMS:0000106 a disease stage which is characterized by the lack of a manifestation of a disease. A part of a disease course in which the extent or rate of change of the signs and symptoms of a disorder has decreased. Albert Goldfain Richard Scheuermann Sagar Jain http://code.google.com/p/ogms/issues/detail?id=73 10 NOV 2015 remission OGMS:0000107 A planned process that has the objective to support the objective of a health care process without directly involving the treatment, diagnosis, or prevention of disease or injury of a patient. 2017-04-18 Sagar Jain ancillary health care process OGMS:0000108 A health care process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. creation: 16MAY2017 Sagar Jain health care process assay OGMS:0000109 A health care process which results in physical changes in a specified input material creation: 16MAY2017 Sagar Jain health care process biomaterial transformation OGMS:0000110 A health care process that produces output from input data creation: 16MAY2017 Sagar Jain health care process data transformation 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. William R. Hogan health care role Mathias Brochhausen 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:00000024 A role inhering in an entity realized by social interactions in human society. Mathias Brochhausen Previous definition: A role played by an entity in human social processes. role in human social processes PATO:0000011 age A time quality inhering in a bearer by virtue of how long the bearer has existed. age PATO:0000049 intensity PATO:0000051 morphology PATO:0000052 shape PATO:0000057 occurrence PATO:0000068 qualitative PATO:0000069 deviation(from_normal) PATO:0000122 length A 1-D extent quality which is equal to the distance between two points. length PATO:0000125 mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. mass PATO:0000128 weight PATO:0000141 structure PATO:0000146 A physical quality of the thermal energy of a system. temperature PATO:0000161 A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. rate rate PATO:0000396 severe intensity PATO:0000402 branched PATO:0000460 abnormal PATO:0000583 decreased weight PATO:0000912 increased rate PATO:0001018 physical quality PATO:0001025 A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. pressure PATO:0001035 force PATO:0001199 linear PATO:0001236 process quality 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 PATO:0001509 functionality PATO:0001818 progressive PATO:0001873 cylindrical PATO:0001874 discoid PATO:0002007 convex 3-D shape PATO:0002009 branchiness PATO:0002062 physical quality of a process PATO:0002124 laminar PATO:0002246 decreased force PATO:0002266 3-D shape PATO:0002300 increased quality PATO:0002301 decreased quality PATO:0002303 decreased object quality PATO:0002304 increased process quality PATO:0002323 temporal distribution quality A fiat object part that is either a modified amino-acid residue or an unmodified amino-acid residue. amino-acid residue protein PR:000036907 Category=external. Note: This entity is distinct from CHEBI: "amino-acid residue" in that it includes residues that are technically not part of that class. [PRO:JSG] amino acid chain component PR:000036907 RO:0002577 A material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 Chris Mungall http://www.jbiomedsem.com/content/4/1/43 system UO:0000001 length unit A unit which is a standard measure of the distance between two points. length unit UO:0000002 mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit UO:0000003 time unit A unit which is a standard measure of the dimension in which events occur in sequence. time unit VSO:0000001 auscultatory blood pressure measurement process VSO:0000002 auscultatory pulse rate measurement process VSO:0000003 The temperature of the axillary fossa. axillary temperature VSO:0000004 blood pressure The pressure exerted by circulating blood on the walls of blood vessels. Unless otherwise specified, a clinical report of a blood pressure is systolic left ventricular pressure over diastolic left ventricular pressure. Albert Goldfain http://en.wikipedia.org/wiki/Blood_pressure blood pressure VSO:0000005 blood pressure measurement datum VSO:0000006 blood pressure measurement process VSO:0000007 The temperature of a part of the human body Albert Goldfain body temperature VSO:0000008 body temperature measurement datum VSO:0000009 body temperature measurement process VSO:0000010 The pulse rate of the brachial artery. brachial pulse rate VSO:0000011 These phases belong in some OBO foundry ontology of cardiac physiology. Should include the subprocesses of systole and diastole as illustrated here http://en.wikipedia.org/wiki/Cardiac_cycle . cardiac cycle phase VSO:0000012 The pulse rate of the carotid artery. carotid pulse rate VSO:0000013 core body temperature VSO:0000014 The phase of the cardiac cycle in which the heart fills with blood. diastole VSO:0000015 The blood pressure during diastole. diastolic blood pressure VSO:0000016 The diastolic blood pressure in the thoracic vena cava. diastolic central venous pressure VSO:0000017 The left ventricular pressure during diastole. diastolic left ventricular pressure VSO:0000018 The pulmonary artery pressure during diastole. diastolic pulmonary artery pressure VSO:0000019 The right ventricular pressure during diastole. diastolic right ventricular pressure VSO:0000020 The pulse rate of the dorsalis pedis artery. dorsalis pedis pulse rate VSO:0000021 The pulse rate of the facial artery. facial pulse rate VSO:0000022 The pulse rate of the femoral artery. femoral pulse rate VSO:0000023 invasive blood pressure measurement process VSO:0000024 noninvasive blood pressure measurement process VSO:0000025 The temperature of the oral cavity. oral temperature VSO:0000026 oscillometric blood pressure measurement process VSO:0000028 The pulse rate of the popliteal artery. popliteal pulse rate VSO:0000029 The rate at which an artery pulses (i.e., participates in expansion-contraction cycles) as blood passes through it. Albert Goldfain pulse rate VSO:0000030 pulse rate measurement datum VSO:0000031 pulse rate measurement process VSO:0000032 The pulse rate of the radial artery. radial pulse rate VSO:0000033 The temperature of the lumen of the rectum. rectal temperature VSO:0000034 The rate at which an organism breathes. respiratory rate VSO:0000035 respiratory rate measurement datum VSO:0000036 respiratory rate measurement process VSO:0000037 The phase of the cardiac cycle in which the heart contracts. systole VSO:0000038 The blood pressure during systole. systolic blood pressure VSO:0000039 The systolic blood pressure in the thoracic vena cava. systolic central venous pressure VSO:0000040 The left ventricular pressure during systole. systolic left ventricular pressure VSO:0000041 The pulmonary artery pressure during systole. systolic pulmonary artery pressure VSO:0000042 The right ventricular pressure during systole. systolic right ventricular pressure VSO:0000043 The pulse rate of the temporal artery. temporal pulse rate VSO:0000044 The pulse rate of the tibialis posterior artery. tibialis posterior pulse rate VSO:0000045 The temperature of the external acoustic tube. tympanic temperature VSO:0000046 The pulse rate of the ulnar artery. ulnar pulse rate VSO:0000047 The temperature of the lumen of the vagina. vaginal temperature palpatory pulse rate measurement process This class should be imported from OBI. https://github.com/OGMS/ogms/issues/105 disease stage A homeostatic process in which an organism modulates its internal body temperature. regulation of temperature Any process that modulates the frequency or rate of heart contraction. regulation of heart rate The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. blood circulation Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure. regulation of blood pressure Any process that modulates the frequency, rate or extent of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc. regulation of biological quality oboInOwl:DbXref oboInOwl:Definition oboInOwl:Subset oboInOwl:Synonym oboInOwl:SynonymType owl:Thing Person:Alan Ruttenberg has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part BFO:0000051 protein has_part has_part has part has part has_part realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in 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]) has measurement unit label This document is about information artifacts and their representations is_about is 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 person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. denotes is 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 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes. From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input. This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. Alan Ruttenberg is quality measurement of has material basis in has_specified_input see is_input_of example_of_usage 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. 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input is_specified_input_of has_specified_output 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. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output 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 value specification inheres in this fragility inheres in this vase this red color inheres in this apple 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 A dependent inheres in its bearer at all times for which the dependent exists. inheres_in RO:0000052 inheres_in inheres_in inheres in inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer of has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant 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 RO:0000086 protein has_quality false has_quality has quality has_quality inverse of has disposition disposition of A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). Chris Mungall has phenotype has phenotype A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. disease arises from feature See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo. 02:03:2018 14:00 disease_ontology 1.2 lschriml The Disease Ontology content is available via the Creative Commons Public Domain Dedication CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0/). Chris Mungall Courtney Hum Joie Davis Mark Engelstad Melissa Haendel Nicole Vasilevsky Sandra Doelken Peter N Robinson Sebastian Koehler The Human Phenotype Ontology Consortium The Monarch Initiative see http://www.human-phenotype-ontology.org Peter Robinson, Sebastian Koehler, The Human Phenotype Ontology Consortium, and The Monarch Initiative Phenotypic abnormalities encountered in human disease human_phenotype has_part Peter Robinson, Sebastian Koehler, Sandra Doelken, Chris Mungall, Melissa Haendel, Nicole Vasilevsky, Monarch Initiative, et al. Please see license of HPO at http://www.human-phenotype-ontology.org MONDO: Monarch Disease Ontology A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. 1.2 Includes Ontology(OntologyID(Anonymous-31)) [Axioms: 86367 Logical Axioms: 0] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/mondo/imports/equivalencies.owl>) VersionIRI(<null>))) [Axioms: 184582 Logical Axioms: 81364] http://obofoundry.org/ontology/mondo.html Autogenerated by OWLTools-NCBIConverter. The Ontology of Medically Related Social Entities OBO-Edit 2.0 15:02:2018 08:11 protein 1.2 ceci The PRotein Ontology is licensed under CC BY 4.0. Please see http://obofoundry.org/ontology/pr for details. Use reasoner in OBO Edit to see the correct hierarchy. IAO_0021000-IAO_0021999 IAO_0020000-IAO_0020999 Amanda Hicks Chris Stoeckert Danielle Mowery Mark A. Miller Hypertension Ontology For Clinical Data 2019-05-20