Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management. Next generation biobanking ontology(NGBO). 2024-08-27 term source 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 example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status definition English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. 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 DEFINITION 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 definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people 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 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 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 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 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.obolibrary.org/obo/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 assertion to expand assertion to 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 has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg has associated axiom(fol) has axiom label term replaced by IAO_0000125 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 Use on obsolete terms, relating the term to another term that can be used as a substitute Add as annotation triples in the granting ontology Person:Alan Ruttenberg Person:Alan Ruttenberg Person:Alan Ruttenberg term replaced by term replaced by 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 Contributor 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. http://purl.org/dc/elements/1.1/creator uberon dc-creator true dc-creator An entity primarily responsible for making the content of the resource. Creator Creator 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 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 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 Format 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 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 Subject and Keywords Typically, a Title will be a name by which the resource is formally known. A name given to the resource. Title Title has_obo_namespace shorthand is defined by is defined by This is an experimental annotation label label http://www.w3.org/2000/01/rdf-schema#seeAlso uberon seeAlso true seeAlso see also 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 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 part of http://www.obofoundry.org/ro/#OBO_REL:part_of 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 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 realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility 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 OBO Foundry Please note that, as stated on one of the RO documentation pages (https://code.google.com/p/obo-relations/wiki/ROAndBFO), some of the relations RO makes use are either uncontroversial (non-temporalized) parts of BFO2, or will be incorporated in the future. In the case of BFO_0000063, it is not currently in BFO2, but may be in the future. The RO ontologists assume this is the transitive form. For a full definition, refer to the inverse of this property, BFO_0000060. (Allyson Lister) 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. is preceded by preceded_by preceded by precedes The assertion P 'followed by' P1 tells us something about Ps in general: that is, it tells us something about what happened later, given what we know about what happened earlier. 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 preceded by some instance of P. Note that assertions using this property only are rather weak. Typically we will be interested in stronger relations, for example in the relation 'directly followed by'. 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. Modified by Allyson Lister from the preceded_by (which is the inverse of precedes / 'followed by') definition within RO: http://www.obofoundry.org/ro/ro.owl OBO Foundry Please note that, as stated on one of the RO documentation pages (https://code.google.com/p/obo-relations/wiki/ROAndBFO), some of the relations RO makes use are either uncontroversial (non-temporalized) parts of BFO2, or will be incorporated in the future. In the case of BFO_0000060, it is not currently in BFO2, but may be in the future. The RO ontologists assume this is the transitive form. (Allyson Lister) followed by 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 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 has temporal occupant [copied from inverse property 'has history'] b has_history c iff c history_of b [XXX-001 history of member of has measurement unit label 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 relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of 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 x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context.. Mathias Brochhausen designates p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context. Mathias Brochhausen is designated by A relation that is used to follow traceability of specimen activity trace_from A relation that is used to track specimen activity track_to A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Person: Jie Zheng, Chris Stoeckert Penn Group has maximum capacity A relation that relates a container to a measurement datum that specifies the actual amount of material in the container. Person: Jie Zheng, Chris Stoeckert Penn Group has actual load provides_service_consumer_with The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client. A relation between a service and the primary processual part of the service that is performed by the provider for the consumer. provides_service_consumer_with is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of is_manufactured_by http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. Alan Ruttenberg Liju Fan has_make has_manufacturer is_manufactured_by is member of organization Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it. Person:Alan Ruttenberg Person:Helen Parkinson Person:Alan Ruttenberg Person:Helen Parkinson 2009/09/28 Alan Ruttenberg. Fucoidan-use-case is member of organization has organization member Relating an organization to a legal person or organization. See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178 Person: Jie Zheng has organization member specifies value of A relation between a value specification and an entity which the specification is about. specifies value of has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification Mathias Brochhausen Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. owns a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred from c to a. Mathias Brochhausen Mathias Brochhausen A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl administrates a is contact information for b, if a is a information content entity, b is a human being or an organization and a identifies a physical location or electronic resource that allows to initiate communication with a. Mathias Brochhausen is contact information about a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b. Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. is owned by BFO relation takes precedence. We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation. is-aggregate-of true 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 at all times' 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 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 bearer_of is bearer of bearer of bearer_of is bearer of 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 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 has_participant concretizes 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. http://purl.obolibrary.org/obo/obi.owl It is recommended to not use this if possible in OMRSE. According to OntoBee this relation has been obsoleted and replaced with 'concretization of at all times'. As of Dec. 2, 2013 iao-main still uses this relation. 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 has_role this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime location_of RO:0001015 uberon location_of location_of location of 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 RO:0001019 uberon contains contains contains contains 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 RO:0001025 uberon located_in located in located in located_in located_in (type level) This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 David Osumi-Sutherland aligned with A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. David Osumi-Sutherland x 'cell expresses' y iff: cell(x) AND gene(y) AND exists some 'transcription, DNA templated (GO_0006351)'(t) AND t occurs_in x AND t has_input y cell expresses 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. has component 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 inverse of has phenotype Chris Mungall phenotype of 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process Chris Mungall expressed in temporal relation move to BFO? Allen A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporal relation starts inverse of starts with Chris Mungall Allen starts p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input 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 Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. related via exposure to g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background. over-expressed in g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background. under-expressed in x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. Chris Mungall ubiquitously expressed in Inverse of 'expressed in' Chris Mungall expresses inverse of ubiquiotously expressed in Chris Mungall ubiquitously expresses Inverse of 'is substance that treats' cjm is treated by substance holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to 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 output Chris Mungall output of 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 A relation that holds between a disease or an organism and a phenotype Chris Mungall has symptom 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 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 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 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 process' process has causal agent A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Groups both positive and negative correlation correlated with 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 (e.g. a genotype, genetic variation, chemical, or environmental exposure) 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. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. causes or contributes to condition A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. condition ameliorated by A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. condition exacerbated by Do not use this relation directly. It is intended as a grouping for a more specific relations cjm 2017-11-05T02:38:20Z condition has genetic basis in cjm 2017-11-05T03:20:01Z realizable has basis in cjm 2017-11-05T03:20:29Z is basis for realizable cjm 2017-11-05T03:26:47Z disease has basis in A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) cjm 2017-11-05T03:29:32Z disease has basis in dysfunction of A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) cjm 2017-11-05T03:37:52Z disease has basis in disruption of 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. cjm 2017-11-05T03:46:07Z disease has basis in feature Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. cjm 2017-11-05T03:50:54Z causal relationship with disease as subject A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) cjm 2017-11-05T03:51:09Z disease causes disruption of disease causes dysfunction of (disease to anatomical entity) cjm 2017-11-05T03:58:20Z disease causes dysfunction of A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. cjm 2017-11-05T04:06:02Z disease has location A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity cjm 2017-12-26T19:37:31Z disease has inflammation site A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. cjm 2017-12-26T19:45:49Z realized in response to stimulus A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. cjm 2017-12-26T19:50:53Z RO:0004029 disease_has_feature disease has feature A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. cjm 2017-12-26T19:58:44Z disease arises from structure A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. Austin Meier Chris Mungall David Osumi-Sutherland Marie Angelique Laporte triggered by process realized in response to https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit triggered by process RO:cjm Genetic information generically depend on molecules of DNA. The novel *War and Peace* generically depends on this copy of the novel. The pattern shared by chess boards generically depends on any chess board. The score of a symphony g-depends on a copy of the score. This pdf file generically depends on this server. A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. [072-ISO] g-depends on generically depends on Molecules of DNA are carriers of genetic information. This copy of *War and Peace* is carrier of the novel written by Tolstoy. This hard drive is carrier of these data items. *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* [072-ISO] is carrier of This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. cjm 2018-09-26T00:00:32Z disease relationship SIO_000001 'is related to' is the top level relation in SIO core relations+ is related to SIO_000008 core has attribute SIO_000011 is attribute of SIO_000254 is annotation of SIO_000255 document x is annotated with the keywords 'ontology','semantic web' has annotation SIO_000671 has identifier SIO_000672 is identifier for SIO_000673 has unique identifier SIO_000674 is unique identifier for has form Microsoft version 2007 is directly preceded by Microsoft version 2003. Entity A is 'directly preceded by' entity B if there are no intermediate entities temporally between the two entities. WIthin SWO this property is mainly used to describe versions of entities such as software. Allyson Lister OBO Foundry directly preceded by 'directly followed by' is an object property which further specializes the parent 'followed by' property. In the assertion 'C directly followed by C1', says that Cs generally are immediately followed by C1s. Allyson Lister directly followed by Has format specification is a type of "is encoded in" relationship which specifically describes the relationship between data and a data format specification. Allyson Lister has format specification A data property that set user email ID userEmailId A data property that set user ID userID A data property that set user password userPassword A data property that set user name userName edamontology:data_1093 beta12orEarlier A persistent, unique identifier of a molecular sequence database entry. Damion Dooley EDAM A persistent, unique identifier of a molecular sequence database entry. Sequence accession number Sequence accession sequence accession BFO:0000001 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 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 BFO:0000002 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 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 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 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. 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. 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 a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) 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 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. 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 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 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 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 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 an infinitely thin plane in space. the surface of a sphere-shaped part of space (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] BFO:0000011 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 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 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 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. 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 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. 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 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 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. 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 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 (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] BFO:0000019 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 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] quality 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 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. 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 (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] 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. per discussion with Barry Smith BFO:0000023 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. (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] BFO:0000024 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 (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object fiat object part (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 an edge of a cube-shaped portion of space. (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] BFO:0000027 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. (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. (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 a cube-shaped region of space a sphere-shaped region of space, (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] BFO:0000029 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) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] BFO:0000030 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 object BFO:0000031 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 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. (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] BFO:0000035 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 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). (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] BFO:0000040 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. 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. 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] material entity 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 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 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 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 (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 (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 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]) (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]) (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 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 (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 (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 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. (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 (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 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. (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] BrendaTissueOBO BTO:0000152 infected cell BTO:0000152 Endothelial cell of or involving the cerebrum and the blood vessels supplying it. BrendaTissueOBO BTO:0000238 cerebrovascular endothelial cell BTO:0000238 Cancer cell of the blood-forming tissues in which large numbers of immature, abnormal red blood cells are found in the blood and bone marrow. BrendaTissueOBO BTO:0000426 erythroleukemia cell BTO:0000426 BTO:0000551 Cancer cell of the major organ of respiration the lung. lung cancer cell BrendaTissueOBO BTO:0000583 bone marrow cancer cell BTO:0000583 A malignant tumour cell of glandular origin in the prostate. Over 95% are adenocarcinomas. BrendaTissueOBO prostate cancer cell prostate carcinoma cell prostate tumor cell prostate tumour cell BTO:0001130 prostate gland cancer cell BTO:0001130 BrendaTissueOBO CRC cell colorectal carcinoma cell BTO:0001615 colorectal cancer cell BTO:0001615 BTO:0001899 A cell culture at the plateau of the growth curve after log growth in a culture, during which cell number remains constant. New cells are produced at the same rate as older cells die. stationary phase culture BTO:0001903 A cell culture at the steepest slope of the growth curve of a culture-- at the phase of vigorous growth during which cell number doubles every 20-30 minutes. logarithmic phase culture BTO:0002842 A rare type of hepatocellular carcinoma arising from the cholangioles, composed of tumor cells resembling the epithelial cells of the cholangioles arranged in cords consisting of two layers of cells surrounding a minute lumen. cholangioma cell BTO:0002844 Infiltrating ductal carcinoma is one of several recognized specific patterns of cancer of the breast. It is so named because it begins in the cells forming the ducts of the breast. It is the most common form of breast cancer, comprising 65-85% of all cases. breast invasive ductal carcinoma cell BTO:0004298 corneal epithelial cell mgr 2010-04-11T12:13:16Z BrendaTissueOBO VSMC cell BTO:0004578 vascular smooth muscle cell BTO:0004578 CARO:0000007 immaterial anatomical entity CHEBI:23367 molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well molecular entity molecular entity CL:0000002 A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite growth/propagation in vitro as part of a immortal cell line. immortal cell line cell CL:0000007 A cell found in the embryo before the formation of all the gem layers is complete. early embryonic cell CL:0000015 James Malone male germ cell CL:0000023 A female germ cell that has entered meiosis. Tomasz Adamusiak NCIt:C12598 SNOMEDCT:86082002 ZFA:0009008 oocyte CL:0000034 A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. James Malone NCIt:C12662 SNOMEDCT:419758009 stem cell CL:0000037 A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4,CD5,CD8 alpha chain, CD14, CD19, CD20, integrin alpha-M, neural cell adhesion molecule 1, lymphocyte antigen 6G, lymphocyte antigen 76. James Malone Tomasz Adamusiak NCIt:C12551 SNOMEDCT:418318001 hematopoietic stem cell CL:0000038 A progenitor cell committed to the erythroid lineage. A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative). Tomasz Adamusiak NCIt:C12526 erythroid progenitor cell CL:0000040 NCIt:C13014 SNOMEDCT:53945006 monoblast CL:0000041 mature eosinophil CL:0000042 neutrophilic myeloblast CL:0000043 mature basophil CL:0000047 Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors. James Malone NCIt:C12985 neuronal stem cell CL:0000048 A stem cell that can give rise to mulitple lineages of cells. A stem cell that can give rise to multiple lineages of cells. James Malone NCIt:C43419 multipotent stem cell CL:0000049 common myeloid progenitor CL:0000050 megakaryocyte-erythroid progenitor cell CL:0000051 common lymphoid progenitor CL:0000055 A precursor cell with a limited number of potential fates. Tomasz Adamusiak NCIt:C12918 SNOMEDCT:312256009 blast cell CL:0000056 An embryonic (precursor) cell of the myogenic lineage that develops from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. An embryonic cell that becomes a cell of muscle fiber. James Malone NCIt:C33151 myoblast CL:0000057 A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. A connective-tissue cell of mesenchymal origin that secretes proteins and especially molecular collagen from which the extracellular fibrillar matrix of connective tissue forms. A large, flat, oval cell found in connective tissue and responsible for the formation of fibers. James Malone Tomasz Adamusiak NCIt:C12482 NIFSTD:nlx_cell_20090201 SNOMEDCT:52547004 fibroblast CL:0000062 A bone-forming cell which secretes an extracellular matrix. Hydroxyapatite crystals are then deposited into the matrix to form bone. James Malone NCIt:C12568 SNOMEDCT:48156001 osteoblast CL:0000065 A neurectoderm derived cell that lines the neural lumen. [ JB:jb GOC:tfm PMID:9550134 ] ependymal cell CL:0000066 A cell that is usually found in a two-dimensional sheet with a free surface. A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. Cell that cover the surface of the body and line its cavities. Cell that line the inner and outer surfaces of the body by forming cellular layers (epithelium) or masses (MSH). James Malone Tomasz Adamusiak NCIt:C12578 NIFSTD:sao441624014 SNOMEDCT:4212006 epithelial cell CL:0000071 The endothelial cells that line the vasculature. James Malone blood vessel endothelial cell CL:0000077 A flattened epithelial cell of mesenchymal origin that lines the serous cavity. James Malone NCIt:C33104 SNOMEDCT:58966000 mesothelial cell CL:0000080 A cell which moves among different tissues of the body, via blood, lymph, or other medium. Ele Holloway James Malone ZFA:0009043 circulating cell CL:0000081 A cell found predominately in the blood. Tomasz Adamusiak SNOMEDCT:63370004 blood cell CL:0000083 An epithelial cell of the pancreas. Cells of the pancreas that secrete digestive enzymes, the archetypal secretory cell upon which much of the early work on the sequence of events in the secretory process was done. Jie Zheng Tomasz Adamusiak NCIt:C93173 exocrine pancreas cell CL:0000091 NCIt:C12564 SNOMEDCT:256002 Kupffer cell CL:0000092 NCIt:C12570 SNOMEDCT:27770000 osteoclast CL:0000094 A leukocyte with abundant granules in the cytoplasm. A polymorphonuclear white blood cell with granule-containing cytoplasm. A polymorphonuclear white blood cell with granule-containing cytoplasm.nIn humans the granulocytes are also classified as polymorphonuclear leucocytes and are subdivided according to the staining properties of the granules into eosinophils, basophils and neutrophils, some invertebrate blood cells are also referred to, not very helpfully, as granulocytes. James Malone Tomasz Adamusiak NCIt:C12530 SNOMEDCT:256909001 granulocyte CL:0000096 mature neutrophil CL:0000097 NCIt:C12747 SNOMEDCT:6445007 mast cell CL:0000099 Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. James Malone NCIt:C12625 interneuron CL:0000100 An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes movement. Neurons which activate muscle cells (MSH). Tomasz Adamusiak NCIt:C12644 NIFSTD:sao1460710779 SNOMEDCT:31513005 motor neuron CL:0000101 Any neuron having a sensory function; an afferent neuron conveying sensory impulses. Ele Holloway James Malone NCIt:C12628 sensory neuron CL:0000112 James Malone columnar neuron CL:0000115 An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. The main type of cell found in the inside lining of blood vessels, lymph vessels, and the heart. James Malone NCIt:C12865 SNOMEDCT:45709008 endothelial cell CL:0000125 A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. (Reichenbach and Wolburg) MERGED DEFINITION:nTARGET DEFINITION: The delicate network of branched cells and fibers that supports the tissue of the central nervous system.n--------------------nSOURCE DEFINITION: The cells of the supportive tissue of the central nervous system (neuroglia). These non-neural cells are of three kinds: astrocytes, oligodendrocytes (collectively termed macroglia) and microglia. The delicate network of branched cells and fibers that supports the tissue of the central nervous system. James Malone Tomasz Adamusiak MSH:D009457 NCIt:C12615 NIFSTD:sao313023570 SNOMEDCT:2156000 glial cell CL:0000127 A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from "star" cells) are irregularly shaped with many long processes, including those with "end feet" which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and "reactive astrocytes" (along with microglia) respond to injury (MSH). A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury. cells) are irregularly shaped with many long processes, including those with "end feet" which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and James Malone Tomasz Adamusiak NCIt:C12477 NIFSTD:sao1394521419 SNOMEDCT:78399007 http://purl.obolibrary.org/obo/BTO_0000099 astrocyte CL:0000128 A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system. A class of large neuroglial (macroglial) cells in the central nervous system. Oligodendroglia may be called interfascicular, perivascular, or perineuronal (not the same as satellite cells, perineuronal of ganglia) according to their location. They form the insulating myelin sheath of axons in the central nervous system (MSH). Tomasz Adamusiak MSH:D009836 NCIt:C12618 NIFSTD:sao844118448 SNOMEDCT:66254009 oligodendrocyte CL:0000129 A central nervous system macrophage found in the parenchyma of the central nervous system. A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive. A small, migratory, phagocytic, interstitial cell of hematopoietic origin found in the central nervous system. Microglial cells are of various forms and may have slender branched processes. MERGED DEFINITION:nTARGET DEFINITION: The small, non-neural, interstitial cells of mesodermal origin that form part of the supporting structure of the central nervous system. They are of various forms and may have slender branched processes. They are migratory and act as phagocytes to waste products of nerve tissue. n--------------------nSOURCE DEFINITION: One of the small interstitial phagocytic cells of the microglia. The small, non-neural, interstitial cells of mesodermal origin that form part of the supporting structure of the central nervous system. They are of various forms and may have slender branched processes. They are migratory and act as phagocytes to waste products of nerve tissue. James Malone Tomasz Adamusiak MSH:D017628 NCIt:C12616 NIFSTD:sao789292116 SNOMEDCT:63483002 microglial cell CL:0000136 A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides. A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of tryglycerides. James Malone NCIt:C12556 NCIt:C32991 SNOMEDCT:24826007 fat cell CL:0000138 Polymorphic cell that form cartilage. James Malone NCIt:C12557 SNOMEDCT:433180002 SNOMEDCT:81272008 chondrocyte CL:0000148 A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. An epidermal cell that produces melanin. Tomasz Adamusiak NCIt:C12591 SNOMEDCT:9683001 melanocyte CL:0000151 A cell that specializes in controlled release of one or more substances. Tomasz Adamusiak NCIt:C13055 secretory cell CL:0000160 A cell of the epithelial lining that produce and secrete mucins. MESH:A03.492.411.369.320 cell goblet cell CL:0000162 A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl. James Malone NCIt:C12594 parietal cell CL:0000163 A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions. MESH:A06.407 cell endocrine cell CL:0000165 A neuron that has the specialized function to produce and secrete hormones, and that constitutes, in whole or in part, an endocrine organ or system. Neuroendocrine cells are cells that receive neuronal input (neurotransmitters released by nerve cells) and, as a consequence of this input, release message molecules (hormones) to the blood. An example of a neuroendocrine cell is the cell of the adrenal medulla which releases adrenalin to the blood. The major center of neuroendocrine integration in the body is found in the hypothalamus and the pituitary gland. Here hypothalamic neurosecretory cells release factors to the blood. Neuroendocrine cells are cells that receive neuronal input (neurotransmitters released by nerve cells) and, as a consequence of this input, release message molecules (hormones) to the blood. In this way they bring about and integration between the nervous system and the endocrine system, a process known as neuroendocrine integration. An example of a neuroendocrine cell is the cell of the adrenal medulla (innermost part of the adrenal gland) which releases adrenalin to the blood. The adrenal medullary cells are controlled by the sympathetic division of the autonomic nervous system. These cells are modified postganglionic neurons. Autonomic nerve fibers lead directly to them from the central nervous system. The major center of neuroendocrine integration in the body is found in the hypothalamus and the pituitary gland. Here hypothalamic neurosecretory cells release factors to the blood. Some of these these factors, release at the median eminence, control the secretion of pituitary hormones, while others (the hormones oxytocin and vasopressin) are released directly to the peripheral circulation. Tomasz Adamusiak NCIt:C12485 neuroendocrine cell CL:0000168 A cell that composes the bulk of the islets of Langerhans and secretes insulin. James Malone Tomasz Adamusiak NCIt:C32199 beta cell CL:0000169 A cell that secretes insulin and is located towards the center of the islets of Langerhans. GOC:tfm ISBN:0517223651 NCIT:C32199 type B pancreatic cell CL:0000171 A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon. Jie Zheng Tomasz Adamusiak NCIt:C32052 pancreatic A cell CL:0000173 A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin. GOC:tfm cell pancreatic D cell CL:0000178 A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis. James Malone NCIt:C12609 Leydig cell CL:0000182 A liver cell. The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. James Malone NCIt:C12588 hepatocyte CL:0000185 Contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament. [ GOC:tfm ISBN:0721662544 ] myoepithelial cell CL:0000187 A mature contractile cell, commonly known as a myocyte, that forms one of three kinds of muscle. A mature contractile cell, commonly known as a myocyte, that forms one of three kinds of muscle. This cell has as part of its cytoplasm myofibrils organized in various patterns. Mature contractile cells, commonly known as myocytes, that form one of three kinds of muscle. The three types of muscle cells are skeletal (muscle fibers), cardiac (myocytes, cardiac), and smooth (myocytes, smooth muscle). They are derived from embryonic (precursor) muscle cells called myoblasts (MSH). James Malone Tomasz Adamusiak NCIt:C12612 NIFSTD:sao519252327 muscle cell CL:0000192 A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast). Non-striated, elongated, spindle-shaped cells found lining the digestive tract, uterus, and blood vessels. They are derived from specialized myoblasts (myoblasts, smooth muscle) (MSH). James Malone Tomasz Adamusiak NCIt:C13001 NIFSTD:sao676858164 smooth muscle cell CL:0000202 A mechanoreceptor cell located in the inner ear that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system. A mechanoreceptor cell located in the organ of Corti that is sensitive to auditory stimuli and in the vestibular apparatus that is sensitive to movement of the head. In each case the accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system. James Malone Tomasz Adamusiak NIFSTD:sao630986029 cochlear hair cell CL:0000211 A cell whose function is determined by the generation or the reception of an electric signal. cell electrically active cell CL:0000216 A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier. Tomasz Adamusiak NCIt:C12595 Sertoli cell CL:0000218 A neuroglial cell of the peripheral nervous system which forms the insulating myelin sheaths of peripheral axons. James Malone NCIt:C12620 Schwann cell CL:0000222 A cell of the middle germ layer of the embryo. James Malone NCIt:C33936 mesodermal cell CL:0000232 A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. A red blood cell. In mammals, mature erythrocytes are non-nucleated, biconcave disks containing hemoglobin whose function is to transport oxygen. Any of the hemoglobin-containing cells that carry oxygen to the tissues and are responsible for the red color of vertebrate blood. James Malone Tomasz Adamusiak NCIt:C12521 SNOMEDCT:41898006 erythrocyte CL:0000233 A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation. James Malone Tomasz Adamusiak MSH:D001792 NCIt:C12520 SNOMEDCT:16378004 true platelet CL:0000235 A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. A mononuclear phagocyte which differentiates from monocytes, is typically resident in a particular tissue, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells (Cell Ontology). Relatively long-lived phagocytic cell of mammalian tissues, derived from blood monocyte. Macrophages from different sites have distinctly different properties. Main types are peritoneal and alveolar macrophages, tissue macrophages (histiocytes), Kuppfer cells of the liver, and osteoclasts. In response to foreign materials may become stimulated or activated. Macrophages play an important role in killing of some bacteria, protozoa, and tumour cells, release substances that stimulate other cells of the immune system, and are involved in antigen presentation. May further differentiate within chronic inflammatory lesions to epithelioid cells or may fuse to form foreign body giant cells or Langhans' giant cells. James Malone Tomasz Adamusiak NCIt:C12558 NIFSTD:sao185843373 SNOMEDCT:58986001 macrophage CL:0000236 A lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. A lymphocyte of B lineage with the phenotype CD19-positive and surface immunoglobulin-positive. Immunologically important lymphocyte that is not thymus-dependent, is either short-lived and naive or long-lived and of memory phenotype, and resembles the bursa-derived lymphocyte of birds in that it is responsible for the production of immunoglobulins. James Malone Tomasz Adamusiak MSH:D001402 NCIt:C12474 SNOMEDCT:112130006 B cell CL:0000286 A cell of a filament of a fungal mycelium. cell hyphal cell CL:0000292 One of a pair of cells flanking the stomatal pore and causing the opening and closing of the pore by changes in turgor. Tomasz Adamusiak guard cell CL:0000333 A cell of the strip of specialized ectoderm flanking each side of the embryonal neural plate, which after the closure of the neural tube, forms a column of isolated cells along the dorsal aspect of the neural tube. Most of the cranial and all of the spinal sensory ganglion cells arise by differentiation of neural crest cells. James Malone NCIt:C33937 neural crest cell CL:0000337 An embryonic cell that develops into a nerve cell or neuron. James Malone Tomasz Adamusiak NCIt:C12991 neuroblast (sensu Vertebrata) CL:0000346 A specialized mesenchymal cell that resides in the dermal papilla located at the bottom of hair follicles. This cell plays a pivotal roles in hair formation, growth, and cycling. Helen Parkinson hair follicle dermal papilla cell CL:0000349 A cell which is part of an extraembryonic structure associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. extra-embryonic cell extraembryonic cell CL:0000351 A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface. trophoblastic cell trophoblast cell CL:0000352 A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. James Malone epiblast cell CL:0000362 An epithelial cell of the integument (the outer layer of an organism). epidermal cell CL:0000371 The cell protoplasm after removal of the cell wall. Tomasz Adamusiak NCIt:C12659 protoplast CL:0000384 Tomasz Adamusiak ligament cell CL:0000387 A blood cell especially of an invertebrate animal. Tomasz Adamusiak hemocyte CL:0000390 blood cell (sensu Nematoda and Protostomia) CL:0000398 cell polygonal cell CL:0000415 A cell whose nucleus has two haploid genomes. cell diploid cell CL:0000421 A free floating cell, including amebocytes and eleocytes, in the coelom of certain animals, especially annelids. cell coelomocyte CL:0000442 A cell with extensive dendritic processes found in the B cell areas (primary follicles and germinal centers) of lymphoid tissue. They are unrelated to the dendritic cell associated with T cells. Follicular dendritic cells have Fc receptors and C3b receptors, but unlike other dendritic cells, they do not process or present antigen in a way that allows recognition by T cells. Instead, they hold antigen in the form of immune complexes on their surfaces for long periods and can present antigen to B cells during an immune response. ISBN:127520252 NCIt:C12622 SNOMEDCT:56685008 cell Due to its unique lineage and distinct function, this is not a type of dendritic cell; CL:0000451. follicular dendritic cell CL:0000451 A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. A special type of cell that is a key regulator of the immune system, acting as a professional antigen-presenting cell, APC, capable of activating naive T cells and stimulating the growth and differentiation of B cells. Dendritic cells are found, for example, in the lymph nodes and spleen. As an APC, a dendritic cell can retain antigen for long periods on its surface, present the antigen to a T or B cell and so influence their behavior. Large, stellate fibroblast found along the network of collagen fibers of the reticulum of the spleen; synthesize the matrix components of the reticulum. James Malone Tomasz Adamusiak NCIt:C12583 SNOMEDCT:127942009 SNOMEDCT:24333000 SNOMEDCT:37510001 dendritic cell CL:0000453 NCIt:C12584 Langerhans cell CL:0000477 James Malone follicle cell CL:0000484 connective tissue type mast cell CL:0000485 mucosal type mast cell CL:0000499 A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere. Tomasz Adamusiak NCIt:C12571 stromal cell CL:0000501 A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors. NCIt:C12587 granulosa cell CL:0000510 An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix. NCIt:C12593 SNOMEDCT:84907006 paneth cell CL:0000514 A precursor cell destined to differentiate into smooth muscle myocytes. Tomasz Adamusiak NCIt:C33516 smooth muscle myoblast CL:0000515 A myoblast that differentiates into skeletal muscle fibers. Helen Parkinson http://purl.obolibrary.org/obo/CL_0000515 skeletal muscle myoblast CL:0000520 cell prokaryotic cell CL:0000521 cell fungal cell CL:0000525 A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo. It It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy. Tomasz Adamusiak syncytiotrophoblast cell CL:0000540 A grayish or reddish granular cell with specialized processes that is the fundamental functional unit of nervous tissue. The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. The basic cellular units of nervous tissue. Neurons are polarized cells with defined regions consisting of the cell body, an axon, and dendrites, although some types of neurons lack axons or dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. James Malone Tomasz Adamusiak NCIt:C12623 NIFSTD:sao1417703748 SNOMEDCT:47220008 neuron CL:0000547 An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers. Jie Zheng Tomasz Adamusiak NCIt:C13129 SNOMEDCT:16671004 proerythroblast CL:0000549 A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers. Jie Zheng Tomasz Adamusiak NCIt:C13130 SNOMEDCT:115610004 SNOMEDCT:464005 basophilic erythroblast CL:0000550 NCIt:C13131 SNOMEDCT:16779009 polychromatophilic erythroblast CL:0000552 orthochromatic erythroblast CL:0000553 The earliest cytologically identifiable precursor in the thrombocytic series. The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative). James Malone Tomasz Adamusiak NCIt:C13122 SNOMEDCT:27852005 SNOMEDCT:50284009 megakaryocyte progenitor cell CL:0000556 A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm. A large cell that has a lobulated nucleus, is found especially in the bone marrow, and is the source of blood platelets. James Malone Tomasz Adamusiak NCIt:C12553 SNOMEDCT:23592000 megakaryocyte CL:0000557 A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata-1, Gata2 but do express C/EBPa, and Pu.1. A progenitor cell that has plasma membrane part CD123, CD34, and CD45RA, lacks plasma membrane part CD19 and CD3, and is committed to the granulocyte and monocyte lineages. Tomasz Adamusiak granulocyte monocyte progenitor cell CL:0000558 An immature erythrocyte showing a basophilic reticulum under vital staining. An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. Jie Zheng Tomasz Adamusiak NCIt:C12528 SNOMEDCT:52802009 reticulocyte CL:0000559 NCIt:C13121 SNOMEDCT:1075005 promonocyte CL:0000560 band form neutrophil CL:0000562 nucleate erythrocyte CL:0000564 SNOMEDCT:34254002 neutrophilic promyelocyte CL:0000576 A mononuclear phagocytic leukocyte, 13 to 25 mm in diameter, with an ovoid or kidney-shaped nucleus, containing lacy, linear chromatin and abundant gray-blue cytoplasm filled with fine reddish and azurophilic granules. Formed in the bone marrow from promonocytes, monocytes are transported to tissues such as the lung and liver, where they develop into macrophages. Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. James Malone Tomasz Adamusiak MSH:D009000 NCIt:C12547 SNOMEDCT:55918008 true monocyte CL:0000579 A follicle cell that migrates from the anterior pole of the egg chamber, between the nurse cells, to the anterior of the oocyte where they participate in formation of the micropyle. About 6-10 border cells per egg chamber migrate as a tightly associated cluster. A follicle cell that migrates from the anterior pole of the egg chamber, between the nurse cells, to the anterior of the oocyte where they participate in formation of the micropyle. About 6-10 border cells per egg chamber migrate as a tightly associated cluster. Tomasz Adamusiak border follicle cell CL:0000580 SNOMEDCT:4717004 neutrophilic myelocyte CL:0000581 NCIt:C12566 peritoneal macrophage CL:0000582 SNOMEDCT:50134008 neutrophilic metamyelocyte CL:0000583 NCIt:C12565 SNOMEDCT:33956004 alveolar macrophage CL:0000584 An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen. SANBI:mhl cell enterocyte CL:0000586 The reproductive cell in multicellular organisms. Jie Zheng Tomasz Adamusiak NCIt:C12597 germ cell CL:0000588 odontoclast CL:0000595 enucleate erythrocyte CL:0000598 A projection neuron in the cerebral cortex and the hippocampus. Pyramidal cells have a pyramid-shaped soma with the apex and an apical dendrite pointed toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their cortical region. GOC:tfm NCIt:C12652 NIF_Cell:sao862606388 SNOMEDCT:17522008 cell pyramidal cell CL:0000599 An asexual, nonmotile spore formed by higher fungi; conidia are usually made from the side or tip of specialized sporogenous cells and do not form by progressive cleavage of the cytoplasm. FAO:0000024 SNOMEDCT:14127004 cell conidium CL:0000611 eosinophil progenitor cell CL:0000612 SNOMEDCT:90961003 eosinophilic myelocyte CL:0000613 basophil progenitor cell CL:0000614 SNOMEDCT:17295002 basophilic myelocyte CL:0000617 A neuron that uses GABA as a vesicular neurotransmitter James Malone GABAergic neuron CL:0000622 A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus). Jie Zheng Tomasz Adamusiak NCIt:C13077 acinar cell CL:0000628 A cell that can perform photosynthesis, in which carbohydrates are synthesized from carbon dioxide and water, using light as the energy source. cell see PMID:21177950, The making of a photosynthetic animal. photosynthetic cell CL:0000632 A cell that is found in the perisinusoidal space of the liver that is capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components that can contribute to liver fibrosis. This activated state has a myofibroblast-like phenotype, though it's not clear in the literature if this is terminally differentiated. This cell type comprises approximately 8-15% of total cells in the liver. NCIt:C32734 Ito cell hepatic perisinusoidal cell perisinusoidal cell cell fat-storing cell lipocyte vitamin A-storing cells Hepatic stellate cells are CD271-positive, desmin-positive, DDR-2-positive, GFAP-positive, synamin-positive, synaptophysin-positive, vimentin-positive, They are capable of producing angiotensin II, fibronectin, laminin, MMP-1, MMP-2, MMP-3, MMP-9, MMP-11, TGF-beta1, TIMP-1, TIMP-2, type I collagen, type III collagen, type IV collagen, and type VI collagen. hepatic stellate cell CL:0000646 Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament. James Malone NCIt:C12475 basal cell CL:0000647 multinucleated giant cell CL:0000669 *Slender, contractile, mesenchymal-like cell found in close association with capillary walls. They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells. (From OBO Cell Type Ontology). *A flattened, or elongated, stellate-shaped solitary cell with multiple cytoplasmic processes encircling the capillary endothelium and contacting a large abluminal vessel area. It may be equivalent to the vascular smooth muscle cell, although this identify has not been conclusively determined yet (Armulik et al., Circ Res 97: 512, 2005). A slender, contractile, mesenchymal-like cell found in close association with capillary walls. They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells. (From Stedman, 26th ed). An elongated, contractile cell found wrapped about precapillary arterioles outside the basement membrane. They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells. Tomasz Adamusiak NCIt:C12656 NIFSTD:nifext_171 SNOMEDCT:34773004 pericyte CL:0000670 A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells. James Malone NCIt:C33401 primordial germ cell CL:0000679 James Malone glutamatergic neuron CL:0000700 A neuron that releases dopamine as a neurotransmitter. NCIt:C26454 dopaminergic neuron CL:0000711 Cumulus cell is a specialized granulosa cell that surrounds and nourishes the oocyte. This cell-type surrounds the fully-grown oocyte to form a cumulus-oocyte complex (abbr. COC). The terms cumulus oophorus cells, cumulus granulosa cells, cumulus oophorous granulosa cells, granulosa-cumulus cells are used to make a distinction between this cell and the other functionally different subpopulation of granulosa cells at the wall of the Graafian follicle. cell cumulus cell CL:0000723 A stem cell that can give rise to cell types of the body other than those of the germ-line. SNOMEDCT:417904004 cell somatic stem cell CL:0000738 A nucleated cell of the myeloid or lymphoid lineages, found in blood or other tissue. An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. Any of the blood cells that are colorless, lack hemoglobin, contain a nucleus, and include the lymphocytes, monocytes, neutrophils, eosinophils, and basophils. James Malone Tomasz Adamusiak NCIt:C12529 SNOMEDCT:52501007 leukocyte CL:0000746 A heart muscle cell. A myocyte located in the heart. The contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei. A striated muscle cell found in the heart. They develop from cardiac myoblasts. Striated muscle cells found in the heart. They are derived from cardiac myoblasts (myoblasts, cardiac (MSH). James Malone Tomasz Adamusiak NCIt:C13002 NIFSTD:sao658938043 SNOMEDCT:86441007 cardiac muscle cell CL:0000762 nucleated thrombocyte CL:0000763 A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. Any of the immature blood cells that develop in the bone marrow, such as those involved in hematopoiesis. James Malone Tomasz Adamusiak NCIt:C12549 myeloid cell CL:0000764 A immature or mature cell in the lineage leading to and including erythrocytes. erythroid lineage cell CL:0000765 A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers. A nucleated precursor of an erythrocyte. James Malone Tomasz Adamusiak NCIt:C12527 SNOMEDCT:84227004 erythroblast CL:0000766 myeloid leukocyte CL:0000767 Granular leukocytes characterized by a relatively pale-staining, lobate nucleus and cytoplasm containing coarse dark-staining granules of variable size and stainable by basic dyes. Dani Welter MSH:D001491 NCIt:C12531 SNOMEDCT:30061004 true basophil CL:0000768 immature basophil CL:0000769 SNOMEDCT:63369000 basophilic metamyelocyte CL:0000770 band form basophil CL:0000771 Granular leukocytes with a nucleus that usually has two lobes connected by a slender thread of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and stainable by eosin. Dani Welter MSH:D004804 NCIt:C12532 SNOMEDCT:14793004 true eosinophil CL:0000772 immature eosinophil CL:0000773 SNOMEDCT:80036001 eosinophilic metamyelocyte CL:0000774 band form eosinophil CL:0000775 A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. Ele Holloway James Malone Tomasz Adamusiak MSH:D009504 NCIt:C12533 SNOMEDCT:116712007 true neutrophil CL:0000776 immature neutrophil CL:0000777 A tissue-resident macrophage of the renal glomerular mesangium involved in the disposal and degradation of filtration residues, presentation of antigen to T cells and in tissue remodeling. A tissue-resident macrophage of the renal glomerular mesangium. James Malone Tomasz Adamusiak NCIt:C13159 SNOMEDCT:24259000 mesangial phagocyte CL:0000778 mononuclear osteoclast CL:0000779 multinuclear osteoclast CL:0000782 myeloid dendritic cell CL:0000784 A dendritic cell type of distinct morphology, localization, and surface marker expression from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection. James Malone Tomasz Adamusiak NCIt:C45236 plasmacytoid dendritic cell CL:0000785 A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen. James Malone Tomasz Adamusiak NCIt:C33058 mature B cell CL:0000786 A terminally differentiated cell of the B lymphocyte lineage that produces antibodies; plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern. A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. James Malone Tomasz Adamusiak NCIt:C12486 SNOMEDCT:113335003 plasma cell CL:0000787 memory B cell CL:0000788 naive B cell CL:0000816 An immature B cell is a precursor B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation. James Malone Tomasz Adamusiak NCIt:C32766 immature B cell CL:0000817 A precursor B cell is a B cell with the phenotype CD10-positive (P08473/NEP_HUMAN; PIRSF001194). A precursor B cell is a B cell with the phenotype CD10-positive. James Malone Tomasz Adamusiak precursor B cell CL:0000818 transitional stage B cell CL:0000819 B-1 B cell CL:0000820 B-1a B cell CL:0000821 B-1b B cell CL:0000822 A conventional B cell subject to antigenic stimulation and dependent on T cell help and with a distinct surface marker expression pattern from B-1 B cells. These cells are CD43-negative. James Malone Tomasz Adamusiak B-2 B cell CL:0000828 thromboblast CL:0000829 basophilic myeloblast CL:0000830 SNOMEDCT:71170001 basophilic promyelocyte CL:0000831 mast cell progenitor CL:0000832 SNOMEDCT:259719000 eosinophilic myeloblast CL:0000833 SNOMEDCT:4029003 eosinophilic promyelocyte CL:0000834 neutrophil progenitor cell CL:0000835 NCIt:C13015 SNOMEDCT:15622002 myeloblast CL:0000836 NCIt:C13114 SNOMEDCT:43446009 promyelocyte CL:0000837 A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans. A progenitor cell of any hematopoietic lineage, potentially multipotent. Jie Zheng Tomasz Adamusiak hematopoietic multipotent progenitor cell CL:0000838 lymphoid lineage restricted progenitor cell CL:0000839 A progenitor cell of any myeloid lineage, potentially multipotent. A progenitor cell restricted to the myeloid lineage. Tomasz Adamusiak myeloid lineage restricted progenitor cell CL:0000840 immature conventional dendritic cell CL:0000841 mature conventional dendritic cell CL:0000843 follicular B cell CL:0000844 germinal center B cell CL:0000845 marginal zone B cell CL:0000860 classical monocyte CL:0000861 elicited macrophage CL:0000862 suppressor macrophage CL:0000863 inflammatory macrophage CL:0000864 tissue-resident macrophage CL:0000865 gastrointestinal tract (lamina propria) macrophage CL:0000866 thymic macrophage CL:0000867 secondary lymphoid organ macrophage CL:0000868 lymph node macrophage CL:0000869 tonsillar macrophage CL:0000870 Peyer's patch macrophage CL:0000871 splenic macrophage CL:0000872 splenic marginal zone macrophage CL:0000873 splenic metallophillic macrophage CL:0000874 splenic red pulp macrophage CL:0000875 non-classical monocyte CL:0000876 splenic white pulp macrophage CL:0000878 central nervous system macrophage CL:0000879 meningeal macrophage CL:0000880 choroid-plexus macrophage CL:0000881 perivascular macrophage CL:0000882 thymic medullary macrophage CL:0000883 thymic cortical macrophage CL:0000884 mucosa-associated lymphoid tissue macrophage CL:0000885 gut-associated lymphoid tissue macrophage CL:0000886 nasal and broncial associated lymphoid tissue macrophage CL:0000887 lymph node subcapsular sinus macrophage CL:0000888 lymph node tingible body macrophage CL:0000889 myeloid suppressor cell CL:0000890 alternatively activated macrophage CL:0000936 early lymphoid progenitor CL:0000941 thymic conventional dendritic cell CL:0000942 thymic plasmacytoid dendritic cell CL:0000943 Be1 Cell CL:0000944 Be2 cell CL:0000947 IgE plasma cell CL:0000948 IgE memory B cell CL:0000949 IgD plasmablast CL:0000950 IgE plasmablast CL:0000951 IgE short lived plasma cell CL:0000961 Bm1 B cell CL:0000962 Bm2 B cell CL:0000963 Bm3-delta B cell CL:0000964 Bm2' B cell CL:0000965 Bm3 B cell CL:0000966 Bm4 B cell CL:0000967 Bm5 B cell CL:0000968 Be cell CL:0000969 NCIt:C113502 regulatory B cell CL:0000970 unswitched memory B cell CL:0000971 IgM memory B cell CL:0000972 class switched memory B cell CL:0000973 IgA memory B cell CL:0000974 long lived plasma cell CL:0000975 short lived plasma cell CL:0000976 IgA short lived plasma cell CL:0000977 IgG short lived plasma cell CL:0000978 IgM short lived plasma cell CL:0000979 IgG memory B cell CL:0000980 NCIt:C37082 SNOMEDCT:2579009 plasmablast CL:0000981 double negative memory B cell CL:0000982 IgG plasmablast CL:0000983 IgM plasmablast CL:0000984 IgA plasmablast CL:0000985 IgG plasma cell CL:0000986 IgM plasma cell CL:0000987 IgA plasma cell CL:0000988 A blood cell. A cell found predominately in the blood. A cell of a hematopoietic lineage. Tomasz Adamusiak hematopoietic cell CL:0000989 CD11c-low plasmacytoid dendritic cell CL:0000990 conventional dendritic cell CL:0000991 CD11c-negative plasmacytoid dendritic cell CL:0000992 immature CD11c-low plasmacytoid dendritic cell CL:0000993 mature CD11c-low plasmacytoid dendritic cell CL:0000994 immature CD11c-negative plasmacytoid dendritic cell CL:0000995 CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor CL:0000996 mature CD11c-negative plasmacytoid dendritic cell CL:0000998 CD8_alpha-negative CD11b-negative dendritic cell CL:0000999 CD4-positive CD11b-positive dendritic cell CL:0001000 CD8_alpha-positive CD11b-negative dendritic cell CL:0001001 immature CD8_alpha-negative CD11b-negative dendritic cell CL:0001002 mature CD8_alpha-negative CD11b-negative dendritic cell CL:0001004 immature CD8_alpha-positive CD11b-negative dendritic cell CL:0001005 mature CD8_alpha-positive CD11b-negative dendritic cell CL:0001006 dermal dendritic cell CL:0001007 interstitial dendritic cell CL:0001008 Kit and Sca1-positive hematopoietic stem cell CL:0001009 immature dermal dendritic cell CL:0001010 mature dermal dendritic cell CL:0001011 immature interstitial dendritic cell CL:0001012 CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor CL:0001013 mature interstitial dendritic cell CL:0001014 CD1a-positive Langerhans cell CL:0001015 CD8_alpha-low Langerhans cell CL:0001019 CD115-positive monocyte OR common dendritic progenitor CL:0001022 CD115-positive monocyte CL:0001024 CD34-positive, CD38-negative hematopoietic stem cell CL:0001029 common dendritic progenitor CL:0001030 CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor CL:0001063 An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism. GOC:add GOC:cg GOC:wdd NCIt:C12922 cell neoplastic cell CL:0002000 Kit-positive erythroid progenitor cell CL:0002001 CD34-positive, CD38-positive granulocyte monocyte progenitor CL:0002002 Kit-positive granulocyte monocyte progenitor CL:0002003 CD34-positive, GlyA-negative erythroid progenitor cell CL:0002004 CD34-negative, GlyA-negative proerythroblast CL:0002007 Kit-low, CD34-positive eosinophil progenitor cell CL:0002008 CD34-positive, CD38-positive eosinophil progenitor cell CL:0002009 macrophage dendritic cell progenitor CL:0002010 pre-conventional dendritic cell CL:0002012 Kit-low proerythroblast CL:0002013 GlyA-positive basophillic erythroblast CL:0002014 Kit-negative, Ly-76 high basophilic erythroblast CL:0002015 Kit-negative, Ly-76 high polychromatophilic erythroblast CL:0002016 CD71-low, GlyA-positive polychromatic erythroblast CL:0002017 Kit-negative, Ly-76 high orthochromatophilic erythroblasts CL:0002018 CD71-negative, GlyA-positive orthochromatic erythroblast CL:0002019 Ly-76 high reticulocyte CL:0002020 GlyA-positive reticulocytes CL:0002021 GlyA-positive erythrocyte CL:0002022 Ly-76 high positive erythrocyte CL:0002023 CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell CL:0002024 Kit-positive megakaryocyte progenitor cell CL:0002025 CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell CL:0002026 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell CL:0002027 CD9-positive, CD41-positive megakaryocyte cell CL:0002028 basophil mast progenitor cell CL:0002029 Fc-epsilon RIalpha-low mast cell progenitor CL:0002030 Fc-epsilon RIalpha-high basophil progenitor cell CL:0002031 hematopoietic lineage restricted progenitor cell CL:0002032 hematopoietic oligopotent progenitor cell CL:0002035 Slamf1-negative multipotent progenitor cell CL:0002036 Slamf1-positive multipotent progenitor cell CL:0002043 CD34-positive, CD38-negative multipotent progenitor cell CL:0002044 Kit-positive, integrin beta7-high basophil mast progenitor cell CL:0002056 Fraction F mature B cell CL:0002057 CD14-positive, CD16-negative classical monocyte CL:0002058 Gr1-low non-classical monocyte CL:0002059 CD8alpha-positive thymic conventional dendritic cell CL:0002060 melanophage CL:0002079 Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH. GOC:tfm PMID:14740223 cell pancreatic ductal cell CL:0002087 nongranular leukocyte CL:0002092 A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. [ GOC:tfm ISBN:0618947256 ] MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. bone marrow cell CL:0002101 CD38-positive naive B cell CL:0002102 CD38-negative naive B cell CL:0002103 IgG-positive double negative memory B cell CL:0002104 IgG-negative double negative memory B cell CL:0002105 CD38-positive IgG memory B cell CL:0002106 IgD-positive CD38-positive IgG memory B cell CL:0002107 IgD-negative CD38-positive IgG memory B cell CL:0002108 CD38-negative IgG memory B cell CL:0002109 B220-positive CD38-positive naive B cell CL:0002110 B220-low CD38-positive naive B cell CL:0002111 CD38-negative unswitched memory B cell CL:0002112 B220-positive CD38-negative unswitched memory B cell CL:0002113 B220-low CD38-negative unswitched memory B cell CL:0002114 CD38-positive unswitched memory B cell CL:0002115 B220-positive CD38-positive unswitched memory B cell CL:0002116 B220-low CD38-positive unswitched memory B cell CL:0002117 IgG-negative class switched memory B cell CL:0002118 CD38-negative IgG-negative class switched memory B cell CL:0002119 CD38-positive IgG-negative class switched memory B cell CL:0002120 CD24-positive CD38-negative IgG-negative class switched memory B cell CL:0002121 CD24-negative CD38-negative IgG-negative class switched memory B cell CL:0002122 B220-positive CD38-positive IgG-negative class switched memory B cell CL:0002123 B220-low CD38-positive IgG-negative class switched memory B cell CL:0002144 An endothelial cell found in capillaries. tmeehan 2010-08-24T10:15:00Z cell capillary endothelial cell CL:0002150 epitheloid cell CL:0002151 late promyelocyte CL:0002154 early promyelocyte CL:0002155 echinocyte CL:0002191 granulocytopoietic cell CL:0002192 NCIt:C13116 SNOMEDCT:83321009 metamyelocyte CL:0002193 A cell derived from a promyelocyte. It differentiates into a metamyelocyte. It has a diameter of 10-18 micrometer, and an oval or round nucleus with finely granulated chromatin. A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses. Jie Zheng Tomasz Adamusiak NCIt:C13115 SNOMEDCT:127915008 myelocyte CL:0002194 monopoietic cell CL:0002204 A cell type found in the gastrointestinal and respiratory tracts that is characterized by the presence of a tuft of blunt, squat microvilli (120-140 per cell). Function of this cell type is not known. GOC:tfm ISBN:0517223651 PMID:15817800 cell tuft cell CL:0002231 An epithelial cell of the prostate. GOC:tfm cell epithelial cell of prostate CL:0002246 NCIt:C12946 SNOMEDCT:419583006 peripheral blood stem cell CL:0002247 pleural macrophage CL:0002248 A pluripotent stem cell has the ability to form cells from all three germ layers (ectoderm, mesoderm, and endoderm). However, unlike totipotent stem cells, they cell can not generate all the cells of the whole organism such as placenta. NCIt:C12977 tmeehan 2010-09-07T04:26:06Z cell pluripotent stem cell CL:0002253 An epithelial cell of the large intestine. tmeehan 2010-09-08T09:28:22Z CL:1000292 cell epithelial cell of colon epithelial cell of large intestine CL:0002275 A PP cell located in the islets of the pancreas. GOC:tfm cell pancreatic PP cell CL:0002318 periperhal blood mesothelial cell CL:0002319 neural cell CL:0002321 A cell of the embryo. Tomasz Adamusiak NCIt:C13054 embryonic cell CL:0002322 Totipotent cell cultured from early embryo. Have the advantage that following modification in vitrothey can be used to produce chimeric embryos and thus transgenic animals. James Malone Tomasz Adamusiak NCIt:C12935 SNOMEDCT:419965008 embryonic stem cell CL:0002327 An epithelial cell of the mammary gland. GOC:tfm PMID:19022771 cell mammary epithelial cell CL:0002334 A precursor to an adipocyte. An undifferentiated fibroblast that can be stimulated to form a fat cell. James Malone Tomasz Adamusiak preadipocyte CL:0002342 A circulating endothelial cell of the phenotype CD146-positive, CD105-positive, CD45-negative. This cell type is indicative of recent vascular damage. PMID:19022771 cell circulating endothelial cell CL:0002351 A multi-fate stem cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1. Jie Zheng Tomasz Adamusiak http://en.wikipedia.org/wiki/Pancreas progenitor cell of endocrine pancreas CL:0002352 gestational hematopoietic stem cell CL:0002353 A hematopoietic stem cell that resides in the fetal liver. In mice, this cell type is first observed at E10.5. This cell type is MHC-positive, HSA-positive, AA4.1-positive, CD45-positive, Sca-1 positive, CD150-positive, CD48-negative and CD244-negative. Jie Zheng Tomasz Adamusiak fetal liver hematopoietic progenitor cell CL:0002355 primitive red blood cell CL:0002356 primitive reticulocyte CL:0002357 fetal derived definitive erythrocyte CL:0002358 pyrenocyte CL:0002361 primitive erythroid progenitor CL:0002363 A keratocyte is a specialized fibroblast residing in the stroma that has a flattened, dendritic cell located between the lamellae with a large flattened nucleus and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratin sulfate. A keratocyte is a specialized fibroblast residing in the stroma that has a flattened, dendritic cell located between the lamellae with a large flattened nucleus and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratin sulfate. Ele Holloway James Malone Tomasz Adamusiak SNOMEDCT:397052000 keratocyte CL:0002364 An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells. [ PMID:18403190 GOC:tfm ] cortical thymic epithelial cell CL:0002365 An epithelial cell located in the inner portion of the thymus where the T lymphocytes become mature and are released into the circulation. An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output. James Malone Tomasz Adamusiak NCIt:C45702 medullary thymic epithelial cell CL:0002368 An endo-epithelial cell of the respiratory tract. Epithelium of the respiratory portion of the bronchial tree. Tomasz Adamusiak respiratory epithelial cell CL:0002371 A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). One of the cells of the body that compose the tissues, organs, and parts of that individual other than the germ cells. James Malone Tomasz Adamusiak NCIt:C12949 somatic cell CL:0002393 intermediate monocyte CL:0002394 CD141-positive myeloid dendritic cell CL:0002395 Gr1-high classical monocyte CL:0002396 CD14-low, CD16-positive monocyte CL:0002397 CD14-positive, CD16-positive monocyte CL:0002398 Gr1-positive, CD43-positive monocyte CL:0002399 CD1c-positive myeloid dendritic cell CL:0002402 Peyer's patch B cell CL:0002410 A cell that is found in the periacinar space of the exocrine pancreas and in perivascular and periductal regions of the pancreas, and has long cytoplasmic processes that encircle the base of the acinus. Expresses several intermediate filament proteins including vimentin and nestin. Shares many of the characteristics of hepatatic stellate cells, but not stellate cells of the central nervous system. Upon activation, this cell type undergoes morphological and gene expression changes that make the cell suggestive of being a type of myofibroblast. GOC:mah GOC:tfm PMID:17200706 cell pancreatic stellate cell CL:0002417 primitive erythroid lineage cell CL:0002421 nucleated reticulocyte CL:0002422 enucleated reticulocyte CL:0002451 A multi-fate stem cell that is the source of cells for growth of the mammary gland during puberty and gestation. This cell type gives rise to both the luminal and myoepithelial cell types of the gland, and have been shown to have the ability to regenerate the entire organ in mice. This cell type also plays an important role in carcinogenesis of the breast. This cell type is Lin-, CD24-positive, CD29-hi. [ PMID:16397499 GOC:tfm PMID:17851544 GOC:hjd PMID:15987436 ] mammary stem cell CL:0002453 The cell type from which oligodendrocytes develop. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons. GOC:tfm PMID:2014242 cell oligodendrocyte precursor cell CL:0002454 Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell CL:0002455 CD8_alpha-negative plasmactyoid dendritic cell CL:0002456 CD8_alpha-positive plasmactyoid dendritic cell CL:0002457 SNOMEDCT:127854005 epidermal Langerhans cell CL:0002458 langerin-positive dermal dendritic cell CL:0002459 langerin-negative dermal dendritic cell CL:0002460 CD8alpha-negative thymic conventional dendritic cell CL:0002461 CD103-positive dendritic cell CL:0002462 adipose dendritic cell CL:0002465 CD11b-positive dendritic cell CL:0002466 small intestine serosal dendritic cell CL:0002467 Gr1-high myeloid suppressor cell CL:0002468 Gr1-low myeloid suppressor cell CL:0002469 MHC-II-negative classical monocyte CL:0002470 MHC-II-positive classical monocyte CL:0002471 MHC-II-negative non-classical monocyte CL:0002472 MHC-II-low non-classical monocyte CL:0002473 MHC-II-high non-classical monocyte CL:0002474 lymphoid MHC-II-negative classical monocyte CL:0002475 lymphoid MHC-II-negative non-classical monocyte CL:0002476 bone marrow macrophage CL:0002477 adipose macrophage CL:0002478 F4/80-negative adipose macrophage CL:0002479 F4/80-positive adipose macrophage CL:0002507 langerin-positive lymph node dendritic cell CL:0002508 langerin-negative, CD103-negative lymph node dendritic cell CL:0002509 CD103-positive, langerin-positive lymph node dendritic cell CL:0002510 CD103-negative, langerin-positive lymph node dendritic cell CL:0002511 CD11b-low, CD103-negative, langerin-negative lymph node dendritic cell CL:0002512 CD11b-high, CD103-negative, langerin-negative lymph node dendritic cell CL:0002526 CD14-positive dermal dendritic cell CL:0002529 CD1a-positive dermal dendritic cell CL:0002532 CD16-positive myeloid dendritic cell CL:0002540 A mesenchymal stem cell that is part of the bone marrow. [ GOC:tfm ] mesenchymal stem cell of the bone marrow CL:0002551 fibroblast that is part of dermis Sirarat Sarntivijai tmeehan 2011-02-28T05:05:33Z cell fibroblast of dermis CL:0002553 A fibroblast that is part of lung http://purl.obolibrary.org/obo/CL_0002553 lung fibroblast CL:0002563 An epithelial cell of the intestine. [ GOC:tfm ] tmeehan cell intestinal epithelial cell CL:0002598 tmeehan 2011-03-06T05:46:39Z cell bronchial smooth muscle cell CL:0002601 A smooth muscle cell of the uterus. tmeehan 2011-03-06T05:53:28Z cell uterine smooth muscle cell CL:0002608 A neuron of the hippocampus. hippocampal neuron CL:0002617 A fat cell that is part of the breast. adipocyte of breast CL:0002618 An endothelial cell of the umbilical vein. [ GOC:tfm ] endothelial cell of umbilical vein CL:0002619 An adult angioblastic cell released from the bone marrow, capable of blood circulation and participation in angiogenesis by differentiating into blood vessel endothelial cells. Their existence is controversial. [ GOC:tfm PMID:20807818 PMID:9020076 ] adult endothelial progenitor cell CL:0002633 A basal cell in the respiratory tract. [ PMID:20699479 GOC:tfm ] repiratory basal cell CL:0005019 Ghrelin secreting cells found in the found in the exocrine pancreas. PMID:14970313 cell pancreatic epsilon cell CL:0009004 Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. PMID:10702418 retinal cell CL:1000488 An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts. [ PMID:18356246 PMID:16550043 GOC:tfm ] cholangiocyte CL:1000497 KUPO:0001010 cell kidney cell CL:2000018 Any endothelial cell of artery that is part of a coronary artery. [ GOC:TermGenie ] endothelial cell of coronary artery CL:2000058 Any osteoblast that is part of a skull. [ GOC:TermGenie ] calvarial osteoblast CL:2000074 Any leukocyte that is part of a spleen. [ GOC:TermGenie ] Splenocytes is a vague term that refers to any one of the different white blood cell types in the spleen. This name is seen many references as such and is not explained further, necessitating a need for this terminology. splenocyte DOID:162 A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. malignant neoplasm malignant tumor primary cancer cancer FLU:0001019 A specimen barcode is a specimen identification number formatted as an optical machine-readable representation. PERSON: Melanie Courtot WEB: http://en.wikipedia.org/wiki/Barcode specimen barcode GAZ:00000448 geographic location A reference to a place on the Earth, by its name or by its geographical location. geographic location GENEPIO:0001562 Identifier for a reference genome (used to build or compare an assembly) that is used in the genome browsers and in the community Damion Dooley GENEPIO reference genome identifier GENEPIO:0001795 help:In this dataset, selected data have been de-identified (anonymized) for access by dataset users. A 'de-identified data' role between a user and given data entails that the user is authorized to see only those fields (including those that are encrypted) which do not contain information that could be use to identify particular individuals (whether patients or medical practitioners) or potentially organizations in the case where an investigation may implicate them. Damion Dooley's note: There is a case in the "draft tuberculosis contextual data standard" that has this be a boolean selection. If a categorical field is linked directly, and it has no underlings, this indicates that it is being treated as a boolean feature. Damion Dooley Generally de-identified data should include HIPAA patient privacy fields as indicated in https://www.hipaa.com/hipaa-protected-health-information-what-does-phi-include/ de-identified data GENEPIO:0001800 sequence identifier GENEPIO:0001888 /^((:<FSA>[ABCEGHJKLMNPRSTVXY][0-9][ABCEGHJKLMNPRSTVWXYZ])) ?(:<LDU>[0-9][ABCEGHJKLMNPRSTVWXYZ][0-9])$/i, $FSA $LDU A Canadian postal code is a postal code that pertains to a geographic region of Canada. Note that a Canadian postal code can cover multiple communities. Secondly, postal codes can be retired, and then reintroduced elsewhere. Historical data associations may need to take the date of postal code mapping into account. Canada postal code GENO:0000815 The location of a sequence feature as defined by its start and end position on some reference coordinate system. 1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms). 2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there. sequence feature location GENO:0000902 The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future. We don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences. In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed. For example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus). genomic location genomic locus VMC:Location 1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. 2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus. 3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there. genomic feature location 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:0000010 software Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI software IAO:0000027 data item Data 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. 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: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 entity 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: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: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: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 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 http://www.ebi.ac.uk/efo/EFO_0001444 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: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: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: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: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: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: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: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 Damion Dooley's note: See https://www.w3.org/TR/NOTE-datetime for ISO 8601 time standards time measurement datum 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: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: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: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: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: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: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: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: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:0020000 A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. Mathias Brochhausen identifier proper name IAO:0020015 A personal name is a proper name identifying an individual person. Mathias Brochhausen http://en.wikipedia.org/wiki/Personal_name Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name) personal name ICO:0000001 A document that explains all relevant study information to assist a human subject in understanding the expectations and requirements of participation in a research study. This form document is presented to and signed by the study subject. AK, FM, YH, YL, MH, EE NCIt C16468 informed consent form ICO:0000023 an informed consent form that has been filled with all required contents. YH completely filled informed consent form ICO:0000024 an informed consent form that has been partically filled with required contents. YH partially filled informed consent form ICO:0000058 a one-dimensional temporal region that is a period of an informed consented study YH informed consented study period ICO:0000088 a temporal interval that represent the time of someone (for example the study subject) participating the study or the research. YL, MH, AK, EE, YH participation duration ICO:0000089 Total length of time of subject's participation in a clinical study; from the time of enrollment to the completion of follow-up. This duration is different with the 'planned duration of study subject participation' YL actual duration of study subject participation ICO:0000126 a termporal interval that represents a period of time during which a signed informed consent form is stored. YH, EE, YL, AK, MH WEB: http://answers.hhs.gov/ohrp/questions/7223 storage duration of signed informed consent form ICO:0000127 a participation time that is the total length of time of subject's participation in a research study; from the time of enrollment to the completion of follow-up. The term definition is adapted from NCIt definition of "Planned Duration of Study Subject Participation" (C70707) with modification. Compared to the NCIt definition, the ICO definition specifies research research study instead of a clinical study. This duration is different with the 'planned duration of study subject participation' YL planned duration of study subject participation ICO:0000146 A realizable entity that represents the eligibility of a candidate according to a study protocol. Frank Manion, Oliver He eligibility of candidate participation IDO:0000619 A disposition whose realization negatively regulates an immune response. Albert Goldfain Alexander Diehl Lindsay Cowell immunosuppressive disposition NCBITaxon:117571 Euteleostomi bony vertebrates Euteleostomi NCBITaxon:2759 Eukaryota eucaryotes eukaryotes Eukaryota NCBITaxon:314146 Euarchontoglires Euarchontoglires NCBITaxon:32523 Tetrapoda tetrapods Tetrapoda NCBITaxon:32524 Amniota amniotes Amniota NCBITaxon:33154 Opisthokonta Opisthokonta NCBITaxon:33213 Bilateria Bilateria NCBITaxon:40674 Mammalia mammals Mammalia NCBITaxon:7742 Vertebrata <Metazoa> Vertebrata vertebrates Vertebrata <Metazoa> NCBITaxon:9606 Homo sapiens human human being man Homo sapiens NCIT:C25621 Any system designed to expedite the sorting and delivery of mail by assigning a series of alphanumeric codes to each delivery area. Also used to refer to any individual delivery area code. Postal Code NCIT:C25690 The street name and building number where a person or organization can be found. Street Address NCIT:C25720 /^(:<zip>\d{5}(-\d{4})?)/, $zip A system designed to expedite the sorting and delivery of mail by assigning a series of numbers to each delivery area in the United States. Also used to refer to any individual delivery area code. Zip Code NCIT:C29719 A record of an individual's background in regard to smoking tobacco. This would include such factors as start date, end date (if applicable), number of cigarette smoked, attempts to quit, and others. Smoking History Smoking History NCIT:C40978 A sequence of decimal digits (0-9) that is used for identifying a destination telephone line or other device in a telephone network. Telephone Number NCIT:C42775 A text string identifier for a location to which e-mail can be delivered. Damion Dooley's note: It can also be used as an authorization token in some identification processes. E-mail Address NCIT:C81229 A description of an individual's current and past experience with alcoholic beverage consumption. Alcohol Use History Alcohol Use History NGBO:0000037 Data item which represents a normalized probability of observing the new amino acid at that position and ranges from 0 to 1. SIFT score impact NGBO:0000038 A processed specimen which is the output of preparing a DNA sample for further analysis. Dalia Alghamdi DNA processed specimen NGBO:0000055 Same amino acid change as a previously established pathogenic variant regardless of nucleotide change PS1 criteria NGBO:0000056 De novo (both maternity and paternity confirmed) in a patient with the disease and no family history PS2 criteria NGBO:0000057 The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls PS4 criteria NGBO:0000058 Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation PM1 criteria NGBO:0000059 Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or ExAC PM2 criteria NGBO:0000060 Assumed de novo, but without confirmation of paternity and maternity PM6 criteria NGBO:0000061 For recessive disorders, detected in trans with a pathogenic variant PM3 criteria NGBO:0000062 Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants PM4 criteria NGBO:0000063 ACMG guidelines for classification of variants of strong variants classification ACMG strong variants classification NGBO:0000064 Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product PS3 criteria NGBO:0000065 ACMG guidelines for classification of variants of moderate classification ACMG moderate classification criteria NGBO:0000066 ACMG guidelines for classification of variants of very strong classification ACMG very strong classification criteria NGBO:0000067 ACMG guidelines for classification of variants of spporting classification ACMG supporting classification criteria NGBO:6000003 inferred from the College of American Pathologists (CAP) requirements Information content entity that is a standard way that information is encoded for storage in a computer file. Dalia Alghamdi https://en.wikipedia.org/wiki/File_format data file format NGBO:6000004 inferred from https://en.wikipedia.org/wiki/Variant_Call_Format A file format which represent represent the format of a text file used in bioinformatics for storing gene sequence variations Dalia Alghamdi VCF format NGBO:6000005 A file format which represent a text-based format for storing biological sequences aligned to a reference sequence Dalia Alghamdi https://en.wikipedia.org/wiki/SAM_(file_format) SAM format NGBO:6000006 A file format which represent represent a text-based format for representing either nucleotide sequences or peptide sequences, in which base pairs or amino acids are represented using single-letter codes Dalia Alghamdi https://zhanglab.ccmb.med.umich.edu/FASTA/ FASTA format NGBO:6000007 A file format which represent text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores Dalia Alghamdi https://en.wikipedia.org/wiki/FASTQ_format FASTQ format NGBO:6000009 A fixed tissue slide specimen that is contain unstained tissue section(s) inferred from KFMC SOP unstained fixed tissue slide NGBO:6000012 A file format which represent a binary file format designed for storing a genome consists of multiple chromosomal sequences Dalia Alghamdi https://biojulia.net/BioSequences.jl/stable/io/twobit.html 2bit format NGBO:6000014 A file format which represent a data format allows display of continuous-valued data in track format Dalia Alghamdi https://genome.ucsc.edu/goldenPath/help/bedgraph.html bed graph format NGBO:6000019 A file format which represent represent format provides a flexible way to define the data lines that are displayed in an annotation track Dalia Alghamdi https://genome.ucsc.edu/FAQ/FAQformat.html bed format NGBO:6000021 A file format which represent binary format for storing sequence data. Dalia Alghamdi https://genome.sph.umich.edu/wiki/BAM BAM format NGBO:6000029 A standard operating procedure for shipping and receiving of sample shipping and receiving of samples SOP NGBO:6000057 A reference genome datum which represent reference genome edition reference genome version number NGBO:6000058 inferred from College of American Pathologists (CAP) requirments A reference genome datum which represent a location where reference genome can be accessed online Dalia Alghamdi reference genome URI NGBO:6000081 Information about data storage location information content entity which represent any physical hardware such as external hard drives, flash drives, and CD https://www.kelsercorp.com/blog/pros-and-cons-of-local-and-cloud-data-storage information about local data storage NGBO:6000083 Information about data storage location information content entity which represent information about the basic containers that hold your data in cloud storage Dalia Alghamdi https://cloud.google.com/storage/docs/key-terms information about cloud storage bucket NGBO:6000089 A personal name that designates the human being donated specimen name of specimen donor NGBO:6000092 A document which represent a contract that governs the transfer of tangible research materials between two organizations, when the recipient intends to use it for his or her own research purposes. Dalia Alghamdi https://en.wikipedia.org/wiki/Material_transfer_agreement material transfer agreement NGBO:6000093 inferred from ISBER A document information content entity established between organisations that governs the transfer of one or more data sets from the owner/provider to a third party Dalia Alghamdi https://www.medschl.cam.ac.uk/research/information-governance/information-governance-data-transfer-agreements/ data transfer agreement NGBO:6000098 An assay kit processed material comprises a sterile device for collecting a sample, a collection and dispersing device for depositing and holding the sample, a device for transferring the sample, and a container for storing the sample to be tested. There may also be a labeling system for identifying the sample and for diluting the sample Dalia Alghamdi specimen collection kit NGBO:6000099 A container which used to ship temperature sensitive products such as foods, pharmaceuticals, organs, blood, biologic materials, and chemicals. They are used as part of a cold chain to help maintain product freshness and efficacy. Dalia Alghamdi https://en.wikipedia.org/wiki/Insulated_shipping_container insulated shipping container NGBO:6000103 A one-dimensional temporal region that is a period of an duration of standard operation procedure Dalia Alghamdi When a procedure is discontinued or replaced, a paper or electronic copy is maintained for at least 2 years, recording initial date of use, and retirement date. standard operating procedure actual use duration NGBO:6000105 inferred from the College of American Pathologists (CAP) requirements A material processing process which attaches synthetic oligonucleotides of a known sequence to one or both ends of cDNA fragments Dalia Alhgamdi https://www.ebi.ac.uk/training/online/glossary/adapter-ligation adapter ligation process NGBO:6000106 A specimen which is a recognizable part or product taken from specimen Dalia Alghamdi specimen derivative NGBO:6000122 A data transformation which involeves curation, processing and analysis of complex biological data Dalia Alghamdi bioinformatics analysis NGBO:6000123 A gene expression level analysis is a bioinformatics analysis that compares the RNA expression levels of multiple genes (profiling) and/or multiple samples (screening) Dalia Alghamdi inferred from https://www.thermofisher.com/ca/en/home/life-science/gene-expression-analysis-genotyping/gene-expression-profiling.html gene expression level analysis NGBO:6000124 Variant calling is the process by which we identify variants from sequence data. Dalia Alghamdi https://www.ebi.ac.uk/training/online/course/human-genetic.../variant.../what-variant variant calling assay NGBO:6000125 A genetic variation analysis which assign a formal classification to a detected genetic variant. variant interpretation variant classification assay NGBO:6000128 A bioinformatics analysis which attempt to group biological sequences that are somehow related Dalia Alghamdi https://en.wikipedia.org/wiki/Sequence_clustering sequence clustring NGBO:6000140 A file format which represent alignment files are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. The axtNet and axtChain alignments are produced by processing the alignment files with additional utilities written by Jim Kent at UCSC Dalia Alghamdi http://genome.ucsc.edu/goldenPath/help/axt.html axt file format NGBO:6000148 required quality check list for the procedure of paraffin embedding and/or fixation. Dalia Alghamdi paraffin embedding and Fixation quality check report NGBO:6000150 a specimen which represent remaining portion of a specimen obtained for clinical purposes that is no longer needed for its original purpose and that would otherwise be discarded Dalia Alghamdi CAP accreditation program, Biorepository checklist remnant specimen NGBO:6000157 A specimen that derives from an organism and might contain infectious materials. specimen with potentially infectious materials NGBO:6000160 A training manual is a book or booklet of instructions, designed to improve the quality of a performed task. Dalia Alghamdi https://en.wikipedia.org/wiki/Training_manual training manual NGBO:6000161 A data item infromation content entity that represent any data that could potentially identify a specific individual. Any information that can be used to distinguish one person from another and can be used for de-anonymizing anonymous data can be considered PII. Dalia Alghamdi https://searchfinancialsecurity.techtarget.com/definition/personally-identifiable-information personally identifiable information NGBO:6000166 A sequencing assay which involves the determination of the arrangement of the amino acid sequence of a protein. Dalia Alghamdi protein sequencing NGBO:6000175 inferred from College of American Pathologists (CAP) requirments A database which represent libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. Dalia Alghamdi https://en.wikipedia.org/wiki/Biological_database biological database NGBO:6000179 A bioinformatics analysis data transformation which two or more things are positioned in a straight line or parallel to each other https://dictionary.cambridge.org/dictionary/english/alignment alignment NGBO:6000181 A bioinformatics analysis that produces data structure that improves the speed of data retrieval operations on a database table at the cost of additional writes and storage space to maintain the index data structure Dalia Alghamdi https://en.wikipedia.org/wiki/Database_index database index NGBO:6000182 A bioinformatics analysis which referes to the process of compressing to reduze the size of genome file Dalia Alghamdi genome indexing NGBO:6000185 A measured expression level which refers to the characteristic of preferentially expressing a parental allele in the hybrid due to variations in regulatory sequences from the parental genomes. Dalia Alghamdi https://www.pnas.org/content/116/12/5653 ASE_SNP_CNV_Expression, Allele-Specific Expression Allele-specific expression data NGBO:6000186 A measured expression level measurement datum which represent copy number variation (CNV) obtained by microarray Dalia Alghamdi microarray CNV genotypes data NGBO:6000190 A measured expression level measurement datum which refers to represent small non-coding RNAs of 19-24 nucleotides in length that downregulate gene expression during various crucial cell processes such as apoptosis, differentiation and development. Dalia Alghamdi microRNA expression data NGBO:6000193 A measured expression level which refers to activity (the expression) of thousands of genes at once, to create a global picture of cellular function. Dalia Alghamdi https://en.wikipedia.org/wiki/Gene_expression_profiling gene expression profile data NGBO:6000195 inferred from the College of American Pathologists (CAP) requirements. A mesurement datum that represent all of the protein-coding regions of genes in a genome (known as the exome) Dalia Alghamdi whole exome sequence data NGBO:6000198 A single molecule real time sequencing data is DNA sequence data generated from parallelized single molecule DNA sequencing method. Dalia Alghamdi inferred from https://en.wikipedia.org/wiki/Single-molecule_real-time_sequencing single molecule real time sequencing data NGBO:6000199 inferred from the College of American Pathologists (CAP) requirements A DNA sequence data which represent the the complete DNA sequence of an organism's genome at a single time Dalia Alghamdi https://en.wikipedia.org/wiki/Whole_genome_sequencing whole genome sequence data NGBO:6000200 DNA sequence data which represent genomic DNA obtained from environmental samples Dalia Alghamdi metagenomics sequence data NGBO:6000201 RNA sequence data which represent the complete complement of transcripts in a sample, at a given time Dalia Alghamdi inferred from https://sequencing.roche.com/en/ whole transcriptome sequence data NGBO:6000204 Inffered from clinical lab standard operating procedure 16s RNA sequence data is used to identify bacteria at the species level in order to differentiate between closely related species. RNA sequence data which is about the 16s gene of one or more organisms. Dalia Alghamdi https://www.sciencedirect.com/topics/neuroscience/16s-ribosomal-rna 16s RNA sequence data NGBO:6000207 A genetic variation analysis which involves identifying biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes. Dalia Alghamdi Bioinformatics operations, data types, formats, identifiers and topics ontology (operation_3226) variant prioritisation NGBO:6000212 An assay which attempt to select highly confident variants and remove the ones that are falsely called Dalia Alghamdi https://www.sevenbridges.com/smart-variant-filtering/ genetic variants filtration assay NGBO:6000216 A sequence alignment which align every residue in every sequence Dalia Alghamdi https://en.wikipedia.org/wiki/Sequence_alignment global sequence alignment NGBO:6000217 A sequence alignment which align dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context Dalia Alghamdi https://en.wikipedia.org/wiki/Sequence_alignment#Global_and_local_alignments local sequence alignment NGBO:6000218 A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. Dalia Alghamdi https://en.wikipedia.org/wiki/Multiple_sequence_alignment replace with OBIws multiple sequence alignment NGBO:6000219 A sequence alignment bioinformatics analysis which identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid) Dalia Alghamdi https://www.ebi.ac.uk/Tools/psa/ pairwise sequence alignment NGBO:6000225 A bioinformatics analysis which attempt to searching sequence databases by using alignment to a query sequence Dalia Alghamdi https://www.ebi.ac.uk/Tools/sss/ sequence similarity search NGBO:6000227 inferred from College of American Pathologists (CAP) requirments appropriate command line flags for running bioinformatics pipline, for example, bwa - Burrows-Wheeler Alignment Tool options found here: http://bio-bwa.sourceforge.net/bwa.shtml A symbol that is used to specify options for command line programs. command line argument command line parameter command line flag NGBO:6000229 Functional annotation is a bioinformatics analysis consists of attaching biological information to genomic elements such as: biochemical function, biological function, involved regulation and interactions and expression Dalia Alghamdi functional annotation NGBO:6000232 A planned process which ensure data have undergone data cleansing to ensure they have data quality, that is, that they are both correct and useful. Dalia Alghamdi https://en.wikipedia.org/wiki/Data_validation data validation NGBO:6000233 A data validation process that checks that the data is in a specified format (template), e.g., dates have to be in the format DD/ MM/YYYY is correct Dalia Alghamdi https://en.wikipedia.org/wiki/Data_validation format validation NGBO:6000235 inferred from College of American Pathologists (CAP) requirments A data validating whech validate sequencing quality scores and measure the probability that a base is called incorrectly. Dalia alghamdi sequence data quality validation NGBO:6000236 inffered from the College of American Pathologists (CAP) requirments A processed material which contain a set of articles or equipment needed for a specific purpose. Dalia Alghamdi assay kit NGBO:6000237 A process material which contains DNA fragments that represent the entire genome of an organism. Dalia Alghamdi https://www.thermofisher.com/ca/en/home/life-science/cloning/cloning-applications/library-construction.html DNA library NGBO:6000238 inffered from the College of American Pathologists (CAP) requirments An assay kit used for the technique of isolating DNA in a biological sample Dalia Alghamdi DNA extraction assay kit NGBO:6000244 A data item which represent datum related to reference genome used as a standard for comparison in basic research and clinical settings Dalia Alghamdi reference genome datum NGBO:6000246 inferred from College of American Pathologists (CAP) requirments A URL at which the data file file is stored. data file URL NGBO:6000248 A database is an information content entity that describe a structured set of data held in a computer, especially one that is accessible in various ways. Dalia Alghamdi https://en.oxforddictionaries.com/definition/database database NGBO:6000255 inferred from College of American Pathologists (CAP) requirments An assay kit processed material that include a set of articles or equipment needed for library construction Dalia Alghamdi library construction kit NGBO:6000257 A report that represent the process of data collection and analysis through which the degree of conformity to predetermined standards and criteria are exemplified Dalia Alghamdi https://pubmed.ncbi.nlm.nih.gov/1604740/ quality assesment report NGBO:6000258 A material processing that has as its input a specimen and as its output a sample derivative. Dalia Alghamdi sample derivative from specimen creation process NGBO:6000259 A data item that represent sort of archive that contains one or more files that have been reduced in size through file compression process inferred from https://support.microsoft.com/en-us/windows/zip-and-unzip-files-8d28fa72-f2f9-712f-67df-f80cf89fd4e5 compressed file NGBO:6000261 A bioinformatics analysis which analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model. Dalia Alghamdi Bioinformatics operations, data types, formats, identifiers and topics EDAM genetic variantion analysis NGBO:6000264 An assay which represent the process of targeting detected known disease causing genetic variant for validation purposes validation of known variant assay NGBO:6000265 inferred from the College of American Pathologists (CAP) requirements A validation of known variant assay which permits the direct detection of any point mutation in human DNA by analyzing the PCR products in an ethidium bromide-stained agarose or polyacrylamide gel https://www.sciencedirect.com/science/article/pii/S1046202305801240 allele specific PCR NGBO:6000269 A molecular quality that represent the number of copies of a particular gene varies from one individual to the next (germline mutation) Dalia Alghamdi inferred from https://www.genome.gov/genetics-glossary/Copy-Number-Variation copy number variation NGBO:6000270 A molecular quality that describe changes in copy number that have arisen in somatic tissues. Dalia Alghamdi Li, W., Lee, A. & Gregersen, P.K. Copy-number-variation and copy-number-alteration region detection by cumulative plots. BMC Bioinformatics 10, S67 (2009). https://doi.org/10.1186/1471-2105-10-S1-S67 copy number alteration NGBO:6000271 Secure file transfer is a planned process that represent data sharing via a secure, reliable delivery method. It is used to safeguard proprietary and personal data in transit and at rest. Most secure file sharing methods use standard protocols, including: Secure File Transfer Protocol (SFTP) https://www.globalscape.com/solutions/secure-file-transfer secure file transfer process NGBO:6000272 A data transfer protocol is a network protocol that provides file access, file transfer, and file management over any reliable data stream https://en.wikipedia.org/wiki/SSH_File_Transfer_Protocol secure file transfer protocol NGBO:6000273 A protocol plan specification which describes the process of data transfer between two entities data transfer protocol NGBO:6000274 A data transfer protocol, and extension of the Hypertext Transfer Protocol (HTTP). It is used for secure communication over a computer network, and is widely used on the Internet Dalia Alghamdi https://en.wikipedia.org/wiki/HTTPS hypertext transfer protocol secure NGBO:6000276 A protocol plan specification which describes the process of generating a collection of DNA fragments for sequencing library preparation protocol NGBO:6000278 Protocol for acceptence or rejcetion must be based on metrics and quality control parameters established during test optimization and utilized during validation result acceptance or rejection protocol NGBO:6000279 A protocol which describe the criteria for acceptance or rejection of a specimen specimen acceptance or rejection protocol NGBO:6000281 Sequencing quality scores measure the probability that a base is called incorrectly. to review sequencing quality scores NGBO:6000282 inferred from the College of American Pathologists (CAP) requirements A biological database that contains genes nomenclature created by the HUGO Gene Nomenclature Committee (HGNC) that sets the standards for human gene nomenclature. Dalia Alghamdi HUGO gene nomenclature committee gene name NGBO:6000283 A specimen that is divided into separate parts which are typically stored in separate containers as individual samples aliquot NGBO:6000286 inferred from ISBER A protocol that ensure that biospecimens can be tracked accurately from the collection site through biospecimen arrival and subsequent specimen tracking protocol NGBO:6000288 Each freezer, refrigerator, room temperature stor- age cabinet, or other unit appropriate to the collec- tions should have a unique identifier. storage unit identifier NGBO:6000289 A data item which represent the availability of other specimen from the same donor Availability of other specimen from the same donor NGBO:6000290 inferred from ISBER An identifier which denotes number assigned by a shipper of specimen. Dalia Alghamdi specimen shipment identifier NGBO:6000292 A version number denotes standard operating procedure Dalia Alghamdi inferred from College of American Pathologists (CAP) requirments standard operating procedure version number NGBO:6000293 A unique SOP name which captures the essence of the practice described. standard operating procedure title NGBO:6000294 A temperature which represent specimen temperature during shipment. specimen shipping temperature NGBO:6000296 A specimen shipping tempruture which represent a Refrigerated temperature (2 to 8°C) - wet ice or gel packs (conditioned at –15°C, designed for refrigerated temperatures, or phase change material rated for refrigerated transport). Dalia Alghamdi refrigerated specimen temperature NGBO:6000298 inferred from ISBER A planned process with the objective to destroy an entire collection or specific specimen. specimen destruction assay NGBO:6000299 inferred from ISBER A specimen culling is the process of reviewing and eliminating specimens in a collection or an entire collection either by destruction or transfer to a new custodian specimen culling NGBO:6000302 A data item representing a variant’s significance in relation to a disease or phenotype. clinical variant interpretation NGBO:6000303 inferred from College of American Pathologists (CAP) requirments A clinical variant interpretation that represents a sequence variant that is previously reported and is a recognized cause of the disorder. disease causing mutation predisposing variant sasceptibility gene susceptibility gene mutation pathogenic variant 1 2 1 4 2 2 3 1 NGBO:6000304 inferred from College of American Pathologists (CAP) requirments A clinical variant interpretation that represents a sequence variant that is previously unreported and is of the type which is expected to cause the disorder. likely pathogenic variant NGBO:6000305 inferred from College of American Pathologists (CAP) requirments A clinical variant interpretation that represents a sequence variant that is previously unreported and is of the type which may or may not be causative of the disorder. VUS variant of uncertain significance variant of unknown significance NGBO:6000306 inferred from College of American Pathologists (CAP) requirments A clinical variant interpretation that represents a sequence variant that is previously unreported and is probably not causative of disease likely benign variant NGBO:6000307 inferred from College of American Pathologists (CAP) requirements A clinical variant interpretation that represents a sequence variant previously classified or reported as a recognized neutral variant benign variant NGBO:6000318 A genomic feature location which represent the expression quantitative trait loci are genomic loci that explain all or a fraction of variation in expression levels of mRNAs Dalia Alghamdi https://en.wikipedia.org/wiki/Expression_quantitative_trait_loci expression quantitative trait loci NGBO:6000319 RNA sequence data that represent the sequence of single-stranded RNA molecule that is complementary to one of the DNA strands of a gene. The mRNA is an RNA version of the gene that leaves the cell nucleus and moves to the cytoplasm where proteins are made. https://www.genome.gov/genetics-glossary/messenger-rna messenger RNA sequence data NGBO:6000320 inferred from use case discussion A data item which indicates availability of specimen associated data Dalia Alghamdi measurement datum availability statement NGBO:6000323 A material processing which capture specific regions of interest after library preparation for next generation sequencing. https://sequencing.roche.com/en/products-solutions/products/sample-preparation/dna-reagents/target-enrichment.html#:~:text=Target%20enrichment%20is%20a%20cost,reduced%20cost%20and%20simplified%20analysis. target region enrichment assay NGBO:6000352 A bioinformatics analysis which involves any edit or change to a molecular sequence file. Dalia Alghamdi raw sequence file editing NGBO:6000353 An assay which generate OMICS data through a wet bench process such as sequencing techniques. Dalia Alghamdi omics data generation assay NGBO:6000354 A protocol that describe the process of assigning a formal classification to the detected variant Dalia Alghamdi interpretation of clinical variant protocol NGBO:6000355 inffered from College of American Pathologists (CAP) requirment A protocol which describes the guidance for the interpretation of sequence variants suggested by The American College of Medical Genetics and Genomics (ACMG). Dalia Alghamdi https://pubmed.ncbi.nlm.nih.gov/25741868/ ACMG guidelines for classification of variants NGBO:6000359 inffered from whole exome sequencing clinical report An algorithm which perform mapping of low-divergent sequences against a large reference genome, such as the human genome. Dalia Alghamdi http://bio-bwa.sourceforge.net/#:~:text=It%20consists%20of%20three%20algorithms,ranged%20from%2070bp%20to%201Mbp.&text=BWA%2DMEM%20also%20has%20better,for%2070%2D100bp%20Illumina%20reads. Burrows-Wheeler Aligner algorithm NGBO:6000360 inferred from the College of American Pathologists (CAP) requirements http://purl.obolibrary.org/obo/IAO_0000428 A protocol which describes the process of attaching synthetic oligonucleotides with known sequences to both or either ends of complementary DNA (cDNA) fragments as a prepration for sequencing rev Dalia Alghamdi adapter ligation protocol NGBO:6000362 inferred from College of American Pathologists (CAP) requirments A protocol which describe the process of validation of known variant Dalia Alghamdi inferred from Rodenburg RJ. The functional genomics laboratory: functional validation of genetic variants. J Inherit Metab Dis. 2018;41(3):297-307. doi:10.1007/s10545-018-0146-7 validation of known variant protocol NGBO:6000364 inferred from the College of American Pathologists (CAP) requirements A protocol which describes the process of Allele-specific polymerase chain reaction (PCR) Dalia Alghamdi allele specific PCR protocol NGBO:6000365 inferred from ISBER A protocol plan specification which describes the process of reducing the likelihood that the data can identify an individual. Dalia Alghamdi data anonymization protocol NGBO:6000377 Bioinformatics analysis which performs gapped alignment for single-end reads, supports paired-end mapping, generates mapping quality, and gives multiple hits if required inferred from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705234/ BWA assembly process NGBO:6000382 A software designed to extract meaningful information from the mass of molecular biology data bioinformatics analysis software NGBO:6000385 inferred from College of American Pathologists (CAP) requirments A data item that represent information on data storage. Dalia Alghamdi data storage datum NGBO:6000394 An objective specification to determine attaching synthetic oligonucleotides with known sequences to both or either ends of complementary DNA (cDNA) fragments Dalia Alghamdi inferred from the College of American Pathologists (CAP) requirements inferred from https://www.cytivalifesciences.com/en/us/solutions/genomics/knowledge-center/glossary/adapter-ligation ligation objective NGBO:6000395 inferred from the College of American Pathologists (CAP) requirements A protocol which describes the workflow to capture specific regions of interest after library preparation for NGS and has many advantages over whole genome sequencing (WGS). Dalia Alghamdi target enrichment protocol NGBO:6000397 inferred from the College of American Pathologists (CAP) requirements use case clinial report A data item that which represent information about subset of genes or specific regions of interest of the genome. inferred from https://www.bgi.com/us/sequencing-services/dna-sequencing/target-region-sequencing/ target sequence information NGBO:6000399 An information content entity that is about the location of data storage information about data storage location NGBO:6000400 inferred from use case A library preparation material processing which uses bead-linked transposomes for a more uniform tagmentation reaction compared to in-solution tagmentation reactions Dalia Alghamdi https://www.illumina.com/techniques/sequencing/ngs-library-prep/tagmentation.html in-bead tagmentation library prepration NGBO:6000402 A personal name that designates the person who executed the sequencing run. Dalia Alghamdi name of data generation assay executor NGBO:6000405 A version number of assay kit. assay kit version NGBO:6000406 inffered from whole exome sequencing clinical report A personal name that designates the person who executed the bioinformatics analysis. name of bioinformatics analysis executor NGBO:6000407 A data file which contain the output of data transformation process Dalia Alghamdi output data file NGBO:6000408 A data file which contain the input for data transformation process Dalia Alghamdi input data file NGBO:6000409 Information content entity about bioinformatics software information about software NGBO:6000410 Information about software includes software name bioinformatics software name NGBO:6000411 Information about software includes information on software version number. software version number NGBO:6000412 Information about software includes information on software parameter value. software parameter value NGBO:6000413 Information about software includes information on software parameter name. bioinformatics software parameter name NGBO:6000414 A time measurement datum of the bioinformatics analysis execution date. bioinformatics analysis execution date NGBO:6000415 Information about software includes software description. software description NGBO:6000416 Information about software includes software documentation URI software Documentation URI NGBO:6000417 An identifier which denotes the bioinformatics analysis ID. software run identifier NGBO:6000418 A description of the file that contain raw data generated by a measurement device. data file description NGBO:6000419 A document part of relevant notes or instructions regarding data generation assay execution assay execution note NGBO:6000439 A conclusion based on data about a permanent change in the DNA sequence that makes up a gene detected gene mutation NGBO:6000472 Any data file as generated by some acquisition computer or console. http://nmrML.org/nmrCV#NMR:1400267 data file NGBO:6000473 A data item which represents the substitution of one or more amino acids. amino acid substitution NGBO:6000474 A planned process of making the decision of the data transfer. data transfer agreement document act NGBO:6000475 An Identifier of an oligonucleotide probe. probe ID NGBO:6000476 A region of short stretches of single-stranded DNA or RNA used to detect the presence of complementary nucleic acid sequences (target sequences) by hybridization. oligonucleotide probe NGBO:6000477 A data item that describe expression quantitative trait loci. expression quantitative trait loci data NGBO:6000627 An assay kit used for the technique of target enrichment target enrichment kit NGBO:6000685 A software pipeline that is composed of a wide array of software algorithms to process biological raw data. Dalia Alghamdi https://www.sciencedirect.com/science/article/pii/S1525157817303732 bioinformatics pipeline NGBO:6000689 An information content entity about user authentication information. This term is used for to store users information registered in a federated service https://github.com/Dalalghamdi/NGBOSemanticWebApplication user information OBIB:0000029 A material entity that is bearer of a medication role. Person: Chris Stoeckert, Jie Zheng Penn Group medication material OBIB:0000033 A planned process for receiving specimens such as into a laboratory. Person: Jie Zheng, Chris Stoeckert Penn Group specimen receiving OBIB:0000034 An adding a material entity into a target process where a collected specimen is added to a specimen container. (note, not used for other specimen process that produce new specimens) Person: Jie Zheng, Chris Stoeckert Penn Group adding specimen into a container OBIB:0000035 An adding specimen into a container process that spots the blood from an organism on the blood spot card. Person: Jie Zheng, Chris Stoeckert Penn Group blood spotting OBIB:0000036 A processed specimen which is the output of a density gradient centrifugation of an anticoagulated blood specimen that contains most of the white blood cells and platelets. Person: Jie Zheng, Chris Stoeckert http://en.wikipedia.org/wiki/Buffy_coat buffy coat specimen OBIB:0000039 A blood specimen that is located on a blood spot card. Person: Jie Zheng, Chris Stoeckert Penn Group A specimen that located in a blood spot card via blood spotting process. blood specimen on blood spot card OBIB:0000041 A duration time of smoking about how long a person has been smoking regularly. (better to have criteria of regularly mean, such as smoke everyday) Person: Jie Zheng, Chris Stoeckert Penn Group duration time of smoking regularly OBIB:0000051 A time measurement datum which is the start date of a smoking behavior. Person: Jie Zheng, Chris Stoeckert Penn Group smoking start date OBIB:0000053 A time measurement datum about how long a person has been smoking. Person: Jie Zheng, Chris Stoeckert Penn Group duration time of smoking OBIB:0000054 A time measurement datum which is the end date of a smoking behavior. Person: Jie Zheng, Chris Stoeckert Penn Group smoking end date OBIB:0000060 A time measurement datum that states the duration during which a specimen was submerged in fixative. more general than time in formalin Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB time in fixative measurement OBIB:0000068 An identifier that refers to a collection packet used in a specimen collection process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Kit ID OBIB NCI BBRB collection packet identifier OBIB:0000070 A protocol that is a set of step-by-step instructions compiled by an organization for carrying out routine operations. Person: Chris Stoeckert, Helena Ellis, Jie Zheng SOP https://en.wikipedia.org/wiki/Standard_operating_procedure NCI BBRB standard operating procedure OBIB:0000071 A standard operating procedure for the transportation of specimens. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB specimen transport SOP OBIB:0000072 A standard operating procedure for collecting specimens from organism. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB tissue procurement SOP OBIB:0000073 A standard operating procedure for properly and completely filling out a case report form. Person: Chris Stoeckert, Helena Ellis, Jie Zheng CRF completion protocol OBIB NCI BBRB case report form completion SOP OBIB:0000086 specimen collected with GTEx Pink Kit A specimen from organism that is collected with a collection packet that is designed to collect specimens of a particular type for a particular purpose. Person: Chris Stoeckert, Helena Ellis, Jie Zheng specimen collected with specific kit OBIB NCI BBRB specimen collected with specific collection packet OBIB:0000093 A time measurement datum that states the duration during which the specimen donor's body was refrigerated. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB time donor body refrigerated measurement OBIB:0000131 A time measurement datum of the period between organ resection and the time of first clamping perfomed in vivo. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB in vivo intraoperative ischemic period OBIB:0000150 A time measurement datum of the duration of fasting by the specimen donor prior to surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB Duration of fasting by specimen donor prior to surgery OBIB:0000200 BPV SOP governing receipt and dissection of surgical tissue in the Tissue Bank A standard operating procedure for the receipt and dissection of surgical tissue in a biobank. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB receipt and dissection of surgical specimen SOP OBIB:0000202 A personal name that designates the person who received a specimen in the biobank. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of biobank person receiving specimen OBIB:0000204 Parent Tissue Specimen ID of required study tumor tissue received in Tissue Bank from the Pathology Gross Room A specimen ID denoting a specimen that is used to create a specimen family. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB parent specimen ID OBIB:0000205 A personal name that designates the person who performed the dissection of a surgical specimen to create a specimen family. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of dissector of parent specimen OBIB:0000220 A quality that inheres in buffered formalin by virtue of its usage and processing. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB buffered formalin condition OBIB:0000222 A standard operating procedure for collection and processing of blood specimens. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB blood specimen collection and processing SOP OBIB:0000232 A personal name that designates the person who performed the collection of a blood specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB name of person performing blood draw OBIB:0000240 A personal name that designates the person who received a blood specimen in the laboratory. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of person receiving blood specimen in laboratory OBIB:0000243 DNA PAXgene tube Specimen Barcode ID A specimen barcode that is associated with a vacutainer. need specimen barcode Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB vacutainer specimen barcode OBIB:0000246 A personal name that designates the person who stored a specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of person storing specimen OBIB:0000250 An identifier that specifically identifies a particular conical centrifuge tube. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Conical centrifuge Tube code NCI BBRB, OBIB NCI BBRB conical centrifuge tube identifier OBIB:0000252 A specimen barcode that is associated with a blood plasma specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB blood plasma specimen barcode OBIB:0000255 A specimen barcode that is associated with a cryovial. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB cryovial specimen barcode OBIB:0000257 A personal name that designates the person who processed a blood specimen to generate aliquots of blood plasma specimens. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB name of person processing blood plasma specimen aliquots OBIB:0000258 A personal name that designates the person who transferred blood plasma specimens to freezer. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB name of person transferring blood plasma specimens to freezer OBIB:0000263 Whole Cell Pellet Aliquot Specimen Barcode ID A specimen barcode that is associated with a cell pellet specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB cell pellet specimen barcode OBIB:0000266 A personal name that designates the person who performed processing of the blood cell pellet specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB name of person processing blood cell pellet specimen OBIB:0000272 A role borne by an organization that is the provider of a specimen that is transported to another organization. Person: Chris Stoeckert, Helena Ellis, Jie Zheng specimen shipping organization NCI BBRB, OBIB NCI BBRB specimen transporting organization OBIB:0000273 A role borne by an organization that is the recipient of a specimen that is transported from another organization. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB specimen receiving organization OBIB:0000274 A personal name that designates the person who is responsible for the transport of a specimen to another organization. Person: Chris Stoeckert, Helena Ellis, Jie Zheng name of person responsible for specimen shipment NCI BBRB, OBIB NCI BBRB name of person responsible for specimen transport OBIB:0000275 A personal name that designates the person who verified the specimen transport was according to best practice, international standards, and industry regulations as trained by the IATA. Person: Chris Stoeckert, Helena Ellis, Jie Zheng name of IATA-trained person verifying specimen shipment http://www.iata.org/training/pages/index.aspx NCI BBRB name of IATA-trained person verifying specimen transport OBIB:0000285 A personal name that designates the person who performed a quality control inspection of the specimen that is to be transported to another organization. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB name of quality control inspector of specimen OBIB:0000286 A personal name that designates the person who performed the data entry process for filling in a tissue recovery case report form. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of data entry person for tissue recovery form OBIB:0000287 A personal name that designates the person who is the leader of the team responsible for entering the tissue recovery form data. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of team leader for filling out tissue recovery form OBIB:0000288 A standard operating procedure for fixation of a tissue to the state where it is completely infiltrated with a suitable histological wax and can be embedded ready for section cutting on the microtome for a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng http://www.leicabiosystems.com/pathologyleaders/an-introduction-to-specimen-processing/ NCI BBRB FFPE tissue processing SOP OBIB:0000292 An information content entity that indicates whether duration of the alcohol stage followed that prescribed in the FFPE tissue processing SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence of alcohol stage duration to FFPE tissue processing SOP OBIB:0000293 A time measurement datum that is the result of measuring the duration of the alcohol stage in a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE alcohol stage duration OBIB:0000294 An information content entity that indicates whether duration of the dehydration process followed that prescribed in the FFPE tissue processing SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence of dehydration process duration to FFPE tissue processing SOP OBIB:0000295 A time measurement datum that is the result of measuring the duration of the dehydration process in the formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB FFPE dehydration process duration OBIB:0000296 An information content entity that indicates whether temperature of the dehydration process followed that prescribed in the FFPE tissue processing SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence of dehydration process temperature to FFPE tissue processing SOP OBIB:0000298 An information content entity that indicates whether the number of stages and replicates followed that prescribed in the FFPE tissue processing SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence of stage and replicate numbers to FFPE tissue processing SOP OBIB:0000300 An information content entity that indicates whether the duration in clearing agent followed that prescribed in the FFPE tissue processing SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence of duration in clearing agent to FFPE tissue processing SOP OBIB:0000301 A time measurement datum that is the result of measuring the duration in clearing agent in the formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB FFPE clearing agent duration OBIB:0000302 An information content entity that indicates whether the temperature of clearing agent followed that prescribed in the FFPE tissue processing SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence of temperature of clearing agent to FFPE tissue processing SOP OBIB:0000304 An information content entity that indicates whether the paraffin impregnation method followed that prescribed in the FFPE tissue processing SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence to paraffin impregnation method in FFPE tissue processing SOP OBIB:0000306 An information content entity that indicates whether the paraffin temperature followed that prescribed in the FFPE tissue processing SOP. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence of paraffin temperature to FFPE tissue processing SOP OBIB:0000309 A standard operating procedure for the paraffin embedding of a formalin-fixed paraffin-embedded (FFPE) tissue. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE tissue paraffin embedding SOP OBIB:0000313 A time measurement datum that is the result of measuring the total time that freshly poured blocks were cooled in the formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB total time FFPE freshly poured blocks were cooled OBIB:0000314 A standard operating procedure for the handling, tracking, and storing of a formalin-fixed paraffin-embedded (FFPE) tissue block. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE tissue block handling, tracking, and storage SOP OBIB:0000315 An information content entity that indicates whether the FFPE tissue block storage SOP was followed. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB adherence to FFPE tissue block storage SOP OBIB:0000318 A personal name that designates the person who performed a specimen slide preparation. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Slide Prep Technician Name NCI BBRB, OBIB NCI BBRB name of specimen slide preparation technician OBIB:0000319 A standard operating procedure for the preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE tissue section preparation SOP OBIB:0000320 An age that inheres in a microtome blade. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB microtome blade age OBIB:0000321 A microtome blade age that indicates that the microtome blade is as new as possible. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB fresh microtome blade OBIB:0000334 A standard operating procedure for the hematoxylin and eosin (H&E) staining and slide mounting of a formalin-fixed paraffin-embedded (FFPE) tissue section. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE tissue section H&E staining and mounting SOP OBIB:0000335 A time measurement datum that is the result of measuring the duration in an oven for the hematoxylin and eosin staining of a formalin-fixed paraffin-embedded (FFPE) tissue section. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB FFPE tissue section H&E staining in oven duration OBIB:0000341 A planned process involving the manual performance of the FFPE tissue section H&E deparaffinization protocol. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB manual FFPE tissue section H&E deparaffinization OBIB:0000342 A planned process involving the manual performance of the FFPE tissue section H&E staining protocol. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB manual FFPE tissue section H&E staining OBIB:0000343 A planned process involving the manual performance of the FFPE tissue section H&E clearing protocol. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB manual FFPE tissue section H&E clearing OBIB:0000344 A planned process involving the manual performance of the FFPE tissue section H&E cover slip protocol. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB manual FFPE tissue section H&E cover slipping OBIB:0000349 A specimen barcode associated with the specific chart (key) used to randomly assign specimens to one of several distinct experimental protocols. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB specimen randomization key ID OBIB:0000360 An identifier that specifically identifies a particular component of a collection packet. Person: Chris Stoeckert, Helena Ellis, Jie Zheng kit component ID NCI BBRB, OBIB NCI BBRB collection packet component ID OBIB:0000365 A specimen ID that specifically identifies a particular tissue cassete used in a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB FFPE tissue cassette ID OBIB:0000368 A time measurement datum that is the result of measuring the duration of the the planned delay of placing the tissue cassette in fixative in the formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB placement of tissue cassette in FFPE fixative delay duration OBIB:0000374 A time measurement datum that is the result of measuring the time between FFPE tissue processor cycle completion and embedding in a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB measurement of time between FFPE tissue processor cycle completion and embedding OBIB:0000380 A personal name that designates the person who performed the dissection of a normal tissue adjacent to a tumor for a formalin-fixed paraffin-embedded (FFPE) process. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of dissector of normal adjacent tissue to tumor for FFPE OBIB:0000385 An identifier that specifically identifies a particular specimen image. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB specimen image ID OBIB:0000387 name of submitter of pathology case summary report. Person: Chris Stoeckert, Helena Ellis, Jie Zheng name of submitting pathologist NCI BBRB, OBIB NCI BBRB name of submitter of pathology case summary report. OBIB:0000389 A personal name that designates the person who served as the reviewer for quality assurance purposes of a pathology case summary report. Person: Chris Stoeckert, Helena Ellis, Jie Zheng name of submitting pathologist NCI BBRB, OBIB NCI BBRB name of reviewer of pathology case summary report. OBIB:0000402 An information content entity that is an indicator of whether the local pathology review of a formalin-fixed paraffin-embedded (FFPE) hematoxylin and eosin (H&E)-stained tumor tissue slide confirmed the histological type. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB confirmation of histologic type of FFPE H&E tumor slide OBIB:0000408 A personal name that designates the person who served as the pathologist reviewing a specimen slide at an organization conducting specimen collection from organisms. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of reviewing pathologist at organization conducting specimen collection OBIB:0000410 A personal name that designates the person who performed the data entry process for filling in a local pathology review form. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of data entry person for local pathology review form OBIB:0000413 A personal name that designates the person who received a specimen in a pathology gross room from an associated operating room (OR). Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of person in gross room receiving OR specimen OBIB:0000414 A specimen transport SOP governing the transport of tissue from the operating room (OR) to the pathology gross room. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB specimen transport from OR to gross room SOP OBIB:0000419 A personal name that designates the person who performed the gross evaluation of a resected tissue specimen. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB name of performer of gross evaluation of resected tissue specimen OBIB:0000445 An information content entity that is an indicator of whether a tumor specimen was obtained and processed with a particular FFPE fixation delay protocol other than meeting the top priority for tissue procurement. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB additional tumor specimen was obtained and processed with a particular FFPE fixation delay protocol OBIB:0000474 An centrally registered identifier symbol assigned by an Institutional Review Board (IRB) that identifies a particular protocol at a given site. Person: Chris Stoeckert, Helena Ellis, Jie Zheng protocol number at a site NCI BBRB, OBIB NCI BBRB identification number of a protocol at a particular site OBIB:0000477 A personal name that designates who performed the screening of a potential specimen donor for a research study. Person: Chris Stoeckert, Helena Ellis, Jie Zheng specimen donor screener NCI BBRB, OBIB NCI BBRB name of person screening specimen donors OBIB:0000478 A personal name of an individual with research obtainer role who approaches a person's legal representative and informs them of key facts about potential risks and benefits, and asks them for authorization for post-mortem specimen donation for research for the person they legally represent. Person: Chris Stoeckert, Helena Ellis, Jie Zheng Research authorization obtainer for post-mortem specimen donation NCI BBRB, OBIB NCI BBRB name of person obtaining authorization from legally authorized representative for post-mortem specimen donation OBIB:0000480 An identifier that uniquely identifies a particular legally authorized representative in a research study. Person: Chris Stoeckert, Helena Ellis, Jie Zheng legal representative identifier NCI BBRB, OBIB NCI BBRB identifier for legally authorized representative OBIB:0000481 A relationship that may be biological or legal, between the specimen donor and the legally authorized representative who signed the research authorization. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB relationship between person signing research authorization and specimen donor OBIB:0000499 A time measurement datum that is the result of measuring the time elapsed since radiation therapy prior to surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB time since radiation therapy was received prior to surgery OBIB:0000500 A time measurement datum that is the result of measuring the time elapsed since chemotherapy prior to surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB time since chemotherapy was received prior to surgery OBIB:0000501 A time measurement datum that is the result of measuring the time elapsed since immunotherapy prior to surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB time since immunotherapy was received prior to surgery OBIB:0000502 A time measurement datum that is the result of measuring the time elapsed since hormonal therapy prior to surgery. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB time since hormonal therapy was received prior to surgery OBIB:0000507 An Alcohol Use History in which there is no alcohol consumption. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB lifelong non-drinker of alcohol OBIB:0000508 An Alcohol Use History in which there was alcohol consumption in the past but is currently a non-drinker of alcohol. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB current non-drinker of alcohol OBIB:0000509 An Alcohol Use History in which alcohol consumption was equal to or less than 2 drinks per day for men and 1 drink or less per day for women. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB moderate alcohol consumption history OBIB:0000510 An Alcohol Use History in which alcohol consumption was more than 2 drinks per day for men and more than 1 drink per day for women. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB greater than moderate alcohol consumption history OBIB:0000511 A time measurement datum that is the result of measuring the duration of greater than moderate alcohol consumption (more than 2 drinks per day for a man or more than 1 drink per day for a woman) prior to study enrollment. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB duration of greater than moderate alcohol consumption prior to enrollment OBIB:0000512 Less than 100 cigarettes smoked in lifetime A Smoking History in which there was no or an insignificant level of smoking. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB lifelong non-smoker history OBIB:0000513 A Smoking History in which there is current smoking either on a daily or non-daily basis. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB current smoker history OBIB:0000514 A Smoking History in which there is no current smoking and has not been smoking for more than 15 years. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB current reformed smoker for more than 15 years history OBIB:0000515 A Smoking History in which there is no current smoking and has not been smoking for less than 15 years. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB current reformed smoker for less than 15 years history OBIB:0000526 A time measurement datum that is the result of measuring the duration of use of hormonally based birth control prior to enrollment in a study. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB duration of hormonal birth control use prior to enrollment OBIB:0000527 A time measurement datum that is the result of measuring the time elapsed since the participant last used hormonally based birth control. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB time since last usage of hormonal birth control OBIB:0000529 A time measurement datum that is the result of measuring the duration of hormone replacement therapy prior to enrollment in a study. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB duration of hormone replacement therapy prior to enrollment OBIB:0000530 A time measurement datum that is the result of measuring the time elapsed since the participant last used hormonally replacement therapy. Person: Chris Stoeckert, Helena Ellis, Jie Zheng NCI BBRB, OBIB NCI BBRB time since last usage of hormone replacement therapy OBIB:0000543 A clinical history in which there is a history of sepsis. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of sepsis OBIB:0000544 A clinical history in which there is a history of pneumonia. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of pneumonia OBIB:0000545 A clinical history in which there is a history of open wounds. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of open wounds OBIB:0000546 A clinical history in which there is a history of a high unexplained fever . Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of high unexplained fever OBIB:0000547 A clinical history in which there is a history of positive blood cultures. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of positive blood cultures OBIB:0000548 A clinical history in which there is a history of abnormal white blood cell levels. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of abnormal white blood cell levels OBIB:0000549 A clinical history in which there is a history of fungal infections. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of fungal infections OBIB:0000550 A clinical history in which there is a history of the presence of ascites fluid. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of ascites OBIB:0000551 A clinical history in which there is a history of cellulitis. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of cellulitis OBIB:0000552 A clinical history in which there is a history of receiving a blood transfusion while in another country. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of blood transfusion in foreign country OBIB:0000553 A clinical history in which there is a history of receiving a human tissue or organ transplant . Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of human tissue transplant OBIB:0000554 A clinical history in which there is a history of receiving an animal tissue or organ xenotransplant. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of animal tissue xenotransplant OBIB:0000555 A clinic history in which there is a history of a recent of smallpox vaccination. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of smallpox vaccination OBIB:0000556 A clinical history in which there is a history of contact with someone who recently had smallpox. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB a clinical history of contact with someone with smallpox OBIB:0000557 The patient had a clinical history of dialysis treatment three times a week for longer than one month. A clinical history in which there is a history of significant regular dialysis treatment. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of dialysis OBIB:0000558 A clinical history in which there is a current diagnosis of cancer at death. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of cancer at death OBIB:0000559 A clinical history in which there is a history of cancer diagnosis in the preceding five years. A clinical history in which there is a history of cancer diagnosis within a specified time frame. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of cancer within a time period before death OBIB:0000560 A clinical history in which there is a history of tuberculosis . Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of tuberculosis OBIB:0000561 A clinical history in which there was active meningitis at death. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of meningitis at death OBIB:0000562 A clinical history in which there was active encephalitis at death. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of encephalitis OBIB:0000563 A clinical history in which there is a history of long term steroid use. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of long term steroid use OBIB:0000564 A clinical history in which there is a history of osteomyelitis. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of osteomyelitis OBIB:0000565 A clinical history in which there is a history of unexplained seizures. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of unexplained seizures OBIB:0000566 A clinical history in which there is a history of unexplained weakness and fatigue described as flu-like symptoms. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of unexplained weakness and fatigue OBIB:0000567 A clinical history in which there is a history of exposure to toxic substances that may have led to chronic conditions. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of exposure to toxins OBIB:0000568 A clinical history in which there is a history of an animal bite in the last 12 months, from an animal suspected to have rabies. A clinical history in which there is a history of an animal bite in recent past, from an animal suspected to have rabies. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of exposure to rabies OBIB:0000573 A clinical history in which there is a history of clotting disorders, such as hemophilia, requiring treatment with human-derived clotting factors. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of clotting disorders OBIB:0000574 A clinical history in which there is a history of growth hormone use. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of growth hormone use OBIB:0000575 A clinical history in which there is a history of the donor not being able to be tested for Human Immunodeficiency Virus (HIV) because of hemodilution. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of inability to have Human Immunodeficiency Virus testing due to hemodilution OBIB:0000576 A clinical history in which there is a history of unexplained weight loss. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of unexplained weight loss OBIB:0000577 A clinical history in which there is a history of night sweats. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of night sweats OBIB:0000578 A clinical history in which there is a of blue or purple spots on the skin or mucus membranes (typical of Kaposi's sarcoma). Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of blue or purple spots on skin or mucous membranes OBIB:0000579 A clinical history in which there is a history of unexplained lymphadenopathy lasting more than one month. A clinical history in which there is a history of unexplained lymphadenopathy of a specific duration. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of unexplained lymphadenopathy OBIB:0000580 A clinical history in which there is a history of fever of at least 38.6 Celsius for more than 10 days. A clinical history in which there is a history of fever of at least 38.6 Celsius for a specified duration. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of a prolonged fever OBIB:0000581 A clinical history in which there is are active signs of unexplained persistent cough and/or shortness of breath. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of an unexplained cough or shortness of breath OBIB:0000582 A clinical history in which there is a history of opportunistic infections. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of opportunistic infections OBIB:0000583 A clinical history in which there is a history of sexually transmitted diseases Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of sexually transmitted disease OBIB:0000584 A clinical history in which there is a history of drug abuse. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of drug abuse OBIB:0000585 A clinical history in which there is a history of a Severe Acute Respiratory Syndrome (SARS) diagnosis. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of Severe Acute Respiratory Syndrome OBIB:0000586 A clinical history in which there is a history of recent contact with someone who has Severe Acute Respiratory Syndrome (SARS). Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of exposure to Severe Acute Respiratory Syndrome OBIB:0000587 A clinical history in which there is a history of West Nile Virus (WNV) infection. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of West Nile Virus OBIB:0000588 A clinical history in which there is a history of contact with a human or animal who has West Nile Virus (WNV). Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of West Nile Virus exposure OBIB:0000589 A clinical history in which there is a history of current gonorrhea infection or treatment for gonorrhea in the last 12 months. A clinical history in which there is a history of active gonorrhea infection or treatment for gonorrhea in the recent past. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of gonorrhea OBIB:0000590 A clinical history in which there is a history of current syphilis infection or treatment for syphilis in the last 12 months. A clinical history in which there is a history of active syphilis infection or treatment for syphilis in the recent past. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of syphilis OBIB:0000591 A clinical history in which there is a history of Hepatitis B infection. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of Hepatitis B OBIB:0000592 A clinical history in which there is a history of Hepatitis C infection. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of Hepatitis C OBIB:0000593 A clinical history in which there is a history of Human Immunodeficiency Virus (HIV). Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of Human Immunodeficiency Virus OBIB:0000594 A clinical history in which there is a history of systemic lupus Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of lupus OBIB:0000595 A clinical history in which there is a history of sarcoidosis. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of sarcoidosis OBIB:0000596 A clinical history in which there is a history of scleroderma. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of scleroderma OBIB:0000597 A clinical history in which there is a history of Reye's Syndrome. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of Reye's Syndrome OBIB:0000598 A clinical history in which there is a history of rheumatoid arthritis. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of rheumatoid arthritis OBIB:0000599 A clinical history in which there is a history of idiopathic heart disease. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of idiopathic heart disease OBIB:0000600 A clinical history in which there is a history of Alzheimer's Disease. Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of Alzheimer's disease OBIB:0000601 A clinical history in which there is a history of dementia with unknown cause that is not caused by a previous Cerebrovascular Accident (CVA) infection, head trauma or brain tumor). Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of dementia of unknown cause OBIB:0000602 A clinical history in which there is a history of Multiple Sclerosis (MS). Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of Multiple Sclerosis OBIB:0000603 A clinical history in which there is a history of Amyotrophic Lateral Sclerosis (ALS) Person: Chris Stoeckert, Helena Ellis, Jie Zheng OBIB NCI BBRB clinical history of Amyotrophic Lateral Sclerosis OBI:0000011 planned process planned process Injecting mice with a vaccine in order to test its efficacy A processual entity that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process OBI:0000015 biological feature identification objective Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature. Jennifer Fostel biological feature identification objective OBI:0000018 material supplier role Jackson Labs is an organization which provide mice as experimental material a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. Supplier role is a special kind of service, e.g. biobank PERSON:Jennifer Fostel material provider role supplier material supplier role OBI:0000038 chromatography column Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms. Frank Gibson http://en.wikipedia.org/wiki/Column_chromatography open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 chromatography column OBI:0000047 processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material OBI:0000051 liquid chromatography mass spectrometry platform A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI. OBI instrument branch OBI Instrument branch liquid chromatography mass spectrometry platform OBI:0000055 software optimization objective Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software. Jennifer Fostel software optimization objective OBI:0000070 assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method assay OBI:0000086 reagent role Buffer, dye, a catalyst, a solvating agent. A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. PERSON:Matthew Brush reagent PERSON:Matthew Brush Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). reagent role OBI:0000093 patient role a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778 a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider GROUP:Role Branch patient OBI, CDISC CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably patient role OBI:0000094 material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing OBI:0000096 protocol testing objective Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols. Jennifer Fostel protocol testing objective OBI:0000101 measured expression level Examples are quantified data from an expression microarray experiment, PCR measurements, etc. A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts. person:Chris Stoeckert OBI Data Transformation branch measured expression level OBI:0000112 specimen role liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. GROUP: Role Branch OBI specimen role OBI:0000113 sequence feature identification objective Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide. Jennifer Fostel sequence feature identification objective OBI:0000131 molecular feature identification objective Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications. Jennifer Fostel molecular feature identification objective OBI:0000134 hardware testing objective Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner. Jennifer Fostel hardware testing objective OBI:0000151 filter paper a device manufacture with the intent to provide a porous unsized paper used for filtering. Frank Gibson sep:00107 filter paper OBI:0000186 protocol optimization objective Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol. Jennifer Fostel protocol optimization objective OBI:0000192 microtiter plate A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA) A microtiter_plate is a flat plate with multiple wells used as small test tubes. Melanie Courtot microplate http://en.wikipedia.org/wiki/Microtiter_plate microtiter plate OBI:0000208 methodology testing objective Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies. Jennifer Fostel methodology testing objective OBI:0000219 cellular feature identification objective Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation. Jennifer Fostel cellular feature identification objective OBI:0000232 hardware optimization objective Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware. Jennifer Fostel hardware optimization objective OBI:0000242 software testing objective Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software. Jennifer Fostel software testing objective OBI:0000245 organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization OBI:0000257 DNA extraction A DNA extraction is a nucleic acid extraction where the desired output material is DNA. PlanAndPlannedProcess Branch OBI branch derived DNA extraction OBI:0000260 plan The plan of researcher X to perform an experiment according to a protocol. A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. AR, BP, JM, MC, PRS branch derived plan OBI:0000268 organism feature identification objective Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle. Jennifer Fostel organism feature identification objective OBI:0000272 protocol PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol protocol OBI:0000274 adding a material entity into a target Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water. is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'. Class was renamed from 'administering substance', as this is commonly used only for additions into organisms. BP branch derived adding a material entity into a target OBI:0000338 interpreting data Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion PERSON: Bjoern Peters PERSON: Jennifer Fostel Bjoern Peters drawing a conclusion based on data OBI:0000345 mass analyzer The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply. Frank Gibson PERSON: Daniel Schober http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer mass analyzer OBI:0000370 contain function A syringe, a beaker A contain function is a function to constrain a material entities location in space Bill Bug Daniel Schober Frank Gibson Melanie Courtot contain function OBI:0000371 heat function A heat function is a function that increases the internal kinetic energy of a material Bill Bug Daniel Schober Frank Gibson Melanie Courtot heat function OBI:0000372 material separation function A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality. Bill Bug Daniel Schober Frank Gibson Melanie Courtot material separation function OBI:0000379 mechanical function A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force). Bill Bug Daniel Schober Frank Gibson Melanie Courtot http://en.wikipedia.org/wiki/Mechanical_work mechanical function OBI:0000387 cool function A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material. Daniel Schober Frank Gibson Melanie Courtot cool function OBI:0000399 solid support function Taped, glued, pinned, dried or molecularly bonded to a solid support A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement Daniel Schober Frank Gibson Melanie Courtot solid support function OBI:0000401 environment control function An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature. Bill Bug Daniel Schober Frank Gibson Melanie Courtot environment control function OBI:0000405 primer role a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation. (cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer primer role OBI:0000407 viral RNA extraction The AccuPrepTM Viral RNA Extraction Kit is designed for the rapid and convenient extraction of viral RNA from cell-free samples as serum, plasma, CSF, urine, etc - http://www.biokits.com/moreinfos.html?id=2703 The extraction of RNA from an input material that specifically isolates viral RNA Person:Bjoern Peters viral RNA extraction OBI:0000415 polymerase chain reaction Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413 PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified. OBI Plan PCR adapted from wikipedai polymerase chain reaction OBI:0000423 extract Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923 an extract is a material entity which results from an extraction process PERSON: Philippe Rocca-Serra extracted material GROUP: OBI Biomatrial Branch extract OBI:0000424 transcription profiling assay Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858 An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity. This term should encompass transcription and post-transcription, but before translation into protein. So 'gene expression' itself is too broad, and we use 'transcription profiling identification objective' to constrain the scope of this term. Philippe Rocca-Serra gene expression profiling transcription profiling OBI transcription profiling assay OBI:0000425 averaging objective A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi averaging objective OBI:0000433 DNA sequence feature detection assay genotyping using an Affymetrix chip An assay with the objective to determine a sequence feature of DNA Bjoern Peters Philippe Rocca-Serra OBI DNA sequence feature detection assay OBI:0000434 adding material objective creating a mouse infected with LCM virus is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity BP adding material objective OBI:0000436 needle Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569 a needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture. Philippe Rocca-Serra OBI Instrument needle OBI:0000437 analyte measurement objective The objective to measure the concentration of glucose in a blood sample an assay objective to determine the presence or concentration of an analyte in the evaluant PERSON: Bjoern Peters PPPB branch analyte measurement objective OBI:0000438 DNA sequence variation detection assay Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641 An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule. Philippe Rocca-Serra OBI Biomaterial DNA sequence variation detection assay OBI:0000441 assay objective the objective to determine the weight of a mouse. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) PPPB branch PPPB branch assay objective OBI:0000444 target of material addition role peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application. target of material addition role is a role realized by an entity into which a material is added in a material addition process From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role. GROUP: Role Branch OBI target of material addition role OBI:0000448 packed column A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube. PERSON:Daniel Schober WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218 packed column OBI:0000450 regulatory agency The US Environmental Protection Agency A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. GROUP: OBI Biomaterial Branch WEB: en.wikipedia.org/wiki/Regulator regulatory agency OBI:0000453 measure function A glucometer measures blood glucose concentration, the glucometer has a measure function. Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. PERSON: Daniel Schober PERSON: Helen Parkinson PERSON: Melanie Courtot PERSON:Frank Gibson measure function OBI:0000456 material transformation objective The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch material transformation objective OBI:0000457 manufacturing Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process Manufacturing implies reproducibility and responsibility AR This includes a single scientist making a processed material for personal use. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing OBI:0000458 manufacturing objective is the objective to manufacture a material of a certain function (device) PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing objective OBI:0000465 organic acid column An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099 organic acid column OBI:0000468 protein column A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238 refactor as defined class protein column OBI:0000482 normal phase column A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097 normal phase column OBI:0000485 chromatography instrument Any instrument that is used to carry out a chromatography experiment. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01262 chromatography device, defined class? chromatography instrument OBI:0000490 cation exchange column A cation exchange column is a chromatography column that is used in cation exchange chromatography. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096 cation exchange column OBI:0000496 capillary column A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066 capillary column OBI:0000510 reversed phase column A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106 reversed phase column OBI:0000515 chromatofocusing column A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind. PERSON:Daniel Schober WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209 chromatofocusing column OBI:0000518 trap column A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01261 trap column OBI:0000533 affinity column An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094 affinity column OBI:0000535 gel filtration column A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104 gel filtration column OBI:0000560 ion exchange column An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105 ion exchange column OBI:0000570 spin column A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232 spin column OBI:0000574 high temperature column A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233 high temperature column OBI:0000584 anion exchange column An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095 anion exchange column OBI:0000586 plunger column A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108 plunger column OBI:0000603 liquid chromatography column A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227 liquid chromatography column OBI:0000606 open tubular column An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube. PERSON:Daniel Schober WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219 open tubular column OBI:0000609 glass column A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101 glass column OBI:0000618 size exclusion column A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100 size exclusion column OBI:0000621 custom made column A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234 custom made column OBI:0000622 gel permeation column A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size. PERSON:Daniel Schober WEB:<http://composite.about.com/od/glossaries/l/bldef_g2419.htm> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103 gel permeation column OBI:0000626 DNA sequencing assay Illumina (Solexa) sequencing is an example of DNA sequencing A sequencing assay which determines information on the sequence of a DNA molecule. Philippe Rocca-Serra nucleotide sequencing url:https://en.wikipedia.org/wiki/DNA_sequencing DNA sequencing assay OBI:0000628 carbon nanotube column Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well. PERSON:Daniel Schober WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107 carbon nanotube column OBI:0000636 acquisition computer A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013 NMR instrument acquisition computer OBI:0000639 material separation objective The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. is an objective to transform a material entity into spatially separated components. PPPB branch PPPB branch material separation objective OBI:0000651 urine specimen a portion of urine collected from an organism 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant. This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active are we happy calling collection of urine a material separation? urine specimen OBI:0000652 material combination Mixing two fluids. Adding salt into water. Injecting a mouse with PBS. is a material processing with the objective to combine two or more material entities as input into a single material entity as output. created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes. bp bp material combination OBI:0000653 fuzzy clustering objective A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori. James Malone PERSON: James Malone PERSON: Ryan Brinkman fuzzy clustering objective OBI:0000655 blood specimen blood drawn from a human for glucose assay a material entity derived from a portion of blood collected from an organism Bjoern Peters Bjoern Peters blood specimen OBI:0000659 specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation A planned process with the objective of collecting a specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process OBI:0000671 sample from organism a material obtained from an organism in order to be a representative of the whole 5/29: This is a helper class for now we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about. sample from organism OBI:0000675 statistical hypothesis test objective is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation James Malone Person:Helen Parkinson hypothesis test objective WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing statistical hypothesis test objective OBI:0000678 portioning objective The objective to obtain multiple aliquots of an enzyme preparation. A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. portioning objective OBI:0000679 average value A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. PERSON: James Malone PERSON: Monnie McGee arithmetic mean average value OBI:0000681 separation into different composition objective The objective to obtain cells contained in a sample of blood. A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives separation into different composition objective OBI:0000684 specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective OBI:0000686 material combination objective is an objective to obtain an output material that contains several input materials. PPPB branch bp material combination objective OBI:0000689 454 Genome Sequence 20 PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20. is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. Philippe Rocca-Serra GS 20 454 Genome Sequence 20 OBI:0000691 ABI 377 automated sequencer is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers. Philippe Rocca-Serra Applied Biosystems ABI 377 automated sequencer OBI:0000696 AB SOLiD System PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57. is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation Philippe Rocca-Serra Applied Biosystems AB SOLiD System OBI:0000702 454 Genome Sequencer FLX PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B. J Biotechnol. 2008 Aug 31;136(1-2):3-10. is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. Philippe Rocca-Serra 454 GS FLX GS-FLX adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay 454 Genome Sequencer FLX OBI:0000703 Illumina Genome Analyzer II PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57. is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology Philippe Rocca-Serra Illumina Corporation Illumina Genome Analyzer II OBI:0000704 decision tree induction objective A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. James Malone decision tree induction objective OBI:0000710 Li-Cor 4300 DNA Analysis System is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing Philippe Rocca-Serra OBI and Li-Cor Li-Cor 4300 DNA Analysis System OBI:0000711 library preparation PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120. is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors. Philippe Rocca-Serra library construction library preparation OBI:0000713 GenePattern software a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. James Malone Person:Helen Parkinson WEB: http://www.broadinstitute.org/cancer/software/genepattern/ GenePattern software OBI:0000717 HeliScope Single Molecule Sequencer is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry Philippe Rocca-Serra HeliScope Single Molecule Sequencer OBI:0000722 paired-end library PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y. is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs Philippe Rocca-Serra mate-paired library paired-end tag (PET) library adapted from information provided by Solid web site paired-end library OBI:0000723 DNA sequencing by ligation assay ABI Solid Sequencing uses the ligation-based DNA sequencing technology (https://en.wikipedia.org/wiki/ABI_Solid_Sequencing). A DNA sequencing assay that performs chain extension during the sequencing reaction step using DNA ligase Philippe Rocca-Serra url:https://en.wikipedia.org/wiki/Sequencing_by_ligation DNA sequencing by ligation assay OBI:0000734 DNA sequencing by synthesis assay Roche-454 pyrosequencing and Illumina (Solexa) sequencing use synthesis-based method for DNA sequencing A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. Philippe Rocca-Serra url:https://www.illumina.com/technology/next-generation-sequencing/sequencing-technology.html DNA sequencing by synthesis assay OBI:0000736 single fragment library is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs Philippe Rocca-Serra fragment library single fragment library OBI:0000740 material sample role a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. material sample role OBI:0000747 material sample blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material entity that has the material sample role OBI: workshop sample population sample material sample OBI:0000791 multiple testing correction objective Application of the Bonferroni correction A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously multiple comparison correction objective http://en.wikipedia.org/wiki/Multiple_Testing_Correction multiple testing correction objective OBI:0000796 purification objective the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides. The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest PERSON:Bjoern Peters isolation objective BP 10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality purification objective OBI:0000806 material maintenance objective An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters PERSON: Bjoern Peters material maintenance objective OBI:0000810 informed consent process A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#informed 2009/09/28 Alan Ruttenberg. Fucoidan-use-case informed consent process OBI:0000811 primary structure of DNA macromolecule a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. placeholder for SO BP et al primary structure of DNA macromolecule OBI:0000828 research organization The SALK institute is a research organization. An organization formed with a goal to have its members conduct investigations Person:Bjoern Peters research organization OBI:0000832 measurement device A ruler, a microarray scanner, a Geiger counter. A device in which a measure function inheres. GROUP:OBI Philly workshop OBI measurement device OBI:0000835 manufacturer A person or organization that has a manufacturer role manufacturer OBI:0000839 labeled oligonucleotide a labeled oligonucleotide is a short nucleic acid which underwent a labeling process resulting in a radioactive isotope such as P32 or P33 added to its backbone for instance by end labeling with polynucleotide kinase which added radiolabeled ATP to the 5' end of oligonucleotide 2010-01-31: Philippe Rocca-Serra placeholder Person: Philippe Rocca-Serra labeled oligonucleotide OBI:0000844 hospital human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660] A medical organization at which sick or injured people are given clinical care Person:Alan Ruttenberg Person:Helen Parkinson http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n modified from the wording of the wordnet definition 2009/09/28 Alan Ruttenberg. Fucoidan-use-case hospital OBI:0000845 primary structure of RNA molecule The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together Person:Bjoern Peters primary structure of RNA molecule OBI:0000848 polyA RNA extraction A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA. Person: Chris Stoeckert Person: Jie Zheng UPenn Group polyA RNA extraction OBI:0000849 organellar RNA extraction A RNA extraction process in which the desired output material is RNA in the organelle(s). Person: Chris Stoeckert Person: Jie Zheng UPenn Group organellar RNA extraction OBI:0000855 total RNA extraction A RNA extraction process in which total cellular and organelle RNA are extracted. Person: Chris Stoeckert Person: Jie Zheng UPenn Group total RNA extraction OBI:0000857 complementary nucleotide probe role A primer in a PCR reaction. A probe on an Affymetrix chip. A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence PERSON:Bjoern Peters complementary nucleotide probe role OBI:0000859 cytoplasmic RNA extraction A RNA extraction process in which the desired output material is RNA in the cytoplasm. Person: Chris Stoeckert Person: Jie Zheng UPenn Group cytoplasmic RNA extraction OBI:0000868 pattern matching objective A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees. Tina Boussard http://en.wikipedia.org/wiki/Pattern_matching pattern matching objective OBI:0000880 RNA extract an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. PERSON: Chris Stoeckert PERSON: Jie Zheng Group: UPenn Group RNA extract OBI:0000888 nuclear RNA extraction A RNA extraction process in which the desired output material is RNA in the nucleus. Person: Chris Stoeckert Person: Jie Zheng UPenn Group nuclear RNA extraction OBI:0000893 real time polymerase chain reaction assay An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. Bjoern Peters Melanie Courtot Q-PCR kinetic polymerase chain reaction qPCR quantitative real time polymerase chain reaction url:http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction real time polymerase chain reaction assay OBI:0000924 labeled specimen A specimen that has been modified in order to be able to detect it in future experiments added during call 3/1/2010 OBI group labeled specimen OBI:0000932 material separation device flow cytometer A device with a separation function realized in a planed process material separation device OBI:0000941 service consumer role A biologist who uses a sequencing services fulfills the role of a service consumer a role which inheres in a person who uses a service Person:Helen Parkinson OBI service consumer role OBI:0000947 service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person PERSON:Helen Parkinson service provider role OBI:0000949 accessed material role the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism is realized in a planned process where the bearer participates AR: rent a DNA sequencer for a period of time. two realizations, payment for the service and also when the person who pays for the service uses it accessed material role OBI:0000953 processed specimen A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. processed specimen OBI:0000960 reagent application function An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations. A function that is realized when a reagent is automatically added to some research material. PERSON: Nicole Vasilevsky, Matthew Brush PERSON: Nicole Vasilevsky, Matthew Brush 4/10/2011: It is unclear if we need / want this, or what this is supposed to be for. Lots of the functions we have are reagent specific. Will this only confuse people? reagent application function OBI:0000962 training objective A training objective is fulfilled by e.g. a bioconductor tutorial which instructs the user in the use of a package An objective specification which is fulfilled by the provision of some training. Helen Parkinson OBI training objective OBI:0000967 container A device that can be used to restrict the location of material entities over time 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) PERSON: Bjoern Peters container OBI:0000968 device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. device OBI:0000973 sequence data example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. Person:Chris Stoeckert GROUP: OBI sequence data OBI:0000989 PCR instrument A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. 03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent. PCR instrument OBI:0000993 service provision objective A sequencing centre has a service provision objective An objective which is fulfilled by the provision of some service e.g. a training service Helen Parkinson OBI service provision objective OBI:0000996 device creation objective an objective which aims to create a device with a specified function PERSON: Helen Parkinson OBI device creation objective OBI:0001010 nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. PERSON: Jie Zheng UPenn Group nucleic acid extract OBI:0001047 pH meter A device that is used to measure the pH (acidity or alkalinity) of a liquid. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/PH_meter pH meter OBI:0001050 RNA extraction/purification instrument A device that is used to isolate and collect RNA for subsequent molecular analysis. PERSON: Erik Segerdell PERSON: Erik Segerdell RNA extraction/purification instrument OBI:0001051 DNA extract The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. Person: Jie Zheng Group: UPenn group DNA extract OBI:0001063 automatic staining machine A device that is used to automatically stain tissue sections on slides or tissue specimens. PERSON: Erik Segerdell PERSON: Erik Segerdell automatic staining machine OBI:0001064 automatic tissue processor A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue. PERSON: Erik Segerdell United States Patent 3762362 automatic tissue processor OBI:0001092 computer cluster A group of linked computers, working together closely so that in many respects they form a single computer. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Cluster_(computing) computer cluster OBI:0001100 microcentrifuge A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Laboratory_centrifuge microcentrifuge OBI:0001101 electronic repeater pipette A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations. PERSON: Erik Segerdell http://www.faqs.org/patents/app/20090196797 electronic repeater pipette OBI:0001107 tissue embedding station A device that is used to perform paraffin embedding of tissue specimens. PERSON: Erik Segerdell PERSON: Erik Segerdell tissue embedding station OBI:0001108 nucleic acid sequencer An device that is used to determine the order of nucleotides in nucleic acid sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell nucleic acid sequencer OBI:0001110 real-time PCR machine An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction real-time PCR machine OBI:0001113 microplate washer A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY?? PERSON: Erik Segerdell http://www.articlesnatch.com/Article/Microplate-Readers-And-Washers-For-Laboratories/948037 microplate washer OBI:0001114 nucleic acid extraction/purification instrument A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis. PERSON: Erik Segerdell PERSON: Erik Segerdell nucleic acid extraction/purification instrument OBI:0001115 ELISA microplate washer A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA). PERSON: Erik Segerdell PERSON: Erik Segerdell ELISA microplate washer OBI:0001117 DNA extraction/purification instrument A device that is used to isolate and collect DNA for subsequent molecular analysis. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/DNA_extraction DNA extraction/purification instrument OBI:0001127 freeze substitution system A device or system for dehydrating and then chemically fixing electron microscopy samples at low temperatures in preparation for various treatments including embedding in resins. PERSON: Erik Segerdell doi:10.1017/S143192760707866X freeze substitution system OBI:0001128 micropipette A microinjection device that is used to measure very small volumes of liquids. PERSON: Erik Segerdell http://www.answers.com/topic/micropipette micropipette OBI:0001137 protein sequencer An device that is used to determine the order of amino acids in protein sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell protein sequencer OBI:0001143 labeled nucleic acid extract a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. Person: Jie Zheng labeled extract MO_221 labeledExtract labeled extract labeled nucleic acid extract OBI:0001153 genetic transformation objective a material transformation objective aims to create genetically modified organism or cell Person: Jie Zheng Person: Jie Zheng suggested to be added by BP and AR during Oct 25, 2010 dev call genetic transformation objective OBI:0001160 assay validation objective an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results PERSON: Chris Stoeckert, Jie Zheng GROUP: Penn Group assay validation objective OBI:0001166 validation by real time PCR design a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results PERSON: Chris Stoeckert, Jie Zheng MO_434 real_time_PCR_quality_control validation by real time PCR design 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:0001175 selective organism creation objective an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms. PERSON: Chris Stoeckert, Jie Zheng WEB: wikipedia http://en.wikipedia.org/wiki/Cultivar http://en.wikipedia.org/wiki/Ecotype http://en.wikipedia.org/wiki/Strain_%28biology%29 selective organism creation objective OBI:0001177 RNA sequencing assay An assay that determines the sequence of an RNA molecule. Bjoern Peters Bjoern Peters RNA sequencing assay OBI:0001204 SNP microarray a DNA microarray used to detect polymorphisms in DNA samples Person: Helen Parkinson EFO_0002703 SNP array SNP microarray OBI:0001235 transcription profiling by tiling array assay A transcription profiling by array assay that uses a tiling path array. James Malone EFO:0002769 transcription profiling by tiling array assay OBI:0001271 RNA-seq assay An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance. James Malone transcription profiling by high throughput sequencing EFO:0002770 RNA-seq assay OBI:0001307 tiling microarray a DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. Person: Helen Parkinson genome tiling array EFO_0002704: tiling array tiling microarray OBI:0001331 transcription profiling identification objective A molecular feature identification objective that aims to characterize the abundance of transcripts Person: Chris Stoeckert, Jie Zheng Group: Penn Group transcription profiling identification objective OBI:0001335 microRNA profiling by array assay An assay that analyses the microRNA component of the transcriptome using a microRNA array. James Malone EFO:0000753 microRNA profiling by array assay OBI:0001361 transcription profiling by RT-PCR assay A transcription profiling assay that uses reverse transcription PCR (RT-PCR). Anna Farne EFO:0002943 transcription profiling by RT-PCR assay OBI:0001463 transcription profiling by array assay A transcription profiling assay that uses array technology. James Malone RNA profiling by array assay EFO:0002768 https://sourceforge.net/p/obi/obi-terms/757/ transcription profiling by array assay OBI:0001472 specimen with known storage state A specimen for which it is known whether it has been subjected to storage of a specified type. PERSON: Chris Stoeckert, Jie Zheng MO_95 BiosourceType specimen with known storage state OBI:0001479 specimen from organism A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). PERSON: Chris Stoeckert, Jie Zheng tissue specimen MO_954 organism_part specimen from organism OBI:0001483 cell collecting A planned process that collects cells from culture. PERSON: Chris Stoeckert, Jie Zheng MO_982 harvest cell collecting OBI:0001494 linear amplification An example is the use of the T7 promoter for amplification by transcribing many RNA copies. An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template. PERSON: Chris Stoeckert, Jie Zheng MO_997 linear_amplification linear amplification OBI:0001522 sequence assembly algorithm An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Assembly Algorithm NIAID GSCID-BRC sequence assembly algorithm OBI:0001573 DNA sequence data The part of a FASTA file that contains the letters ACTGGGAA A sequence data item that is about the primary structure of DNA OBI call; Bjoern Peters OBI call; Melanie Courtout 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there. DNA sequence data OBI:0001615 investigation description A textual entity that describes an investigation. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group study description project description NIAID GSCID-BRC NCBI BioProject investigation description OBI:0001616 specimen identifier A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation. Person: Chris Stoeckert, Jie Zheng specimen ID NIAID GSCID-BRC metadata working group Specimen ID NIAID GSCID-BRC sample identifier specimen identifier OBI:0001618 average depth of sequence coverage An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Depth of Coverage - Average NIAID GSCID-BRC average depth of sequence coverage OBI:0001619 specimen collection time measurement datum A time measurement datum that is the measure of the time when the specimens are collected. Person: Chris Stoeckert, Jie Zheng collection date NIAID GSCID-BRC metadata working group Specimen Collection Date NIAID GSCID-BRC specimen collection time measurement datum OBI:0001623 organism identification objective A biological feature identification objective to identify the organism species in a specimen. Person: Chris Stoeckert, Jie Zheng Penn Group organism identification objective OBI:0001625 sequence annotation algorithm An algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Annotation Algorithm NIAID GSCID-BRC sequence annotation algorithm OBI:0001626 Bioinformatics Resource Center An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them. Person: Chris Stoeckert, Jie Zheng BRC Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers NIAID GSCID-BRC Bioinformatics Resource Center OBI:0001673 nano-cap analysis of gene expression assay Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan._PMID:20543846 A transcription profiling assay that is performed using a very low amount (nanogram scale) of mRNA samples using Cap analysis gene expression (CAGE). Marcus Chibucos Philippe Rocca-Serra nano-CAGE PMID:20543846 nano-cap analysis of gene expression assay OBI:0001674 cap analysis of gene expression assay 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. PMID:22362160 A transcription profiling assay which measures RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome Marcus Chibucos Philippe Rocca-Serra CAGE PMID:14663149 cap analysis of gene expression assay OBI:0001690 molecular function identification objective is an objective specification which aims to discover molecular function realized by a molecular entity PERSON:Philippe Rocca-Serra OBI group molecular function identification objective OBI:0001691 cellular structure feature identification objective is an objective specification which aims to discover cellular structure properties PERSON:Philippe Rocca-Serra OBI group cellular structure feature identification objective OBI:0001849 structural analysis by paired-end tag sequencing assay Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419] An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants. Chris Stoeckert Jie Zheng Venkat Malladi DNA-PET DNA-PET assay PMID:23029419 structural analysis by paired-end tag sequencing assay OBI:0001850 transcript analysis by paired-end tag sequencing assay Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299] A transcription profiling assay that determines transcripts, gene structures, and gene expressions using Paired-End Tags and sequencing technology. Chris Stoeckert Jie Zheng Venkat Malladi RNA-PET RNA-PET assay PMID:22113299 transcript analysis by paired-end tag sequencing assay OBI:0001851 transcription start site identification objective A transcription profiling identification objective that aims to characterize the transcription start sites of genes. Person: Chris Stoeckert, Jie Zheng Penn Group transcription start site identification objective OBI:0001852 paired-end library preparation A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process. Person: Venkat Malladi, Jie Zheng Venkat Malladi, Jie Zheng ENCODE project paired-end library preparation OBI:0001853 DNase I hypersensitive sites sequencing assay Sabo, et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. [PMID:15550541] An assay that identifies the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I. Chris Stoeckert Jie Zheng Venkat Malladi url:http://en.wikipedia.org/wiki/DNase-Seq DNase I hypersensitive sites sequencing assay OBI:0001854 protein and RNA interaction identification objective A sequence feature identification objective that aims to characterize the interactions between protein and RNA. JZ: Term added for ENCODE project requested assays. Definition adapted from 'protein and DNA interaction identification objective'. Person: Jie Zheng Jie Zheng protein and RNA interaction identification objective OBI:0001859 formaldehyde-assisted isolation of regulatory elements assay Giresi, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17 (6): 877_�_85. [PMID:17179217] An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. Chris Stoeckert Jie Zheng Venkat Malladi FAIRE-seq FAIRE-seq assay url:http://en.wikipedia.org/wiki/FAIRE-Seq formaldehyde-assisted isolation of regulatory elements assay OBI:0001864 RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248] An transcription profiling assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing. Chris Stoeckert Jie Zheng Venkat Malladi RAMPAGE PMID:22936248 RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay OBI:0001865 assay array A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg Penn Group assay array OBI:0001867 establishing cell line a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset). 2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time. Person: Matthew Brush PERSON:Matthew Brush establishing cell line OBI:0001869 Illumina BeadChip An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides. PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi http://www.illumina.com/technology/beadarray_technology.ilmn Illumina BeadChip OBI:0001870 Illumina methylation BeadChip A BeadChip made for an analyte assay that generates information about DNA methylation. PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg Penn Group Illumina methylation BeadChip OBI:0001872 sequence assembly process A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs). PRS/AGB: changed to restrictions by adding 2 possible specified outputs (N50 and genome coverage) for sequence assembly. Alejandra Gonzalez-Beltran PERSON: Jie Zheng, Chris Stoeckert Philippe Rocca-Serra NIAID GSCID-BRC metadata working group NIAID GSCID-BRC sequence assembly process OBI:0001879 reagent A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output. 2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device. PERSON:Matthew Brush PERSON:Matthew Brush (copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). reagent OBI:0001880 organization of specimen provider principal investigator An organization that is the affiliation of the principal investigator providing the specimens for the investigation PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider PI's Institution NIAID GSCID-BRC organization of specimen provider principal investigator OBI:0001881 organization of Bioinformatics Resource Center contact person An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact's Institution NIAID GSCID-BRC organization of Bioinformatics Resource Center contact person OBI:0001885 specimen repository organization An organization that provides a service to store and distribute specimens PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository NIAID GSCID-BRC specimen repository organization OBI:0001891 sequencing facility organization An organization that provides sequence determination service PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility NIAID GSCID-BRC sequencing facility organization OBI:0001892 specification of data to be generated in an investigation Some examples of Project Objectives are Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation, Epigenetic markers, expression, maps, phenotype An objective specification which indicates the type of data that will be generated and submitted to a database. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Project Objectives NIAID GSCID-BRC specification of data to be generated in an investigation OBI:0001893 organization of specimen collector An organization that is the affiliation of the person collecting the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector's Institution NIAID GSCID-BRC organization of specimen collector OBI:0001897 organization of sequencing facility contact person An organization that is the affiliation of the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact's Institution NIAID GSCID-BRC organization of sequencing facility contact person OBI:0001900 specimen identifier assigned by specimen repository A specimen identifier which is assigned by a specimen repository PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository Sample ID NIAID GSCID-BRC specimen identifier assigned by specimen repository OBI:0001901 specimen identifier assigned by sequencing facility A specimen identifier which is assigned by a sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample ID - Sequencing Facility NIAID GSCID-BRC specimen identifier assigned by sequencing facility OBI:0001909 conclusion based on data The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". An information content entity that is inferred from data. In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group Group:2013 Philly Workshop group conclusion based on data OBI:0001916 DNA replication identification objective A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time. Chris Stoeckert, Jie Zheng Group: Penn Group DNA replication identification objective OBI:0001917 chromosome conformation identification objective A molecular feature identification objective that aims to determine spatial organization of chromatin. Chris Stoeckert, Jie Zheng Group: Penn Group chromosome conformation identification objective OBI:0001922 microRNA profiling by high throughput sequencing assay Juhlia et al. MicroRNA expression profiling reveals miRNA families regulating_specific biological pathways in mouse frontal cortex and hippocampus. PLoS One. 2011;6(6). PMID: 21731767 A microRNA profiling assay that analyzes the microRNA component of the transcriptome using high throughput sequencing technology. Chris Stoeckert Jie Zheng Venkat Malladi miRNA-HTS miRNA-seq microRNA-seq microRNA-seq assay url:http://www.ebi.ac.uk/efo/EFO_0002896 microRNA profiling by high throughput sequencing assay OBI:0001924 micrococcal nuclease digestion followed by high throughput sequencing assay Cui et al.Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq. Methods Mol Biol. 2012;833:413-9. [PMID:22183607] An assay that identifies nucleosome positioning by genome wide sequencing of regions sensitive to digestion by micrococal nuclease Chris Stoeckert Jie Zheng Venkat Malladi MNase-seq MNase-seq assay PMID:17038564 micrococcal nuclease digestion followed by high throughput sequencing assay OBI:0001926 microRNA profiling assay A transcription profiling assay that quantifies the microRNA species within a biological sample. Chris Stoeckert Jie Zheng Venkat Malladi miRNA expression assay microRNA expression assay PMID: 23382819 microRNA profiling assay OBI:0001928 selection PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria. this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary) Person: Philippe Rocca-Serra selection process OBI selection OBI:0001936 molecular-labeled material a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay PERSON:Matthew Brush OBI developer call, 3-12-12 molecular-labeled material OBI:0001942 grant agency An organization that provides funding support for projects such as investigations. PERSON: Jie Zheng, Chris Stoeckert funding organization NIAID GSCID-BRC metadata working group NIAID GSCID-BRC grant agency 'funding organization' http://vivoweb.org/ontology/core#FundingOrganization OBI:0001943 software pipeline A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements. PERSON: Jie Zheng, Chris Stoeckert WEB: http://en.wikipedia.org/wiki/Pipeline_%28software%29 NIAID GSCID-BRC software pipeline OBI:0001944 sequence annotation A sequence annotation bioinformatics analysis that identifies and reports sequence features (e.g. protein coding regions) in sequence data. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group NIAID GSCID-BRC sequence annotation OBI:0001962 target gene specification http://www.ncbi.nlm.nih.gov/pubmed/25367129 "performing a profiling of microbial phylogenetic composition using sequencing of 16S rRNA gene (used as target gene) is a directive information specifying a coding genomic region which is the focus of a planned process such as an assay, for instance in a environmental gene survey PERSON:Philippe Rocca-Serra PRS for OBI target gene target gene specification OBI:0001964 decision-theoretic analysis objective An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric. The best action to take is typically defined as the one that maximizes expected utility. PERSON: Bill Hogan decision analysis objective PERSON: Bill Hogan decision-theoretic analysis objective OBI:0001969 biodiversity assessment objective biodiversity assessment objective is an objective of a planned process aimed at producing data item whose interpretation should provide insight about variety of biological species found in a biological sample at macroscopic or microscopic level PERSON:Philippe Rocca-Serra PRS for OBI biodiversity assessment objective OBI:0002004 Methylation 450K BeadChip surgical cancer treatment Naumov, Vladimir A., et al. "Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips." Epigenetics 8.9 (2013): 0-1. PMID: 23867710 A cancer therapeutic procedure that involves a surgical procedure as a main part. A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. Chris Stoeckert, Helena Ellis PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina Infinium Human Methylation 450K BeadChip NCI BBRB, OBIB http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn NCI BBRB ENCODE project Methylation 450K BeadChip surgical cancer treatment OBI:0002005 Methylation 27K BeadChip specimen gross appearance of metastatic tumor Polidoro, Silvia, et al. "Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139 A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. A specimen gross appearance of a tumor that has spread from its original site by discontinuous (not direct) spread, e.g. by blood or lymphatics. Chris Stoeckert, Helena Ellis PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina Infinium Human Methylation 27K BeadChip NCI BBRB, OBIB http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf NCI BBRB ENCODE project Methylation 27K BeadChip specimen gross appearance of metastatic tumor OBI:0002006 1M-Duo Infinium HD BeadChip specimen gross appearance of tumor center Edwards, Todd L., et al. "Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease." Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850 A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis. A specimen gross appearance of the most internal topographic location of the tumor. Chris Stoeckert, Helena Ellis PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina Human 1M-Duo Infinium HD BeadChip NCI BBRB, OBIB http://www.illumina.com/technology/infinium_hd_assay.ilmn NCI BBRB ENCODE project 1M-Duo Infinium HD BeadChip specimen gross appearance of tumor center OBI:0002007 SOLiD 3 Plus System specimen gross appearance of tumor edge Vissers, Lisenka ELM, et al. "A de novo paradigm for mental retardation." Nature genetics 42.12 (2010): 1109-1112. PMID:21076407 A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. A specimen gross appearance of the border of the tumor with non-tumorous tissue. Chris Stoeckert, Helena Ellis PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Applied Biosystems SOLiD 3 Plus System NCI BBRB, OBIB http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf NCI BBRB ENCODE project SOLiD 3 Plus System specimen gross appearance of tumor edge OBI:0002008 Mouse 385K Whole Genome CGH Tiling Array research authorization for post mortem specimen donation for a specific tissue or fluid Miller, Becky Akiko. Detection and biological assessment of genome structural variation in Plasmodium falciparum. Diss. University of Notre Dame, 2012. http://etd.nd.edu/ETD-db/theses/available/etd-04182012-114744/ A research authorization documentation for postmortem specimen donation in which the authorization is for a specified tissue or biological fluid. A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 385,000 features. Chris Stoeckert, Helena Ellis PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Nimblegen Mouse 385K Whole Genome CGH Tiling Array NCI BBRB, OBIB http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf NCI BBRB ENCODE project Mouse 385K Whole Genome CGH Tiling Array research authorization for post mortem specimen donation for a specific tissue or fluid OBI:0002009 Mouse 3x720K Whole Genome CGH Tiling Array Wartman, Lukas D., et al. "Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression." The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584 A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features. An autolysis value specification that indicates no apparent autolytic destruction of an organism cells or tissues. Chris Stoeckert, Helena Ellis PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array NCI BBRB, OBIB http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf NCI BBRB ENCODE project 0-non autolyis Mouse 3x720K Whole Genome CGH Tiling Array OBI:0002010 Human 3x720K Whole Genome CGH Tiling Array Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism PMID:21091464 A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 3x720,000 features. An autolysis value specification that indicates slight autolytic destruction of an organism cells or tissues. Chris Stoeckert, Helena Ellis PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Nimblegen Human 3x720K Whole Genome CGH Tiling Array NCI BBRB, OBIB http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf NCI BBRB ENCODE project 1-slight autolysis Human 3x720K Whole Genome CGH Tiling Array OBI:0002011 Human 2.1M Whole-Genome CGH Tiling Array v2.0 Filges, Isabel, et al. "Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome." Journal of medical genetics 48.2 (2011): 117-122. PMID:21037274 A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 2.1 million features. An autolysis value specification that indicates moderate autolytic destruction of an organism cells or tissues. Chris Stoeckert, Helena Ellis PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Nimblegen Human 2.1M Whole-Genome CGH Tiling Array v2.0 NCI BBRB, OBIB http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf NCI BBRB ENCODE project 2-moderate autolysis Human 2.1M Whole-Genome CGH Tiling Array v2.0 OBI:0002012 PacBio RS II Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. An autolysis value specification that indicates severe autolytic destruction of an organism cells or tissues. Chris Stoeckert, Helena Ellis PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Pacific Biosciences RS II NCI BBRB, OBIB http://www.pacificbiosciences.com/products/ NCI BBRB ENCODE project 3-severe autolysis PacBio RS II OBI:0002015 transcription profiling by MPSS assay A transcription profiling assay that uses Massive Parallel Signature Sequencing (MPSS). Chris Stoeckert Jie Zheng expression MPSS url:http://en.wikipedia.org/wiki/Massively_parallel_signature_sequencing transcription profiling by MPSS assay OBI:0002021 NextSeq 500 A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Illumina NextSeq 500 http://systems.illumina.com/systems/nextseq-sequencer.html ENCODE project NextSeq 500 OBI:0002022 Illumina HiSeq 1000 A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng HiSeq 1000 http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf ENCODE project Illumina HiSeq 1000 OBI:0002023 Human Genome U133 Plus 2.0 tiling array A tiling array which is a comprehensive whole human genome expression array manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 47,000 transcripts and variants. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Affymetrix HT Human Genome U133 Plus 2 Array Plate Set HG-U133 Plus 2 HG-U133 Plus 2 array http://www.affymetrix.com/estore/esearch/search.jsp?pd=131455&N=4294967292 ENCODE project Human Genome U133 Plus 2.0 tiling array OBI:0002024 SOLiD 4 System An AB SOLid System which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Applied Biosystems SOLiD 4 System SOLiD 4 http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/next-generation-systems/solid-4-system.html?CID=FL-091411_solid4 ENCODE project SOLiD 4 System OBI:0002025 Human Exon 1.0 ST tilling array A tiling microarray which is manufactured by the Affymetrix corporation. Built to analyze 3' DNA sequence copy number by comparative genomic hybridization for human DNA against 28,000 genes. It can be used for gene expression and alternative splicing assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Affymetrix Human Exon 1.0 St Array Human Exon 1.0 Human Exon 1.0 ST Array http://www.affymetrix.com/catalog/131453/AFFY/Human+Gene+ST+Arrays#1_1 ENCODE project Human Exon 1.0 ST tilling array OBI:0002026 Human Genome U133 tiling array A tiling array which is manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 39,000 transcripts and variants. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Affymetrix HT Human Genome U133 Array Plate Set HG-U133 HG-U133 array http://www.affymetrix.com/estore/esearch/search.jsp?pd=131441&N=4294967292 ENCODE project Human Genome U133 tiling array OBI:0002027 Genome Analyzer IIe An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Illumina GA IIe Illumina Genome Analyzer IIe http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf ENCODE project Genome Analyzer IIe OBI:0002028 SAGE ditag library preparation A library preparation in which tags identifiying transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library. Related tracker:https://sourceforge.net/p/obi/obi-terms/720/ Person:Chris Stoeckert PMID:15905473 SAGE ditag library preparation OBI:0002029 serial analysis of gene expression assay PMID:15905473 A transcription profiling assay that quantifies RNA through creating short signature tags of the messages and ligating them into a larger molecule than was sequenced. Chris Stoeckert Janos Demeter Jie Zheng SAGE PMID:7570003 https://sourceforge.net/p/obi/obi-terms/720/ serial analysis of gene expression assay OBI:0002033 translation-associated transcript leader sequencing assay pmid:23580730 An RNA-seq assay that combines TL-seq with polysome fractionation Chris Stoeckert Janos Demeter TATL-seq PMID:23580730 https://sourceforge.net/p/obi/obi-terms/725/ translation-associated transcript leader sequencing assay OBI:0002034 transcript leader sequencing assay pmid:23580730 An RNA-seq assay that combines enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. Chris Stoeckert Janos Demeter TL-seq PMID:23580730 https://sourceforge.net/p/obi/obi-terms/725/ transcript leader sequencing assay OBI:0002038 ribosomal profiling by sequencing assay Aspden et al., (August 2014). "Extensive translation of small open reading frames revealed by poly-ribo-seq." eLIFE 2014;3:e03528 A RNA-seq assay that sequences only mRNA protected by the ribosome during translation. Chris Stoeckert Jie Zheng Venkat Malladi Ribo-seq Ribo-seq assay ribosomal profiling PMID:24468696 ribosomal profiling by sequencing assay OBI:0002041 self-transcribing active regulatory region sequencing assay Bohla et al., (September 2014). "A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking." PLoS One 9(9):e107765. doi: 10.1371/journal.pone.0107765. An RNA-seq assay that identifies the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA. Chris Stoeckert Jie Zheng Venkat Malladi STARR-seq STARR-seq assay self-transcribing active regulatory region sequencing PMID:23328393 self-transcribing active regulatory region sequencing assay OBI:0002044 RNA Bind-n-Seq assay An RNA-seq assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs). Chris Stoeckert Jie Zheng Venkat Malladi RBNS RNA Bind-n-Seq RNBS assay doi: 10.1016/j.molcel.2014.04.016 RNA Bind-n-Seq assay OBI:0002045 poly(A)-site sequencing assay Wu et al., (July 2014). "Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 2014 Jul 21;15:615. doi: 10.1186/1471-2164-15-615. A RNA-seq assay that quantitatively profiles RNA polyadenylation at the transcriptome level. Chris Stoeckert Jie Zheng Venkat Malladi PAS-seq PAS-seq assay Poly(A)-site sequencing doi: 10.1261/rna.2581711 poly(A)-site sequencing assay OBI:0002048 Illumina HiSeq 3000 A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. PERSON: Sagar Jain, Richard Scheuermann HiSeq 3000 http://www.illumina.com/systems/hiseq-3000-4000.html Illumina HiSeq 3000 OBI:0002049 Illumina HiSeq 4000 A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. PERSON: Sagar Jain, Richard Scheuermann HiSeq 4000 http://www.illumina.com/systems/hiseq-3000-4000.html Illumina HiSeq 4000 OBI:0002076 collection of specimens Blood cells collected from multiple donors over the course of a study. A material entity that has two or more specimens as its parts. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Person: Chris Stoeckert, Jie Zheng OBIB, OBI Biobank collection of specimens OBI:0002088 specimen container COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube A container with the function of containing a specimen. For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/ Chris Stoeckert Duke Biobank, OBIB Biobank Specimen containers are typically constructed or treated in a particular manner in order to perform their containing a specimen function. This will be a defined class so that any container (e.g., cryotube, vacutainer, conical test tube) with the function of containing a specimen will be inferred to be a specimen container. specimen container OBI:0002109 Human 6x630K CGH Whole Genome Tiling Array A tiling array which is manufactured by the Nimblegen corporation to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 6x630,000 features. Term request: https://sourceforge.net/p/obi/obi-terms/791/ Jason Hilton, Chris Stoeckert, Bjoern Peters, OBI-group NimbleGen Human 6x630K CGH Whole Genome Tiling Array http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=snolquwezzwdxuj&acc=GPL18318 Human 6x630K CGH Whole Genome Tiling Array OBI:0002112 small RNA sequencing assay An RNA-seq assay which is targeting small RNA (< 200 bp) sequences such as, but not exclusive to, miRNAs using, for example, small RNA library preparation kits. Chris Stoeckert Jason Hilton Mark A. Miller short RNA-seq small RNA-seq url:http://science.sciencemag.org/content/316/5830/1484.full url:http://www.illumina.com/techniques/sequencing/rna-sequencing/small-rna-seq.html https://github.com/obi-ontology/obi/issues/859 small RNA sequencing assay OBI:0002113 bromouridine labeling and sequencing assay An RNA-seq assay to identify spans of nascent transcription in the genome through isolation of recent bromouridine (Bru) labelled RNAs. Chris Stoeckert Jason Hilton Bru-seq PMC:4009065 bromouridine labeling and sequencing assay OBI:0002114 bromouridine pulse-chase and sequencing assay An RNA-seq assay to identify RNA populations of specific ages through isolation of RNAs first labelled with bromouridine (Bru) followed by chasing in uridine for different periods of time. Chris Stoeckert Jason Hilton BruChase-seq PMC:4009065 bromouridine pulse-chase and sequencing assay OBI:0002117 whole genome sequencing assay WGS permits comprehensive sequencing of introns and exons, whereas whole exome sequencing (WES) allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS. A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. ImmPort WGS PMID:23095910 PMID:25827230 whole genome sequencing assay OBI:0002118 exome sequencing assay DNA was extracted from the Ficoll pellet of blood taken from congenital asplenia patients. Unamplified, high-molecular weight, RNase-treated genomic DNA (4_6 _g) was used for whole exome sequencing (WES) with the use of Agilent 71 Mb (V4 + UTR) singlesample capture and an Illumina HiSeq 2000. Sequencing was carried out so as to obtain 30_ coverage from 2 _ 100-bp paired-end reads. We used the Annovar tool (25) to annotate the resulting highquality (HQ) variants. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and13,325, respectively. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called. A mean of 105 coding HQ SNVs and 32 indels was identified. A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons). ImmPort WES PMID:25827230 exome sequencing assay OBI:0002125 H&E-stained fixed tissue slide specimen A fixed tissue slide specimen that is the output of H&E slide staining. Chris Stoeckert, Ned Haubein OBIB, OBI H&E-stained fixed tissue slide specimen OBI:0002126 IHC-stained fixed tissue slide specimen A fixed tissue slide specimen that is the output of immunohistochemistry slide staining. Chris Stoeckert, Ned Haubein immunohistochemistry slide specimen OBIB, OBI IHC-stained fixed tissue slide specimen OBI:0002128 Illumina Genome Analyzer A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. Person: Chris Stoeckert, Jason Hilton Illumina Genome Analyzer I http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html ENCODE project Illumina Genome Analyzer OBI:0002129 Illumina HiSeq X Ten A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann HiSeq X Ten http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html ENCODE project Illumina HiSeq X Ten OBI:0002130 Illumina Infinium Omni5Exome-4 Kit An Illumina BeadChip which is an array that interrogates over 4.3 million whole-genome variants for genotyping and copy number variation. Person: Chris Stoeckert, Jason Hilton http://www.illumina.com/products/by-type/microarray-kits/infinium-omni5-exome.html ENCODE project Illumina Infinium Omni5Exome-4 Kit OBI:0002131 Illumina Infinium MethylationEPIC BeadChip An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. Person: Chris Stoeckert, Jason Hilton http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf ENCODE project Illumina Infinium MethylationEPIC BeadChip OBI:0002142 Nanostring nCounter miRNA expression assay A microRNA profiling assay using digital molecular barcoding technology to quantify target microRNA molecules without the need for amplification. Chris Stoeckert Jason Hilton microRNA counts PMID:26729350 url:http://www.nanostring.com/applications/technology https://github.com/obi-ontology/obi/issues/806 ENCODE DCC Nanostring nCounter miRNA expression assay OBI:0002143 bromouride labeling and sequencing after UV exposure An RNA-seq assay to identify transcription start sites and active enhancer elements through isolation of bromouridine (Bru) labelled RNAs after UV light exposure introduces transcription-blocking lesions. Chris Stoeckert Jason Hilton BruUV-seq PMC:4675984 https://github.com/obi-ontology/obi/issues/827 ENCODE DCC bromouride labeling and sequencing after UV exposure OBI:0002144 extrachromosomal circular DNA sequencing assay An assay which aims at identifying the endogenous population of extrachromosomal circular DNA originating from a subset of genomic loci and potentially having profound consequences on the regulatory and coding capabilities of these regions. The assay includes creation of a library out of the circular DNA molecules and subsequent sequencing using parallelized sequencing methods. Chris Stoeckert Jason Hilton circulome-seq eccDNA-seq url:http://biorxiv.org/content/early/2017/04/19/128686 https://github.com/obi-ontology/obi/issues/830 ENCODE DCC extrachromosomal circular DNA sequencing assay OBI:0002190 courier organization An organization that delivers messages, packages, and mail. Chris Stoeckert, Helena Ellis courier https://en.wikipedia.org/wiki/Courier NCI BBRB courier organization OBI:0002191 courier tracking number A centrally registered identifier symbol assigned by a courier organization in order to track the delivery of an item. Chris Stoeckert, Helena Ellis OBIB NCI BBRB courier tracking number OBI:0002192 Leica Peloris rapid tissue processor An automatic tissue processor that is a dual retort tissue processor manufactured by the Leica company to provide fast, high quality tissue processing for histology laboratories. Chris Stoeckert, Helena Ellis http://drp8p5tqcb2p5.cloudfront.net/fileadmin/downloads_lbs/Leica%20PELORIS/User%20Manuals/Leica_Peloris_manual_EN.pdf NCI BBRB Leica Peloris rapid tissue processor OBI:0002198 molecular analysis facility organization An analysis facility that includes analysis of molecular metabolites, as well as the various DNAs and RNAs. An organization that provides molecular analysis service. Chris Stoeckert, Helena Ellis MAF NCI BBRB, OBIB NCI BBRB molecular analysis facility organization OBI:0002368 clinical history of cancer A clinical history in which there is a diagnosis of cancer. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB clinical history of cancer OBI:0002369 clinical history devoid of cancer A clinical history in which there was no diagnosis of cancer. Chris Stoeckert, Helena Ellis clinical history of no cancer NCI BBRB, OBIB NCI BBRB clinical history devoid of cancer OBI:0002370 unknown clinical history of cancer A clinical history in which it is not known whether there was a diagnosis of cancer. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB unknown clinical history of cancer OBI:0002372 family clinical history of cancer A clinical history in which there is a diagnosis of cancer in a blood relative. Chris Stoeckert, Helena Ellis family history of cancer NCI BBRB, OBIB NCI BBRB family clinical history of cancer OBI:0002373 aunt clinical history of cancer A clinical history in which there is a diagnosis of cancer in the female sibling of a parent. Chris Stoeckert, Helena Ellis OBIB NCI BBRB aunt clinical history of cancer OBI:0002374 brother clinical history of cancer A clinical history in which there is a diagnosis of cancer in a male sibling. Chris Stoeckert, Helena Ellis OBIB NCI BBRB brother clinical history of cancer OBI:0002375 daughter clinical history of cancer A clinical history in which there is a diagnosis of cancer in a person's female child. Chris Stoeckert, Helena Ellis OBIB NCI BBRB daughter clinical history of cancer OBI:0002376 father clinical history of cancer A clinical history in which there is a diagnosis of cancer in a male parent. Chris Stoeckert, Helena Ellis OBIB NCI BBRB father clinical history of cancer OBI:0002377 mother clinical history of cancer A clinical history in which there is a diagnosis of cancer in a female parent. Chris Stoeckert, Helena Ellis OBIB NCI BBRB mother clinical history of cancer OBI:0002378 sister clinical history of cancer A clinical history in which there is a diagnosis of cancer in a female sibling. Chris Stoeckert, Helena Ellis OBIB NCI BBRB sister clinical history of cancer OBI:0002379 son clinical history of cancer A clinical history in which there is a diagnosis of cancer in a person's male child. Chris Stoeckert, Helena Ellis OBIB NCI BBRB son clinical history of cancer OBI:0002380 uncle clinical history of cancer A clinical history in which there is a diagnosis of cancer in a male sibling of a parent. Chris Stoeckert, Helena Ellis OBIB NCI BBRB uncle clinical history of cancer OBI:0002381 grandmother clinical history of cancer A clinical history in which there is a diagnosis of cancer in a female parent of a parent. Chris Stoeckert, Helena Ellis OBIB NCI BBRB grandmother clinical history of cancer OBI:0002382 grandfather clinical history of cancer A clinical history in which there is a diagnosis of cancer in a male parent of a parent. Chris Stoeckert, Helena Ellis OBIB NCI BBRB grandfather clinical history of cancer OBI:0002383 nephew clinical history of cancer A clinical history in which there is a diagnosis of cancer in a male child of a sibling. Chris Stoeckert, Helena Ellis OBIB NCI BBRB nephew clinical history of cancer OBI:0002384 niece clinical history of cancer A clinical history in which there is a diagnosis of cancer in a female child of a sibling. Chris Stoeckert, Helena Ellis OBIB NCI BBRB niece clinical history of cancer OBI:0002389 clinical history of repeated HIV assays A clinical history in which there is repeated reactive screening assays for human immunodeficiency virus (1 or 2) antibodies regardless of the results of supplemental assays. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB clinical history of repeated HIV assays OBI:0002390 exposure to second hand smoke A clinical history in which there has been second hand exposure to tobacco smoking. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB exposure to second hand smoke OBI:0002391 exposure to second hand smoke in household during childhood An exposure to second hand smoke that occurred in the (patient's) household when the person was a child. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB exposure to second hand smoke in household during childhood OBI:0002392 exposure to second hand smoke in current household An exposure to second hand smoke in person's current household. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB exposure to second hand smoke in current household OBI:0002393 pregnancy history A clinical history in which a female has had a pregnancy. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB pregnancy history OBI:0002397 gynecologic surgery history A clinical history in which a woman has had gynecologic surgery in the past. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB gynecologic surgery history OBI:0002398 hysterectomy history A gynecologic surgery history in which a woman has had a hysterectomy. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB hysterectomy history OBI:0002399 unilateral oophorectomy history A gynecologic surgery history in which a woman has had a unilateral oophorectomy. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB unilateral oophorectomy history OBI:0002400 neither hysterectomy nor oophorectomy history A gynecologic surgery history in which a woman has not had either a hysterectomy or an oophorectomy. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB neither hysterectomy nor oophorectomy history OBI:0002405 hormonal replacement therapy history A clinical history in which an individual has had hormonal replacement therapy in the past. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB hormonal replacement therapy history OBI:0002445 transcription start site mapping by primer extension assay A transcription profiling assay in which the transcription start site for a gene is determined by identifying the 5' end of mRNA. A radio-labeled primer is annealed to a complementary mRNA sequence near the 3' end, then cDNA is synthesized until the 5' end is reached. Rebecca Tauber PMID:23378648 url:https://en.wikipedia.org/wiki/Primer_extension transcription start site mapping by primer extension assay OBI:0002457 precision nuclear run-on sequencing assay An RNA-seq assay that maps the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution by using biotin-labeled ribonucleotide triphosphate analogs (biotin-NTP) for nuclear run-on reactions, allowing the efficient affinity purification of nascent RNAs for high throughput sequencing from their 3' ends. Rebecca Tauber PRO-Seq precision nuclear run-on and sequencing assay PMID:23430654 https://github.com/obi-ontology/obi/issues/876 precision nuclear run-on sequencing assay OBI:0002466 alignment counting algorithm An algorithm used to assign aligned sequence reads, resulting from a reference genome transcriptome alignment algorithm, to sequence features (e.g. genes or transcripts). Stephen A. Fisher, Junhyong Kim, Dan Berrios alignment counting algorithm OBI:0002467 alignment counting application A software application that implements an alignment counting algorithm, used to count the overlap of aligned sequencing reads with genes. Stephen A. Fisher, Junhyong Kim, Dan Berrios doi:10.1093/bioinformatics/btu638 alignment counting application OBI:0002469 base calling application A base-calling application that implments a base-calling algorithm to convert BCL (binary base call) files, (e.g., those generated by Illumina sequencing systems) to standard FASTQ file formats for downstream analysis. Stephen A. Fisher, Junhyong Kim, Dan Berrios base calling application OBI:0002470 bcl2fastq software application A base calling application that implments a base calling algorithm to convert BCL (binary base call) files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. Stephen A. Fisher, Junhyong Kim, Dan Berrios https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html bcl2fastq software application OBI:0002478 reference genome-transcriptome alignment algorithm An algorithm that attempts to align a nucleic acid sequence to a reference genome and transcriptome. Stephen A. Fisher, Junhyong Kim, Dan Berrios reference genome-transcriptome alignment algorithm OBI:0002484 star algorithm A reference genome transcriptome alignment algorithm that is a standalone RNA-seq alignment algorithm that uses uncompressed suffix arrays and a mapping algorithm similar to those used in large-scale genome alignment tools to align RNA-seq reads to a genomic reference. Stephen A. Fisher, Junhyong Kim, Dan Berrios https://www.ncbi.nlm.nih.gov/pubmed/23104886 star algorithm OBI:0002487 microraft A material separation device also commerically known as Isoraft, that is used to isolate single cells. Stephen A. Fisher, Junhyong Kim, Dan Berrios https://en.wikipedia.org/wiki/Microrafts microraft OBI:0002500 amniotic fluid specimen A specimen that is derived from amniotic fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank amniotic fluid specimen OBI:0002501 bile specimen A specimen that is derived from bile. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank bile specimen OBI:0002502 cerebrospinal fluid specimen A specimen that is derived from cerbrospinal fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank cerebrospinal fluid specimen OBI:0002503 feces specimen A specimen that is derived from feces. Chris Stoeckert stool specimen Chris Stoeckert, Penn Medicine Biobank feces specimen OBI:0002504 digestive system fluid or secretion specimen A specimen that is derived from digestive system fluid or secretion. Chris Stoeckert gastric fluid specimen Chris Stoeckert, Penn Medicine Biobank digestive system fluid or secretion specimen OBI:0002505 milk specimen A specimen that is derived from milk. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank milk specimen OBI:0002506 pericardial fluid specimen A specimen that is derived from pericardial fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank pericardial fluid specimen OBI:0002507 saliva specimen A specimen that is derived from saliva. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank saliva specimen OBI:0002508 sputum specimen A specimen that is derived from sputum. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank sputum specimen OBI:0002509 sweat specimen A specimen that is derived from sweat. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank sweat specimen OBI:0002510 synovial fluid specimen A specimen that is derived from synovial fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank synovial fluid specimen OBI:0002511 vitreous humor specimen A specimen that is derived from vireous humor. Chris Stoeckert vitreous fluid specimen Chris Stoeckert, Penn Medicine Biobank vitreous humor specimen OBI:0002512 bone marrow specimen A specimen that is derived from bone marrow. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank bone marrow specimen OBI:0002513 placenta specimen A specimen that is derived from placenta. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank placenta specimen OBI:0002514 peritoneal fluid specimen A specimen that is derived from peritoneal fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank peritoneal fluid specimen OBI:0002515 pleural fluid specimen A specimen that is derived from pleural fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank pleural fluid specimen OBI:0002516 brain specimen A specimen that is derived from brain. Chris Stoeckert Chris Stoeckert, NCI BBRB brain specimen OBI:0002517 hair specimen A specimen that is derived from hair. Chris Stoeckert Chris Stoeckert, NCI BBRB hair specimen OBI:0002518 prostate gland specimen A specimen that is derived from prostate gland. Chris Stoeckert Chris Stoeckert, NCI BBRB prostate gland specimen OBI:0002519 skeletal muscle tissue specimen A specimen that is derived from skeletal muscle. Chris Stoeckert Chris Stoeckert, NCI BBRB skeletal muscle tissue specimen OBI:0002520 heart specimen A specimen that is derived from heart. Chris Stoeckert Chris Stoeckert, NCI BBRB heart specimen OBI:0002521 renal medulla specimen A specimen that is derived from renal medulla. Chris Stoeckert kidney medulla specimen Chris Stoeckert, NCI BBRB renal medulla specimen OBI:0002522 adrenal gland specimen A specimen that is derived from adrenal gland. Chris Stoeckert Chris Stoeckert, NCI BBRB adrenal gland specimen OBI:0002523 breast specimen A specimen that is derived from breast. Chris Stoeckert mammary tissue specimen Chris Stoeckert, NCI BBRB breast specimen OBI:0002524 urinary bladder specimen A specimen that is derived from urinary bladder. Chris Stoeckert Chris Stoeckert, NCI BBRB urinary bladder specimen OBI:0002525 tibial artery specimen A specimen that is derived from tibial artery. Chris Stoeckert Chris Stoeckert, NCI BBRB tibial artery specimen OBI:0002526 skin of body specimen A specimen that is derived from skin. Chris Stoeckert skin specimen Chris Stoeckert, NCI BBRB skin of body specimen OBI:0002527 pancreas specimen A specimen that is derived from pancreas. Chris Stoeckert Chris Stoeckert, NCI BBRB pancreas specimen OBI:0002528 stomach specimen A specimen that is derived from stomach. Chris Stoeckert Chris Stoeckert, NCI BBRB stomach specimen OBI:0002529 pituitary gland specimen A specimen that is derived from pituitary gland. Chris Stoeckert Chris Stoeckert, NCI BBRB pituitary gland specimen OBI:0002530 adipose tissue specimen A specimen that is derived from adipose tissue. Chris Stoeckert Chris Stoeckert, NCI BBRB adipose tissue specimen OBI:0002531 cortex of kidney specimen A specimen that is derived from cortex of kidney. Chris Stoeckert kidney cortex specimen Chris Stoeckert, NCI BBRB cortex of kidney specimen OBI:0002532 esophagus mucosa specimen A specimen that is derived from esophagus mucosa. Chris Stoeckert Chris Stoeckert, NCI BBRB esophagus mucosa specimen OBI:0002533 colon specimen A specimen that is derived from colon. Chris Stoeckert Chris Stoeckert, NCI BBRB colon specimen OBI:0002534 lung specimen A specimen that is derived from lung. Chris Stoeckert Chris Stoeckert, NCI BBRB lung specimen OBI:0002535 esophagus muscularis mucosa specimen A specimen that is derived from esophagus muscularis mucosa. Chris Stoeckert esophagus muscularis specimen Chris Stoeckert, NCI BBRB esophagus muscularis mucosa specimen OBI:0002536 cerebral cortex specimen A specimen that is derived from cerebral cortex. Chris Stoeckert brain cortex specimen Chris Stoeckert, NCI BBRB cerebral cortex specimen OBI:0002537 thyroid gland specimen A specimen that is derived from thyroid gland. Chris Stoeckert Chris Stoeckert, NCI BBRB thyroid gland specimen OBI:0002538 cerebellum specimen A specimen that is derived from cerebellum. Chris Stoeckert brain cerebellum specimen Chris Stoeckert, NCI BBRB cerebellum specimen OBI:0002539 tibial nerve specimen A specimen that is derived from tibial nerve. Chris Stoeckert Chris Stoeckert, NCI BBRB tibial nerve specimen OBI:0002540 coronary artery specimen A specimen that is derived from coronary artery. Chris Stoeckert Chris Stoeckert, NCI BBRB coronary artery specimen OBI:0002541 spleen specimen A specimen that is derived from spleen. Chris Stoeckert Chris Stoeckert, NCI BBRB spleen specimen OBI:0002542 aorta specimen A specimen that is derived from aorta. Chris Stoeckert Chris Stoeckert, NCI BBRB aorta specimen OBI:0002543 atrial appendage specimen A specimen that is derived from the atrium auricular region. Chris Stoeckert Chris Stoeckert, NCI BBRB atrial appendage specimen OBI:0002544 esophagogastric junction specimen A specimen that is derived from the esophagogastric junction. Chris Stoeckert Chris Stoeckert, NCI BBRB esophagogastric junction specimen OBI:0002545 ileum specimen A specimen that is derived from ileum. Chris Stoeckert Chris Stoeckert, NCI BBRB ileum specimen OBI:0002546 liver specimen A specimen that is derived from liver. Chris Stoeckert Chris Stoeckert, NCI BBRB liver specimen OBI:0002547 minor salivary gland specimen A specimen that is derived from minor salivary gland. Chris Stoeckert Chris Stoeckert, NCI BBRB minor salivary gland specimen OBI:0002548 omentum specimen A specimen that is derived from omentum. Chris Stoeckert Chris Stoeckert, NCI BBRB omentum specimen OBI:0002549 ovary specimen A specimen that is derived from female gonad. Chris Stoeckert Chris Stoeckert, NCI BBRB ovary specimen OBI:0002550 sigmoid colon specimen A specimen that is derived from sigmoid colon. Chris Stoeckert Chris Stoeckert, NCI BBRB sigmoid colon specimen OBI:0002551 suprapubic skin specimen A specimen that is derived from suprapubic skin. Chris Stoeckert Chris Stoeckert, NCI BBRB suprapubic skin specimen OBI:0002552 testis specimen A specimen that is derived from testis. Chris Stoeckert Chris Stoeckert, NCI BBRB testis specimen OBI:0002553 uterus specimen A specimen that is derived from uterus. Chris Stoeckert Chris Stoeckert, NCI BBRB uterus specimen OBI:0002554 vagina specimen A specimen that is derived from vagina. Chris Stoeckert Chris Stoeckert, NCI BBRB vagina specimen OBI:0002565 adapter-sequence trimming A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed). Dan Berrios Dan Berrios adapter-sequence trimming OBI:0002566 file merge A data transformation in which data contained in 2 or more files are merged into a single file. Dan Berrios Dan Berrios file merge OBI:0002567 sequence alignment A data transformation in which one or more sequences (reads) are positioned on a reference sequence template (often a reference set of genes), according to the genetic base-pairing paradigm. Dan Berrios Dan Berrios sequence alignment OBI:0002570 nCounter Mouse miRNA Expression array Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819 A mouse array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller added based on http://purl.obolibrary.org/obo/OBI_0002013 https://www.nanostring.com/products/mirna-assays/mirna-panels 2018-05-11T14:04:41Z ENCODE project nCounter Mouse miRNA Expression array OBI:0002571 polyA-selected RNA sequencing assay An RNA-seq assay to study transcriptomes through the enrichment of polyadenylated transcripts or removal of ribosomal RNA prior to high-throughput sequencing. Jason Hilton Mark A. Miller mRNA-seq url:https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-419 ENCODE polyA-selected RNA sequencing assay OBI:0002572 polyA-depleted RNA sequencing assay An RNA-seq assay to study non-polyadenylated transcripts, such as, but not exclusive to unspliced and circular isoforms, through the depletion of polyadenylated transcripts prior to high-throughput sequencing. Jason Hilton Mark A. Miller polyA-depleted RNA-seq url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030733 url:http://www.tandfonline.com/doi/full/10.1080/15476286.2015.1110676 ENCODE polyA-depleted RNA sequencing assay OBI:0002574 RNA extraction with polyA depletion A RNA extraction process in which only RNAs lacking a polyA tail are retained Mark A. Miller, based on OBI_0000848 UPenn Group 2018-05-11T15:01:14Z RNA extraction with polyA depletion OBI:0002575 isoform sequencing Novel transcript forms were assessed by isoform sequencing. A method for sequencing isoforms by enriching a cDNA library for full-length reads spanning entire transcript isoforms. ISO-seq url:http://www.pacb.com/blog/intro-to-iso-seq-method-full-leng/ isoform sequencing OBI:0002578 adapter sequence data Nucleotide sequences of molecules that are ligated to assay samples prior to sequencing of these samples; these sequences are provided by assay kit manufacturers and typically used to combine sequencing of multiple samples in one assay run. Dan Berrios Dan Berrios adapter sequence data OBI:0002579 adapter-trimmed sequence data The results of a data transformation of sequence data in which reference subsequences corresponding to ligated library adapters are removed. Dan Berrios Dan Berrios adapter-trimmed sequence data OBI:0002580 aligned sequence data The results of a sequence alignment. Dan Berrios Dan Berrios aligned sequence data OBI:0002581 merged aligned sequence data The results of a data transformation of sequence data in which files containing aligned sequence data are merged together Dan Berrios Dan Berrios merged aligned sequence data OBI:0002583 DNA methylation profiling data The results of a DNA methylation profiling assay DNA methylation profiling data OBI:0002585 sequence trimming A data transformation in which subsequences of a molecular sequence are cut (removed). sequence trimming OBI:0002623 whole metagenome sequencing assay A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. Whole metagenome sequencing has been used to explore the composition and metabolic capability of communities of microbes found in the environment (e.g. in soil, water, etc.) and in humans and other species (e.g. in the gut, oral cavity, etc.). Rebecca Jackson WMS Bjoern Peters Michelle Giglio https://github.com/obi-ontology/obi/issues/1056 whole metagenome sequencing assay OBI:0002689 detection of pathogenic organisms objective An organism feature identification objective that aims to detect whether an organism contains pathogenic organisms. Jie Zheng VEuPathDB https://github.com/obi-ontology/obi/issues/1117 VEuPathDB detection of pathogenic organisms objective OBI:0002690 insecticide resistance detection objective An organism feature identification objective that aims to detect insecticide resistance of an insect. Jie Zheng VEuPathDB https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance detection objective OBI:0002768 whole virome sequencing assay A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. Michelle Giglio Rebecca Jackson Suvarna Nadendla OBI:0002623 CFDE whole virome sequencing assay OBI:0100016 blood plasma specimen PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA. PERSON: Maura Gasparetto PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra plasma WEB: http://en.wikipedia.org/wiki/Blood_plasma blood plasma specimen OBI:0100017 blood serum specimen PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy. A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. PERSON: Maura Gasparetto PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/Blood_plasma blood serum specimen OBI:0100026 organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism OBI:0100051 specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen OBI:0100067 bronchial alveolar lavage solution containing lung derived T cells, eosinophils, and TNFa. Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space. PERSON: Bjoern Peters BAL GROUP: IEDB bronchial alveolar lavage OBI:0200000 data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A data transformation is a process which produces output data from input data A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors data transformation OBI:0200005 feature extraction objective A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image. Elisabetta Manduchi James Malone TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction feature extraction objective OBI:0200031 differential expression analysis objective Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions. Elisabetta Manduchi PERSON: Elisabetta Manduchi differential expression analysis objective OBI:0200078 descriptive statistical calculation objective A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. Elisabetta Manduchi James Malone Melanie Courtot Monnie McGee PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Monnie McGee descriptive statistical calculation objective OBI:0200081 sequence analysis objective A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns. James Malone PERSON: James Malone sequence analysis objective OBI:0200083 survival analysis objective Kaplan meier data transformation A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables PERSON: James Malone PERSON: Tina Boussard survival analysis http://en.wikipedia.org/wiki/Survival_analysis survival analysis objective OBI:0200091 inter-rater reliability objective A study was conducted to determine the inter-rater reliability of common clinical examination procedures proposed to identify patients with lumbar segmental instability. Examples include joint-probability of agreement, Cohen's kappa and the related Fleiss' kappa, inter-rater correlation, concordance correlation coefficient and intra-class correlation. a data transformation objective of determining the concordance or agreement between human judges. Person:Alan Ruttenberg Person:Helen Parkinson inter-rater agreement http://en.wikipedia.org/wiki/Inter-rater_reliability inter-rater reliability objective OBI:0200111 data visualization Generation of a heatmap from a microarray dataset An planned process that creates images, diagrams or animations from the input data. Elisabetta Manduchi James Malone Melanie Courtot Tina Boussard data encoding as image visualization PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Tina Boussard Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding data visualization OBI:0200157 data vector reduction objective Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k. James Malone Richard H. Scheuermann PERSON: Richard H. Scheuermann data vector reduction objective OBI:0200166 data transformation objective normalize objective An objective specification to transformation input data into output data Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone data transformation objective OBI:0200167 data normalization objective Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons. Elisabetta Manduchi Helen Parkinson James Malone PERSON: Elisabetta Manduchi PERSON: Helen Parkinson PERSON: James Malone data normalization objective OBI:0200168 correction objective Type I error correction A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself James Malone PERSON: James Malone PERSON: Melanie Courtot correction objective OBI:0200172 partitioning objective A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi partitioning objective OBI:0200173 background correction objective A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi background correction objective OBI:0200174 curve fitting objective A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi curve fitting objective OBI:0200177 center calculation objective A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average. A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. James Malone PERSON: James Malone center calculation objective OBI:0200178 class discovery objective A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. James Malone clustering objective discriminant analysis objective unsupervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class discovery objective OBI:0200179 class prediction objective A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. James Malone classification objective supervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class prediction objective OBI:0200180 spread calculation objective Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set Awaiting English definition from Monnie McGee James Malone Person:Helen Parkinson spread calculation objective OBI:0200183 scaling objective Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13 is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum Awaiting English definition from Monnie McGee James Malone Person:Helen Parkinson scaling objective OBI:0200186 error correction objective Application of a multiple testing correction method An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself. James Malone, Helen Parkinson PERSON: James Malone error correction objective OBI:0200187 sequence analysis data transformation A sequence analysis data transformation is a data transformation that has objective sequence analysis and has the aim of analysing ordered biological data for sequential patterns. James Malone EDITOR sequence analysis data transformation OBI:0200188 cross validation objective A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. James Malone rotation estimation objective WEB: http://en.wikipedia.org/wiki/Cross_validation cross validation objective OBI:0200189 merging objective merging of columns from two different data sets A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets. James Malone combining objective PERSON: Data Transformation Branch merging objective OBI:0200196 correlation study objective A data transformation objective in which correlation is obtained (often measured as a correlation coefficient, ρ) which indicates the strength and direction of a relationship between two random variables. PERSON: Tina Boussard correlation study objective OBI:0200197 spectrum analysis objective Calculation of characteristic path length in mass spectrometry is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process. PERSON: Tina Boussard Person:Helen Parkinson spectrum analysis objective OBI:0302884 extraction nucleic acid extraction using phenol chloroform A material separation in which a desired component of an input material is separated from the remainder Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future. Person:Bjoern Peters Philippe Rocca-Serra extraction OBI:0302885 filtration PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4. filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device Philippe Rocca-Serra OBI-Branch: adapted from wikipedia and wordnet filtration OBI:0302886 centrifugation PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12. centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation Philippe Rocca-Serra adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm centrifugation OBI:0302888 washing PMID: 6874122. Dialysis leucopenia--no correction after prolonged washing of the membrane. Int J Artif Organs. 1983 May;6(3):113-4. washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow. Philippe Rocca-Serra OBI-Branch washing OBI:0302903 nucleic acid hybridization PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27. a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity. Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization] hybridization assay nucleic acid hybridization OBI:0302906 DNA Subtraction PMID: 10718422. Identification of genes overexpressed in head and neck squamous cell carcinoma using a combination of complementary DNA subtraction and microarray analysis. Laryngoscope. 2000 Mar;110(3 Pt 1):374-81 a material separation process by which repetitive genomic DNA is removed during the construction of cDNA library. Philippe Rocca-Serra OBI-Branch DNA Subtraction OBI:0302908 document editing Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL. Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292 is a planned process with specified input original document and specified output edited document Philippe Rocca-Serra and OBI consortium adapted from wikipedia document editing OBI:0400043 flow cell Biofilm Flow Cell Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell. Person:John Quinn flow_cell http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm flow cell OBI:0400045 fluid pressure regulator LSR2 fluid pressure regulator Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less frequently nitrogen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank. Person: John Quinn Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 fluid pressure regulator OBI:0400103 DNA sequencer ABI 377 DNA Sequencer, ABI 310 DNA Sequencer A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. Trish Whetzel MO DNA sequencer OBI:0400105 arrayer BioRobotics Microgrid II TAS, Affymetrix GMS 417 a device which deposits biological material onto a substrate in a defined pattern. Trish Whetzel MO_697 arrayer arrayer OBI:0400106 centrifuge A device with a rapidly rotating container that applies centrifugal force to its contents Melanie Courtot Person: Jennifer Fostel Trish Whetzel http://en.wikipedia.org/wiki/Centrifuge centrifuge OBI:0400107 computer Apple PowerBook, Dell OptiPlex A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. Melanie Courtot Trish Whetzel http://en.wikipedia.org/wiki/Computer computer OBI:0400147 microarray An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays. A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position. Daniel Schober PERSON: Chris Stoeckert microarray OBI:0400148 DNA microarray Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115 A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample. PERSON: Daniel Schober PERSON: Frank Gibson DNA Chip DNA-array Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03 DNA microarray OBI:0400149 protein microarray The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions. A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions. Daniel Schober PERSON: Daniel Schober protein microarray OBI:0400170 microscope slide PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay. a microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument PERSON: Phillippe Rocca-Serra OBI biomaterial branch microscope slide OBI:0600004 human subject enrollment enlisting familiy members of HIV patients into a study A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent. As with group assignment, should the specified output here be an organism which bears a role Bjoern Peters IEDB criteria come from plan / clinical trial branch human subject enrollment OBI:0600005 collecting specimen from organism taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation PERSON:Bjoern Peters IEDB collecting specimen from organism OBI:0600014 material component separation Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification a material processing in which components of an input material become segregated in space Bjoern Peters IEDB material component separation OBI:0600016 pooling specimens http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points physical combination of several instances of like material PlanAndPlannedProcess Branch sample pooling OBI branch derived like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class. pooling specimens OBI:0600018 material portioning pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock a material processing in which the input substance is partitioned into a number of portions that are similar in composition. PERSON:Bjoern Peters aliquoting apportioning OBI branch derived material portioning OBI:0600036 'establishing cell culture' a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). PERSON:Matthew Brush PERSON:Matthew Brush A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. establishing cell culture OBI:0600037 cell culture splitting The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media. The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing PlanAndPlannedProcess Branch cell culture passaging OBI branch derived An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone. cell culture splitting OBI:0600038 addition of molecular label The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+. a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay PERSON:Matthew Brush labeling OBI developer call, 3-12-12 addition of molecular label OBI:0600044 lavage the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid This is not washing, in which case the material of interest is not the resulting fluid PlanAndPlannedProcess Branch OBI branch derived lavage OBI:0600047 sequencing assay sequencing assay The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template An assay the uses chemical or biochemical means to infer the sequence of a biomaterial the use of a chemical or biochemical means to infer the sequence of a biomaterial has_output should be sequence of input; we don't have sequence well defined yet PlanAndPlannedProcess Branch PlanAndPlannedProcess Branch OBI branch derived OBI branch derived Sequencing Technology SA4 NIAID GSCID-BRC sequencing assay sequencing assay OBI:0600049 DNA polymerase amplification The use of taq polymerase to amplify a DNA fragment during a PCR. DNA polymerase amplification is an enzymatic amplification which uses DNA polymerase enzyme to make copies of a DNA contained in biomaterial used as input PERSON:Kevin Clancy Philippe Rocca-Serra OBI branch derived DNA polymerase amplification OBI:0600052 dialysis the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition PERSON:Kevin Clancy OBI branch derived dialysis OBI:0600057 enzymatic DNA replication the use of enzymes to duplicate DNA molecules the use of enzymes to duplicate DNA molecule any process used to make additional copies of a biomaterial PERSON:Kevin Clancy OBI branch derived enzymatic DNA replication OBI:0600058 enzymatic amplification the use of a polymerase chain reaction to amplify a fragment of DNA the use of enzymes to increase the number of molecules of a biomaterial PERSON:Kevin Clancy OBI branch derived enzymatic amplification OBI:0666666 RNA extraction A RNA extraction is a nucleic acid extraction where the desired output material is RNA PlanAndPlannedProcess Branch OBI branch derived requested by Helen Parkinson for MO RNA extraction OBI:0666667 nucleic acid extraction Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet. a material separation to recover the nucleic acid fraction of an input material PlanAndPlannedProcess Branch OBI branch derived requested by Helen Parkinson for MO. Could be defined class nucleic acid extraction OBI:1110087 donor A T cell line from a PPD(+) donor. A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro. IEDB donor role IEDB Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended. donor OBI:1110095 blood harvesting A material separation where blood is taken from an organism. IEDB IEDB blood harvesting OBI:1110109 target of material addition A cell culture into which a mixture of peptides is being added. A material entity into which another is being added in a material combinatino process 10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export. IEDB target of material addition OBIws:0000192 A sequence data that is about the primary structure of RNA. ITPPR ITPPR RNA sequence data OGMS:0000015 clinical history A series of statements representing health-relevant qualities of a patient and of a patient's family. clinical history OGMS:0000023 phenotype 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. phenotype 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 disease 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 disorder OMIABIS:0000000 A biobank is a collections of samples of biological substances (e.g. tissue, blood, DNA) which are linked to data about the samples and their donors. They have a dual nature as collections of samples and data. Mathias Brochhausen definition derived from the definition of 'human biobank', based on http://www.ethikrat.org/files/der_opinion_human-biobanks.pdf biobank OMIABIS:0000003 An identifier in natural language referring to a biobank. Mathias Brochhausen Name of biobank biobank proper name OMIABIS:0000004 An identifier that consists of two letters, is part of the ISO 3166-1, and designates countries, dependent territories, and special areas of geographical interest. Mathias Brochhausen http://en.wikipedia.org/wiki/ISO_3166-1_alpha-2 Two-letter country codes defined in ISO 3166-1, part of the ISO 3166 standard published by the International Organization for Standardization (ISO), to designate countries, dependent territories, and special areas of geographical interest. ISO 3166-1 alpha-2 code OMIABIS:0000005 A biobank identifier that has an ISO 3166-1 alpha-2 code as a part. Mathias Brochhausen Biobank ID Textual string of letters starting with the country code (according to standard ISO1366 alpha2) followed by the underscore “_” and post-fixed by a biobank ID or name specified by its juristic person (nationally specific). biobank idenfier with ISO 3166-1 alpha-2 code OMIABIS:0000007 The ISO 3166-1 alpha-2 code that is part of the sample collection or study contact's postal address. Mathias Brochhausen Sample Collection/Study contact country ISO 3166-1 alpha-2 code for sample collection or study contact OMIABIS:0000012 A role borne by a human being that is part of an group of individuals and acts as contact person for the group. This role gets realized by the bearer being a participant in a contacting process. Mathias Brochhausen contact role OMIABIS:0000014 A personal name that designates the person acting as contact for a sample collection or a study. Mathias Brochhausen Biobank contact person name of biobank contact person OMIABIS:0000024 A post-office box is material entity that is a box on the premises of a post office station and is uniquely addressable. Mathias Brochhausen http://en.wikipedia.org/wiki/Post-office_box post-office box OMIABIS:0000028 The ISO 3166-1 alpha-2 code that is part of the biobank contact person's postal address. Mathias Brochhausen Biobank country code ISO 3166-1 alpha-2 code for biobank contact person OMIABIS:0000037 A proper name that designates a study. Mathias Brochhausen Study name study proper name OMIABIS:0000038 A personal name that designates the human being responsible for a sample collection or the human being being the principal investigator in a study. Mathias Brochhausen Sample Collection Responsible / Principal Investigator name of sample collection responsible or principal investigator OMIABIS:0000039 A personal name that designates the person acting as contact for a sample collection or a study. Mathias Brochhausen Sample Collection/Study contact person name of sample collection or study contact person OMIABIS:0000045 An ISO 3166-1 alpha-2 code that designates the country a biobank is located in. Mathias Brochhausen Biobank country code biobank location ISO 3166-1 alpha-2 code OMIABIS:0000046 An identifier for an organization that is assigned to that organization by the Cancer Therapy Evaluation Program. Mathias Brochhausen CTEP organization identifier OMIABIS:0000047 A biobank identifier that has both an ISO 3166-1 alpha-2 code and a CTEP organization code. Mathias Brochhausen biobank identifier with ISO 3166-1 alpha-2 code and CTEP organization identifier OMIABIS:0000050 fixed tissue specimen A processed specimen that is the output of a fixation process. Alice Nzinga Mathias Brochhausen fixed tissue specimen OMIABIS:0000051 A fixed tissue specimen that is in block form. fixed tissue block specimen OMIABIS:0000052 fixed tissue slide specimen A fixed tissue specimen that is placed in a slide. fixed tissue slide specimen OMIABIS:0000057 A specimen that has been procured from a histology slide under direct microscopic visualization. Alice Nzinga http://www.ncbi.nlm.nih.gov/pubmed/11269646 microdissected specimen OMIABIS:0000093 A contact role borne by a member of a biobank organization and realized by serving as the contact for one of its biobanks. A contact role borne by a member of a sample collection or study organization and realized by serving as the contact for the collection or the study. biobank contact role OMIABIS:0000094 sample collection or study contact role OMIABIS:0000911 A material processing that uses chemical process by which biological tissues are preserved from decay. Fixation terminates any ongoing biochemical reactions and may increase stability of the treated tissues. http://en.wikipedia.org/wiki/Fixation_%28histology%29 http://sharedresources.fhcrc.org/training/tips-about-fixation-and-formalin The choice of fixation depends on the type of study. fixation OMIABIS:0001040 Mathias Brochhausen adherance to specification All specimens that meet the set parameters to be procured on. specimen meeting specification OMIABIS:0001042 A personal name that designates the person who prepared the specimen. Alice Nzinga specimen preparation contact OMIABIS:0001043 15min A time measurement datum that states the duration during which a specimen was submerged in formalin. Alice Nzinga time in formalin measurement OMIABIS:0001047 An identifier that refers to a specimen donor who is participating in specimen collection process for tissue procurement purposes and is usually assigned at the time of donor procurement. Alice Nzinga http://biospecimens.cancer.gov/resources/sops/GTEx_SOPs/II/A/GTEx%20Tissue%20Procurement%20SOP%20%28PR-0004%20v1.2.1%29.pdf case ID OMIABIS:0001054 A specimen that is normal. normal specimen OMIABIS:0001079 Alice Nzinga Mathias Brochhausen sample donor A Homo sapiens who contributes specimen. specimen donor OMIABIS:0001080 A planned process of preparing and submitting specimens to storage. specimen handling http://www.exchangenetwork.net/standards/SampleHandling_01_06_2006_Final.pdf sample handling OMIT:0025630 DNA fragmentation is the separation or breaking of DNA strands into pieces. It can be done intentionally by laboratory personnel or by cells, or can occur spontaneously DNA Fragmentation 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:00000012 A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism. Mathias Brochhausen William R. Hogan health care provider role OMRSE: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 OMRSE:00000038 A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law. Mathias Brochhausen Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008. We are aware of the fact that Wikipedia's definition differs from ours by saying that "Legal personality (...) is the characteristic of a non-living entity regarded by law to have the status of personhood" (http://en.wikipedia.org/wiki/Legal_personality) However, Shaw explicates: "In any legal system, certain entities, whether they be individuals or companies, will be regarded as possessing rights and duties enforceable at law. Thus an individual may prosecute or be prosecuted for assault and a company can sue for breach of contract. They are able to do this because the law recognises them as 'legal persons' possessing the capacity to have and to maintain certain rights, and being subject to perform specific duties. (...) In municipal law individuals, limited companies and public corporations are recognized as each possessing a distinct legal personality, the terms of which are circumscribed by the relevant legislation" (Shaw MN: International Law. Sixth Edition. Cambridge University Press, Cambridge, 2008). We hold that Shaw's position is ontological more prolific since it not only allows to explain how groups of individuals become recognized as unities at law, but also how different individuals can hold different legal personality roles (always against the context of one legal system). The latter will proof useful when dealing with the representing comatous patients or minorsat law in ontologies. legal person role PATO:0000011 age A time quality inhering in a bearer by virtue of how long the bearer has existed. age biological sex An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny. The assemblage of physical properties or qualities by which male is distinguished from female; the physical difference between male and female; the distinguishing peculiarity of male or female. James Malone Jie Zheng Tomasz Adamusiak MSH:D012723 NCIt:C28421 PATO:0000047 quality PATO:0000047 biological sex sex PATO:0000047 An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. MGED:MGED 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 A physical quality inhering in a bearer that has mass near a gravitational body. weight PATO:0000140 A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. position PATO:0000146 temperature A physical quality of the thermal energy of a system. Damion's Note: Future use might prefer: CMO_0000015 body temperature. temperature female A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. James Malone Jie Zheng Tomasz Adamusiak MSH:D005260 NCIt:C16576 PATO:0000383 SNOMEDCT:248152002 quality PATO:0000383 female PATO:0000383 A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. MGED:MGED male A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. James Malone Jie Zheng Tomasz Adamusiak MSH:D008297 NCIt:C20197 PATO:0000384 SNOMEDCT:248153007 quality PATO:0000384 male PATO:0000384 A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. MGED:MGED PATO:0000918 volume A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. volume PATO:0001018 A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0002079 Wikipedia:Physical_property relational physical quality physical 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 A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality PATO:0001241 A quality which inheres in a continuant. PATOC:GVG hermaphrodite A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. An organism having both male and female sexual characteristics and organs. James Malone Jie Zheng Tomasz Adamusiak DOID:3763 NCIt:C45909 PATO:0001340 SNOMEDCT:237821001 intersex quality PATO:0001340 hermaphrodite PATO:0001340 A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. MGED:MGED A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of one sex and external sexual characteristics of the other sex. quality PATO:0001827 pseudohermaphrodite PATO:0001827 A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of one sex and external sexual characteristics of the other sex. WordNet:WordNet An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. quality PATO:0001894 phenotypic sex PATO:0001894 PATO:0001985 frozen A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. frozen organismal quality A quality that inheres in an entire organism or part of an organism. quality PATO:0001995 organismal quality PATO:0001995 A quality that inheres in an entire organism or part of an organism. PATOC:CJM PATO:0015009 A quality inhering in air by virtue of the partial pressure exerted by the bearer's water vapour content. humidity PO:0004010 A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall. meristematic cell http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern meristematic cell http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PO:0006204 A native plant cell (PO:0025606) which is diploid (2n), and undergoes meiosis (GO:0007126) to produce four haploid (1n) plant spores (PO:0025017). sporocyte http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A native plant cell (PO:0025606) which is diploid (2n), and undergoes meiosis (GO:0007126) to produce four haploid (1n) plant spores (PO:0025017). http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern sporocyte http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PO:0009002 A cell which is a plant structure (PO:0009011). Sirarat Sarntivijai Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall. plant cell PO:0020099 A native plant cell (PO:0025606) that is the larger cell of a microgametophyte (PO:0025280) in seed plants. It does not divide further and develops into a pollen tube cell (PO:0025195). microgametophyte vegetative cell http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A native plant cell (PO:0025606) that is the larger cell of a microgametophyte (PO:0025280) in seed plants. It does not divide further and develops into a pollen tube cell (PO:0025195). http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern microgametophyte vegetative cell http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PO:0020132 Cell that constitutes the central part of the root cap, arranged in longitudinal files. columella root cap cell http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern Cell that constitutes the central part of the root cap, arranged in longitudinal files. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern columella root cap cell http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PO:0025606 A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment). A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004). native plant cell http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment). http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004). http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern native plant cell http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PO:0030007 A single meristematic cell (PO:0004010) at the tip of a plant structure where apical growth occurs. Apical cells occur only at the tip of a shoot axis apex, leaf apex, root apex, thallus apex, or protonema in bryophytes and some pteridophytes. Apical growth results from division of a single meristematic cell located at the tip of an apical meristem or plant organ, rather than from a population of meristematic cells located at the tip of an apical meristem. The apical cell may be tetrahedral shaped, with three (in shoots) or four (in roots) cutting faces, or wedge-shaped (lenticular) with two cutting faces (in non-vascular leaves or thalli). An apical cell may be established upon germination of a spore or upon the first cell division of an embryo, or later. meristematic apical cell http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A single meristematic cell (PO:0004010) at the tip of a plant structure where apical growth occurs. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern Apical cells occur only at the tip of a shoot axis apex, leaf apex, root apex, thallus apex, or protonema in bryophytes and some pteridophytes. Apical growth results from division of a single meristematic cell located at the tip of an apical meristem or plant organ, rather than from a population of meristematic cells located at the tip of an apical meristem. The apical cell may be tetrahedral shaped, with three (in shoots) or four (in roots) cutting faces, or wedge-shaped (lenticular) with two cutting faces (in non-vascular leaves or thalli). An apical cell may be established upon germination of a spore or upon the first cell division of an embryo, or later. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern meristematic apical cell http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PO:0030014 An apical cell that is part of a whole plant in the gametophytic phase. Occurs bryophytes and pteridophytes. gametophyte meristematic apical cell http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern An apical cell that is part of a whole plant in the gametophytic phase. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern Occurs bryophytes and pteridophytes. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern gametophyte meristematic apical cell http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern PO:0030015 A meristematic apical cell that is part of a whole plant in the sporophytic phase. Occurs in pteridophytes and the sporophyte of bryophytes. sporophyte meristematic apical cell http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern A meristematic apical cell that is part of a whole plant in the sporophytic phase. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern Occurs in pteridophytes and the sporophyte of bryophytes. http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern sporophyte meristematic apical cell http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern REO:0000171 molecular label role a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role) molecular tracer role OBI developer call, 3-12-12 molecular label role SO:0000001 region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. primary structure of sequence macromolecule sequence region SO:0000104 polypeptide A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. polypeptide sequence polypeptide SO:0000148 supercontig One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. supercontig SO:0000149 contig A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. contig SO:0000276 miRNA Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. miRNA SO:0000353 sequence_assembly A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. sequence_assembly SO:0001248 assembly A region of the genome of known length that is composed by ordering and aligning two or more different regions. assembly A pancreatic cell that produces and secretes hormones such as insulin and glucagon. An Islet cell is a pancreatic cell that produces and secretes hormones such as insulin and glucagon. The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin[GO]. Jie Zheng Tomasz Adamusiak NCIt:C32885 SNOMEDCT:360555004 SNOMEDCT:361339003 TAO:0001260 ZFA:0001260 uberon UBERON:0000016 Editor notes - endocrine and exocrine pancrease are not co-associated in hagfishes or lampreys [PMID:20959416] - create a separate class for these? endocrine pancreas UBERON:0000016 The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin[GO]. GOC:GO Wikipedia:Islets_of_Langerhans A cell collecting process used to isolate PBMCs, including T cells, from whole blood using density gradient centrifugation (e.g., Ficoll-Paque). PBMC Separation peripheral blood mononuclear cell isolation resource:SIO_000026 SIO_000026 object quality resource:SIO_000078 SIO_000078 nlp+ language entity resource:SIO_000079 SIO_000079 visual language entity resource:SIO_000115 SIO_000115 identifier resource:SIO_000116 SIO_000116 name resource:SIO_000119 SIO_000119 brand name resource:SIO_000120 SIO_000120 scientific name resource:SIO_000136 SIO_000136 description resource:SIO_000179 SIO_000179 label resource:SIO_000181 SIO_000181 first name resource:SIO_000182 SIO_000182 last name resource:SIO_000183 SIO_000183 personal name resource:SIO_000184 SIO_000184 legal name resource:SIO_000651 SIO_000651 textual entity resource:SIO_000653 SIO_000653 version label resource:SIO_000675 SIO_000675 unique identifier resource:SIO_000785 SIO_000785 answer resource:SIO_000811 A Uniform Resource Locator or Universal Resource Locator (URL) is a specific character string that constitutes a reference to an Internet resource. URL resource:SIO_000942 SIO_000942 numeric label resource:SIO_001041 SIO_001041 study design resource:SIO_001166 SIO_001166 annotation resource:SIO_001196 SIO_001196 history resource:SIO_001383 a gene symbol is a short name assigned to a gene. SIO_001383 gene symbol resource:SIO_010053 SIO_010053 evolutionary lineage resource:SIO_010060 SIO_010060 family history resource:SIO_010673 SIO_010673 medical history efo:EFO_0000187 A malignant neoplasm characterized by a vascular proliferation which usually contains blunt endothelial cells. Erythrocyte extravasation and hemosiderin deposition are frequently present. The most frequent site of involvement is the skin; however it may also occur internally. It generally develops in people with compromised immune systems including those with acquired immune deficiency syndrome (AIDS). A multicentric, malignant neoplastic vascular proliferation characterized by bluish-red cutaneous nodules, usually on the legs, toes, or feet, that slowly increase in size and number and spread to more proximal sites. The tumors have endothelium-lined channels and vascular spaces mixed with aggregates of spindle-shaped cells; they may remain confined to skin and subcutaneous tissue, but widespread visceral involvement may occur. James Malone Tomasz Adamusiak OMIM:148000 Kaposi's sarcoma cell efo:EFO_0000324 epithelial, glial. A cell type is a distinct morphological or functional form of cell. Examples are epithelial, glial etc. James Malone Jie Zheng Tomasz Adamusiak cell type efo:EFO_0000572 An immature lymphocyte that has enlarged in response to antigenic stimulation. Often referred to as a blast cell. Unlike other usages of the suffix -blast a lymphoblast is a further differentiation of a lymphocyte, T- or B-, occasioned by an antigenic stimulus. The lymphoblast usually develops by enlargement of a lymphocyte, active re-entry to the S phase of the cell cycle, mitogenesis and production of much m-RNA and ribosomes. James Malone NCIt:C13013 SNOMEDCT:15433008 lymphoblast efo:EFO_0000586 James Malone NCIt:C43423 SNOMEDCT:418124002 mesenchymal stem cell efo:EFO_0000700 Cell coming from the intergument, organ that constitutes the external surface of the body. The intergument consists of the epidermis, dermis, and skin appendages. James Malone integumental cell efo:EFO_0002433 Tomasz Adamusiak http://en.wikipedia.org/wiki/Ovulation cumulus-oocyte complex efo:EFO_0002439 Tomasz Adamusiak PO:0004006 mesophyll cell efo:EFO_0002451 A convenient source of human endothelial cells are those that line the large vein in the umbilical cord which is usually discarded together with the placenta after childbirth. The cells can be removed as a fairly pure suspension by mild enzymatic treatment of the vein followed by some mechanical distraction and will grow relatively easily in culture, retaining their differentiated characteristics for several passages. Tomasz Adamusiak HUVEC cell efo:EFO_0002534 Jie Zheng Tomasz Adamusiak MSH:D005312 fetal blood cell efo:EFO_0002540 Jie Zheng Tomasz Adamusiak PMID: 11246871 nestin positive islet-derived progenitor cell efo:EFO_0002572 Jie Zheng Tomasz Adamusiak large adipocyte efo:EFO_0002573 Jie Zheng Tomasz Adamusiak small adipocyte efo:EFO_0002661 dendritic cell-derived intermediate cell efo:EFO_0002662 dendritic cell-derived osteoclast efo:EFO_0002665 monocyte-derived intermediate cell efo:EFO_0002666 monocyte-derived osteoclast efo:EFO_0002955 reproductive system cell efo:EFO_0002956 musculo-skeletal system cell efo:EFO_0002958 experimental cell is a cell which is experimentally derived such as a cell line cell, or a cell differentiated in culture. Experimentally derived cells may have diffrent properties from the cell from which they originally derived, such as through gene expression changes. Helen Parkinson experimental cell efo:EFO_0002962 animal reproductive system cell efo:EFO_0002963 nervous system cell efo:EFO_0002966 pancreatic cell efo:EFO_0002968 neural stem cells experimentally derived from ES cells embryonic stem cell derived neuronal stem cell efo:EFO_0003036 A cell with empty-appearing cytoplasm when viewed with a light microscope. Tomasz Adamusiak NCIt:C12478 clear cell efo:EFO_0003076 An epithelial cell lining the thyroid follicle. Tomasz Adamusiak thyrocyte efo:EFO_0003919 An aspect of personal behavior or lifestyle, environmental exposure, or inborn or inherited characteristic, which, on the basis of epidemiologic evidence, is known to be associated with a health-related condition considered important to prevent. Any aspect of an individual's life, behavior, an environmental exposure, or an inborn or inherited characteristic that increases the likelihood of a disease, condition or injury. Factor, Risk Factors, Risk Risk Factors risk factor efo:EFO_0003970 mouse erythroleukemia cell efo:EFO_0004038 mouse embryonic stem cell Mikkelsen et al. (2007). Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560 mouse embryonic stem cell efo:EFO_0004039 mouse neural progenitor cell efo:EFO_0004040 Mouse embryonic fibroblast cell James Malone mouse embryonic fibroblast cell efo:EFO_0004905 Induced pluripotent stem cells (iPS cells or iPSCs) are a type of pluripotent stem cell artificially derived from a non-pluripotent cell. Various methods exist to revert cells to pluripotency such as reprogramming mediated through a mature metaphase II oocyte as in somatic cell nuclear transfer. James Malone Sirarat Sarntivijai Submitted by Nancy Mah induced pluripotent stem cell efo:EFO_0004950 The point in time at which an individual was born. date of birth efo:EFO_0004953 The point at which a clinical diagnosis is made. date of diagnosis efo:EFO_0004987 A cell which bears embryonal carcinoma. James Malone embryonal carcinoma cell efo:EFO_0005023 A adult mesenchymal stem cell derived from adipose tisssue Helen Parkinson adipose tissue derived mesenchymal stem cell efo:EFO_0005024 A pericyte derived from the placenta. Helen Parkinson placental pericyte efo:EFO_0005289 The mural granulosa cells form during antral folliculogenesis, process in which a single antral cavity is formed, separating two functionally distinct granulosa cell populations. The mural granulosa cells line the wall of the follicle and are critical for steroidogenesis and ovulation. Drashtti Vasant mural granulosa cell efo:EFO_0005293 B-lymphoblast efo:EFO_0005495 Neuron class of two pharyngeal neurosecretory-motor neurons. Dani Welter NSM efo:EFO_0005497 type of cells that make up muscle layers in the pharynx in worms such as C. elegans Dani Welter pharyngeal muscle cell efo:EFO_0005934 disease cell type efo:EFO_0009498 Induced pluripotent stem cell line from a Caucasian male with type 2 diabetes, same donor as of MSLCL cell line. PMID:24136358 MSiPS efo:EFO_0009501 Induced pluripotent stem cells derived from MSC658 fibroblasts. http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode%2Fcv.ra&term=%22iPS_CWRU1%22 CWRU1 efo:EFO_1000343 lympoid tissue efo:EFO_1000615 utering smooth muscle cell efo:EFO_1001464 glial brain cell efo:EFO_1001468 mantle cell efo:EFO_1001470 merkel cell owl:Thing address 2024-08-27 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 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 has part 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 is about is_supported_by_data The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI Philly 2011 workshop is_supported_by_data has_specified_input 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 has_specified_output 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 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 is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective has performer performer relation covers the need to report on who performed a planned processed. it has to cover processes done by People or Devices (such as a robot controlled by software WF management system) has performer this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality has quality relationship between a planned process and the plan specification that it carries out; it is defined as equivalent to the composed relationship (realizes o concretizes) Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra AGB executes Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management. Next generation biobanking ontology(NGBO). 2024-08-27