Ontology for BIoBanking (OBIB)
type: Ontology
version IRI: obib.owl
contributor: Alice Nzinga
contributor: Chris Stoeckert
contributor: Jan-Eric Litton
contributor: Jie Zheng
contributor: Loreana Norlin
contributor: Maria Anderberg
contributor: Martin N. Fransson
contributor: Mathias Brochhausen
contributor: Mikael Eriksson
contributor: Roxana Merino-Martinez
contributor: Sanela Kjellqvist
contributor: William R. Hogan
description: The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology.
source: MIABIS_v2_accepted and UPenn Biobank ontology
license: http://creativecommons.org/licenses/by/4.0/
version info: 2023-04-05

BFO OWL specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
curator note: Really of interest to developers only
sub property of: label

BFO CLIF specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
definition source: Person:Alan Ruttenberg
curator note: Really of interest to developers only
sub property of: label

editor preferred term
type: AnnotationProperty
editor preferred term: editor preferred term
has curation status: ready for release
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

example of usage
type: AnnotationProperty
editor preferred term: example of usage
has curation status: ready for release
definition: 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.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

in branch
type: AnnotationProperty
editor preferred term: in branch
definition: An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
term editor: GROUP:OBI
definition source: OBI_0000277

has curation status
type: AnnotationProperty
editor preferred term: has curation status
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bill Bug
term editor: PERSON:Melanie Courtot

definition
type: AnnotationProperty
editor preferred term: definition
has curation status: ready for release
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 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.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

editor note
type: AnnotationProperty
editor preferred term: editor note
has curation status: ready for release
definition: 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.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>

term editor
type: AnnotationProperty
editor preferred term: term editor
has curation status: ready for release
definition: 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
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

alternative label
type: AnnotationProperty
editor preferred term: alternative label
has curation status: pending final vetting
definition: A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
term editor: OBO Operations committee
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
comment: Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).

definition source
type: AnnotationProperty
editor preferred term: definition source
has curation status: ready for release
definition: 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
term editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has obsolescence reason
type: AnnotationProperty
editor preferred term: has obsolescence reason
definition: 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.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot

curator note
type: AnnotationProperty
editor preferred term: curator note
has curation status: ready for release
definition: An administrative note of use for a curator but of no use for a user
term editor: PERSON:Alan Ruttenberg

term tracker item
type: AnnotationProperty
editor preferred term: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
has curation status: pending final vetting
definition: An IRI or similar locator for a request or discussion of an ontology term.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.

ontology term requester
type: AnnotationProperty
editor preferred term: ontology term requester
has curation status: pending final vetting
definition: The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'term requester' can credit the person, organization or project who request the ontology term.

is denotator type
type: AnnotationProperty
editor preferred term: is denotator type
definition: Relates an class defined in an ontology, to the type of it's denotator
editor note: In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
term editor: Alan Ruttenberg

imported from
type: AnnotationProperty
editor preferred term: imported from
has curation status: pending final vetting
definition: For external terms/classes, the ontology from which the term was imported
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

expand expression to
type: AnnotationProperty
editor preferred term: expand expression to
example of usage: ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
definition: 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
term editor: Chris Mungall

expand assertion to
type: AnnotationProperty
editor preferred term: expand assertion to
example of usage: ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
term editor: Chris Mungall

first order logic expression
type: AnnotationProperty
editor preferred term: first order logic expression
term editor: PERSON:Alan Ruttenberg

antisymmetric property
type: AnnotationProperty
editor preferred term: antisymmetric property
example of usage: part_of antisymmetric property xsd:true
definition: Use boolean value xsd:true to indicate that the property is an antisymmetric property
term editor: Alan Ruttenberg
sub property of: logical characteristic of object property

OBO foundry unique label
type: AnnotationProperty
editor preferred term: OBO foundry unique label
has curation status: pending final vetting
definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: 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 .
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

has ID digit count
type: AnnotationProperty
editor preferred term: has ID digit count
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
term editor: Person:Alan Ruttenberg

has ID range allocated to
type: AnnotationProperty
editor preferred term: has ID range allocated
example of usage: Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
definition: Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
term editor: Person:Alan Ruttenberg

has ID policy for
type: AnnotationProperty
editor preferred term: has ID policy for
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relating an ontology used to record id policy to the ontology namespace whose policy it manages
term editor: Person:Alan Ruttenberg

has ID prefix
type: AnnotationProperty
editor preferred term: has ID prefix
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
term editor: Person:Alan Ruttenberg

elucidation
type: AnnotationProperty
editor preferred term: elucidation
term editor: person:Alan Ruttenberg
definition source: Person:Barry Smith
elucidation: Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms

has associated axiom(nl)
type: AnnotationProperty
editor preferred term: has associated axiom(nl)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom associated with a term expressed using natural language

has associated axiom(fol)
type: AnnotationProperty
editor preferred term: has associated axiom(fol)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom expressed in first order logic using CLIF syntax

is allocated id range
type: AnnotationProperty
editor preferred term: is allocated id range
definition: Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
term editor: PERSON:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

has ontology root term
type: AnnotationProperty
editor preferred term: has ontology root term
definition: Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
term editor: Nicolas Matentzoglu

may be identical to
type: AnnotationProperty
editor preferred term: may be identical to
definition: A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
term editor: David Osumi-Sutherland
term tracker item: #40
ontology term requester: VFB
comment: Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.

scheduled for obsoletion on or after
type: AnnotationProperty
editor preferred term: scheduled for obsoletion on or after
definition: Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
term editor: Chris Mungall, Jie Zheng
term tracker item: https://github.com/geneontology/go-ontology/issues/15532
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/32
ontology term requester: GO ontology
range: dateTime

has axiom label
type: AnnotationProperty
editor preferred term: has axiom id
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI

term replaced by
type: AnnotationProperty
editor preferred term: term replaced by
has curation status: pending final vetting
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

ISA alternative term
type: AnnotationProperty
editor preferred term: ISA alternative term
has curation status: ready for release
definition: An alternative term used by the ISA tools project (http://isa-tools.org).
editor note: Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
term editor: Person: Alejandra Gonzalez-Beltran
term editor: Person: Philippe Rocca-Serra
definition source: ISA tools project (http://isa-tools.org)

NIAID GSCID-BRC alternative term
type: AnnotationProperty
editor preferred term: NIAID GSCID-BRC alternative term
has curation status: ready for release
definition: An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group

IEDB alternative term
type: AnnotationProperty
editor preferred term: IEDB alternative term
has curation status: ready for release
definition: An alternative term used by the IEDB.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB

logical characteristic of object property
type: AnnotationProperty
definition: This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
definition source: OBO Operations call
created by: http://orcid.org/0000-0001-5208-3432

defined by construct
type: AnnotationProperty
example of usage: 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . }
definition: Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
term tracker item: https://github.com/ontodev/robot/issues/963
contributor: https://orcid.org/0000-0002-7356-1779
contributor: https://orcid.org/0000-0002-8688-6599

temporal interpretation
type: AnnotationProperty
definition: An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.

logical macro assertion
type: AnnotationProperty
definition: An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.

logical macro assertion on a property
type: AnnotationProperty
definition: A logical macro assertion whose domain is an IRI for a property

logical macro assertion on an object property
type: AnnotationProperty
definition: Used to annotate object properties to describe a logical meta-property or characteristic of the object property.

has broad synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/18
sub property of: alternative label

has exact synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/20
sub property of: alternative label

has narrow synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/19
sub property of: alternative label

has related synonym
type: AnnotationProperty
definition: An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/21
sub property of: alternative label

label
type: AnnotationProperty

part of
type: ObjectProperty
inverse of: has part
type: TransitiveProperty
editor preferred term: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: 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.
editor note: 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: 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'.
alternative label: part_of
temporal interpretation: RO_0001901

has part
type: ObjectProperty
type: TransitiveProperty
editor preferred term: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: 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.
editor note: 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: 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'.
alternative label: has_part
temporal interpretation: RO_0001901

realized in
type: ObjectProperty
inverse of: realizes
domain: realizable entity
range: process
editor preferred term: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative label: is realized by
alternative label: realized_in
elucidation: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: 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

realizes
type: ObjectProperty
domain: process
range: realizable entity
editor preferred term: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
elucidation: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: 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

preceded by
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
definition: 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.
alternative label: is preceded by
alternative label: preceded_by
imported from: ro.owl

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
definition: 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.
imported from: ro.owl

occurs in
type: ObjectProperty
inverse of: contains process
domain: occurrent
range: independent continuant
property chain axiom: part of
editor preferred term: occurs in
definition: 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
alternative label: occurs_in
alternative label: unfolds in
alternative label: unfolds_in
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

contains process
type: ObjectProperty
editor preferred term: site of
definition: [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

has temporal occupant
type: ObjectProperty
range: occurrent
BFO OWL specification label: span-of
BFO CLIF specification label: spanOf
imported from: bfo.owl
elucidation: [copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])

history of
type: ObjectProperty
sub property of: occurs in
inverse of: has history
type: FunctionalProperty
type: InverseFunctionalProperty
domain: process
range: material entity
BFO OWL specification label: history-of
BFO CLIF specification label: historyOf
definition: [copied from inverse property 'has history'] b has_history c iff c history_of b [XXX-001
imported from: bfo.owl
elucidation: b history_of c if c is a material entity or site and b is a history that is the unique history of cAxiom: if b history_of c and b history_of d then c=d [XXX-001

has history
type: ObjectProperty
sub property of: contains process
type: FunctionalProperty
type: InverseFunctionalProperty
domain: material entity
range: process
BFO OWL specification label: has-history
BFO CLIF specification label: hasHistory
definition: b has_history c iff c history_of b [XXX-001
imported from: bfo.owl
elucidation: [copied from inverse property 'history of'] b history_of c if c is a material entity or site and b is a history that is the unique history of cAxiom: if b history_of c and b history_of d then c=d [XXX-001

is subordinate authority of
type: ObjectProperty
definition: A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1's jurisdiction falls within the relevant jurisdiction of G2.
imported from: geo.owl
comment: 'is subordinate authority of' Domain: governing organization Range: governing organization Formal properties: transitive, anti-symmetric, irreflexive Natural language definition: A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1 falls within the relevant jurisdiction of G2.

has measurement unit label
type: ObjectProperty
sub property of: has part
imported from: iao.owl

is about
type: ObjectProperty
example of usage: This document is about information artifacts and their representations
has curation status: pending final vetting
definition: A (currently) primitive relation that relates an information artifact to an entity.
editor note: 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.
term editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
imported from: iao.owl

denotes
type: ObjectProperty
sub property of: is about
example of usage: 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.
definition: 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
editor note: 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
term editor: person:Alan Ruttenberg
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
imported from: iao.owl

is quality measurement of
type: ObjectProperty
sub property of: is about
definition: 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
editor note: 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
editor note: 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.
editor note: 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.
editor note: 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.
editor note: 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.
term editor: Alan Ruttenberg
imported from: iao.owl

denoted by
type: ObjectProperty
definition: inverse of the relation 'denotes'
term editor: Person: Jie Zheng, Chris Stoeckert, Mike Conlon
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/206
imported from: iao.owl

is duration of
type: ObjectProperty
sub property of: is about
has curation status: metadata complete
definition: relates a process to a time-measurement-datum that represents the duration of the process
term editor: Person:Alan Ruttenberg
imported from: iao.owl

is quality measured as
type: ObjectProperty
has curation status: metadata complete
definition: inverse of the relation of is quality measurement of
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
term editor: Person:Alan Ruttenberg
imported from: iao.owl

has time stamp
type: ObjectProperty
sub property of: has part
has curation status: metadata incomplete
definition: relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
term editor: Alan Ruttenberg
imported from: iao.owl

has measurement datum
type: ObjectProperty
sub property of: has part
has curation status: metadata incomplete
definition: relates a time stamped measurement datum to the measurement datum that was measured
term editor: Alan Ruttenberg
imported from: iao.owl

designates
type: ObjectProperty
inverse of: is designated by
type: AsymmetricProperty
type: IrreflexiveProperty
domain: information content entity
range: entity
definition: 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..
term editor: Mathias Brochhausen

is designated by
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
definition: p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context.
term editor: Mathias Brochhausen

results_in
type: ObjectProperty
imported from: ido.owl

has maximum capacity
type: ObjectProperty
domain: container
range: measurement datum
definition: A relation that relates a container to a measurement datum that specifies the maximum capacity of the container.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

has actual load
type: ObjectProperty
domain: container
range: measurement datum
definition: A relation that relates a container to a measurement datum that specifies the actual amount of material in the container.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

owns
type: ObjectProperty
sub property of: topObjectProperty
inverse of: is owned by
type: AsymmetricProperty
domain: Class
  union of: Homo sapiens
  union of: organization
  union of: collection of humans
  union of: aggregate of organizations
range: Class
  union of: material entity
  union of: information content entity
term editor: Mathias Brochhausen
elucidation: This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal.
source: Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.

administrates
type: ObjectProperty
type: AsymmetricProperty
domain: Class
  union of: Homo sapiens
  union of: organization
  union of: collection of humans
  union of: aggregate of organizations
range: Class
  union of: material entity
  union of: information content entity
definition: 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.
term editor: Mathias Brochhausen
comment: A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl

is contact information about
type: ObjectProperty
sub property of: is about
type: AsymmetricProperty
type: IrreflexiveProperty
domain: information content entity
range: Class
  union of: Homo sapiens
  union of: organization
definition: 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.
term editor: Mathias Brochhausen

is owned by
type: ObjectProperty
type: AsymmetricProperty
domain: Class
  union of: material entity
  union of: information content entity
range: Class
  union of: Homo sapiens
  union of: organization
  union of: collection of humans
  union of: aggregate of organizations
definition: 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.
definition source: Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.

provides_service_consumer_with
type: ObjectProperty
sub property of: has part
editor preferred term: provides_service_consumer_with
example of usage: 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.
has curation status: metadata incomplete
definition: A relation between a service and the primary processual part of the service that is performed by the provider for the consumer.
imported from: obi.owl

is_supported_by_data
type: ObjectProperty
editor preferred term: is_supported_by_data
example of usage: 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.
has curation status: ready for release
definition: 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
term editor: OBI
definition source: OBI
definition source: Philly 2011 workshop
imported from: obi.owl

has_specified_input
type: ObjectProperty
equivalent property:
  inverse of: is_specified_input_of
sub property of: has participant
editor preferred term: has_specified_input
example of usage: see is_input_of example_of_usage
has curation status: ready for release
definition: The inverse property of is_specified_input_of
editor note: 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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Coutot
imported from: obi.owl

is_specified_input_of
type: ObjectProperty
sub property of: participates in
editor preferred term: is_specified_input_of
example of usage: 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
has curation status: ready for release
definition: 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.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters
imported from: obi.owl

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: has participant
editor preferred term: has_specified_output
has curation status: ready for release
definition: The inverse property of is_specified_output_of
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Courtot
imported from: obi.owl

is_specified_output_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_output
sub property of: participates in
editor preferred term: is_specified_output_of
has curation status: ready for release
definition: 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.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters
imported from: obi.owl

achieves_planned_objective
type: ObjectProperty
editor preferred term: achieves_planned_objective
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
has curation status: metadata complete
definition: 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.
term editor: BP, AR, PPPB branch
definition source: PPPB branch derived
curator note: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
imported from: obi.owl

has grain
type: ObjectProperty
sub property of: has part
editor preferred term: has grain
has curation status: metadata complete
definition: the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
editor note: Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
term editor: PERSON: Alan Ruttenberg
definition source: PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
imported from: obi.owl

objective_achieved_by
type: ObjectProperty
editor preferred term: objective_achieved_by
has curation status: ready for release
definition: This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
term editor: OBI
definition source: OBI
imported from: obi.owl

is member of organization
type: ObjectProperty
editor preferred term: is member of organization
has curation status: metadata complete
definition: 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.
editor note: 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
editor note: 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.
term editor: Person:Alan Ruttenberg
term editor: Person:Helen Parkinson
definition source: Person:Alan Ruttenberg
definition source: Person:Helen Parkinson
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
imported from: obi.owl

has disposition to bind
type: ObjectProperty
editor preferred term: has disposition to bind
has curation status: metadata incomplete
definition: A relationship between two material entitites that each have disposition to form a complex with the other.
editor note: This is a shortcut relation, and should expand to say that the two material entities have dispositions, point to the process in which they from a complex that realizes those dispositions, and points to the complex in which the two entities are 'bound to' each other
definition source: IEDB
imported from: obi.owl

has organization member
type: ObjectProperty
editor preferred term: has organization member
has curation status: metadata incomplete
definition: Relating an organization to a legal person or organization.
editor note: See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
term editor: Person: Jie Zheng
imported from: obi.owl

specifies value of
type: ObjectProperty
sub property of: is about
editor preferred term: specifies value of
has curation status: metadata incomplete
definition: A relation between a value specification and an entity which the specification is about.
imported from: obi.owl

has value specification
type: ObjectProperty
sub property of: has part
editor preferred term: has value specification
has curation status: metadata complete
definition: A relation between an information content entity and a value specification that specifies its value.
term editor: PERSON: James A. Overton
definition source: OBI
imported from: obi.owl

obsolete owns
type: ObjectProperty
term editor: Mathias Brochhausen
term replaced by: owns
deprecated: true

obsolete administrates
type: ObjectProperty
term editor: Mathias Brochhausen
term replaced by: administrates
deprecated: true

obsolete is contact information about
type: ObjectProperty
term editor: Mathias Brochhausen
term replaced by: is contact information about
deprecated: true

obsolete is owned by
type: ObjectProperty
definition source: Reinach, A. S�mtliche Werke. Texkritische Ausgabe, M�nchen: Philosophia Verlag, 1989, p.189-204.
term replaced by: is owned by
deprecated: true

is-aggregate-of
type: ObjectProperty
sub property of: topObjectProperty
has obsolescence reason: BFO relation takes precedence.
imported from: omrse.owl
comment: 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.
deprecated: true

characteristic of
type: ObjectProperty
inverse of: has characteristic
type: FunctionalProperty
editor preferred term: inheres in
example of usage: this fragility is a characteristic of this vase
example of usage: this red color is a characteristic of this apple
definition: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
alternative label: inheres_in
temporal interpretation: RO_0001901
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
range: specifically dependent continuant
editor preferred term: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: Inverse of characteristic_of
editor note: 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.
alternative label: bearer_of
alternative label: is bearer of
temporal interpretation: RO_0001901

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
editor preferred term: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative label: participates_in

has participant
type: ObjectProperty
domain: occurrent
range: continuant
editor preferred term: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: 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.
alternative label: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: 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).
definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.

concretizes
type: ObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
example of usage: 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).
example of usage: 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).
definition: 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.

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: 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.
alternative label: function_of
alternative label: is function of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

quality of
type: ObjectProperty
sub property of: characteristic of
inverse of: has quality
example of usage: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
alternative label: is quality of
alternative label: quality_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

role of
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: 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.
alternative label: is role of
alternative label: role_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has function
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: 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.
alternative label: has_function
imported from: ro.owl

has quality
type: ObjectProperty
sub property of: has characteristic
range: quality
example of usage: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: 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.
alternative label: has_quality

has role
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: 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.
alternative label: has_role

has disposition
type: ObjectProperty
sub property of: has characteristic
inverse of: disposition of
domain: independent continuant
range: disposition
definition: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

disposition of
type: ObjectProperty
sub property of: characteristic of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

derives from
type: ObjectProperty
inverse of: derives into
example of usage: this cell derives from this parent cell (cell division)
example of usage: this nucleus derives from this parent nucleus (nuclear division)
has curation status: pending final vetting
definition: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
alternative label: derives_from

derives into
type: ObjectProperty
example of usage: this parent cell derives into this cell (cell division)
example of usage: this parent nucleus derives into this nucleus (nuclear division)
has curation status: pending final vetting
definition: 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
editor note: 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'.
alternative label: derives_into

location of
type: ObjectProperty
inverse of: located in
type: TransitiveProperty
editor preferred term: is location of
example of usage: my head is the location of my brain
example of usage: this cage is the location of this rat
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
alternative label: location_of
temporal interpretation: RO_0001901

located in
type: ObjectProperty
type: TransitiveProperty
domain: independent continuant
domain: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
range: independent continuant
range: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
editor preferred term: located in
example of usage: my brain is located in my head
example of usage: this rat is located in this cage
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
editor note: 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
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
alternative label: located_in
temporal interpretation: RO_0001901
source: http://www.obofoundry.org/ro/#OBO_REL:located_in

Axiom
annotated source: located in
annotated property: domain
annotated target: independent continuant
editor note: 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.

Axiom
annotated source: located in
annotated property: range
annotated target: independent continuant
editor note: 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.

2D boundary of
type: ObjectProperty
inverse of: has 2D boundary
example of usage: the surface of my skin is a 2D boundary of my body
definition: a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative label: 2D_boundary_of
alternative label: boundary of
alternative label: is 2D boundary of
alternative label: is boundary of
temporal interpretation: RO_0001901

has 2D boundary
type: ObjectProperty
domain: material entity
range: immaterial entity
example of usage: my body has 2D boundary the surface of my skin
definition: a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative label: has boundary
alternative label: has_2D_boundary
temporal interpretation: RO_0001901

has component
type: ObjectProperty
sub property of: has part
definition: 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.
imported from: ro.owl

regulates
type: ObjectProperty
sub property of: causally upstream of
definition: p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
imported from: ro.owl

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
definition: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
imported from: ro.owl

temporally related to
type: ObjectProperty
imported from: ro.owl

starts
type: ObjectProperty
sub property of: temporally related to
definition: inverse of starts with
imported from: ro.owl

has input
type: ObjectProperty
sub property of: has participant
definition: 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.
alternative label: consumes
imported from: ro.owl

has output
type: ObjectProperty
sub property of: has participant
definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
alternative label: produces
imported from: ro.owl

results in developmental progression of
type: ObjectProperty
sub property of: developmentally related to
definition: p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
imported from: ro.owl

results in formation of
type: ObjectProperty
sub property of: has output
sub property of: results in developmental progression of
example of usage: an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
example of usage: every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
imported from: ro.owl

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
definition: p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
imported from: ro.owl

developmentally related to
type: ObjectProperty
definition: A relationship that holds between entities participating in some developmental process (GO:0032502)
imported from: ro.owl

member of
type: ObjectProperty
sub property of: part of
inverse of: has member
example of usage: An organism that is a member of a population of organisms
definition: is member of is a mereological relation between a item and a collection.
alternative label: is member of
alternative label: member part of
definition source: SIO
temporal interpretation: RO_0001901

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
definition: has member is a mereological relation between a collection and an item.
definition source: SIO
imported from: ro.owl
temporal interpretation: RO_0001901

input of
type: ObjectProperty
sub property of: participates in
definition: inverse of has input
imported from: ro.owl

output of
type: ObjectProperty
sub property of: participates in
definition: inverse of has output
imported from: ro.owl

causally related to
type: ObjectProperty
definition: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
imported from: ro.owl

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
definition: p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
imported from: ro.owl

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
definition: p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
alternative label: influences (processual)
imported from: ro.owl

causal relation between processes
type: ObjectProperty
sub property of: causally related to
definition: 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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
imported from: ro.owl

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
imported from: ro.owl

DEPRECATED inheres in
type: ObjectProperty
comment: DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information.
deprecated: true

DEPRECATED bearer of
type: ObjectProperty
deprecated: true

lacks_part
type: ObjectProperty
imported from: cl.owl
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y
has OBO namespace: RO

has measurement value
type: DatatypeProperty
imported from: iao.owl

has specified numeric value
type: DatatypeProperty
sub property of: has specified value
editor preferred term: has specified numeric value
has curation status: metadata complete
definition: A relation between a value specification and a number that quantifies it.
editor note: A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
term editor: PERSON: James A. Overton
definition source: OBI
imported from: obi.owl

has specified value
type: DatatypeProperty
editor preferred term: has specified value
has curation status: metadata incomplete
definition: A relation between a value specification and a literal.
editor note: This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
definition source: OBI
imported from: obi.owl

count
type: Class
subclass of: measurement datum
definition: A measurement datum that is the output of counting.
term editor: Mathias Brochhausen
imported from: apollo sv.owl
elucidation: A measurement datum that is the output of counting.
APOLLO SV 0000040: count

counting
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has_specified_output
    some values from: count
subclass of: planned process
definition: The planned process of finding the number of elements in a finite set of objects.
term editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Counting
imported from: apollo sv.owl
elucidation: The planned process of finding the number of elements in a finite set of objects.

age data in age brackets data set
type: Class
subclass of: data set
editor preferred term: age structure data set
definition: A data set consisting of measurements of age organized in age brackets.
imported from: apollo sv.owl
elucidation: A data set consisting of measurements of age organized in age brackets.

ORCID
type: Class
subclass of: identifier
definition: An identifier curated by ORCID, Inc. to denote some academic author.
term editor: Matthew Diller
term editor: William R. Hogan
imported from: apollo sv.owl
elucidation: An identifier curated by ORCID, Inc. to denote some academic author.
term replaced by: http://purl.obolibrary.org/obo/IAO_0000708
APOLLO SV 0000040: orcId
deprecated: true

entity
type: Class
subclass of: Thing
BFO OWL specification label: entity
BFO CLIF specification label: Entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
editor note: 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
editor note: 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
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

Axiom
annotated source: entity
annotated property: editor note
annotated target: 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
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith

Axiom
annotated source: entity
annotated property: elucidation
annotated target: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/001-001

continuant
type: Class
subclass of: entity
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
definition: 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.
editor note: 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
editor note: 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
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

Axiom
annotated source: continuant
annotated property: editor note
annotated target: 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
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000007

Axiom
annotated source: continuant
annotated property: elucidation
annotated target: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

occurrent
type: Class
subclass of: entity
disjoint with: Restriction
  on property: part of
  some values from: continuant
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
editor note: 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
editor note: 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.
editor note: 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.
editor note: 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.
elucidation: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000012

Axiom
annotated source: occurrent
annotated property: elucidation
annotated target: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/077-002

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

independent continuant
type: Class
subclass of: continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
definition: 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])
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (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]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

Axiom
annotated source: independent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

spatial region
type: Class
subclass of: immaterial entity
disjoint with: site
disjoint with: continuant fiat boundary
BFO OWL specification label: s-region
BFO CLIF specification label: SpatialRegion
editor note: BFO 2 Reference: Spatial regions do not participate in processes.
editor note: 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.
elucidation: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
has associated axiom(nl): All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has associated axiom(fol): (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has associated axiom(fol): (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]

Axiom
annotated source: spatial region
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000002
comment: per discussion with Barry Smith

Axiom
annotated source: spatial region
annotated property: elucidation
annotated target: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(nl)
annotated target: All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

temporal region
type: Class
subclass of: occurrent
disjoint with: spatiotemporal region
disjoint with: process
disjoint with: process boundary
BFO OWL specification label: t-region
BFO CLIF specification label: TemporalRegion
editor note: 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
elucidation: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
has associated axiom(nl): All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has associated axiom(fol): (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has associated axiom(fol): (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has associated axiom(fol): (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]

Axiom
annotated source: temporal region
annotated property: editor note
annotated target: 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
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000003
comment: per discussion with Barry Smith

Axiom
annotated source: temporal region
annotated property: elucidation
annotated target: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

two-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 2d-s-region
BFO CLIF specification label: TwoDimensionalSpatialRegion
example of usage: an infinitely thin plane in space.
example of usage: the surface of a sphere-shaped part of space
elucidation: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has associated axiom(fol): (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]

Axiom
annotated source: two-dimensional spatial region
annotated property: elucidation
annotated target: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

Axiom
annotated source: two-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

spatiotemporal region
type: Class
subclass of: occurrent
BFO OWL specification label: st-region
BFO CLIF specification label: SpatiotemporalRegion
example of usage: the spatiotemporal region occupied by a human life
example of usage: the spatiotemporal region occupied by a process of cellular meiosis.
example of usage: the spatiotemporal region occupied by the development of a cancer tumor
elucidation: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has associated axiom(nl): All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has associated axiom(nl): Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has associated axiom(nl): Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has associated axiom(nl): Every spatiotemporal region occupies_spatiotemporal_region itself.
has associated axiom(nl): Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has associated axiom(fol): (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has associated axiom(fol): (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has associated axiom(fol): (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

Axiom
annotated source: spatiotemporal region
annotated property: elucidation
annotated target: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

process
type: Class
subclass of: occurrent
BFO OWL specification label: process
BFO CLIF specification label: Process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
definition: 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])
editor note: 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)
has associated axiom(fol): (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]

Axiom
annotated source: process
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
annotated source: process
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

disposition
type: Class
subclass of: realizable entity
disjoint with: role
BFO OWL specification label: disposition
BFO CLIF specification label: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: 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.
elucidation: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has associated axiom(nl): 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])
has associated axiom(fol): (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]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

Axiom
annotated source: disposition
annotated property: elucidation
annotated target: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

Axiom
annotated source: disposition
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

realizable entity
type: Class
subclass of: specifically dependent continuant
disjoint with: quality
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: 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.
elucidation: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (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]
has associated axiom(fol): (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]

Axiom
annotated source: realizable entity
annotated property: elucidation
annotated target: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(nl)
annotated target: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

zero-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 0d-s-region
BFO CLIF specification label: ZeroDimensionalSpatialRegion
elucidation: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]

Axiom
annotated source: zero-dimensional spatial region
annotated property: elucidation
annotated target: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

Axiom
annotated source: zero-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

quality
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: quality
BFO CLIF specification label: Quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
elucidation: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (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]

Axiom
annotated source: quality
annotated property: elucidation
annotated target: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

specifically dependent continuant
type: Class
subclass of: continuant
disjoint with: generically dependent continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
example of usage: 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
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: 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.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: 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.
definition: 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])
editor note: 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.
has associated axiom(fol): (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]

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: specifically dependent continuant
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

role
type: Class
subclass of: realizable entity
BFO OWL specification label: role
BFO CLIF specification label: Role
example of usage: 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.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
definition: 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.
editor note: 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.
elucidation: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

Axiom
annotated source: role
annotated property: elucidation
annotated target: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

Axiom
annotated source: role
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

fiat object part
type: Class
subclass of: material entity
BFO OWL specification label: fiat-object-part
BFO CLIF specification label: FiatObjectPart
example of usage: 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
example of usage: the FMA:regional parts of an intact human body.
example of usage: the Western hemisphere of the Earth
example of usage: the division of the brain into regions
example of usage: the division of the planet into hemispheres
example of usage: the dorsal and ventral surfaces of the body
example of usage: the upper and lower lobes of the left lung
editor note: BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
elucidation: b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
has associated axiom(fol): (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]

Axiom
annotated source: fiat object part
annotated property: elucidation
annotated target: b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

Axiom
annotated source: fiat object part
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

one-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 1d-s-region
BFO CLIF specification label: OneDimensionalSpatialRegion
example of usage: an edge of a cube-shaped portion of space.
elucidation: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]

Axiom
annotated source: one-dimensional spatial region
annotated property: elucidation
annotated target: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

Axiom
annotated source: one-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

object aggregate
type: Class
subclass of: material entity
BFO OWL specification label: object-aggregate
BFO CLIF specification label: ObjectAggregate
example of usage: a collection of cells in a blood biobank.
example of usage: a swarm of bees is an aggregate of members who are linked together through natural bonds
example of usage: a symphony orchestra
example of usage: 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)
example of usage: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
example of usage: defined via attributive delimitations such as: the patients in this hospital
example of usage: the aggregate of bearings in a constant velocity axle joint
example of usage: the aggregate of blood cells in your body
example of usage: the nitrogen atoms in the atmosphere
example of usage: the restaurants in Palo Alto
example of usage: your collection of Meissen ceramic plates.
editor note: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
editor note: 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).
definition source: 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.
elucidation: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
has associated axiom(fol): (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]

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000011

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000301

Axiom
annotated source: object aggregate
annotated property: definition source
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000300

Axiom
annotated source: object aggregate
annotated property: elucidation
annotated target: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

Axiom
annotated source: object aggregate
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

three-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 3d-s-region
BFO CLIF specification label: ThreeDimensionalSpatialRegion
example of usage: a cube-shaped region of space
example of usage: a sphere-shaped region of space,
elucidation: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has associated axiom(fol): (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]

Axiom
annotated source: three-dimensional spatial region
annotated property: elucidation
annotated target: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

Axiom
annotated source: three-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

site
type: Class
subclass of: immaterial entity
BFO OWL specification label: site
BFO CLIF specification label: Site
example of usage: Manhattan Canyon)
example of usage: a hole in the interior of a portion of cheese
example of usage: a rabbit hole
example of usage: an air traffic control region defined in the airspace above an airport
example of usage: the Grand Canyon
example of usage: the Piazza San Marco
example of usage: the cockpit of an aircraft
example of usage: the hold of a ship
example of usage: the interior of a kangaroo pouch
example of usage: the interior of the trunk of your car
example of usage: the interior of your bedroom
example of usage: the interior of your office
example of usage: the interior of your refrigerator
example of usage: the lumen of your gut
example of usage: your left nostril (a fiat part – the opening – of your left nasal cavity)
elucidation: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
has associated axiom(fol): (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]

Axiom
annotated source: site
annotated property: elucidation
annotated target: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002

Axiom
annotated source: site
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002

object
type: Class
subclass of: material entity
BFO OWL specification label: object
BFO CLIF specification label: Object
example of usage: atom
example of usage: cell
example of usage: cells and organisms
example of usage: engineered artifacts
example of usage: grain of sand
example of usage: molecule
example of usage: organelle
example of usage: organism
example of usage: planet
example of usage: solid portions of matter
example of usage: star
editor note: 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.
editor note: 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).
editor note: 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
editor note: BFO 2 Reference: an object is a maximal causally unified material entity
editor note: BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
elucidation: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])

Axiom
annotated source: object
annotated property: elucidation
annotated target: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/024-001

generically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
example of usage: 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.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: 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.
definition: 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])
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

Axiom
annotated source: generically dependent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

Axiom
annotated source: generically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

function
type: Class
subclass of: disposition
BFO OWL specification label: function
BFO CLIF specification label: Function
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
editor note: 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.
elucidation: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

Axiom
annotated source: function
annotated property: elucidation
annotated target: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

Axiom
annotated source: function
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

process boundary
type: Class
subclass of: occurrent
BFO OWL specification label: p-boundary
BFO CLIF specification label: ProcessBoundary
example of usage: the boundary between the 2nd and 3rd year of your life.
definition: 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])
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has associated axiom(fol): (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has associated axiom(fol): (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]

Axiom
annotated source: process boundary
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

Axiom
annotated source: process boundary
annotated property: has associated axiom(nl)
annotated target: Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

one-dimensional temporal region
type: Class
subclass of: temporal region
disjoint with: zero-dimensional temporal region
BFO OWL specification label: 1d-t-region
BFO CLIF specification label: OneDimensionalTemporalRegion
example of usage: the temporal region during which a process occurs.
editor note: 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).
elucidation: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]

Axiom
annotated source: one-dimensional temporal region
annotated property: elucidation
annotated target: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

Axiom
annotated source: one-dimensional temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: 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
editor note: 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.
editor note: 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.
elucidation: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (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]
has associated axiom(fol): (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]

Axiom
annotated source: material entity
annotated property: elucidation
annotated target: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

continuant fiat boundary
type: Class
subclass of: immaterial entity
BFO OWL specification label: cf-boundary
BFO CLIF specification label: ContinuantFiatBoundary
definition: 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])
editor note: 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.
editor note: 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
editor note: 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.
has associated axiom(nl): Every continuant fiat boundary is located at some spatial region at every time at which it exists
has associated axiom(fol): (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]

Axiom
annotated source: continuant fiat boundary
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

Axiom
annotated source: continuant fiat boundary
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000008

Axiom
annotated source: continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

immaterial entity
type: Class
subclass of: independent continuant
BFO OWL specification label: immaterial
BFO CLIF specification label: ImmaterialEntity
editor note: 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

one-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
disjoint with: two-dimensional continuant fiat boundary
disjoint with: zero-dimensional continuant fiat boundary
BFO OWL specification label: 1d-cf-boundary
BFO CLIF specification label: OneDimensionalContinuantFiatBoundary
example of usage: The Equator
example of usage: all geopolitical boundaries
example of usage: all lines of latitude and longitude
example of usage: the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
example of usage: the median sulcus of your tongue
elucidation: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
has associated axiom(fol): (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

process profile
type: Class
subclass of: process
disjoint with: history
BFO OWL specification label: process-profile
BFO CLIF specification label: ProcessProfile
example of usage: 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
example of usage: 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.
example of usage: 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.
definition: 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])
elucidation: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
has associated axiom(fol): (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]
has associated axiom(fol): (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]

Axiom
annotated source: process profile
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

Axiom
annotated source: process profile
annotated property: elucidation
annotated target: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

relational quality
type: Class
subclass of: quality
BFO OWL specification label: r-quality
BFO CLIF specification label: RelationalQuality
example of usage: 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.
example of usage: a marriage bond, an instance of requited love, an obligation between one person and another.
definition: 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])
has associated axiom(fol): (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]

Axiom
annotated source: relational quality
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

Axiom
annotated source: relational quality
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

two-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 2d-cf-boundary
BFO CLIF specification label: TwoDimensionalContinuantFiatBoundary
elucidation: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
has associated axiom(fol): (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

zero-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 0d-cf-boundary
BFO CLIF specification label: ZeroDimensionalContinuantFiatBoundary
example of usage: the geographic North Pole
example of usage: the point of origin of some spatial coordinate system.
example of usage: the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
editor note: 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.
elucidation: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
has associated axiom(fol): (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000001
comment: requested by Melanie Courtot

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

zero-dimensional temporal region
type: Class
subclass of: temporal region
BFO OWL specification label: 0d-t-region
BFO CLIF specification label: ZeroDimensionalTemporalRegion
example of usage: a temporal region that is occupied by a process boundary
example of usage: right now
example of usage: the moment at which a child is born
example of usage: the moment at which a finger is detached in an industrial accident
example of usage: the moment of death.
alternative label: temporal instant.
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]

Axiom
annotated source: zero-dimensional temporal region
annotated property: elucidation
annotated target: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

Axiom
annotated source: zero-dimensional temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

history
type: Class
subclass of: process
BFO OWL specification label: history
BFO CLIF specification label: History
elucidation: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])

Axiom
annotated source: history
annotated property: elucidation
annotated target: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/138-001

fentanyl
type: Class
subclass of: molecular entity
definition: A monocarboxylic acid amide resulting from the formal condensation of the aryl amino group of N-phenyl-1-(2-phenylethyl)piperidin-4-amine with propanoic acid.
alternative label: N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide
imported from: chebi.owl

ethanol
type: Class
subclass of: alcohol
definition: A primary alcohol that is ethane in which one of the hydrogens is substituted by a hydroxy group.
alternative label: ETHANOL
alternative label: Ethanol
alternative label: ethanol
imported from: chebi.owl

peptide
type: Class
subclass of: macromolecule
definition: Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
alternative label: Peptide
alternative label: peptides
imported from: chebi.owl

formaldehyde
type: Class
subclass of: molecular entity
definition: An aldehyde resulting from the formal oxidation of methanol.
alternative label: FORMALDEHYDE
alternative label: Formaldehyde
alternative label: formaldehyde
imported from: chebi.owl

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
alternative label: Deoxyribonucleic acid
alternative label: deoxyribonucleic acids
imported from: chebi.owl

dinitrogen oxide
type: Class
subclass of: molecular entity
definition: A nitrogen oxide consisting of linear unsymmetrical molecules with formula N2O. While it is the most used gaseous anaesthetic in the world, its major commercial use, due to its solubility under pressure in vegetable fats combined with its non-toxicity in low concentrations, is as an aerosol spray propellant and aerating agent for canisters of 'whipped' cream.
alternative label: Dinitrogen oxide
alternative label: dinitrogen oxide
alternative label: oxidodinitrogen(N--N)
imported from: chebi.owl

morphine
type: Class
subclass of: molecular entity
definition: A morphinane alkaloid that is a highly potent opiate analgesic psychoactive drug. Morphine acts directly on the central nervous system (CNS) to relieve pain but has a high potential for addiction, with tolerance and both physical and psychological dependence developing rapidly. Morphine is the most abundant opiate found in Papaver somniferum (the opium poppy).
alternative label: 17-methyl-7,8-didehydro-4,5alpha-epoxymorphinan-3,6alpha-diol
alternative label: Morphine
imported from: chebi.owl

nicotine
type: Class
subclass of: molecular entity
definition: A racemate composed of equimolar amounts of (R)- and (S)-nicotine.
alternative label: rac-3-(1-methylpyrrolidin-2-yl)pyridine
imported from: chebi.owl

molecular entity
type: Class
subclass of: material entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
alternative label: molecular entity
imported from: chebi.owl

xylene
type: Class
subclass of: molecular entity
alternative label: xylene
imported from: chebi.owl

alcohol
type: Class
subclass of: molecular entity
definition: A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom.
alternative label: Alcohol
alternative label: alcohols
imported from: chebi.owl

bupivacaine
type: Class
subclass of: molecular entity
definition: A racemate composed of equimolar amounts of dextrobupivacaine and levobupivacaine. Used (in the form of its hydrochloride hydrate) as a local anaesthetic.
alternative label: Bupivacaine
alternative label: rac-1-butyl-N-(2,6-dimethylphenyl)piperidine-2-carboxamide
imported from: chebi.owl

atom
type: Class
subclass of: material entity
definition: A chemical entity constituting the smallest component of an element having the chemical properties of the element.
alternative label: atom
imported from: chebi.owl

antimicrobial agent
type: Class
subclass of: medication role
definition: A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.
imported from: chebi.owl

nucleic acid
type: Class
subclass of: macromolecule
definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
alternative label: nucleic acids
imported from: chebi.owl

ribonucleic acid
type: Class
subclass of: macromolecule
definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
alternative label: ribonucleic acid
alternative label: ribonucleic acids
imported from: chebi.owl

macromolecule
type: Class
subclass of: molecular entity
definition: A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
alternative label: macromolecule
imported from: chebi.owl

steroid
type: Class
subclass of: molecular entity
definition: Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene.
alternative label: Steroid
alternative label: steroids
imported from: chebi.owl

opioid analgesic
type: Class
subclass of: medication role
definition: A narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood.
imported from: chebi.owl

sedative
type: Class
subclass of: medication role
definition: A central nervous system depressant used to induce drowsiness or sleep or to reduce psychological excitement or anxiety.
imported from: chebi.owl

local anaesthetic
type: Class
subclass of: anaesthetic
definition: Any member of a group of drugs that reversibly inhibit the propagation of signals along nerves. Wide variations in potency, stability, toxicity, water-solubility and duration of action determine the route used for administration, e.g. topical, intravenous, epidural or spinal block.
alternative label: local anaesthetic
imported from: chebi.owl

anaesthetic
type: Class
subclass of: medication role
definition: Substance which produces loss of feeling or sensation.
alternative label: anaesthetic
imported from: chebi.owl

inhalation anaesthetic
type: Class
subclass of: anaesthetic
imported from: chebi.owl

intravenous anaesthetic
type: Class
subclass of: anaesthetic
imported from: chebi.owl

EDTA(4-)
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has role
  some values from: blood additive role
definition: A tetracarboxylic acid anion formed by deprotonation of all four carboxy groups in ethylenediaminetetraacetic acid (EDTA).
alternative label: (ethane-1,2-diyldinitrilo)tetraacetate
imported from: chebi.owl

propofol
type: Class
subclass of: molecular entity
definition: A phenol resulting from the formal substitution of the hydrogen at the 2 position of 1,3-diisopropylbenzene by a hydroxy group.
alternative label: 2,6-bis(propan-2-yl)phenol
alternative label: Propofol
imported from: chebi.owl

droperidol
type: Class
subclass of: molecular entity
definition: An organofluorine compound that is haloperidol in which the hydroxy group has been eliminated with the introduction of a double bond in the piperidine ring, and the 4-chlorophenyl group has been replaced by a benzimidazol-2-on-1-yl group. It is used in the management of chemotherapy-induced nausea and vomiting, and in conjunction with an opioid analgesic such as fentanyl to maintain the patient in a calm state of neuroleptanalgesia with indifference to surroundings but still able to cooperate with the surgeon.
alternative label: 1-{1-[4-(4-fluorophenyl)-4-oxobutyl]-1,2,3,6-tetrahydropyridin-4-yl}-1,3-dihydro-2H-benzimidazol-2-one
imported from: chebi.owl

etomidate
type: Class
subclass of: molecular entity
definition: The ethyl ester of 1-[(1R)-1-phenylethyl]-1H-imidazole-5-carboxylic acid. It is an intravenous general anaesthetic with no analgesic activity.
alternative label: Etomidate
alternative label: ethyl 1-[(1R)-1-phenylethyl]-1H-imidazole-5-carboxylate
imported from: chebi.owl

diazepam
type: Class
subclass of: molecular entity
definition: A 1,4-benzodiazepinone that is 1,3-dihydro-2H-1,4-benzodiazepin-2-one substituted by a chloro group at position 7, a methyl group at position 1 and a phenyl group at position 5.
alternative label: 7-chloro-1-methyl-5-phenyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one
alternative label: Diazepam
imported from: chebi.owl

fixative
type: Class
subclass of: role
definition: Any compound used for the purpose of preserving biological tissues from decay in such a way as to allow for the preparation of thin, stained sections for subsequent histological study.
imported from: chebi.owl

antiemetic
type: Class
subclass of: medication role
definition: A drug used to prevent nausea or vomiting. An antiemetic may act by a wide range of mechanisms: it might affect the medullary control centres (the vomiting centre and the chemoreceptive trigger zone) or affect the peripheral receptors.
imported from: chebi.owl

muscle relaxant
type: Class
subclass of: medication role
definition: A drug used to produce muscle relaxation (excepting neuromuscular blocking agents). Its primary clinical and therapeutic use is the treatment of muscle spasm and immobility associated with strains, sprains, and injuries of the back and, to a lesser degree, injuries to the neck. Also used for the treatment of a variety of clinical conditions that have in common only the presence of skeletal muscle hyperactivity, for example, the muscle spasms that can occur in multiple sclerosis.
imported from: chebi.owl

lormetazepam
type: Class
subclass of: molecular entity
definition: A 1,4-benzodiazepinone compound having a methyl substituent at the 1-position, a hydroxy substituent at the 3-position, a 2-chlorophenyl group at the 5-position and a chloro substituent at the 7-position.
alternative label: 7-chloro-5-(2-chlorophenyl)-3-hydroxy-1-methyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one
alternative label: Lormetazepam
imported from: chebi.owl

sodium citrate
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has role
  some values from: blood additive role
definition: The trisodium salt of citric acid.
alternative label: trisodium 2-hydroxypropane-1,2,3-tricarboxylate
imported from: chebi.owl

hydromorphone
type: Class
subclass of: molecular entity
definition: A morphinane alkaloid that is a hydrogenated ketone derivative of morphine. A semi-synthetic drug, it is a centrally acting pain medication of the opioid class.
alternative label: 3-hydroxy-17-methyl-4,5alpha-epoxymorphinan-6-one
alternative label: Hydromorphone
imported from: chebi.owl

isoflurane
type: Class
subclass of: molecular entity
alternative label: 2-chloro-2-difluoromethoxy-1,1,1-trifluoroethane
alternative label: Isoflurane
imported from: chebi.owl

ketamine
type: Class
subclass of: molecular entity
definition: A member of the class of cyclohexanones in which one of the hydrogens at position 2 is substituted by a 2-chlorophenyl group, while the other is substituted by a methylamino group.
alternative label: 2-(2-chlorophenyl)-2-(methylamino)cyclohexanone
alternative label: KETAMINE
alternative label: Ketamine
imported from: chebi.owl

succinylcholine chloride (anhydrous)
type: Class
subclass of: molecular entity
definition: A chloride salt in which the negative charge of the chloride ions is balanced by succinylcholine dications.
alternative label: 2,2'-[(1,4-dioxobutane-1,4-diyl)bis(oxy)]bis(N,N,N-trimethylethanaminium) dichloride
imported from: chebi.owl

lidocaine
type: Class
subclass of: molecular entity
definition: The monocarboxylic acid amide resulting from the formal condensation of N,N-diethylglycine with 2,6-dimethylaniline.
alternative label: Lidocaine
alternative label: N-(2,6-dimethylphenyl)-N(2),N(2)-diethylglycinamide
imported from: chebi.owl

antacid
type: Class
subclass of: medication role
definition: Any substance which is used to neutralise stomach acidity.
imported from: chebi.owl

pethidine
type: Class
subclass of: molecular entity
definition: A piperidinecarboxylate ester that is piperidine which is substituted by a methyl group at position 1 and by phenyl and ethoxycarbonyl groups at position 4. It is an analgesic which is used for the treatment of moderate to severe pain, including postoperative pain and labour pain.
alternative label: ethyl 1-methyl-4-phenylpiperidine-4-carboxylate
imported from: chebi.owl

methohexital sodium
type: Class
subclass of: molecular entity
definition: The sodium salt of methohexital.
alternative label: sodium 5-(hex-3-yn-2-yl)-1-methyl-4,6-dioxo-5-(prop-2-en-1-yl)-1,4,5,6-tetrahydropyrimidin-2-olate
imported from: chebi.owl

Ondansetron
type: Class
subclass of: molecular entity
alternative label: Ondansetron
imported from: chebi.owl

pancuronium
type: Class
subclass of: molecular entity
definition: A steroid ester in which a 5alpha-androstane skeleton is C-3alpha- and C-17beta-disubstituted with acetoxy groups and 2beta- and 16beta-disubstituted with 1-methylpiperidinium-1-yl groups. It is a non-depolarizing curare-mimetic muscle relaxant.
alternative label: 3alpha,17beta-diacetoxy-2beta,16beta-bis(1-methylpiperidinium-1-yl)-5alpha-androstane
alternative label: Pancuronium
imported from: chebi.owl

procaine
type: Class
subclass of: molecular entity
definition: A benzoate ester, formally the result of esterification of 4-aminobenzoic acid with 2-diethylaminoethanol but formed experimentally by reaction of ethyl 4-aminobenzoate with 2-diethylaminoethanol.
alternative label: 2-(diethylamino)ethyl 4-aminobenzoate
alternative label: Procaine
imported from: chebi.owl

ranitidine
type: Class
subclass of: molecular entity
definition: A member of the class of furans used to treat peptic ulcer disease (PUD) and gastroesophageal reflux disease.
alternative label: (E)-N-{2-[({5-[(dimethylamino)methyl]-2-furyl}methyl)sulfanyl]ethyl}-N'-methyl-2-nitroethene-1,1-diamine
imported from: chebi.owl

thiopental sodium
type: Class
subclass of: molecular entity
definition: An organic sodium salt having thiopental(1-) as the counter-ion.
alternative label: sodium 5-ethyl-4,6-dioxo-5-(pentan-2-yl)-1,4,5,6-tetrahydropyrimidine-2-thiolate
imported from: chebi.owl

vecuronium
type: Class
subclass of: molecular entity
definition: A 5alpha-androstane compound having 3alpha-acetoxy-, 17beta-acetoxy-, 2beta-piperidino- and 16beta-N-methylpiperidinium substituents.
alternative label: (2beta,3alpha,5alpha,16beta,17beta)-3,17-diacetoxy-16-(1-methylpiperidinium-1-yl)-2-(piperidin-1-yl)androstane
imported from: chebi.owl

cell line cell
type: Class
subclass of: secondary cultured cell
definition: A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
imported from: clo.owl

immortal cell line cell
type: Class
subclass of: cell line cell
definition: A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line.
alternative label: continuous cell line cell
alternative label: permanent cell line cell
imported from: clo.owl

cell line
type: Class
subclass of: secondary cultured cell population
example of usage: He, Tong-Chuan, et al., Identification of c-MYC as a target of the APC pathway. Science 281.5382 (1998): 1509-1512.: "To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene". Note that common usage in the literature is often of the form "a human colorectal cancer cell line", as seen above. But such references to studies in "a line" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'.
definition: A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
imported from: clo.owl

immortal cell line
type: Class
subclass of: cell line
definition: A cell line that is expected to be capable of indefinite propagation in an vitro culture.
alternative label: permanent cell line
imported from: clo.owl

cell
type: Class
subclass of: material entity
definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
imported from: cl.owl

primary cultured cell
type: Class
subclass of: cultured cell
definition: A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged.
imported from: cl.owl

native cell
type: Class
subclass of: cell
definition: A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
imported from: cl.owl

cultured cell
type: Class
subclass of: experimentally modified cell in vitro
definition: A cell in vitro that is or has been maintained or propagated as part of a cell culture.
imported from: cl.owl

erythrocyte
type: Class
subclass of: cell
definition: A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
imported from: cl.owl

reticulocyte
type: Class
subclass of: cell
definition: 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.
imported from: cl.owl

experimentally modified cell in vitro
type: Class
subclass of: cell in vitro
definition: A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
imported from: cl.owl

leukocyte
type: Class
subclass of: cell
definition: An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
imported from: cl.owl

cell in vitro
type: Class
subclass of: cell
definition: A cell that is maintained or propagated in a controlled artificial environment for use in an investigation.
imported from: cl.owl

Paraffin
type: Class
subclass of: processed material
imported from: dron.owl

environmental material
type: Class
subclass of: material entity
definition: A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.
imported from: envo.owl

specimen barcode
type: Class
subclass of: specimen ID
definition: A specimen barcode is a specimen identification number formatted as an optical machine-readable representation.
imported from: flu.owl

Cortex of left kidney
type: Class
subclass of: organ part
alternative label: Left renal cortex
imported from: fma.owl

Wall of distal part of ileum
type: Class
subclass of: organ part
alternative label: Wall of distal ileum
imported from: fma.owl

Anterior wall of vagina
type: Class
subclass of: organ part
alternative label: Paries anterior (vagina)
imported from: fma.owl

Posterior wall of vagina
type: Class
subclass of: organ part
alternative label: Paries posterior (vagina)
imported from: fma.owl

Right tibial nerve
type: Class
subclass of: tibial nerve
imported from: fma.owl

Left tibial nerve
type: Class
subclass of: tibial nerve
imported from: fma.owl

Cortex of right frontal lobe
type: Class
subclass of: organ part
alternative label: Right frontal lobe cortex
imported from: fma.owl

Right leg
type: Class
subclass of: material anatomical entity
imported from: fma.owl

Left leg
type: Class
subclass of: material anatomical entity
imported from: fma.owl

Skin of right leg
type: Class
subclass of: skin of body
alternative label: Right leg skin
imported from: fma.owl

Skin of left leg
type: Class
subclass of: skin of body
alternative label: Left leg skin
imported from: fma.owl

Left posterior tibial artery
type: Class
subclass of: tibial artery
imported from: fma.owl

Anatomical location
type: Class
subclass of: immaterial entity
definition: Spatial association relationship which describes the containment, adjacency and anatomical coordinates of physical anatomical entities. Examples: anatomical containment, anatomical adjacency, anatomical coordinate.
imported from: fma.owl

Right mammary gland
type: Class
subclass of: material anatomical entity
imported from: fma.owl

Mucosa of abdominal part of esophagus
type: Class
subclass of: esophagus mucosa
imported from: fma.owl

Muscularis mucosae of abdominal part of esophagus
type: Class
subclass of: esophagus muscularis mucosa
imported from: fma.owl

Right hemisphere of cerebellum
type: Class
subclass of: organ part
imported from: fma.owl

subnational entity
type: Class
equivalent class: Class
  intersection of: governmental organization
  intersection of: Restriction
    on property: is subordinate authority of
    some values from: sovereign state
subclass of: governmental organization
definition: a governmental organization that has a local, regional, or territorial government that recognizes a sovereign state as its higher political authority
term editor: Amanda Hicks
term editor: William R. Hogan
imported from: geo.owl

geopolitical dependency
type: Class
subclass of: subnational entity
definition: A subnational entity that does not possess full political independence or sovereignty as a sovereign state, but remains politically outside of the controlling state and controls a geographical region that is outside the controlling state's integral region.
term editor: Amanda Hicks
term editor: William R. Hogan
imported from: geo.owl
comment: Typically, the common feature is that the dependency does not conduct foreign affairs, and relegates this authority to the sovereign state. But otherwise, it is largely or completely autonomous relative to the administrative subdivisions. Examples include Puerto Rico (U.S.), Guam (U.S.), Greenland (Denmark), French Polynesia (France), and Falkland Islands (United Kingdom).

geographical entity
type: Class
subclass of: material entity
editor preferred term: geographical entity of astronomical body
definition: A material entity that is (1) a bona fide or fiat object part of the crust, any bodies of liquid on or contained within the crust, or planetary boundary layer (if present) of a terrestrial planet (including Earth), dwarf planet, exoplanet, natural satellite, planetesimal, or small Solar System body, and that (2) overlaps the planetary surface (including having a boundary that coincides with part of the planetary surface).
term editor: Mathias Brochhausen
term editor: Matt Diller
term editor: William R. Hogan
imported from: geo.owl
comment: Includes atmosphere, crust, geographical regions (e.g., the geographical region over which the state of Florida has jurisdiction), bodies of water, mountains, etc. Generally, an individual organism is a distinct object that is not a part of the Earth, although this requires more thought. But the intent is definitely for this class to NOT subsume organism universally. Human beings are contained within, but not part of, the Earth, for example.
comment: Note that despite the word 'planetary' in 'planetary surface', it refers generally to surface of dwarf planets, asteroids, moons, etc.
comment: We note that not all planets have a surface per se (e.g., gas giants such as Jupiter and Saturn). So only planets, natural satellites, etc. with a planetary surface (with or without a planetary boundary layer) have geographical entities.
comment: We note that the term 'geography' is also applied to the Earth's moon, Mars, Venus, and possibly even other moons and planets in our own solar system and beyond. Thus, we are attempting to define things generally enough that they could be reused for the geographical entities/features on the Moon, Mars, other planets, exoplanets, other natural satellites (a.k.a moons), asteroids, etc.

geographical region
type: Class
subclass of: geographical entity
definition: A geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface.
term editor: François Modave
term editor: Mathias Brochhausen
term editor: Matt Diller
term editor: William R. Hogan
imported from: geo.owl

sovereign state
type: Class
subclass of: governmental organization
definition: A governmental organization with a defined territory on which it exercises internal and external sovereignty, a permanent population, a government, and the capacity to enter into relations with other sovereign states.
term editor: William R. Hogan
alternative label: de facto sovereign state
alternative label: de facto state
alternative label: nation
alternative label: nation state
definition source: http://en.wikipedia.org/wiki/Sovereign_state
imported from: geo.owl
comment: Per Wikipedia, the word 'nation' does not always refer to soverign states. For example, the "nation of Islam".

governmental organization
type: Class
subclass of: organization
definition: An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii). Note: this definition was taken over from "geopolitical organization".
term editor: Amanda Hicks
imported from: geo.owl
comment: IMPORTANT: The label "geopolitical organization" was previously used for OMRSE_00000044 (governmental organization). "geopoli organization" is a label for a new and different class.

immune response
type: Class
subclass of: biological_process
definition: Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
imported from: go.owl

biological_process
type: Class
subclass of: process
definition: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
imported from: go.owl

immunoglobulin complex
type: Class
subclass of: protein-containing complex
definition: A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
imported from: go.owl

protein-containing complex
type: Class
subclass of: material entity
definition: A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
imported from: go.owl

ancestry category
type: Class
subclass of: population
definition: Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data
imported from: hancestro.owl

Asian
type: Class
subclass of: ancestry category
definition: Includes individuals that either self-report or have been described as Asian but there was not sufficient information to allow classification as East Asian, Central Asian, South Asian or South-East Asian.
imported from: hancestro.owl

Hispanic or Latin American
type: Class
subclass of: ancestry category
definition: Includes individuals who either self-report or are described by authors as Hispanic, Latino, Latin American or one of the sub-populations from this region. This category includes individuals with known admixture of primarily European, African and Native American ancestries, though some may have also a degree of Asian (e.g. Peru). We also note that the levels of admixture vary depending on the country, with Caribbean countries carrying higher levels of African admixture when compared to South American countries, for example. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CLM, MXL, PEL and PUR populations
imported from: hancestro.owl

Japanese
type: Class
subclass of: Asian
imported from: hancestro.owl

Chinese
type: Class
subclass of: Asian
imported from: hancestro.owl

American
type: Class
subclass of: ancestry category
imported from: hancestro.owl

Indian
type: Class
subclass of: Asian
imported from: hancestro.owl

African American
type: Class
subclass of: American
imported from: hancestro.owl

European American
type: Class
subclass of: American
imported from: hancestro.owl

conditional specification
type: Class
subclass of: directive information entity
editor preferred term: conditional specification
has curation status: metadata complete
definition: A directive information entity that specifies what should happen if the trigger condition is fulfilled.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
definition source: OBI_0000349
imported from: iao.owl

measurement unit label
type: Class
subclass of: datum label
editor preferred term: measurement unit label
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
has curation status: pending final vetting
definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
editor note: 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
editor note: 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
imported from: iao.owl

objective specification
type: Class
subclass of: directive information entity
editor preferred term: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has curation status: ready for release
definition: 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.
editor note: 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."
editor note: 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.
editor note: Answers the question, why did you do this experiment?
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
alternative label: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
imported from: iao.owl

action specification
type: Class
subclass of: directive information entity
example of usage: Pour the contents of flask 1 into flask 2
has curation status: ready for release
definition: A directive information entity that describes an action the bearer will take.
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
imported from: iao.owl

datum label
type: Class
subclass of: information content entity
editor preferred term: datum label
has curation status: metadata incomplete
definition: A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
term editor: GROUP: IAO
curator note: 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
imported from: iao.owl

data item
type: Class
subclass of: information content entity
editor preferred term: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: pending final vetting
definition: 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.
editor note: 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.
editor note: 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.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: 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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
alternative label: data
imported from: iao.owl

symbol
type: Class
subclass of: information content entity
editor preferred term: symbol
example of usage: a serial number such as "12324X"
example of usage: a stop sign
example of usage: a written proper name such as "OBI"
has curation status: pending final vetting
definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
editor note: 20091104, MC: this needs work and will most probably change
editor note: 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).
term editor: PERSON: James A. Overton
term editor: PERSON: Jonathan Rees
definition source: based on Oxford English Dictionary
imported from: iao.owl

numeral
type: Class
subclass of: symbol
editor preferred term: numeral
has curation status: metadata incomplete
definition: A symbol that denotes a number.
term editor: PERSON: Jonathan Rees
imported from: iao.owl

information content entity
type: Class
subclass of: generically dependent continuant
editor preferred term: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: ready for release
definition: A generically dependent continuant that is about some thing.
editor note: 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).
editor note: 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.
term editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
imported from: iao.owl

scalar measurement datum
type: Class
subclass of: measurement datum
example of usage: 10 feet. 3 ml.
has curation status: metadata complete
definition: A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
editor note: 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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
imported from: iao.owl

directive information entity
type: Class
subclass of: information content entity
has curation status: ready for release
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 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.
editor note: 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.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: 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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
imported from: iao.owl

algorithm
type: Class
subclass of: plan specification
editor preferred term: algorithm
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
has curation status: metadata complete
definition: 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.
term editor: Philippe Rocca-Serra
term editor: PlanAndPlannedProcess Branch
definition source: OBI_0000270
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
imported from: iao.owl

curation status specification
type: Class
equivalent class: Class
  one of: example to be eventually removed
  one of: metadata complete
  one of: organizational term
  one of: ready for release
  one of: metadata incomplete
  one of: uncurated
  one of: pending final vetting
  one of: to be replaced with external ontology term
  one of: requires discussion
subclass of: data about an ontology part
editor preferred term: curation status specification
has curation status: pending final vetting
definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
term editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266

data set
type: Class
subclass of: data item
editor preferred term: data set
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
has curation status: pending final vetting
definition: 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.
editor note: 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
editor note: 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.
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
definition source: OBI_0000042
definition source: group:OBI
imported from: iao.owl

image
type: Class
subclass of: figure
editor preferred term: image
has curation status: ready for release
definition: An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
term editor: person:Alan Ruttenberg
term editor: person:Allyson
term editor: person:Chris Stoeckert
definition source: OBI_0000030
definition source: group:OBI
imported from: iao.owl

data about an ontology part
type: Class
subclass of: data item
editor preferred term: data about an ontology part
definition: Data about an ontology part is a data item about a part of an ontology, for example a term
term editor: Person:Alan Ruttenberg
imported from: iao.owl

plan specification
type: Class
subclass of: directive information entity
editor preferred term: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: ready for release
definition: A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
editor note: 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.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
term editor: Alan Ruttenberg
term editor: Clint Dowland
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
imported from: iao.owl
comment: 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

measurement datum
type: Class
subclass of: data item
editor preferred term: measurement datum
example of usage: 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,}.
has curation status: pending final vetting
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
editor note: 2/2/2009 is_specified_output of some assay?
term editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI
imported from: iao.owl

version number
type: Class
subclass of: symbol
editor preferred term: version number
has curation status: metadata incomplete
definition: 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.
editor note: 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
term editor: GROUP: IAO
imported from: iao.owl

lot number
type: Class
subclass of: symbol
editor preferred term: lot number
has curation status: metadata incomplete
definition: 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.
term editor: GROUP: IAO
alternative label: batch number
imported from: iao.owl

setting datum
type: Class
subclass of: data item
has curation status: metadata incomplete
definition: A settings datum is a datum that denotes some configuration of an instrument.
editor note: 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.
editor note: Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
imported from: iao.owl

conclusion textual entity
type: Class
subclass of: textual entity
editor preferred term: conclusion textual entity
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has curation status: metadata complete
definition: A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/23 Alan Ruttenberg: We need to work on the definition still
term editor: Person:Alan Ruttenberg
imported from: iao.owl

material information bearer
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has characteristic
    some values from: Restriction
      on property: concretizes
      some values from: information content entity
subclass of: material entity
editor preferred term: material information bearer
example of usage: 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.
example of usage: a brain
example of usage: a hard drive
has curation status: ready for release
definition: A material entity in which a concretization of an information content entity inheres.
term editor: GROUP: IAO
imported from: iao.owl

obsolescence reason specification
type: Class
equivalent class: Class
  one of: failed exploratory term
  one of: placeholder removed
  one of: terms merged
  one of: term imported
  one of: term split
  one of: out of scope
subclass of: data about an ontology part
editor preferred term: obsolescence reason specification
has curation status: pending final vetting
definition: The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

textual entity
type: Class
subclass of: information content entity
editor preferred term: textual entity
example of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
has curation status: metadata incomplete
definition: 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.
editor note: 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.
editor note: 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.
term editor: PERSON: Lawrence Hunter
alternative label: text
imported from: iao.owl

document title
type: Class
subclass of: textual entity
editor preferred term: document title
example of usage: Textual characteristics of traditional and Open Access scientific journals are similar
has curation status: pending final vetting
definition: A textual entity that names a document
term editor: PERSON: Lawrence Hunter
imported from: iao.owl

figure
type: Class
subclass of: information content entity
editor preferred term: figure
example of usage: Any picture, diagram or table
has curation status: metadata complete
definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
term editor: PERSON: Lawrence Hunter
imported from: iao.owl

document
type: Class
subclass of: information content entity
editor preferred term: document
example of usage: A journal article, patent application, laboratory notebook, or a book
has curation status: metadata complete
definition: A collection of information content entities intended to be understood together as a whole
term editor: PERSON: Lawrence Hunter
imported from: iao.owl

running title
type: Class
subclass of: document title
editor preferred term: running title
has curation status: pending final vetting
definition: A shorter version of a document title
term editor: PERSON: Lawrence Hunter
imported from: iao.owl

length measurement datum
type: Class
subclass of: scalar measurement datum
has curation status: metadata incomplete
definition: A scalar measurement datum that is the result of measurement of length quality
term editor: Alan Ruttenberg
imported from: iao.owl

denotator type
type: Class
equivalent class: Class
  one of: universal
  one of: defined class
  one of: named class expression
subclass of: data about an ontology part
editor preferred term: denotator type
example of usage: The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
term editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters

mass measurement datum
type: Class
subclass of: scalar measurement datum
has curation status: metadata incomplete
definition: A scalar measurement datum that is the result of measurement of mass quality
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg
imported from: iao.owl

time measurement datum
type: Class
subclass of: scalar measurement datum
has curation status: metadata incomplete
definition: A scalar measurement datum that is the result of measuring a temporal interval
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg
imported from: iao.owl

postal address
type: Class
subclass of: textual entity
has curation status: metadata incomplete
definition: A textual entity that is used as directive to deliver something to a person, or organization
editor note: 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59
imported from: iao.owl

email address
type: Class
subclass of: information content entity
editor preferred term: email address
has curation status: metadata incomplete
editor note: Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583
term editor: Person:Alan Ruttenberg
term editor: Person:Chris Stoeckart
imported from: iao.owl

documenting
type: Class
subclass of: planned process
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
has curation status: pending final vetting
definition: A planned process in which a document is created or added to by including the specified input in it.
editor note: 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
term editor: Bjoern Peters
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting
imported from: iao.owl

centrally registered identifier symbol
type: Class
subclass of: symbol
example of usage: 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.
has curation status: metadata complete
definition: A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
alternative label: CRID symbol
definition source: Original proposal from Bjoern, discussions at IAO calls
imported from: iao.owl

centrally registered identifier
type: Class
subclass of: information content entity
example of usage: 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.
has curation status: metadata complete
definition: An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
editor note: 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
editor note: Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
editor note: Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
alternative label: CRID
definition source: Original proposal from Bjoern, discussions at IAO calls
imported from: iao.owl

centrally registered identifier registry
type: Class
subclass of: data set
example of usage: PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles.
has curation status: metadata complete
definition: A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process.
term editor: Justin Whorton
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
alternative label: CRID registry
definition source: Original proposal from Bjoern, discussions at IAO calls
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/237
imported from: iao.owl

time stamped measurement datum
type: Class
subclass of: measurement datum
has curation status: metadata incomplete
imported from: iao.owl

postal code
type: Class
subclass of: identifier
definition: An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail.
term editor: Mathias Brochhausen
imported from: iao.owl

identifier
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: designates
    some values from: entity
  intersection of: Restriction
    on property: is_specified_output_of
    all values from: dubbing process
subclass of: information content entity
editor preferred term: identifier
definition: 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.
term editor: Justin Whorton
term editor: Mathias Brochhausen
alternative label: proper name
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/237
imported from: iao.owl
creator: Mathias Brochhausen
comment: Sep 29, 2016: The current definition has been amended from the previous version: "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." to more accuratly reflect the necessary and sufficient condition on the class. (MB)

dubbing process
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: identifier
subclass of: planned process
definition: A dubbing process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
term editor: Mathias Brochhausen

personal name
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: designates
    all values from: Homo sapiens
subclass of: identifier
definition: A personal name is a proper name identifying an individual person.
term editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Personal_name
comment: 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)

given name
type: Class
subclass of: personal name
subclass of: Restriction
  on property: part of
  some values from: personal name
definition: A given name, in Western contexts often referred to as a first name, is a personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name
term editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Given_name

family name
type: Class
subclass of: personal name
subclass of: Restriction
  on property: part of
  some values from: personal name
definition: A family name (in Western contexts often referred to as a surname or last name) is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children.
term editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Family_name

identity document
type: Class
equivalent class: Class
  intersection of: document
  intersection of: Restriction
    on property: is about
    some values from: documented identity
  intersection of: Restriction
    on property: is concretized as
    some values from: Class
      intersection of: specifically dependent continuant
      intersection of: Restriction
        on property: characteristic of
        some values from: Restriction
  intersection of: Restriction
    on property: is concretized as
    all values from: Class
      intersection of: specifically dependent continuant
      intersection of: Restriction
        on property: characteristic of
        some values from: Restriction
subclass of: document
definition: A document that denotes some identity and is concretized by the bearer of some credential role.
term editor: Amanda Hicks

documented identity
type: Class
subclass of: information content entity
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: information content entity
  intersection of: Restriction
    on property:
      inverse of: is about
    some values from: identity document
  intersection of: Restriction
    on property: has part
    all values from: information content entity
definition: A documented identity is the aggregate of all data items about an entity. Notice that a documented identity is not itself a document since a document is intended to be understood as a whole and data items about an individual are usually scattered across different documents.
term editor: Amanda Hicks
comment: is an aggregate of ICEs also an ICE? yes Is part_of the appropriate relation to use for data items and documented identities?

authentication
type: Class
subclass of: process
subclass of: Class
  intersection of: process
  intersection of: Restriction
    on property: realizes
    some values from: credential role
  intersection of: Restriction
    on property: has participant
    some values from: data item
  intersection of: Restriction
    on property: has participant
    some values from: Restriction
      on property:
        inverse of: is about
      some values from: data item
example of usage: I order a beer and the bartender authenticates my age by looking at my DOB on my driver's license. I sign into my email account, and the system authenticates my permission to read the email by checking the password I enter against my password listed in the database.
definition: Authentication is the act of checking or verifying an identity claim (that is either tacit or explicit).
term editor: Amanda Hicks

credential role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: realized in
    some values from: authentication
  intersection of: Restriction
    on property: characteristic of
    some values from: Restriction
      on property: has characteristic
      some values from: Restriction
        on property: concretizes
        some values from: identity document
subclass of: role
definition: A role that inheres in a concretization of an identity document and is realized by an authentication process.
term editor: Amanda Hicks

ontology module
type: Class
subclass of: data about an ontology part
editor preferred term: ontology module
editor note: I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
alternative label: ontology file
curator note: This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.

base ontology module
type: Class
subclass of: ontology module
editor preferred term: base ontology module
definition: An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.

editors ontology module
type: Class
subclass of: ontology module
editor preferred term: editors ontology module
definition: An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
alternative label: source ontology module

main release ontology module
type: Class
subclass of: ontology module
editor preferred term: main release ontology module
definition: An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
editor note: TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module

bridge ontology module
type: Class
subclass of: ontology module
editor preferred term: bridge ontology module
definition: An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.

import ontology module
type: Class
subclass of: subset ontology module
editor preferred term: import ontology module
definition: A subset ontology module that is intended to be imported from another ontology.
editor note: TODO: add axioms that indicate this is the output of a module extraction process.
alternative label: import file

subset ontology module
type: Class
subclass of: ontology module
editor preferred term: subset ontology module
definition: An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
alternative label: ontology slim
alternative label: subset ontology

curation subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: curation subset ontology module
definition: A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.

analysis subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: analysis ontology module
definition: An ontology module that is intended for usage in analysis or discovery applications.

single layer subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: single layer ontology module
definition: A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
alternative label: ribbon subset

exclusion subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: exclusion subset ontology module
definition: A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
alternative label: antislim

external import ontology module
type: Class
subclass of: import ontology module
editor preferred term: external import ontology module
definition: An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
alternative label: external import

species subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: species subset ontology module
definition: A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
alternative label: taxon subset

reasoned ontology module
type: Class
subclass of: ontology module
editor preferred term: reasoned ontology module
definition: An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.

generated ontology module
type: Class
subclass of: ontology module
editor preferred term: generated ontology module
definition: An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
editor note: TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process

template generated ontology module
type: Class
subclass of: generated ontology module
editor preferred term: template generated ontology module
definition: An ontology module that is automatically generated from a template specification and fillers for slots in that template.

taxonomic bridge ontology module
type: Class
subclass of: bridge ontology module
editor preferred term: taxonomic bridge ontology module

ontology module subsetted by expressivity
type: Class
subclass of: subset ontology module
editor preferred term: ontology module subsetted by expressivity

obo basic subset ontology module
type: Class
subclass of: ontology module subsetted by expressivity
editor preferred term: obo basic subset ontology module
definition: A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports

ontology module subsetted by OWL profile
type: Class
subclass of: ontology module subsetted by expressivity
editor preferred term: ontology module subsetted by OWL profile

EL++ ontology module
type: Class
subclass of: ontology module subsetted by OWL profile
editor preferred term: EL++ ontology module

informed consent form
type: Class
subclass of: document
definition: A document that explains all relevant information to assist a human being in understanding the expectations and requirements of participation in a process, and is an instrument in obtaining consent and, after having obtained consent, is a record that such a consent has occurred.
alternative label: informed consent document
imported from: ico.owl

completely filled informed consent form
type: Class
subclass of: informed consent form
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: form filling
    intersection of: Restriction
      on property: has_specified_input
      some values from: data confirm questionnaire
    intersection of: Restriction
      on property: has participant
      some values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
    intersection of: Restriction
      on property: has participant
      some values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
definition: An informed consent form that has been filled with all required contents.
imported from: ico.owl

partially filled informed consent form
type: Class
subclass of: informed consent form
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: form filling
    intersection of: Restriction
      on property: has_specified_input
      some values from: data confirm questionnaire
    intersection of: Restriction
      on property: has participant
      some values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
    intersection of: Restriction
      on property: has participant
      some values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
definition: An informed consent form that has been partially filled with required contents.
imported from: ico.owl

act of authorizing
type: Class
subclass of: planned process
definition: A planned process of making the decision of the competent authorities in form of a letter, document, or verbal or electronic form, that confirms that somebody has permission to do something or be somewhere, e.g. to realize a given project.
alternative label: permission
imported from: ico.owl

obsolete authorization document
type: Class
subclass of: document
definition: A document that is the output of an authorization process.
imported from: ico.owl

eligibility of candidate participation
type: Class
subclass of: realizable entity
definition: A role that represents the eligibility of a candidate according to a study protocol.
imported from: ico.owl

candidate eligible for study role
type: Class
subclass of: eligibility of candidate participation
definition: A role inhering in a participant who meets all eligibility criteria defined within a study protocol.
imported from: ico.owl

candidate ineligible for study role
type: Class
subclass of: eligibility of candidate participation
definition: A role inhering in a participant who does not meet all eligibility criteria defined within the study protocol.
imported from: ico.owl

pathogenic disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: characteristic of
    some values from: material entity
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: results in formation of
        some values from: disorder
definition: A disposition to initiate processes that result in a disorder.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative label: pathogenicity
imported from: ido.owl
comment: A pathogenic disposition is realized in processes that create a disorder.
comment: The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition. By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition.

immunosuppressed organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: participates in
    some values from: Class
      union of: pathologic immunosuppression
      union of: pregnancy-induced immunosuppression
subclass of: organism
definition: An organism that is experiencing pregnancy-induced or pathologic immunosuppression.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl

pathogen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has disposition
    some values from: pathogenic disposition
subclass of: material entity
definition: A material entity with a pathogenic disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl

immunosuppression
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: negatively regulates
    some values from: immune response
subclass of: process
definition: A process that attenuates an immune response.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl

pathologic immunosuppression
type: Class
subclass of: immunosuppression
definition: An immunosuppression process which arises as the result of a disorder.
editor note: Disorders that result in immunosuppression include those that result from infection, stress, malnutrition, and treatments such as chemotherapy or calcineurin inhibition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl

immunosuppressive disposition
type: Class
subclass of: disposition
definition: A disposition whose realization negatively regulates an immune response.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl

pregnancy-induced immunosuppression
type: Class
subclass of: immunosuppression
definition: An immunosuppression induced by progesterone and other factors upregulated in pregnant women.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl

immunosuppressed human experiencing HIV-based immunosuppression
type: Class
subclass of: immunosuppressed organism
definition: An immunosuppressed organism that is a human experiencing HIV-based immunosuppression.
term editor: Alex Diehl
term editor: Lindsay Cowell
ontology term requester: NCI BBRB
imported from: ido.owl

immunosuppressed human experiencing chronic systemic steroid use-based immunosuppression
type: Class
subclass of: immunosuppressed organism
definition: An immunosuppressed organism that is a human experiencing chronic systemic steroid use-based immunosuppression.
term editor: Alex Diehl
term editor: Lindsay Cowell
ontology term requester: NCI BBRB
imported from: ido.owl

immunosuppressed human experiencing drug-based immunosuppression due to organ transplant
type: Class
subclass of: immunosuppressed organism
definition: A pathologically immunosuppressed organism that is a human experiencing drug-based immunosuppression.
term editor: Alex Diehl
term editor: Lindsay Cowell
ontology term requester: NCI BBRB
imported from: ido.owl

Viruses
type: Class
subclass of: organism
imported from: ncbitaxon.owl

Herpesviridae
type: Class
subclass of: Viruses
imported from: ncbitaxon.owl

Cytomegalovirus
type: Class
subclass of: Herpesviridae
imported from: ncbitaxon.owl

Human gammaherpesvirus 4
type: Class
subclass of: Herpesviridae
alternative label: Epstein Barr virus
alternative label: Epstein-Barr virus
alternative label: Epstein-Barr virus EBV
alternative label: Human herpesvirus 4
alternative label: Human herpesvirus type 4
imported from: ncbitaxon.owl

Hepatitis B virus
type: Class
subclass of: Viruses
alternative label: Human hepatitis B virus
alternative label: hepatitis B virus (HBV)
alternative label: hepatitis B virus HBV
alternative label: hepatitis B virus, HBV
alternative label: human hepatitis B virus HBV
imported from: ncbitaxon.owl

Hepacivirus C
type: Class
subclass of: Viruses
alternative label: Hepatitis C virus
alternative label: hepatitis C virus HCV
alternative label: human hepatitis C virus
alternative label: human hepatitis C virus HCV
alternative label: human hepatitis virus C HCV
alternative label: post-transfusion hepatitis non A non B virus
imported from: ncbitaxon.owl

Lentivirus
type: Class
subclass of: Viruses
alternative label: Lentivirinae
imported from: ncbitaxon.owl

Human immunodeficiency virus 1
type: Class
subclass of: Lentivirus
alternative label: human immunodeficiency virus 1 HIV-1
alternative label: human immunodeficiency virus HIV-1
alternative label: human immunodeficiency virus type 1 HIV 1
alternative label: human immunodeficiency virus type 1 HIV1
alternative label: human immunodeficiency virus type 1, HIV-1
alternative label: human immunodeficiency virus type I HIV-1
alternative label: human immunodeficiency virus type-1 HIV-1
alternative label: human immunodeficiency virus-1 HIV-1
imported from: ncbitaxon.owl

Human immunodeficiency virus 2
type: Class
subclass of: Lentivirus
alternative label: HIV type 2
alternative label: Human immunodeficiency virus type 2
alternative label: Human immunodeficiency virus-2
alternative label: human immunodeficiency virus type 2 HIV-2
alternative label: human immunodeficiency virus type 2, HIV-2
imported from: ncbitaxon.owl

Euteleostomi
type: Class
subclass of: Vertebrata <vertebrates>
alternative label: bony vertebrates
imported from: ncbitaxon.owl

Bacteria
type: Class
subclass of: organism
alternative label: eubacteria
imported from: ncbitaxon.owl

Archaea
type: Class
subclass of: organism
imported from: ncbitaxon.owl

Eukaryota
type: Class
subclass of: organism
alternative label: eucaryotes
alternative label: eukaryotes
imported from: ncbitaxon.owl

Euarchontoglires
type: Class
subclass of: Mammalia
imported from: ncbitaxon.owl

Tetrapoda
type: Class
subclass of: Euteleostomi
alternative label: tetrapods
imported from: ncbitaxon.owl

Amniota
type: Class
subclass of: Tetrapoda
alternative label: amniotes
imported from: ncbitaxon.owl

Opisthokonta
type: Class
subclass of: Eukaryota
imported from: ncbitaxon.owl

Bilateria
type: Class
subclass of: Opisthokonta
imported from: ncbitaxon.owl

HIV-1 group O
type: Class
subclass of: Human immunodeficiency virus 1
imported from: ncbitaxon.owl

Mammalia
type: Class
subclass of: Amniota
alternative label: mammals
imported from: ncbitaxon.owl

Vertebrata <vertebrates>
type: Class
subclass of: Bilateria
alternative label: Vertebrata
alternative label: vertebrates
imported from: ncbitaxon.owl

Homo sapiens
type: Class
subclass of: Euarchontoglires
alternative label: human
imported from: ncbitaxon.owl

Birth Control Method
type: Class
subclass of: plan specification
definition: The method by which conception or impregnation is prevented. This may be achieved through the use of devices, drugs or surgery.
alternative label: BCMETHOD
alternative label: Birth Control Method
imported from: ncit.owl

Tubulocystic Renal Cell Carcinoma
type: Class
subclass of: DOID 4451
definition: A rare, cytologically high grade carcinoma that arises from the renal parenchyma. It is characterized by the presence of prominently dilated cystic spaces in a bland, fibrotic stroma. The lining cells have large irregular nuclei with prominent nucleoli and abundant eosinophilic cytoplasm. Necrosis and mitotic figures are not present. It rarely metastasizes.
alternative label: Tubulocystic Renal Cell Cancer
alternative label: Tubulocystic Renal Cell Carcinoma
alternative label: Tubulocystic renal cell carcinoma
imported from: ncit.owl

Central African
type: Class
subclass of: population
definition: Denotes a person whose ancestry is in any of the countries of the central part of the African continent: Burundi, the Central African Republic, Chad, the Democratic Republic of the Congo, and Rwanda.
alternative label: Central African
imported from: ncit.owl

North African
type: Class
subclass of: population
definition: Denotes a person whose ancestry is in any of the countries of the northern part of the African continent: Algeria, Egypt, Libya, Morocco, Sudan, Tunisia, and Western Sahara.
alternative label: North African
imported from: ncit.owl

South African
type: Class
subclass of: population
definition: Denotes a person whose ancestry is in the country of South Africa.
alternative label: South African
imported from: ncit.owl

Southeast Asian
type: Class
subclass of: population
definition: Denotes a person whose ancestry is in any of the Asian countries south of China, east of India, west of New Guinea and north of Australia.
alternative label: SOUTHEAST ASIAN
alternative label: Southeast Asian
imported from: ncit.owl

Central Asian
type: Class
subclass of: population
definition: Denotes a person whose ancestry is in any of the Asian countries between the Caspian Sea in the west, China in the east, Afghanistan in the south, and Russia in the north.
alternative label: CENTRAL ASIAN
alternative label: Central Asian
imported from: ncit.owl

Australian
type: Class
subclass of: population
definition: Denotes a person whose ancestry is in the country or continent of Australia.
alternative label: Australian
imported from: ncit.owl

New Zealander
type: Class
subclass of: population
definition: Denotes a person whose ancestry is in the country of New Zealand.
alternative label: New Zealander
imported from: ncit.owl

Scandinavian
type: Class
subclass of: population
definition: Denotes a person whose ancestry is in the countries of Scandinavia: Denmark, Norway and Sweden. Finland and Iceland are generally included as part of the Scandinavian region.
alternative label: Scandinavian
imported from: ncit.owl

Australian/New Zealand Ethnicity
type: Class
subclass of: ancestry category
definition: A collection of ethnic geographical categories including Australian and New Zealander.
alternative label: Australian/New Zealand
alternative label: Australian/New Zealand Ethnicity
imported from: ncit.owl

Prior Radiation Therapy
type: Class
subclass of: treatment
definition: An indicator that a person previously received radiation treatment for the same condition.
alternative label: Prior RT
alternative label: Prior Radiation
alternative label: Prior Radiation Therapy
alternative label: Prior Radiotherapy
alternative label: previously irradiated
alternative label: previously_irradiated
imported from: ncit.owl

Adjuvant Therapy
type: Class
subclass of: Cancer Therapeutic Procedure
definition: Any therapy that is administered to augment or stimulate other treatment modalities or to minimize or prevent disease recurrence subsequent to the main treatment plan.
alternative label: AJ-Adjuvant Therapy
alternative label: Adjuvant Therapy
alternative label: adjunct therapy
alternative label: adjunctive therapy
alternative label: adjuvant therapy
imported from: ncit.owl

Prior Immunotherapy
type: Class
subclass of: treatment
definition: Originally, therapeutic administration of serum or gamma globulin containing preformed antibodies produced by another individual; currently, immunotherapy includes nonspecific systemic stimulation, adjuvants, active specific immunotherapy, and adoptive immunotherapy. New forms of immunotherapy include the use of monoclonal antibodies. This approach has been widely adopted by cancer specialists, often in cases which fail to respond to other treatment. Immunotherapy aims to boost immune system function, as with the administration of interferons and interleukin-2, or to attack cancerous cells directly, as with the injection of monoclonal antibodies. Various immunotherapeutic techniques have also been employed among AIDS patients. In addition, a number of alternative medical practices are claimed to enhance immune function, and various over-the-counter substances (e.g., goldenseal, lysine have gained popularity for this supposed property.
alternative label: Prior Immunotherapy
imported from: ncit.owl

Prior Chemotherapy
type: Class
subclass of: treatment
definition: Previous chemotherapy administered as treatment for this cancer.
alternative label: Prior Chemotherapy
alternative label: Prior Chemotherapy Regimens
imported from: ncit.owl

Prior Hormone Therapy
type: Class
subclass of: treatment
definition: An indication that an individual has been previously treated with hormonal therapy.
alternative label: Prior Hormone Therapy
alternative label: prior hormonal therapy
imported from: ncit.owl

Cancer Therapeutic Procedure
type: Class
subclass of: treatment
definition: Any intervention for management of a malignant neoplasm.
alternative label: Cancer Therapeutic Procedure
alternative label: Cancer Therapy
alternative label: Cancer Treatment
alternative label: Malignant Neoplasm Therapy
alternative label: Malignant Neoplasm Treatment
alternative label: anticancer therapy
imported from: ncit.owl

Renal Cell Carcinoma Associated with Xp11.2 Translocations/TFE3 Gene Fusions
type: Class
subclass of: DOID 4451
definition: A group of renal cell carcinomas characterized by the presence of different translocations involving the chromosome Xp11.2. These translocations result in the creation of gene fusions involving the TFE3 gene. Patients are usually children and young adults. Morphologically, the malignant epithelial cells form papillary patterns.
alternative label: Renal Cell Cancer Associated with Xp11.2 Translocations/TFE3 Gene Fusions
alternative label: Renal Cell Carcinoma Associated with Xp11.2 Translocations/TFE3 Gene Fusions
alternative label: TFE3-Rearranged Renal Cell Carcinoma
alternative label: Xp11.2 Translocation-Related Renal Cell Carcinoma
alternative label: tRCC
imported from: ncit.owl

Tobacco Smoking History
type: Class
subclass of: information content entity
definition: 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.
alternative label: Smoking History
alternative label: Tobacco Smoking History
imported from: ncit.owl

Borderline Ovarian Mucinous Tumor, Intestinal Type
type: Class
subclass of: DOID 6067
definition: A neoplasm of low malignant potential arising from the ovary. It is characterized by the proliferation of neoplastic mucinous epithelial cells that resemble intestinal epithelial cells. There is no evidence of stromal invasion.
alternative label: Borderline Ovarian Mucinous Tumor, Intestinal Type
imported from: ncit.owl

Borderline Ovarian Mucinous Tumor, Endocervical-Like
type: Class
subclass of: DOID 6067
definition: A neoplasm of low malignant potential arising from the ovary. It is characterized by the proliferation of neoplastic epithelial cells that resemble endocervical epithelial cells. There is no evidence of stromal invasion.
alternative label: Borderline Ovarian Mucinous Tumor, Endocervical-Like
imported from: ncit.owl

Borderline Ovarian Clear Cell Tumor
type: Class
subclass of: DOID_0050934
definition: An epithelial neoplasm with low malignant potential affecting the ovary. It is characterized by the presence of clear or hobnail cells. In some cases, the cells may display nuclear atypia and prominent nucleoli. When such cells are present, they remain confined to the glands. There is no evidence of stromal invasion.
alternative label: Borderline Ovarian Clear Cell Neoplasm
alternative label: Borderline Ovarian Clear Cell Tumor
alternative label: Clear cell cystic tumor of borderline malignancy
imported from: ncit.owl

Borderline Ovarian Transitional Cell Tumor
type: Class
subclass of: DOID 4000
definition: An ovarian epithelial neoplasm that resembles the transitional cell neoplasms found in the urinary tract. It is characterized by the presence of atypia and absence of stromal invasion.
alternative label: Borderline Ovarian Transitional Cell Neoplasm
alternative label: Borderline Ovarian Transitional Cell Tumor
imported from: ncit.owl

South Asian
type: Class
subclass of: population
definition: Denotes a person whose ancestry is in the countries of the Indian sub-continent, including India, Pakistan, Bangladesh, and Sri Lanka.
alternative label: SOUTH ASIAN
alternative label: South Asian
alternative label: South Asians
imported from: ncit.owl

European
type: Class
subclass of: population
definition: Denotes the inhabitants of any of the countries of Europe, a person from there, or their descendants elsewhere.
alternative label: EUROPEAN
alternative label: European
imported from: ncit.owl

Ovarian Undifferentiated Carcinoma
type: Class
subclass of: DOID 2394
definition: An aggressive carcinoma arising from the ovary. Most patients present with advanced disease. Microscopically, it is characterized by significant cytologic atypia, increased mitotic activity, and necrosis. The prognosis is usually poor.
alternative label: Anaplastic Carcinoma of Ovary
alternative label: Anaplastic Carcinoma of the Ovary
alternative label: Anaplastic Ovarian Carcinoma
alternative label: Ovarian Undifferentiated Carcinoma
alternative label: Undifferentiated Carcinoma of Ovary
alternative label: Undifferentiated Carcinoma of the Ovary
alternative label: Undifferentiated Ovarian Cancer
alternative label: Undifferentiated Ovarian Carcinoma
imported from: ncit.owl

Lung Squamous Cell Carcinoma, Papillary Variant
type: Class
subclass of: DOID 3907
definition: A morphologic variant of squamous cell lung carcinoma characterized by the presence of papillary structures.
alternative label: Lung Squamous Cell Carcinoma, Papillary Variant
alternative label: Squamous Cell Lung Carcinoma, Papillary Variant
imported from: ncit.owl

Lung Squamous Cell Carcinoma, Clear Cell Variant
type: Class
subclass of: DOID 3907
definition: A morphologic variant of squamous cell lung carcinoma characterized by the presence of clear cells.
alternative label: Lung Squamous Cell Carcinoma, Clear Cell Variant
alternative label: Squamous Cell Lung Carcinoma, Clear Cell Variant
imported from: ncit.owl

Lung Squamous Cell Carcinoma, Small Cell Variant
type: Class
subclass of: DOID 3907
definition: A poorly differentiated morphologic variant of squamous cell lung carcinoma characterized by the presence of small tumor cells with focal squamous differentiation.
alternative label: Lung Squamous Cell Carcinoma, Small Cell Variant
alternative label: Squamous Cell Lung Carcinoma, Small Cell Variant
imported from: ncit.owl

Lung Colloid Adenocarcinoma
type: Class
subclass of: DOID 3910
definition: A morphologic variant of lung adenocarcinoma characterized by the presence of mucin pools containing islands of well differentiated adenocarcinoma cells.
alternative label: Lung Colloid Adenocarcinoma
alternative label: Lung Mucinous Cystadenocarcinoma
alternative label: Lung Mucinous Cystic Tumor of Borderline Malignancy
alternative label: Mucinous cystic tumor of borderline malignancy
imported from: ncit.owl

Lung Signet Ring Cell Carcinoma
type: Class
subclass of: DOID 3910
definition: A morphologic variant of lung adenocarcinoma characterized by the presence of signet ring cells.
alternative label: Lung Signet Ring Cell Carcinoma
alternative label: Lung Signet-Ring Cell Carcinoma
imported from: ncit.owl

Borderline Ovarian Serous Tumor
type: Class
subclass of: DOID_0050933
definition: A low grade serous epithelial neoplasm arising from the ovary. It is characterized by an atypical proliferation of serous-type epithelial cells without evidence of stromal invasion. It is often asymptomatic but rarely it may present with abdominal pain or abdominal enlargement due to rupture or torsion.
alternative label: Borderline Ovarian Serous Neoplasm
alternative label: Borderline Ovarian Serous Tumor
alternative label: Borderline Serous Neoplasm of Ovary
alternative label: Borderline Serous Neoplasm of the Ovary
alternative label: Borderline Serous Tumor of Ovary
alternative label: Borderline Serous Tumor of the Ovary
alternative label: Ovarian Serous Neoplasm of Low Malignant Potential
alternative label: Ovarian Serous Tumor of Low Malignant Potential
alternative label: Proliferating Ovarian Serous Neoplasm
alternative label: Proliferating Ovarian Serous Tumor
alternative label: Proliferating Serous Neoplasm of Ovary
alternative label: Proliferating Serous Neoplasm of the Ovary
alternative label: Proliferating Serous Tumor of Ovary
alternative label: Proliferating Serous Tumor of the Ovary
alternative label: Serous Neoplasm of Ovary with Low Malignant Potential
alternative label: Serous Neoplasm of the Ovary with Low Malignant Potential
alternative label: Serous Ovarian Neoplasm of Low Malignant Potential
alternative label: Serous Ovarian Tumor of Low Malignant Potential
alternative label: Serous Tumor of Ovary with Low Malignant Potential
alternative label: Serous Tumor of the Ovary with Low Malignant Potential
imported from: ncit.owl

Solid Lung Adenocarcinoma
type: Class
subclass of: DOID 3910
definition: A morphologic variant of lung adenocarcinoma characterized by the presence of polygonal malignant cells forming sheets. Acinar, papillary, micropapillary, or lepidic growth patterns are absent. If the tumor is 100 percent solid, intracellular mucin should be present in at least five tumor cells in each of two high-power fields and confirmed with mucin immunohistochemical stains. Tumors formerly classified as large cell carcinomas expressing pneumocyte immunohistochemical markers, even if intracellular mucin is absent, are now included in this category.
alternative label: Lung Solid Adenocarcinoma with Mucin
alternative label: Pulmonary Solid Adenocarcinoma with Mucin
alternative label: Solid Adenocarcinoma of Lung with Mucin
alternative label: Solid Adenocarcinoma of the Lung with Mucin
alternative label: Solid Lung Adenocarcinoma
alternative label: Solid adenocarcinoma
imported from: ncit.owl

Colon Undifferentiated Carcinoma
type: Class
subclass of: DOID 1520
definition: An invasive malignant epithelial tumor that arises from the colon. There is no morphologic, immunophenotypic, or molecular biological evidence of glandular or squamous differentiation.
alternative label: Carcinoma Simplex of the Colon.
alternative label: Colon Anaplastic Carcinoma
alternative label: Colon Undifferentiated Carcinoma
alternative label: Undifferentiated Carcinoma of Colon
alternative label: Undifferentiated Carcinoma of the Colon
alternative label: Undifferentiated Colon Cancer
alternative label: Undifferentiated Colonic Carcinoma
imported from: ncit.owl

Borderline Ovarian Seromucinous Tumor/Atypical Proliferative Ovarian Seromucinous Tumor
type: Class
subclass of: DOID 2152
definition: A low grade, non-invasive ovarian epithelial neoplasm characterized by the presence of atypical neoplastic serous and mucinous cells.
alternative label: Borderline Ovarian Seromucinous Tumor/Atypical Proliferative Ovarian Seromucinous Tumor
imported from: ncit.owl

Pack Year
type: Class
subclass of: measurement unit label
definition: A quantification of lifetime tobacco exposure defined as (number of cigarettes smoked per day x number of years smoked)/20. One pack-year is smoking 20 cigarettes a day for one year.
alternative label: Pack Year
alternative label: Pack Year: The number of cigarettes smoked per day times the number of years smoked divided by 20 (the number of cigarettes in a pack)
alternative label: Pack-Year
alternative label: pack year
alternative label: pack years smoked
alternative label: pack_years_smoked
alternative label: {Pack Year}
imported from: ncit.owl

Mediterranean
type: Class
subclass of: population
definition: Denotes a person having origins in any of the countries abutting the Mediterranean Sea, principally those of Europe.
alternative label: MEDITERRANEAN
alternative label: Mediterranean
imported from: ncit.owl

Western European
type: Class
subclass of: European
definition: Denotes a person having origins in any of the countries of Western Europe such as Spain, Portugal, or France.
alternative label: WESTERN EUROPEAN
alternative label: Western European
imported from: ncit.owl

Eastern European
type: Class
subclass of: European
definition: Denotes a person having origins in any of the countries of Eastern Europe such as Czechoslovakia, Poland, Croatia, Hungary, Slovenia, Former Soviet Union, or Finland. It also includes persons who call themselves Gypsies from this region.
alternative label: EASTERN EUROPEAN
alternative label: Eastern European
imported from: ncit.owl

Middle Eastern
type: Class
subclass of: population
definition: Denotes a person having origins in the region of southwest Asia, between the India subcontinent and Europe, including Kuwait, Turkey, Lebanon, Israel, Iraq, Iran, Jordan, Saudi Arabia, lands east of Pakistan or the other countries of the Arabian Peninsula. Also includes people of Jewish ethnicity including Sephardic and Ashkenazic.
alternative label: MIDDLE EASTERN
alternative label: Middle Eastern
imported from: ncit.owl

Borderline Ovarian Endometrioid Tumor/Atypical Proliferative Ovarian Endometrioid Tumor
type: Class
subclass of: DOID 5828
definition: An epithelial neoplasm that arises from the ovary characterized by the presence of glandular or cystic spaces which contain atypical glandular epithelial cells resembling endometrial cells. The surrounding ovarian stroma is often fibrotic. There is no evidence of stromal invasion.
alternative label: Borderline Endometrioid Neoplasm of Ovary
alternative label: Borderline Endometrioid Neoplasm of the Ovary
alternative label: Borderline Endometrioid Tumor of Ovary
alternative label: Borderline Endometrioid Tumor of the Ovary
alternative label: Borderline Ovarian Endometrioid Neoplasm
alternative label: Borderline Ovarian Endometrioid Tumor
alternative label: Borderline Ovarian Endometrioid Tumor/Atypical Proliferative Ovarian Endometrioid Tumor
alternative label: EBT/APET
alternative label: Endometrioid Neoplasm of Low Malignant Potential
alternative label: Endometrioid Neoplasm with Proliferating Activity, Ovarian
alternative label: Endometrioid Tumor of Low Malignant Potential
alternative label: Endometrioid Tumor with Proliferating Activity, Ovarian
alternative label: Endometrioid tumor of low malignant potential
alternative label: Low Malignant Potential Endometrioid Neoplasm of Ovary
alternative label: Low Malignant Potential Endometrioid Neoplasm of the Ovary
alternative label: Low Malignant Potential Endometrioid Tumor of Ovary
alternative label: Low Malignant Potential Endometrioid Tumor of the Ovary
alternative label: Low Malignant Potential Ovarian Endometrioid Neoplasm
alternative label: Low Malignant Potential Ovarian Endometrioid Tumor
alternative label: Ovarian Endometrioid Borderline Neoplasm
alternative label: Ovarian Endometrioid Borderline Tumor
alternative label: Ovarian Endometrioid Neoplasm of Low Malignant Potential
alternative label: Ovarian Endometrioid Neoplasm with Proliferating Activity
alternative label: Ovarian Endometrioid Tumor of Low Malignant Potential
alternative label: Ovarian Endometrioid Tumor with Proliferating Activity
alternative label: Proliferating Endometrioid Neoplasm of Ovary
alternative label: Proliferating Endometrioid Neoplasm of the Ovary
alternative label: Proliferating Endometrioid Tumor of Ovary
alternative label: Proliferating Endometrioid Tumor of the Ovary
alternative label: Proliferating Ovarian Endometrioid Neoplasm
alternative label: Proliferating Ovarian Endometrioid Tumor
imported from: ncit.owl

Alcohol Use History
type: Class
subclass of: information content entity
definition: A description of an individual's current and past experience with alcoholic beverage consumption.
alternative label: Alcohol History
alternative label: Alcohol Use
alternative label: Alcohol Use History
alternative label: alcohol history
alternative label: alcohol_history
imported from: ncit.owl

colectomy
type: Class
subclass of: surgical procedure
definition: A surgery that is a surgical procedure to remove all or part of your colon.
imported from: oae.owl

biobank description in english
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: biobank
definition: A textual entity providing information about a biobank and that is written in English.
term editor: Mathias Brochhausen
alternative label: biobank description

sample collection identifier
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: designates
    some values from: Class
      intersection of: object aggregate
      intersection of: Restriction
        on property: has part
        all values from: specimen
subclass of: identifier
definition: A proper name that refers to a sample collection.
term editor: Mathias Brochhausen

freezer shelf
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: solid support function
definition: A device that is part of a freezer and consists of a solid horizontal surface to keep material in the freezer on a flat surface.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

discarding
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: located in
      some values from: trash container
definition: A planned process that gets rid of a material that is no longer useful or desirable.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

human subject recuiter role
type: Class
subclass of: worker role
definition: A worker role of recruiting human subjects to partcipate in a clinical investigation in which data about human subject is collected.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

cryovial box
type: Class
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: contain function
definition: A device that is intended to hold cryovials.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

trash container
type: Class
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: contain function
definition: A container that is used for discarded material.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

freezer rack
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: solid support function
definition: A device that is part of a freezer for keeping material in the freezer in a defined position and prevents movement.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

blood spot card box
type: Class
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: contain function
definition: A device that is designed to contain blood spot cards.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

data confirm questionnaire
type: Class
subclass of: questionnaire
definition: A questionnaire that comprises a set of questions about patient, such as height, weight, race, biological sex, clinical history, etc., which will be filled by a recruiter based on an Electronic Medical Record (EMR).
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

form filling
type: Class
subclass of: document editing
definition: A document editing process in which one or more fields in a form are filled with related information, such as when answering a questionnare.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

filled patient questionnaire
type: Class
subclass of: patient questionnaire
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: form filling
    intersection of: Restriction
      on property: has_specified_input
      some values from: patient questionnaire
    intersection of: Restriction
      on property: has participant
      some values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
definition: A patient questionnaire which has been filled out by a patient.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

patient questionnaire
type: Class
subclass of: questionnaire
definition: A questionnaire that comprises a set of demographic and medical questions about a patient which will be filled by the patient or their legally authorized representative.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

collection packet with specimen and information material
type: Class
subclass of: collection packet with specimen
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has characteristic
      some values from: Restriction
        on property: concretizes
        some values from: Class
definition: A collection packet which contains a container with a specimen and a form filled with information about the collected specimen and specimen source.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

blood additive role
type: Class
subclass of: material to be added role
definition: A material to be added role that is born by a chemical entity which is added into a blood collection containter to optimize specific blood component(s) preservation and/or separation.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

lab technician role
type: Class
subclass of: worker role
definition: A worker role that performs the practical hands-on work in laboratories and is realized during study design execution.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

collection packet with specimen
type: Class
subclass of: collection packet
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: specimen
    intersection of: Restriction
      on property: located in
      some values from: container
definition: A collection packet which contains a container with a specimen.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

collection packet with empty container
type: Class
subclass of: collection packet
subclass of: Restriction
  on property: lacks_part
  some values from: material information bearer
subclass of: Restriction
  on property: lacks_part
  some values from: specimen
definition: A collection packet which contains an empty container that will be used for holding a specimen.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

obsolete medication role
type: Class
subclass of: Obsolete Class
definition: A role borne by some material entity which can be delivered/administrated into some organism and the role is realized during a clinical treatment process aiming to treat symptoms, signs or diagnosed disease.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: Penn Group
has obsolescence reason: term imported
term tracker item: https://github.com/biobanking/biobanking/issues/79
term replaced by: medication role
deprecated: true

filled data confirm questionnaire
type: Class
subclass of: data confirm questionnaire
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: form filling
    intersection of: Restriction
      on property: has_specified_input
      some values from: data confirm questionnaire
    intersection of: Restriction
      on property: has participant
      some values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
definition: A data confirm questionnaire which has been filled out by a human subject recruiter.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

collection packet
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: container
definition: A material entity used for specimen collection. It can contain a container to hold a specimen and material (e.g. paper) carrying information about the specimen and the specimen source (e.g. patient).
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

medication material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: medication role
subclass of: material entity
definition: A material entity that is bearer of a medication role.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: Penn Group

blood spot card
type: Class
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: contain function
subclass of: Restriction
  on property: has function
  some values from: solid support function
definition: A device that is designed to collect, ship and store blood specimens in an easy and inexpensive way.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

cryovial
type: Class
subclass of: container
definition: A test tube that designed to store materials at very low temperatures.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

vacutainer
type: Class
subclass of: container
definition: A test tube which is either a sterile glass or plastic tube with a closure that is evacuated to create a vacuum inside the tube facilitating the draw of a predetermined volume of liquid. Most commonly used to draw a blood sample directly from the vein, these also are used to collect urine samples. Vacutainer tube may contain additives designed to stabilize and preserve the specimen prior to analytical testing.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Vacutainer

specimen receiving
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: collection packet
    intersection of: Restriction
      on property: located in
      some values from: Laboratory
definition: A planned process for receiving specimens such as into a laboratory.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

adding specimen into a container
type: Class
subclass of: adding a material entity into a target
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: specimen
    intersection of: Restriction
      on property: has role
      some values from: material to be added role
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: container
        intersection of: Restriction
definition: 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)
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

blood spotting
type: Class
subclass of: adding specimen into a container
subclass of: Restriction
  on property: has_specified_input
  some values from: blood specimen
subclass of: Restriction
  on property: has participant
  some values from: blood spot card
definition: An adding specimen into a container process that spots the blood from an organism on the blood spot card.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

buffy coat specimen
type: Class
subclass of: processed specimen
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: centrifugation
    intersection of: Restriction
      on property: has_specified_input
      some values from: blood specimen
definition: 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.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Buffy_coat

blood specimen on blood spot card
type: Class
subclass of: blood specimen
subclass of: processed specimen
subclass of: Restriction
  on property: is_specified_output_of
  some values from: blood spotting
subclass of: Restriction
  on property: located in
  some values from: blood spot card
definition: A blood specimen that is located on a blood spot card.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group
comment: A specimen that located in a blood spot card via blood spotting process.

collection packet with empty container and unfilled information material
type: Class
subclass of: collection packet
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has characteristic
      some values from: Restriction
        on property: concretizes
        some values from: information content entity
subclass of: Restriction
  on property: lacks_part
  some values from: specimen
definition: A collection packet which contains a container without a specimen and an unfilled form that will be used to fill in information about specimen to be collected.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

duration time of smoking regularly
type: Class
subclass of: duration time of smoking
definition: 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)
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

average daily use of cigarette datum
type: Class
subclass of: average value
subclass of: Restriction
  on property: is_specified_output_of
  some values from: averaging data transformation
definition: An average value of use of cigarettes per day.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

nicotine patch
type: Class
subclass of: nicotine material
subclass of: Restriction
  on property: has part
  some values from: nicotine
definition: A processed material that contains nicotine in the form of a transdermal patch which releases nicotine into the body through the skin. It is commonly used as an aid in nicotine replacement therapy (NRT), a process for smoking cessation.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Nicotine_patch

cigarette
type: Class
subclass of: nicotine material
subclass of: tobacco material
subclass of: Restriction
  on property: has part
  some values from: nicotine
subclass of: Restriction
  on property: derives from
  some values from: tobacco
definition: A processed material which is a small cylinder of finely cut tobacco leaves rolled in thin paper for smoking.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Cigarette

nicotine gum or lozenge
type: Class
subclass of: nicotine material
subclass of: Restriction
  on property: has part
  some values from: nicotine
definition: A processed material contains nicotine in a form of a chewing gum or a candy-like tablet. It delivers nicotine to the body via absorption by the tissues of the mouth. It is commonly used as an aid in nicotine replacement therapy (NRT), a process for smoking cessation.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Nicotine_gum

cigar
type: Class
subclass of: nicotine material
subclass of: tobacco material
subclass of: Restriction
  on property: has part
  some values from: nicotine
subclass of: Restriction
  on property: derives from
  some values from: tobacco
definition: A processed material which is a tightly-rolled bundle of dried and fermented tobacco that is ignited so that its smoke may be drawn into the mouth.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Cigar

chewing tobacco
type: Class
subclass of: tobacco material
subclass of: Restriction
  on property: derives from
  some values from: tobacco
definition: A processed material which is a kind of smokeless tobacco product consumed by placing a portion of the tobacco between the cheek and gum or upper lip teeth and chewing.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Chewing_tobacco

nicotine material
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: Restriction
    on property: has part
    some values from: nicotine
subclass of: processed material
definition: A processed material that contains nicotine.
term editor: Person: Jie Zheng, Chris Stoeckert
alternative label: nicotine product
definition source: Penn Group

smoking pipe
type: Class
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: contain function
definition: A device made to allow the user to inhale or taste smoke or vapor derived from the burning or vaporization of some substance.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Smoking_pipe

nicotine e-cigarette
type: Class
subclass of: nicotine material
subclass of: Restriction
  on property: has part
  some values from: nicotine
definition: A processed material that vaporizes a liquid solution containing nicotine and simulates tobacco smoking by producing an aerosol that resembles smoke.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Electronic_cigarette

smoking start date
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is about
  some values from: smoking behavior
definition: A time measurement datum which is the start date of a smoking behavior.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

pipe smoking behavior
type: Class
subclass of: smoking behavior
subclass of: Restriction
  on property: has_specified_input
  some values from: pipe tobacco
subclass of: Restriction
  on property: has participant
  some values from: smoking pipe
definition: A smoking behavior that uses a smoking pipe to inhale or taste tobacco material.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

duration time of smoking
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is duration of
  some values from: smoking behavior
definition: A time measurement datum about how long a person has been smoking.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

smoking end date
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is about
  some values from: smoking behavior
definition: A time measurement datum which is the end date of a smoking behavior.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

pipe tobacco
type: Class
subclass of: tobacco material
subclass of: Restriction
  on property: derives from
  some values from: tobacco
definition: A processed material which is made from tobacco for smoking tobacco using a pipe.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

tobacco
type: Class
subclass of: Eukaryota
definition: A Eukaryota that is within the genus Nicotiana of the Solanaceae (nightshade) family.
term editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

tobacco material
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: Restriction
    on property: derives from
    some values from: tobacco
subclass of: processed material
definition: A processed material that is made from tobacco. Typically, tobacco material is meant to be used as a source of nicotine as tobacco contains a higher concentration of nicotine than most other plants.
term editor: Person: Jie Zheng, Chris Stoeckert
alternative label: tobacco product
definition source: Penn Group

Location below resection
type: Class
subclass of: Anatomical location
definition: An anatomical location that is just below (1 cm) the site of surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

Location adjacent to tissue fixation
type: Class
subclass of: Anatomical location
example of usage: adjacent to tissue for PAXgene fixation.
definition: An anatomical location that is adjacent to the site where tissue was collected and subjected to fixation.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

time in fixative measurement
type: Class
subclass of: time measurement datum
definition: A time measurement datum that states the duration during which a specimen was submerged in fixative.
editor note: more general than time in formalin
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

postmortem collecting specimen from organism
type: Class
subclass of: collecting specimen from organism
definition: A collection from organism that occurs after the organism is dead.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

collecting specimen from organism during organ donation
type: Class
subclass of: collecting specimen from organism
definition: A collecting specimen from organism that occurs during the process of organ donation.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

internal body temperature measurement assay
type: Class
subclass of: temperature measurement assay
definition: A temperature measurement assay to obtain the body temperature of an organism through placement of a thermometer in an internal cavity or organ.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: core body temperature
definition source: OBIB
ontology term requester: NCI BBRB

rectal temperature measurement assay
type: Class
subclass of: internal body temperature measurement assay
definition: An internal body temperature measurement assay where the thermometer is placed in the rectum.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

organ temperature measurement assay
type: Class
subclass of: internal body temperature measurement assay
definition: An internal body temperature measurement assay where the thermometer is placed in an organ.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

anesthesia probe temperature measurement assay
type: Class
subclass of: internal body temperature measurement assay
definition: An internal body temperature measurement assay where the temperature probe interfaces with the anesthesia vent monitor. Typically the thermometer is a rectal probe with a wire and connector that hooks up to the ekg/pulse ox/co2 monitor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

collection packet identifier
type: Class
subclass of: identifier
definition: An identifier that refers to a collection packet used in a specimen collection process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Kit ID
definition source: OBIB
ontology term requester: NCI BBRB

prosector role
type: Class
subclass of: role
definition: A role which inheres in a person and is realized in the dissection of a body for anatomical instruction or pathological examination.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: http://medical-dictionary.thefreedictionary.com/prosector
ontology term requester: NCI BBRB

standard operating procedure
type: Class
subclass of: protocol
definition: A protocol that is a set of step-by-step instructions compiled by an organization for carrying out routine operations.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: SOP
definition source: https://en.wikipedia.org/wiki/Standard_operating_procedure
ontology term requester: NCI BBRB

specimen transport SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for the transportation of specimens.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

tissue procurement SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for collecting specimens from organism.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

case report form completion SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for properly and completely filling out a case report form.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: CRF completion protocol
definition source: OBIB
ontology term requester: NCI BBRB

SOP memorandum
type: Class
subclass of: textual entity
definition: A textual entity that is a short communication to provide advisory or informative matter about a standard operating procedure.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://www.merriam-webster.com/dictionary/memorandum
ontology term requester: NCI BBRB

SOP adjustment
type: Class
subclass of: protocol
definition: A protocol that provides deviations or changes to part of an existing standard operating procedure.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

first blood draw date
type: Class
subclass of: date of specimen collection
definition: A date of specimen collection for the first collection of blood from a donor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

first tissue removed date
type: Class
subclass of: date of specimen collection
definition: A date of specimen collection for the first collection of a tissue from a donor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

date of form data verification
type: Class
subclass of: data item
definition: A data item that reports the calendar date when the data collected on a form was verified.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

blood draw time
type: Class
subclass of: data item
definition: A data item that reports the time of day when a blood specimen was collected.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

first blood draw time
type: Class
subclass of: blood draw time
definition: A blood draw time for the first collection of a blood specimen from a donor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

first tissue removed time
type: Class
subclass of: time of surgical removal of specimen
definition: A time of surgical removal of specimen for the first removal of tissue from a donor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

time of surgical ligature for specimen collection
type: Class
subclass of: data item
definition: A data item that reports the time of day when a clamp or ligature was applied to an organ for specimen collection.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

form data verification process
type: Class
subclass of: planned process
definition: A planned process to assess the correctness of data entered on a form.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

surgical ligature process
type: Class
subclass of: planned process
definition: A planned process to stop blood flow for an organ during a surgical procedure using a clamp or ligature.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

organization conducting specimen collection from organism
type: Class
subclass of: organization
definition: An organization at which the process of collecting a specimen from an organism occurred.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: biospecimen source site
alternative label: tissue source site
definition source: OBIB
ontology term requester: NCI BBRB

specimen collected with specific collection packet
type: Class
subclass of: specimen from organism
example of usage: specimen collected with GTEx Pink Kit
definition: 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.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: specimen collected with specific kit
definition source: OBIB
ontology term requester: NCI BBRB

autolysis value specification
type: Class
subclass of: categorical value specification
definition: A categorical value specification that is used to record the destruction of an organism cells or tissues by the organisms' own enzymes or processes with nominal categories ranging from none to severe.
editor note: Add instances 0-non, 1-slight, 2-moderate, 3-severe
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

followup required for specimen collection issue
type: Class
subclass of: data item
example of usage: follow up needed for Pathology Resource Center identified issue for Postmortem/Organ Procurement Tissue Collection
definition: A data item that is an indicator of whether further followup on a specimen collection issue is required.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

resolved specimen collection issue
type: Class
subclass of: data item
example of usage: resolution of Pathology Resource Center identified issue for Postmortem/Organ Procurement Tissue Collection
definition: A data item that is an indicator of whether a specimen collection issue is resolved.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

reason for not collecting frozen specimens
type: Class
subclass of: comment from tissue procurement
definition: A comment from tissue procurement that is an explanation as to why frozen specimens were not collected.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on resolved specimen collection issue
type: Class
subclass of: comment from tissue procurement
definition: A comment from tissue procurement made in regards to the resolution of an issue with the tissue.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen donor body refrigerated indicator
type: Class
subclass of: data item
definition: A data item indicating whether the body of the specimen donor was refrigerated after death but prior to specimen collection.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

time donor body refrigerated measurement
type: Class
subclass of: time measurement datum
definition: A time measurement datum that states the duration during which the specimen donor's body was refrigerated.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

cessation of brain activity death
type: Class
subclass of: life-death temporal boundary
definition: A life-death temporal boundary marked by the irreversible end of all brain activity (including involuntary activity necessary to sustain life).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: brain death
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

cessation of cardiac activity death
type: Class
subclass of: life-death temporal boundary
definition: A life-death temporal boundary marked by the natural cessation of cardiac activity.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: cardiac death
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

positive serological assay result
type: Class
subclass of: data item
definition: A data item that indicates the amount of a serum analyte is at a level above a threshold considered to be present.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

negative serological assay result
type: Class
subclass of: data item
definition: A data item that indicates the amount of a serum analyte is at a level below a threshold considered to be present.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

indeterminate serological assay result
type: Class
subclass of: data item
definition: A data item that indicates the amount of a serum analyte is approximately at a threshold considered to be present and therefore can not be confidently scored as positive or negative.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

non-performance of an assay
type: Class
subclass of: information content entity
definition: An information content entity that is about the status of an assay and indicates that the assay has not been started or completed.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

date of surgical removal of specimen
type: Class
subclass of: date of specimen collection
definition: A date of specimen collection on which the surgery was performed during which the specimen was collected.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

preoperative intravenous administration of sedative
type: Class
subclass of: planned process
definition: A planned process to administer sedation drugs intravenously prior to surgery in order to induce total or partial loss of sensation especially tactile sensation and pain.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

preoperative intravenous administration of opioid analgesic
type: Class
subclass of: planned process
definition: A planned process to administer opioid analgesics intravenously prior to surgery in order to induce total or partial loss of sensation especially tactile sensation and pain.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

preoperative intravenous administration of antiemetic
type: Class
subclass of: planned process
definition: A planned process to administer antiemetic agents intravenously prior to surgery to prevent nausea or vomiting.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

preoperative intravenous administration of antacid
type: Class
subclass of: planned process
definition: A planned process to administer antacid intravenously prior to surgery in order to relieve and reduce the symptoms of ulcers in the stomach and upper small intestine.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

preoperative intravenous administration of medication
type: Class
subclass of: planned process
definition: A planned process to administer medication intravenously prior to surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

administration of local anaesthetic
type: Class
subclass of: planned process
example of usage: administered prior to organ removal
definition: A planned process to administer anaesthetic to a restricted or localized area in order to produce a loss of feeling.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

administration of regional anaesthetic
type: Class
subclass of: planned process
example of usage: epidural administration prior to organ removal
definition: A planned process to administer anaesthetic to a restricted area or part of the body in order to produce a loss of feeling.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

administration of intravenous anaesthetic
type: Class
subclass of: planned process
example of usage: administered prior to organ removal
definition: A planned process to administer anaesthetic within or into a vein or veins in order to produce a loss of feeling.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

intravenous administration of opioid analgesic
type: Class
subclass of: planned process
example of usage: administered prior to organ removal
definition: A planned process to administer opioid analgesics intravenously in order to induce total or partial loss of sensation especially tactile sensation and pain.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

intravenous administration of muscle relaxant
type: Class
subclass of: planned process
example of usage: administered prior to organ removal
definition: A planned process to administer muscle relaxant intravenously in order to relax skeletal muscles and reduce muscle contraction.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

administration of inhalation anaesthetic
type: Class
subclass of: planned process
example of usage: administered prior to organ removal
definition: A planned process to administer anaesthetic in the form of a gas aerosol or fine powder via the respiratory tract usually by oral or nasal inhalation for local or systemic effect.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

administration of anaesthetic
type: Class
subclass of: planned process
definition: A planned process to administer anaesthetic in order to produce a loss of feeling.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

administration of insulin during surgery
type: Class
subclass of: planned process
definition: A planned process to administer insulin during a surgical procedure.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

administration of steroid during surgery
type: Class
subclass of: planned process
definition: A planned process to administer steroid during a surgical procedure.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

administration of antimicrobial agent during surgery
type: Class
subclass of: planned process
definition: A planned process to administer antimicrobial agent(s) during a surgical procedure.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

administration of medication during surgery
type: Class
subclass of: planned process
definition: A planned process to administer medication(s) during a surgical procedure.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

time of first surgical incision
type: Class
subclass of: data item
definition: A data item that reports the time of day at which the first incision is made during surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

abdominoperineal resection
type: Class
subclass of: surgical procedure
definition: A surgical procedure in which the anus, rectum, and sigmoid colon are removed.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://my.clevelandclinic.org/health/articles/laparoscopic-abdominoperineal-resection-basic-surgical-steps
ontology term requester: NCI BBRB

left hemicolectomy
type: Class
subclass of: colectomy
definition: A colectomy that is the surgical removal of the left side of the large intestine.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: left colectomy
definition source: http://emedicine.medscape.com/article/1965606-overview
ontology term requester: NCI BBRB

sigmoid colectomy
type: Class
subclass of: colectomy
definition: A colectomy that is the surgical removal of the sigmoid colon.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: http://emedicine.medscape.com/article/1965606-overview
ontology term requester: NCI BBRB

right hemicolectomy
type: Class
subclass of: colectomy
definition: A colectomy that involves removing the cecum, the ascending colon, the hepatic flexure (where the ascending colon joins the transverse colon), the first one-third of the transverse colon, and part of the terminal ileum, along with fat and lymph nodes.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: right colectomy
definition source: http://emedicine.medscape.com/article/1535001-overview
ontology term requester: NCI BBRB

subtotal colectomy
type: Class
subclass of: colectomy
definition: A colectomy that is complete resection of the colon
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://en.wikipedia.org/wiki/Colectomy
ontology term requester: NCI BBRB

total colectomy
type: Class
subclass of: colectomy
definition: A colectomy that is resection of part of the colon or a resection of all of the colon without complete resection of the colon
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://en.wikipedia.org/wiki/Colectomy
ontology term requester: NCI BBRB

transverse colectomy
type: Class
subclass of: colectomy
definition: A colectomy that is resection of the transverse colon along with the middle colic vessels and its mesentery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: http://ether.stanford.edu/abdominal_surgery_rotation/documents/Colon%20surgeries%20vm%20071512.pdf
ontology term requester: NCI BBRB

low anterior resection
type: Class
subclass of: surgical procedure
definition: A surgical procedure that is done to treat cancer of the rectum in which the part of the rectum containing the cancer is removed. The remaining part of the rectum is reconnected to the colon.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: LAR
definition source: https://www.mskcc.org/cancer-care/patient-education/about-your-low-anterior-resection-surgery
ontology term requester: NCI BBRB

proctectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove all or part of the rectum. It is often needed to treat rectal cancer.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: http://www.hopkinsmedicine.org/healthlibrary/test_procedures/gastroenterology/proctectomy_135,53/
ontology term requester: NCI BBRB

proctocolectomy
type: Class
subclass of: colectomy
definition: A colectomy that is the surgical removal of the rectum and all or part of the colon.[
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://en.wikipedia.org/wiki/Proctocolectomy
ontology term requester: NCI BBRB

rectosigmoidectomy
type: Class
subclass of: colectomy
definition: A colectomy that is the surgical removal of the rectum and sigmoid colon.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: http://medical-dictionary.thefreedictionary.com/rectosigmoidectomy
ontology term requester: NCI BBRB

time of first clamp for specimen removal
type: Class
subclass of: data item
definition: A data item that reports the time of day when the first clamp was applied to the vasculature of an organ for specimen collection.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

time of second clamp for specimen removal
type: Class
subclass of: data item
definition: A data item that reports the time of day when the second clamp was applied to the vasculature of an organ for specimen collection.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

in vivo intraoperative ischemic period
type: Class
subclass of: time measurement datum
definition: A time measurement datum of the period between organ resection and the time of first clamping perfomed in vivo.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

vital sign blood pressure variance early in organ excision
type: Class
subclass of: data item
definition: A data item on the duration of blood pressure variances of greater than 20 mmHg from a patient's pre-operative baseline from the time of anesthesia induction to 15 minutes post.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: BP excursions from time of anesthesia induction to 15 minutes post
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

vital sign blood pressure variance late in organ excision
type: Class
subclass of: data item
definition: A data item on the duration of blood pressure variances of greater than 20 mmHg from a patient's pre-operative baseline from 15 minutes post anesthesia induction to the organ excision.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: BP excursions from 15 minutes post anesthesia induction to organ excision
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

first temperature recorded in operating room of specimen donor
type: Class
subclass of: time stamped measurement datum
definition: A time stamped measurement datum that is the first temperature recorded in the operating room of the specimen donor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

second temperature recorded in operating room of specimen donor
type: Class
subclass of: time stamped measurement datum
definition: A time stamped measurement datum that is the second temperature recorded in the operating room of the specimen donor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

oxygen desaturation epochs prior to organ excision description
type: Class
subclass of: comment from tissue procurement
definition: A comment from tissue procurement of the epochs of oxygen desaturation of less than 92% for more than 5 minutes prior to organ excision.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

carbon dioxide level of specimen donor recorded at time closest to organ excision
type: Class
subclass of: measurement datum
definition: A measurement datum of the level of carbon dioxide gas at time closest to organ exiscion from the specimen donor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

albumin volume administered intraoperatively
type: Class
subclass of: measurement datum
definition: A measurement datum of the volume of albumin administered during surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

amount of packed red blood cells administered intraoperatively
type: Class
subclass of: count
definition: A count of the number of units of packed red blood cells administered during surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

platelet volume administered intraoperatively
type: Class
subclass of: measurement datum
definition: A measurement datum of the volume of platelets administered during surgery measured.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

amount of fresh frozen plasma administered intraoperatively
type: Class
subclass of: count
definition: A count of the number of units of fresh frozen plasma administered during surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen donor intraoperative blood loss volume measurement datum
type: Class
subclass of: measurement datum
definition: A measurement datum of the volume of intraoperative blood loss from the specimen donor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: intraoperative blood loss of specimen donor
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen donor intraoperative blood loss prior to organ excision volume measurement datum
type: Class
subclass of: specimen donor intraoperative blood loss volume measurement datum
definition: A specimen donor intraoperative blood loss volume measurement datum obtained prior to organ excision.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: intraoperative blood loss of specimen donor prior to organ excision
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen donor intraoperative blood loss at end of surgery volume measurement datum
type: Class
subclass of: specimen donor intraoperative blood loss volume measurement datum
definition: A specimen donor intraoperative blood loss volume measurement datum obtained at the end of surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: intraoperative blood loss of specimen donor at end of surgery
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen donor intraoperative urine excreted volume measurement datum
type: Class
subclass of: measurement datum
definition: A measurement datum of the volume of intraoperative urine excreted obtained from the specimen donor during surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: intraoperative urine volume excreted
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen donor intraoperative urine excreted prior to organ excision volume measurement datum
type: Class
subclass of: specimen donor intraoperative urine excreted volume measurement datum
definition: A specimen donor intraoperative urine excreted volume measurement datum obtained during prior to organ excision.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: intraoperative urine volume excreted of specimen donor prior to organ excision
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen donor intraoperative urine excreted at end of surgery volume measurement datum
type: Class
subclass of: specimen donor intraoperative urine excreted volume measurement datum
definition: A specimen donor intraoperative urine excreted volume measurement datum obtained at the end of surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: intraoperative urine volume excreted of specimen donor at end of surgery
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

indicator of ascites fluid collection during surgery
type: Class
subclass of: information content entity
definition: An information content entity that is an indication of whether ascites fluid was collected from the specimen donor during organ excision.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

ascites fluid from specimen donor during surgery volume measurement datum
type: Class
subclass of: measurement datum
definition: A measurement datum of the volume of ascites fluid collected from the specimen donor during surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

Duration of fasting by specimen donor prior to surgery
type: Class
subclass of: time measurement datum
definition: A time measurement datum of the duration of fasting by the specimen donor prior to surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on donor pre-operative bowel preparation prior to surgery
type: Class
subclass of: comment from tissue procurement
definition: A comment from tissue procurement of the pre-operative bowel preparation performed prior to surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on notable events during donor surgery
type: Class
subclass of: comment from tissue procurement
definition: A comment from tissue procurement of notable events that occurred during surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

time specimen left operating room
type: Class
subclass of: data item
definition: A data item indicating the time at which the surgical specimen left the operating for delivery to the pathology gross room.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

hysterectomy with bilateral salpingo-oophorectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure with the removal of the uterus, cervix, fallopian tubes, and ovaries. This is the most common surgery done for endometrial cancer.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: http://www.webmd.com/cancer/cervical-cancer/hysterectomy-for-endometrial-cancer
ontology term requester: NCI BBRB

hysterectomy with left salpingo-oophorectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure with the removal of the uterus, cervix, left fallopian tube, and left ovary.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

hysterectomy with right salpingo-oophorectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure with the removal of the uterus, cervix, right fallopian tube, and right ovary.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

bilateral oophorectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure with the removal of both ovaries.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: http://www.mayoclinic.org/tests-procedures/oophorectomy/home/ovc-20314905
ontology term requester: NCI BBRB

left oophorectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure with the removal of the left ovary.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

right oophorectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure with the removal of the right ovary.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

pelvic exenteration
type: Class
subclass of: surgical procedure
definition: A surgical procedure that removes all organs from a person's pelvic cavity including the urinary bladder, urethra, rectum, and anus.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://en.wikipedia.org/wiki/Pelvic_exenteration
ontology term requester: NCI BBRB

pelvic mass excision
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove a mass (growth or tumor) on the ovary or in the pelvis.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://innovativegyn.com/conditions/ovarian-cyst-and-pelvic-mass/
ontology term requester: NCI BBRB

bilateral salpingo-oophorectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove both ovaries and both fallopian tubes.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://www.cancer.gov/publications/dictionaries/cancer-terms
ontology term requester: NCI BBRB

left salpingo-oophorectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove the left ovary and left fallopian tube.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

right salpingo-oophorectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove the right ovary and right fallopian tube.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

surgical method
type: Class
subclass of: protocol
definition: A protocol providing the action or system by which the surgical procedure is to be performed.
term editor: Person: Chris Stoeckert, Jie Zheng
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

abdominal surgical method
type: Class
subclass of: surgical method
definition: A surgical method in which operations are performed through the abdomen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
ontology term requester: NCI BBRB

vaginal surgical method
type: Class
subclass of: surgical method
definition: A surgical method in which operations are performed through the vagina.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
ontology term requester: NCI BBRB

laparoscopic surgical method
type: Class
subclass of: surgical method
definition: A surgical method in which operations are performed far from their location through small incisions (usually 0.5���1.5��cm) elsewhere in the body.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://en.wikipedia.org/wiki/Laparoscopic_surgery
ontology term requester: NCI BBRB

laparoscopically assisted vaginal surgical method
type: Class
subclass of: surgical method
example of usage: Laparoscopically Assisted Vaginal Hysterectomy (LAVH)
definition: A surgical method in which operations are performed through the vagina aided by laparoscopic tools and techniques.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
ontology term requester: NCI BBRB

supracervical hysterectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure in which the body of the uterus is removed but the cervix is kept intact, as compared to the more common total hysterectomy, in which the uterus, cervix and fundus (the part of the uterus above the fallopian tube openings) are removed.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://www.floridahospital.com/supracervical-hysterectomy
ontology term requester: NCI BBRB

robotic surgical method
type: Class
subclass of: surgical method
definition: A surgical method using very small tools attached to a robotic arm. The surgeon controls the robotic arm with a computer.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://medlineplus.gov/ency/article/007339.htm
ontology term requester: NCI BBRB

indicator of pelvic washings collected during ovarian surgery
type: Class
subclass of: information content entity
definition: An information content entity that is an indication of whether pelvic washings were collected during ovarian surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

left kidney biopsy
type: Class
subclass of: biopsy
definition: A biopsy of the left kidney.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Kidney biopsy (left)
definition source: OBIB
ontology term requester: NCI BBRB

right kidney biopsy
type: Class
subclass of: biopsy
definition: A biopsy of the right kidney.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Kidney biopsy (right)
definition source: OBIB
ontology term requester: NCI BBRB

left kidney mass excision
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove a mass (growth or tumor) in the left kidney.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Kidney mass excision (left)
definition source: OBIB
ontology term requester: NCI BBRB

left partial nephrectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove part of the left kidney.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Nephrectomy (partial left)
definition source: OBIB
ontology term requester: NCI BBRB

left radical nephrectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove the entire left kidney.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Nephrectomy (radical left)
definition source: OBIB
ontology term requester: NCI BBRB

left nephroureterectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure that is minimally invasive to remove a patient's left renal pelvis, kidney, ureter, and bladder cuff.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Nephroureterectomy (left)
definition source: https://my.clevelandclinic.org/health/articles/nephroureterectomy
ontology term requester: NCI BBRB

right kidney mass excision
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove a mass (growth or tumor) in the right kidney.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Kidney mass excision (right)
definition source: OBIB
ontology term requester: NCI BBRB

right partial nephrectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove part of the right kidney.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Nephrectomy (partial right)
definition source: OBIB
ontology term requester: NCI BBRB

right radical nephrectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove the entire right kidney.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Nephrectomy (radical right)
definition source: OBIB
ontology term requester: NCI BBRB

right nephroureterectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure that is minimally invasive to remove a patient's right renal pelvis, kidney, ureter, and bladder cuff.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Nephroureterectomy (right)
definition source: https://my.clevelandclinic.org/health/articles/nephroureterectomy
ontology term requester: NCI BBRB

open surgical method
type: Class
subclass of: surgical method
definition: A surgical method in which an incision is made using a scalpel. Open surgery is the traditional type of surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: open surgery
definition source: https://www.verywell.com/open-surgery-3157124
ontology term requester: NCI BBRB

left lung biopsy
type: Class
subclass of: biopsy
definition: A biopsy of the left lung.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

right lung biopsy
type: Class
subclass of: biopsy
definition: A biopsy of the right lung.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

left lung lobectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove one of the lobes of the left lung.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: http://www.hopkinsmedicine.org/healthlibrary/test_procedures/pulmonary/lobectomy_92,P07749/
ontology term requester: NCI BBRB

right lung lobectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove one of the lobes of the right lung.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: http://www.hopkinsmedicine.org/healthlibrary/test_procedures/pulmonary/lobectomy_92,P07749/
ontology term requester: NCI BBRB

left lung mass excision
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove a mass (growth or tumor) in the left lung.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

right lung mass excision
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove a mass (growth or tumor) in the right lung.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

left pneumonectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure performed to remove an entire left lung
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: http://www.cancercenter.com/treatments/pneumonectomy/
ontology term requester: NCI BBRB

right pneumonectomy
type: Class
subclass of: surgical procedure
definition: A surgical procedure performed to remove an entire right lung
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: http://www.cancercenter.com/treatments/pneumonectomy/
ontology term requester: NCI BBRB

wedge resection of left lung
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove a triangle-shaped slice of tissue from the left lung. It may be used to remove a tumor or some other type of tissue that requires removal and typically includes a small amount of normal tissue around it.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://en.wikipedia.org/wiki/Wedge_resection
ontology term requester: NCI BBRB

wedge resection of right lung
type: Class
subclass of: surgical procedure
definition: A surgical procedure to remove a triangle-shaped slice of tissue from the right lung. It may be used to remove a tumor or some other type of tissue that requires removal and typically includes a small amount of normal tissue around it.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://en.wikipedia.org/wiki/Wedge_resection
ontology term requester: NCI BBRB

indicator of collected and banked pre-operative blood specimens
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether pre-operative/pre-anesthesia blood samples were collected from the participant and were successfully banked in a biobank.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

reason for not banking pre-operative blood specimen
type: Class
subclass of: comment from tissue procurement
example of usage: The reason(s) that the pre-operative/pre-anesthesia blood samples were not received in the tissue bank as per the BPV Collection and Processing SOP.
definition: A comment from tissue procurement providing a reason that the pre-operative/pre-anesthesia blood samples were not received in a biobank as per SOP.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

blood not received in biobank
type: Class
subclass of: reason for not banking pre-operative blood specimen
definition: A reason for not banking pre-operative blood specimen which is the blood specimen was not received in the biobank.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

minimum amount of required pre-op blood not drawn
type: Class
subclass of: reason for not banking pre-operative blood specimen
definition: A reason for not banking pre-operative blood specimen which is a minimum amount of required pre-op blood was not drawn.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

minimum number of aliquots not banked
type: Class
subclass of: reason for not banking pre-operative blood specimen
definition: A reason for not banking pre-operative blood specimen which is a minimum number of aliquots was not banked.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

blood was hemolyzed or not useable
type: Class
subclass of: reason for not banking pre-operative blood specimen
definition: A reason for not banking pre-operative blood specimen which is the blood was hemolyzed or not useable.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

receipt and dissection of surgical specimen SOP
type: Class
subclass of: standard operating procedure
example of usage: BPV SOP governing receipt and dissection of surgical tissue in the Tissue Bank
definition: A standard operating procedure for the receipt and dissection of surgical tissue in a biobank.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

data and time of biobank receipt of specimen
type: Class
subclass of: data item
example of usage: Date and time tissue specimens were received in Tissue Bank from the Pathology Gross Room
definition: A data item indicating the date and time at which the specimen was received in the biobank.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of biobank person receiving specimen
type: Class
subclass of: personal name
definition: A personal name that designates the person who received a specimen in the biobank.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment from specimen receipt
type: Class
subclass of: textual entity
definition: A textual entity that states a comment or issue regarding specimen receipt or deviations from a standard operating procedure for specimen receipt.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

parent specimen ID
type: Class
subclass of: specimen ID
example of usage: Parent Tissue Specimen ID of required study tumor tissue received in Tissue Bank from the Pathology Gross Room
definition: A specimen ID denoting a specimen that is used to create a specimen family.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of dissector of parent specimen
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed the dissection of a surgical specimen to create a specimen family.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

beginning time of parent specimen dissection.
type: Class
subclass of: data item
definition: A data item indicating the time that the dissection of a specimen for specimen family creation began.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

ending time of parent specimen dissection.
type: Class
subclass of: data item
definition: A data item indicating the time that the dissection of a specimen for specimen family creation ended.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen gross appearance
type: Class
subclass of: data item
example of usage: The gross appearance of the parent sample as determined in the pathology gross room.
definition: A data item on manifestations of disease produced from macroscopic analysis of a specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://en.wikipedia.org/wiki/Gross_pathology
ontology term requester: NCI BBRB

specimen gross appearance of tumor
type: Class
subclass of: specimen gross appearance
definition: A specimen gross appearance of a tumor manifestation.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

obsolete fine needle biopsy
type: Class
subclass of: Obsolete Class
definition: A biopsy that uses a thin, hollow needle to draw cells from a body.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: needle biopsy
definition source: http://www.mayoclinic.org/tests-procedures/needle-biopsy/basics/what-you-can-expect/prc-20012926
has obsolescence reason: term imported
ontology term requester: NCI BBRB
term replaced by: fine needle aspiration biopsy
deprecated: true

obsolete core needle biopsy
type: Class
subclass of: Obsolete Class
definition: A biopsy that uses a hollow tube that allows extracting a core of tissue for testing. This type of needle biopsy uses a wider needle than does fine-needle aspiration.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: core biopsy
definition source: http://www.mayoclinic.org/tests-procedures/needle-biopsy/basics/what-you-can-expect/prc-20012926
has obsolescence reason: term imported
ontology term requester: NCI BBRB
term replaced by: core needle biopsy
deprecated: true

PAXgene fixation reagent
type: Class
subclass of: processed material
definition: A processed material that is a non-carcinogenic, non-cross-linking mixture of different alcohols, acid and a soluble organic compound that rapidly preserves morphology and all bio-molecules.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: PAXgene Tissue FIX
definition source: http://journals.plos.org/plosone/article
ontology term requester: NCI BBRB

neutral buffered formalin
type: Class
subclass of: processed material
example of usage: 10% neutral buffered formalin (4% neutral buffered formaldehyde)
definition: A processed material that is a mixture of formalin (formaldehyde), phosphates, and water used as a standard fixative for diagnostic preparations.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: buffered formalin
definition source: http://stainsfile.info/StainsFile/prepare/fix/fixatives/formalin-buffered.htm
ontology term requester: NCI BBRB

buffer formula for specimen fixative
type: Class
subclass of: protocol
definition: A protocol specifying the buffer formula of the fixative in which tissue specimens are processed.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Fixative formula (buffer)
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

medical product expiration date
type: Class
subclass of: data item
definition: A data item that indicates the the date determined by appropriate stability testing of the medical product, lot, batch or item after which the product may not meet the appropriate regulatory agencies requirements.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

fixative product manufacturer
type: Class
subclass of: manufacturer
definition: A manufacturer that produces fixatives used in specimen collection.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

commercial manufacturer
type: Class
subclass of: manufacturer
definition: A manufacturer that produces materials to be sold for profit.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: commercial source
definition source: OBIB
ontology term requester: NCI BBRB

in-house manufacturer
type: Class
subclass of: manufacturer
definition: A manufacturer that produces materials internally for the internal needs of the organization.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: In-house source
definition source: OBIB
ontology term requester: NCI BBRB

recycled buffered formalin condition
type: Class
subclass of: buffered formalin condition
definition: A buffered formalin condition by virtue of the formalin having undergone a recycling process such as fractional distillation by temperature.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: recycled formalin
definition source: OBIB
ontology term requester: NCI BBRB

buffered formalin condition
type: Class
subclass of: quality
definition: A quality that inheres in buffered formalin by virtue of its usage and processing.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

fresh buffered formalin condition
type: Class
subclass of: buffered formalin condition
definition: A buffered formalin condition by virtue of being newly prepared with formalin that has not been previously used.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: fresh formalin
definition source: OBIB
ontology term requester: NCI BBRB

blood specimen collection and processing SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for collection and processing of blood specimens.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

minimum required pre-operative blood tubes collected
type: Class
subclass of: information content entity
definition: An information content entity indicating whether the minimum requirement according to a standard operating procedure was met for pre-operative blood collection.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

approval to proceed with collection
type: Class
subclass of: information content entity
definition: An information content entity indicating whether approval was received to proceed with collection.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

phlebotomist role
type: Class
subclass of: health care provider role
definition: A health care provider role borne by a person trained to draw blood from a patient for clinical or medical testing, transfusions, donations, or research. Phlebotomists collect blood primarily by performing venipunctures.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://en.wikipedia.org/wiki/Phlebotomy
ontology term requester: NCI BBRB

anesthesiologist role
type: Class
subclass of: health care provider role
definition: A health care provider role borne by a medical practitioner trained in anesthesia and perioperative medicine.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://en.wikipedia.org/wiki/Anesthesiologist
ontology term requester: NCI BBRB

nurse anesthetist role
type: Class
subclass of: nurse role
definition: A nurse role borne by a nurse who specializes in the administration of anesthesia.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: https://en.wikipedia.org/wiki/Nurse_anesthetist
ontology term requester: NCI BBRB

operating room technician
type: Class
subclass of: health care provider role
definition: A health care provider role borne by a person whose duties are to prepare operating rooms, set up equipment and surgical tools, and assist doctors and nurses during surgeries as instructed.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: O.R. technician
alternative label: surgical technician
definition source: http://work.chron.com/become-operating-room-technician-12460.html
ontology term requester: NCI BBRB

date and time of blood collection
type: Class
subclass of: data item
definition: A data item indicating the date and time when a blood specimen was collected.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Date and Time Blood Was Drawn
definition source: OBIB
ontology term requester: NCI BBRB

pre-operative blood specimen collection
type: Class
subclass of: blood specimen collection
definition: A blood specimen collection that occurs pre-operatively or pre-anesthesia relative to surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: pre-operative blood draw
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

blood specimen collection
type: Class
subclass of: collecting specimen from organism
definition: A collecting specimen from organism that results in a blood specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: blood draw
definition source: OBIB
ontology term requester: NCI BBRB

name of person performing blood draw
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed the collection of a blood specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

blood specimen container with EDTA
type: Class
subclass of: specimen container
definition: A specimen container for collecting blood and has ethylenediaminetetraacetic acid (EDTA) as an anticoagulant.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: lavender top tube
definition source: http://www.mayomedicallaboratories.com/customer-service/faq/specimen/collection-tubes
ontology term requester: NCI BBRB

PAXgene DNA vacutainer
type: Class
subclass of: specimen container
definition: A specimen container developed by PreAnalytiX that is intended to collect, anticoagulate, stabilize, transport, and store a venous whole blood sample for preparation of high quality DNA for use with molecular diagnostic test methods that require DNA.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: http://www.preanalytix.com/sites/default/files/handbooks/PAXgene%20Blood%20DNA%20Tube%20IVD%20Product%20Circular.pdf
ontology term requester: NCI BBRB

PAXgene RNA vacutainer
type: Class
subclass of: specimen container
definition: A specimen container developed by PreAnalytiX that contains a proprietary reagent for stabilization of intracellular RNA immediately upon collection.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: http://www.preanalytix.com/products/blood/RNA/paxgene-blood-rna-tube
ontology term requester: NCI BBRB

blood specimen volume
type: Class
subclass of: scalar measurement datum
example of usage: Volume of blood collected in milliliters
definition: A scalar measurement datum that is the output of a volume measurement assay that has a blood specimen as evaluant.
editor note: need volume measurement assay from OBI first
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

fresh venous needle blood specimen collection
type: Class
subclass of: blood specimen collection
definition: A blood specimen collection that is performed with a fresh needle inserted into a vein.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: fresh venous needle stick
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment from blood specimen collection
type: Class
subclass of: textual entity
definition: A textual entity that states additional information about the blood specimen or donor that is deemed relevant for the specimen collection process.
editor note: Consider generalizing label of ���comment from tissue procurement��
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

data and time of laboratory receipt of specimen
type: Class
subclass of: data item
definition: A data item indicating the date and time at which the specimen was received in the laboratory for processing.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of person receiving blood specimen in laboratory
type: Class
subclass of: personal name
definition: A personal name that designates the person who received a blood specimen in the laboratory.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

temperature in lab when blood specimen was received
type: Class
subclass of: scalar measurement datum
definition: A scalar measurement datum that is the output of a temperature measurement assay occurring in a laboratory and performed when a blood specimen is received.
editor note: need temperature measurement assay from OBI and humidity from PATO
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

humidity in lab when blood specimen was received
type: Class
subclass of: measurement datum
definition: A measurement datum that is the output of an assay of humidity occurring in a laboratory and performed when a blood specimen is received.
editor note: need humidity from PATO
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

vacutainer specimen barcode
type: Class
subclass of: specimen barcode
example of usage: DNA PAXgene tube Specimen Barcode ID
definition: A specimen barcode that is associated with a vacutainer.
editor note: need specimen barcode
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

time of specimen freezing at approximately -20 degrees C
type: Class
subclass of: time of specimen freezing
example of usage: Time DNA PAXgene tube was frozen at -20�_C �� 2�_C
definition: A time of specimen freezing which occurred at approximately -20�_C.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

time of specimen freezing at -70 to -80 degrees C
type: Class
subclass of: time of specimen freezing
example of usage: Time DNA PAXgene tube was transferred to storage at -75�_C �� 5�_C
definition: A time of specimen freezing which occurred at -75�_ �� 5�_C.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

name of person storing specimen
type: Class
subclass of: personal name
definition: A personal name that designates the person who stored a specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen was collected and stored in accordance with the specified SOP
type: Class
subclass of: information content entity
example of usage: DNA PAXgene tube was collected and stored in accordance with the specified SOP
definition: An information content entity indicating whether the specimen was collected and stored in accordance with the specified SOP.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment from blood specimen storage
type: Class
subclass of: textual entity
example of usage: DNA PAXgene tube storage comments
definition: A textual entity that states additional information about the blood specimen or donor that is deemed relevant for the specimen storage process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

time of blood processing
type: Class
subclass of: data item
example of usage: Time plasma processing began.
definition: A data item indicating the time when a blood specimen was processed.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

conical centrifuge tube identifier
type: Class
subclass of: identifier
definition: An identifier that specifically identifies a particular conical centrifuge tube.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Conical centrifuge Tube code
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

blood specimen volume in conical centrifuge tube
type: Class
subclass of: blood specimen volume
definition: A blood specimen volume of blood contained in a conical centrifuge tube.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

blood plasma specimen barcode
type: Class
subclass of: specimen barcode
definition: A specimen barcode that is associated with a blood plasma specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

blood plasma specimen volume
type: Class
subclass of: scalar measurement datum
definition: A scalar measurement datum that is the output of a volume measurement assay that has a blood plasma specimen as evaluant.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

time of blood plasma specimen placement on dry ice
type: Class
subclass of: data item
definition: A data item indicating the time when a blood plasma specimen was placed on dry ice.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

cryovial specimen barcode
type: Class
subclass of: specimen barcode
definition: A specimen barcode that is associated with a cryovial.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

time of blood plasma specimen transfer to freezer
type: Class
subclass of: data item
definition: A data item indicating the time when a blood plasma specimen was transferred to a freezer.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

name of person processing blood plasma specimen aliquots
type: Class
subclass of: personal name
definition: A personal name that designates the person who processed a blood specimen to generate aliquots of blood plasma specimens.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

name of person transferring blood plasma specimens to freezer
type: Class
subclass of: personal name
definition: A personal name that designates the person who transferred blood plasma specimens to freezer.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

specimen was processed in accordance with the specified SOP
type: Class
subclass of: information content entity
example of usage: Plasma Processing Was Performed in Accordance With Specified SOP
definition: An information content entity indicating whether the specimen was processed in accordance with the specified SOP.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment from blood specimen processing
type: Class
subclass of: textual entity
example of usage: Plasma Processing Comments
definition: A textual entity that states additional information about the blood specimen or donor that is deemed relevant for specimen processing.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

presence of gross hemolysis of plasma observed
type: Class
subclass of: information content entity
definition: An information content entity indicating whether the presence of gross hemolysis of plasma was observed.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

cell pellet volume
type: Class
subclass of: scalar measurement datum
example of usage: Volume in ml of Whole Cell Pellet
definition: A scalar measurement datum that is the output of a volume measurement assay that has a cell pellet as evaluant.
editor note: need volume measurement assay from OBI first
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

cell pellet specimen barcode
type: Class
subclass of: specimen barcode
example of usage: Whole Cell Pellet Aliquot Specimen Barcode ID
definition: A specimen barcode that is associated with a cell pellet specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

time of completion of blood cell pellet processing
type: Class
subclass of: data item
definition: A data item indicating the time when processing of a blood cell pellet specimen was completed.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

time of blood cell pellet transfer to storage
type: Class
subclass of: data item
definition: A data item indicating the time when the blood cell pellet specimen was transferred to storage.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

name of person processing blood cell pellet specimen
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed processing of the blood cell pellet specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

date of specimen placement on dry ice for transport
type: Class
subclass of: data item
definition: A data item indicating the calendar date when a specimen was placed on dry ice for transport.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

time of specimen placement on dry ice for transport
type: Class
subclass of: data item
definition: A data item indicating the time when a specimen was placed on dry ice for transport.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

date of specimen freezing at -70 to -80 degrees C
type: Class
subclass of: data item
definition: A data item indicating the calendar date when a specimen was stored at -75_ � 5_C.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

date of specimen transport
type: Class
subclass of: data item
definition: A data item indicating the calendar date when a specimen was transported to another institution.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: date of specimen shipment
definition source: OBIB
ontology term requester: NCI BBRB

time of specimen transport
type: Class
subclass of: data item
definition: A data item indicating the time when a specimen was transported to another institution.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: time of specimen shipment
definition source: OBIB
ontology term requester: NCI BBRB

specimen transporting organization
type: Class
subclass of: role
definition: A role borne by an organization that is the provider of a specimen that is transported to another organization.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: specimen shipping organization
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen receiving organization
type: Class
subclass of: role
definition: A role borne by an organization that is the recipient of a specimen that is transported from another organization.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of person responsible for specimen transport
type: Class
subclass of: personal name
definition: A personal name that designates the person who is responsible for the transport of a specimen to another organization.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: name of person responsible for specimen shipment
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of IATA-trained person verifying specimen transport
type: Class
subclass of: personal name
definition: 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.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: name of IATA-trained person verifying specimen shipment
definition source: http://www.iata.org/training/pages/index.aspx
ontology term requester: NCI BBRB

date of receiving specimen transport
type: Class
subclass of: data item
definition: A data item indicating the calendar date when a specimen was received after transport from another institution.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: date of receiving specimen shipment
definition source: OBIB
ontology term requester: NCI BBRB

time of receiving specimen transport
type: Class
subclass of: data item
definition: A data item indicating the time when a specimen was received after transport from another institution.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: time of receiving specimen shipment
definition source: OBIB
ontology term requester: NCI BBRB

temperature of specimen collection packet at time of receipt
type: Class
subclass of: scalar measurement datum
definition: A scalar measurement datum that is the output of a temperature measurement assay performed on a collection packet when it is received with a specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: temperature of interior kit at time of receipt
definition source: OBIB
ontology term requester: NCI BBRB

name of person receiving specimen shipment
type: Class
subclass of: data item
definition: A personal name that designates the person who received the specimen that was transported from another organization.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

specimen shipment received in good condition
type: Class
subclass of: information content entity
definition: An information content entity indicating that the physical condition of a specimen upon receipt after transport was good.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

specimen shipment received in poor condition
type: Class
subclass of: information content entity
definition: An information content entity indicating that the physical condition of a specimen upon receipt after transport was poor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

comment on specimen integrity after transport
type: Class
subclass of: textual entity
definition: A textual entity that states information about the physical integrity or wholeness of the specimen that is deemed relevant for the specimen transport process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

date of specimen receipt for pathologist processing
type: Class
subclass of: data item
definition: A data item indicating the calendar date when a specimen arrives in the gross pathology room for processing and review.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

time of receipt for pathologist processing
type: Class
subclass of: data item
definition: A data item indicating the time when a specimen arrives in the gross pathology room for processing and review.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of quality control inspector of specimen
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed a quality control inspection of the specimen that is to be transported to another organization.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

name of data entry person for tissue recovery form
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed the data entry process for filling in a tissue recovery case report form.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of team leader for filling out tissue recovery form
type: Class
subclass of: personal name
definition: A personal name that designates the person who is the leader of the team responsible for entering the tissue recovery form data.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE tissue processing SOP
type: Class
subclass of: standard operating procedure
definition: 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.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: http://www.leicabiosystems.com/pathologyleaders/an-introduction-to-specimen-processing/
ontology term requester: NCI BBRB

equipment maintained as per manufacturer recommendations
type: Class
subclass of: information content entity
definition: An information content entity that indicates whether equipment was maintained following the manufacturers recommendations.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on maintenance discrepancy from manufacturer recommendations
type: Class
subclass of: textual entity
definition: A textual entity that states information about maintenance discrepancies from manufacturer recommendations.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

FFPE clearing agent role
type: Class
subclass of: role
definition: A role borne by a chemical that is realized in the formalin-fixed paraffin-embedded (FFPE) processes to remove alcohol used for specimen dehydration, remove stains, and prepare a specimen for infiltration medium.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

adherence of alcohol stage duration to FFPE tissue processing SOP
type: Class
subclass of: information content entity
definition: An information content entity that indicates whether duration of the alcohol stage followed that prescribed in the FFPE tissue processing SOP.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE alcohol stage duration
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the duration of the alcohol stage in a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

adherence of dehydration process duration to FFPE tissue processing SOP
type: Class
subclass of: information content entity
definition: An information content entity that indicates whether duration of the dehydration process followed that prescribed in the FFPE tissue processing SOP.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE dehydration process duration
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the duration of the dehydration process in the formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

adherence of dehydration process temperature to FFPE tissue processing SOP
type: Class
subclass of: information content entity
definition: An information content entity that indicates whether temperature of the dehydration process followed that prescribed in the FFPE tissue processing SOP.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE dehydration process temperature
type: Class
subclass of: scalar measurement datum
definition: A scalar measurement datum that is the output of a temperature measurement assay performed on a specimen in alcohol during the dehydration process in a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

adherence of stage and replicate numbers to FFPE tissue processing SOP
type: Class
subclass of: information content entity
definition: An information content entity that indicates whether the number of stages and replicates followed that prescribed in the FFPE tissue processing SOP.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

number of FFPE stages/replicates
type: Class
subclass of: data item
definition: A data item that indicates the number of stages and replicates in a FFPE process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

adherence of duration in clearing agent to FFPE tissue processing SOP
type: Class
subclass of: information content entity
definition: An information content entity that indicates whether the duration in clearing agent followed that prescribed in the FFPE tissue processing SOP.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE clearing agent duration
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the duration in clearing agent in the formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

adherence of temperature of clearing agent to FFPE tissue processing SOP
type: Class
subclass of: information content entity
definition: An information content entity that indicates whether the temperature of clearing agent followed that prescribed in the FFPE tissue processing SOP.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE clearing agent temperature
type: Class
subclass of: scalar measurement datum
definition: A scalar measurement datum that is the output of a temperature measurement assay performed on a specimen in clearing agent in a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

adherence to paraffin impregnation method in FFPE tissue processing SOP
type: Class
subclass of: information content entity
definition: An information content entity that indicates whether the paraffin impregnation method followed that prescribed in the FFPE tissue processing SOP.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE paraffin impregnation method
type: Class
subclass of: protocol
definition: A protocol for the paraffin impregnation step of a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

adherence of paraffin temperature to FFPE tissue processing SOP
type: Class
subclass of: information content entity
definition: An information content entity that indicates whether the paraffin temperature followed that prescribed in the FFPE tissue processing SOP.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE paraffin temperature
type: Class
subclass of: scalar measurement datum
definition: A scalar measurement datum that is the output of a temperature measurement assay performed on paraffin in a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

comment on FFPE tissue processing
type: Class
subclass of: textual entity
definition: A textual entity that states information relevant to tissue processing in a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE tissue paraffin embedding SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for the paraffin embedding of a formalin-fixed paraffin-embedded (FFPE) tissue.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE paraffin processing for embedding temperature
type: Class
subclass of: scalar measurement datum
definition: A scalar measurement datum that is the output of a temperature measurement assay performed during the paraffin processing for embedding in a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

fresh paraffin
type: Class
subclass of: Paraffin
definition: A paraffin that has not been previously used or recycled.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

age of paraffin
type: Class
subclass of: scalar measurement datum
definition: A scalar measurement datum that is the output of an age measurement assay performed on paraffin.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

total time FFPE freshly poured blocks were cooled
type: Class
subclass of: time measurement datum
definition: 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.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE tissue block handling, tracking, and storage SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for the handling, tracking, and storing of a formalin-fixed paraffin-embedded (FFPE) tissue block.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

adherence to FFPE tissue block storage SOP
type: Class
subclass of: information content entity
definition: An information content entity that indicates whether the FFPE tissue block storage SOP was followed.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on FFPE tissue block storage
type: Class
subclass of: textual entity
example of usage: discrepancies from a FFPE tissue block storage SOP.
definition: A textual entity that states information relevant to storage of a formalin-fixed paraffin-embedded (FFPE) tissue block.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on paraffin embedding of FFPE tissue
type: Class
subclass of: textual entity
definition: A textual entity that states information relevant to paraffin embedding of a formalin-fixed paraffin-embedded (FFPE) tissue.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of specimen slide preparation technician
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed a specimen slide preparation.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Slide Prep Technician Name
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE tissue section preparation SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for the preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

microtome blade age
type: Class
subclass of: age
definition: An age that inheres in a microtome blade.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

fresh microtome blade
type: Class
subclass of: microtome blade age
definition: A microtome blade age that indicates that the microtome blade is as new as possible.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

preparation of FFPE block face for sectioning protocol
type: Class
subclass of: protocol
definition: A protocol describing the preparation on the faced block prior to sectioning of a formalin-fixed paraffin-embedded (FFPE) tissue.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

description of glass slide charge
type: Class
subclass of: textual entity
definition: A textual entity that describes the carge on a glass slide.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Slide Charge
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

charged glass slide indicator
type: Class
subclass of: information content entity
definition: An information content entity that indicates that a glass slide has been positively charged.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: charged slide
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

uncharged glass slide indicator
type: Class
subclass of: information content entity
definition: An information content entity that indicates that a glass slide has not been positively charged.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: uncharged slide
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE water bath temperature
type: Class
subclass of: scalar measurement datum
definition: A scalar measurement datum that is the output of a temperature measurement assay performed on a water bath used in a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

microtome maintenance frequency
type: Class
subclass of: information content entity
definition: An information content entity that indicates the frequency with which microtome maintenance is performed and recorded.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

daily microtome maintenance
type: Class
subclass of: microtome maintenance frequency
definition: A microtome maintenance frequency that indicates that microtome maintenance is performed and recorded daily.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on deviations from microtome daily maintenance SOP
type: Class
subclass of: textual entity
definition: A textual entity that states information about deviations from a microtome daily maintenance standard operating procedure.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

water bath maintenance frequency
type: Class
subclass of: information content entity
definition: An information content entity that indicates the frequency with which water bath maintenance is performed and recorded.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

daily water bath maintenance
type: Class
subclass of: water bath maintenance frequency
definition: A water bath maintenance frequency that indicates that microtome maintenance is performed and recorded daily.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on deviations from water bath daily maintenance SOP
type: Class
subclass of: textual entity
definition: A textual entity that states information about deviations from a water bath daily maintenance standard operating procedure.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

comment on preparation of FFPE tissue section
type: Class
subclass of: textual entity
definition: A textual entity that states information relevant to preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE tissue section H&E staining and mounting SOP
type: Class
subclass of: standard operating procedure
definition: A standard operating procedure for the hematoxylin and eosin (H&E) staining and slide mounting of a formalin-fixed paraffin-embedded (FFPE) tissue section.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE tissue section H&E staining in oven duration
type: Class
subclass of: time measurement datum
definition: 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.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

oven temperature during FFPE tissue section H&E staining
type: Class
subclass of: scalar measurement datum
definition: A scalar measurement datum that is the output of a temperature measurement assay performed on a oven during a formalin-fixed paraffin-embedded (FFPE) tissue section hematoxylin and eosin (H&E) staining.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

FFPE tissue section H&E deparaffinization protocol
type: Class
subclass of: protocol
definition: A protocol describing the deparaffinization method used during the hematoxylin and eosin (H&E) stained slide preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: H&E deparaffinization method
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE tissue section H&E staining protocol
type: Class
subclass of: protocol
definition: A protocol describing the staining method used during the hematoxylin and eosin (H&E) stained slide preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: H&E staining method
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE tissue section H&E clearing protocol
type: Class
subclass of: protocol
definition: A protocol describing the clearing method used during the hematoxylin and eosin (H&E) stained slide preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: H&E clearing method
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE tissue section H&E cover slip protocol
type: Class
subclass of: protocol
definition: A protocol describing the method for applying a cover slip used during the hematoxylin and eosin (H&E) stained slide preparation of a formalin-fixed paraffin-embedded (FFPE) tissue section.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: H&E cover slipping method
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

manual FFPE tissue section H&E deparaffinization
type: Class
subclass of: planned process
definition: A planned process involving the manual performance of the FFPE tissue section H&E deparaffinization protocol.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

manual FFPE tissue section H&E staining
type: Class
subclass of: planned process
definition: A planned process involving the manual performance of the FFPE tissue section H&E staining protocol.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

manual FFPE tissue section H&E clearing
type: Class
subclass of: planned process
definition: A planned process involving the manual performance of the FFPE tissue section H&E clearing protocol.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

manual FFPE tissue section H&E cover slipping
type: Class
subclass of: planned process
definition: A planned process involving the manual performance of the FFPE tissue section H&E cover slip protocol.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

comment on preparation of FFPE H&E stained slide
type: Class
subclass of: textual entity
definition: A textual entity that states information relevant to the preparation of a formalin-fixed paraffin-embedded (FFPE) hematoxylin and eosin (H&E) stained slide.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

H&E staining equipment maintenance performed and recorded frequency
type: Class
subclass of: data item
definition: A data item that indicates the frequency with which hematoxylin and eosin (H&E) staining equipment maintenance is performed and recorded.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

H&E staining equipment maintenance performed and recorded frequency value specification
type: Class
subclass of: categorical value specification
definition: A categorical value specification that is used to record the frequency with which hematoxylin and eosin (H&E) staining equipment maintenance is performed and recorded. Categories include daily, weekly, bi-monthly, and per SOP.
editor note: Add instances: daily, weekly, bi-monthly, per SOP
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on deviations from H&E equipment maintenance SOP
type: Class
subclass of: textual entity
definition: A textual entity that states information about deviations from a hemtoxylin and eosin (H&E) equipment maintenance standard operating procedure.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

specimen randomization key ID
type: Class
subclass of: specimen barcode
definition: A specimen barcode associated with the specific chart (key) used to randomly assign specimens to one of several distinct experimental protocols.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

manager of human research protocol requirements role
type: Class
subclass of: role
definition: A role borne by personnel responsible for managing human research protocol requirements including but not limited to screening, obtaining authorization, consenting and/or enrollment activities.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Consent or Research Analyst/Coordinator role
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

transplant alert associated with specimen donor
type: Class
subclass of: textual entity
definition: A textual entity that is a notification within a clinical data repository that a specimen donor was a transplant recipient.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

serology alert associated with specimen donor
type: Class
subclass of: textual entity
definition: A textual entity that is a notification within a clinical data repository that specimen donor serology results include positive infectious disease data.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

data and time parent specimen ID was recorded
type: Class
subclass of: data item
definition: A data item indicating the date and time at which the parent specimen ID was recorded.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on tissue specimen processing
type: Class
subclass of: textual entity
definition: A textual entity that states additional information deemed relevant for tissue specimen processing.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

human brain biobank
type: Class
subclass of: biobank
example of usage: Brain Endowment Bank at Miller School of Medicine, of the University of Miami.
definition: A biobank that focuses on the special requirements of the human brain with regards to preservation, handling, and analysis.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: brain bank
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

central biobank
type: Class
subclass of: biobank
definition: A biobank which receives its specimens primarily/exclusively from tissue source sites.� Activities include receipt, some processing, production of slides/images of the tissue, storage, and retrieval/shipping of materials on-demand.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Central Biospecimen Repository
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

laboratory, data analysis, and coordinating center for human specimens
type: Class
subclass of: Laboratory
definition: A laboratory that specializes in acquiring human tissues and analyzing components such as DNA and RNA from them.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: LDACC
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

pathology research center
type: Class
subclass of: Laboratory
definition: A laboratory that performs a rigorous review of images of tissue specimens by a group of senior pathologists not involved in the specimen collection typically to evaluate and characterize the tissue (e.g., % necrosis).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: PRC
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

time specimen place in stabilizer
type: Class
subclass of: data item
definition: A data item indicating the time when a specimen was placed in a container with stabilizing reagent.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

collection packet component ID
type: Class
subclass of: identifier
definition: An identifier that specifically identifies a particular component of a collection packet.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: kit component ID
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

data and time specimen was frozen in liquid nitrogen
type: Class
subclass of: data item
definition: A data item indicating the date and time at which a specimen was frozen by placement in liguid nitrogen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

weight of frozen tissue specimen
type: Class
subclass of: mass measurement datum
example of usage: weight of frozen tumor block after freezing in liquid nitrogen
definition: A mass measurement datum that is the result of measuring the weight of a frozen tissue specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE fixation protocol
type: Class
subclass of: protocol
definition: A protocol for the fixation step of a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE fixation delay protocol
type: Class
subclass of: FFPE fixation protocol
definition: A FFPE fixation protocol that specifies the planned delay to fixation time.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE tissue cassette ID
type: Class
subclass of: specimen ID
definition: A specimen ID that specifically identifies a particular tissue cassete used in a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

data and time FFPE tissue cassette ID was recorded
type: Class
subclass of: data item
definition: A data item indicating the date and time at which the FFPE tissue cassette ID was recorded.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

date and time FFPE tissue cassette placed in fixative
type: Class
subclass of: data item
definition: A data item indicating the date and time when a tissue cassette was placed in fixative as part of a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

placement of tissue cassette in FFPE fixative delay duration
type: Class
subclass of: time measurement datum
definition: 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.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

date and time FFPE tissue cassette placed in processor
type: Class
subclass of: data item
definition: A data item indicating the date and time when a tissue cassette was placed in a tissue processor as part of a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

date and time FFPE tissue processor cycle ended
type: Class
subclass of: data item
definition: A data item indicating the date and time when a tissue processor cycle ended as part of a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

time in FFPE fixative measurement
type: Class
subclass of: time in fixative measurement
definition: A time in fixative measurement that states the duration during which a specimen was submerged in fixative as part of a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

date and time FFPE tissue cassette removed from processor
type: Class
subclass of: data item
definition: A data item indicating the date and time when a tissue cassette was removed from a tissue processor as part of a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

date and time FFPE tissue embedding started
type: Class
subclass of: data item
definition: A data item indicating the date and time when a tissue embedding started as part of a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

measurement of time between FFPE tissue processor cycle completion and embedding
type: Class
subclass of: time measurement datum
definition: 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.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

date and time FFPE tissue cassette was frozen
type: Class
subclass of: data item
definition: A data item indicating the date and time when a tissue cassette was frozen as part of a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE freezing protocol
type: Class
subclass of: protocol
definition: A protocol for the freezing step of a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: FFPE freezing method
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE freezing by dry ice protocol
type: Class
subclass of: protocol
definition: A FFPE freezing protocol that involves the use of dry ice.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE freezing by LN2 vapor phase protocol
type: Class
subclass of: protocol
definition: A FFPE freezing protocol that involves the use of liquid nitrogen vapor phase.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

date and time FFPE tissue cassette transferred to storage
type: Class
subclass of: data item
example of usage: Date/Time Tissue Cryosettes Were Transferred to Storage
definition: A data item indicating the date and time when a tissue cassette was transferred to storage after a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of dissector of normal adjacent tissue to tumor for FFPE
type: Class
subclass of: personal name
definition: 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.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen was processed in accordance with the FFPE SOP
type: Class
subclass of: specimen was processed in accordance with the specified SOP
definition: A specimen was processed in accordance with the specified SOP where the specified SOP is for a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

date and time FFPE tissue was preserved
type: Class
subclass of: data item
definition: A data item indicating the date and time when a specimen tissue was fixed or frozen as part of a formalin-fixed paraffin-embedded (FFPE) process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen was processed in accordance with the FFPE SOP including <1 hour delay to fixation and 23 hour time in fixative
type: Class
subclass of: specimen was processed in accordance with the specified SOP
definition: A specimen was processed in accordance with the specified SOP where the specified SOP is for a formalin-fixed paraffin-embedded (FFPE) process and includes less than 1 hour delay in fixation and 23 hour time in fixative.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on procurement site restriction
type: Class
subclass of: comment from tissue procurement
definition: A comment from tissue procurement made in regards to all non-consent issues related to or creating a limitation on tissues that can be procured including tissue type and reason for restriction.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen image ID
type: Class
subclass of: identifier
definition: An identifier that specifically identifies a particular specimen image.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on FFPE slide image
type: Class
subclass of: textual entity
definition: A textual entity that states information relevant to an image from a formalin-fixed paraffin-embedded (FFPE) slide.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of submitter of pathology case summary report.
type: Class
subclass of: personal name
definition: A personal name that designates the person who was the submitter of a pathology case summary report.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: name of submitting pathologist
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

date of submission of pathology case summary report
type: Class
subclass of: data item
definition: A data item that reports the calendar date when a pathology case summary report was submitted.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

name of reviewer of pathology case summary report.
type: Class
subclass of: personal name
definition: A personal name that designates the person who served as the reviewer for quality assurance purposes of a pathology case summary report.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: name of reviewing pathologist
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

date of review of pathology case summary report
type: Class
subclass of: data item
definition: A data item that reports the calendar date when a pathology case summary report was reviewed.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

pathologist submitted specimen procurement feedback
type: Class
subclass of: comment from tissue procurement
definition: A comment from tissue procurement that was submitted as feedback by a pathologist
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

greatest tumor dimension on slide
type: Class
subclass of: length measurement datum
example of usage: The largest dimension of the tumor on the slide measured in millimeters.
definition: A length measurement datum that is the result of measuring the maximum length of a tumor specimen as presented on a slide.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

percentage of cross-sectional surface area of entire slide composed of tumor focus
type: Class
subclass of: data item
definition: A data item that is the result of determining the percentage of cross-sectional surface area of an entire specimen slide composed of tumor focus including necrotic tumor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

percentage of tumor cellularity by cell count of the entire slide.
type: Class
subclass of: data item
definition: A data item that is the result of determining the percentage of tumor nuclei by cell count of the entire specimen slide (number of tumor epithelial cell nuclei as compared to all cell nuclei).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

percentage of cross-sectional surface area of entire slide composed of necrotic tissue
type: Class
subclass of: data item
definition: A data item that is the result of determining the percentage of cross-sectional surface area of an entire specimen slide that is composed of necrotic tissue.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

histologic profile quantitative assessment of tumor slide specimen surface area
type: Class
subclass of: data item
definition: A data item that is made up of percentages of different histology-based assessments of a tumor slide specimen that in aggregate describe the total tumor surface area (i.e. add up to 100%).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

percentage of viable tumor slide specimen by surface area
type: Class
subclass of: data item
definition: A data item that is the result of determining the percentage of a tumor slide specimen that is viable based on surface area not including stroma.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

percentage of necrotic tumor slide specimen by surface area
type: Class
subclass of: data item
definition: A data item that is the result of determining the percentage of a tumor slide specimen that is necrotic based on surface area.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

percentage of tumor slide specimen stroma by surface area
type: Class
subclass of: data item
definition: A data item that is the result of determining the percentage of a tumor slide specimen that is stroma based on surface area.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

percentage of non-cellular component of tumor slide specimen by surface area
type: Class
subclass of: data item
example of usage: Percent non-cellular component consisting of mucin, hemorrhage, blood clot, etc.
definition: A data item that is the result of determining the percentage of a tumor slide specimen that is non-cellular based on surface area.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

non-cellular component of tumor slide specimen description
type: Class
subclass of: textual entity
definition: A textual entity that describes the non-cellular component of a tumor slide specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

confirmation of histologic type of FFPE H&E tumor slide
type: Class
subclass of: information content entity
definition: 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.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE slide meets necrosis percentage and tumor content criteria
type: Class
subclass of: information content entity
example of usage: This Slide Meets the Microscopic Analysis Criteria of the BPV Project of Necrosis Percentage of <20% AND Tumor Content of _50% Tumor Nuclei
definition: An information content entity that is an indicator of whether a formalin-fixed paraffin-embedded (FFPE) slide meets the microscopic analysis criteria with respect to necrosis percentage and tumor content.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE slide findings that do not meet microscopic analysis criteria
type: Class
subclass of: textual entity
definition: A textual entity that describes findings upon review of a formalin-fixed paraffin-embedded (FFPE) slide that do not meet microscopic analysis criteria.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment from pathology review of FFPE slide
type: Class
subclass of: textual entity
definition: A textual entity that states information relevant to a review by a pathologist of a formalin-fixed paraffin-embedded (FFPE) slide.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE slide consistent with findings of diagnostic pathology report
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether a formalin-fixed paraffin-embedded (FFPE) slide was consistent with findings of diagnostic pathology report.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

FFPE slide inconsistencies with findings of diagnostic pathology report
type: Class
subclass of: textual entity
definition: A textual entity that describes inconsistencies with findings of diagnostic pathology report upon review of a formalin-fixed paraffin-embedded (FFPE) slide.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of reviewing pathologist at organization conducting specimen collection
type: Class
subclass of: personal name
definition: A personal name that designates the person who served as the pathologist reviewing a specimen slide at an organization conducting specimen collection from organisms.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

date of FFPE slide review by the pathologist
type: Class
subclass of: data item
definition: A data item that reports the calendar date when a formalin-fixed paraffin-embedded (FFPE) slide was reviewed by a pathologist.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

name of data entry person for local pathology review form
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed the data entry process for filling in a local pathology review form.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

presence of sarcomatoid features on specimen slide
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether examination of a tissue specimen slide revealed the presence of sarcomatoid features.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

sarcomatoid features observed on FFPE slide
type: Class
subclass of: textual entity
definition: A textual entity that describes sarcomatoid features observed on a formalin-fixed paraffin-embedded (FFPE) slide.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of person in gross room receiving OR specimen
type: Class
subclass of: personal name
definition: A personal name that designates the person who received a specimen in a pathology gross room from an associated operating room (OR).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen transport from OR to gross room SOP
type: Class
subclass of: specimen transport SOP
definition: A specimen transport SOP governing the transport of tissue from the operating room (OR) to the pathology gross room.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen transport from OR to gross room was performed as per SOP
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether transport of tissue from the operating room (OR) to the pathology gross room was performed in accordance with the relevant standard operating procedure (SOP).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen transport from OR to gross room issues or deviations from SOP
type: Class
subclass of: textual entity
definition: A textual entity that describes issues with the transport of tissue from the operating room (OR) to the pathology gross room or deviations from the relevant standard operating procedure (SOP).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

temperature in gross room when specimen arrived from OR
type: Class
subclass of: scalar measurement datum
definition: A scalar measurement datum that is the output of a temperature measurement assay occurring in a pathology gross room and performed when a specimen arrived from the operating room (OR).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

humidity in gross room when specimen arrived from OR
type: Class
subclass of: measurement datum
definition: A measurement datum that is the output of an assay of humidity occurring in a pathology gross room and performed when a specimen arrived from the operating room (OR).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of performer of gross evaluation of resected tissue specimen
type: Class
subclass of: personal name
definition: A personal name that designates the person who performed the gross evaluation of a resected tissue specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

resected tissue specimen mass measurement datum
type: Class
subclass of: mass measurement datum
definition: A mass measurement datum that is the output of an assay to measure the weight of a resected tissue specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: resected tissue weight
definition source: OBIB
ontology term requester: NCI BBRB

gross appearance of disease in resected tissue
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether gross appearance of disease was observed in a resected tissue specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on gross evaluation of resected tissue specimen
type: Class
subclass of: textual entity
definition: A textual entity that states information relevant to gross evaluation of a resected tissue specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

gross diagnosis of resected tissue
type: Class
subclass of: diagnosis
definition: A diagnosis that is based on the gross evaluation of a resected tissue specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

photograph of tissue was taken in pathology gross room
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether a photograph was taken in the pathology gross room of a resected tissue specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

reason for not taking a photograph of resected tissue in pathology gross room
type: Class
subclass of: textual entity
definition: A textual entity that describes the reason no photographs were taken of a resected tissue specimen in the pathology gross room.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

pathology ink used on resected tissue specimen
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether pathology ink was used to mark the resected tissue specimen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

ink used for marking surgical margin
type: Class
subclass of: processed material
example of usage: India ink
definition: A processed material that is used to mark the margin of a surgical excision of a resected tissue. It is used to evaluate whether the margin is free of tumor tissue.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: pathology ink
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248492/
ontology term requester: NCI BBRB

tumor tissue was released to the biobank
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether a tumor tissue specimen was released to a biobank.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

explanation of why tumor tissue specimen was not released to a biobank
type: Class
subclass of: textual entity
definition: A textual entity that describes the reason why a tumor tissue specimen was not released to a biobank.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

percentage of gross area of necrosis of a specimen sent to biobank
type: Class
subclass of: data item
definition: A data item that is the result of determining the percentage of gross area of necrosis of a specimen sent to a biobank.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

percentage of tumor content of specimen sent to biobank
type: Class
subclass of: data item
definition: A data item that is the result of determining the percentage of tumor content of a specimen sent to a biobank.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

second piece of tumor tissue was collected
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether a second piece of tumor was collected and released to a biobank.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

dimensions of each specimen meet the criteria specified within the relevant tissue procurement SOP
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether the dimensions of each specimen meet the criteria specified within the relevant tissue procurement standard operating procedure (SOP).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on deviations in specimen dimensions from a tissue procurement SOP
type: Class
subclass of: textual entity
definition: A textual entity that states information relevant to deviations from a tissue procurement SOP with regards to specimen dimensions.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

normal adjacent tissue released to the biobank in addition to tumor tissue
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether normal adjacent tissue was released to the biobank in addition to the tumor tissue.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

time of specimen transfer from pathology gross room to a biobank
type: Class
subclass of: data item
definition: A data item indicating the time when a specimen was transferred from a pathology gross room to a biobank.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

no recurrence of tumor
type: Class
subclass of: information content entity
definition: An information content entity that is about the status of a tumor and indicates that there has not been a recurrence.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

follow-up on donor outcome comment from tissue procurement
type: Class
subclass of: comment from tissue procurement
definition: A comment from tissue procurement that was submitted as part of a follow-up documenting donor outcome after initial specimen collection.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

participant signed and dated informed consent form
type: Class
subclass of: information content entity
example of usage: Did the participant sign and date the informed consent for HRRC/IRB#11-279?
definition: An information content entity that is an indicator of whether the participant signed and dated a specified informed consent form.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen collection quality review comment
type: Class
subclass of: textual entity
definition: A textual entity that states information relevant to a review to determine if requirements were met for a specimen collection from a donor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: case quality review comment
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

minimum required pre-operative RNA and DNA PAXgene tubes were collected
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether the minimum required pre-operative RNA and DNA PAXgene tubes were collected from a donor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

desired plasma and serum aliquots were obtained
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether the desired plasma and serum aliquots were obtained from a specimen donor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

top priority tumor specimen was obtained and processed with a particular FFPE fixation delay protocol
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether a tumor specimen was obtained and processed with a particular FFPE fixation delay protocol to meet the top priority for tissue procurement.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

additional tumor specimen was obtained and processed with a particular FFPE fixation delay protocol
type: Class
subclass of: information content entity
definition: 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.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

local pathology review of QC FFPE tumor tissue H&E slide was completed
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether the local pathology review of a hematoxylin (H&E) slide derived from a quality control (QC) formalin-fixed paraffin-embedded (FFPE) tumor tissue was completed.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

local pathology review was consistent with site of tissue procurement diagnostic pathology report
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether the local pathology review was consistent with the findings of the diagnostic pathology report from the site of specimen collection from a donor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen donor clinical data entry was completed
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether clinical data entry was completed for a specimen donor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: case clinical data entry was completed
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

tumor specimen satisfied criteria of necrosis percentage and tumor content
type: Class
subclass of: information content entity
example of usage: Required tumor module satisfies the project criteria of necrosis percentage of less than 20% and tumor content of greater than or equal to 50% tumor cells by surface area
definition: An information content entity that is an indicator of whether the tumor specimen obtained satisfied criteria of necrosis percentage and tumor content of tumor cells by surface area.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

all requirements for an investigation are met enabling release of specimen for shipment.
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether all requirements for an investigation were met such that a specimen from a particular donor is released for shipment.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: case meets all requirements for an investigation and is released for shipment.
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

activity related to a particular specimen donor was stopped.
type: Class
subclass of: information content entity
definition: An information content entity that is an indicator of whether activity related to a particular specimen donor was stopped.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: case was stopped
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

activity related to a particular specimen donor was stopped because not enough blood collected
type: Class
subclass of: activity related to a particular specimen donor was stopped.
definition: An activity related to a particular specimen donor was stopped that is because there was not enough blood collected.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: case was stopped because not enough blood collected
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

activity related to a particular specimen donor was stopped because not enough tissue
type: Class
subclass of: activity related to a particular specimen donor was stopped.
definition: An activity related to a particular specimen donor was stopped that is because there was not enough tissue.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: case was stopped because not enough tissue
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

activity related to a particular specimen donor was stopped because tissue was too necrotic
type: Class
subclass of: activity related to a particular specimen donor was stopped.
definition: An activity related to a particular specimen donor was stopped that is because the tissue was too necrotic.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: case was stopped because tissue was too necrotic
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

activity related to a particular specimen donor was stopped because tissue was benign
type: Class
subclass of: activity related to a particular specimen donor was stopped.
definition: An activity related to a particular specimen donor was stopped that is because the tissue was benign.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: case was stopped because tissue was benign
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

activity related to a particular specimen donor was stopped because tissue was not released to a biobank
type: Class
subclass of: activity related to a particular specimen donor was stopped.
definition: An activity related to a particular specimen donor was stopped that is because the tissue was not released to a biobank.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: case was stopped because tissue was not released to biobank
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

research authorization for post mortem specimen donation
type: Class
subclass of: act of authorizing
definition: An authorization in which a legally authorized individual is asked to give permission for general research for post mortem specimen donation from a person they represent.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

research authorization obtainer role for post mortem donation of specimens from a legally authorized representative
type: Class
subclass of: role
definition: A role borne by a person 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 general research for the person they legally represent.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: obtainer of research authorization for post-mortem specimen donation
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

research authorization documentation for post mortem specimen donation
type: Class
subclass of: obsolete authorization document
definition: An authorization documentation that is the output of a research authorization for post mortem specimen donation.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

research authorization for post mortem specimen donation was obtained
type: Class
subclass of: information content entity
definition: An information content entity that indicates whether research authorization for post mortem specimen donation was obtained.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

research authorization documentation for post mortem specimen donation that is affirmative
type: Class
subclass of: research authorization documentation for post mortem specimen donation
definition: A research authorization documentation for post mortem specimen donation establishing agreement for post-mortem donation and use in general research.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: agreed to research authorization for post mortem specimen donation
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

research authorization documentation for post mortem specimen donation that is negative
type: Class
subclass of: research authorization documentation for post mortem specimen donation
definition: A research authorization documentation for post mortem specimen donation establishing the lack of agreement for post-mortem donation and use in general research.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: refused research authorization documentation for post mortem specimen donation
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

research authorization for post mortem specimen donation not obtained due to religious reasons
type: Class
subclass of: research authorization documentation for post mortem specimen donation
definition: A research authorization documentation for post mortem specimen donation in which the reason authorization was not obtained was due to due to religious reasons.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: refused due to religious reasons
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

research authorization for post mortem specimen donation not obtained due to surgeon's recommendation
type: Class
subclass of: research authorization documentation for post mortem specimen donation
definition: A research authorization documentation for post mortem specimen donation in which authorization was not obtained because the donors surgeon did not recommend it.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: refused due to surgeon's recommendation
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

research authorization for post mortem specimen donation not obtained because legally authorized representative felt pressured
type: Class
subclass of: research authorization documentation for post mortem specimen donation
definition: A research authorization documentation for post mortem specimen donation because the legally authorized representative felt pressured into making a decision.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: refused because legally authorized representative felt pressured
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

research authorization for post mortem specimen donation not obtained because legally authorized representative felt too distraught
type: Class
subclass of: research authorization documentation for post mortem specimen donation
definition: A research authorization documentation for post mortem specimen donation in which authorization was not obtained because the the legally authorized representative felt too distraught.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: refused because legally authorized representative too distraught
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

research authorization for post mortem specimen donation not obtained because legally authorized representative needed more time to make a decision
type: Class
subclass of: research authorization documentation for post mortem specimen donation
definition: A research authorization documentation for post mortem specimen donation in which authorization was not obtained because the the legally authorized representative needed more time to make a decision.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: refused because legally authorized representative needed more time to make a decision
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

research authorization for post mortem specimen donation not obtained because legally authorized representative was uncomfortable with the risks
type: Class
subclass of: research authorization documentation for post mortem specimen donation
definition: A research authorization documentation for post mortem specimen donation in which authorization was not obtained because the the legally authorized representative was uncomfortable with the risks of the request.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: refused because legally authorized representative was uncomfortable with the risks
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

research authorization for post mortem specimen donation not obtained because legally authorized representative was afraid the decision might affect the surgery plans of donor
type: Class
subclass of: research authorization documentation for post mortem specimen donation
definition: A research authorization documentation for post mortem specimen donation in which authorization was not obtained because the the legally authorized representative was afraid the decision might affect the surgery plans for the donor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: refused because legally authorized representative was afraid the decision would affect surgery plans
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

research authorization for post mortem specimen donation not obtained because legally authorized representative did not agree with the activity of biobanking
type: Class
subclass of: research authorization documentation for post mortem specimen donation
definition: A research authorization documentation for post mortem specimen donation in which authorization was not obtained because the the legally authorized representative did not agree with the activity of biobanking.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: refused because legally authorized representative did not agree with the activity of biobanking.
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

research authorization for post mortem specimen donation not obtained because legally authorized representative did not show up to the appointment as scheduled
type: Class
subclass of: research authorization documentation for post mortem specimen donation
definition: A research authorization documentation for post mortem specimen donation in which authorization was not obtained because the the legally authorized representative did not show up to the appointment as scheduled.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: refused because legally authorized representative did not show up to the appointment as scheduled.
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

date of research protocol approval as determined by an institutional review board
type: Class
subclass of: data item
definition: A data item that indicates the calendar date on which a research protocol was approved by an Institutional Review Board related to where the research will take place.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: IRB approval date
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

date of research protocol expiration as determined by an institutional review board
type: Class
subclass of: data item
definition: A data item that indicates the calendar date on which a research protocol expires and becomes inactive as determined by an Institutional Review Board.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: IRB expiration date
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

identification number of a protocol at a particular site
type: Class
subclass of: centrally registered identifier symbol
definition: An centrally registered identifier symbol assigned by an Institutional Review Board (IRB) that identifies a particular protocol at a given site.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: protocol number at a site
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

date that research authorization for post mortem specimen donation was witnessed
type: Class
subclass of: data item
definition: A data item that indicates the calendar date on which the signing of the research authorization for post mortem specimen donation by the legally authorized individual was witnessed.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

date of research authorization verification
type: Class
subclass of: data item
definition: A data item that indicates the calendar date on which the receipt of the research authorization was verified by study personnel.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: research authorization verification date
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of person screening specimen donors
type: Class
subclass of: personal name
definition: A personal name that designates who performed the screening of a potential specimen donor for a research study.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: specimen donor screener
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

name of person obtaining authorization from legally authorized representative for post-mortem specimen donation
type: Class
subclass of: personal name
definition: 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.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Research authorization obtainer for post-mortem specimen donation
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

date on which research authorization was obtained from legally authorized representative
type: Class
subclass of: data item
definition: A data item that indicates the calendar date on which a research authorization was obtained from a specimen donor's legally authorized representative.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: Research authorization date
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

identifier for legally authorized representative
type: Class
subclass of: identifier
definition: An identifier that uniquely identifies a particular legally authorized representative in a research study.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: legal representative identifier
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

relationship between person signing research authorization and specimen donor
type: Class
subclass of: specifically dependent continuant
definition: A relationship that may be biological or legal, between the specimen donor and the legally authorized representative who signed the research authorization.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen donor's date of birth
type: Class
subclass of: date of birth
definition: A date of birth that signifies the calendar date on which a particular donor of a specimen was born.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: donor's date of birth
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

donor's biological sex
type: Class
subclass of: biological sex
definition: Biological sex of the person who bears the role of donor.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: donor's gender
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

post mortem donor role
type: Class
subclass of: role
definition: A role borne by a person who has died from whom specimens are collected.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

age of specimen donor at time that authorization from legally authorized representative was obtained
type: Class
subclass of: age measurement datum
definition: An age measurement datum that indicates the age of the specimen donor at the time that authorization from their legally authorized representative was obtained.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

indicator of whether specimen donor has reached the age of majority
type: Class
subclass of: information content entity
definition: An Information content entity that indicates whether the specimen donor has reached the age of majority as defined by the appropriate regulation.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: age of majority indicator
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comments related to research authorization process
type: Class
subclass of: textual entity
definition: A textual entity that provides additional information that may be relevant to the research authorization verification process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: research authorization comments
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

willingness to be contacted for a research study
type: Class
subclass of: information content entity
definition: An information content entity that signifies the willingness of an individual to be contacted for a research study.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: recontact indicator
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

agreement to a specified research addendum
type: Class
subclass of: obsolete authorization document
definition: An authorization documentation in which a legally authorized individual agrees to a specific research addendum for the person they represent.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: research addendum authorization
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

authorization documentation for postmortem specimen donation for a specified purpose
type: Class
subclass of: obsolete authorization document
definition: An authorization documentation for postmortem specimen donation in which specimens are to be used for a specified purpose (e.g., transplantation, research, education).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: authorization for anatomical gift
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

authorization for postmortem specimen donation for transplantation purposes only
type: Class
subclass of: authorization documentation for postmortem specimen donation for a specified purpose
definition: An authorization documentation for postmortem specimen donation for a specified purpose which is solely for the purpose of transplantation to another person or persons.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: tissue donation for transplant only
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

authorization for postmortem specimen donation for transplantation and research
type: Class
subclass of: authorization documentation for postmortem specimen donation for a specified purpose
definition: An authorization documentation for postmortem specimen donation for a specified purpose which is for transplantation, research, education and the advancement of science.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: tissue donation for transplant and research
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

authorization not obtained for whole brain donation
type: Class
subclass of: authorization documentation for postmortem specimen donation for a specified purpose
definition: An authorization documentation for post mortem specimen donation in which authorization is not obtained for whole brain donation.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

limitations on research authorization for use of donated specimens
type: Class
subclass of: authorization documentation for postmortem specimen donation for a specified purpose
definition: An authorization documentation for postmortem specimen donation in which authorization includes specific limitations or additional information related to the use of tissue for research.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: tissue use limitations
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

presence of metastatic tumor exclusion criterion
type: Class
subclass of: exclusion criterion
definition: An exclusion criterion that defines whether a metastatic tumor is present, which if met, makes an individual unsuitable for a given task or participation in a given process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

presence of a tumor larger than a specified size exclusion criterion
type: Class
subclass of: exclusion criterion
definition: An exclusion criterion that defines whether a tumor is larger than a specified size, which if met, makes an individual unsuitable for a given task or participation in a given process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

authorization to collect of minimum number of organ/tissue types for a specific study inclusion criterion
type: Class
subclass of: inclusion criterion
definition: An inclusion criterion that defines whether the specimen donor has provided authorization to allow for the minimum number of organs/tissue types for a specific study to be collected, which when met, makes a specimen donor suitable for a given task or participation in a given process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

tissue collection timing and placed in fixative inclusion criterion
type: Class
subclass of: inclusion criterion
example of usage: A challenging inclusion criterion is defined as whether it is likely that tissue collection can be started AND the first tissue can be placed in fixative within eight hours of death.
definition: An inclusion criterion that is defined by whether it is likely that tissue collection can be started AND the first tissue can be placed in fixative within a specified period of time from cardiac cessation or recorded time of death (observed or presumed) for a specimen donor, which if met, makes a specimen donor suitable for a given task or participation in a given process.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

time since radiation therapy was received prior to surgery
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the time elapsed since radiation therapy prior to surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

time since chemotherapy was received prior to surgery
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the time elapsed since chemotherapy prior to surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

time since immunotherapy was received prior to surgery
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the time elapsed since immunotherapy prior to surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

time since hormonal therapy was received prior to surgery
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the time elapsed since hormonal therapy prior to surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

date of radiation therapy prior to surgery
type: Class
subclass of: data item
definition: A data item that reports the calendar date when radiation therapy was received prior to surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

date of chemotherapy prior to surgery
type: Class
subclass of: data item
definition: A data item that reports the calendar date when chemotherapy was received prior to surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

date of immunotherapy prior to surgery
type: Class
subclass of: data item
definition: A data item that reports the calendar date when immunotherapy was received prior to surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

date of hormonal therapy prior to surgery
type: Class
subclass of: data item
definition: A data item that reports the calendar date when hormonal therapy was received prior to surgery.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

lifelong non-drinker of alcohol
type: Class
subclass of: Alcohol Use History
definition: An Alcohol Use History in which there is no alcohol consumption.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

current non-drinker of alcohol
type: Class
subclass of: Alcohol Use History
definition: An Alcohol Use History in which there was alcohol consumption in the past but is currently a non-drinker of alcohol.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

moderate alcohol consumption history
type: Class
subclass of: Alcohol Use History
definition: 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.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

greater than moderate alcohol consumption history
type: Class
subclass of: Alcohol Use History
definition: 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.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

duration of greater than moderate alcohol consumption prior to enrollment
type: Class
subclass of: time measurement datum
definition: 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.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

lifelong non-smoker history
type: Class
subclass of: Tobacco Smoking History
example of usage: Less than 100 cigarettes smoked in lifetime
definition: A Smoking History in which there was no or an insignificant level of smoking.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

current smoker history
type: Class
subclass of: Tobacco Smoking History
definition: A Smoking History in which there is current smoking either on a daily or non-daily basis.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

current reformed smoker for more than 15 years history
type: Class
subclass of: Tobacco Smoking History
definition: A Smoking History in which there is no current smoking and has not been smoking for more than 15 years.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

current reformed smoker for less than 15 years history
type: Class
subclass of: Tobacco Smoking History
definition: A Smoking History in which there is no current smoking and has not been smoking for less than 15 years.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

timing of scoring performance status
type: Class
subclass of: one-dimensional temporal region
definition: A one-dimensional temporal region during which a cancer patient's performance status (general well-being and activities of daily life) was assessed.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

preoperative performance status score
type: Class
subclass of: timing of scoring performance status
definition: A timing of scoring performance status that occurs prior to an operation to treat cancer.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

pre-adjuvant performance status score
type: Class
subclass of: timing of scoring performance status
definition: A timing of scoring performance status that occurs prior to adjuvant therapy to treat cancer.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

post adjuvant performance status score
type: Class
subclass of: timing of scoring performance status
definition: A timing of scoring performance status that occurs after adjuvant therapy to treat cancer.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment from clinical data entry form
type: Class
subclass of: textual entity
definition: A textual entity that states additional information relevant to the filling out of a clinical data entry form.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

pill-based hormonal birth control method
type: Class
subclass of: Birth Control Method
definition: A birth control method that involves the use of an oral hormone-based contraceptive typically taken as a pill.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

injection-based hormonal birth control method
type: Class
subclass of: Birth Control Method
definition: A birth control method that involves the injection of hormones.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

intrauterine device-based hormonal birth control method
type: Class
subclass of: Birth Control Method
definition: A birth control method that involves the use of an intrauterine device (IUD) to deliver hormones.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: IUD-based hormonal birth control method
definition source: OBIB
ontology term requester: NCI BBRB

patch-based hormonal birth control method
type: Class
subclass of: Birth Control Method
definition: A birth control method that involves the administration of hormones through a transdermal patch delivery system.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

vaginal ring-based hormonal birth control method
type: Class
subclass of: Birth Control Method
definition: A birth control method that involves the administration of hormones through a vaginal ring.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

duration of hormonal birth control use prior to enrollment
type: Class
subclass of: time measurement datum
definition: 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.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

time since last usage of hormonal birth control
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the time elapsed since the participant last used hormonally based birth control.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on the use of hormonally based birth control
type: Class
subclass of: textual entity
definition: A textual entity that states additional information relevant to the use of hormonally based birth control.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

duration of hormone replacement therapy prior to enrollment
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the duration of hormone replacement therapy prior to enrollment in a study.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

time since last usage of hormone replacement therapy
type: Class
subclass of: time measurement datum
definition: A time measurement datum that is the result of measuring the time elapsed since the participant last used hormonally replacement therapy.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on the use of hormone replacement therapy
type: Class
subclass of: textual entity
definition: A textual entity that states additional information relevant to the use of hormone replacement therapy.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

comment on exposure to environmental and workplace carcinogens
type: Class
subclass of: textual entity
definition: A textual entity that states additional information relevant to the history of exposure to environmental and workplace carcinogens.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

colorectal cancer risk factor
type: Class
subclass of: risk factor
definition: A risk factor that is associated with increased likelihood of colorectal cancer.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

high meat diet colorectal cancer risk factor
type: Class
subclass of: colorectal cancer risk factor
example of usage: a diet that is high in beef, lamb, or liver and hot dogs and some luncheon meats.
definition: A colorectal cancer risk factor that is having a diet that is high in red meats and processed meats.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

obesity colorectal cancer risk factor
type: Class
subclass of: colorectal cancer risk factor
definition: A colorectal cancer risk factor that is having been obese.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

Type II diabetes colorectal cancer risk factor
type: Class
subclass of: colorectal cancer risk factor
definition: A colorectal cancer risk factor that is having Type II diabetes mellitus.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

previous colorectal polyps colorectal cancer risk factor
type: Class
subclass of: colorectal cancer risk factor
definition: A colorectal cancer risk factor that is having had colorectal polyps.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

familial adenomatous polyposis colorectal cancer risk factor
type: Class
subclass of: colorectal cancer risk factor
definition: A colorectal cancer risk factor that is having familial adenomatous polyposis or having a family member with familial adenomatous polyposis.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

estrogen alone hormone replacement therapy
type: Class
subclass of: hormone replacement therapy
definition: A hormone replacement therapy where the hormone is estrogen.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

estrogen with progestin hormone replacement therapy
type: Class
subclass of: hormone replacement therapy
definition: A hormone replacement therapy where the hormones are estrogen and progestin.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

progestin alone hormone replacement therapy
type: Class
subclass of: hormone replacement therapy
definition: A hormone replacement therapy where the hormone is progestin.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

testosterone hormone replacement therapy
type: Class
subclass of: hormone replacement therapy
definition: A hormone replacement therapy where the hormone is testosterone.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of sepsis
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of sepsis.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of pneumonia
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of pneumonia.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of open wounds
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of open wounds.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of high unexplained fever
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of a high unexplained fever .
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of positive blood cultures
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of positive blood cultures.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of abnormal white blood cell levels
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of abnormal white blood cell levels.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of fungal infections
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of fungal infections.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of ascites
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of the presence of ascites fluid.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of cellulitis
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of cellulitis.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of blood transfusion in foreign country
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of receiving a blood transfusion while in another country.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of human tissue transplant
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of receiving a human tissue or organ transplant .
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of animal tissue xenotransplant
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of receiving an animal tissue or organ xenotransplant.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of smallpox vaccination
type: Class
subclass of: clinical history
definition: A clinic history in which there is a history of a recent of smallpox vaccination.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

a clinical history of contact with someone with smallpox
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of contact with someone who recently had smallpox.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of dialysis
type: Class
subclass of: clinical history
example of usage: The patient had a clinical history of dialysis treatment three times a week for longer than one month.
definition: A clinical history in which there is a history of significant regular dialysis treatment.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of cancer at death
type: Class
subclass of: clinical history
definition: A clinical history in which there is a current diagnosis of cancer at death.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of cancer within a time period before death
type: Class
subclass of: clinical history
example of usage: A clinical history in which there is a history of cancer diagnosis in the preceding five years.
definition: A clinical history in which there is a history of cancer diagnosis within a specified time frame.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of tuberculosis
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of tuberculosis .
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of meningitis at death
type: Class
subclass of: clinical history
definition: A clinical history in which there was active meningitis at death.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of encephalitis
type: Class
subclass of: clinical history
definition: A clinical history in which there was active encephalitis at death.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of long term steroid use
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of long term steroid use.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of osteomyelitis
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of osteomyelitis.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of unexplained seizures
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of unexplained seizures.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of unexplained weakness and fatigue
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of unexplained weakness and fatigue described as flu-like symptoms.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of exposure to toxins
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of exposure to toxic substances that may have led to chronic conditions.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of exposure to rabies
type: Class
subclass of: clinical history
example of usage: 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.
definition: A clinical history in which there is a history of an animal bite in recent past, from an animal suspected to have rabies.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

indication of heroin use
type: Class
subclass of: information content entity
definition: An information content entity that indicates whether an individual ever used heroin in any manner.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

Indication of recent cocaine use
type: Class
subclass of: information content entity
example of usage: The participant's clinical history included cocaine use in the last 5 years.
definition: An information content entity that indicates whether an individual recently used cocaine.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

indication of male homosexual sexual activity
type: Class
subclass of: information content entity
definition: An information content entity in that indicates whether a man has ever had sex with another man.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

an indication of illegal injectable drug use
type: Class
subclass of: information content entity
example of usage: An information content entity in which the individual used illegal injectable drugs in the last 5 years.
definition: An information content entity that indicates whether an individual recently used injectable drugs for non-medical purposes in the recent past.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of clotting disorders
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of clotting disorders, such as hemophilia, requiring treatment with human-derived clotting factors.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of growth hormone use
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of growth hormone use.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of inability to have Human Immunodeficiency Virus testing due to hemodilution
type: Class
subclass of: clinical history
definition: 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.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of unexplained weight loss
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of unexplained weight loss.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of night sweats
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of night sweats.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of blue or purple spots on skin or mucous membranes
type: Class
subclass of: clinical history
definition: A clinical history in which there is a of blue or purple spots on the skin or mucus membranes (typical of Kaposi's sarcoma).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of unexplained lymphadenopathy
type: Class
subclass of: clinical history
example of usage: A clinical history in which there is a history of unexplained lymphadenopathy lasting more than one month.
definition: A clinical history in which there is a history of unexplained lymphadenopathy of a specific duration.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of a prolonged fever
type: Class
subclass of: clinical history
example of usage: A clinical history in which there is a history of fever of at least 38.6 Celsius for more than 10 days.
definition: A clinical history in which there is a history of fever of at least 38.6 Celsius for a specified duration.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of an unexplained cough or shortness of breath
type: Class
subclass of: clinical history
definition: A clinical history in which there is are active signs of unexplained persistent cough and/or shortness of breath.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of opportunistic infections
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of opportunistic infections.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of sexually transmitted disease
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of sexually transmitted diseases
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of drug abuse
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of drug abuse.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of Severe Acute Respiratory Syndrome
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of a Severe Acute Respiratory Syndrome (SARS) diagnosis.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of exposure to Severe Acute Respiratory Syndrome
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of recent contact with someone who has Severe Acute Respiratory Syndrome (SARS).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of West Nile Virus
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of West Nile Virus (WNV) infection.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of West Nile Virus exposure
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of contact with a human or animal who has West Nile Virus (WNV).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of gonorrhea
type: Class
subclass of: clinical history
example of usage: A clinical history in which there is a history of current gonorrhea infection or treatment for gonorrhea in the last 12 months.
definition: A clinical history in which there is a history of active gonorrhea infection or treatment for gonorrhea in the recent past.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of syphilis
type: Class
subclass of: clinical history
example of usage: A clinical history in which there is a history of current syphilis infection or treatment for syphilis in the last 12 months.
definition: A clinical history in which there is a history of active syphilis infection or treatment for syphilis in the recent past.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of Hepatitis B
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of Hepatitis B infection.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of Hepatitis C
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of Hepatitis C infection.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of Human Immunodeficiency Virus
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of Human Immunodeficiency Virus (HIV).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of lupus
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of systemic lupus
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of sarcoidosis
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of sarcoidosis.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of scleroderma
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of scleroderma.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of Reye's Syndrome
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of Reye's Syndrome.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of rheumatoid arthritis
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of rheumatoid arthritis.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of idiopathic heart disease
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of idiopathic heart disease.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of Alzheimer's disease
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of Alzheimer's Disease.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of dementia of unknown cause
type: Class
subclass of: clinical history
definition: 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).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of Multiple Sclerosis
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of Multiple Sclerosis (MS).
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

clinical history of Amyotrophic Lateral Sclerosis
type: Class
subclass of: clinical history
definition: A clinical history in which there is a history of Amyotrophic Lateral Sclerosis (ALS)
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

indication of having resided in a Northern European military base
type: Class
subclass of: information content entity
example of usage: An information content entity in which there is an indication of whether an individual resided on a Northern European military base for 6 months from 1980-1990.
definition: An information content entity in which there is an indication of whether an individual resided on a Northern European military base for a specified duration during a specific time frame.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

indication of having resided in Europe during a specific time frame
type: Class
subclass of: information content entity
example of usage: An information content entity in which there is an indication of whether an individual resided in Europe from 1980-1996.
definition: An information content entity in which there is an indication of whether an individual resided in Europe during a specific time frame
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

indication of performing sexual acts in exchange for money or drugs
type: Class
subclass of: information content entity
definition: An information content entity in which there is an indication of whether an individual ever performed sexual acts in exchange for money or drugs.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

indication of time in jail
type: Class
subclass of: information content entity
example of usage: An information content entity in which there is an indication of whether an individual spent more than 72 hours in a correction/detention center in the last year.
definition: An information content entity in which there is an indication of whether an individual spent more than 72 hours in a correction/detention center in the recent past.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: indication of jail time
definition source: OBIB
ontology term requester: NCI BBRB

indication of a tattoo from unregulated tattoo parlor
type: Class
subclass of: information content entity
example of usage: An information content entity in which there is an indication of whether an individual had a tattoo done in a state that does not regulate tattoo parlors, in the last year.
definition: An information content entity in which there is an indication of whether an individual had a tattoo done in a state that does not regulate tattoo parlors, in the recent past.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

indication of illegal prescription drug use
type: Class
subclass of: information content entity
definition: An information content entity in which there is an indication of whether an individual has used prescription pills that were not prescribed to them.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

indication of intravenous drug use
type: Class
subclass of: information content entity
example of usage: An information content entity in which there is an indication of whether an individual has used illegal intravenous drugs in the past 5 years.
definition: An information content entity in which there is an indication of whether an individual has used illegal intravenous drugs in a specified time frame.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

indication of having lived in the United Kingdom during specific time frame
type: Class
subclass of: information content entity
example of usage: An information content entity in which there is an indication of whether an individual spent a total of three or more months in the United Kingdom, any time from 1980-1996.
definition: An information content entity in which there is an indication of whether an individual spent a total of three or more months in the United Kingdom, in a specified time frame.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

indication of body piercing from non-professional
type: Class
subclass of: information content entity
definition: An information content entity in which there is an indication of whether an individual has signs of non-professional body piercing.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

indication of tattoo from non-professional
type: Class
subclass of: information content entity
definition: An information content entity in which there is an indication of whether an individual has signs of non-professional tattoos.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

indication of residence in state-run group home at time of death
type: Class
subclass of: information content entity
definition: An information content entity in which there is an indication of whether an individual was a resident of a state-run group home at time of death.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

indication of having resided in Europe during specific time frame
type: Class
subclass of: information content entity
example of usage: An indication of whether an individual lived in Europe for at least 5 years since 1980.
definition: An information content entity in which there is an indication of whether an individual lived in Europe for at least 5 years during a specific time.
term editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

biobank
type: Class
subclass of: object aggregate
definition: 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.
term editor: Mathias Brochhausen
definition source: definition derived from the definition of 'human biobank', based on http://www.ethikrat.org/files/der_opinion_human-biobanks.pdf

human biobank
type: Class
subclass of: biobank
definition: A human biobank is a collections of samples of human body substances (e.g. Tissue, blood, DNA) which are linked to personal data and socio deographic information about the donors of the material. They have a dual nature as collections of samples and data."
definition source: Deutscher Ethikrat: Human biobanks for research. Opinion. Berlin, 2010. http://www.ethikrat.org/files/der_opinion_human-biobanks.pdf

settlement part of address of sample collection or study contact
type: Class
equivalent class: Class
  intersection of: settlement part of address
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: postal address
      intersection of: Restriction
        on property: is contact information about
        some values from: Class
subclass of: settlement part of address
definition: The part of a sample collection or study contact's adress denoting a settlement.
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study contact city

biobank proper name
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: designates
    some values from: biobank
subclass of: identifier
definition: An identifier in natural language referring to a biobank.
term editor: Mathias Brochhausen
alternative label: Name of biobank

ISO 3166-1 alpha-2 code
type: Class
subclass of: identifier
subclass of: Restriction
  on property: designates
  some values from: Class
    union of: geopolitical dependency
    union of: sovereign state
definition: 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.
term editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/ISO_3166-1_alpha-2
comment: 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.

biobank idenfier with ISO 3166-1 alpha-2 code
type: Class
subclass of: biobank proper name
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: ISO 3166-1 alpha-2 code
  intersection of: Restriction
    on property: designates
    some values from: biobank
definition: A biobank identifier that has an ISO 3166-1 alpha-2 code as a part.
term editor: Mathias Brochhausen
alternative label: Biobank ID
comment: 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).

ISO 3166-1 alpha-2 code for sample collection or study contact
type: Class
equivalent class: Class
  intersection of: ISO 3166-1 alpha-2 code
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: postal address
      intersection of: Restriction
        on property: is contact information about
        some values from: Class
subclass of: ISO 3166-1 alpha-2 code
definition: The ISO 3166-1 alpha-2 code that is part of the sample collection or study contact's postal address.
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study contact country

biobank organization
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Class
    union of: Restriction
      on property: owns
      some values from: biobank
    union of: Restriction
      on property: administrates
      some values from: biobank
  intersection of: Restriction
    on property: has characteristic
    some values from: legal person role
subclass of: organization
subclass of: Restriction
  on property: has organization member
  some values from: biobank contact person
definition: An organization bearing legal personality that owns or adminstrates a biobank.
term editor: Mathias Brochhausen
alternative label: biobank juristic person

contacting
type: Class
subclass of: planned process
definition: A planned process that involves a human being and is intended to initiate a communication with another human being.
term editor: Mathias Brochhausen
comment: Contacting is the process of one human being starting a communication process with another human being. Contacting can be done using all modes of communication used by humans.

contact role
type: Class
subclass of: role in human social processes
subclass of: Restriction
  on property: realized in
  some values from: contacting
subclass of: Restriction
  on property: realized in
  all values from: contacting
subclass of: Restriction
  on property: characteristic of
  all values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: is member of organization
      some values from: organization
definition: 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.
term editor: Mathias Brochhausen

biobank contact person
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: is member of organization
    some values from: biobank organization
  intersection of: Restriction
    on property: has characteristic
    some values from: biobank contact role
subclass of: Homo sapiens
definition: A human being that is member of a biobank organization and bears the organization contact role.
term editor: Mathias Brochhausen

name of biobank contact person
type: Class
equivalent class: Restriction
  on property: designates
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: is member of organization
      some values from: biobank organization
    intersection of: Restriction
      on property: has characteristic
      some values from: biobank contact role
subclass of: personal name
definition: A personal name that designates the person acting as contact for a biobank.
term editor: Mathias Brochhausen
alternative label: Biobank contact person

email address of biobank contact person
type: Class
equivalent class: Class
  intersection of: email address
  intersection of: Restriction
    on property: is contact information about
    some values from: Class
      intersection of: Homo sapiens
      intersection of: Restriction
        on property: is member of organization
        some values from: biobank organization
      intersection of: Restriction
        on property: has characteristic
        some values from: biobank contact role
subclass of: email address
definition: An email address for the purpose of contacting a biobank contact person.
term editor: Mathias Brochhausen
alternative label: Biobank contact email

postal address of biobank contact person
type: Class
equivalent class: Class
  intersection of: postal address
  intersection of: Restriction
    on property: is contact information about
    some values from: biobank contact person
subclass of: postal address
definition: Postal address used as a directive for deliveries to the biobank contact person.
term editor: Mathias Brochhausen

department
type: Class
subclass of: organization
subclass of: Class
  intersection of: Class
    complement of: Restriction
      on property: has characteristic
      some values from: legal person role
  intersection of: Restriction
    on property: is member of organization
    some values from: Class
      intersection of: organization
      intersection of: Restriction
        on property: has characteristic
        some values from: legal person role
definition: An organization with a specific responsibility that is a part of a larger organization with a specific responsibility.
definition source: http://en.wikipedia.org/wiki/Department

department of biobank contact
type: Class
equivalent class: Class
  intersection of: department
  intersection of: Restriction
    on property: has organization member
    some values from: Class
      intersection of: Homo sapiens
      intersection of: Restriction
        on property: is member of organization
        some values from: biobank organization
      intersection of: Restriction
        on property: has characteristic
        some values from: biobank contact role
subclass of: department
definition: A department that has a contact person for a biobank as an organizational member.
term editor: Mathias Brochhausen
alternative label: Biobank contact department

unique resource locator
type: Class
subclass of: centrally registered identifier
definition: A CRID that constitutes a reference to an Internet resource.
term editor: Mathias Brochhausen
alternative label: uri
definition source: http://en.wikipedia.org/wiki/Uniform_resource_locator

biobank's unique resource locator
type: Class
subclass of: unique resource locator
definition: A unique resource locator referring to the homepage of a biobank.
term editor: Mathias Brochhausen
alternative label: Biobank URL

telephone number
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: has part
  all values from: numeral
definition: A telephone number is a textual entity consisting of a sequence of digits used to call from one telephone line to another in a public switched telephone network.
term editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Telephone_number
comment: MB: This class should probably be a subclass to CRID. However, the textual definition of CRID right now states that each instance has the CRID identifier as a part. This is not the case for telephone numbers. Therefore, they cannot be subsumed under CRID now. I am looking into changing IAO accordingly. Once that is done, the class ought to be a subclass of CRID.

telephone number of biobank contact
type: Class
equivalent class: Class
  intersection of: telephone number
  intersection of: Restriction
    on property: is contact information about
    some values from: Class
      intersection of: Homo sapiens
      intersection of: Restriction
        on property: is member of organization
        some values from: biobank organization
      intersection of: Restriction
        on property: has characteristic
        some values from: biobank contact role
subclass of: telephone number
definition: A telephone number that is contact information about a biobank contact person.
term editor: Mathias Brochhausen
alternative label: Biobank contact phone

post-office box number
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: denotes
    all values from: post-office box
subclass of: identifier
definition: An identifier denoting a post-office box.
term editor: Mathias Brochhausen

post-office box
type: Class
subclass of: material entity
definition: A post-office box is material entity that is a box on the premises of a post office station and is uniquely addressable.
term editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Post-office_box

telephone number of sample collection or study contact
type: Class
equivalent class: Class
  intersection of: telephone number
  intersection of: Restriction
    on property: is contact information about
    some values from: Class
      intersection of: Homo sapiens
      intersection of: Class
        union of: Class
subclass of: telephone number
definition: A telephone number that is contact information about a sample collection or study contact person.
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study contact phone

postal code of biobank contact
type: Class
equivalent class: Class
  intersection of: postal code
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: postal address
      intersection of: Restriction
        on property: is contact information about
        some values from: Class
subclass of: postal code
definition: The postal code that is part of the postal address of the biobank contact person.
term editor: Mathias Brochhausen
alternative label: Biobank contact ZIP

ISO 3166-1 alpha-2 code for biobank contact person
type: Class
equivalent class: Class
  intersection of: ISO 3166-1 alpha-2 code
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: postal address
      intersection of: Restriction
        on property: is contact information about
        some values from: Class
subclass of: ISO 3166-1 alpha-2 code
definition: The ISO 3166-1 alpha-2 code that is part of the biobank contact person's postal address.
term editor: Mathias Brochhausen

settlement part of address
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: geographical region
definition: A textual entity that is part of a postal address and denotes a human settlement for the purpose of delivering mail.
term editor: Mathias Brochhausen

settlement part of address biobank contact
type: Class
equivalent class: Class
  intersection of: settlement part of address
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: postal address
      intersection of: Restriction
        on property: is contact information about
        some values from: Class
subclass of: settlement part of address
definition: The part of a biobank contact's adress denoting a settlement.
term editor: Mathias Brochhausen
alternative label: Biobank contact city

intra-settlement specification part of address
type: Class
equivalent class: Class
  intersection of: textual entity
  intersection of: Restriction
    on property: part of
    some values from: postal address
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: identifier
      intersection of: Restriction
        on property: designates
        some values from: Class
subclass of: textual entity
definition: A textual entity that is part of a postal address and specifies the location inside the settlement (which is specified by another part of the address). This can be a street name and a house number, or just a number or a post-office box number.
term editor: Mathias Brochhausen

intra-settlement specification part of address of biobank contact
type: Class
equivalent class: Class
  intersection of: intra-settlement specification part of address
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: postal address
      intersection of: Restriction
        on property: is contact information about
        some values from: Class
subclass of: intra-settlement specification part of address
definition: An intra-settlement specification part of address that is part of a biobank contact's postal address.
term editor: Mathias Brochhausen
alternative label: Biobank contact address

hosted study collection
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: object aggregate
    intersection of: Restriction
      on property: has part
      all values from: specimen
  intersection of: Restriction
    on property: part of
    some values from: biobank
  intersection of: Restriction
    on property: participates in
    some values from: study design execution
subclass of: object aggregate
subclass of: collection of specimens
definition: A object aggregate that consists of specimens, participates in a study and is part of a biobank.
term editor: Mathias Brochhausen
alternative label: Hosted studies

name of hosted study collection
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: designates
    some values from: hosted study collection
subclass of: sample collection identifier
definition: The proper name that designates a hosted study collection.
term editor: Mathias Brochhausen

email address of sample collection or study contact
type: Class
equivalent class: Class
  intersection of: email address
  intersection of: Restriction
    on property: is contact information about
    some values from: Class
      intersection of: Homo sapiens
      intersection of: Class
        union of: Class
subclass of: email address
definition: An email address for the purpose of contacting a sample collection or study contact person.
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study contact email

sample collection or study aim description
type: Class
equivalent class: Class
  intersection of: textual entity
  intersection of: Restriction
    on property: is about
    some values from: Class
      union of: Class
        intersection of: object aggregate
        intersection of: Restriction
      union of: Restriction
        on property: is about
        some values from: Class
subclass of: textual entity
definition: A textual entity describing a study aim or a sample collection.
term editor: Mathias Brochhausen
alternative label: Sample collection or study description

study proper name
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: designates
    some values from: study design execution
subclass of: identifier
definition: A proper name that designates a study.
term editor: Mathias Brochhausen
alternative label: Study name

name of sample collection responsible or principal investigator
type: Class
equivalent class: Restriction
  on property: designates
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Class
      union of: Class
        intersection of: Restriction
      union of: Class
        intersection of: Restriction
subclass of: personal name
definition: A personal name that designates the human being responsible for a sample collection or the human being being the principal investigator in a study.
term editor: Mathias Brochhausen
alternative label: Sample Collection Responsible / Principal Investigator

name of sample collection or study contact person
type: Class
equivalent class: Restriction
  on property: designates
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Class
      union of: Class
        intersection of: Restriction
      union of: Class
        intersection of: Restriction
subclass of: personal name
definition: A personal name that designates the person acting as contact for a sample collection or a study.
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study contact person

department of sample collection or study contact
type: Class
equivalent class: Class
  intersection of: department
  intersection of: Restriction
    on property: has organization member
    some values from: Class
      intersection of: Homo sapiens
      intersection of: Class
        union of: Class
subclass of: department
definition: A department that has a contact person for a sample collection or a study as an organizational member.
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study contact department

street
type: Class
subclass of: material entity
definition: A street is a thoroughfare in a built environment.
term editor: Mathias Brochhausen

intra-settlement specification part of address of sample collection or study contact
type: Class
equivalent class: Class
  intersection of: intra-settlement specification part of address
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: postal address
      intersection of: Restriction
        on property: is contact information about
        some values from: Class
subclass of: intra-settlement specification part of address
definition: An intra-settlement specification part of address that is part of a sample collection or study contact's postal address.
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study contact address

postal code for sample collection or study contact
type: Class
equivalent class: Class
  intersection of: postal code
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: postal address
      intersection of: Restriction
        on property: is contact information about
        some values from: Class
subclass of: postal code
definition: Postal code that is part of the address of a human being serving as sample collection or study contact.
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study contact ZIP

biobank location ISO 3166-1 alpha-2 code
type: Class
equivalent class: Class
  intersection of: ISO 3166-1 alpha-2 code
  intersection of: Restriction
    on property: designates
    some values from: Class
      intersection of: geographical region
      intersection of: Restriction
        on property: location of
        some values from: biobank
subclass of: ISO 3166-1 alpha-2 code
definition: An ISO 3166-1 alpha-2 code that designates the country a biobank is located in.
term editor: Mathias Brochhausen
alternative label: Biobank country code

CTEP organization identifier
type: Class
subclass of: identifier
subclass of: Restriction
  on property: designates
  some values from: organization
definition: An identifier for an organization that is assigned to that organization by the Cancer Therapy Evaluation Program.
term editor: Mathias Brochhausen

biobank identifier with ISO 3166-1 alpha-2 code and CTEP organization identifier
type: Class
subclass of: biobank idenfier with ISO 3166-1 alpha-2 code
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: ISO 3166-1 alpha-2 code
      intersection of: Class
        intersection of: CTEP organization identifier
        intersection of: Restriction
  intersection of: Restriction
    on property: designates
    some values from: biobank
definition: A biobank identifier that has both an ISO 3166-1 alpha-2 code and a CTEP organization code.
term editor: Mathias Brochhausen

fixed tissue specimen
type: Class
subclass of: processed specimen
subclass of: Restriction
  on property: is_specified_output_of
  some values from: fixation
definition: A processed specimen that is the output of a fixation process.
term editor: Alice Nzinga
term editor: Mathias Brochhausen

fixed tissue block specimen
type: Class
subclass of: fixed tissue specimen
definition: A fixed tissue specimen that is in block form.

fixed tissue slide specimen
type: Class
subclass of: fixed tissue specimen
definition: A fixed tissue specimen that is placed in a slide.

flash frozen specimen
type: Class
subclass of: frozen specimen
definition: A frozen specimen that has been instantly/quickly frozen by subjecting the specimen to cryogenic temperatures, or in direct contact with liquid nitrogen at -320.8F 0r -196C.
definition source: http://en.wikipedia.org/wiki/Flash_freezing

fresh tissue specimen
type: Class
subclass of: fresh specimen
definition: A fresh specimen that is in a tissue form.

frozen tissue block specimen
type: Class
subclass of: frozen specimen
definition: A frozen specimen is a tissue sample preserved in a block.

frozen tissue slide specimen
type: Class
subclass of: frozen specimen
definition: A frozen specimen that has been sliced from a tissue block into thin layers that are placed on a glass to be examined under a microscope.

microdissected specimen
type: Class
subclass of: specimen
definition: A specimen that has been procured from a histology slide under direct microscopic visualization.
term editor: Alice Nzinga
definition source: http://www.ncbi.nlm.nih.gov/pubmed/11269646

survey data
type: Class
equivalent class: Class
  intersection of: data item
  intersection of: Restriction
    on property: is_specified_output_of
    all values from: survey execution
subclass of: data item
definition: A data item that contains the outcome of a survey.
term editor: Alice Nzinga
term editor: Mathias Brochhausen

sampling specimens for biobank
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: object aggregate
      intersection of: Restriction
        on property: part of
        some values from: biobank
      intersection of: Restriction
        on property: has part
        all values from: Class
subclass of: planned process
definition: The process of collecting or selecting an aggregate of specimens into a biobank.
term editor: Mathias Brochhausen

biobank contact role
type: Class
subclass of: contact role
definition: A contact role borne by a member of a biobank organization and realized by serving as the contact for one of its biobanks.

sample collection or study contact role
type: Class
subclass of: contact role
definition: 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.

sample collection or study contact person
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Class
    union of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: has characteristic
        some values from: sample collection or study contact role
    union of: Class
      intersection of: Restriction
        on property: has characteristic
        some values from: sample collection or study contact role
      intersection of: Restriction
        on property: participates in
        some values from: study design execution
subclass of: Homo sapiens
definition: A human being acting as bearing the contact role for a sample collection or a study.

specimen disease state datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: specimen
definition: A data item that indicates the pathological assessment of a specimen.

diseased state specimen datum
type: Class
subclass of: specimen disease state datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: specimen
    intersection of: Restriction
      on property: has part
      some values from: disorder
definition: A specimen disease state datum item that specifies that the specimen in question consists of a disorder.

mixed state specimen datum
type: Class
subclass of: specimen disease state datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: specimen
    intersection of: Restriction
      on property: has part
      some values from: normal specimen
    intersection of: Restriction
      on property: has part
      some values from: disorder
definition: A specimen disease state datum that specifies that the specimen in question consists of partially normal tissue and a disorder.

normal state specimen datum
type: Class
subclass of: specimen disease state datum
subclass of: Restriction
  on property: is about
  some values from: normal specimen
definition: A specimen disease state datum that specifies that the specimenin questions consists of normal tissue.

fixation
type: Class
subclass of: material processing
definition: 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.
definition source: http://en.wikipedia.org/wiki/Fixation_%28histology%29
definition source: http://sharedresources.fhcrc.org/training/tips-about-fixation-and-formalin
comment: The choice of fixation depends on the type of study.

age interval information
type: Class
subclass of: information content entity
subclass of: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: Restriction
        on property: part of
        some values from: data set
      intersection of: Restriction
        on property: is about
        some values from: Class
definition: An information content entity that is about a data set that has age information and specifies the range of age information in that data set.
term editor: Alice Nzinga
term editor: Martin Fransson
term editor: Mathias Brochhausen
comment: Example: age interval is 18-65

average age
type: Class
subclass of: average value
subclass of: Class
  intersection of: average value
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: Class
        intersection of: measurement datum
        intersection of: Restriction
      intersection of: Restriction
        on property: part of
        some values from: data set
definition: An average value of age for a certain group of individuals.
term editor: Alice Nzinga
term editor: Mathias Brochhausen

patient registry data
type: Class
subclass of: data set
subclass of: Restriction
  on property: is about
  some values from: Homo sapiens
definition: A data set of collected secondary data related to patients with a specific diagnosis, condition, or procedure and plays an important role in post marketing surveillance of pharmaceuticals.
term editor: Alice Nzinga
term editor: Martin Fransson
alternative label: patient register data
comment: It can be said to be a formal record of an internationally agreed minimum amount of information about clinical trial.

date of data entry
type: Class
subclass of: data item
subclass of: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: one-dimensional temporal region
      intersection of: Restriction
        on property: has part
        some values from: Class
disjoint with: date of data update
disjoint with: end date of sampling for biobank
disjoint with: start date of sampling for biobank
definition: A data item that indicates the time when data about the sample collection was reported into a database.
term editor: Alice Nzinga
comment: It is denoted by Date in ISO-standard (8601) time format.

date of data update
type: Class
subclass of: data item
subclass of: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: one-dimensional temporal region
      intersection of: Restriction
        on property: has part
        some values from: Class
disjoint with: end date of sampling for biobank
disjoint with: start date of sampling for biobank
definition: A data item that indicates the time when data about the sample collection was last updated in a database.
term editor: Alice Nzinga
comment: It is expressed as a Date in ISO-standard (8601) time format.

end date of sampling for biobank
type: Class
subclass of: data item
subclass of: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: one-dimensional temporal region
      intersection of: Restriction
        on property: has part
        some values from: Restriction
disjoint with: start date of sampling for biobank
definition: A data item that indicates the time when the sampling of specimens for a biobank ended.
term editor: Alice Nzinga
comment: It is denoted by Date in ISO-standard (8601) time format.

start date of sampling for biobank
type: Class
subclass of: data item
subclass of: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: one-dimensional temporal region
      intersection of: Restriction
        on property: has part
        some values from: Restriction
definition: A data item that indicates the time when the sampling of specimens for a biobank started.
term editor: Alice Nzinga
comment: It is denoted by Date in ISO-standard (8601) time format.

comorbidity
type: Class
subclass of: diagnosis
disjoint with: primary diagnosis
definition: A diagnosis that is the outcome of a diagnostic process targeting a second or additional health problem.
term editor: Alice Nzinga
term editor: Mathias Brochhausen
alternative label: secondary infection, nosocomial infection
definition source: amended from http://en.wikipedia.org/wiki/Comorbidity
comment: It is argued that Comorbidity occurs due to a disposition established by a prior infection with a pathogenic organism of a different kind.

primary diagnosis
type: Class
subclass of: diagnosis
definition: A diagnosis that is the main reason for the inducement of medical care.
term editor: Alice Nzinga
alternative label: main diagnosis
definition source: Hint: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

count of current sampled human study participant
type: Class
subclass of: count
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: object aggregate
    intersection of: Restriction
      on property: has part
      all values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
disjoint with: physiological measurement data
definition: A count that is about the aggregate of individuals who have contributed biological specimens in a study.
term editor: Alice Nzinga

count of current total human study participant
type: Class
subclass of: count
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: object aggregate
    intersection of: Restriction
      on property: has part
      all values from: Class
        intersection of: Homo sapiens
        intersection of: Class
disjoint with: physiological measurement data
definition: A count that is about the aggregate of individuals who have been recruited to participate in a study.
term editor: Alice Nzinga

physiological measurement data
type: Class
subclass of: data item
subclass of: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      union of: disease
      union of: disorder
      union of: treatment
      union of: Class
        intersection of: function
        intersection of: Restriction
definition: A measurement datum that contains the assessment information about the functioning of a major organ system, the extent of disease or disability,as well as the provision and/or response to therapeutic interventions.
term editor: Alice Nzinga
term editor: Mathias Brochhausen
definition source: http://www.improvement.nhs.uk/physiologydiagnostics/documents/WhatisPhysiologicalMeasurement.pdf
comment: Examples: Audiology, Cardiac Physiology, GI Physiology, Neurophysiology, Ophthalmic and Vision Science, Respiratory and Sleep Physiology, Urodynamics, Vascular Technology

storage temperature setting
type: Class
subclass of: setting datum
definition: A setting datum that specifies the temperature inside a container participating in a storage process.
term editor: Alice Nzinga
term editor: Mathias Brochhausen
comment: Examples: -18 °C to -35 °C, -60 °C to -85 °C, Liquid nitrogen, Room temperature etc

omics experiment on specimen
type: Class
subclass of: study design execution
subclass of: Class
  intersection of: planned process
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes
      some values from: study design
  intersection of: Restriction
    on property: has participant
    some values from: specimen
definition: An objective specification that aims at the collective characterization and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.
term editor: Alice Nzinga
term editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Omics
comment: A tentative procedure that is aimed at discovering some characteristic of a large familiy of cellular molecules, having named by appending suffix "-omics."
comment: Technologies that measure some characteristic of a large family of cellular molecules, such as genes, proteins, or small metabolites, have been named by appending the suffix "-omics," as in "genomics." Omics refers to the collective technologies used to explore the roles, relationships, and actions of the various types of molecules that make up the cells of an organism.
comment: interrelated experiments.

number of sampled human study participants objective
type: Class
subclass of: objective specification
subclass of: Restriction
  on property: part of
  some values from: study design
disjoint with: number of total human study participant objective
definition: An objective specification that specifies the number of individuals to participate in a study and provide biological specimens to the study.
term editor: Alice Nzinga
term editor: Mathias Brochhausen

number of total human study participant objective
type: Class
subclass of: objective specification
subclass of: Restriction
  on property: part of
  some values from: study design
definition: An objective specification that specifies the total number of individuals who are planned to participate in study.
term editor: Alice Nzinga

case control study design
type: Class
subclass of: study design
disjoint with: cross sectional study design
disjoint with: longitudinal study design
disjoint with: population based study design
disjoint with: quality control study design
disjoint with: twin study design
definition: A study design that compares two groups of subjects; those with the disease or condtion under study and a similar group of subjects who do not have the condition.
term editor: Alice Nzinga

cross sectional study design
type: Class
subclass of: study design
disjoint with: longitudinal study design
disjoint with: population based study design
disjoint with: quality control study design
disjoint with: twin study design
definition: A study design in which all participants or a representative subset of participants are examined at only a single time for characteristics of a interest (e.g. a specific disease).
term editor: Alice Nzinga

longitudinal study design
type: Class
subclass of: study design
disjoint with: population based study design
disjoint with: quality control study design
disjoint with: twin study design
definition: A study design that involves repeated observations of the same entity over time. In the biobank context, longitudinal studies sample a group of people in a given time period, and study them at intervals by the acquisition and analyses of data and/or samples over time.
term editor: Alice Nzinga

cohort study design
type: Class
subclass of: longitudinal study design
disjoint with: panel study design
definition: A longitudinal study that aims to study a case-defined population who presently have a certain condition or recepient of a particular treatment that are followed over time and are compared with a similar group who do not have condition.

panel study design
type: Class
subclass of: longitudinal study design
definition: A longitudinal study that samples a cross-section and studies it at regular intervals.

population based study design
type: Class
subclass of: study design
disjoint with: quality control study design
disjoint with: twin study design
definition: A study design that is multidisciplinary done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment.
term editor: Alice Nzinga

quality control study design
type: Class
subclass of: study design
disjoint with: twin study design
definition: A study design where some aspect of the experiment is quality controlled for the purposes of quality assurance.
term editor: Alice Nzinga

twin study design
type: Class
subclass of: study design
definition: A study design usually in behavior genetics which aids the study of individual differences between genetically identical twins by highlighting the role of environmental and genetic causes on behavior.
term editor: Alice Nzinga

survey plan specification
type: Class
subclass of: plan specification
definition: A plan specification that is realized by process of gathering information (e.g. by asking questions).
term editor: Alice Nzinga
term editor: Mathias Brochhausen

medical record
type: Class
subclass of: document
definition: A document that contains information representing health-relevant qualities of a patient written in a chronological manner and that is primarily used for patient care in a clinical setting.
term editor: Martin Fransson
comment: It is a chronological written account of examination, treatment, medical history or complaints.
comment: It is used interchangeably with health record and medical chart. https://en.wikipedia.org/wiki/Medical_record

sample medical record
type: Class
subclass of: medical record
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Class
      intersection of: Restriction
        on property: has role
        some values from: participant under investigation role
      intersection of: Restriction
        on property: has role
        some values from: donor
definition: A medical record of a specimen donor.
term editor: Alice Nzinga

sample handling summary
type: Class
equivalent class: Class
  intersection of: document
  intersection of: Restriction
    on property: is about
    some values from: sample handling
subclass of: document
definition: A document that outlines the procedures employed to preserve and protect the material collected during specimen collection as an indication of sample quality.
term editor: Alice Nzinga
comment: It could be argued as to why this class was not created as an 'objective specification'. However, the emphasis here is to 'a briefing of how the specimen in the sample collection have been handled as an indication of specimen quality.'
comment: It could be freeze chain, freze time, SPREC compliant, etc.

age interval information for sampled donors
type: Class
subclass of: age interval information
subclass of: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: is about
    some values from: Restriction
      on property: part of
      some values from: Class
        intersection of: data set
        intersection of: Restriction
definition: Age interval information that is age information of specimen donors.
term editor: Alice Nzinga
alternative label: sampled group age interval
definition source: http://www.abta.org/Dictionary/67

donor patient registry data
type: Class
subclass of: patient registry data
subclass of: Restriction
  on property: is about
  some values from: donor
definition: Registry data for a patient who participates as a donor in a study.
term editor: Alice Nzinga

study subject survey data
type: Class
subclass of: survey data
subclass of: Class
  intersection of: survey data
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: Restriction
        on property: has characteristic
        some values from: participant under investigation role
      intersection of: Restriction
        on property: has characteristic
        some values from: donor
definition: A survey data for a specimen donor.
term editor: Alice Nzinga
term editor: Mathias Brochhausen
comment: Examples: Individual Disease History, Individual History of Injuries, Medication, Perception of Health, Women's Health, Reproductive History, Familial Disease History, Life Habits/Behaviors, Sociodemographic Characteristics, Socioeconomic Characteristics, Physical Environment, Mental Health, Other.

sample collection data entry
type: Class
subclass of: planned process
definition: A planned process that involves the initial entering of data about sample collection into a database.

sample collection data update
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: date of data update
definition: A planned process which involves editing of specimen collection data into a database after its initial entry.

survey execution
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes
      some values from: survey plan specification
  intersection of: Restriction
    on property: has_specified_output
    some values from: survey data
subclass of: planned process
definition: A planned process that realizes the concretization of a survey to generate an output(survey data.)

temperature regulating
type: Class
subclass of: planned process
definition: A planned process that aims to control or maintain the temperature of a material entity to a given or required measurement datum.
comment: As per placing the term as a planned process, it can be argued that nature does play a role in the final output of the actual temperature.

comment from tissue procurement
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: Class
    union of: sampling specimens for biobank
    union of: Restriction
      on property: participates in
      some values from: sampling specimens for biobank
definition: A textual entity that states additional information about the specimen or donor that is deemed relevant for the specimen collection process.
definition source: Alice Nzinga

specimen measurement
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: measurement datum
  intersection of: Restriction
    on property: has part
    some values from: length measurement datum
  intersection of: Restriction
    on property: is about
    some values from: specimen
example of usage: 3mm X 3mm X 3mm
definition: A measurement datum that is the result of measurement of the three dimensions of a specimen.
term editor: Alice Nzinga
term editor: Mathias Brochhausen

date of specimen collection
type: Class
subclass of: data item
subclass of: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: one-dimensional temporal region
      intersection of: Restriction
        on property: has part
        some values from: Class
definition: A data item that indicates the time when the collection of a specimen occurred.
term editor: Alice Nzinga
term editor: Mathias Brochhausen
alternative label: date of specimen preparation
comment: It is denoted by Date in ISO-standard (8601) time format.

specimen meeting specification
type: Class
subclass of: specimen
definition: All specimens that meet the set parameters to be procured on.
term editor: Mathias Brochhausen
alternative label: adherance to specification

surgical procedure
type: Class
subclass of: planned process
example of usage: mastectomy / craniotomy / liver resection e.t.c.
definition: A planned process that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury, or to help improve bodily function or appearance.
definition source: http://en.wikipedia.org/wiki/Surgery

specimen preparation contact
type: Class
subclass of: personal name
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Class
      union of: Restriction
        on property: participates in
        some values from: specimen collection process
      union of: Restriction
        on property: participates in
        some values from: material maintenance
    intersection of: Restriction
      on property: has characteristic
      some values from: contact role
definition: A personal name that designates the person who prepared the specimen.
term editor: Alice Nzinga

time in formalin measurement
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: Class
      union of: one-dimensional temporal region
      union of: zero-dimensional temporal region
    intersection of: Restriction
      on property: has temporal occupant
      some values from: Class
        intersection of: sample handling
        intersection of: Restriction
example of usage: 15min
definition: A time measurement datum that states the duration during which a specimen was submerged in formalin.
term editor: Alice Nzinga

specimen surgical removal
type: Class
subclass of: collecting specimen from organism
definition: A collecting specimen from organism process that involves removing the specimen from an individual through a surgical procedure.

specimen freezing
type: Class
equivalent class: Class
  intersection of: freezing storage
  intersection of: Restriction
    on property: has participant
    some values from: specimen
subclass of: freezing storage
definition: A freezing storage for the specimen.

specimen ID
type: Class
subclass of: identifier
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: centrally registered identifier symbol
  intersection of: Restriction
    on property: is about
    some values from: specimen
definition: A proper name that identifies a specimen and is usually in form of a label included in the specimen cassette.
term editor: Alice Nzinga
definition source: http://biospecimens.cancer.gov/resources/sops/GTEx_SOPs/II/A/GTEx%20Tissue%20Procurement%20SOP%20%28PR-0004%20v1.2.1%29.pdf

case ID
type: Class
subclass of: identifier
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: participates in
      some values from: specimen collection process
    intersection of: Restriction
      on property: has role
      some values from: donor
definition: 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.
term editor: Alice Nzinga
definition source: http://biospecimens.cancer.gov/resources/sops/GTEx_SOPs/II/A/GTEx%20Tissue%20Procurement%20SOP%20%28PR-0004%20v1.2.1%29.pdf

specimen measurement specification
type: Class
subclass of: objective specification
definition: An directive information entity that states the technical standard measurement set and values that determines if a specimen qualifies for procurement or not.
term editor: Alice Nzinga
definition source: http://en.wikipedia.org/wiki/Specification_(technical_standard)
comment: A specification (often abbreviated as spec) may refer to an explicit set of requirements to be satisfied by a material, design, product, or service.

time of specimen freezing
type: Class
subclass of: data item
subclass of: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: one-dimensional temporal region
      intersection of: Restriction
        on property: has temporal occupant
        some values from: specimen freezing
definition: A data item that reports the time when a specimen was frozen.
term editor: Alice Nzinga
term editor: Mathias Brochhausen

time of surgical removal of specimen
type: Class
subclass of: data item
subclass of: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: one-dimensional temporal region
      intersection of: Restriction
        on property: has temporal occupant
        some values from: specimen surgical removal
definition: A data item that reports the time when a specimen was collected by a surgical procedure.
term editor: Alice Nzinga
term editor: Mathias Brochhausen

normal specimen
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Class
    complement of: Restriction
      on property: has part
      some values from: disorder
subclass of: specimen
definition: A specimen that is normal.

hosting biobank
type: Class
equivalent class: Class
  intersection of: biobank
  intersection of: Restriction
    on property: participates in
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: part of
        some values from: study design execution
subclass of: biobank
definition: A biobank that collects and stores specimen during specimen collection primarily for the purposes of some study.
term editor: Alice Nzinga

specimen donor
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: has characteristic
    some values from: Class
      intersection of: role
      intersection of: Restriction
        on property: realized in
        some values from: specimen collection process
subclass of: Homo sapiens
definition: A Homo sapiens who contributes specimen.
term editor: Alice Nzinga
term editor: Mathias Brochhausen
alternative label: sample donor

sample handling
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Class
    intersection of: Restriction
      on property: has_specified_input
      some values from: Restriction
        on property: is_specified_output_of
        some values from: specimen collection process
    intersection of: Restriction
      on property: has_specified_output
      some values from: Class
        intersection of: specimen
        intersection of: Restriction
subclass of: planned process
definition: A planned process of preparing and submitting specimens to storage.
alternative label: specimen handling
definition source: http://www.exchangenetwork.net/standards/SampleHandling_01_06_2006_Final.pdf

start of sampling specimens for biobank
type: Class
subclass of: process boundary
subclass of: Restriction
  on property: part of
  some values from: sampling specimens for biobank
definition: The process boundary marking the beginning of a sampling of specimens into a biobank.
term editor: Mathias Brochhausen

end of sampling specimens for biobank
type: Class
subclass of: process boundary
subclass of: Restriction
  on property: part of
  some values from: sampling specimens for biobank
definition: The process boundary marking the end of a sampling of specimens into a biobank.
term editor: Mathias Brochhausen

specimen position
type: Class
equivalent class: Class
  intersection of: position
  intersection of: Restriction
    on property: characteristic of
    all values from: specimen
subclass of: position
editor preferred term: specimen position
example of usage: left side of specimen
has curation status: ready for release
definition: A position inhering in a specimen.
editor note: https://github.com/biobanking/biobanking/issues/24
term editor: Anna Maria Masci, Chris Stoeckert
alternative label: specimen laterality
definition source: OBIB

specimen integrity
type: Class
equivalent class: Class
  intersection of: wholeness
  intersection of: Restriction
    on property: characteristic of
    all values from: specimen
subclass of: wholeness
editor preferred term: specimen integrity
has curation status: ready for release
definition: A wholeness that inheres in a specimen.
editor note: https://github.com/biobanking/biobanking/issues/24
term editor: Anna Maria Masci, Chris Stoeckert
definition source: OBIB

specimen weight
type: Class
equivalent class: Class
  intersection of: mass measurement datum
  intersection of: Restriction
    on property: is about
    some values from: specimen
subclass of: mass measurement datum
editor preferred term: specimen weight
has curation status: ready for release
definition: A mass measurement datum that is the result of an assay to measure the weight of a specimen.
editor note: https://github.com/biobanking/biobanking/issues/24
term editor: Anna Maria Masci, Chris Stoeckert
definition source: OBIB

specimen slide ID
type: Class
subclass of: identifier
editor preferred term: specimen slide ID
definition: An identifier that specifically identifies a particular specimen slide.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

surgical cancer treatment
type: Class
subclass of: Cancer Therapeutic Procedure
editor preferred term: surgical cancer treatment
definition: A cancer therapeutic procedure that involves a surgical procedure as a main part.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen gross appearance of metastatic tumor
type: Class
subclass of: specimen gross appearance of tumor
editor preferred term: specimen gross appearance of metastatic tumor
definition: 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.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen gross appearance of tumor center
type: Class
subclass of: specimen gross appearance of tumor
editor preferred term: specimen gross appearance of tumor center
definition: A specimen gross appearance of the most internal topographic location of the tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

specimen gross appearance of tumor edge
type: Class
subclass of: specimen gross appearance of tumor
editor preferred term: specimen gross appearance of tumor edge
definition: A specimen gross appearance of the border of the tumor with non-tumorous tissue.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

research authorization for post mortem specimen donation for a specific tissue or fluid
type: Class
subclass of: research authorization documentation for post mortem specimen donation
editor preferred term: research authorization for post mortem specimen donation for a specific tissue or fluid
definition: A research authorization documentation for postmortem specimen donation in which the authorization is for a specified tissue or biological fluid.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

tissue specimen suitability for molecular analysis
type: Class
subclass of: conclusion textual entity
editor preferred term: tissue specimen suitability for molecular analysis
has curation status: ready for release
definition: A conclusion textual entity that signifies whether a specimen is acceptable for molecular analysis based on the assessment by a pathologist of a tissue specimen based on qualities such as purity and size.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
subclass of: process
editor preferred term: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: ready for release
definition: A process that realizes a plan which is the concretization of a plan specification.
editor note: '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.)
editor note: 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.
term editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: 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)
imported from: obi.owl

regulator role
type: Class
subclass of: regulatory role
editor preferred term: regulator role
example of usage: Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
has curation status: metadata complete
definition: a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
term editor: Person:Jennifer Fostel
alternative label: regulator
definition source: OBI
imported from: obi.owl

regulatory role
type: Class
subclass of: role
editor preferred term: regulatory role
example of usage: Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
has curation status: metadata complete
definition: a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
term editor: GROUP: Role branch
definition source: OBI, CDISC
curator note: govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent
imported from: obi.owl

material supplier role
type: Class
subclass of: service provider role
editor preferred term: material supplier role
example of usage: Jackson Labs is an organization which provide mice as experimental material
has curation status: metadata complete
definition: a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
editor note: Supplier role is a special kind of service, e.g. biobank
term editor: PERSON:Jennifer Fostel
alternative label: material provider role
alternative label: supplier
imported from: obi.owl

processed material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: material processing
subclass of: material entity
editor preferred term: processed material
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
has curation status: ready for release
definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg
imported from: obi.owl

investigation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: documenting
subclass of: Restriction
  on property: has part
  some values from: drawing a conclusion based on data
subclass of: Restriction
  on property: has part
  some values from: study design execution
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: planning
    intersection of: Restriction
      on property: has_specified_output
      some values from: study design
editor preferred term: investigation
example of usage: Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
has curation status: ready for release
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
term editor: Bjoern Peters
definition source: OBI branch derived
curator note: Could add specific objective specification
curator note: Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
imported from: obi.owl
ISA alternative term: study

evaluant role
type: Class
subclass of: material entity role
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: assay
editor preferred term: evaluant role
example of usage: When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
has curation status: ready for release
definition: a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
editor note: Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
editor note: examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
term editor: GROUP: Role Branch
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
imported from: obi.owl

assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: evaluant role
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
editor preferred term: assay
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
has curation status: ready for release
definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
editor note: 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.
term editor: PlanAndPlannedProcess Branch
alternative label: measuring
alternative label: scientific observation
definition source: OBI branch derived
imported from: obi.owl
ISA alternative term: study assay
IEDB alternative term: any method

culture medium
type: Class
subclass of: processed material
editor preferred term: culture medium
example of usage: A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
has curation status: ready for release
definition: a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
editor note: changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
term editor: Person: Jennifer Fostel, Jie Zheng
definition source: OBI
imported from: obi.owl

reagent role
type: Class
subclass of: role
editor preferred term: reagent role
example of usage: Buffer, dye, a catalyst, a solvating agent.
has curation status: metadata complete
definition: 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.
term editor: PERSON:Matthew Brush
alternative label: reagent
definition source: PERSON:Matthew Brush
curator note: 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.
imported from: obi.owl
comment: (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 t…

patient role
type: Class
subclass of: material entity role
subclass of: Restriction
  on property: characteristic of
  some values from: Homo sapiens
editor preferred term: patient role
example of usage: a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
has curation status: metadata complete
definition: 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
term editor: GROUP:Role Branch
alternative label: patient
definition source: OBI, CDISC
curator note: 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
imported from: obi.owl

material processing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: has_specified_input
  all values from: material entity
editor preferred term: material processing
example of usage: A cell lysis, production of a cloning vector, creating a buffer.
has curation status: ready for release
definition: A planned process which results in physical changes in a specified input material
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca Serra
alternative label: material transformation
definition source: OBI branch derived
imported from: obi.owl

participant under investigation role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: study design execution
editor preferred term: study subject role
example of usage: Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
has curation status: ready for release
definition: A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
editor note: A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
term editor: GROUP: Role Branch
definition source: OBI
curator note: Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS
imported from: obi.owl

responsible party role
type: Class
subclass of: investigation agent role
editor preferred term: responsible party role
example of usage: he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm
has curation status: metadata complete
definition: a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
term editor: Person: Jennifer Fostel
alternative label: responsible party
definition source: OBI
imported from: obi.owl

principal investigator role
type: Class
subclass of: responsible party role
editor preferred term: principal investigator role
has curation status: metadata incomplete
definition: a responsible party role played by a person responsible for the overall conduct of a study
term editor: Person: Jennifer Fostel
alternative label: principal investigator
curator note: CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC)
imported from: obi.owl

specimen role
type: Class
subclass of: material entity role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
editor preferred term: specimen role
example of usage: 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.
has curation status: ready for release
definition: 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
editor note: 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.
editor note: 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.
editor note: 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.
editor note: 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.
term editor: GROUP: Role Branch
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/1013
imported from: obi.owl

worker role
type: Class
subclass of: investigation agent role
editor preferred term: worker role
example of usage: Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html
has curation status: metadata complete
definition: a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline
editor note: "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
term editor: Person:Jennifer Fostel
alternative label: worker
definition source: OBI
imported from: obi.owl

filter paper
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: filter function
editor preferred term: filter paper
has curation status: metadata complete
definition: A device manufacture with the intent to provide a porous unsized paper used for filtering.
term editor: Frank Gibson
definition source: sep:00107
imported from: obi.owl

population
type: Class
subclass of: material entity
editor preferred term: population
example of usage: PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
has curation status: pending final vetting
definition: a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
editor note: 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/
term editor: PERSON: Philippe Rocca-Serra
definition source: adapted from Oxford English Dictionnary
curator note: rem1: collection somehow always involve a selection process
imported from: obi.owl

investigation agent role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: characteristic of
    some values from: Restriction
      on property: has characteristic
      some values from: Restriction
        on property: concretizes
        some values from: Restriction
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: investigation
editor preferred term: investigation agent role
example of usage: The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
has curation status: ready for release
definition: A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
editor note: Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
editor note: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
term editor: GROUP: Role Branch
alternative label: investigator
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
imported from: obi.owl
ISA alternative term: study person role
comment: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)

organization
type: Class
subclass of: material entity
editor preferred term: organization
example of usage: 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.
has curation status: ready for release
definition: 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.
editor note: 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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
term editor: PERSON: Susanna Sansone
definition source: GROUP: OBI
imported from: obi.owl

DNA extraction
type: Class
subclass of: nucleic acid extraction
subclass of: Restriction
  on property: has_specified_output
  some values from: deoxyribonucleic acid
editor preferred term: DNA extraction
has curation status: metadata incomplete
definition: A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl

plan
type: Class
subclass of: realizable entity
editor preferred term: plan
example of usage: The plan of researcher X to perform an experiment according to a protocol.
has curation status: pending final vetting
definition: A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
editor note: 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.
term editor: AR, BP, JM, MC, PRS
definition source: branch derived
imported from: obi.owl

protocol
type: Class
subclass of: plan specification
editor preferred term: protocol
example of usage: 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.
has curation status: ready for release
definition: 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.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
imported from: obi.owl
ISA alternative term: study protocol

adding a material entity into a target
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
subclass of: material combination
subclass of: Restriction
  on property: realizes
  some values from: material to be added role
subclass of: Restriction
  on property: realizes
  some values from: target of material addition role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: material to be added role
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
editor preferred term: adding a material entity into a target
example of usage: Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
has curation status: ready for release
definition: 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'.
editor note: Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
term editor: BP
definition source: branch derived
imported from: obi.owl

analyte role
type: Class
subclass of: measurand role
subclass of: Restriction
  on property: role of
  some values from: Class
    union of: molecular entity
    union of: atom
editor preferred term: analyte role
example of usage: Glucose in blood (measured in an assay to determine the concentration of glucose).
has curation status: ready for release
definition: A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
editor note: interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
editor note: pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
editor note: qualities such as weight, color are not assayed but measured, so they do not fall into this category.
term editor: GROUP: Role Branch
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
imported from: obi.owl

material to be added role
type: Class
subclass of: role
editor preferred term: material to be added role
example of usage: drug added to a buffer contained in a tube; substance injected into an animal;
has curation status: metadata complete
definition: A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role is added into another material entity (the target).
term editor: Role Branch
definition source: OBI
curator note: 9 March 09 from discussion with PA branch
imported from: obi.owl

drawing a conclusion based on data
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: conclusion based on data
editor preferred term: interpreting data
example of usage: 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.
has curation status: ready for release
definition: 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
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
definition source: Bjoern Peters
imported from: obi.owl

planning
type: Class
subclass of: process
subclass of: Class
  intersection of: process
  intersection of: Restriction
    on property: has participant
    some values from: plan specification
editor preferred term: planning
example of usage: The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
has curation status: ready for release
definition: a process of creating or modifying a plan specification
editor note: 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
term editor: Bjoern Peters
definition source: Bjoern Peters
definition source: Plans and Planned Processes Branch
imported from: obi.owl

contain function
type: Class
subclass of: function
editor preferred term: contain function
example of usage: A syringe, a beaker
has curation status: ready for release
definition: A contain function is a function to constrain a material entities location in space
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

heat function
type: Class
subclass of: function
editor preferred term: heat function
has curation status: ready for release
definition: A heat function is a function that increases the internal kinetic energy of a material
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

material separation function
type: Class
subclass of: function
editor preferred term: material separation function
has curation status: ready for release
definition: 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.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

filter function
type: Class
subclass of: material separation function
editor preferred term: filter function
has curation status: ready for release
definition: A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
term editor: Frank Gibson
imported from: obi.owl

mechanical function
type: Class
subclass of: function
editor preferred term: mechanical function
has curation status: ready for release
definition: A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition source: http://en.wikipedia.org/wiki/Mechanical_work
imported from: obi.owl

transfer function
type: Class
subclass of: function
editor preferred term: transfer function
has curation status: ready for release
definition: A transfer function is a function to displace a material from one location to another.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

cool function
type: Class
subclass of: function
editor preferred term: cool function
has curation status: ready for release
definition: 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.
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

image acquisition function
type: Class
subclass of: measure function
subclass of: Restriction
  on property: characteristic of
  some values from: image creation device
subclass of: Restriction
  on property: realized in
  all values from: image creation
editor preferred term: image acquisition function
has curation status: ready for release
definition: An image acquisition function is a function to acquire an image of a material
term editor: Frank Gibson
imported from: obi.owl

image creation device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: image acquisition function
subclass of: measurement device
editor preferred term: image acquisition device
has curation status: metadata incomplete
definition: An image creation device is a device which captures a digitized image of an object
term editor: Frank Gibson
alternative label: image acquisition device
definition source: sep:00096
imported from: obi.owl

solid support function
type: Class
subclass of: function
editor preferred term: solid support function
example of usage: Taped, glued, pinned, dried or molecularly bonded to a solid support
has curation status: ready for release
definition: 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
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

environment control function
type: Class
subclass of: function
editor preferred term: environment control function
has curation status: ready for release
definition: 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.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

extract
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: extraction
editor preferred term: extract
example of usage: 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
has curation status: metadata complete
definition: an extract is a material entity which results from an extraction process
term editor: PERSON: Philippe Rocca-Serra
alternative label: extracted material
definition source: GROUP: OBI Biomatrial Branch
imported from: obi.owl

averaging objective
type: Class
subclass of: data transformation objective
editor preferred term: averaging objective
example of usage: 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.
has curation status: ready for release
definition: An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
term editor: Elisabetta Manduchi
term editor: James Malone
definition source: PERSON: Elisabetta Manduchi
imported from: obi.owl

adding material objective
type: Class
subclass of: material combination objective
editor preferred term: adding material objective
example of usage: creating a mouse infected with LCM virus
has curation status: ready for release
definition: 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
term editor: BP
imported from: obi.owl

needle
type: Class
subclass of: device
editor preferred term: needle
example of usage: 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
has curation status: metadata complete
definition: 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.
term editor: Philippe Rocca-Serra
definition source: OBI Instrument
imported from: obi.owl

analyte measurement objective
type: Class
subclass of: assay objective
editor preferred term: analyte measurement objective
example of usage: The objective to measure the concentration of glucose in a blood sample
has curation status: ready for release
definition: an assay objective to determine the presence or concentration of an analyte in the evaluant
term editor: PERSON: Bjoern Peters
definition source: PPPB branch
imported from: obi.owl

assay objective
type: Class
subclass of: objective specification
editor preferred term: assay objective
example of usage: the objective to determine the weight of a mouse.
has curation status: ready for release
definition: an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
term editor: PPPB branch
definition source: PPPB branch
imported from: obi.owl

analyte assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement datum
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
editor preferred term: analyte assay
example of usage: example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
has curation status: ready for release
definition: An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
term editor: Alan Ruttenberg
term editor: Bjoern Peters
term editor: Helen Parkinson
term editor: Philippe Rocca-Serra
definition source: Alan Ruttenberg
definition source: Bjoern Peters
definition source: Helen Parkinson
definition source: OBI Planned process branch
definition source: Philippe Rocca-Serra
imported from: obi.owl

target of material addition role
type: Class
subclass of: material entity role
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: adding a material entity into a target
editor preferred term: target of material addition role
example of usage: peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
has curation status: metadata complete
definition: A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role (the target) receives the addition of another material entity.
editor note: 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.
term editor: GROUP: Role Branch
definition source: OBI
imported from: obi.owl

regulatory agency
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: has role
    some values from: regulator role
subclass of: organization
editor preferred term: regulatory agency
example of usage: The US Environmental Protection Agency
has curation status: ready for release
definition: A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
term editor: GROUP: OBI Biomaterial Branch
definition source: WEB: en.wikipedia.org/wiki/Regulator
imported from: obi.owl

measure function
type: Class
subclass of: function
subclass of: Restriction
  on property: function of
  some values from: processed material
subclass of: Restriction
  on property: realized in
  all values from: Restriction
    on property: has_specified_output
    some values from: measurement datum
editor preferred term: measure function
example of usage: A glucometer measures blood glucose concentration, the glucometer has a measure function.
has curation status: ready for release
definition: 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.
term editor: PERSON: Daniel Schober
term editor: PERSON: Helen Parkinson
term editor: PERSON: Melanie Courtot
term editor: PERSON:Frank Gibson
imported from: obi.owl

material transformation objective
type: Class
subclass of: objective specification
editor preferred term: material transformation objective
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
has curation status: ready for release
definition: an objective specifiction that creates an specific output object from input materials.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
alternative label: artifact creation objective
definition source: GROUP: OBI PlanAndPlannedProcess Branch
imported from: obi.owl

manufacturing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: manufacturing objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
editor preferred term: manufacturing
has curation status: ready for release
definition: 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
editor note: Manufacturing implies reproducibility and responsibility AR
editor note: This includes a single scientist making a processed material for personal use.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch
imported from: obi.owl

manufacturing objective
type: Class
subclass of: material transformation objective
editor preferred term: manufacturing objective
has curation status: ready for release
definition: is the objective to manufacture a material of a certain function (device)
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch
imported from: obi.owl

study design execution
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes
      some values from: study design
subclass of: planned process
editor preferred term: study design execution
example of usage: injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
has curation status: ready for release
definition: a planned process that carries out a study design
editor note: removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
definition source: branch derived
curator note: 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
imported from: obi.owl

manufacturer role
type: Class
subclass of: material entity role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    union of: Homo sapiens
    union of: organization
subclass of: Restriction
  on property: realized in
  all values from: manufacturing
editor preferred term: manufacturer role
example of usage: With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
has curation status: metadata incomplete
definition: Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
term editor: GROUP: Role Branch
definition source: OBI
imported from: obi.owl

material separation objective
type: Class
equivalent class: Class
  union of: portioning objective
  union of: separation into different composition objective
subclass of: material transformation objective
editor preferred term: material separation objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
has curation status: ready for release
definition: is an objective to transform a material entity into spatially separated components.
term editor: PPPB branch
definition source: PPPB branch
imported from: obi.owl

urine specimen
type: Class
subclass of: specimen from organism
subclass of: Restriction
  on property: is_specified_output_of
  some values from: collecting specimen from organism
subclass of: Restriction
  on property: has role
  some values from: specimen role
subclass of: Restriction
  on property: derives from
  some values from: urine
editor preferred term: urine specimen
has curation status: metadata complete
definition: a portion of urine collected from an organism
editor note: 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
editor note: 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
editor note: are we happy calling collection of urine a material separation?
imported from: obi.owl

material combination
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material combination objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
editor preferred term: material combination
example of usage: Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
has curation status: ready for release
definition: is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
editor note: created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
term editor: bp
definition source: bp
imported from: obi.owl

blood specimen
type: Class
subclass of: bodily fluid specimen
subclass of: Restriction
  on property: is_specified_output_of
  some values from: collecting specimen from organism
subclass of: Restriction
  on property: has role
  some values from: specimen role
subclass of: Restriction
  on property: derives from
  some values from: blood
editor preferred term: blood specimen
example of usage: blood drawn from a human for glucose assay
has curation status: ready for release
definition: a material entity derived from a portion of blood collected from an organism
term editor: Bjoern Peters
definition source: Bjoern Peters
imported from: obi.owl

specimen collection process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
editor preferred term: specimen collection process
example of usage: 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
has curation status: ready for release
definition: A planned process with the objective of collecting a specimen.
editor note: 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.
editor note: 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.
editor note: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
editor note: label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
term editor: Bjoern Peters
alternative label: specimen collection
curator note: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
curator note: 6/9/09: used at workshop
imported from: obi.owl

sample from organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: collecting specimen from organism
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: material sample
subclass of: specimen from organism
subclass of: Restriction
  on property: derives from
  some values from: material anatomical entity
editor preferred term: sample from organism
has curation status: example to be eventually removed
definition: a material obtained from an organism in order to be a representative of the whole
editor note: 5/29: This is a helper class for now
editor note: 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.
imported from: obi.owl

portioning objective
type: Class
subclass of: material separation objective
editor preferred term: portioning objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation.
has curation status: metadata incomplete
definition: A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
imported from: obi.owl

average value
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: averaging data transformation
subclass of: data item
editor preferred term: average value
has curation status: pending final vetting
definition: A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative label: arithmetic mean
imported from: obi.owl

separation into different composition objective
type: Class
subclass of: material separation objective
editor preferred term: separation into different composition objective
example of usage: The objective to obtain cells contained in a sample of blood.
has curation status: metadata complete
definition: 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).
editor note: We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
imported from: obi.owl

specimen collection objective
type: Class
subclass of: objective specification
editor preferred term: specimen collection objective
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
has curation status: ready for release
definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
term editor: Bjoern Peters
definition source: Bjoern Peters
imported from: obi.owl

material combination objective
type: Class
subclass of: material transformation objective
editor preferred term: material combination objective
has curation status: ready for release
definition: is an objective to obtain an output material that contains several input materials.
term editor: PPPB branch
definition source: bp
imported from: obi.owl

material sample role
type: Class
subclass of: specimen role
editor preferred term: material sample role
example of usage: 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.
has curation status: pending final vetting
definition: A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
editor note: 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.
term tracker item: https://github.com/obi-ontology/obi/issues/1013
imported from: obi.owl

material sample
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: specimen
editor preferred term: material sample
example of usage: 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.
has curation status: metadata incomplete
definition: A material entity that has the material sample role
term editor: OBI: workshop
alternative label: sample population
term tracker item: https://github.com/obi-ontology/obi/issues/1013
imported from: obi.owl
ISA alternative term: sample

material maintenance objective
type: Class
subclass of: objective specification
editor preferred term: material maintenance objective
has curation status: ready for release
definition: An objective specification maintains some or all of the qualities of a material over time.
term editor: PERSON: Bjoern Peters
definition source: PERSON: Bjoern Peters
imported from: obi.owl

informed consent process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: Homo sapiens
subclass of: Restriction
  on property: has participant
  some values from: Restriction
    on property: has role
    some values from: investigation agent role
editor preferred term: informed consent process
has curation status: ready for release
definition: 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.
editor note: 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.
term editor: Person:Alan Ruttenberg
definition source: http://clinicaltrials.gov/ct2/info/glossary#informed
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
imported from: obi.owl

measurement device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: measure function
subclass of: device
editor preferred term: measurement device
example of usage: A ruler, a microarray scanner, a Geiger counter.
has curation status: ready for release
definition: A device in which a measure function inheres.
term editor: GROUP:OBI Philly workshop
definition source: OBI
imported from: obi.owl

manufacturer
type: Class
equivalent class: Class
  intersection of: Class
    union of: Homo sapiens
    union of: organization
  intersection of: Restriction
    on property: has role
    some values from: manufacturer role
subclass of: material entity
editor preferred term: manufacturer
has curation status: metadata incomplete
definition: A person or organization that has a manufacturer role
imported from: obi.owl

test tube
type: Class
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: contain function
editor preferred term: test tube
has curation status: metadata complete
definition: A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material
term editor: Bjoern Peters
alternative label: collection tube
alternative label: sample tube
definition source: http://en.wikipedia.org/wiki/Test_tube
imported from: obi.owl

material maintenance
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: planned process
editor preferred term: material maintenance
has curation status: metadata incomplete
definition: a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
imported from: obi.owl

record of missing knowledge
type: Class
subclass of: information content entity
editor preferred term: record of missing knowledge
example of usage: A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
has curation status: metadata complete
definition: An information content entity created to indicate that information about something is not available to the person recording it.
editor note: This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately.
term editor: Bjoern Peters
imported from: obi.owl

pre-mortem specimen
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: specimen collection process
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        intersection of: organism
        intersection of: Restriction
subclass of: specimen with pre- or post-mortem status
editor preferred term: pre-mortem specimen
example of usage: material obtained through a liver biopsy from a human patient
has curation status: metadata complete
definition: a specimen that was taken from a live organism
term editor: Bjoern Peters
definition source: MO_705 premortem
imported from: obi.owl

RNA extract
type: Class
subclass of: nucleic acid extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: RNA extraction
subclass of: Restriction
  on property: has grain
  some values from: ribonucleic acid
editor preferred term: RNA extract
has curation status: metadata complete
definition: an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: Group: UPenn Group
imported from: obi.owl

freezing storage
type: Class
subclass of: storage
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has quality
        some values from: frozen
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has quality
        some values from: frozen
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred term: freezing storage
example of usage: a fozen pellet used for later assay
has curation status: metadata complete
definition: A storage process in temperature that maintenance the frozen status of the stored entities.
editor note: 2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance" 2014/2/3 OBI dev call: "prepare for maintenance" is a separate process. For example, 'freezing' and 'flash freezing' are defined and can be used to produce frozen material for storage. Updated both textual and logical definition. Both input and output material of freezing storage have quality frozen.
term editor: Person: Alan Ruttenberg, Mathias Brochhausen
definition source: MO_481 frozen_storage
definition source: OBI
imported from: obi.owl

nasal swab specimen
type: Class
subclass of: swab specimen
subclass of: Restriction
  on property: is_specified_output_of
  some values from: collecting specimen with swab
subclass of: Restriction
  on property: has role
  some values from: specimen role
editor preferred term: nasal swab specimen
example of usage: type of sample used in the PCIRN influenza network
has curation status: metadata complete
definition: A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination.
term editor: PERSON: Melanie Courtot
definition source: WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
imported from: obi.owl

frozen specimen
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: freezing storage
      intersection of: Restriction
        on property: has_specified_input
        some values from: Restriction
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: specimen with known storage state
editor preferred term: frozen specimen
example of usage: Frozen blood plasma
has curation status: metadata incomplete
definition: A specimen that has been frozen in order to store it.
term editor: Person:Alan Ruttenberg
definition source: MO_610 frozen_sample
imported from: obi.owl

lyophilization storage
type: Class
subclass of: storage
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred term: lyophilization storage
has curation status: metadata incomplete
definition: a storage process with input material entity and output freeze dried material for long time storage
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
imported from: obi.owl
comment: can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed

material separation device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: material separation function
subclass of: device
editor preferred term: material separation device
example of usage: flow cytometer
has curation status: metadata incomplete
definition: A device with a separation function realized in a planed process
imported from: obi.owl

service consumer role
type: Class
subclass of: material entity role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    union of: Homo sapiens
    union of: organization
editor preferred term: service consumer role
example of usage: A biologist who uses a sequencing services fulfills the role of a service consumer
has curation status: metadata complete
definition: a role which inheres in a person who uses a service
term editor: Person:Helen Parkinson
definition source: OBI
imported from: obi.owl

service provider role
type: Class
subclass of: material entity role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    union of: Homo sapiens
    union of: organization
subclass of: Restriction
  on property: realized in
  all values from: planned process
editor preferred term: service provider role
example of usage: Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
has curation status: metadata incomplete
definition: 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
term editor: PERSON:Helen Parkinson
imported from: obi.owl

paraffin specimen
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: paraffin storage
      intersection of: Restriction
        on property: has_specified_input
        some values from: Restriction
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: specimen with known storage state
editor preferred term: paraffin specimen
example of usage: liver tissue embedded in paraffin
has curation status: metadata incomplete
definition: a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: MO_990 paraffin_sample
imported from: obi.owl

processed specimen
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: specimen
subclass of: processed material
subclass of: specimen
editor preferred term: processed specimen
example of usage: 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.
has curation status: ready for release
definition: A specimen that has been intentionally physically modified.
term editor: Bjoern Peters
definition source: Bjoern Peters
imported from: obi.owl
comment: A tissue sample that has been sliced and stained for a histology study.

reagent application function
type: Class
subclass of: function
editor preferred term: reagent application function
example of usage: An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations.
has curation status: metadata complete
definition: A function that is realized when a reagent is automatically added to some research material.
term editor: PERSON: Nicole Vasilevsky, Matthew Brush
definition source: PERSON: Nicole Vasilevsky, Matthew Brush
curator note: 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?
imported from: obi.owl

lyophilized specimen
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: lyophilization storage
      intersection of: Restriction
        on property: has_specified_input
        some values from: Restriction
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: specimen with known storage state
editor preferred term: lyophilized specimen
example of usage: freezing dried DNA
has curation status: metadata incomplete
definition: a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: MO_589 freeze_dried_sample
imported from: obi.owl

container
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: contain function
subclass of: device
subclass of: Restriction
  on property: has maximum capacity
  some values from: measurement datum
subclass of: Restriction
  on property: has actual load
  some values from: measurement datum
editor preferred term: container
has curation status: metadata incomplete
definition: A device that can be used to restrict the location of material entities over time
editor note: 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?)
term editor: PERSON: Bjoern Peters
imported from: obi.owl

device
type: Class
subclass of: processed material
editor preferred term: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
has curation status: ready for release
definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor note: 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…
term editor: PERSON: Helen Parkinson
alternative label: instrument
definition source: OBI development call 2012-12-17.
imported from: obi.owl

fresh specimen
type: Class
subclass of: specimen with known storage state
editor preferred term: fresh specimen
example of usage: a liver freshly removed from a rat
has curation status: metadata incomplete
definition: a specimen that is output of a specimen creation process used for an investigation without storage.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: MO_730 fresh_sample
imported from: obi.owl

paraffin storage
type: Class
subclass of: storage
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: organism
    union of: material anatomical entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred term: paraffin storage
has curation status: metadata complete
definition: a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
imported from: obi.owl
comment: need to specify paraffin or wax is one of specified input of the process

agar stab specimen
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: agar stab storage
    intersection of: Restriction
      on property: has_specified_input
      some values from: Restriction
        on property: has role
        some values from: specimen role
subclass of: specimen with known storage state
editor preferred term: agar stab specimen
has curation status: metadata incomplete
definition: a specimen that is output of a process that cell culture inoculated into agar for long term storage.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: MO_971 agar_stab
imported from: obi.owl

computed tomography scanner
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
editor preferred term: computed tomography scanner
has curation status: metadata complete
definition: An image acquisition device that generates a three-dimensional image of the inside of an object from a large series of two-dimensional X-ray images taken around a single axis of rotation.
term editor: PERSON:Bjoern Peters
alternative label: CT scanner
alternative label: X-ray computed tomography scanner
definition source: http://en.wikipedia.org/wiki/X-ray_computed_tomography
imported from: obi.owl

questionnaire
type: Class
subclass of: document
editor preferred term: questionnaire
has curation status: metadata complete
definition: A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
editor note: JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
editor note: Need to clarify if this is a document or a directive information entity (or what their connection is))
term editor: PERSON: Jessica Turner
definition source: Merriam-Webster
imported from: obi.owl

agar stab storage
type: Class
subclass of: storage
subclass of: Restriction
  on property: has_specified_input
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred term: agar stab storage
has curation status: metadata complete
definition: a storage process with input cell culture and agar and output agar stab for long time storage
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
imported from: obi.owl
comment: need to specify that agar is one of input for this process

image creation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: image
editor preferred term: image acquisition
example of usage: Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
has curation status: metadata incomplete
definition: A planned process that captures an image of an object.
term editor: PERSON: Jie Zheng
alternative label: image acquisition
imported from: obi.owl

nucleic acid extract
type: Class
subclass of: extract
subclass of: processed specimen
subclass of: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: nucleic acid extraction
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: Restriction
  on property: has grain
  some values from: nucleic acid
editor preferred term: nucleic acid extract
has curation status: metadata complete
definition: An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
term editor: PERSON: Jie Zheng
definition source: UPenn Group
imported from: obi.owl

environmental control device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: Class
      union of: heat function
      union of: cool function
      union of: environment control function
subclass of: device
editor preferred term: environmental control device
example of usage: A growth chamber is an environmental control device.
has curation status: metadata complete
definition: An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
term editor: Helen Parkinson
definition source: OBI
imported from: obi.owl

DNA extract
type: Class
subclass of: nucleic acid extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: DNA extraction
subclass of: Restriction
  on property: has grain
  some values from: deoxyribonucleic acid
editor preferred term: DNA extract
has curation status: metadata complete
definition: The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
term editor: Person: Jie Zheng
definition source: Group: UPenn group
imported from: obi.owl

automatic tissue processor
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
subclass of: Restriction
  on property: has function
  some values from: reagent application function
editor preferred term: automatic tissue processor
has curation status: metadata complete
definition: 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.
term editor: PERSON: Erik Segerdell
definition source: United States Patent 3762362
imported from: obi.owl

age since planting measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since planting measurement datum
has curation status: metadata complete
definition: An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_495 planting
curator note: Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. Term proposed by Bjoern on Nov 8, 2010 dev call Supported by Alan on Nov 15, 2010 dev call
imported from: obi.owl

age since hatching measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since hatching measurement datum
has curation status: metadata complete
definition: An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_745 hatching
imported from: obi.owl

age since egg laying measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since egg laying measurement datum
has curation status: metadata complete
definition: An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_767 egg laying
imported from: obi.owl

age since germination measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since germination measurement datum
has curation status: metadata complete
definition: An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth.
editor note: Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_590 germination
imported from: obi.owl

age since eclosion measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since eclosion measurement datum
has curation status: metadata complete
definition: An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_876 eclosion
imported from: obi.owl

age since sowing measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since sowing measurement datum
has curation status: metadata complete
definition: An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_748 sowing
imported from: obi.owl

age since coitus measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since coitus measurement datum
has curation status: metadata complete
definition: An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_783 coitus
imported from: obi.owl

age measurement datum
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is quality measurement of
  some values from: age
editor preferred term: age measurement datum
has curation status: metadata complete
definition: A time measurement datum that is the result of measurement of age of an organism
editor note: 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.
term editor: PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
definition source: MO_178 Age
curator note: 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
curator note: discussed on Nov 15, dev call All subtype will be defined by textual definition now.
imported from: obi.owl

age since fertilization measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since fertilization measurement datum
has curation status: metadata complete
definition: An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote.
editor note: Definition of fertilization comes from GO.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_701 fertilization
imported from: obi.owl

age since birth measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since birth measurement datum
has curation status: metadata complete
definition: An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_710 birth
imported from: obi.owl

service
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: service consumer role
    intersection of: Restriction
      on property: realizes
      some values from: service provider role
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: planned process
editor preferred term: service
example of usage: providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony.
has curation status: metadata complete
definition: A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
term editor: Carlo; Matt
definition source: OBI workshop San Diego 2011
imported from: obi.owl

genetic characteristics information
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: region
    intersection of: Restriction
      on property: is concretized as
      some values from: Restriction
        on property: characteristic of
        some values from: Class
editor preferred term: genetic characteristics information
has curation status: metadata complete
definition: a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_66 IndividualGeneticCharacteristics
curator note: MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)
imported from: obi.owl

specimen with known storage state
type: Class
equivalent class: Class
  union of: fresh specimen
  union of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: storage
subclass of: specimen
editor preferred term: specimen with known storage state
has curation status: metadata incomplete
definition: A specimen for which it is known whether it has been subjected to storage of a specified type.
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_95 BiosourceType
imported from: obi.owl

specimen from organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has role
    some values from: specimen role
  intersection of: Restriction
    on property: derives from
    some values from: Class
      union of: material anatomical entity
      union of: anatomical cluster
subclass of: specimen
editor preferred term: specimen from organism
has curation status: ready for release
definition: 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).
term editor: PERSON: Chris Stoeckert, Jie Zheng
alternative label: tissue specimen
definition source: MO_954 organism_part
imported from: obi.owl

specimen with pre- or post-mortem status
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: specimen collection process
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        intersection of: organism
        intersection of: Restriction
subclass of: specimen
editor preferred term: specimen with pre- or post-mortem status
has curation status: metadata complete
definition: A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
editor note: organizational term, used in description of specimen that is created from known pre- or post-mortem status
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_84 OrganismStatus
imported from: obi.owl

material service
type: Class
equivalent class: Class
  intersection of: service
  intersection of: Restriction
    on property: provides_service_consumer_with
    some values from: Class
      union of: Restriction
        on property: has_specified_input
        some values from: material entity
      union of: Restriction
        on property: has_specified_output
        some values from: material entity
subclass of: service
editor preferred term: material service
example of usage: A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization
has curation status: pending final vetting
definition: A service which has a material entity as specified input and/or specified output.
term editor: PERSON: Carlo Torniai
term editor: PERSON: Matthew Brush
definition source: PERSON: Carlo Torniai
imported from: obi.owl

material analysis service
type: Class
equivalent class: Class
  intersection of: material service
  intersection of: Restriction
    on property: provides_service_consumer_with
    some values from: assay
subclass of: material service
editor preferred term: material analysis service
example of usage: Services performing DNA sequencing or Cell Analysis
has curation status: pending final vetting
definition: A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer.
term editor: PERSON: Carlo Torniai
term editor: PERSON: Matthew Brush
definition source: PERSON: Matthew Brush
imported from: obi.owl

material transport service
type: Class
subclass of: material service
editor preferred term: material transport service
example of usage: A service for chemical disposal
has curation status: pending final vetting
definition: A service in which a service provider facilitates the transport of some material entity to a specified destination for the service consumer.
term editor: PERSON: Carlo Torniai
term editor: PERSON: Matthew Brush
definition source: PERSON: Carlo Torniai
imported from: obi.owl

specimen collection time measurement datum
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: process boundary
    intersection of: Restriction
      on property: starts
      some values from: specimen collection process
editor preferred term: specimen collection time measurement datum
has curation status: metadata complete
definition: A time measurement datum that is the measure of the time when the specimens are collected.
term editor: Person: Chris Stoeckert, Jie Zheng
alternative label: collection date
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
NIAID GSCID-BRC alternative term: Specimen Collection Date
source: NIAID GSCID-BRC

selection criterion
type: Class
subclass of: directive information entity
editor preferred term: selection criterion
example of usage: rats should be aged between 6 and 8 weeks and weight between 180-250grams
has curation status: ready for release
definition: A directive information entity which defines and states a principle of standard by which selection process may take place.
term editor: Person: Philippe Rocca-Serra
alternative label: selection rule
definition source: OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/
imported from: obi.owl

secondary cultured cell
type: Class
subclass of: cultured cell
subclass of: Class
  union of: Restriction
    on property: is_specified_output_of
    some values from: cell culture splitting
  union of: Restriction
    on property: derives from
    some values from: Restriction
      on property: is_specified_output_of
      some values from: cell culture splitting
subclass of: Restriction
  on property: derives from
  some values from: primary cultured cell
editor preferred term: secondary cultured cell
has curation status: metadata complete
definition: A cultured cell that has been passaged or derives from a cell that has been passaged in culture.
editor note: The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
term editor: Person: Matthew Brush
definition source: PERSON: Matthew Brush
imported from: obi.owl
comment: A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture.

establishing cell line
type: Class
subclass of: establishing cell culture
subclass of: Restriction
  on property: has_specified_output
  some values from: cell line
editor preferred term: establishing cell line
has curation status: metadata complete
definition: 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).
editor note: 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.
term editor: Person: Matthew Brush
definition source: PERSON:Matthew Brush
imported from: obi.owl

reagent
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: reagent role
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
editor preferred term: reagent
has curation status: metadata complete
definition: 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.
editor note: 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.
term editor: PERSON:Matthew Brush
definition source: PERSON:Matthew Brush
imported from: obi.owl
comment: (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…

secondary cultured cell population
type: Class
subclass of: cultured cell population
subclass of: Restriction
  on property: is_specified_output_of
  some values from: cell culture splitting
subclass of: Restriction
  on property: has grain
  some values from: secondary cultured cell
subclass of: Restriction
  on property: has grain
  all values from: secondary cultured cell
editor preferred term: secondary cultured cell population
has curation status: metadata complete
definition: A cultured cell population that is derived through one or more passages in culture.
editor note: The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
term editor: PERSON:Matthew Brush
alternative label: secondary cell culture sample
definition source: PERSON:Matthew Brush
imported from: obi.owl
comment: The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally.

conclusion based on data
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: drawing a conclusion based on data
editor preferred term: conclusion based on data
example of usage: 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".
has curation status: ready for release
definition: An information content entity that is inferred from data.
editor note: 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.
term editor: Group:2013 Philly Workshop group
definition source: Group:2013 Philly Workshop group
imported from: obi.owl

cell freezing medium
type: Class
subclass of: processed material
editor preferred term: cell freezing medium
has curation status: metadata complete
definition: A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
term editor: PERSON: Matthew Brush
imported from: obi.owl

selection
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: selection criterion
subclass of: planned process
editor preferred term: selection
example of usage: 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.
has curation status: ready for release
definition: A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria.
editor note: 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)
term editor: Person: Philippe Rocca-Serra
alternative label: selection process
definition source: OBI
imported from: obi.owl

categorical value specification
type: Class
subclass of: value specification
editor preferred term: categorical value specification
has curation status: metadata incomplete
definition: A value specification that is specifies one category out of a fixed number of nominal categories
term editor: PERSON:Bjoern Peters
imported from: obi.owl

scalar value specification
type: Class
subclass of: value specification
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has specified numeric value
  min cardinality: 1
editor preferred term: scalar value specification
has curation status: metadata incomplete
definition: A value specification that consists of two parts: a numeral and a unit label
term editor: PERSON:Bjoern Peters
imported from: obi.owl

value specification
type: Class
subclass of: information content entity
editor preferred term: value specification
example of usage: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
has curation status: ready for release
definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
editor note: This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
term editor: PERSON:Bjoern Peters
imported from: obi.owl

molecular-labeled material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has part
    some values from: molecular label
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: addition of molecular label
subclass of: processed material
editor preferred term: molecular-labeled material
has curation status: pending final vetting
definition: 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
term editor: PERSON:Matthew Brush
definition source: OBI developer call, 3-12-12
imported from: obi.owl

collection of specimens
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has member
    all values from: specimen
subclass of: material entity
editor preferred term: collection of specimens
example of usage: Blood cells collected from multiple donors over the course of a study.
has curation status: pending final vetting
definition: A material entity that has two or more specimens as its parts.
editor note: Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: OBIB, OBI
imported from: obi.owl
source: Biobank

specimens derived from shared ancestor
type: Class
subclass of: collection of specimens
editor preferred term: specimens derived from shared ancestor
example of usage: Aliquoting one specimen to multiple tubes and the collection of the aliquoted specimens are a specimen family. Slicing a tissue specimen into multiple sections for microscopy.
has curation status: ready for release
definition: A collection of specimens derived from one common specimen via one or more material processing process(es).
editor note: Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
term editor: Chris Stoeckert, Jie Zheng
alternative label: specimen family
definition source: Duke Biobank, OBIB, OBI
imported from: obi.owl
source: Biobank

containing a specimen function
type: Class
subclass of: contain function
editor preferred term: containing a specimen function
has curation status: ready for release
definition: A contain function that involves physical contact with a specimen. This function is typically performed in such a way that the specimen is usable for an investigation or assay.
editor note: For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/
term editor: Chris Stoeckert
definition source: Duke Biobank, OBIB
imported from: obi.owl
source: Biobank

specimen container
type: Class
equivalent class: Class
  intersection of: container
  intersection of: Restriction
    on property: has function
    some values from: containing a specimen function
subclass of: container
editor preferred term: specimen container
example of usage: COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube
has curation status: ready for release
definition: A container with the function of containing a specimen.
editor note: For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/
term editor: Chris Stoeckert
definition source: Duke Biobank, OBIB
imported from: obi.owl

physical store
type: Class
equivalent class: Class
  intersection of: container
  intersection of: Restriction
    on property: has function
    some values from: environment control function
subclass of: container
subclass of: environmental control device
editor preferred term: physical store
example of usage: a freezer. a humidity controlled box.
has curation status: ready for release
definition: A container with an environmental control function.
editor note: For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/
term editor: Chris Stoeckert
definition source: Duke Biobank, OBIB
imported from: obi.owl

specimen family creation
type: Class
subclass of: material processing
subclass of: Class
  intersection of: material processing
  intersection of: Restriction
    on property: has_specified_input
    some values from: specimen
  intersection of: Restriction
    on property: has_specified_output
    some values from: specimens derived from shared ancestor
editor preferred term: specimen family creation
example of usage: Aliquoting one specimen to multiple tubes, slicing a tissue specimen into multiple sections, processing blood into buffy coat, red cells, and serum.
has curation status: ready for release
definition: A material processing that has as its input a specimen and as its output a collection of specimens.
editor note: For details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
term editor: Mathias Brochhausen, Chris Stoeckert, Jie Zheng
definition source: OBI, OBIB
imported from: obi.owl
source: Biobank

IHC slide staining
type: Class
subclass of: staining
subclass of: Class
  intersection of: staining
  intersection of: Restriction
    on property: has_specified_input
    some values from: obsolete fixed tissue slide specimen
editor preferred term: IHC slide staining
has curation status: pending final vetting
definition: A staining using labeled antibodies, i.e. the analytical part of immunohistochemistry. The staining is applied to fixed specimens on slides to identify biomarkers in tissues.
term editor: Chris Stoeckert, Ned Haubein
definition source: http://www.agilent.com/cs/library/technicaloverviews/public/08002_ihc_staining_methods.pdf
imported from: obi.owl

H&E slide staining
type: Class
subclass of: staining
subclass of: Class
  intersection of: staining
  intersection of: Restriction
    on property: has_specified_input
    some values from: obsolete fixed tissue slide specimen
editor preferred term: H&E slide staining
has curation status: pending final vetting
definition: A staining using hematoxylin and eosin. The staining is applied to fixed specimens on slides to observe the whole structure and morphology of cells in a tissue; nuclei are stained dark blue/purple while cytoplasm is stained pink.
term editor: Chris Stoeckert, Ned Haubein
definition source: http://www.histalim.com/accueil/activities/our-services/histology/hematoxylin-eosin-2/
imported from: obi.owl

H&E-stained fixed tissue slide specimen
type: Class
subclass of: continuant
subclass of: obsolete fixed tissue slide specimen
subclass of: Class
  intersection of: obsolete fixed tissue slide specimen
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: H&E slide staining
editor preferred term: H&E-stained fixed tissue slide specimen
has curation status: pending final vetting
definition: A fixed tissue slide specimen that is the output of H&E slide staining.
term editor: Chris Stoeckert, Ned Haubein
definition source: OBIB, OBI
imported from: obi.owl

IHC-stained fixed tissue slide specimen
type: Class
subclass of: continuant
subclass of: obsolete fixed tissue slide specimen
subclass of: Class
  intersection of: obsolete fixed tissue slide specimen
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: IHC slide staining
editor preferred term: IHC-stained fixed tissue slide specimen
has curation status: pending final vetting
definition: A fixed tissue slide specimen that is the output of immunohistochemistry slide staining.
term editor: Chris Stoeckert, Ned Haubein
alternative label: immunohistochemistry slide specimen
definition source: OBIB, OBI
imported from: obi.owl

RNA Integrity Number calculation
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: has value specification
      some values from: RNA Integrity Number value specification
editor preferred term: RNA Integrity Number calculation
has curation status: pending final vetting
definition: A data transformation using the RIN algorithm to generate a quality measure of RNA based on features from an electrophoretic trace.
term editor: Chris Stoeckert, Bjoern Peters
alternative label: RIN calculation
definition source: https://www.agilent.com/cs/library/applications/5989-1165EN.pdf
imported from: obi.owl

RNA Integrity Number value specification
type: Class
subclass of: value specification
editor preferred term: RNA Integrity Number value specification
has curation status: ready for release
definition: A value specification that specifies the value of the RNA Integrity Number as a real value between 1 (most degraded) and 10 (most intact).
term editor: Chris Stoeckert, Bjoern Peters
alternative label: RIN value specification
definition source: OBI
imported from: obi.owl

temperature value specification
type: Class
subclass of: value specification
editor preferred term: temperature value specification
has curation status: ready for release
definition: A value specification that specifies the temperature of some thing.
term editor: Chris Stoeckert
definition source: OBI
imported from: obi.owl

volume value specification
type: Class
subclass of: value specification
subclass of: Class
  intersection of: Restriction
    on property: specifies value of
    some values from: volume
  intersection of: Restriction
    on property: has measurement unit label
    all values from: volume unit
editor preferred term: volume value specification
has curation status: ready for release
definition: A value specification that specifies the volume of some thing.
term editor: Chris Stoeckert
definition source: OBI
imported from: obi.owl

temperature measurement assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: has value specification
      some values from: temperature value specification
editor preferred term: temperature measurement assay
has curation status: ready for release
definition: An assay to determine the temperature of an evaluant.
term editor: Bjoern Peters
term editor: Chris Stoeckert
definition source: OBI
imported from: obi.owl

volume measurement assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: has value specification
      some values from: volume value specification
editor preferred term: volume measurement assay
has curation status: ready for release
definition: An assay to determine the volume of an evaluant.
term editor: Bjoern Peters
term editor: Chris Stoeckert
definition source: OBI
imported from: obi.owl

antigen specific antibodies assay
type: Class
subclass of: analyte assay
editor preferred term: antigen specific antibodies assay
example of usage: Test performed using antibodies produced by human B-cells that bind with human immunodeficiency virus (HIV) antigens
has curation status: metadata complete
definition: An analyte assay that measures the presence or amount of antibodies to a specified antigen.
term editor: Bjoern Peters
term editor: Chris Stoeckert
term editor: James Overton
term editor: Randi Vita
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/825
ontology term requester: NCI BBRB
imported from: obi.owl

HIV antibody assay
type: Class
subclass of: antigen specific antibodies assay
editor preferred term: HIV antibody assay
has curation status: metadata complete
definition: An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens.
editor note: HIV-1 and HIV-2 are two different viruses (http://i-base.info/qa/36)
term editor: Bjoern Peters
term editor: Chris Stoeckert
term editor: James Overton
term editor: Randi Vita
alternative label: HIV I/II Ab assay
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/825
ontology term requester: NCI BBRB
imported from: obi.owl

HIV group O antibody assay
type: Class
subclass of: antigen specific antibodies assay
editor preferred term: HIV group O antibody assay
has curation status: metadata complete
definition: An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) group O antigens.
editor note: https://www.cdc.gov/mmwr/preview/mmwrhtml/00042810.htm
term editor: Bjoern Peters
term editor: Chris Stoeckert
term editor: James Overton
term editor: Randi Vita
alternative label: HIV I/II Plus O assay
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/825
ontology term requester: NCI BBRB
imported from: obi.owl

surface HBV antibody assay
type: Class
subclass of: antigen specific antibodies assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: immunoglobulin complex
      intersection of: Restriction
        on property: has disposition to bind
        some values from: Hepatitis B virus
editor preferred term: surface HBV antibody assay
has curation status: metadata complete
definition: An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) surface antigens.
term editor: Bjoern Peters
term editor: Chris Stoeckert
term editor: James Overton
term editor: Randi Vita
alternative label: HBsAb assay
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/825
ontology term requester: NCI BBRB
imported from: obi.owl

core HBV antibody assay
type: Class
subclass of: antigen specific antibodies assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: immunoglobulin complex
      intersection of: Restriction
        on property: has disposition to bind
        some values from: Hepatitis B virus
editor preferred term: core HBV antibody assay
has curation status: metadata complete
definition: An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) core antigens.
term editor: Bjoern Peters
term editor: Chris Stoeckert
term editor: James Overton
term editor: Randi Vita
alternative label: HBcAb assay
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/825
ontology term requester: NCI BBRB
imported from: obi.owl

core HBV IgM antibody assay
type: Class
subclass of: antigen specific antibodies assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: immunoglobulin complex
      intersection of: Restriction
        on property: has disposition to bind
        some values from: Hepatitis B virus
editor preferred term: core HBV IgM antibody assay
has curation status: metadata complete
definition: An antigen specific antibodies assay that is meant to detectimmunoglobulin M (IgM) antibodies that bind to hepatitis B virus (HBV) core antigens.
term editor: Bjoern Peters
term editor: Chris Stoeckert
term editor: James Overton
term editor: Randi Vita
alternative label: HBcAb-IgM assay
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/825
ontology term requester: NCI BBRB
imported from: obi.owl

HCV antibody assay
type: Class
subclass of: antigen specific antibodies assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: immunoglobulin complex
      intersection of: Restriction
        on property: has disposition to bind
        some values from: Hepacivirus C
editor preferred term: HCV antibody assay
has curation status: metadata complete
definition: An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens.
term editor: Bjoern Peters
term editor: Chris Stoeckert
term editor: James Overton
term editor: Randi Vita
alternative label: HCV Ab assay
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/825
ontology term requester: NCI BBRB
imported from: obi.owl

EBV IgG antibody assay
type: Class
subclass of: antigen specific antibodies assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: immunoglobulin complex
      intersection of: Restriction
        on property: has disposition to bind
        some values from: Human gammaherpesvirus 4
editor preferred term: EBV IgG antibody assay
has curation status: metadata complete
definition: An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens.
term editor: Bjoern Peters
term editor: Chris Stoeckert
term editor: James Overton
term editor: Randi Vita
alternative label: EBV IgG Ab assay
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/825
ontology term requester: NCI BBRB
imported from: obi.owl

EBV IgM antibody assay
type: Class
subclass of: antigen specific antibodies assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: immunoglobulin complex
      intersection of: Restriction
        on property: has disposition to bind
        some values from: Human gammaherpesvirus 4
editor preferred term: EBV IgM antibody assay
has curation status: metadata complete
definition: An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens.
term editor: Bjoern Peters
term editor: Chris Stoeckert
term editor: James Overton
term editor: Randi Vita
alternative label: EBV IgM Ab assay
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/825
ontology term requester: NCI BBRB
imported from: obi.owl

CMV antibody assay
type: Class
subclass of: antigen specific antibodies assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: immunoglobulin complex
      intersection of: Restriction
        on property: has disposition to bind
        some values from: Cytomegalovirus
editor preferred term: CMV antibody assay
has curation status: metadata complete
definition: An antigen specific antibodies assay that is meant to detect antibodies that bind to cytomegalovirus (CMV) antigens.
term editor: Bjoern Peters
term editor: Chris Stoeckert
term editor: James Overton
term editor: Randi Vita
alternative label: CMV Ab assay
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/825
ontology term requester: NCI BBRB
imported from: obi.owl

venereal disease research laboratory test
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: immunoglobulin complex
  intersection of: Restriction
    on property: has_specified_input
    some values from: immunoglobulin complex
editor preferred term: venereal disease research laboratory test
has curation status: metadata complete
definition: An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood.
term editor: Bjoern Peters
term editor: Chris Stoeckert
term editor: James Overton
term editor: Randi Vita
alternative label: VDRL test
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/825
ontology term requester: NCI BBRB
imported from: obi.owl

rapid plasma reagin test
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: immunoglobulin complex
  intersection of: Restriction
    on property: has_specified_input
    some values from: immunoglobulin complex
editor preferred term: rapid plasma reagin test
has curation status: metadata complete
definition: An analyte assay that is meant to detect with the aid of carbon or charcoal particles general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. RPR tests can be done without a microscope.
term editor: Bjoern Peters
term editor: Chris Stoeckert
term editor: James Overton
term editor: Randi Vita
alternative label: RPR assay
definition source: url:http://www.differencebetween.net/science/health/difference-between-vdlr-and-rpr/
term tracker item: https://github.com/obi-ontology/obi/issues/825
ontology term requester: NCI BBRB
imported from: obi.owl

HBV surface antigen assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: measurand role
      intersection of: Restriction
        on property: characteristic of
        some values from: Hepatitis B virus
  intersection of: Restriction
    on property: has_specified_input
    some values from: Hepatitis B virus
editor preferred term: HBV surface antigen assay
has curation status: metadata complete
definition: An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens.
term editor: Bjoern Peters
term editor: Chris Stoeckert
term editor: James Overton
term editor: Randi Vita
alternative label: HBsAg assay
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/825
ontology term requester: NCI BBRB
imported from: obi.owl

HIV-1 nucleic acid testing
type: Class
subclass of: analyte assay
editor preferred term: HIV-1 nucleic acid testing
has curation status: metadata complete
definition: An analyte assay that is meant to detect human immunodeficiency virus (HIV-1) nucleic acids.
term editor: Bjoern Peters
term editor: Chris Stoeckert
term editor: James Overton
term editor: Randi Vita
alternative label: HIV-1 NAT
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/825
ontology term requester: NCI BBRB
imported from: obi.owl

HCV nucleic acid testing
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: nucleic acid
      intersection of: Restriction
        on property: part of
        some values from: Hepacivirus C
editor preferred term: HCV nucleic acid testing
has curation status: metadata complete
definition: An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids.
term editor: Bjoern Peters
term editor: Chris Stoeckert
term editor: James Overton
term editor: Randi Vita
alternative label: HCV NAT
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/825
ontology term requester: NCI BBRB
imported from: obi.owl

courier organization
type: Class
subclass of: organization
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: service provider role
    intersection of: Restriction
      on property: realized in
      some values from: material transport service
editor preferred term: courier organization
has curation status: ready for release
definition: An organization that delivers messages, packages, and mail.
term editor: Chris Stoeckert, Helena Ellis
alternative label: courier
definition source: https://en.wikipedia.org/wiki/Courier
ontology term requester: NCI BBRB
imported from: obi.owl

courier tracking number
type: Class
subclass of: centrally registered identifier symbol
editor preferred term: courier tracking number
has curation status: ready for release
definition: A centrally registered identifier symbol assigned by a courier organization in order to track the delivery of an item.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

Leica Peloris rapid tissue processor
type: Class
subclass of: automatic tissue processor
editor preferred term: Leica Peloris rapid tissue processor
has curation status: ready for release
definition: 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.
term editor: Chris Stoeckert, Helena Ellis
definition source: http://drp8p5tqcb2p5.cloudfront.net/fileadmin/downloads_lbs/Leica%20PELORIS/User%20Manuals/Leica_Peloris_manual_EN.pdf
ontology term requester: NCI BBRB
imported from: obi.owl

Microm Ergostar HM200
type: Class
subclass of: microtome
editor preferred term: Microm Ergostar HM200
has curation status: ready for release
definition: A microtome that is manufactured by Microm and uses a vertical cutting stroke common to all rotary microtomes engaged by a horizontal sliding movement. An operating arm replaces the handwheel and is attached to both sides of the instrument for greater convenience to permit control of sectioning from the left or right.
term editor: Chris Stoeckert, Helena Ellis
definition source: http://www.ultra-medical.com/Microm-Ergostar-HM200-Microtome/en
ontology term requester: NCI BBRB
imported from: obi.owl

microtome blade
type: Class
subclass of: device
editor preferred term: microtome blade
has curation status: ready for release
definition: A device that is the part of a microtome used to slice specimens to a desired thickness.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://en.wikipedia.org/wiki/Microtome
ontology term requester: NCI BBRB
imported from: obi.owl

Sakura Low profile Accu-Edge microtome blade
type: Class
subclass of: microtome blade
editor preferred term: Sakura Low profile Accu-Edge microtome blade
has curation status: ready for release
definition: A microtome blade that is manufactured by Feather and is disposable. The ultra-sharp blades section specimens without striations, distortion or chattering.
term editor: Chris Stoeckert, Helena Ellis
definition source: http://www.sakura.eu/Our-products/item/8/Microtomy/29/Accu-Edge-Disposable-Microtome-Blades
ontology term requester: NCI BBRB
imported from: obi.owl

tissue section thickness
type: Class
subclass of: length measurement datum
editor preferred term: tissue section thickness
has curation status: ready for release
definition: A length measurement datum that is the result of an assay measuring the thickness of a tissue section.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

molecular analysis facility organization
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: has role
    some values from: Class
      intersection of: service provider role
      intersection of: Restriction
        on property: realized in
        some values from: material analysis service
subclass of: organization
editor preferred term: molecular analysis facility organization
example of usage: An analysis facility that includes analysis of molecular metabolites, as well as the various DNAs and RNAs.
has curation status: ready for release
definition: An organization that provides molecular analysis service.
term editor: Chris Stoeckert, Helena Ellis
alternative label: MAF
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

reason for lack of data item
type: Class
subclass of: information content entity
editor preferred term: reason for lack of data item
example of usage: cannot be assessed, not applicable, unknown
has curation status: metadata complete
definition: An information content entity that provides an explanation why a data item is not provided.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBI
ontology term requester: NCI BBRB
imported from: obi.owl

cannot be assessed determination
type: Class
subclass of: reason for lack of data item
editor preferred term: cannot be assessed determination
has curation status: metadata complete
definition: A reason for lack of data item that is the negative output of a determination if assay will provide reliable results.
term editor: Chris Stoeckert, Helena Ellis
alternative label: cannot be assessed
definition source: OBI
ontology term requester: NCI BBRB
imported from: obi.owl

determination if assay will provide reliable results
type: Class
subclass of: planned process
editor preferred term: determination if assay will provide reliable results
has curation status: metadata complete
definition: A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBI
ontology term requester: NCI BBRB
imported from: obi.owl

GX
type: Class
subclass of: cannot be assessed determination
editor preferred term: GX
example of usage: AJCC 7th edition GX: cannot be assessed.
has curation status: metadata complete
definition: A cannot be assessed determination for histologic tumor grade.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBI
ontology term requester: NCI BBRB
imported from: obi.owl

pTX
type: Class
subclass of: cannot be assessed determination
editor preferred term: pTX
example of usage: AJCC 7th edition pTX: cannot be assessed.
has curation status: metadata complete
definition: A cannot be assessed determination for pathologic primary tumor staging.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBI
ontology term requester: NCI BBRB
imported from: obi.owl

pNX
type: Class
subclass of: cannot be assessed determination
editor preferred term: pNX
example of usage: AJCC 7th edition pNX: cannot be assessed.
has curation status: metadata complete
definition: A cannot be assessed determination of pathologic staging of lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBI
ontology term requester: NCI BBRB
imported from: obi.owl

histologic grade according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred term: histologic grade according to AJCC 7th edition
example of usage: G1:Well differentiated
example of usage: G4: Undifferentiated
has curation status: metadata complete
definition: A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

histologic grade according to the Fuhrman Nuclear Grading System
type: Class
subclass of: categorical value specification
editor preferred term: histologic grade according to the Fuhrman Nuclear Grading System
has curation status: metadata complete
definition: A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Histologic Grade (Fuhrman Nuclear Grading System)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

histologic grade for ovarian tumor
type: Class
subclass of: categorical value specification
editor preferred term: histologic grade for ovarian tumor
has curation status: metadata complete
definition: A categorical value specification that is a histologic grade assigned to a ovarian tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

histologic grade for ovarian tumor according to a two-tier grading system
type: Class
subclass of: histologic grade for ovarian tumor
editor preferred term: histologic grade for ovarian tumor according to a two-tier grading system
has curation status: metadata complete
definition: A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

histologic grade for ovarian tumor according to the World Health Organization
type: Class
subclass of: histologic grade for ovarian tumor
editor preferred term: histologic grade for ovarian tumor according to the World Health Organization
has curation status: metadata complete
definition: A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred term: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative label: pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

pathologic primary tumor stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred term: pathologic primary tumor stage for lung according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative label: pT: Pathologic spread lung primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

pathologic primary tumor stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred term: pathologic primary tumor stage for kidney according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative label: pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

pathologic primary tumor stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred term: pathologic primary tumor stage for ovary according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative label: pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

pathologic lymph node stage for colon and rectum according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred term: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative label: pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

pathologic lymph node stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred term: pathologic lymph node stage for lung according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative label: pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

pathologic lymph node stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred term: pathologic lymph node stage for kidney according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative label: pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

pathologic lymph node stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred term: pathologic lymph node stage for ovary according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative label: pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

pathologic distant metastases stage for colon according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred term: pathologic distant metastases stage for colon according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative label: M: colon distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

pathologic distant metastases stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred term: pathologic distant metastases stage for lung according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative label: M: lung distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

pathologic distant metastases stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred term: pathologic distant metastases stage for kidney according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative label: M: kidney distant Metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

pathologic distant metastases stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred term: pathologic distant metastases stage for ovary according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative label: M: ovarian distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

clinical tumor stage group according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred term: clinical tumor stage group according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Clinical tumor stage group (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

International Federation of Gynecology and Obstetrics cervical cancer stage value specification
type: Class
subclass of: categorical value specification
editor preferred term: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
has curation status: metadata complete
definition: A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Clinical FIGO stage
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
type: Class
subclass of: categorical value specification
editor preferred term: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

performance status value specification
type: Class
subclass of: categorical value specification
editor preferred term: performance status value specification
has curation status: metadata complete
definition: A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life).
term editor: Chris Stoeckert, Helena Ellis
alternative label: Performance Status Scale
definition source: https://en.wikipedia.org/wiki/Performance_status
ontology term requester: NCI BBRB
imported from: obi.owl

Eastern Cooperative Oncology Group score value specification
type: Class
subclass of: performance status value specification
editor preferred term: Eastern Cooperative Oncology Group score value specification
has curation status: metadata complete
definition: A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient.
term editor: Chris Stoeckert, Helena Ellis
alternative label: ECOG score
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Karnofsky score vaue specification
type: Class
subclass of: performance status value specification
editor preferred term: Karnofsky score vaue specification
has curation status: metadata complete
definition: A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Karnofsky Score
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

clinical history of cancer
type: Class
subclass of: clinical history
editor preferred term: clinical history of cancer
has curation status: metadata complete
definition: A clinical history in which there is a diagnosis of cancer.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

clinical history devoid of cancer
type: Class
subclass of: clinical history
editor preferred term: clinical history devoid of cancer
has curation status: metadata complete
definition: A clinical history in which there was no diagnosis of cancer.
term editor: Chris Stoeckert, Helena Ellis
alternative label: clinical history of no cancer
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

unknown clinical history of cancer
type: Class
subclass of: clinical history
editor preferred term: unknown clinical history of cancer
has curation status: metadata complete
definition: A clinical history in which it is not known whether there was a diagnosis of cancer.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

diagnosis of cancer
type: Class
subclass of: diagnosis
editor preferred term: diagnosis of cancer
has curation status: metadata complete
definition: A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has cancer.
term editor: Chris Stoeckert, Helena Ellis
alternative label: cancer diagnosis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

family clinical history of cancer
type: Class
subclass of: clinical history
editor preferred term: family clinical history of cancer
has curation status: metadata complete
definition: A clinical history in which there is a diagnosis of cancer in a blood relative.
term editor: Chris Stoeckert, Helena Ellis
alternative label: family history of cancer
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

aunt clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred term: aunt clinical history of cancer
has curation status: metadata complete
definition: A clinical history in which there is a diagnosis of cancer in the female sibling of a parent.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

brother clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred term: brother clinical history of cancer
has curation status: metadata complete
definition: A clinical history in which there is a diagnosis of cancer in a male sibling.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

daughter clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred term: daughter clinical history of cancer
has curation status: metadata complete
definition: A clinical history in which there is a diagnosis of cancer in a person's female child.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

father clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred term: father clinical history of cancer
has curation status: metadata complete
definition: A clinical history in which there is a diagnosis of cancer in a male parent.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

mother clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred term: mother clinical history of cancer
has curation status: metadata complete
definition: A clinical history in which there is a diagnosis of cancer in a female parent.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

sister clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred term: sister clinical history of cancer
has curation status: metadata complete
definition: A clinical history in which there is a diagnosis of cancer in a female sibling.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

son clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred term: son clinical history of cancer
has curation status: metadata complete
definition: A clinical history in which there is a diagnosis of cancer in a person's male child.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

uncle clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred term: uncle clinical history of cancer
has curation status: metadata complete
definition: A clinical history in which there is a diagnosis of cancer in a male sibling of a parent.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

grandmother clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred term: grandmother clinical history of cancer
has curation status: metadata complete
definition: A clinical history in which there is a diagnosis of cancer in a female parent of a parent.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

grandfather clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred term: grandfather clinical history of cancer
has curation status: metadata complete
definition: A clinical history in which there is a diagnosis of cancer in a male parent of a parent.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

nephew clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred term: nephew clinical history of cancer
has curation status: metadata complete
definition: A clinical history in which there is a diagnosis of cancer in a male child of a sibling.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

niece clinical history of cancer
type: Class
subclass of: family clinical history of cancer
editor preferred term: niece clinical history of cancer
has curation status: metadata complete
definition: A clinical history in which there is a diagnosis of cancer in a female child of a sibling.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

diagnosis of infectious disease
type: Class
subclass of: diagnosis
editor preferred term: diagnosis of infectious disease
has curation status: metadata complete
definition: A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has an infectious disease.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

diagnosis of hepatitis B
type: Class
subclass of: diagnosis of infectious disease
editor preferred term: diagnosis of hepatitis B
has curation status: metadata complete
definition: A diagnosis of infectious disease caused by the hepatitis B virus.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

diagnosis of hepatitis C
type: Class
subclass of: diagnosis of infectious disease
editor preferred term: diagnosis of hepatitis C
has curation status: metadata complete
definition: A diagnosis of infectious disease caused by the hepatitis C virus.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

diagnosis of HIV
type: Class
subclass of: diagnosis of infectious disease
editor preferred term: diagnosis of HIV
has curation status: metadata complete
definition: A diagnosis of infectious disease caused by the human immunodeficiency virus (1 or 2).
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

clinical history of repeated HIV assays
type: Class
subclass of: clinical history
editor preferred term: clinical history of repeated HIV assays
has curation status: metadata complete
definition: 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.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

exposure to second hand smoke
type: Class
subclass of: clinical history
editor preferred term: exposure to second hand smoke
has curation status: metadata complete
definition: A clinical history in which there has been second hand exposure to tobacco smoking.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

exposure to second hand smoke in household during childhood
type: Class
subclass of: exposure to second hand smoke
editor preferred term: exposure to second hand smoke in household during childhood
has curation status: metadata complete
definition: An exposure to second hand smoke that occurred in the (patient's) household when the person was a child.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

exposure to second hand smoke in current household
type: Class
subclass of: exposure to second hand smoke
editor preferred term: exposure to second hand smoke in current household
has curation status: metadata complete
definition: An exposure to second hand smoke in person's current household.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

pregnancy history
type: Class
subclass of: clinical history
editor preferred term: pregnancy history
has curation status: metadata complete
definition: A clinical history in which a female has had a pregnancy.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

number of pregnancies
type: Class
subclass of: measurement datum
editor preferred term: number of pregnancies
has curation status: metadata complete
definition: A measurement datum of the total number of pregnancies a woman has had.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

number of live births
type: Class
subclass of: measurement datum
editor preferred term: number of live births
has curation status: metadata complete
definition: A measurement datum of the total number of live births a female has had.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

age when gave birth to first child
type: Class
subclass of: age measurement datum
editor preferred term: age when gave birth to first child
has curation status: metadata complete
definition: An age measurement datum performed on a female when her first biological child was born.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

gynecologic surgery history
type: Class
subclass of: clinical history
editor preferred term: gynecologic surgery history
has curation status: metadata complete
definition: A clinical history in which a woman has had gynecologic surgery in the past.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

hysterectomy history
type: Class
subclass of: gynecologic surgery history
editor preferred term: hysterectomy history
has curation status: metadata complete
definition: A gynecologic surgery history in which a woman has had a hysterectomy.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

unilateral oophorectomy history
type: Class
subclass of: gynecologic surgery history
editor preferred term: unilateral oophorectomy history
has curation status: metadata complete
definition: A gynecologic surgery history in which a woman has had a unilateral oophorectomy.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

neither hysterectomy nor oophorectomy history
type: Class
subclass of: gynecologic surgery history
editor preferred term: neither hysterectomy nor oophorectomy history
has curation status: metadata complete
definition: A gynecologic surgery history in which a woman has not had either a hysterectomy or an oophorectomy.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

hormonal birth control use history
type: Class
subclass of: information content entity
editor preferred term: hormonal birth control use history
has curation status: metadata complete
definition: An information content entity that indicates whether a woman has ever used oral contraceptives in order to block ovulation and prevent the occurrence of pregnancy.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

hormonal birth control former use history
type: Class
subclass of: hormonal birth control use history
editor preferred term: hormonal birth control former use history
has curation status: metadata complete
definition: A hormonal birth control use history that indicates an individual has previously been a hormonal birth control user but is not a current user.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

hormonal birth control current use history
type: Class
subclass of: hormonal birth control use history
editor preferred term: hormonal birth control current use history
has curation status: metadata complete
definition: A hormonal birth control use history that indicates an individual is currently a hormonal birth control user.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

no hormonal birth control use history
type: Class
subclass of: hormonal birth control use history
editor preferred term: no hormonal birth control use history
has curation status: metadata complete
definition: A hormonal birth control use history that indicates an individual has not ever been a hormonal birth control user.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

hormonal replacement therapy history
type: Class
subclass of: clinical history
editor preferred term: hormonal replacement therapy history
has curation status: metadata complete
definition: A clinical history in which an individual has had hormonal replacement therapy in the past.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

delivery form for hormonal replacement therapy
type: Class
subclass of: processed material
editor preferred term: delivery form for hormonal replacement therapy
has curation status: metadata complete
definition: A processed material used for delivery of hormones in hormone replacement therapy.
term editor: Chris Stoeckert, Helena Ellis
alternative label: form of hormone replacement therapy
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

pill delivery form for hormonal replacement therapy
type: Class
subclass of: delivery form for hormonal replacement therapy
editor preferred term: pill delivery form for hormonal replacement therapy
has curation status: metadata complete
definition: A delivery form for hormonal replacement therapy that is a pill for oral administration.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

patch delivery form for hormonal replacement therapy
type: Class
subclass of: delivery form for hormonal replacement therapy
editor preferred term: patch delivery form for hormonal replacement therapy
has curation status: metadata complete
definition: A delivery form for hormonal replacement therapy that is a patch for transdermal administration.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

cream delivery form for hormonal replacement therapy
type: Class
subclass of: delivery form for hormonal replacement therapy
editor preferred term: cream delivery form for hormonal replacement therapy
has curation status: metadata complete
definition: A delivery form for hormonal replacement therapy that is a cream for transdermal administration.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

menopausal status
type: Class
subclass of: information content entity
editor preferred term: menopausal status
has curation status: metadata complete
definition: An information content entity that indicates the state of a female's cessation of menstruation.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

indeterminate menopausal status
type: Class
subclass of: menopausal status
editor preferred term: indeterminate menopausal status
has curation status: metadata complete
definition: A menopausal status that is neither pre- nor post-menopausal.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

premenopausal status
type: Class
subclass of: menopausal status
editor preferred term: premenopausal status
has curation status: metadata complete
definition: A menopausal status indicating that less than 6 months has passed since the last menstrual period and there has not been prior bilateral oophorectomy and not on estrogen replacement.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

perimenopausal status
type: Class
subclass of: menopausal status
editor preferred term: perimenopausal status
has curation status: metadata complete
definition: A menopausal status indicating that it has been 6-12 months since last menstrual period.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

postmenopausal status
type: Class
subclass of: menopausal status
editor preferred term: postmenopausal status
has curation status: metadata complete
definition: A menopausal status indicating that it has been more than 12 months since the last menstrual period with no prior hysterectomy or that there has been a prior bilateral oophorectomy.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

exposure to environmental and workplace carcinogens history
type: Class
subclass of: information content entity
editor preferred term: exposure to environmental and workplace carcinogens history
has curation status: metadata complete
definition: An information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

exposure to arsenic history
type: Class
subclass of: exposure to environmental and workplace carcinogens history
editor preferred term: exposure to arsenic history
has curation status: metadata complete
definition: An exposure to environmental and workplace carcinogens history where the carcinogen is arsenic.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

exposure to asbestos history
type: Class
subclass of: exposure to environmental and workplace carcinogens history
editor preferred term: exposure to asbestos history
has curation status: metadata complete
definition: An exposure to environmental and workplace carcinogens history where the carcinogen is asbestos.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

exposure to diesel exhaust history
type: Class
subclass of: exposure to environmental and workplace carcinogens history
editor preferred term: exposure to diesel exhaust history
has curation status: metadata complete
definition: An exposure to environmental and workplace carcinogens history where the carcinogen is diesel exhaust.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

exposure to chromium history
type: Class
subclass of: exposure to environmental and workplace carcinogens history
editor preferred term: exposure to chromium history
has curation status: metadata complete
definition: An exposure to environmental and workplace carcinogens history where the carcinogen is chromium.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

exposure to silica history
type: Class
subclass of: exposure to environmental and workplace carcinogens history
editor preferred term: exposure to silica history
has curation status: metadata complete
definition: An exposure to environmental and workplace carcinogens history where the carcinogen is silica.
term editor: Chris Stoeckert, Helena Ellis
definition source: OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

indicator of whether an inclusion criterion was met
type: Class
subclass of: information content entity
editor preferred term: indicator of whether an inclusion criterion was met
has curation status: metadata complete
definition: An information content entity that indicates whether or not an entity has met a specific requirement in order to take part in a given process.
term editor: Chris Stoeckert, Helena Ellis
alternative label: eligibility criterion met
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

indicator of whether all inclusion criteria were met
type: Class
subclass of: information content entity
editor preferred term: indicator of whether all inclusion criteria were met
has curation status: metadata complete
definition: An information content entity that indicates whether or not an entity has met all specific requirements in order to take part in a given process.
term editor: Chris Stoeckert, Helena Ellis
alternative label: all eligibility criteria met
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

age of majority inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred term: age of majority inclusion criterion
has curation status: metadata complete
definition: An inclusion criterion that uses the age of majority for a state or institution, where one is generally considered to be an adult, which if met, makes an individual suitable for a given task or participation in a given process.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

chemotherapy treatment exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred term: chemotherapy treatment exclusion criterion
has curation status: metadata complete
definition: An exclusion criterion that defines whether chemotherapy was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

radiation treatment exclusion criteria
type: Class
subclass of: exclusion criterion
editor preferred term: radiation treatment exclusion criteria
has curation status: metadata complete
definition: An exclusion criterion that defines whether radiation was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

chemotherapy treatment within the recent past exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred term: chemotherapy treatment within the recent past exclusion criterion
example of usage: An exclusion criterion defined by the pathologist is defined as whether the individual received chemotherapy within the last two years.
has curation status: metadata complete
definition: An exclusion criterion that defines whether chemotherapy was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

radiation treatment within the recent past exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred term: radiation treatment within the recent past exclusion criterion
example of usage: An exclusion criterion defined by the pathologist is defined as whether the individual received radiation therapy within the last two years.
has curation status: metadata complete
definition: An exclusion criterion that defines whether radiation was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

BMI range inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred term: BMI range inclusion criterion
example of usage: An important inclusion criterion is for for the individual to have a BMI between 18.5 and 35.0
has curation status: metadata complete
definition: An inclusion criterion that defines and states a Body Mass Index range, which if met, makes an individual suitable for a given task or participation in a given process.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

blood transfusion exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred term: blood transfusion exclusion criterion
example of usage: An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within 48 hours prior to death.
has curation status: metadata complete
definition: An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within a specified time frame prior to death, which if met, makes a specimen donor unsuitable for a given task or participation in a given process.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

history of metastatic cancer exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred term: history of metastatic cancer exclusion criterion
has curation status: metadata complete
definition: An exclusion criterion defined as whether an individual has ever been diagnosed with metastatic cancer (cancer that spread beyond the initial site such as to other organs like brain bone or liver), which if met, makes the individual unsuitable for a given task or participation in a given process.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

intravenous drug use exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred term: intravenous drug use exclusion criterion
example of usage: Donor eligibility based on history of intravenous drug abuse in the last 5 years.
has curation status: metadata complete
definition: An exclusion criterion defined as when an individual has a history of intravenous drug abuse for a specific timeframe, which if met, makes the individual unsuitable for a given task or participation in a given process.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

history of sex with someone with a history of blood borne infection exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred term: history of sex with someone with a history of blood borne infection exclusion criterion
example of usage: Donor eligibility based on whether the donor has a history of sex with someone who has been diagnosed or at risk for HIV/AIDS and/or HCV and/or HBV in the last 5 years.
has curation status: metadata complete
definition: An exclusion criterion defined as whether an individual has a history of sex with someone who has been diagnosed or at risk for a blood borne infections disease in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

history of sex with someone with a history of intravenous drugs exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred term: history of sex with someone with a history of intravenous drugs exclusion criterion
example of usage: Donor eligibility based on whether the donor has a history of sex with someone who has used intravenous drugs in the last 5 years.
has curation status: metadata complete
definition: An exclusion criterion defined as whether an individual has a history of sex with someone who has used intravenous drugs in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

HIV exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred term: HIV exclusion criterion
has curation status: metadata complete
definition: An exclusion criterion defined as whether an individual has a history of repeatedly reactive screening assays for HIV-1 or HIV-2 antibody regardless of the results of supplemental assays, which if met, makes the individual unsuitable for a given task or participation in a given process.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

exposure to blood borne infectious disease exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred term: exposure to blood borne infectious disease exclusion criterion
example of usage: Donor eligibility based on whether the donor has been exposed to HIV/AIDS.
has curation status: metadata complete
definition: An exclusion criterion defined as whether an individual has been exposed to a blood borne infections disease through needle sticks and/or contact with non-intact skin and/or contact with open wounds and/or contact with mucous membranes, which if met, makes the individual unsuitable for a given task or participation in a given process.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

measurand role
type: Class
subclass of: material entity role
subclass of: Restriction
  on property: role of
  some values from: material entity
editor preferred term: measurand role
has curation status: metadata complete
definition: A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.
term editor: Person: Alan Ruttenberg, Jie Zheng
definition source: https://en.wiktionary.org/wiki/measurand
term tracker item: https://github.com/obi-ontology/obi/issues/778
imported from: obi.owl

health status inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred term: health status inclusion criterion
example of usage: ‘diagnosed with Type 2 diabetes mellitus’, ‘E11.4’, ’not finding of hypertension'
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states one or more clinically significant bodily components, dispositions, and/or bodily processes of an entity that are inferred from relevant clinical findings or self-reported, which, if met, makes the entity suitable for a given task or participation in a given process.
term editor: Mathias Brochhausen
ontology term requester: MIABIS2.0
imported from: obi.owl

clinically relevant lifestyle inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred term: clinically relevant lifestyle inclusion criterion
example of usage: 'smoking behavior’
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states one or more clinically relevant planned processes that a human being actively participates in , which, if met, makes the human being suitable for a given task or participation in a given process.
term editor: Mathias Brochhausen
ontology term requester: MIABIS2.0
imported from: obi.owl

clinically relevant exposure inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred term: clinically relevant exposure inclusion criterion
example of usage: 'exposure to cigarette smoke’, ‘exposure to lead through drinking water'
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states one or more clinically relevant histories of exposure of an entity, which, if met, makes the entity suitable for a given task or participation in a given process.
term editor: Mathias Brochhausen
ontology term requester: MIABIS2.0
imported from: obi.owl

gravidity inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred term: gravidity inclusion criterion
example of usage: 'pregnant’, ‘not pregnant'
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states one or more gravidity statuses of an organism, which, if met, makes the entity suitable for a given task or participation in a given process.
term editor: Mathias Brochhausen
ontology term requester: MIABIS2.0
imported from: obi.owl

defined population inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred term: defined population inclusion criterion
example of usage: inclusion based on age, sex, and living region (rural area or specified city).
has curation status: metadata complete
definition: An inclusion criterion that is based on fitting within the defined characteristics of a population based study design.
term editor: Chris Stoeckert, Mathias Brochhausen
definition source: MIABIS 2.0
term tracker item: https://github.com/obi-ontology/obi/issues/920
ontology term requester: MIABIS 2.0
imported from: obi.owl

age since culture seeding measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since culture seeding measurement datum
has curation status: metadata incomplete
definition: An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish).
term editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
alternative label: age of culture
imported from: obi.owl

amniotic fluid specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: amniotic fluid
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: amniotic fluid specimen
has curation status: ready for release
definition: A specimen that is derived from amniotic fluid.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: obi.owl

bile specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: bile
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred term: bile specimen
has curation status: ready for release
definition: A specimen that is derived from bile.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: obi.owl

cerebrospinal fluid specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: cerebrospinal fluid
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred term: cerebrospinal fluid specimen
has curation status: ready for release
definition: A specimen that is derived from cerbrospinal fluid.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: obi.owl

feces specimen
type: Class
subclass of: specimen from organism
editor preferred term: feces specimen
has curation status: ready for release
definition: A specimen that is derived from feces.
term editor: Chris Stoeckert
alternative label: stool specimen
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: obi.owl

digestive system fluid or secretion specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: digestive system secreted substance
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: digestive system fluid or secretion specimen
has curation status: ready for release
definition: A specimen that is derived from digestive system fluid or secretion.
term editor: Chris Stoeckert
alternative label: gastric fluid specimen
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: obi.owl

milk specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: milk
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred term: milk specimen
has curation status: ready for release
definition: A specimen that is derived from milk.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: obi.owl

pericardial fluid specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: pericardial fluid
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred term: pericardial fluid specimen
has curation status: ready for release
definition: A specimen that is derived from pericardial fluid.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: obi.owl

saliva specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: saliva
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: saliva specimen
has curation status: ready for release
definition: A specimen that is derived from saliva.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: obi.owl

sputum specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: sputum
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: sputum specimen
has curation status: ready for release
definition: A specimen that is derived from sputum.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: obi.owl

sweat specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: sweat
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred term: sweat specimen
has curation status: ready for release
definition: A specimen that is derived from sweat.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: obi.owl

synovial fluid specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: synovial fluid
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred term: synovial fluid specimen
has curation status: ready for release
definition: A specimen that is derived from synovial fluid.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: obi.owl

vitreous humor specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: vitreous humor specimen
has curation status: ready for release
definition: A specimen that is derived from vireous humor.
term editor: Chris Stoeckert
alternative label: vitreous fluid specimen
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: obi.owl

bone marrow specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: bone marrow
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: bone marrow biopsy
subclass of: specimen from organism
editor preferred term: bone marrow specimen
has curation status: ready for release
definition: A specimen that is derived from bone marrow.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: obi.owl

placenta specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: placenta specimen
has curation status: ready for release
definition: A specimen that is derived from placenta.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: obi.owl

peritoneal fluid specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: peritoneal fluid
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred term: peritoneal fluid specimen
has curation status: ready for release
definition: A specimen that is derived from peritoneal fluid.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: obi.owl

pleural fluid specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: pleural fluid
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred term: pleural fluid specimen
has curation status: ready for release
definition: A specimen that is derived from pleural fluid.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: obi.owl

brain specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: brain specimen
has curation status: ready for release
definition: A specimen that is derived from brain.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

hair specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: strand of hair
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: hair specimen
has curation status: ready for release
definition: A specimen that is derived from hair.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

prostate gland specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: prostate gland specimen
has curation status: ready for release
definition: A specimen that is derived from prostate gland.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

skeletal muscle tissue specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: skeletal muscle tissue
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: skeletal muscle tissue specimen
has curation status: ready for release
definition: A specimen that is derived from skeletal muscle.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

heart specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: heart specimen
has curation status: ready for release
definition: A specimen that is derived from heart.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

renal medulla specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: renal medulla specimen
has curation status: ready for release
definition: A specimen that is derived from renal medulla.
term editor: Chris Stoeckert
alternative label: kidney medulla specimen
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

adrenal gland specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: adrenal gland specimen
has curation status: ready for release
definition: A specimen that is derived from adrenal gland.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

breast specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: breast specimen
has curation status: ready for release
definition: A specimen that is derived from breast.
term editor: Chris Stoeckert
alternative label: mammary tissue specimen
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

urinary bladder specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: urinary bladder specimen
has curation status: ready for release
definition: A specimen that is derived from urinary bladder.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

tibial artery specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: tibial artery specimen
has curation status: ready for release
definition: A specimen that is derived from tibial artery.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

skin of body specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: skin of body specimen
has curation status: ready for release
definition: A specimen that is derived from skin.
term editor: Chris Stoeckert
alternative label: skin specimen
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

pancreas specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: pancreas specimen
has curation status: ready for release
definition: A specimen that is derived from pancreas.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

stomach specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: stomach specimen
has curation status: ready for release
definition: A specimen that is derived from stomach.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

pituitary gland specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: pituitary gland specimen
has curation status: ready for release
definition: A specimen that is derived from pituitary gland.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

adipose tissue specimen
type: Class
subclass of: specimen from organism
editor preferred term: adipose tissue specimen
has curation status: ready for release
definition: A specimen that is derived from adipose tissue.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

cortex of kidney specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: cortex of kidney specimen
has curation status: ready for release
definition: A specimen that is derived from cortex of kidney.
term editor: Chris Stoeckert
alternative label: kidney cortex specimen
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

esophagus mucosa specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: esophagus mucosa specimen
has curation status: ready for release
definition: A specimen that is derived from esophagus mucosa.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

colon specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: colon specimen
has curation status: ready for release
definition: A specimen that is derived from colon.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

lung specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: lung specimen
has curation status: ready for release
definition: A specimen that is derived from lung.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

esophagus muscularis mucosa specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: esophagus muscularis mucosa specimen
has curation status: ready for release
definition: A specimen that is derived from esophagus muscularis mucosa.
term editor: Chris Stoeckert
alternative label: esophagus muscularis specimen
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

cerebral cortex specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: cerebral cortex specimen
has curation status: ready for release
definition: A specimen that is derived from cerebral cortex.
term editor: Chris Stoeckert
alternative label: brain cortex specimen
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

thyroid gland specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: thyroid gland specimen
has curation status: ready for release
definition: A specimen that is derived from thyroid gland.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

cerebellum specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: cerebellum specimen
has curation status: ready for release
definition: A specimen that is derived from cerebellum.
term editor: Chris Stoeckert
alternative label: brain cerebellum specimen
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

tibial nerve specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: tibial nerve specimen
has curation status: ready for release
definition: A specimen that is derived from tibial nerve.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

coronary artery specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: coronary artery specimen
has curation status: ready for release
definition: A specimen that is derived from coronary artery.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

spleen specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: spleen specimen
has curation status: ready for release
definition: A specimen that is derived from spleen.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

aorta specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: aorta specimen
has curation status: ready for release
definition: A specimen that is derived from aorta.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

atrial appendage specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: atrial appendage specimen
has curation status: ready for release
definition: A specimen that is derived from the atrium auricular region.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

esophagogastric junction specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: esophagogastric junction specimen
has curation status: ready for release
definition: A specimen that is derived from the esophagogastric junction.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

ileum specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: ileum specimen
has curation status: ready for release
definition: A specimen that is derived from ileum.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

liver specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: liver specimen
has curation status: ready for release
definition: A specimen that is derived from liver.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

minor salivary gland specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: minor salivary gland specimen
has curation status: ready for release
definition: A specimen that is derived from minor salivary gland.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

omentum specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: omentum specimen
has curation status: ready for release
definition: A specimen that is derived from omentum.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

ovary specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: ovary specimen
has curation status: ready for release
definition: A specimen that is derived from female gonad.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

sigmoid colon specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: sigmoid colon specimen
has curation status: ready for release
definition: A specimen that is derived from sigmoid colon.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

suprapubic skin specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: skin of body specimen
editor preferred term: suprapubic skin specimen
has curation status: ready for release
definition: A specimen that is derived from suprapubic skin.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

testis specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: testis specimen
has curation status: ready for release
definition: A specimen that is derived from testis.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

uterus specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: uterus specimen
has curation status: ready for release
definition: A specimen that is derived from uterus.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

vagina specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: vagina specimen
has curation status: ready for release
definition: A specimen that is derived from vagina.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: obi.owl

age group inclusion criterion
type: Class
subclass of: inclusion criterion
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: minimum age value specification
  intersection of: Restriction
    on property: has part
    some values from: maximum age value specification
editor preferred term: age group inclusion criterion
example of usage: "18-33 years old"
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process.
term editor: Mathias Brochhausen
term tracker item: https://github.com/obi-ontology/obi/issues/839
imported from: obi.owl

minimum age value specification
type: Class
subclass of: value specification
editor preferred term: minimum age value specification
has curation status: metadata incomplete
definition: A value specifcation that specifies the youngest age when specifying an age range.
term editor: Mathias Brochhausen
imported from: obi.owl

maximum age value specification
type: Class
subclass of: value specification
editor preferred term: maximum age value specification
has curation status: metadata incomplete
definition: A value specifcation that specifies the oldest age when specifying an age range.
term editor: Mathias Brochhausen
imported from: obi.owl

use of medication inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred term: use of medication inclusion criterion
example of usage: "received at least 2 days of vancomycin"
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states a a set of medications, which, if used by an entity, makes that entity suitable for a given task or participation in a given process.
term editor: Mathias Brochhausen
term tracker item: https://github.com/obi-ontology/obi/issues/840
imported from: obi.owl

hospital patient inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred term: hospital patient inclusion criterion
example of usage: "included hospital patients"
has curation status: metadata incomplete
definition: An inclusion criterion defines that a human being has to be a hospital patient to be suitable for a given task or participation in a given process.
term editor: Mathias Brochhausen
imported from: obi.owl

family status inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred term: family status inclusion criterion
example of usage: "included married and unmarried patients", "included divorced individuals"
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states one or more family statuses, which, if met, makes a human being suitable for a given task or participation in a given process.
term editor: Mathias Brochhausen
imported from: obi.owl

sex inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred term: sex inclusion criterion
example of usage: "included males and females", "included male patients"
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states one or more sexes which, if met, makes an entity suitable for a given task or participation in a given process.
term editor: Mathias Brochhausen
imported from: obi.owl

country of residence inclusion criteria
type: Class
subclass of: inclusion criterion
editor preferred term: country of residence inclusion criteria
example of usage: "include US residents"
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states one or more countries of residence which, if met, makes a human being suitable for a given task or participation in a given process.
term editor: Mathias Brochhausen
imported from: obi.owl

ethnicity inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred term: ethnicity inclusion criterion
example of usage: "include only Hispanic individuals"
has curation status: metadata incomplete
definition: An inclusion criteria that defines and states one or more ethnicities which, if met, makes an entity suitable for a given task or participation in a given process.
term editor: Mathias Brochhausen
imported from: obi.owl

swab specimen
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: collecting specimen with swab
subclass of: specimen
editor preferred term: swab specimen
has curation status: ready for release
definition: A specimen that is stored on a swab as the output of a collecting specimen with swab process.
term editor: Chris Stoeckert
definition source: OBIB/OBI
term tracker item: https://github.com/obi-ontology/obi/issues/910
ontology term requester: OBIB
imported from: obi.owl

collecting specimen with swab
type: Class
subclass of: specimen collection process
editor preferred term: collecting specimen with swab
has curation status: ready for release
definition: A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick).
term editor: Chris Stoeckert
definition source: OBIB
term tracker item: https://github.com/obi-ontology/obi/issues/910
ontology term requester: OBIB
imported from: obi.owl

areolar swab specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen with swab
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: Class
        intersection of: specimen collection process
        intersection of: Restriction
subclass of: swab specimen
editor preferred term: areolar swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of an areola of a breast.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: obi.owl

breast swab specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen with swab
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: Class
        intersection of: specimen collection process
        intersection of: Restriction
subclass of: swab specimen
editor preferred term: breast swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of a breast.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: obi.owl

cheek swab specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen with swab
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: Class
        intersection of: specimen collection process
        intersection of: Restriction
subclass of: swab specimen
editor preferred term: cheek swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: obi.owl

nasopharyngeal swab specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen with swab
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: Class
        intersection of: specimen collection process
        intersection of: Restriction
subclass of: swab specimen
editor preferred term: nasopharyngeal swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of a nasopharynx.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: obi.owl

oral swab specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen with swab
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: Class
        intersection of: specimen collection process
        intersection of: Restriction
subclass of: swab specimen
editor preferred term: oral swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the inside surface of a mouth.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: obi.owl

oropharyngeal swab specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen with swab
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: Class
        intersection of: specimen collection process
        intersection of: Restriction
subclass of: swab specimen
editor preferred term: oropharyngeal swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of a oropharynx.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: obi.owl

rectal swab specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen with swab
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: Class
        intersection of: specimen collection process
        intersection of: Restriction
subclass of: swab specimen
editor preferred term: rectal swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of a rectum.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: obi.owl

tongue swab specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen with swab
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: Class
        intersection of: specimen collection process
        intersection of: Restriction
subclass of: swab specimen
editor preferred term: tongue swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of a tongue.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: obi.owl

vagina swab specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen with swab
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: Class
        intersection of: specimen collection process
        intersection of: Restriction
subclass of: swab specimen
editor preferred term: vagina swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of a vagina.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: obi.owl

fecal swab specimen
type: Class
subclass of: swab specimen
editor preferred term: fecal swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of a feces.
term editor: Chris Stoeckert
alternative label: stool swab specimen
definition source: Chris Stoeckert, OBIB
imported from: obi.owl

environmental swab specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen with swab
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: Class
        intersection of: specimen collection process
        intersection of: Restriction
subclass of: swab specimen
editor preferred term: environmental swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of an environmenal material.
term editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: obi.owl

birth cohort study design
type: Class
subclass of: study design
editor preferred term: birth cohort study design
example of usage: The LucKi Birth Cohort Study was designed and started in 2006 to follow children from birth into adulthood on a wide range of determinants, disorders, and diseases.
has curation status: metadata complete
definition: A cohort study design for which the subjects are followed from the time of birth usually including information about gestation and follow up.
term editor: MIABIS
definition source: MIABIS contributors
imported from: obi.owl

disease specific study design
type: Class
subclass of: study design
editor preferred term: disease specific study design
example of usage: A study of the symptoms experienced by patients who have been diagnosed with multiple sclerosis employs a disease specific study design.
has curation status: metadata complete
definition: A study design for which material and information is collected from subjects that have already developed a particular disease.
term editor: MIABIS
definition source: MIABIS contributors
imported from: obi.owl

genealogical record
type: Class
subclass of: document
editor preferred term: genealogical record
example of usage: A family tree is a type of genealogical record.
has curation status: metadata incomplete
definition: A document about the family relationships of persons related as members of a domestic group linked through descent from a common ancestor, marriage, or adoption.
term editor: MIABIS
term editor: Sarah Bost
imported from: obi.owl

national registry
type: Class
subclass of: information content entity
editor preferred term: national registry
example of usage: The Social Security Administration's Death Master File is a national registry in the United States.
has curation status: metadata complete
definition: An information content entity that contains information about a nationwide group of individuals.
term editor: MIABIS
term editor: Sarah Bost
definition source: MIABIS contributors
imported from: obi.owl

national biomedical registry
type: Class
subclass of: national registry
editor preferred term: national biomedical registry
example of usage: The Care Register for Health Care, maintained by the Finnish National Institute for Health and Welfare, is a national biomedical registry.
has curation status: metadata complete
definition: A national registry that contains information about individuals that was accumulated for a biomedical purpose, such as diagnoses, treatments, or outcomes.
term editor: MIABIS
term editor: Sarah Bost
definition source: MIABIS contributors
imported from: obi.owl

biopsy
type: Class
subclass of: collecting specimen from organism
editor preferred term: biopsy
example of usage: Biopsy of a potentially cancerous mole.
has curation status: ready for release
definition: A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive.
term editor: Damion Dooley
term editor: Nicole Vasilevsky
definition source: https://en.wikipedia.org/wiki/Biopsy
imported from: obi.owl

image guided biopsy
type: Class
subclass of: needle biopsy
editor preferred term: image guided biopsy
example of usage: Image-guided needle biopsy allows a doctor to biopsy suspicious areas that aren't readily seen or felt through skin, such as in a prostate gland.
has curation status: ready for release
definition: A biopsy which uses an imaging procedure to guide a needle biopsy.
term editor: Damion Dooley
alternative label: image guided needle biopsy
alternative label: image-guided biopsy
alternative label: imaging guided biopsy
definition source: https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922
imported from: obi.owl

computed tomography assisted biopsy
type: Class
subclass of: image guided biopsy
subclass of: Restriction
  on property: has_specified_input
  some values from: computed tomography scanner
editor preferred term: computed tomography assisted biopsy
example of usage: A CT Guided Biopsy is a procedure performed by a radiologist to obtain a small tissue sample through a needle.
has curation status: ready for release
definition: A needle biopsy guided by real-time computed tomography (CT) scan images.
term editor: Damion Dooley
alternative label: CT Assisted Biopsy
alternative label: CT Guided Biopsy
alternative label: Computed Tomography Assisted Biopsy
alternative label: Computed Tomography-Guided Needle Biopsy
definition source: http://purl.obolibrary.org/obo/NCIT_C137909
imported from: obi.owl

ultrasound-guided needle biopsy
type: Class
subclass of: image guided biopsy
editor preferred term: ultrasound-guided needle biopsy
example of usage: An ultrasound-guided needle biopsy uses sound waves to help locate a nodule or abnormality within the thyroid.
has curation status: ready for release
definition: A needle biopsy guided by ultrasound visualization.
term editor: Damion Dooley
definition source: https://www.oncolink.org/cancer-treatment/procedures-diagnostic-tests/biopsy-procedures/ultrasound-guided-needle-biopsy
imported from: obi.owl

needle biopsy
type: Class
subclass of: biopsy
subclass of: Restriction
  on property: has_specified_input
  some values from: needle
editor preferred term: needle biopsy
example of usage: A needle biopsy is often used on suspicious breast lumps and enlarged lymph nodes that a doctor can feel through a patient's skin.
has curation status: ready for release
definition: A biopsy that uses a hollow needle to extract cells.
term editor: Damion Dooley
definition source: https://www.mayoclinic.org/tests-procedures/needle-biopsy/about/pac-20394749
imported from: obi.owl

fine needle aspiration biopsy
type: Class
subclass of: needle biopsy
editor preferred term: fine needle aspiration biopsy
example of usage: A fine needle aspiration biopsy is commonly performed in order to test for cancer.
has curation status: ready for release
definition: A biopsy that uses a thin needle to extract cells.
term editor: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: FNA
alternative label: FNAB
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/
ontology term requester: NCI BBRB
imported from: obi.owl

core needle biopsy
type: Class
subclass of: needle biopsy
editor preferred term: core needle biopsy
example of usage: A core needle biopsy can remove more tissue than a fine needle biopsy, and therefore can provide more information about the cells and tissue removed.
has curation status: ready for release
definition: A biopsy that uses a hollow tube to collect a core of tissue.
term editor: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative label: CNB
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/
ontology term requester: NCI BBRB
imported from: obi.owl

surgical biopsy
type: Class
subclass of: biopsy
editor preferred term: surgical biopsy
example of usage: Surgical biopsy may be required to collect hard-to-reach tissue.
has curation status: ready for release
definition: A biopsy involving a surgical incision into an organism to access the biopsy material.
term editor: Damion Dooley
alternative label: excisional biopsy
alternative label: open biopsy
definition source: https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922
imported from: obi.owl

abdominal wall fat pad biopsy
type: Class
subclass of: biopsy
subclass of: Restriction
  on property: has_specified_input
  some values from: omental fat pad
editor preferred term: abdominal wall fat pad biopsy
example of usage: The makeup of fat in the abdominal wall can be investigated by fat biopsy.
has curation status: ready for release
definition: A biopsy involving the collection of a small part of the abdominal wall fat pad.
term editor: Nicole Vasilevsky, Damion Dooley
alternative label: abdominal wall biopsy
alternative label: fat biopsy
definition source: https://www.ucsfbenioffchildrens.org/tests/003841.html
imported from: obi.owl

tail biopsy
type: Class
subclass of: biopsy
subclass of: Restriction
  on property: has_specified_input
  some values from: tail
editor preferred term: tail biopsy
example of usage: A mouse tail biopsy was performed to collect material for DNA extraction.
has curation status: ready for release
definition: A biopsy involving the collection of the tip of a mamallian tail.
term editor: Nicole Vasilevsky, Damion Dooley
alternative label: snip
definition source: http://web.jhu.edu/animalcare/policies/Tail%20Biopsy%20of%20Mice.pdf
imported from: obi.owl

bone marrow biopsy
type: Class
subclass of: biopsy
subclass of: Restriction
  on property: has_specified_input
  some values from: bone marrow
editor preferred term: bone marrow biopsy
example of usage: A bone marrow biopsy removes bone with the marrow inside to look at under a microscope
has curation status: ready for release
definition: A biopsy where a small amount of bone and a small amount of fluid and bone marrow are collected.
term editor: Nicole Vasilevsky
definition source: http://www.webmd.com/cancer/bone-marrow-aspiration-and-biopsy
imported from: obi.owl

skinpunch biopsy
type: Class
subclass of: biopsy
subclass of: Restriction
  on property: has_specified_input
  some values from: integument
editor preferred term: skinpunch biopsy
example of usage: A three or four millimeter punch is used in s skinpunch biopsy proceedure.
has curation status: ready for release
definition: A biopsy that involves the collection of a cylinder of skin (including epidermis, dermis and superficial fat) using a punch tool.
term editor: Nicole Vasilevsky
alternative label: punch biopsy; skin biopsy
definition source: http://healthlibrary.epnet.com/GetContent.aspx
imported from: obi.owl

vacuum-assisted biopsy needle
type: Class
subclass of: needle
subclass of: Restriction
  on property: has function
  some values from: transfer function
editor preferred term: vacuum-assisted biopsy needle
example of usage: Vacuum-assisted biopsy needles come in two varieties: a non-tethered design and a needle design requiring tethering cable to a vacuum source.
has curation status: requires discussion
definition: A core biopsy needle integrated with a vacuum system which facilitates the collection of specimen material.
term editor: Damion Dooley
definition source: https://www.researchgate.net/publication/330227873
term tracker item: https://github.com/obi-ontology/obi/issues/1163
imported from: obi.owl

molecular label role
type: Class
subclass of: reagent role
editor preferred term: molecular label role
has curation status: metadata complete
definition: 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.
editor note: MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role). JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced REO_0000171 by newly assigned ID: OBI:0002743.
term editor: Group: OBI
alternative label: molecular tracer role
definition source: OBI developer call, 3-12-12
term tracker item: https://github.com/obi-ontology/obi/issues/1135
imported from: obi.owl

molecular label
type: Class
equivalent class: Class
  intersection of: molecular entity
  intersection of: Restriction
    on property: has role
    some values from: molecular label role
subclass of: molecular entity
subclass of: reagent
editor preferred term: molecular label
has curation status: metadata complete
definition: A molecular reagent 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
editor note: JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced OBI:0002744 by newly assigned ID: OBI:0002744.
term editor: Group: OBI
alternative label: molecular tracer
definition source: OBI developer call, 3-12-12
term tracker item: https://github.com/obi-ontology/obi/issues/1135
imported from: obi.owl

vacuum-assisted biopsy
type: Class
subclass of: needle biopsy
subclass of: Restriction
  on property: has_specified_input
  some values from: vacuum-assisted biopsy needle
editor preferred term: vacuum-assisted biopsy
example of usage: A vacuum assisted biopsy can remove an area of abnormal cells from breast tissue.
has curation status: ready for release
definition: A biopsy performed with a needle augmented with a vacuum device.
term editor: Damion Dooley
alternative label: VAB
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/
imported from: obi.owl

induced sputum specimen
type: Class
subclass of: sputum specimen
subclass of: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: specimen collection process
  intersection of: Restriction
    on property: derives from
    some values from: sputum
subclass of: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: collecting specimen from organism
editor preferred term: induced sputum specimen
has curation status: metadata complete
definition: A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution.
term editor: John Judkins
definition source: PMC3297553
imported from: obi.owl

platelet-poor plasma specimen
type: Class
subclass of: blood plasma specimen
editor preferred term: platelet-poor plasma specimen
has curation status: metadata incomplete
definition: A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter.
term editor: PERSON: Matthew Diller
imported from: obi.owl

platelet-poor plasma preparation process
type: Class
subclass of: material component separation
editor preferred term: platelet-poor plasma preparation process
has curation status: metadata incomplete
definition: A material component separation process in which (1) whole blood is first centrifuged to separate red blood cells from blood plasma, which forms the supernatant, and (2) the blood plasma is then centrifuged to separate platelets from the plasm.
term editor: PERSON: Matthew Diller
imported from: obi.owl

material supplier
type: Class
equivalent class: Class
  intersection of: Class
    union of: Homo sapiens
    union of: organization
  intersection of: Restriction
    on property: has role
    some values from: material supplier role
subclass of: material entity
editor preferred term: material supplier
has curation status: metadata incomplete
definition: A person or organization that provides material supplies to other people or organizations.
term editor: Rebecca Jackson
term tracker item: https://github.com/obi-ontology/obi/issues/1289
imported from: obi.owl

blood plasma specimen
type: Class
subclass of: processed specimen
editor preferred term: blood plasma specimen
example of usage: 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.
has curation status: metadata complete
definition: a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
editor note: 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.
term editor: PERSON: Maura Gasparetto
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
alternative label: plasma
definition source: WEB: http://en.wikipedia.org/wiki/Blood_plasma
imported from: obi.owl

blood serum specimen
type: Class
subclass of: processed specimen
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: Class
      union of: filtration
      union of: centrifugation
      union of: dialysis
    intersection of: Restriction
      on property: has_specified_input
      some values from: blood specimen
subclass of: Restriction
  on property: has role
  some values from: specimen role
editor preferred term: blood serum specimen
example of usage: 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.
has curation status: metadata complete
definition: A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
term editor: PERSON: Maura Gasparetto
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
definition source: WEB: http://en.wikipedia.org/wiki/Blood_plasma
imported from: obi.owl

organism
type: Class
subclass of: material entity
editor preferred term: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
has curation status: ready for release
definition: 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.
editor note: 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')
editor note: 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.
term editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism
imported from: obi.owl

specimen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: material entity
editor preferred term: specimen
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
has curation status: ready for release
definition: A material entity that has the specimen role.
editor note: 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.
term editor: PERSON: James Malone
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI Biomaterial Branch
term tracker item: https://github.com/obi-ontology/obi/issues/1013
imported from: obi.owl

cultured cell population
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: maintaining cell culture
subclass of: Restriction
  on property: has grain
  some values from: cultured cell
subclass of: Restriction
  on property: has grain
  all values from: cultured cell
editor preferred term: cultured cell population
example of usage: A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
has curation status: metadata complete
definition: A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
editor note: 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
term editor: PERSON:Matthew Brush
alternative label: cell culture sample
definition source: PERSON:Matthew Brush
imported from: obi.owl
comment: The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.

bronchial alveolar lavage
type: Class
subclass of: processed specimen
subclass of: Restriction
  on property: has role
  some values from: specimen role
subclass of: Restriction
  on property: is_specified_output_of
  all values from: lavage
editor preferred term: bronchial alveolar lavage
example of usage: solution containing lung derived T cells, eosinophils, and TNFa.
has curation status: metadata complete
definition: 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.
term editor: PERSON: Bjoern Peters
alternative label: BAL
definition source: GROUP: IEDB
imported from: obi.owl

data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: data transformation objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: Class
      intersection of: algorithm
      intersection of: Restriction
        on property: has part
        some values from: objective specification
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
editor preferred term: data transformation
example of usage: 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.
has curation status: ready for release
definition: A planned process that produces output data from input data.
term editor: Elisabetta Manduchi
term editor: Helen Parkinson
term editor: James Malone
term editor: Melanie Courtot
term editor: Philippe Rocca-Serra
term editor: Richard Scheuermann
term editor: Ryan Brinkman
term editor: Tina Hernandez-Boussard
alternative label: data analysis
alternative label: data processing
definition source: Branch editors
imported from: obi.owl

data transformation objective
type: Class
subclass of: objective specification
editor preferred term: data transformation objective
example of usage: normalize objective
has curation status: ready for release
definition: An objective specification to transformation input data into output data
editor note: Modified definition in 2013 Philly OBI workshop
term editor: James Malone
definition source: PERSON: James Malone
imported from: obi.owl

averaging data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: average value
  union of: Restriction
    on property: achieves_planned_objective
    some values from: averaging objective
subclass of: data transformation
editor preferred term: averaging data transformation
has curation status: metadata incomplete
definition: An averaging data transformation is a data transformation that has objective averaging.
term editor: James Malone
definition source: PERSON: James Malone
imported from: obi.owl

pool of specimens
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: material combination
      intersection of: Restriction
        on property: has_specified_input
        all values from: specimen
subclass of: processed specimen
editor preferred term: pool of specimens
has curation status: metadata complete
definition: A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
editor note: check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish
term editor: PERSON: Jennifer Fostel
definition source: GROUP: CEBS
imported from: obi.owl

edited document
type: Class
subclass of: document
subclass of: Restriction
  on property: is_specified_output_of
  some values from: document editing
editor preferred term: edited document
example of usage: The OBI manuscript is (much) edited imformation
has curation status: ready for release
definition: A document which is the output of a document editing process
term editor: Person:Bjoern Peters
term editor: Philippe Rocca-Serra
imported from: obi.owl

extraction
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
editor preferred term: extraction
example of usage: nucleic acid extraction using phenol chloroform
has curation status: metadata incomplete
definition: A material separation in which a desired component of an input material is separated from the remainder
editor note: 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.
term editor: Person:Bjoern Peters
term editor: Philippe Rocca-Serra
imported from: obi.owl

filtration
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
subclass of: Restriction
  on property: has participant
  some values from: filter paper
editor preferred term: filtration
example of usage: PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4.
has curation status: metadata complete
definition: filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
term editor: Philippe Rocca-Serra
definition source: OBI-Branch: adapted from wikipedia and wordnet
imported from: obi.owl

centrifugation
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
subclass of: Restriction
  on property: has participant
  some values from: centrifuge
editor preferred term: centrifugation
example of usage: 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.
has curation status: metadata complete
definition: 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
term editor: Philippe Rocca-Serra
definition source: adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
imported from: obi.owl

staining
type: Class
subclass of: material processing
editor preferred term: staining
example of usage: PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8.
has curation status: pending final vetting
definition: Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
imported from: obi.owl

storage
type: Class
subclass of: material maintenance
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred term: storage
example of usage: PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
has curation status: metadata complete
definition: A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability
term editor: Philippe Rocca-Serra
definition source: OBI-Branch
imported from: obi.owl

document editing
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: document
subclass of: Restriction
  on property: has_specified_output
  some values from: edited document
editor preferred term: document editing
example of usage: 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
has curation status: metadata complete
definition: is a planned process with specified input original document and specified output edited document
term editor: Philippe Rocca-Serra and OBI consortium
definition source: adapted from wikipedia
imported from: obi.owl

digital curation
type: Class
subclass of: documenting
editor preferred term: digital curation
example of usage: PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44.
has curation status: metadata complete
definition: Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally.
term editor: Philippe Rocca-Serra
definition source: wikipedia
imported from: obi.owl

centrifuge
type: Class
subclass of: measurement device
subclass of: material separation device
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: has function
    some values from: contain function
subclass of: Restriction
  on property: has function
  some values from: measure function
subclass of: Restriction
  on property: has function
  some values from: Class
    intersection of: material separation function
    intersection of: Restriction
      on property: realized in
      all values from: centrifugation
editor preferred term: centrifuge
has curation status: ready for release
definition: A device with a rapidly rotating container that applies centrifugal force to its contents
term editor: Melanie Courtot
term editor: Person: Jennifer Fostel
term editor: Trish Whetzel
definition source: http://en.wikipedia.org/wiki/Centrifuge
imported from: obi.owl

microtome
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: microtome
example of usage: PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7.
has curation status: pending final vetting
definition: A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand.
term editor: PERSON: Phillippe Rocca-Serra
definition source: PERSON: Daniel Schober
imported from: obi.owl

study design
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: has part
  some values from: protocol
editor preferred term: study design
example of usage: a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
has curation status: ready for release
definition: A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
editor note: Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
term editor: PERSON: Chris Stoeckert
alternative label: experimental design
curator note: rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
imported from: obi.owl

eligibility criterion
type: Class
subclass of: selection criterion
editor preferred term: eligibility criterion
example of usage: PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
has curation status: ready for release
definition: an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process.
term editor: Person: Philippe Rocca-Serra
alternative label: eligibility rule
definition source: Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
imported from: obi.owl

inclusion criterion
type: Class
subclass of: eligibility criterion
editor preferred term: inclusion criterion
example of usage: PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) .
has curation status: pending final vetting
definition: an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study.
term editor: Person: Philippe Rocca-Serra
alternative label: inclusion condition
alternative label: inclusion rule
definition source: Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
imported from: obi.owl

exclusion criterion
type: Class
subclass of: eligibility criterion
editor preferred term: exclusion rule
example of usage: PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months.
has curation status: pending final vetting
definition: an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study
term editor: Person: Philippe Rocca-Serra
definition source: Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
imported from: obi.owl

human subject enrollment
type: Class
subclass of: selection
subclass of: Restriction
  on property: has part
  some values from: informed consent process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: eligibility criterion
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: population
    intersection of: Restriction
      on property: has part
      some values from: Homo sapiens
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: Class
      intersection of: population
      intersection of: Restriction
        on property: has part
        some values from: Homo sapiens
    intersection of: Restriction
      on property: has role
      some values from: participant under investigation role
editor preferred term: human subject enrollment
example of usage: enlisting familiy members of HIV patients into a study
has curation status: ready for release
definition: 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.
editor note: As with group assignment, should the specified output here be an organism which bears a role
term editor: Bjoern Peters
definition source: IEDB
curator note: criteria come from plan / clinical trial branch
imported from: obi.owl

collecting specimen from organism
type: Class
subclass of: specimen collection process
subclass of: Restriction
  on property: has_specified_input
  some values from: organism
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
editor preferred term: collecting specimen from organism
example of usage: taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
has curation status: ready for release
definition: a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
term editor: PERSON:Bjoern Peters
definition source: IEDB
imported from: obi.owl

material component separation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
editor preferred term: material component separation
example of usage: 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
has curation status: ready for release
definition: a material processing in which components of an input material become segregated in space
term editor: Bjoern Peters
definition source: IEDB
imported from: obi.owl

pooling specimens
type: Class
subclass of: material combination
subclass of: Restriction
  on property: has_specified_input
  some values from: specimen
subclass of: Restriction
  on property: has_specified_output
  some values from: pool of specimens
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material combination objective
subclass of: Restriction
  on property: has_specified_input
  min cardinality: 2
editor preferred term: pooling specimens
example of usage: 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
has curation status: pending final vetting
definition: physical combination of several instances of like material
term editor: PlanAndPlannedProcess Branch
alternative label: sample pooling
definition source: OBI branch derived
curator note: 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.
imported from: obi.owl

material portioning
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: portioning objective
editor preferred term: material portioning
example of usage: pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock
has curation status: metadata incomplete
definition: a material processing in which the input substance is partitioned into a number of portions that are similar in composition.
term editor: PERSON:Bjoern Peters
alternative label: aliquoting
alternative label: apportioning
definition source: OBI branch derived
imported from: obi.owl

maintaining cell culture
type: Class
subclass of: material maintenance
subclass of: Restriction
  on property: has_specified_input
  some values from: cultured cell population
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: culture medium
    union of: cell freezing medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred term: maintaining cell culture
example of usage: When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
has curation status: pending final vetting
definition: a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl

establishing cell culture
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: cell
subclass of: Restriction
  on property: has_specified_input
  some values from: culture medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred term: 'establishing cell culture'
has curation status: metadata complete
definition: 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).
term editor: PERSON:Matthew Brush
definition source: PERSON:Matthew Brush
imported from: obi.owl
comment: 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.

cell culture splitting
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: has_specified_input
  some values from: cultured cell population
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: portioning objective
editor preferred term: cell culture splitting
example of usage: 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.
has curation status: pending final vetting
definition: 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
term editor: PlanAndPlannedProcess Branch
alternative label: cell culture passaging
definition source: OBI branch derived
imported from: obi.owl
comment: 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.

addition of molecular label
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: molecular label
subclass of: Restriction
  on property: has_specified_input
  some values from: target of material addition
subclass of: Restriction
  on property: has_specified_output
  some values from: molecular-labeled material
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred term: addition of molecular label
example of usage: 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+.
has curation status: pending final vetting
definition: 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
term editor: PERSON:Matthew Brush
alternative label: labeling
definition source: OBI developer call, 3-12-12
imported from: obi.owl

lavage
type: Class
subclass of: collecting specimen from organism
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
editor preferred term: lavage
example of usage: the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present
has curation status: metadata complete
definition: A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid
editor note: This is not washing, in which case the material of interest is not the resulting fluid
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl

dialysis
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
editor preferred term: dialysis
example of usage: the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
has curation status: pending final vetting
definition: a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
term editor: PERSON:Kevin Clancy
definition source: OBI branch derived
imported from: obi.owl

RNA extraction
type: Class
subclass of: nucleic acid extraction
subclass of: Restriction
  on property: has_specified_output
  some values from: ribonucleic acid
editor preferred term: RNA extraction
has curation status: pending final vetting
definition: A RNA extraction is a nucleic acid extraction where the desired output material is RNA
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
curator note: requested by Helen Parkinson for MO
imported from: obi.owl

nucleic acid extraction
type: Class
subclass of: extraction
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: sample from organism
    union of: organism
    union of: cultured cell population
subclass of: Restriction
  on property: has_specified_output
  some values from: nucleic acid
editor preferred term: nucleic acid extraction
example of usage: 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.
has curation status: pending final vetting
definition: a material separation to recover the nucleic acid fraction of an input material
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
curator note: requested by Helen Parkinson for MO. Could be defined class
imported from: obi.owl

cell pellet
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: centrifugation
subclass of: Restriction
  on property: derives from
  some values from: Class
    union of: cultured cell population
    union of: bronchial alveolar lavage
editor preferred term: cell pellet
example of usage: Detection of fetal DNA in a cell pellet after centrifugation of mountant. J Forensic Sci. 2003 Jan;48(1):135-6. PMID: 12570214
has curation status: metadata complete
definition: A material entity which results from the aggregation of cells produced by the application of centrifugal force to a liquid containing cells in suspension
term editor: PERSON: Helen Parkinson
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: CEBS
definition source: GROUP: OBI Biomaterial Branch
imported from: obi.owl

donor
type: Class
subclass of: role
editor preferred term: donor
example of usage: A T cell line from a PPD(+) donor.
has curation status: metadata complete
definition: 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.
term editor: IEDB
alternative label: donor role
definition source: IEDB
curator note: Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended.
imported from: obi.owl

target of material addition
type: Class
equivalent class: Restriction
  on property: has role
  some values from: target of material addition role
subclass of: material entity
editor preferred term: target of material addition
example of usage: A cell culture into which a mixture of peptides is being added.
has curation status: ready for release
definition: A material entity that receives the addition of another material entity in an “adding a material entity into a target” process.
editor note: 10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export.
definition source: IEDB
imported from: obi.owl

FFPE specimen
type: Class
subclass of: paraffin specimen
editor preferred term: FFPE specimen
example of usage: Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures. -based on https://lab-ally.com/histopathology-resources/ffpe-samples/
has curation status: metadata complete
definition: A specimen that has been fixed in formalin and embedded in paraffin.
term editor: MIABIS
alternative label: formalin-fixed paraffin-embeded specimen
definition source: what-is-ffpe-tissue
term tracker item: https://github.com/obi-ontology/obi/issues/1019
imported from: obi.owl

uterine cervix specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: uterine cervix specimen
has curation status: metadata complete
definition: A specimen that is derived from some uterine cervix
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

urethra specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: urethra specimen
has curation status: metadata complete
definition: A specimen that is derived from some urethra
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

cervical mucus specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: cervical mucus
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred term: cervical mucus specimen
has curation status: metadata complete
definition: A specimen that is derived from some cervical mucus
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

throat specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: throat specimen
has curation status: metadata complete
definition: A specimen that is derived from some throat
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

eye specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: eye specimen
has curation status: metadata complete
definition: A specimen that is derived from some eye
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

respiratory system specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: respiratory system specimen
has curation status: metadata complete
definition: A specimen that is derived from some respiratory system
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

upper respiratory tract specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: upper respiratory tract specimen
has curation status: metadata complete
definition: A specimen that is derived from some upper respiratory tract
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

nasopharynx specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: nasopharynx specimen
has curation status: metadata complete
definition: A specimen that is derived from some nasopharynx
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

semen specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: semen
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: semen specimen
has curation status: metadata complete
definition: A specimen that is derived from some semen
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

bodily fluid specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: bodily fluid
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: bodily fluid specimen
has curation status: metadata complete
definition: A specimen that is derived from some bodily fluid
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

chorionic villus specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred term: chorionic villus specimen
has curation status: metadata complete
definition: A specimen that is derived from some chorionic villus
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

meconium specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: meconium
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: feces specimen
editor preferred term: meconium specimen
has curation status: metadata complete
definition: A specimen that is derived from some meconium
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

umbilical cord blood specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: umbilical cord blood
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: arterial blood specimen
editor preferred term: umbilical cord blood specimen
has curation status: metadata complete
definition: A specimen that is derived from some umbilical cord blood
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

arterial blood specimen
type: Class
subclass of: bodily fluid specimen
editor preferred term: arterial blood specimen
has curation status: metadata complete
definition: A specimen that is derived from some arterial blood
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

venous blood specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: venous blood
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred term: venous blood specimen
has curation status: metadata complete
definition: A specimen that is derived from some venous blood
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

capillary blood specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: capillary blood
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred term: capillary blood specimen
has curation status: metadata complete
definition: A specimen that is derived from some capillary blood
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

erythrocyte specimen
type: Class
subclass of: swab specimen
editor preferred term: erythrocyte specimen
has curation status: metadata complete
definition: A specimen that is derived from some erythrocytes
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

reticulocyte specimen
type: Class
subclass of: swab specimen
subclass of: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: collecting specimen with swab
subclass of: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has_specified_input
        some values from: reticulocyte
editor preferred term: reticulocyte specimen
has curation status: metadata complete
definition: A specimen that is derived from some reticulocytes
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

leukocyte specimen
type: Class
subclass of: swab specimen
subclass of: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: collecting specimen with swab
subclass of: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has_specified_input
        some values from: leukocyte
editor preferred term: leukocyte specimen
has curation status: metadata complete
definition: A specimen that is derived from some leukocytes
term editor: Christian Stoeckert ORCID:0000-0002-5714-991X
term editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: obi.owl

clinical history
type: Class
subclass of: information content entity
definition: A series of statements representing health-relevant qualities of a patient and of a patient's family.
imported from: ogms.owl

phenotype
type: Class
subclass of: quality
definition: 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.
imported from: ogms.owl

disease
type: Class
subclass of: disposition
definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
imported from: ogms.owl

disorder
type: Class
subclass of: material entity
definition: A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
imported from: ogms.owl

diagnosis
type: Class
subclass of: data item
definition: The representation of a conclusion of a diagnostic process.
imported from: ogms.owl

treatment
type: Class
subclass of: planned process
definition: A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process
imported from: ogms.owl

health care encounter
type: Class
subclass of: process
definition: A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter
imported from: ogms.owl

diagnostic process
type: Class
subclass of: planned process
definition: A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output).
imported from: ogms.owl

medication role
type: Class
subclass of: role
definition: A role borne by some material entity which can be delivered/administrated into some organism and the role is realized during a clinical treatment process aiming to treat symptoms, signs or diagnosed disease.
imported from: ogms.owl

obsolete biobank
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
definition source: definition derived from the definition of 'human biobank', based on http://www.ethikrat.org/files/der_opinion_human-biobanks.pdf
term replaced by: biobank
deprecated: true

obsolete human biobank
type: Class
subclass of: Obsolete Class
definition source: Deutscher Ethikrat: Human biobanks for research. Opinion. Berlin, 2010. http://www.ethikrat.org/files/der_opinion_human-biobanks.pdf
term replaced by: human biobank
deprecated: true

obsolete settlement part of address of sample collection or study contact
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study contact city
definition source: true
term replaced by: settlement part of address of sample collection or study contact
deprecated: true

obsolete biobank proper name
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Name of biobank
term replaced by: biobank proper name
deprecated: true

obsolete ISO 3166-1 alpha-2 code
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/ISO_3166-1_alpha-2
term replaced by: ISO 3166-1 alpha-2 code
deprecated: true

obsolete biobank idenfier with ISO 3166-1 alpha-2 code
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Biobank ID
term replaced by: biobank idenfier with ISO 3166-1 alpha-2 code
deprecated: true

obsolete sample collection or study identifier
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study ID
deprecated: true

obsolete ISO 3166-1 alpha-2 code for sample collection or study contact
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study contact country
term replaced by: ISO 3166-1 alpha-2 code for sample collection or study contact
deprecated: true

obsolete biobank organization
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: biobank juristic person
term replaced by: biobank organization
deprecated: true

obsolete contacting
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
term replaced by: contacting
deprecated: true

obsolete contact role
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
term replaced by: contact role
deprecated: true

obsolete biobank contact person
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
term replaced by: biobank contact person
deprecated: true

obsolete name of biobank contact person
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Biobank contact person
term replaced by: name of biobank contact person
deprecated: true

obsolete email address of biobank contact person
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Biobank contact email
term replaced by: email address of biobank contact person
deprecated: true

obsolete postal address of biobank contact person
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
term replaced by: postal address of biobank contact person
deprecated: true

obsolete department
type: Class
subclass of: Obsolete Class
definition source: http://en.wikipedia.org/wiki/Department
term replaced by: department
deprecated: true

obsolete department of biobank contact
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Biobank contact department
term replaced by: department of biobank contact
deprecated: true

obsolete unique resource locator
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: uri
definition source: http://en.wikipedia.org/wiki/Uniform_resource_locator
term replaced by: unique resource locator
deprecated: true

obsolete biobank's unique resource locator
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Biobank URL
term replaced by: biobank's unique resource locator
deprecated: true

obsolete telephone number
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Telephone_number
term replaced by: telephone number
deprecated: true

obsolete telephone number of biobank contact
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Biobank contact phone
term replaced by: telephone number of biobank contact
deprecated: true

obsolete post-office box number
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
term replaced by: post-office box number
deprecated: true

obsolete post-office box
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Post-office_box
term replaced by: post-office box
deprecated: true

obsolete telephone number of sample collection or study contact
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study contact phone
term replaced by: telephone number of sample collection or study contact
deprecated: true

obsolete postal code
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Postal_code
term replaced by: postal code
deprecated: true

obsolete postal code of biobank contact
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Biobank contact ZIP
term replaced by: postal code of biobank contact
deprecated: true

obsolete ISO 3166-1 alpha-2 code for biobank contact person
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Biobank country code
term replaced by: ISO 3166-1 alpha-2 code for biobank contact person
deprecated: true

obsolete settlement part of address
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
term replaced by: settlement part of address
deprecated: true

obsolete settlement part of address biobank contact
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Biobank contact city
term replaced by: settlement part of address biobank contact
deprecated: true

obsolete intra-settlement specification part of address
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
term replaced by: intra-settlement specification part of address
deprecated: true

obsolete intra-settlement specification part of address of biobank contact
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Biobank contact address
term replaced by: intra-settlement specification part of address of biobank contact
deprecated: true

obsolete hosted study collection
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Hosted studies
term replaced by: hosted study collection
deprecated: true

obsolete name of hosted study collection
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
term replaced by: name of hosted study collection
deprecated: true

obsolete email address of sample collection or study contact
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study contact email
term replaced by: email address of sample collection or study contact
deprecated: true

obsolete sample collection or study aim description
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Sample collection or study description
term replaced by: sample collection or study aim description
deprecated: true

obsolete study proper name
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Study name
term replaced by: study proper name
deprecated: true

obsolete name of sample collection responsible or principal investigator
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Sample Collection Responsible / Principal Investigator
term replaced by: name of sample collection responsible or principal investigator
deprecated: true

obsolete name of sample collection or study contact person
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study contact person
term replaced by: name of sample collection or study contact person
deprecated: true

obsolete department of sample collection or study contact
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study contact department
term replaced by: department of sample collection or study contact
deprecated: true

obsolete street
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
term replaced by: street
deprecated: true

obsolete intra-settlement specification part of address of sample collection or study contact
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study contact address
term replaced by: intra-settlement specification part of address of sample collection or study contact
deprecated: true

obsolete postal code for sample collection or study contact
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Sample Collection/Study contact ZIP
term replaced by: postal code for sample collection or study contact
deprecated: true

obsolete biobank location ISO 3166-1 alpha-2 code
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: Biobank country code
term replaced by: biobank location ISO 3166-1 alpha-2 code
deprecated: true

obsolete CTEP organization identifier
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
term replaced by: CTEP organization identifier
deprecated: true

obsolete biobank identifier with ISO 3166-1 alpha-2 code and CTEP organization identifier
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
term replaced by: biobank identifier with ISO 3166-1 alpha-2 code and CTEP organization identifier
deprecated: true

obsolete bone marrow specimen
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
definition source: http://www.who.int/transplantation/activities/GlobalGlossaryonDonationTransplantation.pdf
deprecated: true

obsolete fixed tissue specimen
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term editor: Mathias Brochhausen
term replaced by: fixed tissue specimen
deprecated: true

obsolete fixed tissue block specimen
type: Class
subclass of: Obsolete Class
term replaced by: fixed tissue block specimen
deprecated: true

obsolete fixed tissue slide specimen
type: Class
subclass of: Obsolete Class
term replaced by: fixed tissue slide specimen
deprecated: true

obsolete flash frozen specimen
type: Class
subclass of: Obsolete Class
definition source: http://en.wikipedia.org/wiki/Flash_freezing
term replaced by: flash frozen specimen
deprecated: true

obsolete fresh tissue specimen
type: Class
subclass of: Obsolete Class
term replaced by: fresh tissue specimen
deprecated: true

obsolete frozen tissue block specimen
type: Class
subclass of: Obsolete Class
term replaced by: frozen tissue block specimen
deprecated: true

obsolete frozen tissue slide specimen
type: Class
subclass of: Obsolete Class
term replaced by: frozen tissue slide specimen
deprecated: true

obsolete microdissected specimen
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
definition source: http://www.ncbi.nlm.nih.gov/pubmed/11269646
term replaced by: microdissected specimen
deprecated: true

obsolete survey data
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term editor: Mathias Brochhausen
term replaced by: survey data
deprecated: true

obsolete sampling specimens for biobank
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
term replaced by: sampling specimens for biobank
deprecated: true

obsolete biobank contact role
type: Class
subclass of: Obsolete Class
term replaced by: biobank contact role
deprecated: true

obsolete sample collection or study contact role
type: Class
subclass of: Obsolete Class
term replaced by: sample collection or study contact role
deprecated: true

obsolete sample collection or study contact person
type: Class
subclass of: Obsolete Class
term replaced by: sample collection or study contact person
deprecated: true

obsolete study principle investigator or responsible
type: Class
subclass of: Obsolete Class
deprecated: true

obsolete specimen disease state datum
type: Class
subclass of: Obsolete Class
term replaced by: specimen disease state datum
deprecated: true

obsolete diseased state specimen datum
type: Class
subclass of: Obsolete Class
term replaced by: diseased state specimen datum
deprecated: true

obsolete mixed state specimen datum
type: Class
subclass of: Obsolete Class
term replaced by: mixed state specimen datum
deprecated: true

obsolete normal state specimen datum
type: Class
subclass of: Obsolete Class
term replaced by: normal state specimen datum
deprecated: true

obsolete unknown state specimen data
type: Class
subclass of: Obsolete Class
deprecated: true

obsolete fixation
type: Class
subclass of: Obsolete Class
definition source: http://en.wikipedia.org/wiki/Fixation_%28histology%29
definition source: http://sharedresources.fhcrc.org/training/tips-about-fixation-and-formalin
term replaced by: fixation
deprecated: true

obsolete addition of molecular label
type: Class
subclass of: Obsolete Class
example of usage: 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+.
term editor: PERSON: Matthew Brush
alternative label: labeling
definition source: OBI developer call, 3-12-12
deprecated: true

obsolete age interval information
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term editor: Martin Fransson
term editor: Mathias Brochhausen
term replaced by: age interval information
deprecated: true

obsolete average age
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term editor: Mathias Brochhausen
term replaced by: average age
deprecated: true

obsolete patient registry data
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term editor: Martin Fransson
alternative label: patient register data
term replaced by: patient registry data
deprecated: true

obsolete survey data
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
deprecated: true

obsolete date of data entry
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: date of data entry
deprecated: true

obsolete date of data update
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: date of data update
deprecated: true

obsolete end date of sampling for biobank
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: end date of sampling for biobank
deprecated: true

obsolete start date of sampling for biobank
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: start date of sampling for biobank
deprecated: true

obsolete comorbidity
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term editor: Mathias Brochhausen
alternative label: secondary infection, nosocomial infection
definition source: amended from http://en.wikipedia.org/wiki/Comorbidity
term replaced by: comorbidity
deprecated: true

obsolete primary diagnosis
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
alternative label: main diagnosis
term replaced by: primary diagnosis
deprecated: true

obsolete count of current sampled human study participant
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: count of current sampled human study participant
deprecated: true

obsolete count of current total human study participant
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: count of current total human study participant
deprecated: true

obsolete physiological measurement data
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term editor: Mathias Brochhausen
definition source: http://www.improvement.nhs.uk/physiologydiagnostics/documents/WhatisPhysiologicalMeasurement.pdf
term replaced by: physiological measurement data
deprecated: true

obsolete storage temperature setting
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term editor: Mathias Brochhausen
term replaced by: storage temperature setting
deprecated: true

obsolete omics experiment on specimen
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Omics
term replaced by: omics experiment on specimen
deprecated: true

obsolete number of sampled human study participants objective
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term editor: Mathias Brochhausen
term replaced by: number of sampled human study participants objective
deprecated: true

obsolete number of total human study participant objective
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: number of total human study participant objective
deprecated: true

obsolete case control study design
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: case control study design
deprecated: true

obsolete cross sectional study design
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: cross sectional study design
deprecated: true

obsolete longitudinal study design
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: longitudinal study design
deprecated: true

obsolete cohort study design
type: Class
subclass of: Obsolete Class
term replaced by: cohort study design
deprecated: true

obsolete panel study design
type: Class
subclass of: Obsolete Class
term replaced by: panel study design
deprecated: true

obsolete population based study design
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: population based study design
deprecated: true

obsolete quality control study design
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: quality control study design
deprecated: true

obsolete twin study design
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: twin study design
deprecated: true

obsolete survey plan specification
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term editor: Mathias Brochhausen
term replaced by: survey plan specification
deprecated: true

obsolete medical record
type: Class
subclass of: Obsolete Class
term editor: Martin Fransson
term replaced by: medical record
deprecated: true

obsolete sample medical record
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: sample medical record
deprecated: true

obsolete sample handling summary
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: sample handling summary
deprecated: true

obsolete age interval information for sampled donors
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
alternative label: sampled group age interval
definition source: http://www.abta.org/Dictionary/67
term replaced by: age interval information for sampled donors
deprecated: true

obsolete donor patient registry data
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: donor patient registry data
deprecated: true

obsolete study subject survey data
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term editor: Mathias Brochhausen
term replaced by: study subject survey data
deprecated: true

obsolete sample collection data entry
type: Class
subclass of: Obsolete Class
term replaced by: sample collection data entry
deprecated: true

obsolete sample collection data update
type: Class
subclass of: Obsolete Class
term replaced by: sample collection data update
deprecated: true

obsolete survey execution
type: Class
subclass of: Obsolete Class
term replaced by: survey execution
deprecated: true

obsolete temperature regulating
type: Class
subclass of: Obsolete Class
term replaced by: temperature regulating
deprecated: true

obsolete comment from tissue procurement
type: Class
subclass of: Obsolete Class
definition source: Alice Nzinga
term replaced by: comment from tissue procurement
deprecated: true

obsolete specimen measurement
type: Class
subclass of: Obsolete Class
example of usage: 3mm X 3mm X 3mm
term editor: Alice Nzinga
term editor: Mathias Brochhausen
term replaced by: specimen measurement
deprecated: true

obsolete date of specimen collection
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term editor: Mathias Brochhausen
alternative label: date of specimen preparation
term replaced by: date of specimen collection
deprecated: true

obsolete specimen meeting specification
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
alternative label: adherance to specification
term replaced by: specimen meeting specification
deprecated: true

obsolete surgical procedure
type: Class
subclass of: Obsolete Class
example of usage: mastectomy / craniotomy / liver resection e.t.c.
definition source: http://en.wikipedia.org/wiki/Surgery
term replaced by: surgical procedure
deprecated: true

obsolete specimen preparation contact
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: specimen preparation contact
deprecated: true

obsolete time in formalin measurement
type: Class
subclass of: Obsolete Class
example of usage: 15min
term editor: Alice Nzinga
term replaced by: time in formalin measurement
deprecated: true

obsolete specimen surgical removal
type: Class
subclass of: Obsolete Class
term replaced by: specimen surgical removal
deprecated: true

obsolete specimen freezing
type: Class
subclass of: Obsolete Class
term replaced by: specimen freezing
deprecated: true

obsolete specimen ID
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
definition source: http://biospecimens.cancer.gov/resources/sops/GTEx_SOPs/II/A/GTEx%20Tissue%20Procurement%20SOP%20%28PR-0004%20v1.2.1%29.pdf
term replaced by: specimen ID
deprecated: true

obsolete case ID
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
definition source: http://biospecimens.cancer.gov/resources/sops/GTEx_SOPs/II/A/GTEx%20Tissue%20Procurement%20SOP%20%28PR-0004%20v1.2.1%29.pdf
term replaced by: case ID
deprecated: true

obsolete specimen measurement specification
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
definition source: http://en.wikipedia.org/wiki/Specification_(technical_standard)
term replaced by: specimen measurement specification
deprecated: true

obsolete time of specimen freezing
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term editor: Mathias Brochhausen
term replaced by: time of specimen freezing
deprecated: true

obsolete time of surgical removal of specimen
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term editor: Mathias Brochhausen
term replaced by: time of surgical removal of specimen
deprecated: true

obsolete normal specimen
type: Class
subclass of: Obsolete Class
term replaced by: normal specimen
deprecated: true

obsolete cerebrospinal fluid specimen
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
definition source: http://www.ncbi.nlm.nih.gov/books/NBK398/
deprecated: true

obsolete faeces specimen
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
deprecated: true

obsolete saliva specimen
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
deprecated: true

obsolete hosting biobank
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term replaced by: hosting biobank
deprecated: true

obsolete specimen donor
type: Class
subclass of: Obsolete Class
term editor: Alice Nzinga
term editor: Mathias Brochhausen
alternative label: sample donor
term replaced by: specimen donor
deprecated: true

obsolete sample handling
type: Class
subclass of: Obsolete Class
alternative label: specimen handling
definition source: http://www.exchangenetwork.net/standards/SampleHandling_01_06_2006_Final.pdf
term replaced by: sample handling
deprecated: true

obsolete start of sampling specimens for biobank
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
term replaced by: start of sampling specimens for biobank
deprecated: true

obsolete end of sampling specimens for biobank
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
term replaced by: end of sampling specimens for biobank
deprecated: true

human health care role
type: Class
subclass of: role in human social processes
subclass of: Restriction
  on property: realized in
  some values from: health care encounter
definition: 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.
term editor: William R. Hogan
alternative label: health care role
imported from: omrse.owl
comment: Mathias Brochhausen

health care provider role
type: Class
subclass of: human health care role
subclass of: Class
  intersection of: Restriction
    on property: characteristic of
    some values from: Class
      union of: Homo sapiens
      union of: organization
  intersection of: Restriction
    on property: characteristic of
    all values from: Class
      union of: Homo sapiens
      union of: organization
definition: 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.
term editor: Mathias Brochhausen
imported from: omrse.owl
comment: William R. Hogan

nurse role
type: Class
subclass of: health care provider role
subclass of: Homo sapiens role
definition: A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life.
term editor: Mathias Brochhausen
alternative label: nurse
definition source: based on: http://en.wikipedia.org/wiki/Nursing
imported from: omrse.owl

collection of humans
type: Class
equivalent class: Restriction
  on property: is-aggregate-of
  some values from: Homo sapiens
subclass of: collection of organisms
definition: An object aggregate all of whose components are human beings.
imported from: omrse.owl
comment: An object aggregate all of whose components are human beings.

aggregate of organizations
type: Class
equivalent class: Class
  intersection of: Class
    complement of: organization
  intersection of: Restriction
    on property: has member
    all values from: organization
  intersection of: Restriction
    on property: has member
    min qualified cardinality: 2
    on class: organization
subclass of: material entity
subclass of: Restriction
  on property: has member
  some values from: organization
definition: An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common
term editor: William R. Hogan Amanda Hicks
imported from: omrse.owl
comment: It is often convenient to group organizations together that otherwise might not even interact with one another.

legal person role
type: Class
subclass of: role in human social processes
subclass of: Class
  intersection of: Restriction
    on property: characteristic of
    some values from: Class
      union of: Homo sapiens
      union of: collection of humans
  intersection of: Restriction
    on property: characteristic of
    all values from: Class
      union of: Homo sapiens
      union of: collection of humans
definition: A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law.
term editor: Mathias Brochhausen
definition source: Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
imported from: omrse.owl
comment: 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.

material entity role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: characteristic of
    some values from: material entity
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
subclass of: Restriction
  on property: characteristic of
  all values from: material entity
imported from: omrse.owl

Homo sapiens role
type: Class
subclass of: material entity role
subclass of: Restriction
  on property: characteristic of
  some values from: Homo sapiens
subclass of: Restriction
  on property: characteristic of
  all values from: Homo sapiens
imported from: omrse.owl

social identity information content entity
type: Class
subclass of: information content entity
definition: An information content entity that is intended to be a truthful statement about some person and whether that person identifies as some particular aspect of social identity—such as a gender, an ethnicity, a race, or a sexual orientation—where the sense of identifying may correspond to either (i) an aspect of one’s cognitive representation of oneself, (ii) how one prefers to be regarded by others within some social context, or (iii) how one chooses to present oneself to others within some social context.
term editor: S. Clint Dowland
imported from: omrse.owl
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: We include (i)-(iii) to acknowledge that there are different senses of "identify" that are relevant here, and that we may not always be sure which sense the person concretizing the social identity information content entity intended. While (i) concerns how one thinks of oneself, (ii) and (iii) are more focused on one's interactions with others. Importantly, some choose not to share with others how they identify in the sense of (i). For example, one can consider oneself to be some certain gender without either wanting others to know or choosing to present oneself in a corresponding way. We distinguish (ii) and (iii) because one can prefer to be regarded some certain way without attempting to present oneself in any corresponding way.

ethnic identity information content entity
type: Class
subclass of: social identity information content entity
definition: A social identity information content entity that is about whether some person identifies as some ethnicity.
term editor: S. Clint Dowland
imported from: omrse.owl
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: Ethnicity is separate from but related to racial identity. It refers more to identifying with a particular culture than with individuals similar in physical appearance. It includes things like Hispanic ethnicity (which spans many nations) and national cultural identities like Irish and ethnic groups within nations such as Catalan and Armenian.

OMB ethnic identity information content entity
type: Class
subclass of: ethnic identity information content entity
definition: An ethnic identity information content entity that uses OMB terminology for ethnicity or terminology that is strictly mapped onto the OMB ethnicity terms.
term editor: S. Clint Dowland
imported from: omrse.owl
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: OMB dichotomizes ethnicity into Hispanic or Latino and Not Hispanic or Latino, and ignores all other forms of ethnicity.

OMB Hispanic or Latino identity information content entity
type: Class
subclass of: OMB ethnic identity information content entity
definition: An OMB ethnic identity information content entity that is about some person's identifying as Hispanic or Latino, which are intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race.
term editor: S. Clint Dowland
imported from: omrse.owl
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: It comprehends people of Portuguese culture or origin in Brazil.

OMB not Hispanic or Latino identity information content entity
type: Class
subclass of: OMB ethnic identity information content entity
definition: An OMB ethnic identity information content entity that is about some person's identifying as neither Hispanic nor Latino, which are intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race.
term editor: S. Clint Dowland
imported from: omrse.owl
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

gender identity information content entity
type: Class
subclass of: social identity information content entity
definition: A social identity information content entity that is about whether some person identifies as some gender.
term editor: S. Clint Dowland
imported from: omrse.owl
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

female gender identity information content entity
type: Class
subclass of: gender identity information content entity
definition: A gender identity information content entity that is about some person's identifying as female in gender.
term editor: S. Clint Dowland
imported from: omrse.owl
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

male gender identity information content entity
type: Class
subclass of: gender identity information content entity
definition: A gender identity information content entity that is about some person's identifying as male in gender.
term editor: S. Clint Dowland
imported from: omrse.owl
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

non-binary identity information content entity
type: Class
subclass of: gender identity information content entity
definition: A gender identity information content entity that is about some person's identifying as non-binary in gender.
term editor: S. Clint Dowland
imported from: omrse.owl
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

racial identity information content entity
type: Class
subclass of: social identity information content entity
definition: A social identity information content entity that is about whether some person identifies as some race.
term editor: S. Clint Dowland
imported from: omrse.owl
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

OMB racial identity information content entity
type: Class
subclass of: racial identity information content entity
definition: A racial identity information content entity that uses OMB terminology and definitions for race or terminology that is strictly mapped onto the OMB race terms.
term editor: S. Clint Dowland
imported from: omrse.owl
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

OMB American Indian or Alaska Native identity information content entity
type: Class
subclass of: OMB racial identity information content entity
definition: An OMB racial identity information content entity that is about some person's identifying as American Indian or Alaska Native, which is intended to mean having origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment.
term editor: S. Clint Dowland
imported from: omrse.owl
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: This definition corresponds to that used by OMB. It is worth noting that the OMB definition from which this one is derived is problematic, in that it implies that one's race cannot be Native American or Alaskan Native unless one maintains tribal affiliations or community attachment.

OMB Asian identity information content entity
type: Class
subclass of: OMB racial identity information content entity
definition: An OMB racial identity information content entity that is about some person's identifying as Asian, which is intended to mean having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent.
term editor: S. Clint Dowland
imported from: omrse.owl
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

OMB black or African American identity information content entity
type: Class
subclass of: OMB racial identity information content entity
definition: An OMB racial identity information content entity that is about some person's identifying as black or African American which is intended to mean having origins in any of the black racial groups of Africa.
term editor: S. Clint Dowland
imported from: omrse.owl
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

OMB Native Hawaiian or other Pacific Islander identity information content entity
type: Class
subclass of: OMB racial identity information content entity
definition: An OMB racial identity information content entity that is about some person's identifying as Native Hawaiian or other Pacific Islander, which is intended to mean having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands.
term editor: S. Clint Dowland
imported from: omrse.owl
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

OMB white identity information content entity
type: Class
subclass of: OMB racial identity information content entity
definition: An OMB racial identity information content entity that is about some person's identifying as white which is intended to mean having origins in any of the original peoples of Europe, the Middle East, or North Africa.
term editor: S. Clint Dowland
imported from: omrse.owl
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

role in human social processes
type: Class
subclass of: material entity role
subclass of: Restriction
  on property: characteristic of
  all values from: material entity
definition: A role inhering in an entity realized by social interactions in human society.
term editor: Matthew Diller
imported from: omrse.owl
contributor: Mathias Brochhausen
comment: Previous definition: A role played by an entity in human social processes.

age
type: Class
subclass of: time
definition: A time quality inhering in a bearer by virtue of how long the bearer has existed.
imported from: pato.owl

biological sex
type: Class
subclass of: organismal quality
definition: 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.
imported from: pato.owl

morphology
type: Class
subclass of: physical object quality
definition: A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
imported from: pato.owl

size
type: Class
subclass of: morphology
definition: A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
imported from: pato.owl

height
type: Class
subclass of: 1-D extent
definition: A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.
imported from: pato.owl

length
type: Class
subclass of: 1-D extent
definition: A 1-D extent quality which is equal to the distance between two points.
imported from: pato.owl

mass
type: Class
subclass of: physical quality
definition: A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
imported from: pato.owl

weight
type: Class
subclass of: physical quality
definition: A physical quality inhering in a bearer that has mass near a gravitational body. Important usage note: Note that this ontology has a class for a similar concept, mass (PATO:0000125). Mass and weight are not equivalent. For most use cases, the class mass is strongly preferred over weight.
imported from: pato.owl

position
type: Class
subclass of: physical quality
definition: A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
imported from: pato.owl

temperature
type: Class
subclass of: physical quality
definition: A physical quality of the thermal energy of a system.
imported from: pato.owl

time
type: Class
subclass of: physical quality
definition: A quality in which events occur in sequence.
imported from: pato.owl

viability
type: Class
subclass of: organismal quality
definition: An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
imported from: pato.owl

volume
type: Class
subclass of: 3-D extent
definition: A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
imported from: pato.owl

physical quality
type: Class
subclass of: physical object quality
definition: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
imported from: pato.owl

physical object quality
type: Class
subclass of: quality
definition: A quality which inheres in a continuant.
imported from: pato.owl

alive
type: Class
subclass of: viability
definition: A viability quality inhering in a bearer by virtue of the bearer's condition before death.
imported from: pato.owl

dead
type: Class
subclass of: viability
definition: A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
imported from: pato.owl

wholeness
type: Class
subclass of: morphology
definition: A structural quality inhering in a bearer by virtue of whether the bearer includes all its components.
imported from: pato.owl

1-D extent
type: Class
subclass of: size
definition: A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
imported from: pato.owl

3-D extent
type: Class
subclass of: size
definition: A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions.
imported from: pato.owl

frozen
type: Class
subclass of: temperature
definition: A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
imported from: pato.owl

organismal quality
type: Class
subclass of: physical object quality
definition: A quality that inheres in an entire organism or part of an organism.
imported from: pato.owl

humidity
type: Class
subclass of: physical quality
definition: A quality inhering in air by virtue of the partial pressure exerted by the bearer's water vapour content.
imported from: pato.owl

collection of organisms
type: Class
subclass of: object aggregate
example of usage: Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
definition: A material entity that consists of two or more organisms, viruses, or viroids.
alternative label: group of organism
alternative label: organism collection
imported from: pco.owl

protein
type: Class
subclass of: molecular entity
definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
imported from: pr.owl

insulin gene translation product
type: Class
subclass of: protein
definition: An insulin family protein that is a translation product of the human INS gene or a 1:1 ortholog thereof.
imported from: pr.owl

region
type: Class
subclass of: generically dependent continuant
definition: 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.
imported from: so.owl

uterine cervix
type: Class
subclass of: material anatomical entity
definition: Lower, narrow portion of the uterus where it joins with the top end of the vagina.
alternative label: canalis cervicis uteri
alternative label: caudal segment of uterus
alternative label: cervical canal of uterus
alternative label: cervix uteri
alternative label: neck of uterus
alternative label: uterine cervix
imported from: uberon.owl

pituitary gland
type: Class
subclass of: material anatomical entity
definition: The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN].
alternative label: glandula pituitaria
alternative label: pituitary
alternative label: pituitary body
imported from: uberon.owl

lymph node
type: Class
subclass of: material anatomical entity
definition: Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph.
imported from: uberon.owl

urethra
type: Class
subclass of: material anatomical entity
definition: The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening.
imported from: uberon.owl

large intestine
type: Class
subclass of: organ part
definition: A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
imported from: uberon.owl

organ part
type: Class
subclass of: material anatomical entity
definition: A multicellular structure that is a part of an organ.
alternative label: cardinal organ part
imported from: uberon.owl

mouth
type: Class
subclass of: material anatomical entity
definition: The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
alternative label: regio oralis
imported from: uberon.owl

amniotic fluid
type: Class
subclass of: organism substance
definition: Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid.
imported from: uberon.owl

blood
type: Class
subclass of: bodily fluid
definition: A fluid that is composed of blood plasma and erythrocytes.
alternative label: portion of blood
alternative label: vertebrate blood
imported from: uberon.owl

breast
type: Class
subclass of: material anatomical entity
definition: The upper ventral region of the torso of an organism.
alternative label: mammary part of chest
alternative label: mammary region
imported from: uberon.owl

cervical mucus
type: Class
subclass of: bodily fluid
definition: A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus.
alternative label: cervix mucus
imported from: uberon.owl

throat
type: Class
subclass of: material anatomical entity
definition: In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted].
imported from: uberon.owl

renal medulla
type: Class
subclass of: multi-tissue structure
definition: The inner portion of the kidney consisting of the renal pyramids.
alternative label: kidney medulla
alternative label: medulla of kidney
alternative label: medulla renalis
alternative label: pyramides renales
alternative label: renal medullae
alternative label: renal medullae set
alternative label: renal pyramids
alternative label: renal pyramids set
imported from: uberon.owl

organism substance
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
alternative label: body fluid or substance
alternative label: body substance
alternative label: organism substance
alternative label: portion of body substance
alternative label: portion of organism substance
imported from: uberon.owl

material anatomical entity
type: Class
subclass of: material entity
definition: Anatomical entity that has mass.
imported from: uberon.owl

testis
type: Class
subclass of: material anatomical entity
definition: A gonad of a male animal. A gonad produces and releases sperm.
alternative label: gonad of male genitalia
alternative label: gonad of male reproductive system
alternative label: male gonad
alternative label: testicle
imported from: uberon.owl

anatomical cluster
type: Class
subclass of: material entity
definition: Anatomical group that has its parts adjacent to one another.
imported from: uberon.owl

tissue
type: Class
subclass of: material anatomical entity
definition: Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
alternative label: portion of tissue
alternative label: tissue portion
imported from: uberon.owl

multi-tissue structure
type: Class
subclass of: material anatomical entity
definition: Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
imported from: uberon.owl

stomach
type: Class
subclass of: material anatomical entity
definition: An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
imported from: uberon.owl

aorta
type: Class
subclass of: material anatomical entity
definition: The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation.
alternative label: trunk of aortic tree
alternative label: trunk of systemic arterial tree
imported from: uberon.owl

heart
type: Class
subclass of: material anatomical entity
definition: A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
alternative label: chambered heart
alternative label: vertebrate heart
imported from: uberon.owl

brain
type: Class
subclass of: material anatomical entity
definition: The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
imported from: uberon.owl

cerebral cortex
type: Class
subclass of: anatomical cluster
definition: The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex.
alternative label: cortex of cerebral hemisphere
imported from: uberon.owl

eye
type: Class
subclass of: material anatomical entity
definition: An organ that detects light.
imported from: uberon.owl

reproductive system
type: Class
subclass of: material anatomical entity
definition: Anatomical system that has as its parts the organs concerned with reproduction.
imported from: uberon.owl

ovary
type: Class
subclass of: material anatomical entity
definition: The gonad of a female organism which contains germ cells.
alternative label: animal ovary
alternative label: female gonad
alternative label: female organism genitalia gonad
alternative label: female organism genitalia gonada
alternative label: female organism reproductive system gonad
alternative label: female organism reproductive system gonada
alternative label: female reproductive system gonad
alternative label: female reproductive system gonada
alternative label: genitalia of female organism gonad
alternative label: genitalia of female organism gonada
alternative label: gonad of female organism genitalia
alternative label: gonad of female organism reproductive system
alternative label: gonad of female reproductive system
alternative label: gonad of genitalia of female organism
alternative label: gonad of reproductive system of female organism
alternative label: gonada of female organism genitalia
alternative label: gonada of female organism reproductive system
alternative label: gonada of female reproductive system
alternative label: gonada of genitalia of female organism
alternative label: gonada of reproductive system of female organism
alternative label: ovum-producing ovary
alternative label: reproductive system of female organism gonad
alternative label: reproductive system of female organism gonada
imported from: uberon.owl

uterus
type: Class
subclass of: organ part
definition: The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth.
imported from: uberon.owl

vagina
type: Class
subclass of: organ part
definition: A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP].
imported from: uberon.owl

respiratory system
type: Class
subclass of: material anatomical entity
definition: Functional system which consists of structures involved in respiration.
alternative label: apparatus respiratorius
alternative label: respiratory system
imported from: uberon.owl

adipose tissue
type: Class
subclass of: tissue
definition: Portion of connective tissue composed of adipocytes enmeshed in areolar tissue.
alternative label: fat
alternative label: fat tissue
alternative label: fatty tissue
imported from: uberon.owl

strand of hair
type: Class
subclass of: material anatomical entity
definition: A filament, mostly protein, that grows from follicles found in the dermis[WP].
alternative label: hair
imported from: uberon.owl

esophagus
type: Class
subclass of: material anatomical entity
definition: Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
alternative label: gullet
alternative label: oesophagus
imported from: uberon.owl

rectum
type: Class
subclass of: organ part
definition: The terminal portion of the intestinal tube, terminating with the anus.
alternative label: terminal portion of intestine
imported from: uberon.owl

pleural fluid
type: Class
subclass of: bodily fluid
definition: Transudate contained in the pleural cavity.
imported from: uberon.owl

urine
type: Class
subclass of: organism substance
definition: Excretion that is the output of a kidney.
imported from: uberon.owl

sweat
type: Class
subclass of: bodily fluid
definition: Secretion produced by a sweat gland.
imported from: uberon.owl

synovial fluid
type: Class
subclass of: bodily fluid
definition: Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
alternative label: joint fluid
imported from: uberon.owl

right lobe of liver
type: Class
subclass of: organ part
definition: The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted].
alternative label: liver right lobe
alternative label: lobus hepaticus dexter
alternative label: right liver lobe
imported from: uberon.owl

right lobe of thyroid gland
type: Class
subclass of: organ part
definition: A lobe of thyroid gland that is in the right side of a thyroid gland.
alternative label: lobus dexter (glandula thyroidea)
alternative label: right thyroid lobe
alternative label: thyroid gland right lobe
imported from: uberon.owl

left lobe of thyroid gland
type: Class
subclass of: organ part
definition: A lobe of thyroid gland that is in the left side of a thyroid gland.
alternative label: left thyroid lobe
alternative label: lobus sinister (glandula thyroidea)
alternative label: thyroid gland left lobe
imported from: uberon.owl

skeletal muscle tissue
type: Class
subclass of: tissue
definition: Muscle tissue that consists primarily of skeletal muscle fibers.
imported from: uberon.owl

body of pancreas
type: Class
subclass of: organ part
definition: The body of the pancreas is a subsection of the pancreas organ in the human body. It is somewhat prismatic in shape, and has three surfaces: anterior, posterior, and inferior. It is at the same level as the transpyloric plane. [WP,unvetted].
alternative label: pancreas body
alternative label: pancreatic body
imported from: uberon.owl

caecum
type: Class
subclass of: organ part
definition: A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
alternative label: caecum
alternative label: cecum
alternative label: intestinum crassum caecum
imported from: uberon.owl

colon
type: Class
subclass of: material anatomical entity
definition: A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal.
alternative label: large bowel
imported from: uberon.owl

ascending colon
type: Class
subclass of: organ part
definition: Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified].
alternative label: colon ascendens
imported from: uberon.owl

transverse colon
type: Class
subclass of: organ part
definition: The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified].
alternative label: colon transversum
imported from: uberon.owl

descending colon
type: Class
subclass of: organ part
definition: The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon.
alternative label: colon descendens
imported from: uberon.owl

sigmoid colon
type: Class
subclass of: organ part
definition: The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity.
imported from: uberon.owl

body of stomach
type: Class
subclass of: organ part
definition: The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO].
alternative label: corpus gastricum (ventriculare)
alternative label: gastric body
alternative label: stomach body
imported from: uberon.owl

cortex of kidney
type: Class
subclass of: material anatomical entity
definition: Outer cortical portion of the kidney, between the renal capsule and the renal medulla.
alternative label: cortex renalis
alternative label: kidney cortex
alternative label: renal cortex
imported from: uberon.owl

right adrenal gland
type: Class
subclass of: adrenal gland
definition: An adrenal gland that is in the right side of the abdomen.
alternative label: glandula suprarenalis dexter
alternative label: right suprarenal gland
imported from: uberon.owl

left adrenal gland
type: Class
subclass of: adrenal gland
definition: An adrenal gland that is in the left side of the abdomen.
alternative label: glandula suprarenalis sinister
alternative label: left suprarenal gland
imported from: uberon.owl

urinary bladder
type: Class
subclass of: material anatomical entity
definition: Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
alternative label: vesica urinaria
imported from: uberon.owl

pancreas
type: Class
subclass of: material anatomical entity
definition: An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO].
imported from: uberon.owl

peritoneal fluid
type: Class
subclass of: bodily fluid
definition: Transudate contained in the peritoneal cavity.
imported from: uberon.owl

tibial nerve
type: Class
subclass of: anatomical cluster
definition: The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted].
alternative label: medial popliteal nerve
imported from: uberon.owl

cerebrospinal fluid
type: Class
subclass of: bodily fluid
definition: A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
alternative label: CSF
alternative label: cerebral spinal fluid
imported from: uberon.owl

gastrocnemius
type: Class
subclass of: skeletal muscle tissue
definition: The most superficial muscle of the triceps surae group, in the posterior portion of the lower hindleg.
alternative label: gastrocnemius muscle
alternative label: m. gastrocnemius
alternative label: m.gastrocnemius
imported from: uberon.owl

ascending aorta
type: Class
subclass of: organ part
definition: The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta[GO]. A portion of the aorta commencing at the upper part of the base of the left ventricle, on a level with the lower border of the third costal cartilage behind the left half of the sternum; it passes obliquely upward, forward, and to the right, in the direction of the heart's axis, as high as the upper border of the second right costal cartilage, describing a slight curve in its course, and being situated, about 6 cm behind the posterior surface of the sternum. The total length is about 5 cm in length [Wikipedia].
alternative label: ascending thoracic aorta
alternative label: pars ascendens aortae
imported from: uberon.owl

upper respiratory tract
type: Class
subclass of: material anatomical entity
definition: The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea.
imported from: uberon.owl

cheek
type: Class
subclass of: material anatomical entity
definition: A fleshy subdivision of one side of the face bounded by an eye, ear and the nose.
imported from: uberon.owl

coronary artery
type: Class
subclass of: material anatomical entity
definition: An artery that supplies the myocardium.
alternative label: coronary arterial tree
imported from: uberon.owl

tongue
type: Class
subclass of: material anatomical entity
definition: A muscular organ in the floor of the mouth.
imported from: uberon.owl

nasopharynx
type: Class
subclass of: material anatomical entity
definition: The section of the pharynx that lies above the soft palate.
alternative label: nasal part of pharynx
alternative label: rhinopharynx
imported from: uberon.owl

oropharynx
type: Class
subclass of: material anatomical entity
definition: The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis.
alternative label: oral part of pharynx
imported from: uberon.owl

vitreous humor
type: Class
subclass of: organism substance
definition: A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina.
alternative label: humor vitreous
alternative label: humor vitreus
alternative label: vitreous
alternative label: whole portion of vitreous humor
imported from: uberon.owl

minor salivary gland
type: Class
subclass of: material anatomical entity
definition: One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP].
imported from: uberon.owl

lower lip
type: Class
subclass of: material anatomical entity
definition: Lip that covers the lower portion of the mouth.[TAO].
alternative label: lower jaw lip
imported from: uberon.owl

saliva
type: Class
subclass of: organism substance
definition: A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
alternative label: salivary gland secretion
imported from: uberon.owl

milk
type: Class
subclass of: bodily fluid
definition: An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.
alternative label: mammary gland milk
imported from: uberon.owl

semen
type: Class
subclass of: organism substance
definition: Organism substance that is composed of sperm cells suspended in seminal fluid.
imported from: uberon.owl

bile
type: Class
subclass of: bodily fluid
definition: Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium.
imported from: uberon.owl

blood vessel
type: Class
subclass of: material anatomical entity
definition: A vessel through which blood circulates in the body.
alternative label: region of vascular tree organ
alternative label: vascular tree organ region
imported from: uberon.owl

placenta
type: Class
subclass of: material anatomical entity
definition: Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
alternative label: allantoic placenta
alternative label: eutherian placenta
imported from: uberon.owl

feces
type: Class
subclass of: organism substance
definition: Portion of semisolid bodily waste discharged through the anus[MW,modified].
alternative label: faeces
alternative label: fecal material
alternative label: fecal matter
alternative label: piece of shit
alternative label: portion of excrement
alternative label: portion of faeces
alternative label: portion of fecal material
alternative label: portion of fecal matter
alternative label: portion of feces
alternative label: portionem cacas
alternative label: stool
imported from: uberon.owl

areola
type: Class
subclass of: material anatomical entity
definition: Subdivision of breast which consists of skin, connective tissue and smooth muscle bundle and modified sebaceous glands and which surrounds the nipple.
imported from: uberon.owl

cerebellum
type: Class
subclass of: multi-tissue structure
definition: Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA].
alternative label: epencephalon-1
imported from: uberon.owl

thyroid gland
type: Class
subclass of: material anatomical entity
definition: A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO].
alternative label: thyroid
imported from: uberon.owl

lung
type: Class
subclass of: material anatomical entity
definition: Respiration organ that develops as an outpocketing of the esophagus.
alternative label: pulmo
imported from: uberon.owl

right cardiac atrium
type: Class
subclass of: cardiac atrium
definition: A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve.
alternative label: cardiac right atrium
alternative label: heart right atrium
alternative label: right atrium
alternative label: right atrium of heart
alternative label: right cardiac atrium
imported from: uberon.owl

cardiac atrium
type: Class
subclass of: organ part
definition: Cardiac chamber in which blood enters the heart.
alternative label: atria
alternative label: atrium
alternative label: atrium of heart
alternative label: cardiac atria
alternative label: heart atrium
imported from: uberon.owl

heart left ventricle
type: Class
subclass of: organ part
definition: A cardiac ventricle that is in the left side of the heart.
alternative label: cardiac left ventricle
alternative label: left cardiac ventricle
alternative label: left ventricle
alternative label: left ventricle of heart
imported from: uberon.owl

skin of body
type: Class
subclass of: material anatomical entity
definition: The organ covering the body that consists of the dermis and epidermis.
alternative label: entire skin
alternative label: skin organ
imported from: uberon.owl

spleen
type: Class
subclass of: material anatomical entity
definition: The organ that functions to filter blood and to store red corpuscles and platelets.
imported from: uberon.owl

liver
type: Class
subclass of: material anatomical entity
definition: An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
imported from: uberon.owl

small intestine
type: Class
subclass of: organ part
definition: Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong].
alternative label: small bowel
alternative label: small intestine
imported from: uberon.owl

kidney
type: Class
subclass of: material anatomical entity
definition: A paired organ of the urinary tract which has the production of urine as its primary function.
imported from: uberon.owl

ileum
type: Class
subclass of: organ part
definition: The portion of the small intestine that extends from the jejunum to the colon.
imported from: uberon.owl

right ovary
type: Class
subclass of: ovary
definition: An ovary that is part of a right side of organism [Automatically generated definition].
imported from: uberon.owl

left ovary
type: Class
subclass of: ovary
definition: An ovary that is part of a left side of organism [Automatically generated definition].
imported from: uberon.owl

right lung
type: Class
subclass of: lung
definition: Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA].
imported from: uberon.owl

left lung
type: Class
subclass of: lung
definition: Lung which consists of the left upper lobe and left lower lobe.[FMA].
imported from: uberon.owl

integument
type: Class
subclass of: material anatomical entity
definition: The dermis, epidermis and hypodermis.
alternative label: dermis plus epidermis plus hypodermis
alternative label: integumentum commune
alternative label: skin and subcutaneous tissue
alternative label: skin plus hypodermis
alternative label: the integument
imported from: uberon.owl

peritoneum
type: Class
subclass of: organ part
definition: A serous membrane that lines the peritoneal cavity[VHOG,modified].
imported from: uberon.owl

prostate gland
type: Class
subclass of: material anatomical entity
definition: The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
alternative label: male prostate
alternative label: prostate
imported from: uberon.owl

endocrine gland
type: Class
subclass of: material anatomical entity
definition: Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
alternative label: ductless gland
alternative label: glandula endocrina
imported from: uberon.owl

adrenal gland
type: Class
subclass of: material anatomical entity
definition: Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO].
alternative label: glandula adrenalis
alternative label: glandula suprarenalis
imported from: uberon.owl

bone marrow
type: Class
subclass of: tissue
definition: The soft tissue that fills the cavities of bones.
alternative label: medulla ossea
alternative label: medulla ossium
imported from: uberon.owl

pericardial fluid
type: Class
subclass of: bodily fluid
definition: Transudate contained in the pericardial cavity.[FMA].
imported from: uberon.owl

tail
type: Class
subclass of: material anatomical entity
definition: An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail.
alternative label: caudal subdivision
imported from: uberon.owl

esophagus mucosa
type: Class
subclass of: material anatomical entity
definition: A mucosa that is part of a esophagus [Automatically generated definition].
alternative label: esophageal mucosa
alternative label: esophageal mucous membrane
alternative label: esophagus mucosa
alternative label: esophagus mucous membrane
alternative label: lamina muscularis mucosae oesophageae
alternative label: mucosa of esophagus
alternative label: mucosa of oesophagus
alternative label: mucous membrane of esophagus
alternative label: mucous membrane of oesophagus
alternative label: oesophageal mucosa
alternative label: oesophagus mucosa
alternative label: oesophagus mucous membrane
alternative label: tunica mucosa esophagi
alternative label: tunica mucosa oesophageae
alternative label: tunica mucosa oesophagi
imported from: uberon.owl

omentum
type: Class
subclass of: organ part
definition: A fold of peritoneum originating at the stomach and supporting the viscera.
imported from: uberon.owl

neural tissue
type: Class
subclass of: material anatomical entity
definition: Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
alternative label: nerve tissue
alternative label: nervous tissue
alternative label: portion of neural tissue
imported from: uberon.owl

fallopian tube
type: Class
subclass of: organ part
definition: Initial section of the oviduct through which the ova pass from the ovary to the uterus.
alternative label: mammalian oviduct
alternative label: uterine tube (sensu Mammalia)
imported from: uberon.owl

left kidney
type: Class
subclass of: kidney
definition: A kidney that is part of a left side of organism [Automatically generated definition].
imported from: uberon.owl

right kidney
type: Class
subclass of: kidney
definition: A kidney that is part of a right side of organism [Automatically generated definition].
imported from: uberon.owl

esophagus muscularis mucosa
type: Class
subclass of: tissue
definition: A muscularis mucosa that is part of a esophagus.
alternative label: esophagus muscularis mucosae
alternative label: lamina muscularis mucosae (oesphagus)
alternative label: lamina muscularis of esophageal mucous membrane
alternative label: muscularis mucosae of esophagus
imported from: uberon.owl

greater omentum
type: Class
subclass of: omentum
definition: The greater omentum (also the great omentum, omentum majus, gastrocolic omentum, epiploön, or, especially in animals, caul) is a large fold of peritoneum that hangs down from the stomach, and extends from the stomach to the posterior abdominal wall after associating with the transverse colon.
imported from: uberon.owl

bodily fluid
type: Class
subclass of: organism substance
definition: Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
alternative label: body fluid
imported from: uberon.owl

atrium auricular region
type: Class
subclass of: multi-tissue structure
definition: A small conical pouch projections located on the upper anterior portion of each atrium of the heart.
alternative label: atrial appendage
alternative label: atrial auricle
alternative label: atrium appendage
alternative label: auricle of atrium
alternative label: auricle of heart
alternative label: auricula (cor)
alternative label: auricula atrii
alternative label: auricular appendage
alternative label: cardiac auricle
alternative label: heart atrial appendage
alternative label: heart atrium auriclular region
imported from: uberon.owl

digestive system secreted substance
type: Class
subclass of: organism substance
alternative label: digestive system fluid or secretion
imported from: uberon.owl

chorionic villus
type: Class
subclass of: material anatomical entity
definition: One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta.
imported from: uberon.owl

meconium
type: Class
subclass of: feces
definition: A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth.
imported from: uberon.owl

sputum
type: Class
subclass of: organism substance
definition: Matter ejected from the lungs, bronchi, and trachea, through the mouth.
imported from: uberon.owl

tibial artery
type: Class
subclass of: material anatomical entity
definition: The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot.
imported from: uberon.owl

esophagogastric junction
type: Class
subclass of: organ part
definition: The junction between the esophagus and the stomach epithelium.
alternative label: cardioesophageal junction
alternative label: gastroesophageal junction
imported from: uberon.owl

lingula of left lung
type: Class
subclass of: organ part
definition: Anterioinferior portion of left upper lung lobe.
alternative label: left pulmonary lingula
alternative label: lingula of lung
alternative label: lingula of the lung
imported from: uberon.owl

body of uterus
type: Class
subclass of: organ part
definition: The part of the uterus above the isthmus and below the orifices of the uterine tubes.
alternative label: corpus uteri
alternative label: uterine body
alternative label: uterine corpus
imported from: uberon.owl

omental fat pad
type: Class
subclass of: adipose tissue
definition: Encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon.
alternative label: omental fat depot
imported from: uberon.owl

umbilical cord blood
type: Class
subclass of: blood
definition: Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP].
imported from: uberon.owl

arterial blood
type: Class
subclass of: blood
definition: A blood that is part of a artery.
alternative label: arterial blood
alternative label: blood in artery
alternative label: portion of arterial blood
imported from: uberon.owl

venous blood
type: Class
subclass of: blood
definition: A blood that is part of a vein.
alternative label: blood in vein
alternative label: portion of venous blood
alternative label: venous blood
imported from: uberon.owl

capillary blood
type: Class
subclass of: blood
definition: A blood that is part of a capillary.
alternative label: blood in capillary
alternative label: portion of blood in capillary
alternative label: portion of capillary blood
imported from: uberon.owl

splenic flexure of colon
type: Class
subclass of: organ part
definition: The splenic (or left colic) flexure is a sharp bend between the transverse and the descending colon in the left upper quadrant of humans. The left colic flexure is near the spleen, and hence called the splenic flexure. There are two colic flexures in the transverse colon — the other being the hepatic flexure in the right upper quadrant.
alternative label: flexura coli splenica
alternative label: left colic flexure
alternative label: splenic flexure
alternative label: splenic flexure of colon
imported from: uberon.owl

hepatic flexure of colon
type: Class
subclass of: organ part
definition: Hepatic (or the right colic) flexure is the sharp bend between the ascending and the transverse colon. The right colic flexure is adjacent to the liver, and is therefore also known as the hepatic flexure. Thus, the left colic flexure is also known as the splenic flexure (as it is close to the spleen). The hepatic flexure lies in the right upper quadrant of the abdomen in humans.
alternative label: flexura coli heaptica
alternative label: hepatic flexure
alternative label: hepatic flexure of colon
alternative label: right colic flexure
imported from: uberon.owl

esophagogastric junction muscularis mucosa
type: Class
subclass of: organ part
definition: Muscularis mucosa from the lowest portion of the esophagus, just proximal to the stomach.
alternative label: gastro-esophageal junction muscularis mucosa
imported from: uberon.owl

life-death temporal boundary
type: Class
subclass of: process boundary
definition: A life cycle temporal boundary that marks the end of the life cycle of the organism.
alternative label: end of life cycle
alternative label: moment of death
alternative label: time of death
imported from: uberon.owl

suprapubic skin
type: Class
subclass of: skin of body
definition: Area of skin in the hypoastric region of the abdomen.
imported from: uberon.owl

rectosigmoid junction
type: Class
subclass of: organ part
definition: An anatomical junction that is between the sigmoid colon and rectum.
imported from: uberon.owl

length unit
type: Class
subclass of: measurement unit label
imported from: uo.owl

mass unit
type: Class
subclass of: measurement unit label
imported from: uo.owl

time unit
type: Class
subclass of: measurement unit label
alternative label: time derived unit
imported from: uo.owl

temperature unit
type: Class
subclass of: measurement unit label
alternative label: temperature derived unit
imported from: uo.owl

concentration unit
type: Class
subclass of: measurement unit label
imported from: uo.owl

volume unit
type: Class
subclass of: measurement unit label
imported from: uo.owl

Laboratory
type: Class
subclass of: organization
editor preferred term: Laboratory
definition: An organizational unit (as opposed to the physical facility) that performs research, provides services, or processes materials
imported from: ero.owl

risk factor
type: Class
subclass of: disposition
definition: 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.
definition: 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.
imported from: efo.owl

hormone replacement therapy
type: Class
subclass of: treatment
definition: Therapeutic use of hormones to alleviate the effects of hormone deficiency.
imported from: efo.owl

smoking behavior
type: Class
subclass of: biological_process
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: cigarette
    union of: cigar
    union of: pipe tobacco
definition: Inhaling and exhaling the smoke of tobacco or something similar to tobacco.
imported from: efo.owl

chewing tobacco behavior
type: Class
subclass of: biological_process
subclass of: Restriction
  on property: has_specified_input
  some values from: chewing tobacco
definition: Mastication of tobacco, correlated with an increased risk of oral cancers.
imported from: efo.owl

date of birth
type: Class
subclass of: time measurement datum
definition: The point in time at which an individual was born.
imported from: efo.owl

date of diagnosis
type: Class
subclass of: time measurement datum
definition: The point at which a clinical diagnosis is made.
imported from: efo.owl

Obsolete Class
type: Class
subclass of: Thing

example to be eventually removed
type: NamedIndividual
type: curation status specification
editor preferred term: example to be eventually removed

failed exploratory term
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: failed exploratory term
definition: The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
term editor: Person:Alan Ruttenberg

metadata complete
type: NamedIndividual
type: curation status specification
editor preferred term: metadata complete
definition: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.

organizational term
type: NamedIndividual
type: curation status specification
editor preferred term: organizational term
definition: Term created to ease viewing/sort terms for development purpose, and will not be included in a release

ready for release
type: NamedIndividual
type: curation status specification
editor preferred term: ready for release
definition: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."

metadata incomplete
type: NamedIndividual
type: curation status specification
editor preferred term: metadata incomplete
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
type: NamedIndividual
type: curation status specification
editor preferred term: uncurated
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: NamedIndividual
type: curation status specification
editor preferred term: pending final vetting
definition: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.

obsolete_core
type: NamedIndividual
definition: Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
has obsolescence reason: placeholder removed
deprecated: true

placeholder removed
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: placeholder removed

terms merged
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: terms merged
editor note: An editor note should explain what were the merged terms and the reason for the merge.

term imported
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: term imported
editor note: This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.

term split
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: term split
editor note: This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.

universal
type: NamedIndividual
type: denotator type
editor preferred term: universal
editor note: Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
term editor: Alan Ruttenberg
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf

defined class
type: NamedIndividual
type: denotator type
editor preferred term: defined class
definition: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
editor note: "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
term editor: Alan Ruttenberg

named class expression
type: NamedIndividual
type: denotator type
editor preferred term: named class expression
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
editor note: named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
term editor: Alan Ruttenberg

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification
editor preferred term: to be replaced with external ontology term
definition: Terms with this status should eventually replaced with a term from another ontology.
term editor: Alan Ruttenberg
definition source: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
editor preferred term: requires discussion
definition: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
term editor: Alan Ruttenberg
definition source: group:OBI

Affymetrix
type: NamedIndividual
type: manufacturer
type: material supplier
editor preferred term: Affymetrix
example of usage: Affymetrix supplied microarray
has curation status: metadata incomplete
definition: An organization which supplies technology, tools and protocols for use in high throughput applications

Thermo
type: NamedIndividual
type: manufacturer
editor preferred term: Thermo
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Waters
type: NamedIndividual
type: manufacturer
editor preferred term: Waters
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

BIO-RAD
type: NamedIndividual
type: manufacturer
editor preferred term: BIO-RAD
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Ambion
type: NamedIndividual
type: manufacturer
editor preferred term: Ambion
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Helicos
type: NamedIndividual
type: manufacturer
editor preferred term: Helicos
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Roche
type: NamedIndividual
type: manufacturer
editor preferred term: Roche
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Illumina
type: NamedIndividual
type: manufacturer
editor preferred term: Illumina
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Agilent
type: NamedIndividual
type: manufacturer
editor preferred term: Agilent
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Li-Cor
type: NamedIndividual
type: manufacturer
editor preferred term: Li-Cor
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Bruker Corporation
type: NamedIndividual
type: manufacturer
editor preferred term: Bruker Corporation
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Applied Biosystems
type: NamedIndividual
type: manufacturer
editor preferred term: Applied Biosystems
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Bruker Daltonics
type: NamedIndividual
type: manufacturer
editor preferred term: Bruker Daltonics
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Sysmex Corporation, Kobe, Japan
type: NamedIndividual
type: manufacturer
editor preferred term: Sysmex Corporation, Kobe, Japan
has curation status: metadata complete
definition source: WEB:http://www.sysmex.com/@2009/08/06

U.S. Food and Drug Administration
type: NamedIndividual
type: regulatory agency
editor preferred term: U.S. Food and Drug Administration
has curation status: metadata incomplete
alternative label: FDA

Edingburgh handedness inventory
type: NamedIndividual
type: questionnaire
editor preferred term: Edingburgh handedness inventory
has curation status: metadata complete
definition: The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Jessica Turner
definition source: PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
definition source: WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html

eBioscience
type: NamedIndividual
type: manufacturer
editor preferred term: eBioscience
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.ebioscience.com/@2011/04/11

Cytopeia
type: NamedIndividual
type: manufacturer
editor preferred term: Cytopeia
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.cytopeia.com/@2011/04/11

Exalpha Biological
type: NamedIndividual
type: manufacturer
editor preferred term: Exalpha Biological
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.exalpha.com/@2011/04/11

Apogee Flow Systems
type: NamedIndividual
type: manufacturer
editor preferred term: Apogee Flow Systems
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.apogeeflow.com/@2011/04/11

Exbio Antibodies
type: NamedIndividual
type: manufacturer
editor preferred term: Exbio Antibodies
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.exbio.cz/@2011/04/11

Becton Dickinson (BD Biosciences)
type: NamedIndividual
type: manufacturer
editor preferred term: Becton Dickinson (BD Biosciences)
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.bdbiosciences.com/@2011/04/11

Dako Cytomation
type: NamedIndividual
type: manufacturer
editor preferred term: Dako Cytomation
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.dakousa.com/@2011/04/11

Millipore
type: NamedIndividual
type: manufacturer
editor preferred term: Millipore
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.guavatechnologies.com/@2011/04/11

Antigenix
type: NamedIndividual
type: manufacturer
editor preferred term: Antigenix
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.antigenix.com/@2011/04/11

Partec
type: NamedIndividual
type: manufacturer
editor preferred term: Partec
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.partec.de/@2011/04/11

Beckman Coulter
type: NamedIndividual
type: manufacturer
editor preferred term: Beckman Coulter
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.beckmancoulter.com/@2011/04/11

Advanced Instruments Inc. (AI Companies)
type: NamedIndividual
type: manufacturer
editor preferred term: Advanced Instruments Inc. (AI Companies)
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.aicompanies.com/@2011/04/11

Miltenyi Biotec
type: NamedIndividual
type: manufacturer
editor preferred term: Miltenyi Biotec
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.miltenyibiotec.com/@2011/04/11

AES Chemunex
type: NamedIndividual
type: manufacturer
editor preferred term: AES Chemunex
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.aeschemunex.com/@2011/04/11

Bentley Instruments
type: NamedIndividual
type: manufacturer
editor preferred term: Bentley Instruments
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://bentleyinstruments.com/@2011/04/11

Invitrogen
type: NamedIndividual
type: manufacturer
editor preferred term: Invitrogen
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.invitrogen.com/@2011/04/11

Luminex
type: NamedIndividual
type: manufacturer
editor preferred term: Luminex
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.luminexcorp.com/@2011/04/11

CytoBuoy
type: NamedIndividual
type: manufacturer
editor preferred term: CytoBuoy
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.cytobuoy.com/@2011/04/11

Nimblegen
type: NamedIndividual
type: manufacturer
editor preferred term: Nimblegen
has curation status: metadata incomplete
definition: An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing.
term editor: Person: Jie Zheng

Pacific Biosciences
type: NamedIndividual
type: manufacturer
editor preferred term: Pacific Biosciences
has curation status: metadata incomplete
definition: An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution.
term editor: Person: Jie Zheng

NanoString Technologies
type: NamedIndividual
type: manufacturer
editor preferred term: NanoString Technologies
has curation status: metadata incomplete
definition: An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules.

0-non autolyis
type: NamedIndividual
type: autolysis value specification
definition: An autolysis value specification that indicates no apparent autolytic destruction of an organism cells or tissues.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

1-slight autolysis
type: NamedIndividual
type: autolysis value specification
definition: An autolysis value specification that indicates slight autolytic destruction of an organism cells or tissues.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

2-moderate autolysis
type: NamedIndividual
type: autolysis value specification
definition: An autolysis value specification that indicates moderate autolytic destruction of an organism cells or tissues.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

3-severe autolysis
type: NamedIndividual
type: autolysis value specification
definition: An autolysis value specification that indicates severe autolytic destruction of an organism cells or tissues.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB

Thermo Fisher Scientific
type: NamedIndividual
type: organization
editor preferred term: Thermo Fisher Scientific
has curation status: metadata complete
definition: An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific

G1: Well differentiated
type: NamedIndividual
type: histologic grade according to AJCC 7th edition
editor preferred term: G1: Well differentiated
has curation status: metadata complete
definition: A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal.
term editor: Chris Stoeckert, Helena Ellis
alternative label: G1
definition source: https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
ontology term requester: NCI BBRB

G2: Moderately differentiated
type: NamedIndividual
type: histologic grade according to AJCC 7th edition
editor preferred term: G2: Moderately differentiated
has curation status: metadata complete
definition: A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade.
term editor: Chris Stoeckert, Helena Ellis
alternative label: G2
definition source: https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
ontology term requester: NCI BBRB

G3: Poorly differentiated
type: NamedIndividual
type: histologic grade according to AJCC 7th edition
editor preferred term: G3: Poorly differentiated
has curation status: metadata complete
definition: A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue.
term editor: Chris Stoeckert, Helena Ellis
alternative label: G3
definition source: https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
ontology term requester: NCI BBRB

G4: Undifferentiated
type: NamedIndividual
type: histologic grade according to AJCC 7th edition
editor preferred term: G4: Undifferentiated
has curation status: metadata complete
definition: A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue.
term editor: Chris Stoeckert, Helena Ellis
alternative label: G4
definition source: https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
ontology term requester: NCI BBRB

G1 (Fuhrman)
type: NamedIndividual
type: histologic grade according to the Fuhrman Nuclear Grading System
editor preferred term: G1 (Fuhrman)
has curation status: metadata complete
definition: A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Grade 1
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G2 (Fuhrman)
type: NamedIndividual
type: histologic grade according to the Fuhrman Nuclear Grading System
editor preferred term: G2 (Fuhrman)
has curation status: metadata complete
definition: A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Grade 2
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G3 (Fuhrman)
type: NamedIndividual
type: histologic grade according to the Fuhrman Nuclear Grading System
editor preferred term: G3 (Fuhrman)
has curation status: metadata complete
definition: A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Grade 3
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G4 (Fuhrman)
type: NamedIndividual
type: histologic grade according to the Fuhrman Nuclear Grading System
editor preferred term: G4 (Fuhrman)
has curation status: metadata complete
definition: A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Grade 4
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

Low grade ovarian tumor
type: NamedIndividual
type: histologic grade for ovarian tumor according to a two-tier grading system
editor preferred term: Low grade ovarian tumor
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Low grade
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

High grade ovarian tumor
type: NamedIndividual
type: histologic grade for ovarian tumor according to a two-tier grading system
editor preferred term: High grade ovarian tumor
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade.
term editor: Chris Stoeckert, Helena Ellis
alternative label: High grade
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G1 (WHO)
type: NamedIndividual
type: histologic grade for ovarian tumor according to the World Health Organization
editor preferred term: G1 (WHO)
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated.
term editor: Chris Stoeckert, Helena Ellis
alternative label: G1
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G2 (WHO)
type: NamedIndividual
type: histologic grade for ovarian tumor according to the World Health Organization
editor preferred term: G2 (WHO)
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated.
term editor: Chris Stoeckert, Helena Ellis
alternative label: G2
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G3 (WHO)
type: NamedIndividual
type: histologic grade for ovarian tumor according to the World Health Organization
editor preferred term: G3 (WHO)
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated.
term editor: Chris Stoeckert, Helena Ellis
alternative label: G3
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G4 (WHO)
type: NamedIndividual
type: histologic grade for ovarian tumor according to the World Health Organization
editor preferred term: G4 (WHO)
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated.
term editor: Chris Stoeckert, Helena Ellis
alternative label: G4
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pT0 (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred term: pT0 (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pTis (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred term: pTis (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT1 (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred term: pT1 (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT2 (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred term: pT2 (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT3 (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred term: pT3 (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT4a (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred term: pT4a (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT4b (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred term: pT4b (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT0 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred term: pT0 (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pTis (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred term: pTis (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT1 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred term: pT1 (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT1a (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred term: pT1a (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT1b (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred term: pT1b (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT2 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred term: pT2 (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT2a (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred term: pT2a (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT2b (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred term: pT2b (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT3 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred term: pT3 (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT4 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred term: pT4 (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT0 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred term: pT0 (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT1 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred term: pT1 (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT1a (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred term: pT1a (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT1b (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred term: pT1b (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT2 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred term: pT2 (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT2a (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred term: pT2a (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT2b (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred term: pT2b (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT3 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred term: pT3 (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT3a (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred term: pT3a (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT3b (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred term: pT3b (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT3c (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred term: pT3c (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT4 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred term: pT4 (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT0 (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred term: pT0 (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT1 (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred term: pT1 (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT1a (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred term: pT1a (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT1b (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred term: pT1b (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT1c (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred term: pT1c (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT2 (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred term: pT2 (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT2a (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred term: pT2a (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT2b (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred term: pT2b (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT2c (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred term: pT2c (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT3 (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred term: pT3 (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT3a (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred term: pT3a (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT3b (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred term: pT3b (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT3c (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred term: pT3c (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pN0 (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred term: pN0 (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN1 (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred term: pN1 (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN1a (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred term: pN1a (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN1b (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred term: pN1b (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN1c (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred term: pN1c (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN2 (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred term: pN2 (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN2a (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred term: pN2a (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN2b (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred term: pN2b (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN0 (lung)
type: NamedIndividual
type: pathologic lymph node stage for lung according to AJCC 7th edition
editor preferred term: pN0 (lung)
has curation status: metadata complete
definition: A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/
ontology term requester: NCI BBRB

pN1 (lung)
type: NamedIndividual
type: pathologic lymph node stage for lung according to AJCC 7th edition
editor preferred term: pN1 (lung)
has curation status: metadata complete
definition: A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/
ontology term requester: NCI BBRB

pN2 (lung)
type: NamedIndividual
type: pathologic lymph node stage for lung according to AJCC 7th edition
editor preferred term: pN2 (lung)
has curation status: metadata complete
definition: A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/
ontology term requester: NCI BBRB

pN3 (lung)
type: NamedIndividual
type: pathologic lymph node stage for lung according to AJCC 7th edition
editor preferred term: pN3 (lung)
has curation status: metadata complete
definition: A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/
ontology term requester: NCI BBRB

pN0 (kidney)
type: NamedIndividual
type: pathologic lymph node stage for kidney according to AJCC 7th edition
editor preferred term: pN0 (kidney)
has curation status: metadata complete
definition: A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/
ontology term requester: NCI BBRB

pN1 (kidney)
type: NamedIndividual
type: pathologic lymph node stage for kidney according to AJCC 7th edition
editor preferred term: pN1 (kidney)
has curation status: metadata complete
definition: A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/
ontology term requester: NCI BBRB

pN0 (ovary)
type: NamedIndividual
type: pathologic lymph node stage for ovary according to AJCC 7th edition
editor preferred term: pN0 (ovary)
has curation status: metadata complete
definition: A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/
ontology term requester: NCI BBRB

pN1 (ovary)
type: NamedIndividual
type: pathologic lymph node stage for ovary according to AJCC 7th edition
editor preferred term: pN1 (ovary)
has curation status: metadata complete
definition: A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/
ontology term requester: NCI BBRB

cM0 (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred term: cM0 (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29
ontology term requester: NCI BBRB

cM1 (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred term: cM1 (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29
ontology term requester: NCI BBRB

cM1a (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred term: cM1a (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

cM1b (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred term: cM1b (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

pM1 (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred term: pM1 (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

pM1a (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred term: pM1a (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

pM1b (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred term: pM1b (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

cM0 (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred term: cM0 (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

cM1 (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred term: cM1 (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

cM1a (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred term: cM1a (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

cM1b (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred term: cM1b (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

pM1 (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred term: pM1 (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

pM1a (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred term: pM1a (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

pM1b (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred term: pM1b (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

cM0 (kidney)
type: NamedIndividual
type: pathologic distant metastases stage for kidney according to AJCC 7th edition
editor preferred term: cM0 (kidney)
has curation status: metadata complete
definition: A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/
ontology term requester: NCI BBRB

cM1 (kidney)
type: NamedIndividual
type: pathologic distant metastases stage for kidney according to AJCC 7th edition
editor preferred term: cM1 (kidney)
has curation status: metadata complete
definition: A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/
ontology term requester: NCI BBRB

pM1 (kidney)
type: NamedIndividual
type: pathologic distant metastases stage for kidney according to AJCC 7th edition
editor preferred term: pM1 (kidney)
has curation status: metadata complete
definition: A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/
ontology term requester: NCI BBRB

cM0 (ovary)
type: NamedIndividual
type: pathologic distant metastases stage for ovary according to AJCC 7th edition
editor preferred term: cM0 (ovary)
has curation status: metadata complete
definition: A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/
ontology term requester: NCI BBRB

cM1 (ovary)
type: NamedIndividual
type: pathologic distant metastases stage for ovary according to AJCC 7th edition
editor preferred term: cM1 (ovary)
has curation status: metadata complete
definition: A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/
ontology term requester: NCI BBRB

pM1 (ovary)
type: NamedIndividual
type: pathologic distant metastases stage for ovary according to AJCC 7th edition
editor preferred term: pM1 (ovary)
has curation status: metadata complete
definition: A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/
ontology term requester: NCI BBRB

Occult Carcinoma (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred term: Occult Carcinoma (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Occult Carcinoma
definition source: http://www.medilexicon.com/dictionary/14371
ontology term requester: NCI BBRB

Stage 0 (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred term: Stage 0 (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 0
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage I (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred term: Stage I (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage I
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIA (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred term: Stage IIA (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIA
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIB (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred term: Stage IIB (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIB
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIC (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred term: Stage IIC (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIC
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIIA (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred term: Stage IIIA (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIIA
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIIB (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred term: Stage IIIB (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIIB
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIIC (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred term: Stage IIIC (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIIC
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IVA (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred term: Stage IVA (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IVA
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IVB (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred term: Stage IVB (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IVB
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IA (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred term: Stage IA (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IA
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IA1 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred term: Stage IA1 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IA1
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IA2 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred term: Stage IA2 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IA2
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IB (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred term: Stage IB (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IB
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IB1 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred term: Stage IB1 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IB1
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IB2 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred term: Stage IB2 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IB2
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIA (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred term: Stage IIA (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIA
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIA1 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred term: Stage IIA1 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIA1
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIA2 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred term: Stage IIA2 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIA2
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIB (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred term: Stage IIB (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIB
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIIA (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred term: Stage IIIA (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIIA
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIIB (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred term: Stage IIIB (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIIB
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IVA (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred term: Stage IVA (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IVA
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IVB (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred term: Stage IVB (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IVB
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage 1 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred term: Stage 1 (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 1
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 1A (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred term: Stage 1A (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 1A
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 1B (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred term: Stage 1B (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 1B
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 1C (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred term: Stage 1C (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 1C
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 2 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred term: Stage 2 (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 2
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 2A (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred term: Stage 2A (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 2A
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 2B (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred term: Stage 2B (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 2B
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 2C (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred term: Stage 2C (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 2C
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 3 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred term: Stage 3 (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0).
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 3
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 3A (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred term: Stage 3A (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 .
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 3A
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 3B (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred term: Stage 3B (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 .
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 3B
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 3C (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred term: Stage 3C (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0).
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 3C
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 4 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred term: Stage 4 (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 4
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage Unknown (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred term: Stage Unknown (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0).
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage Unknown
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

3: symptomatic in bed more than 50% of the day but not bed ridden
type: NamedIndividual
type: Eastern Cooperative Oncology Group score value specification
editor preferred term: 3: symptomatic in bed more than 50% of the day but not bed ridden
has curation status: metadata complete
definition: An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

2: symptomatic but in bed less than 50% of the day
type: NamedIndividual
type: Eastern Cooperative Oncology Group score value specification
editor preferred term: 2: symptomatic but in bed less than 50% of the day
has curation status: metadata complete
definition: An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

4: bed ridden
type: NamedIndividual
type: Eastern Cooperative Oncology Group score value specification
editor preferred term: 4: bed ridden
has curation status: metadata complete
definition: An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

0: asymptomatic
type: NamedIndividual
type: Eastern Cooperative Oncology Group score value specification
editor preferred term: 0: asymptomatic
has curation status: metadata complete
definition: An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

1: symptomatic but fully ambulatory
type: NamedIndividual
type: Eastern Cooperative Oncology Group score value specification
editor preferred term: 1: symptomatic but fully ambulatory
has curation status: metadata complete
definition: An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

100: asymptomatic
type: NamedIndividual
type: Karnofsky score vaue specification
editor preferred term: 100: asymptomatic
has curation status: metadata complete
definition: A Karnofsky score vaue specification indicating that a patient is asymptomatic.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

80-90: symptomatic but fully ambulatory
type: NamedIndividual
type: Karnofsky score vaue specification
editor preferred term: 80-90: symptomatic but fully ambulatory
has curation status: metadata complete
definition: A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

60-70: symptomatic but in bed less than 50% of the day
type: NamedIndividual
type: Karnofsky score vaue specification
editor preferred term: 60-70: symptomatic but in bed less than 50% of the day
has curation status: metadata complete
definition: A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

40-50: symptomatic, in bed more than 50% of the day, but not bed ridden
type: NamedIndividual
type: Karnofsky score vaue specification
editor preferred term: 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden
has curation status: metadata complete
definition: A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

Oxford Nanopore Technologies
type: NamedIndividual
type: manufacturer
editor preferred term: Oxford Nanopore Technologies
has curation status: metadata complete
definition: An organization that is developing and selling nanopore sequencing products and is based in the UK.
term editor: James A. Overton
definition source: https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies

out of scope
type: NamedIndividual
type: obsolescence reason specification
definition: The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
editor note: This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/77
ontology term requester: https://orcid.org/0000-0001-5208-3432

second
type: NamedIndividual
type: time unit
imported from: uo.owl

degree Celsius
type: NamedIndividual
type: temperature unit
imported from: uo.owl

minute
type: NamedIndividual
type: time unit
imported from: uo.owl

hour
type: NamedIndividual
type: time unit
imported from: uo.owl

day
type: NamedIndividual
type: time unit
imported from: uo.owl

week
type: NamedIndividual
type: time unit
imported from: uo.owl

month
type: NamedIndividual
type: time unit
imported from: uo.owl

year
type: NamedIndividual
type: time unit
imported from: uo.owl

molar
type: NamedIndividual
type: concentration unit
imported from: uo.owl

millimolar
type: NamedIndividual
type: concentration unit
imported from: uo.owl

micromolar
type: NamedIndividual
type: concentration unit
imported from: uo.owl

nanomolar
type: NamedIndividual
type: concentration unit
imported from: uo.owl

picomolar
type: NamedIndividual
type: concentration unit
imported from: uo.owl

mass percentage
type: NamedIndividual
type: concentration unit
imported from: uo.owl

mass volume percentage
type: NamedIndividual
type: concentration unit
imported from: uo.owl

volume percentage
type: NamedIndividual
type: concentration unit
imported from: uo.owl

gram per liter
type: NamedIndividual
type: concentration unit
imported from: uo.owl

milligram per milliliter
type: NamedIndividual
type: concentration unit
imported from: uo.owl

degree Fahrenheit
type: NamedIndividual
type: temperature unit
imported from: uo.owl

pH
type: NamedIndividual
type: concentration unit
imported from: uo.owl

milliliter per liter
type: NamedIndividual
type: concentration unit
imported from: uo.owl

gram per deciliter
type: NamedIndividual
type: concentration unit
imported from: uo.owl

colony forming unit per volume
type: NamedIndividual
type: concentration unit
imported from: uo.owl

microgram per liter
type: NamedIndividual
type: concentration unit
imported from: uo.owl

Class
intersection of: one-dimensional temporal region
intersection of: Restriction
  on property: has temporal occupant
  qualified cardinality: 1
  on class: history

Restriction
on property: is about
some values from: Class
  intersection of: one-dimensional temporal region
  intersection of: Restriction
    on property: has temporal occupant
    qualified cardinality: 1
    on class: history

Restriction
on property: is about
some values from: Class
  intersection of: one-dimensional temporal region
  intersection of: Restriction
    on property: has temporal occupant
    qualified cardinality: 1
    on class: Class
      intersection of: history
      intersection of: Restriction
        on property: history of
        some values from: specimen donor