Ontology for Representing CDM Semantics
type: Ontology
version IRI: orcs.owl
contributor: Amanda Hicks
contributor: Josh Hanna
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: S. Clint Dowland
contributor: William R. Hogan
date: 2019-08-03
version info: 2021-11-13

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)
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: editor preferred label

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.
definition 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.
definition editor: GROUP:OBI
definition source: OBI_0000277

has curation status
type: AnnotationProperty
editor preferred term: has curation status
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bill Bug
definition 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.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: textual definition

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.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>

definition 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.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: term editor

alternative term
type: AnnotationProperty
editor preferred term: alternative term
has curation status: pending final vetting
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

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
definition 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.
definition editor: PERSON:Alan Ruttenberg
definition 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
definition editor: PERSON:Alan Ruttenberg
label: curator notes

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.
definition 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.
definition 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')
definition 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
definition editor: PERSON:Alan Ruttenberg
definition 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
definition 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.
definition editor: Chris Mungall

first order logic expression
type: AnnotationProperty
editor preferred term: first order logic expression
definition: An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.
definition editor: PERSON:Alan Ruttenberg
sub property of: logical macro assertion on an object property

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
definition editor: Alan Ruttenberg

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 .
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
definition editor: PERSON:Chris Mungall
definition 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)
definition 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
definition 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
definition 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.
definition editor: Person:Alan Ruttenberg

elucidation
type: AnnotationProperty
editor preferred term: elucidation
definition 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)
definition 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)
definition 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"
definition editor: PERSON:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

retired from use as of
type: AnnotationProperty
editor preferred term: retired from use as of
definition: relates a class of CRID to the date after which further instances should not be made, according to the central authority
editor note: In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp
definition editor: Alan Ruttenberg

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.
definition 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.
definition 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.
definition 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
definition 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

IUI
type: AnnotationProperty
editor preferred term: instance unique identifier
comment: An annotation to be applied to individuals only. Value is a GUID/UUID for use in a referent tracking system.

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
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

has_MedDRA_id
type: AnnotationProperty

U.S. Census PUMS serial number
type: AnnotationProperty
definition: The PUMS serial number assigned to a housing unit, which is only unique within each state, and which explicitly links the housing unit record with person records in PUMS data.

ISO 639-1 code
type: AnnotationProperty
editor preferred term: ISO 639-1 code
definition editor: William R. Hogan
comment: ISO 639-1 assigns two-character identifiers to individual human languages. This annotation property is for use in annotating OWL2 individuals in OMRSE that represent languages with their appropriate ISO 639-1 code that designates them in that standard system.

ISO 639-2/B code
type: AnnotationProperty
editor preferred term: ISO 639-2/B code
definition editor: William R. Hogan
comment: ISO 639-2/B assigns three-character identifiers to individual human languages. This annotation property is for use in annotating OWL2 individuals in OMRSE that represent languages with their appropriate ISO 639-2/B ('B' is for "bibliographic applications") code that designates them in that standard system.

ISO 639-2/T code
type: AnnotationProperty
editor preferred term: ISO 639-2/T code
definition editor: William R. Hogan
comment: ISO 639-2/T assigns three-character identifiers to individual human languages. This annotation property is for use in annotating OWL2 individuals in OMRSE that represent languages with their appropriate ISO 639-2/T ('T' is for "terminology applications") code that designates them in that standard system.

ISO 639-3 code
type: AnnotationProperty
editor preferred term: ISO 639-3 code
definition editor: William R. Hogan
comment: ISO 639-3 assigns three-character identifiers to individual human languages. This annotation property is for use in annotating OWL2 individuals in OMRSE that represent languages with their appropriate ISO 639-3 code that designates them in that standard system.

OOSTT user-centered description
type: AnnotationProperty
definition editor: Mathias Brochhausen

PCORnet CDM comment
type: AnnotationProperty
definition: A verbatim excerpt—such as a definition, comment, or description—from the PCORnet Common Data Model.

inheres in
type: AnnotationProperty
type: ObjectProperty
sub property of: inheres in part of
inverse of: bearer of
type: FunctionalProperty
example of usage: this fragility is a characteristic of this vase
example of usage: this fragility inheres in this vase
definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
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.
editor preferred term: inheres in
label: characteristic of
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
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.
example of usage: this red color inheres in this apple
example of usage: this red color is a characteristic of this apple
temporal interpretation: axiom holds for all times
alternative term: inheres_in

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.
sub property of: logical macro assertion on an object property

never in taxon
type: AnnotationProperty
example of usage: tooth SubClassOf 'never in taxon' value 'Aves'
definition: x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/17921072
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20973947
expand assertion to: ?X DisjointWith RO_0002162 some ?Y
sub property of: taxonomic class assertion

mutually spatially disjoint with
type: AnnotationProperty
definition: A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
alternative term: non-overlapping with
alternative term: shares no parts with
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
expand assertion to: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
sub property of: logical macro assertion on a class

taxonomic class assertion
type: AnnotationProperty
definition: An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.

present_in_taxon
type: AnnotationProperty

defined by inverse
type: AnnotationProperty
sub property of: subset_property

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.

annotation property cardinality
type: AnnotationProperty
definition: An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N.
sub property of: logical macro assertion on an annotation property
range: nonNegativeInteger

logical macro assertion on a class
type: AnnotationProperty
definition: A logical macro assertion whose domain is an IRI for a class
editor note: The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
sub property of: logical macro assertion

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.
sub property of: logical macro assertion on a property

logical macro assertion on an annotation property
type: AnnotationProperty

dispositional interpretation
type: AnnotationProperty
definition: An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one.
sub property of: logical macro assertion on an object property

has no connections with
type: AnnotationProperty
example of usage: 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'
definition: A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
alternative term: shares no connection with
expand assertion to: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))
sub property of: logical macro assertion on a class

inherited annotation property
type: AnnotationProperty

curator guidance link
type: AnnotationProperty
definition: Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)
sub property of: inherited annotation property

always present in taxon
type: AnnotationProperty
example of usage: brain always_present_in_taxon 'Vertebrata'
example of usage: forelimb always_present_in_taxon Euarchontoglires
definition: S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S
editor note: This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed.
alternative term: never lost in
sub property of: present_in_taxon

temporal logical macro assertion on a class
type: AnnotationProperty
curator note: This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans.
sub property of: logical macro assertion on a class

measurement property has unit
type: AnnotationProperty
sub property of: logical macro assertion on an annotation property

has start time value
type: AnnotationProperty
sub property of: temporal logical macro assertion on a class

has end time value
type: AnnotationProperty
sub property of: temporal logical macro assertion on a class

start, days post fertilization
type: AnnotationProperty
definition: Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property.
sub property of: has start time value

end, days post fertilization
type: AnnotationProperty
definition: Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property.
sub property of: has end time value

start, years post birth
type: AnnotationProperty
definition: Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1.
sub property of: has start time value

end, years post birth
type: AnnotationProperty
definition: Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2
sub property of: has end time value

start, months post birth
type: AnnotationProperty
definition: Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1.
sub property of: has start time value

end, months post birth
type: AnnotationProperty
definition: Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2
sub property of: has end time value

month of gestation
type: AnnotationProperty
definition: Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in.
sub property of: temporal logical macro assertion on a class

has developmental stage marker
type: AnnotationProperty
definition: A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process
sub property of: temporal logical macro assertion on a class

start, days post coitum
type: AnnotationProperty
definition: Count of number of days intervening between the start of the stage and the time of coitum.
curator note: For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)
sub property of: has start time value

end, days post coitum
type: AnnotationProperty
definition: Count of number of days intervening between the end of the stage and the time of coitum.
sub property of: has end time value

start, weeks post birth
type: AnnotationProperty
sub property of: has start time value

end, weeks post birth
type: AnnotationProperty
sub property of: has end time value

is asymmetric relational form of process class
type: AnnotationProperty
definition: If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p
sub property of: is relational form of process class

is symmetric relational form of process class
type: AnnotationProperty
definition: If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p
sub property of: is relational form of process class

is relational form of process class
type: AnnotationProperty
definition: R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process
sub property of: is relational form of a class

is direct form of
type: AnnotationProperty
definition: relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
editor note: The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P"
logical macro assertion on an annotation property: If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
creator: Chris Mungall
sub property of: logical macro assertion on an object property

is indirect form of
type: AnnotationProperty
definition: relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y
creator: Chris Mungall
sub property of: logical macro assertion on an object property

logical macro assertion on an axiom
type: AnnotationProperty
sub property of: logical macro assertion

is a defining property chain axiom
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
sub property of: logical macro assertion on an axiom

is a defining property chain axiom where second argument is reflexive
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
sub property of: is a defining property chain axiom

is relational form of a class
type: AnnotationProperty
definition: An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis.
sub property of: logical macro assertion on an object property

logical macro assertion involving identity
type: AnnotationProperty
definition: A shortcut relationship that holds between two entities based on their identity criteria
sub property of: logical macro assertion

in approximate one to one relationship with
type: AnnotationProperty
definition: A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds.
sub property of: logical macro assertion involving identity

is approximately equivalent to
type: AnnotationProperty
definition: x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y
curator note: The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y"
sub property of: in approximate one to one relationship with

is opposite of
type: AnnotationProperty
example of usage: 'anterior end of organism' is-opposite-of 'posterior end of organism'
example of usage: 'increase in temperature' is-opposite-of 'decrease in temperature'
definition: x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
sub property of: in approximate one to one relationship with

is indistinguishable from
type: AnnotationProperty
definition: x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
sub property of: is approximately equivalent to

evidential logical macro assertion on an axiom
type: AnnotationProperty
sub property of: logical macro assertion on an axiom

axiom has evidence
type: AnnotationProperty
definition: A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom
curator note: This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
sub property of: evidential logical macro assertion on an axiom

axiom contradicted by evidence
type: AnnotationProperty
definition: A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom
curator note: This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual.
sub property of: evidential logical macro assertion on an axiom

is representative IRI for equivalence set
type: AnnotationProperty
example of usage: In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context.
definition: this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent.
curator note: If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion
see also: OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member
sub property of: logical macro assertion involving identity

is directional form of
type: AnnotationProperty
definition: Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0"
created by: cjm
creation date: 2018-03-13T23:59:29Z
sub property of: logical macro assertion on an object property

is positive form of
type: AnnotationProperty
created by: cjm
creation date: 2018-03-14T00:03:16Z
sub property of: is directional form of

is negative form of
type: AnnotationProperty
created by: cjm
creation date: 2018-03-14T00:03:24Z
sub property of: is directional form of

is homeomorphic for
type: AnnotationProperty
example of usage: part-of is homeomorphic for independent continuants.
definition: R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.
created by: cjm
creation date: 2018-10-21T19:46:34Z
comment: R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C.
sub property of: logical macro assertion on an object property

external_definition
type: AnnotationProperty

axiom_lost_from_external_ontology
type: AnnotationProperty

homology_notes
type: AnnotationProperty

has_relational_adjective
type: AnnotationProperty

taxon_notes
type: AnnotationProperty

function_notes
type: AnnotationProperty

structure_notes
type: AnnotationProperty

development_notes
type: AnnotationProperty

external_ontology_notes
type: AnnotationProperty

fma_set_term
type: AnnotationProperty

Unique Apollo Label
type: AnnotationProperty

eco subset
type: AnnotationProperty
sub property of: subset_property

contributor
type: AnnotationProperty

subset_property
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has_scope
type: AnnotationProperty

has_synonym_type
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

isDefinedBy
type: AnnotationProperty
OBO foundry unique label: is defined by

Axiom
annotated source: isDefinedBy
annotated property: OBO foundry unique label
annotated target: is defined by
comment: This is an experimental annotation

label
type: AnnotationProperty

see also
type: AnnotationProperty

depicted by
type: AnnotationProperty

part of
type: ObjectProperty
equivalent property:
  inverse of: has part
sub property of: overlaps
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: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
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 term: part_of
imported from: ido.owl
imported from: omrse.owl
temporal interpretation: axiom holds for all times
is homeomorphic for: continuant
is homeomorphic for: occurrent
is homeomorphic for: independent continuant
is homeomorphic for: realizable entity
is homeomorphic for: quality
is homeomorphic for: specifically dependent continuant
is homeomorphic for: generically dependent continuant
in_subset: valid for go annotation extension
in_subset: valid for go gp2term
in_subset: valid for go ontology
in_subset: valid for gocam

has part
type: ObjectProperty
equivalent property:
  inverse of: part of
sub property of: overlaps
sub property of: topObjectProperty
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: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
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 term: has_part
imported from: ido.owl
imported from: omrse.owl
temporal interpretation: axiom holds for all times
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

realized in
type: ObjectProperty
equivalent property:
  inverse of: realizes
sub property of: topObjectProperty
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 term: is realized by
alternative term: realized_in
imported from: ido.owl
imported from: omrse.owl
imported from: http://purl.obolibrary.org/obo/ro.owl
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
equivalent property:
  inverse of: realized in
sub property of: topObjectProperty
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
imported from: ido.owl
imported from: omrse.owl
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

obsolete preceded by
type: ObjectProperty
type: TransitiveProperty
comment: accidentally included in BFO 1.2 proposal - should have been BFO_0000062
deprecated: true

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
property chain axiom: starts during
property chain axiom: happens during
editor preferred term: preceded by
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.
editor note: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
alternative term: is preceded by
alternative term: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in_subset: eco subset

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
editor preferred term: precedes
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.
in_subset: eco subset

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 term: occurs_in
alternative term: unfolds in
alternative term: unfolds_in
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
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

exists at
type: ObjectProperty
inverse of: during which exists
domain: entity
range: temporal region
BFO OWL specification label: exists-at
BFO CLIF specification label: existsAt
editor note: BFO2 Reference: entity
editor note: BFO2 Reference: temporal region
elucidation: b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])

has occurrent part
type: ObjectProperty
sub property of: topObjectProperty
inverse of: part of occurrent
type: TransitiveProperty
domain: occurrent
range: occurrent
BFO OWL specification label: o-has-part
BFO CLIF specification label: hasOccurrentPart
example of usage: [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life
example of usage: [copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
example of usage: [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
definition: b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
editor note: [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
editor note: [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
imported from: http://purl.obolibrary.org/obo/vo.owl
elucidation: [copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
has associated axiom(fol): (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]

has proper occurrent part
type: ObjectProperty
sub property of: has occurrent part
inverse of: proper part of occurrent
type: TransitiveProperty
domain: occurrent
range: occurrent
BFO OWL specification label: o-has-ppart
BFO CLIF specification label: hasProperOccurrentPart
definition: [copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
definition: b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
imported from: http://purl.obolibrary.org/obo/vo.owl

has temporal part
type: ObjectProperty
sub property of: has occurrent part
inverse of: temporal part of
type: TransitiveProperty
domain: occurrent
range: occurrent
BFO OWL specification label: has-t-part
example of usage: [copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
example of usage: [copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life.
example of usage: [copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
definition: [copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
definition: [copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
imported from: http://purl.obolibrary.org/obo/vo.owl

part of occurrent
type: ObjectProperty
sub property of: topObjectProperty
type: TransitiveProperty
domain: occurrent
range: occurrent
BFO OWL specification label: o-part-of
BFO CLIF specification label: occurrentPartOf
example of usage: Mary’s 5th birthday occurrent_part_of Mary’s life
example of usage: The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
example of usage: the first set of the tennis match occurrent_part_of the tennis match.
definition: [copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
editor note: BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
editor note: BFO2 Reference: occurrent
imported from: http://purl.obolibrary.org/obo/vo.owl
elucidation: b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
has associated axiom(nl): occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001])
has associated axiom(nl): occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002])
has associated axiom(nl): occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001])
has associated axiom(nl): occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001])
has associated axiom(nl): occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001])
has associated axiom(fol): (forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001]
has associated axiom(fol): (forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001]
has associated axiom(fol): (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001]
has associated axiom(fol): (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001]
has associated axiom(fol): (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002]

proper part of occurrent
type: ObjectProperty
sub property of: part of occurrent
type: TransitiveProperty
domain: occurrent
range: occurrent
BFO OWL specification label: o-ppart-of
BFO CLIF specification label: properOccurrentPartOf
definition: [copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
definition: b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
has associated axiom(fol): (iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001]

temporal part of
type: ObjectProperty
sub property of: part of occurrent
type: TransitiveProperty
domain: occurrent
range: occurrent
BFO OWL specification label: t-part-of
BFO CLIF specification label: temporalPartOf
example of usage: the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
example of usage: the process boundary which separates the 3rd and 4th years of your life.
example of usage: your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
definition: b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
definition: b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
imported from: http://purl.obolibrary.org/obo/vo.owl
has associated axiom(nl): if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002])
has associated axiom(fol): (forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002]
has associated axiom(fol): (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001]
has associated axiom(fol): (iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003]

occupies temporal region
type: ObjectProperty
sub property of: exists at
inverse of: has temporal occupant
domain: occurrent
range: temporal region
BFO OWL specification label: spans
BFO CLIF specification label: occupiesTemporalRegion
elucidation: 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])

has temporal occupant
type: ObjectProperty
sub property of: during which exists
domain: temporal region
range: occurrent
BFO OWL specification label: span-of
BFO CLIF specification label: spanOf
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])

during which exists
type: ObjectProperty
domain: temporal region
range: entity
BFO OWL specification label: during-which-exists
editor note: [copied from inverse property 'exists at'] BFO2 Reference: entity
editor note: [copied from inverse property 'exists at'] BFO2 Reference: temporal region
elucidation: [copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])

history of
type: ObjectProperty
sub property of: topObjectProperty
inverse of: has history
domain: history
range: material entity
imported from: http://purl.obolibrary.org/obo/bfo/2020/bfo.owl
definition: (Elucidation) b history of c if c is a material entity and b is a history that is the unique history of c
example: This life is the history of this organism.

has history
type: ObjectProperty
sub property of: topObjectProperty
domain: material entity
range: history
imported from: http://purl.obolibrary.org/obo/bfo/2020/bfo.owl
definition: b has history c =Def c history of b
example: This organism has history this life.

has measurement unit label
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
range: measurement unit label

obsolete_specifically denotes
type: ObjectProperty
sub property of: ObsoleteProperty
example of usage: The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend
has curation status: pending final vetting
definition: c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
editor note: 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense
editor note: see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote
definition editor: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
has obsolescence reason: failed exploratory term
deprecated: true

is about
type: ObjectProperty
domain: information content entity
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.
definition editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

mentions
type: ObjectProperty
sub property of: is about
has curation status: pending final vetting
definition: An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
editor note: 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
editor note: 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
definition editor: PERSON: Jonathan Rees
definition editor: Person: Alan Ruttenberg

denotes
type: ObjectProperty
sub property of: is about
inverse of: denoted by
domain: information content entity
range: entity
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
definition editor: person:Alan Ruttenberg
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan

obsolete_materially denotes
type: ObjectProperty
sub property of: ObsoleteProperty
editor note: see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote
has obsolescence reason: failed exploratory term
deprecated: true

is quality measurement of
type: ObjectProperty
sub property of: is about
inverse of: is quality measured as
domain: measurement datum
range: quality
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.
definition editor: Alan Ruttenberg

obsolete_describes
type: ObjectProperty
sub property of: ObsoleteProperty
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_represents
type: ObjectProperty
sub property of: ObsoleteProperty
has obsolescence reason: failed exploratory term
deprecated: true

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

has coordinate unit label
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: length unit
comment: relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point

is duration of
type: ObjectProperty
sub property of: is about
domain: time measurement datum
range: process
has curation status: metadata complete
definition: relates a process to a time-measurement-datum that represents the duration of the process
definition editor: Person:Alan Ruttenberg

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
definition editor: Person:Alan Ruttenberg

is quality specification of
type: ObjectProperty
sub property of: is about
inverse of: quality is specified as
has curation status: metadata complete
definition: A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality.
definition editor: Person:Alan Ruttenberg
definition editor: Person:Bjoern Peters

quality is specified as
type: ObjectProperty
has curation status: metadata complete
definition: inverse of the relation of is quality specification of
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
definition editor: Person:Alan Ruttenberg
definition editor: Person:Bjoern Peters

has time stamp
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
domain: time stamped measurement datum
range: time measurement datum
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
definition editor: Alan Ruttenberg

has measurement datum
type: ObjectProperty
sub property of: has part
domain: time stamped measurement datum
range: Class
  intersection of: measurement datum
  intersection of: Class
    complement of: time measurement datum
has curation status: metadata incomplete
definition: relates a time stamped measurement datum to the measurement datum that was measured
definition editor: Alan Ruttenberg

obsolete_designates
type: ObjectProperty
sub property of: ObsoleteProperty
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..
has obsolescence reason: term imported
term replaced by: denotes
creator: Mathias Brochhausen
deprecated: true

is_borrowed_reference_to
type: ObjectProperty
sub property of: topObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
domain: identifier
range: entity
definition: x is_borrowed_reference_for y, if x is a proper name that is used to refer to one individual among a specific group after the dubbing process took place.
creator: Mathias Brochhausen

is_fixing_reference_to
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
definition: x is_fixed_reference_for y, if x is an utterance or graphemes concretized as writing quality inhering in some independent continuant that is used to single out one individual and refer to the latter among a specific group after the.
creator: 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.
definition editor: Mathias Brochhausen

legally revokes
type: ObjectProperty
sub property of: has_participant
type: FunctionalProperty
type: AsymmetricProperty
type: IrreflexiveProperty
domain: deontic declaration
range: deontic role
definition: d socio-legally revokes s if s participates in d and at the end of d s no longer exists. It is important to note that this going out of existence of s is complete and unlike the going out of existence for material entities which basically always are transformed into something else. After the declaration nothing is left of the socio-legal generically dependent continuant in question.
definition editor: Mathias Brochhausen

obsolete_legally transfers
type: ObjectProperty
sub property of: ObsoleteProperty
type: FunctionalProperty
type: AsymmetricProperty
type: IrreflexiveProperty
definition: d socio-legally transfers l if l participates in d and d has specified input (concretization of l)1 and specified output (concretization of l)2, where (concretization of l)1 and (concretization of l)2 are not identical.
definition editor: Mathias Brochhausen
has obsolescence reason: failed exploratory term
deprecated: true

has_specified_input
type: ObjectProperty
equivalent property:
  inverse of: is_specified_input_of
sub property of: has_participant
inverse of: is_specified_input_of
domain: planned process
editor preferred term: has_specified_input
example of usage: see is_input_of example_of_usage
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.
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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Coutot
imported from: obi.owl

is_specified_input_of
type: ObjectProperty
sub property of: participates in
range: planned process
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.
definition editor: Alan Ruttenberg
definition editor: PERSON:Bjoern Peters

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: has_participant
sub property of: topObjectProperty
inverse of: is_specified_output_of
domain: planned process
editor preferred term: has_specified_output
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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition 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
range: planned process
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.
definition editor: Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
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.
definition editor: Person:Alan Ruttenberg
definition editor: Person:Helen Parkinson
definition source: Person:Alan Ruttenberg
definition source: Person:Helen Parkinson
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

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
definition editor: Person: Jie Zheng

owns
type: ObjectProperty
sub property of: topObjectProperty
domain: Class
  union of: Homo sapiens
  union of: organization
  union of: collection of humans
  union of: aggregate of organizations
definition 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.

administrates
type: ObjectProperty
inverse of: is administered by
domain: Class
  union of: Homo sapiens
  union of: organization
  union of: collection of humans
  union of: aggregate of organizations
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.
definition 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 owned by
type: ObjectProperty
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.

is-aggregate-of
type: ObjectProperty
sub property of: ObsoleteProperty
has obsolescence reason: BFO relation takes precedence.
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.
label: obsolete is-aggregate-of
deprecated: true

obsolete is-component-of-aggregate
type: ObjectProperty
sub property of: ObsoleteProperty
comment: At the instance level, this relation is the named inverse of is-aggregate-of. At the type level, however, not so. We expect BFO 2.0 to have this relation as well, and we will obsolete this property and declare it equivalent to BFO's version when BFO 2.0 comes out.
deprecated: true

is administered by
type: ObjectProperty
type: AsymmetricProperty

is enrolled in school
type: ObjectProperty
type: AsymmetricProperty
domain: Restriction
  on property: bearer of
  some values from: student role
range: school organization

is admitted to hospital
type: ObjectProperty
sub property of: topObjectProperty
domain: Restriction
  on property: bearer of
  some values from: patient role
range: hospital organization

provides service
type: ObjectProperty

bearer of
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
definition: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
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 term: bearer_of
alternative term: is bearer of
temporal interpretation: axiom holds for all times
label: bearer_of
label: has characteristic

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 term: participates_in

has_participant
type: ObjectProperty
domain: occurrent
range: continuant
property chain axiom: has part
property chain axiom: realizes
property chain axiom: inheres in
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 term: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant
label: has participant

is concretized as
type: ObjectProperty
sub property of: topObjectProperty
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
editor preferred term: is concretized as
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.
imported from: http://purl.obolibrary.org/obo/obi.owl

concretizes
type: ObjectProperty
sub property of: topObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
editor preferred term: concretizes
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.
imported from: http://purl.obolibrary.org/obo/obi.owl

function of
type: ObjectProperty
sub property of: inheres in
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 term: function_of
alternative term: 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: inheres in
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 term: is quality of
alternative term: 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: inheres in
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 term: is role of
alternative term: 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: bearer of
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 term: has_function

has quality
type: ObjectProperty
sub property of: bearer of
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 term: has_quality

has role
type: ObjectProperty
sub property of: bearer of
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 term: has_role

has disposition
type: ObjectProperty
sub property of: bearer of
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: inheres in
definition: inverse of has disposition
in_subset: defined by inverse
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 term: derives_from
curator note: This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
in_subset: eco subset

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 term: derives_into
in_subset: eco subset

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/
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
alternative term: location_of
temporal interpretation: axiom holds for all times

contained in
type: ObjectProperty
inverse of: contains
domain: material entity
range: independent continuant
property chain axiom: located in
property chain axiom: part of
editor preferred term: contained in
editor note: Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
editor note: Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
editor note: Intended meaning: domain: material entity range: spatial region or site (immaterial continuant)
alternative term: contained_in
temporal interpretation: axiom holds for all times
in_subset: eco subset

contains
type: ObjectProperty
editor preferred term: contains
temporal interpretation: axiom holds for all times
in_subset: eco subset

is allergic trigger for
type: ObjectProperty
sub property of: causes or contributes to condition
inverse of: has allergic trigger
domain: material entity
example of usage: penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)
definition: A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

is autoimmune trigger for
type: ObjectProperty
sub property of: causes or contributes to condition
inverse of: has autoimmune trigger
domain: material entity
definition: A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

has allergic trigger
type: ObjectProperty
sub property of: causes or contributes to condition
range: material entity
example of usage: penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)
definition: A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

has autoimmune trigger
type: ObjectProperty
sub property of: causes or contributes to condition
range: material entity
definition: A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

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/
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
alternative term: located_in
temporal interpretation: axiom holds for all times
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
sub property of: mereotopologically related to
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 term: 2D_boundary_of
alternative term: boundary of
alternative term: is 2D boundary of
alternative term: is boundary of
temporal interpretation: axiom holds for all times

has 2D boundary
type: ObjectProperty
sub property of: mereotopologically related to
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.
definition editor: David Osumi-Sutherland
alternative term: has boundary
alternative term: has_2D_boundary
temporal interpretation: axiom holds for all times

bounding layer of
type: ObjectProperty
sub property of: part of
range: material entity
definition: X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000
definition editor: David Osumi-Sutherland
in_subset: eco subset
comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.

coincident with
type: ObjectProperty
sub property of: mereotopologically related to
definition: A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
editor note: Note from NCEAS meeting: consider changing primary label
definition editor: David Osumi-Sutherland
in_subset: eco subset
comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.

regulates in other organism
type: ObjectProperty
sub property of: causally upstream of or within
domain: process
range: process
definition: x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
definition editor: David Osumi-Sutherland

regulates transport of
type: ObjectProperty
definition: A relationship that holds between a process that regulates a transport process and the entity transported by that process.
definition editor: David Osumi-Sutherland
in_subset: eco subset

occurent part of
type: ObjectProperty
sub property of: part of
sub property of: causally upstream of or within
domain: occurrent
range: occurrent
definition: A part of relation that applies only between occurents.

has regulatory component activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulated by
definition: A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
created by: dos
creation date: 2017-05-24T09:30:46Z

has negative regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: negatively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
created by: dos
creation date: 2017-05-24T09:31:01Z
comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.

has positive regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: positively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
created by: dos
creation date: 2017-05-24T09:31:17Z
comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.

has necessary component activity
type: ObjectProperty
sub property of: has component activity
sub property of: positively regulated by
created by: dos
creation date: 2017-05-24T09:36:08Z
comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity.

has component activity
type: ObjectProperty
sub property of: has component process
created by: dos
creation date: 2017-05-24T09:44:33Z
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.

has component process
type: ObjectProperty
sub property of: has component
domain: process
range: process
definition: w 'has process component' p if p and w are processes, 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.
created by: dos
creation date: 2017-05-24T09:49:21Z

has ligand
type: ObjectProperty
sub property of: has input
definition: A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.
created by: dos
creation date: 2017-07-19T17:30:36Z

occurs across
type: ObjectProperty
sub property of: has part that occurs in
definition: A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.
created by: dos
creation date: 2017-07-20T17:19:37Z

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates
created by: dos
creation date: 2017-09-17T13:52:24Z
comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.

Axiom
annotated source: directly regulated by
annotated property: comment
annotated target: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
database_cross_reference: GOC:dos

directly negatively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly negatively regulates
definition: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
created by: dos
creation date: 2017-09-17T13:52:38Z

Axiom
annotated source: directly negatively regulated by
annotated property: definition
annotated target: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
database_cross_reference: GOC:dos

directly positively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly positively regulates
definition: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
created by: dos
creation date: 2017-09-17T13:52:47Z

Axiom
annotated source: directly positively regulated by
annotated property: definition
annotated target: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
database_cross_reference: GOC:dos

has effector activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulates
type: FunctionalProperty
definition: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
created by: dos
creation date: 2017-09-22T14:14:36Z
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.

Axiom
annotated source: has effector activity
annotated property: definition
annotated target: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
database_cross_reference: GOC:dos

in register with
type: ObjectProperty
sub property of: mereotopologically related to
definition: A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
creation date: 2017-12-07T12:58:06Z
created by: dos

Axiom
annotated source: in register with
annotated property: definition
annotated target: A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
database_cross_reference: GOC:dos

before or simultaneous with
type: ObjectProperty
sub property of: temporally related to
definition editor: David Osumi-Sutherland
alternative term: <=
in_subset: eco subset
comment: Primitive instance level timing relation between events

simultaneous with
type: ObjectProperty
sub property of: before or simultaneous with
type: TransitiveProperty
definition editor: David Osumi-Sutherland
in_subset: eco subset
comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)

before
type: ObjectProperty
sub property of: before or simultaneous with
type: TransitiveProperty
definition editor: David Osumi-Sutherland
in_subset: eco subset
comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)

during which ends
type: ObjectProperty
sub property of: temporally related to
inverse of: ends during
definition editor: David Osumi-Sutherland
in_subset: eco subset
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

encompasses
type: ObjectProperty
sub property of: during which starts
inverse of: happens during
type: TransitiveProperty
definition editor: David Osumi-Sutherland
alternative term: di
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
property chain axiom: ends during
property chain axiom: preceded by
definition editor: David Osumi-Sutherland
in_subset: eco subset
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
property chain axiom: starts with
property chain axiom: ends with
definition editor: David Osumi-Sutherland
alternative term: starts_at_end_of
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

during which starts
type: ObjectProperty
sub property of: temporally related to
inverse of: starts during
definition editor: David Osumi-Sutherland
in_subset: eco subset
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

starts before
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
property chain axiom: starts during
property chain axiom: obsolete preceded by
definition editor: David Osumi-Sutherland
in_subset: eco subset

immediately precedes
type: ObjectProperty
sub property of: precedes
property chain axiom: ends with
property chain axiom: starts with
definition editor: David Osumi-Sutherland
alternative term: ends_at_start_of
alternative term: meets
is direct form of: precedes
in_subset: eco subset
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

starts during
type: ObjectProperty
sub property of: temporally related to
domain: occurrent
range: occurrent
definition editor: David Osumi-Sutherland
alternative term: io
in_subset: eco subset
comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))

happens during
type: ObjectProperty
sub property of: ends during
type: TransitiveProperty
definition editor: David Osumi-Sutherland
alternative term: d
alternative term: during
in_subset: eco subset
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))

ends during
type: ObjectProperty
sub property of: temporally related to
definition editor: David Osumi-Sutherland
alternative term: o
alternative term: overlaps
in_subset: eco subset
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
property chain axiom: part of
property chain axiom: has part
has curation status: pending final vetting
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
temporal interpretation: axiom holds for all times
in_subset: valid for go annotation extension
in_subset: valid for gocam
in_subset: eco subset

Axiom
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: has part
annotated target: part of
RO_0002582: true

continuous with
type: ObjectProperty
sub property of: mereotopologically related to
domain: independent continuant
range: independent continuant
has curation status: pending final vetting
definition: X continuous_with Y if and only if X and Y share a fiat boundary.
definition editor: David Osumi-Sutherland
alternative term: connected to
curator note: The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
temporal interpretation: axiom holds for all times

partially overlaps
type: ObjectProperty
sub property of: overlaps
has curation status: pending final vetting
definition: x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x
editor note: We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom
alternative term: proper overlaps
first order logic expression: (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x)))))
temporal interpretation: axiom holds for all times
in_subset: eco subset

spatially disjoint from
type: ObjectProperty
sub property of: mereotopologically related to
has curation status: pending final vetting
definition: A is spatially_disjoint_from B if and only if they have no parts in common
editor note: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
curator note: Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
expand expression to: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
temporal interpretation: axiom holds for all times
in_subset: eco subset

connected to
type: ObjectProperty
sub property of: mereotopologically related to
domain: Restriction
  on property: part of
  some values from: system
range: Restriction
  on property: part of
  some values from: system
example of usage: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
definition: a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552

connects
type: ObjectProperty
sub property of: mereotopologically related to
domain: independent continuant
range: Restriction
  on property: part of
  some values from: system
example of usage: The M8 connects Glasgow and Edinburgh
example of usage: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
definition: c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552

supplies
type: ObjectProperty
sub property of: connected to
definition: Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
editor note: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205

has component
type: ObjectProperty
sub property of: has part
has curation status: pending final vetting
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.
editor note: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
curator note: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
temporal interpretation: axiom holds for all times
in_subset: eco subset

phenotype of
type: ObjectProperty
sub property of: topObjectProperty
type: FunctionalProperty
has curation status: pending final vetting
definition: inverse of has phenotype
definition editor: Chris Mungall
in_subset: defined by inverse
in_subset: eco subset

has gene product
type: ObjectProperty
domain: continuant
range: independent continuant
example of usage: every HOTAIR lncRNA is the gene product of some HOXC gene
example of usage: every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
has curation status: pending final vetting
definition: x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y
definition editor: Chris Mungall

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: has effector activity
property chain axiom: ends with
property chain axiom: directly regulates
has curation status: pending final vetting
definition: process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
editor note: We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
definition editor: Chris Mungall
definition editor: David Hill
definition editor: Tanya Berardini
definition source: causal-relations
definition source: GO
curator note: Regulation precludes parthood; the regulatory process may not be within the regulated process.
OBO foundry unique label: regulates (processual)
elucidation: false
in_subset: valid for go annotation extension
in_subset: valid for go gp2term
in_subset: valid for go ontology
in_subset: valid for gocam

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
property chain axiom: ends with
definition: Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
definition editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: negatively regulates (process to process)
is negative form of: regulates
in_subset: valid for go annotation extension
in_subset: valid for go gp2term
in_subset: valid for go ontology
in_subset: valid for gocam

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
property chain axiom: ends with
definition: Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
definition editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: positively regulates (process to process)
is positive form of: regulates
in_subset: valid for go annotation extension
in_subset: valid for go gp2term
in_subset: valid for go ontology
in_subset: valid for gocam

has prototype
type: ObjectProperty
domain: Class
  union of: independent continuant
  union of: process
example of usage: 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
example of usage: heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
has curation status: pending final vetting
definition: x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation.
editor note: Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)
editor note: TODO: add homeomorphy axiom
editor note: This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants.
definition editor: Chris Mungall

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
example of usage: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
example of usage: osteoclast SubClassOf 'capable of' some 'bone resorption'
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
definition editor: Chris Mungall
alternative term: has function realized in
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20123131
definition source: http://www.ncbi.nlm.nih.gov/pubmed/21208450
curator note: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
expand expression to: RO_0000053 some (RO_0000054 only ?Y)
in_subset: eco subset

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: part of
definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
definition editor: Chris Mungall
alternative term: has function in
expand expression to: RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))

Axiom
annotated source: capable of part of
annotated property: propertyChainAxiom
annotated target: capable of
annotated target: part of
RO_0002582: true

actively participates in
type: ObjectProperty
sub property of: participates in
sub property of: ObsoleteProperty
inverse of: obsolete has active participant
definition: OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role
definition: x actively participates in y if and only if x participates in y and x realizes some active role
definition editor: Chris Mungall
alternative term: agent in
comment: Obsoleted as the inverse property was obsoleted.
label: obsolete actively participates in
deprecated: true

obsolete has active participant
type: ObjectProperty
sub property of: has_participant
example of usage: 'heart development' has active participant some Shh protein
has curation status: pending final vetting
definition: x has participant y if and only if x realizes some active role that inheres in y
editor note: This may be obsoleted and replaced by the original 'has agent' relation
definition editor: Chris Mungall
alternative term: has agent
imported from: http://purl.obolibrary.org/obo/ro.owl
in_subset: eco subset
label: has active participant
deprecated: true

surrounded by
type: ObjectProperty
sub property of: adjacent to
inverse of: surrounds
has curation status: pending final vetting
definition: x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
definition editor: Chris Mungall
temporal interpretation: axiom holds for all times

adjacent to
type: ObjectProperty
sub property of: spatially disjoint from
domain: independent continuant
range: independent continuant
example of usage: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
example of usage: The epidermis layer of a vertebrate is adjacent to the dermis.
example of usage: The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
example of usage: The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
has curation status: pending final vetting
definition: x adjacent to y if and only if x and y share a boundary.
editor note: This relation acts as a join point with BSPO
definition editor: Chris Mungall
temporal interpretation: axiom holds for all times

Axiom
annotated source: adjacent to
annotated property: example of usage
annotated target: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.

surrounds
type: ObjectProperty
sub property of: adjacent to
has curation status: pending final vetting
definition: inverse of surrounded by
definition editor: Chris Mungall
temporal interpretation: axiom holds for all times
in_subset: defined by inverse

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent
has curation status: pending final vetting
definition editor: Chris Mungall
definition source: Allen's interval algebra
curator note: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in_subset: eco subset
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

starts
type: ObjectProperty
sub property of: part of
sub property of: temporally related to
inverse of: starts with
has curation status: pending final vetting
definition: inverse of starts with
definition editor: Chris Mungall
definition source: Allen
in_subset: eco subset

starts with
type: ObjectProperty
sub property of: has part
sub property of: temporally related to
type: TransitiveProperty
example of usage: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
has curation status: pending final vetting
definition: x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
definition editor: Chris Mungall
alternative term: started by
in_subset: eco subset

ends
type: ObjectProperty
sub property of: part of
sub property of: temporally related to
inverse of: ends with
has curation status: pending final vetting
definition: inverse of ends with
definition editor: Chris Mungall
in_subset: eco subset

ends with
type: ObjectProperty
sub property of: has part
sub property of: temporally related to
type: TransitiveProperty
has curation status: pending final vetting
definition: x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
definition editor: Chris Mungall
alternative term: finished by
in_subset: eco subset

has start location
type: ObjectProperty
sub property of: has part that occurs in
domain: process
range: independent continuant
property chain axiom: starts with
property chain axiom: occurs in
has curation status: pending final vetting
definition: x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
definition editor: Chris Mungall
alternative term: starts with process that occurs in
in_subset: eco subset

has end location
type: ObjectProperty
sub property of: has part that occurs in
domain: process
range: independent continuant
property chain axiom: ends with
property chain axiom: occurs in
has curation status: pending final vetting
definition: x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
definition editor: Chris Mungall
alternative term: ends with process that occurs in
in_subset: eco subset

has input
type: ObjectProperty
sub property of: has_participant
inverse of: input of
domain: process
range: material entity
property chain axiom: starts with
has curation status: pending final vetting
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.
definition editor: Chris Mungall
alternative term: consumes
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: eco subset

has output
type: ObjectProperty
sub property of: has_participant
inverse of: output of
has curation status: pending final vetting
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 at the beginning of p.
definition editor: Chris Mungall
alternative term: produces
in_subset: eco subset

has exposure receptor
type: ObjectProperty
sub property of: related via exposure to
definition: A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event.
definition source: ExO:0000001

has exposure stressor
type: ObjectProperty
sub property of: has exposure stimulus
definition: A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event.
definition source: ExO:0000000

has exposure route
type: ObjectProperty
sub property of: related via exposure to
definition: A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor
definition source: ExO:0000055

has exposure transport path
type: ObjectProperty
sub property of: related via exposure to
definition: A broad relationship between an exposure event or process and the course takes from the source to the target.
definition source: http://purl.obolibrary.org/obo/ExO_0000004

related via exposure to
type: ObjectProperty
sub property of: causally related to
definition: Any relationship between an exposure event or process and any other entity.
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes.

has active ingredient
type: ObjectProperty
sub property of: has part
inverse of: active ingredient in'
domain: material entity
range: material entity
example of usage: Any portion of roundup 'has active ingredient' some glyphosate
definition: A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.
has_exact_synonym: has active substance
has_related_synonym: has active pharmaceutical ingredient

active ingredient in'
type: ObjectProperty
sub property of: part of
definition: inverse of has active ingredient
in_subset: defined by inverse

connecting branch of
type: ObjectProperty
sub property of: in branching relationship with
inverse of: has connecting branch
definition: b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.

has connecting branch
type: ObjectProperty
sub property of: in branching relationship with
definition: inverse of connecting branch of
in_subset: defined by inverse

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of
example of usage: A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
definition: c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
in_subset: valid for go gp2term

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: enables
property chain axiom: causally upstream of or within
example of usage: A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
definition: c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
has_related_synonym: affects
in_subset: valid for go gp2term

is treated by substance
type: ObjectProperty
sub property of: causally related to
inverse of: is substance that treats
definition: Inverse of 'is substance that treats'
creator: cjm
in_subset: defined by inverse

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
is positive form of: causally upstream of
creator: cjm
in_subset: valid for go annotation extension
in_subset: valid for gocam
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
is negative form of: causally upstream of
creator: cjm
comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y

has exposure stimulus
type: ObjectProperty
sub property of: related via exposure to
definition: A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event.
contributor: Austin Meier
contributor: Chris Mungall
contributor: Marie Angelique Laporte
created by: cjm
creation date: 2017-06-05T17:35:04Z

inheres in part of
type: ObjectProperty
sub property of: depends on
property chain axiom: inheres in
property chain axiom: part of
definition: q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.
editor note: Because part_of is transitive, inheres in is a sub-relation of inheres in part of
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
temporal interpretation: axiom holds for all times

Axiom
annotated source: inheres in part of
annotated property: propertyChainAxiom
annotated target: inheres in
annotated target: part of
RO_0002582: true

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
definition editor: Chris Mungall
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
temporal interpretation: axiom holds for all times

colocalizes with
type: ObjectProperty
sub property of: mereotopologically related to
domain: material entity
range: material entity
example of usage: Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
definition: a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
definition editor: Chris Mungall
definition source: http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with
curator note: In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
creator: Gene Ontology Consortium

contributes to
type: ObjectProperty
sub property of: capable of part of
sub property of: part of structure that is capable of
example of usage: ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
example of usage: Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
example of usage: eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
editor note: We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
definition editor: Chris Mungall
definition source: http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to
curator note: In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has part
property chain axiom: has component activity
example of usage: a particular instances of akt-2 enables some instance of protein kinase activity
definition editor: Chris Mungall
alternative term: catalyzes
alternative term: executes
alternative term: has
alternative term: is catalyzing
alternative term: is executing
curator note: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
curator note: This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
in_subset: valid for go gp2term

functionally related to
type: ObjectProperty
definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
definition editor: Chris Mungall
curator note: This is a grouping relation that collects relations used for the purpose of connecting structure and function

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
property chain axiom: part of
property chain axiom: capable of
definition: this relation holds between c and p when c is part of some c', and c' is capable of p.
definition editor: Chris Mungall
alternative term: false

Axiom
annotated source: part of structure that is capable of
annotated property: propertyChainAxiom
annotated target: part of
annotated target: capable of
is a defining property chain axiom: true

involved in
type: ObjectProperty
sub property of: participates in
sub property of: actively participates in
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: part of
definition: c involved_in p if and only if c enables some process p', and p' is part of p
definition editor: Chris Mungall
alternative term: actively involved in
alternative term: enables part of

regulates levels of
type: ObjectProperty
sub property of: functionally related to
domain: process
range: material entity
example of usage: every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
definition: p regulates levels of c if p regulates some amount (PATO:0000070) of c
definition editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: regulates levels of (process to entity)

enabled by
type: ObjectProperty
sub property of: has_participant
sub property of: functionally related to
definition: inverse of enables
definition editor: Chris Mungall
in_subset: valid for gocam

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
definition: inverse of regulates
definition editor: Chris Mungall
OBO foundry unique label: regulated by (processual)
in_subset: defined by inverse

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
definition editor: Chris Mungall
in_subset: defined by inverse

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
definition editor: Chris Mungall
in_subset: defined by inverse

related via localization to
type: ObjectProperty
domain: process
range: continuant
definition: A relationship that holds via some process of localization
definition editor: Chris Mungall
curator note: Do not use this relation directly. It is a grouping relation.

has target start location
type: ObjectProperty
sub property of: results in transport to from or in
definition: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
definition editor: Chris Mungall

has target end location
type: ObjectProperty
sub property of: results in transport to from or in
definition: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
definition editor: Chris Mungall

results in transport along
type: ObjectProperty
sub property of: related via localization to
definition: Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l
definition editor: Chris Mungall

results in transport across
type: ObjectProperty
sub property of: occurs across
sub property of: results in transport to from or in
definition: Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.
definition editor: Chris Mungall

results in transport to from or in
type: ObjectProperty
sub property of: related via localization to
example of usage: 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
definition editor: Chris Mungall

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 term: is member of
alternative term: member part of
definition source: SIO
temporal interpretation: axiom holds for all times

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
temporal interpretation: axiom holds for all times

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has input
definition editor: Chris Mungall
in_subset: defined by inverse
in_subset: eco subset

output of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has output
definition editor: Chris Mungall
in_subset: defined by inverse
in_subset: eco subset

formed as result of
type: ObjectProperty
sub property of: output of
definition editor: Chris Mungall

has dendrite location
type: ObjectProperty
sub property of: overlaps
definition editor: Chris Mungall
source: http://neurolex.org/wiki/Property:DendriteLocation

in branching relationship with
type: ObjectProperty
sub property of: part of
sub property of: mereotopologically related to
domain: material entity
range: material entity
has curation status: requires discussion
definition: A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
definition editor: Chris Mungall
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
curator note: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)

tributary of
type: ObjectProperty
sub property of: in branching relationship with
example of usage: Deschutes River tributary_of Columbia River
example of usage: inferior epigastric vein tributary_of external iliac vein
has curation status: requires discussion
definition: x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
definition editor: Chris Mungall
alternative term: drains into
alternative term: drains to
alternative term: tributary channel of
definition source: http://en.wikipedia.org/wiki/Tributary
definition source: http://www.medindia.net/glossary/venous_tributary.htm
curator note: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
in_subset: eco subset

distributary of
type: ObjectProperty
sub property of: in branching relationship with
example of usage: Deschutes River distributary_of Little Lava Lake
has curation status: requires discussion
definition: x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x
definition editor: Chris Mungall
alternative term: branch of
alternative term: distributary channel of
definition source: http://en.wikipedia.org/wiki/Distributary
in_subset: eco subset
comment: This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes

anabranch of
type: ObjectProperty
sub property of: distributary of
sub property of:
  inverse of: tributary of
property disjoint with: proper distributary of
property disjoint with: proper tributary of
has curation status: requires discussion
definition: x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y.
definition editor: Chris Mungall
alternative term: anastomoses with
in_subset: eco subset

spatially coextensive with
type: ObjectProperty
sub property of: overlaps
property chain axiom: located in
property chain axiom:
  inverse of: located in
example of usage: A lump of clay and a statue
definition: x spatially_coextensive_with y if and inly if x and y have the same location
definition editor: Chris Mungall
curator note: This relation is added for formal completeness. It is unlikely to be used in many practical scenarios

branching part of
type: ObjectProperty
sub property of: part of
sub property of: in branching relationship with
inverse of: has branching part
has curation status: requires discussion
definition: x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
definition editor: Chris Mungall
in_subset: eco subset

main stem of
type: ObjectProperty
sub property of: in branching relationship with
has curation status: requires discussion
definition: x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path.
definition editor: Chris Mungall
in_subset: eco subset

proper distributary of
type: ObjectProperty
sub property of: distributary of
has curation status: requires discussion
definition: x proper_distributary_of y iff x distributary_of y and x does not flow back into y
definition editor: Chris Mungall
in_subset: eco subset

proper tributary of
type: ObjectProperty
sub property of: tributary of
has curation status: requires discussion
definition: x proper_tributary_of y iff x tributary_of y and x does not originate from y
definition editor: Chris Mungall
in_subset: eco subset

has direct input
type: ObjectProperty
sub property of: has input
example of usage: 'protein catabolic process' SubClassOf has_direct_input some protein
has curation status: requires discussion
definition: p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
definition editor: Chris Mungall
alternative term: directly consumes
curator note: This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'

obsolete has indirect input
type: ObjectProperty
has curation status: requires discussion
definition editor: Chris Mungall
comment: Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
deprecated: true

obsolete has direct output
type: ObjectProperty
example of usage: translation SubClassOf has_direct_output some protein
has curation status: requires discussion
definition: p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c.
definition editor: Chris Mungall
alternative term: directly produces
deprecated: true

obsolete has indirect output
type: ObjectProperty
property chain axiom: causally upstream of
property chain axiom: obsolete has direct output
has curation status: requires discussion
definition editor: Chris Mungall
comment: Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit
deprecated: true

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
inverse of: causally upstream of
has curation status: requires discussion
definition: inverse of upstream of
definition editor: Chris Mungall

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
inverse of: immediately causally upstream of
has curation status: requires discussion
definition editor: Chris Mungall

directly activates
type: ObjectProperty
sub property of: directly positively regulates
has curation status: requires discussion
definition: p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
definition editor: Chris Mungall
alternative term: directly positively regulates
definition source: causal-relations
OBO foundry unique label: directly activates (process to process)

indirectly activates
type: ObjectProperty
sub property of: positively regulates
type: TransitiveProperty
definition: p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
definition editor: Chris Mungall
alternative term: indirectly positively regulates
is indirect form of: positively regulates

directly inhibits
type: ObjectProperty
sub property of: directly negatively regulates
definition editor: Chris Mungall
alternative term: directly negatively regulates
definition source: causal-relations
OBO foundry unique label: directly inhibits (process to process)

indirectly inhibits
type: ObjectProperty
sub property of: negatively regulates
type: TransitiveProperty
has curation status: requires discussion
definition editor: Chris Mungall
alternative term: indirectly negatively regulates
is indirect form of: negatively regulates

causally related to
type: ObjectProperty
has curation status: requires discussion
definition: This relation groups causal relations between material entities and causal relations between processes
editor note: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yiel…
definition editor: Chris Mungall
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
has curation status: requires discussion
definition: p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
definition editor: Chris Mungall
in_subset: valid for go annotation extension
in_subset: valid for gocam

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
has curation status: requires discussion
definition: p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
definition editor: Chris Mungall
is direct form of: causally upstream of

directly provides input for
type: ObjectProperty
sub property of: immediately causally upstream of
sub property of: transitively provides input for
has curation status: requires discussion
definition: p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
editor note: This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit
definition editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: directly provides input for (process to process)

transitively provides input for
type: ObjectProperty
sub property of: causally upstream of
type: TransitiveProperty
domain: process
range: process
has curation status: requires discussion
definition: transitive form of directly_provides_input_for
definition editor: Chris Mungall
curator note: This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')
OBO foundry unique label: transitively provides input for (process to process)

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
definition: p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
editor note: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
definition editor: Chris Mungall
alternative term: influences (processual)
has_related_synonym: affects

differs in
type: ObjectProperty
editor note: false
definition editor: Chris Mungall
comment: This is an exploratory relation

differs in attribute of
type: ObjectProperty
sub property of: differs in
range: Class
  union of: independent continuant
  union of: process
definition editor: Chris Mungall

differs in attribute
type: ObjectProperty
sub property of: differs in
range: specifically dependent continuant
definition editor: Chris Mungall

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
definition editor: Chris Mungall
definition source: causal-relations
in_subset: defined by inverse

involved in regulation of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' regulates some p
definition editor: Chris Mungall

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
definition editor: Chris Mungall
is positive form of: involved in regulation of

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
definition editor: Chris Mungall
is negative form of: involved in regulation of

involved in or involved in regulation of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in process
definition: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
editor note: OWL does not allow defining object properties via a Union
definition editor: Chris Mungall
alternative term: involved in or reguates

is active in
type: ObjectProperty
sub property of: overlaps
sub property of: functionally related to
property chain axiom: enables
property chain axiom: occurs in
example of usage: A protein that enables activity in a cytosol.
definition: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
definition editor: Chris Mungall
alternative term: executes activity in
has_exact_synonym: enables activity in

Axiom
annotated source: is active in
annotated property: propertyChainAxiom
annotated target: enables
annotated target: occurs in
is a defining property chain axiom: true

Axiom
annotated source: is active in
annotated property: definition
annotated target: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
database_cross_reference: GOC:cjm
database_cross_reference: GOC:dos

contributes to morphology of
type: ObjectProperty
sub property of: overlaps
definition: p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
definition editor: Chris Mungall

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: material entity
range: material entity
definition: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
editor note: Considering relabeling as 'pairwise interacts with'
editor note: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
definition editor: Chris Mungall
curator note: Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
has_exact_synonym: in pairwise interaction with
in_subset: eco subset

molecularly interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
definition: An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
definition editor: Chris Mungall
alternative term: binds
alternative term: molecularly binds with

biotically interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
domain: material entity
range: material entity
definition: An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
definition editor: Chris Mungall
alternative term: interacts with on organism level
in_subset: eco subset

participates in a abiotic-biotic interaction with
type: ObjectProperty
sub property of: biotically interacts with
example of usage: Porifiera attaches to substrate
definition: A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.
definition editor: Chris Mungall
has_related_synonym: semibiotically interacts with
in_subset: eco subset

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
editor note: Axiomatization to GO to be added later
definition editor: Chris Mungall
alternative term: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

activity directly regulates activity of
type: ObjectProperty
sub property of: molecularly interacts with
sub property of: causally influences
sub property of: regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
definition: Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
definition: The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
definition editor: Chris Mungall
definition editor: Vasundra Touré
has_exact_synonym: molecularly controls
label: directly regulates activity of

activity directly negatively regulates activity of
type: ObjectProperty
sub property of: activity directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly negatively regulates
property chain axiom: enabled by
definition: Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
definition: The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
definition editor: Chris Mungall
definition editor: Vasundra Touré
alternative term: directly inhibits
alternative term: inhibits
has_exact_synonym: molecularly decreases activity of
label: directly negatively regulates activity of

activity directly positively regulates activity of
type: ObjectProperty
sub property of: activity directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly positively regulates
property chain axiom: enabled by
definition: Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
definition: The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
definition editor: Chris Mungall
definition editor: Vasundra Touré
alternative term: activates
alternative term: directly activates
has_exact_synonym: molecularly increases activity of
label: directly positively regulates activity of

partner in
type: ObjectProperty
sub property of: participates in
definition editor: Chris Mungall
curator note: Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target

subject participant in
type: ObjectProperty
sub property of: partner in
definition editor: Chris Mungall
curator note: Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed.

target participant in
type: ObjectProperty
sub property of: partner in
definition editor: Chris Mungall
curator note: Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed.

helper property (not for use in curation)
type: ObjectProperty
definition editor: Chris Mungall
curator note: This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.

is symbiosis
type: ObjectProperty
sub property of: interaction relation helper property
definition editor: Chris Mungall

is commensalism
type: ObjectProperty
sub property of: is symbiosis
definition editor: Chris Mungall

is mutualism
type: ObjectProperty
sub property of: is symbiosis
definition editor: Chris Mungall

is parasitism
type: ObjectProperty
sub property of: is symbiosis
definition editor: Chris Mungall

is evidence for
type: ObjectProperty
sub property of: related via evidence or inference to
inverse of: has evidence
definition: A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b.
definition editor: Chris Mungall
in_subset: eco subset

composed primarily of
type: ObjectProperty
sub property of: has part
domain: material entity
range: material entity
example of usage: 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
definition: x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
temporal interpretation: axiom holds for all times
in_subset: eco subset

has part that occurs in
type: ObjectProperty
domain: occurrent
range: independent continuant
property chain axiom: has part
property chain axiom: occurs in
definition: p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
definition editor: Chris Mungall
in_subset: eco subset

Axiom
annotated source: has part that occurs in
annotated property: propertyChainAxiom
annotated target: has part
annotated target: occurs in
is a defining property chain axiom: true

is kinase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
definition editor: Chris Mungall

is ubiquitination
type: ObjectProperty
sub property of: molecular interaction relation helper property
definition editor: Chris Mungall

receives input from
type: ObjectProperty
sub property of: connected to
inverse of: sends output to
editor note: See notes for inverse relation
definition editor: Chris Mungall

sends output to
type: ObjectProperty
sub property of: connected to
editor note: This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.
definition editor: Chris Mungall

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
definition source: causal-relations

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: occurrent
range: occurrent
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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
definition editor: Chris Mungall
definition source: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

depends on
type: ObjectProperty
definition editor: Chris Mungall

towards
type: ObjectProperty
sub property of: depends on
definition: q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
editor note: This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205

has intermediate
type: ObjectProperty
sub property of: has_participant
example of usage: 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate
definition: p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c
definition editor: Chris Mungall
alternative term: has intermediate product
in_subset: eco subset

causal relation between entities
type: ObjectProperty
sub property of: causally related to
domain: continuant
domain: material entity
range: continuant
range: material entity
editor note: The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
definition editor: Chris Mungall
definition source: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
label: causal relation between material entities

determined by
type: ObjectProperty
sub property of: part of
sub property of: determined by part of
sub property of: causally influenced by
inverse of: determines
domain: system
range: material entity
example of usage: A coral reef environment is determined by a particular coral reef
definition: s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
editor note: The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/24330602
OBO foundry unique label: determined by (system to material entity)
creator: Chris Mungall
creator: Pier Buttigieg
in_subset: eco subset

determines
type: ObjectProperty
sub property of: causally influences
definition: inverse of determined by
definition editor: Chris Mungall
OBO foundry unique label: determines (material entity to system)
in_subset: defined by inverse
in_subset: eco subset

determined by part of
type: ObjectProperty
sub property of: overlaps
sub property of: causal relation between entities
domain: system
range: material entity
definition: s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
definition editor: Chris Mungall
in_subset: eco subset

transcribed from
type: ObjectProperty
domain: Class
  union of: generically dependent continuant
  union of: material entity
range: Class
  union of: generically dependent continuant
  union of: material entity
definition: x is transcribed from y if and only if x is synthesized from template y
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267

sequentially related to
type: ObjectProperty
definition: A relation that holds between two entities that have the property of being sequences or having sequences.
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect.
curator note: The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene.
cites as authority: 006650.abstract

sequentially adjacent to
type: ObjectProperty
sub property of: does not overlap sequence of
example of usage: Every UTR is adjacent to a CDS of the same transcript
example of usage: Two consecutive DNA residues are sequentially adjacent
example of usage: Two exons on a processed transcript that were previously connected by an intron are adjacent
definition: x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

has start sequence
type: ObjectProperty
sub property of: has subsequence
inverse of: is start sequence of
type: TransitiveProperty
example of usage: Every CDS has as a start sequence the start codon for that transcript
definition: x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence
definition editor: Chris Mungall
alternative term: started by
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is start sequence of
type: ObjectProperty
sub property of: is subsequence of
type: TransitiveProperty
definition: inverse of has start sequence
definition editor: Chris Mungall
alternative term: starts
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
in_subset: defined by inverse

has end sequence
type: ObjectProperty
sub property of: has subsequence
inverse of: is end sequence of
type: TransitiveProperty
example of usage: Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)
definition: x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence
definition editor: Chris Mungall
alternative term: ended by
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is end sequence of
type: ObjectProperty
sub property of: is subsequence of
type: TransitiveProperty
definition: inverse of has end sequence
definition editor: Chris Mungall
alternative term: ends
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract
in_subset: defined by inverse

is consecutive sequence of
type: ObjectProperty
sub property of: has subsequence
definition: x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y.
editor note: In the SO paper, this was defined as an instance-type relation
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is sequentially aligned with
type: ObjectProperty
sub property of: sequentially related to
type: SymmetricProperty
example of usage: Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence.
definition: x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering
definition editor: Chris Mungall
cites as authority: 006650.abstract

bounds sequence of
type: ObjectProperty
sub property of: sequentially related to
inverse of: is bound by sequence of
type: TransitiveProperty
example of usage: The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)
definition: x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y
definition editor: Chris Mungall
cites as authority: 006650.abstract

is bound by sequence of
type: ObjectProperty
sub property of: sequentially related to
type: TransitiveProperty
definition: inverse of bounds sequence of
definition editor: Chris Mungall
cites as authority: 006650.abstract
in_subset: defined by inverse

has subsequence
type: ObjectProperty
sub property of: has part
sub property of: bounds sequence of
sub property of: overlaps sequence of
inverse of: is subsequence of
type: TransitiveProperty
definition: x has subsequence y iff all of the sequence parts of x are sequence parts of y
definition editor: Chris Mungall
alternative term: contains
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
cites as authority: 006650.abstract

is subsequence of
type: ObjectProperty
sub property of: part of
sub property of: is bound by sequence of
sub property of: overlaps sequence of
type: TransitiveProperty
definition: inverse of has subsequence
definition editor: Chris Mungall
alternative term: contained by
cites as authority: 006650.abstract
in_subset: defined by inverse

overlaps sequence of
type: ObjectProperty
sub property of: overlaps
sub property of: sequentially related to
type: SymmetricProperty
definition: x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.
definition editor: Chris Mungall
cites as authority: 006650.abstract

does not overlap sequence of
type: ObjectProperty
sub property of: sequentially related to
type: SymmetricProperty
definition: x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y.
definition editor: Chris Mungall
alternative term: disconnected from
cites as authority: 006650.abstract

is upstream of sequence of
type: ObjectProperty
sub property of: does not overlap sequence of
type: TransitiveProperty
definition: inverse of downstream of sequence of
definition editor: Chris Mungall
cites as authority: 006650.abstract

is downstream of sequence of
type: ObjectProperty
sub property of: does not overlap sequence of
type: TransitiveProperty
definition: x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.
definition editor: Chris Mungall
cites as authority: 006650.abstract

is immediately downstream of sequence of
type: ObjectProperty
sub property of: sequentially adjacent to
sub property of: is downstream of sequence of
example of usage: A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript
definition: x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y
definition editor: Chris Mungall
is direct form of: is downstream of sequence of
cites as authority: 006650.abstract

is immediately upstream of sequence of
type: ObjectProperty
sub property of: sequentially adjacent to
sub property of: is upstream of sequence of
example of usage: A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript
definition: inverse of immediately downstream of
definition editor: Chris Mungall
cites as authority: 006650.abstract

has evidence
type: ObjectProperty
sub property of: related via evidence or inference to
definition: inverse of is evidence for
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/25052702
in_subset: defined by inverse
in_subset: eco subset
comment: x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x.

causally influenced by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences
definition editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: causally influenced by (entity-centric)
OBO foundry unique label: causally influenced by (material entity to material entity)

interaction relation helper property
type: ObjectProperty
sub property of: helper property (not for use in curation)
definition editor: Chris Mungall

molecular interaction relation helper property
type: ObjectProperty
sub property of: interaction relation helper property
definition editor: Chris Mungall

causally influences
type: ObjectProperty
sub property of: causal relation between entities
domain: continuant
range: continuant
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
definition: Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b
definition: The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
definition editor: Chris Mungall
definition editor: Vasundra Touré
definition source: causal-relations
OBO foundry unique label: causally influences (entity-centric)
OBO foundry unique label: causally influences (material entity to material entity)

has branching part
type: ObjectProperty
sub property of: in branching relationship with
definition: inverse of branching part of
definition editor: Chris Mungall
in_subset: defined by inverse
in_subset: eco subset

conduit for
type: ObjectProperty
sub property of: overlaps
domain: material entity
range: material entity
definition: x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.
definition editor: Chris Mungall
definition source: UBERON:cjm
curator note: This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.
in_subset: eco subset

lumen of
type: ObjectProperty
sub property of: part of
range: material entity
definition: x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
definition editor: Chris Mungall
definition source: GOC:cjm
in_subset: eco subset

luminal space of
type: ObjectProperty
sub property of: lumen of
domain: immaterial entity
definition: s is luminal space of x iff s is lumen_of x and s is an immaterial entity
definition editor: Chris Mungall
in_subset: eco subset

has modifier
type: ObjectProperty
domain: specifically dependent continuant
range: specifically dependent continuant
definition: A relation that holds between an attribute or a qualifier and another attribute.
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
curator note: This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are.
in_subset: eco subset

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
definition: Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
definition editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: directly regulates (processual)
is direct form of: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

has part structure that is capable of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: has part
property chain axiom: capable of
example of usage: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
definition: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
definition editor: Chris Mungall

results in breakdown of
type: ObjectProperty
sub property of: has input
definition: p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p

results in catabolism of
type: ObjectProperty
sub property of: results in breakdown of
definition: p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released.

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
definition: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
editor note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
definition editor: Chris Mungall
definition source: causal-relations

capable of regulating
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: regulates
example of usage: pyrethroid -> growth
definition: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
definition source: causal-relations

capable of negatively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: negatively regulates
definition: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
definition source: causal-relations

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
example of usage: renin -> arteriolar smooth muscle contraction
definition: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
definition source: causal-relations

capable of inhibiting or preventing pathological process
type: ObjectProperty
sub property of: capable of negatively regulating
example of usage: pazopanib -> pathological angiogenesis
definition: Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p.
alternative term: treats
definition source: causal-relations
curator note: The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber.

Axiom
annotated source: capable of inhibiting or preventing pathological process
annotated property: alternative term
annotated target: treats
comment: Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship

capable of upregulating or causing pathological process
type: ObjectProperty
sub property of: capable of positively regulating
example of usage: benzene -> cancer [CHEBI]
definition: Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p.
alternative term: causes disease
definition source: causal-relations

is substance that treats
type: ObjectProperty
sub property of: capable of inhibiting or preventing pathological process
definition: c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d.
alternative term: treats
definition source: causal-relations

is marker for
type: ObjectProperty
sub property of: correlated with
definition: c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d.
editor note: May be ceded to OBI

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'
definition source: causal-relations

obsolete related via dependence to
type: ObjectProperty
definition: A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
deprecated: true

correlated with
type: ObjectProperty
definition: A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
curator note: Groups both positive and negative correlation

is evidence with support from
type: ObjectProperty
sub property of: related via evidence or inference to
example of usage: An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support.
definition: A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.
comment: In the Gene Ontology association model, this corresponds to the With/From field

has model
type: ObjectProperty
inverse of: is model of
definition: Inverse of is-model-of

related via evidence or inference to
type: ObjectProperty
curator note: Do not use this relation directly. It is a grouping relation.

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
definition: Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
definition source: causal-relations
OBO foundry unique label: directly positively regulates (process to process)
is positive form of: directly regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
definition: Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
definition source: causal-relations
OBO foundry unique label: directly negatively regulates (process to process)
is negative form of: directly regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

produces
type: ObjectProperty
inverse of: produced by
domain: material entity
range: material entity
has curation status: pending final vetting
definition: a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
definition editor: Melissa Haendel
in_subset: eco subset
comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.

produced by
type: ObjectProperty
domain: material entity
range: material entity
has curation status: pending final vetting
definition: a produced_by b iff some process that occurs_in b has_output a.
definition editor: Melissa Haendel
in_subset: eco subset

represses expression of
type: ObjectProperty
sub property of: activity directly negatively regulates activity of
definition: Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b.
editor note: Logical axioms to be added after the relevant branch of GO is MIREOTed in

increases expression of
type: ObjectProperty
sub property of: activity directly positively regulates activity of
definition: Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b.
editor note: Logical axioms to be added after the relevant branch of GO is MIREOTed in

is model of
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
definition: Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.
editor note: To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?
definition editor: Matthew Brush
comment: The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest.

causes or contributes to condition
type: ObjectProperty
sub property of: causally related to
example of usage: The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.
editor note: Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.

causes condition
type: ObjectProperty
sub property of: causes or contributes to condition
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.

contributes to condition
type: ObjectProperty
sub property of: causes or contributes to condition
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.

contributes to severity of condition
type: ObjectProperty
sub property of: contributes to condition
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual.
alternative term: contributes to expressivity of condition

contributes to frequency of condition
type: ObjectProperty
sub property of: contributes to condition
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population.
alternative term: contributes to penetrance of condition

ameliorates condition
type: ObjectProperty
sub property of: contributes to severity of condition
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.
alternative term: is preventative for condition
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.

correlated with condition
type: ObjectProperty
sub property of: correlated with
definition: A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.

exacerbates condition
type: ObjectProperty
sub property of: contributes to severity of condition
definition: A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.

condition ameliorated by
type: ObjectProperty
sub property of: causally related to
definition: A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity.

condition exacerbated by
type: ObjectProperty
sub property of: causally related to
definition: A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity.

condition has genetic basis in
type: ObjectProperty
sub property of: causally related to
inverse of: is genetic basis for condition
domain: realizable entity
range: Class
  union of: process
  union of: quality
  union of: material entity
curator note: Do not use this relation directly. It is intended as a grouping for a more specific relations
created by: cjm
creation date: 2017-11-05T02:38:20Z

has material basis in gain of function germline mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal gain of function germline mutation of in
created by: cjm
creation date: 2017-11-05T02:45:20Z

has material basis in loss of function germline mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal loss of function germline mutation of in
created by: cjm
creation date: 2017-11-05T02:45:37Z

has material basis in germline mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal germline mutation in
created by: cjm
creation date: 2017-11-05T02:45:54Z

has material basis in somatic mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal somatic mutation in
created by: cjm
creation date: 2017-11-05T02:46:07Z

has major susceptibility factor
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal susceptibility factor for
created by: cjm
creation date: 2017-11-05T02:46:26Z

has partial material basis in germline mutation in
type: ObjectProperty
sub property of: condition has genetic basis in
inverse of: is causal germline mutation partially giving rise to
created by: cjm
creation date: 2017-11-05T02:46:57Z

has primary input or output
type: ObjectProperty
sub property of: has_participant
definition: p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.
created by: cjm
creation date: 2018-12-13T11:26:17Z

has primary output
type: ObjectProperty
sub property of: has output
sub property of: has primary input or output
definition: p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
created by: cjm
creation date: 2018-12-13T11:26:32Z

Axiom
annotated source: has primary output
annotated property: definition
annotated target: p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
database_cross_reference: GOC:cjm
database_cross_reference: GOC:dph
database_cross_reference: GOC:kva
database_cross_reference: GOC:pt
comment: PMID:27812932

has primary input
type: ObjectProperty
sub property of: has input
sub property of: has primary input or output
definition: p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
created by: cjm
creation date: 2018-12-13T11:26:56Z

Axiom
annotated source: has primary input
annotated property: definition
annotated target: p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
database_cross_reference: GOC:cjm
database_cross_reference: GOC:dph
database_cross_reference: GOC:kva
database_cross_reference: GOC:pt
comment: PMID:27812932

is genetic basis for condition
type: ObjectProperty
sub property of: is basis for realizable
range: realizable entity
curator note: Do not use this relation directly. It is intended as a grouping for a more specific relations
created by: cjm
creation date: 2017-11-05T02:53:08Z

is causal gain of function germline mutation of in
type: ObjectProperty
sub property of: is genetic basis for condition
definition: Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:55:51Z

is causal loss of function germline mutation of in
type: ObjectProperty
sub property of: is genetic basis for condition
definition: Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:56:06Z

is causal germline mutation in
type: ObjectProperty
sub property of: is genetic basis for condition
definition: Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:56:40Z

is causal somatic mutation in
type: ObjectProperty
sub property of: is genetic basis for condition
definition: Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:57:07Z

is causal susceptibility factor for
type: ObjectProperty
sub property of: is genetic basis for condition
definition: Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:57:43Z

is causal germline mutation partially giving rise to
type: ObjectProperty
sub property of: is genetic basis for condition
definition: Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet].
created by: cjm
creation date: 2017-11-05T02:58:43Z

realizable has basis in
type: ObjectProperty
sub property of: causally related to
inverse of: is basis for realizable
created by: cjm
creation date: 2017-11-05T03:20:01Z

is basis for realizable
type: ObjectProperty
sub property of: causally related to
created by: cjm
creation date: 2017-11-05T03:20:29Z

disease has basis in
type: ObjectProperty
sub property of: realizable has basis in
domain: disease
created by: cjm
creation date: 2017-11-05T03:26:47Z

disease has basis in disruption of
type: ObjectProperty
sub property of: disease has basis in
range: process
definition: A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process.
OBO foundry unique label: disease has basis in disruption of (disease to process)
created by: cjm
creation date: 2017-11-05T03:37:52Z

realized in response to stimulus
type: ObjectProperty
sub property of: causally related to
domain: realizable entity
range: material entity
property chain axiom: realized in response to
property chain axiom: has input
definition: A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
created by: cjm
creation date: 2017-12-26T19:45:49Z

disease has feature
type: ObjectProperty
domain: disease
definition: A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.
created by: cjm
creation date: 2017-12-26T19:50:53Z

enables subfunction
type: ObjectProperty
sub property of: functionally related to
property chain axiom: enables
property chain axiom: has part
definition: Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
created by: cjm
creation date: 2018-01-25T23:20:13Z

acts upstream of or within, positive effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, positive effect
is positive form of: acts upstream of or within
created by: cjm
creation date: 2018-01-26T23:49:30Z
in_subset: valid for go gp2term

acts upstream of or within, negative effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, negative effect
is negative form of: acts upstream of or within
created by: cjm
creation date: 2018-01-26T23:49:51Z
in_subset: valid for go gp2term

acts upstream of, positive effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, positive effect
property chain axiom: enables
property chain axiom: causally upstream of, positive effect
definition: c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
is positive form of: acts upstream of
created by: cjm
creation date: 2018-01-26T23:53:14Z
in_subset: valid for go gp2term

acts upstream of, negative effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, negative effect
property chain axiom: enables
property chain axiom: causally upstream of, negative effect
definition: c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
is negative form of: acts upstream of
created by: cjm
creation date: 2018-01-26T23:53:22Z
in_subset: valid for go gp2term

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
is negative form of: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
is positive form of: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:19Z

DEPRECATED inheres in
type: ObjectProperty
inverse of: DEPRECATED bearer of
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

has substance added
type: ObjectProperty
type: IrreflexiveProperty
domain: material entity
range: material entity
example of usage: muffin 'has substance added' some 'baking soda'
has curation status: requires discussion
definition: "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time.
editor note: The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients.
definition editor: Damion Dooley

has substance removed
type: ObjectProperty
type: IrreflexiveProperty
domain: material entity
range: material entity
example of usage: 'egg white' 'has substance removed' some 'egg yolk'
has curation status: requires discussion
definition: "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time.
definition editor: Damion Dooley

immersed in
type: ObjectProperty
type: IrreflexiveProperty
domain: material entity
range: material entity
example of usage: sardines 'immersed in' some 'oil and mustard'
has curation status: requires discussion
definition: "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance.
definition editor: Damion Dooley

has primary substance added
type: ObjectProperty
sub property of: has substance added
type: IrreflexiveProperty
example of usage: bread 'has primary substance added' some 'flour'
has curation status: requires discussion
definition: 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance.
definition editor: Damion Dooley

realized in response to
type: ObjectProperty
sub property of: causally related to
domain: realizable entity
range: process
property chain axiom: realized in
property chain axiom: causally downstream of
example of usage: A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
example of usage: An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
example of usage: Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
definition: r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
contributor: Austin Meier
contributor: Chris Mungall
contributor: David Osumi-Sutherland
contributor: Marie Angelique Laporte
has_exact_synonym: triggered by process

Axiom
annotated source: realized in response to
annotated property: has_exact_synonym
annotated target: triggered by process
database_cross_reference: RO:cjm

generically depends on
type: ObjectProperty
inverse of: is carrier of
domain: generically dependent continuant
range: independent continuant
property chain axiom: inheres in
property chain axiom: is concretized as
example of usage: Genetic information generically depend on molecules of DNA.
example of usage: The novel *War and Peace* generically depends on this copy of the novel.
example of usage: The pattern shared by chess boards generically depends on any chess board.
example of usage: The score of a symphony g-depends on a copy of the score.
example of usage: This pdf file generically depends on this server.
definition: A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
definition source: [072-ISO]
has_exact_synonym: g-depends on

is carrier of
type: ObjectProperty
domain: independent continuant
range: generically dependent continuant
property chain axiom: concretizes
property chain axiom: bearer of
example of usage: Molecules of DNA are carriers of genetic information.
example of usage: This copy of *War and Peace* is carrier of the novel written by Tolstoy.
example of usage: This hard drive is carrier of these data items.
definition: *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
definition source: [072-ISO]

regulates activity of
type: ObjectProperty
sub property of: causally influences
domain: material entity
range: material entity
definition: The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
definition editor: Vasundra Touré

in similarity relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: ECO:0000041
database_cross_reference: SO:similar_to
has_exact_synonym: sameness
has_exact_synonym: similar to
has_related_synonym: correspondence
has_related_synonym: resemblance

Axiom
annotated source: in similarity relationship with
annotated property: definition
annotated target: Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
database_cross_reference: HOM_0000000
database_cross_reference: BGEE:curator

Axiom
annotated source: in similarity relationship with
annotated property: has_related_synonym
annotated target: correspondence
database_cross_reference: http://dx.doi.org/10.1007/BF02814479

in homology relationship with
type: ObjectProperty
sub property of: in similarity relationship with
type: SymmetricProperty
property disjoint with: in homoplasy relationship with
definition: Similarity that results from common evolutionary origin.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: homologous to
comment: This broad definition encompasses all the working definitions proposed so far in the literature.

Axiom
annotated source: in homology relationship with
annotated property: definition
annotated target: Similarity that results from common evolutionary origin.
database_cross_reference: bies.950180611
database_cross_reference: jmor.1051730307
database_cross_reference: http://dx.doi.org/10.1007/BF02814480
database_cross_reference: HOM_0000001

in homoplasy relationship with
type: ObjectProperty
sub property of: in similarity relationship with
type: SymmetricProperty
definition: Similarity that results from independent evolution.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: homoplasous to
has_related_synonym: analogy

Axiom
annotated source: in homoplasy relationship with
annotated property: definition
annotated target: Similarity that results from independent evolution.
database_cross_reference: j.jhevol.2006.11.010
database_cross_reference: HOM_0000002

in homocracy relationship with
type: ObjectProperty
sub property of: in similarity relationship with
type: SymmetricProperty
definition: Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: ECO:0000075
has_exact_synonym: homocracous to
comment: Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues.

Axiom
annotated source: in homocracy relationship with
annotated property: definition
annotated target: Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
database_cross_reference: http://dx.doi.org/10.1007/BF02814484
database_cross_reference: s00427-003-0301-4
database_cross_reference: http://dx.doi.org/10.1186/1742-9994-2-15
database_cross_reference: HOM_0000003

in convergence relationship with
type: ObjectProperty
sub property of: in homoplasy relationship with
type: SymmetricProperty
definition: Homoplasy that involves different underlying mechanisms or structures.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_related_synonym: analogy
comment: Convergence usually implies a notion of adaptation.

Axiom
annotated source: in convergence relationship with
annotated property: definition
annotated target: Homoplasy that involves different underlying mechanisms or structures.
database_cross_reference: j.jhevol.2006.11.010
database_cross_reference: HOM_0000004

in parallelism relationship with
type: ObjectProperty
sub property of: in homoplasy relationship with
type: SymmetricProperty
definition: Homoplasy that involves homologous underlying mechanisms or structures.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: parallel evolution
comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage.

Axiom
annotated source: in parallelism relationship with
annotated property: definition
annotated target: Homoplasy that involves homologous underlying mechanisms or structures.
database_cross_reference: j.jhevol.2006.11.010
database_cross_reference: HOM_0000005

in structural homology relationship with
type: ObjectProperty
sub property of: in homology relationship with
type: SymmetricProperty
definition: Homology that is defined by similarity with regard to selected structural parameters.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: ECO:0000071
database_cross_reference: MI:2163
has_exact_synonym: structural homologous to
has_related_synonym: idealistic homology

Axiom
annotated source: in structural homology relationship with
annotated property: definition
annotated target: Homology that is defined by similarity with regard to selected structural parameters.
database_cross_reference: j.jhevol.2006.11.014
database_cross_reference: annurev.es.20.110189.000411
database_cross_reference: HOM_0000006
database_cross_reference: ISBN:0123195837

in historical homology relationship with
type: ObjectProperty
sub property of: in homology relationship with
type: SymmetricProperty
definition: Homology that is defined by common descent.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_broad_synonym: homology
database_cross_reference: ECO:0000080
database_cross_reference: RO_proposed_relation:homologous_to
database_cross_reference: SO:0000330
database_cross_reference: SO:0000853
database_cross_reference: SO:0000857
database_cross_reference: SO:homologous_to
database_cross_reference: TAO:homologous_to
has_exact_synonym: cladistic homology
has_exact_synonym: historical homologous to
has_exact_synonym: phylogenetic homology
has_exact_synonym: taxic homology
has_related_synonym: true homology

Axiom
annotated source: in historical homology relationship with
annotated property: definition
annotated target: Homology that is defined by common descent.
database_cross_reference: S0169-5347(97)01125-7
database_cross_reference: HOM_0000007
database_cross_reference: ISBN:0123195837

in biological homology relationship with
type: ObjectProperty
sub property of: in homology relationship with
type: SymmetricProperty
definition: Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: ECO:0000067
has_exact_synonym: biological homologous to
has_related_synonym: transformational homology
comment: Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism.

Axiom
annotated source: in biological homology relationship with
annotated property: definition
annotated target: Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
database_cross_reference: S0169-5347(97)01125-7
database_cross_reference: annurev.es.20.110189.000411
database_cross_reference: HOM_0000008

in reversal relationship with
type: ObjectProperty
sub property of: in homoplasy relationship with
type: SymmetricProperty
definition: Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: atavism
has_exact_synonym: rudiment
has_related_synonym: reversion

Axiom
annotated source: in reversal relationship with
annotated property: definition
annotated target: Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
database_cross_reference: j.jhevol.2006.11.010
database_cross_reference: HOM_0000009

in syntenic homology relationship with
type: ObjectProperty
sub property of: in structural homology relationship with
type: SymmetricProperty
definition: Structural homology that is detected by similarity in content and organization between chromosomes.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: MeSH:Synteny
database_cross_reference: SO:0000860
database_cross_reference: SO:0005858
has_exact_synonym: syntenic homologous to
has_related_synonym: synteny

Axiom
annotated source: in syntenic homology relationship with
annotated property: definition
annotated target: Structural homology that is detected by similarity in content and organization between chromosomes.
database_cross_reference: HOM_0000010
database_cross_reference: MeSH:Synteny

in paralogy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
property disjoint with: in orthology relationship with
definition: Historical homology that involves genes that diverged after a duplication event.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: SO:0000854
database_cross_reference: SO:0000859
database_cross_reference: SO:paralogous_to
has_exact_synonym: paralogous to

Axiom
annotated source: in paralogy relationship with
annotated property: definition
annotated target: Historical homology that involves genes that diverged after a duplication event.
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000011
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/5449325

in syntenic paralogy relationship with
type: ObjectProperty
sub property of: in syntenic homology relationship with
sub property of: in paralogy relationship with
type: SymmetricProperty
definition: Paralogy that involves sets of syntenic blocks.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: syntenic paralogous to
has_related_synonym: duplicon
has_related_synonym: paralogon

Axiom
annotated source: in syntenic paralogy relationship with
annotated property: definition
annotated target: Paralogy that involves sets of syntenic blocks.
database_cross_reference: 1471-213X-7-100
database_cross_reference: HOM_0000012
database_cross_reference: DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y

in syntenic orthology relationship with
type: ObjectProperty
sub property of: in syntenic homology relationship with
type: SymmetricProperty
definition: Syntenic homology that involves chromosomes of different species.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: syntenic orthologous to

Axiom
annotated source: in syntenic orthology relationship with
annotated property: definition
annotated target: Syntenic homology that involves chromosomes of different species.
database_cross_reference: gr.6380007
database_cross_reference: HOM_0000013

in partial homology relationship with
type: ObjectProperty
sub property of: in structural homology relationship with
type: SymmetricProperty
definition: Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: fractional homology
has_exact_synonym: partial homologous to
has_exact_synonym: segmental homology
has_related_synonym: mixed homology
has_related_synonym: modular homology
has_related_synonym: partial correspondence
has_related_synonym: percent homology

Axiom
annotated source: in partial homology relationship with
annotated property: definition
annotated target: Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
database_cross_reference: HOM_0000014
database_cross_reference: ISBN:0123195837
database_cross_reference: ISBN:978-0471984931

in protein structural homology relationship with
type: ObjectProperty
sub property of: in structural homology relationship with
type: SymmetricProperty
definition: Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: MeSH:Structural_Homology,_Protein
has_exact_synonym: protein structural homologous to

Axiom
annotated source: in protein structural homology relationship with
annotated property: definition
annotated target: Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
database_cross_reference: 0022-2836(76)90195-9
database_cross_reference: HOM_0000015

in non functional homology relationship with
type: ObjectProperty
sub property of: in structural homology relationship with
type: SymmetricProperty
property disjoint with: in equivalogy relationship with
definition: Structural homology that involves a pseudogenic feature and its functional ancestor.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_broad_synonym: pseudogene
database_cross_reference: SO:non_functional_homolog_of
has_exact_synonym: non functional homologous to

Axiom
annotated source: in non functional homology relationship with
annotated property: definition
annotated target: Structural homology that involves a pseudogenic feature and its functional ancestor.
database_cross_reference: HOM_0000016
database_cross_reference: SO:non_functional_homolog_of

in orthology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that involves genes that diverged after a speciation event.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: ECO:00000060
database_cross_reference: SO:0000855
database_cross_reference: SO:0000858
database_cross_reference: SO:orthologous_to
has_exact_synonym: orthologous to
comment: The term is sometimes also used for anatomical structures.

Axiom
annotated source: in orthology relationship with
annotated property: definition
annotated target: Historical homology that involves genes that diverged after a speciation event.
database_cross_reference: http://dx.doi.org/10.1007/BF02814484
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000017
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/5449325

in xenology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: xenologous to
comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis).

Axiom
annotated source: in xenology relationship with
annotated property: definition
annotated target: Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000018

in 1 to 1 homology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that involves two members sharing no other homologs in the lineages considered.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: 1 to 1 homologous to
has_exact_synonym: 1:1 homology
has_exact_synonym: one-to-one homology

Axiom
annotated source: in 1 to 1 homology relationship with
annotated property: definition
annotated target: Historical homology that involves two members sharing no other homologs in the lineages considered.
database_cross_reference: HOM_0000019
database_cross_reference: BGEE:curator

in 1 to 1 orthology relationship with
type: ObjectProperty
sub property of: in orthology relationship with
sub property of: in 1 to 1 homology relationship with
type: SymmetricProperty
definition: Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: 1 to 1 orthologous to
has_exact_synonym: 1:1 orthology
has_exact_synonym: one-to-one orthology

Axiom
annotated source: in 1 to 1 orthology relationship with
annotated property: definition
annotated target: Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
database_cross_reference: http://dx.doi.org/10.1007/BF02814484
database_cross_reference: HOM_0000020
database_cross_reference: homology method.html

in ohnology relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
definition: Paralogy that results from a whole genome duplication event.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: ohnologous to
has_related_synonym: homoeology

Axiom
annotated source: in ohnology relationship with
annotated property: definition
annotated target: Paralogy that results from a whole genome duplication event.
database_cross_reference: http://dx.doi.org/10.1038/75560
database_cross_reference: HOM_0000022

in in-paralogy relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
property disjoint with: in out-paralogy relationship with
definition: Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: in-paralogous to
has_exact_synonym: inparalogy
has_exact_synonym: symparalogy

Axiom
annotated source: in in-paralogy relationship with
annotated property: definition
annotated target: Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000023

in out-paralogy relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
definition: Paralogy that results from a duplication preceding a given speciation event.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: alloparalogy
has_exact_synonym: out-paralogous to
has_exact_synonym: outparalogy

Axiom
annotated source: in out-paralogy relationship with
annotated property: definition
annotated target: Paralogy that results from a duplication preceding a given speciation event.
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000024

in pro-orthology relationship with
type: ObjectProperty
sub property of: in 1 to many orthology relationship with
type: SymmetricProperty
definition: 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: pro-orthologous to

Axiom
annotated source: in pro-orthology relationship with
annotated property: definition
annotated target: 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
database_cross_reference: scdb.1999.0338
database_cross_reference: nrg2099
database_cross_reference: HOM_0000025

in semi-orthology relationship with
type: ObjectProperty
sub property of: in 1 to many orthology relationship with
type: SymmetricProperty
definition: 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: semi-orthologous to
comment: The converse of pro-orthologous.

Axiom
annotated source: in semi-orthology relationship with
annotated property: definition
annotated target: 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
database_cross_reference: scdb.1999.0338
database_cross_reference: nrg2099
database_cross_reference: HOM_0000026

in serial homology relationship with
type: ObjectProperty
sub property of: in iterative homology relationship with
type: SymmetricProperty
definition: Iterative homology that involves structures arranged along the main body axis.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: serial homologous to
has_related_synonym: homonomy

Axiom
annotated source: in serial homology relationship with
annotated property: definition
annotated target: Iterative homology that involves structures arranged along the main body axis.
database_cross_reference: annurev.es.20.110189.000411
database_cross_reference: HOM_0000027

in heterochronous homology relationship with
type: ObjectProperty
sub property of: in biological homology relationship with
type: SymmetricProperty
definition: Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: heterochronous homologous to
has_exact_synonym: heterochrony

Axiom
annotated source: in heterochronous homology relationship with
annotated property: definition
annotated target: Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
database_cross_reference: HOM_0000028
database_cross_reference: ISBN:978-0674639416

in paedomorphorsis relationship with
type: ObjectProperty
sub property of: in heterochronous homology relationship with
type: SymmetricProperty
property disjoint with: in peramorphosis relationship with
definition: Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: juvenification
has_exact_synonym: pedomorphosis

Axiom
annotated source: in paedomorphorsis relationship with
annotated property: definition
annotated target: Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
database_cross_reference: Pedomorphosis
database_cross_reference: HOM_0000029
database_cross_reference: ISBN:978-0674639416

in peramorphosis relationship with
type: ObjectProperty
sub property of: in heterochronous homology relationship with
type: SymmetricProperty
definition: Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated source: in peramorphosis relationship with
annotated property: definition
annotated target: Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
database_cross_reference: Peramorphosis
database_cross_reference: HOM_0000030

in progenesis relationship with
type: ObjectProperty
sub property of: in paedomorphorsis relationship with
type: SymmetricProperty
definition: Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated source: in progenesis relationship with
annotated property: definition
annotated target: Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
database_cross_reference: Progenesis
database_cross_reference: HOM_0000031
database_cross_reference: ISBN:978-0674639416

in neoteny relationship with
type: ObjectProperty
sub property of: in paedomorphorsis relationship with
type: SymmetricProperty
definition: Paedomorphosis that is produced by a retardation of somatic development.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: juvenilization
has_exact_synonym: neotenous to

Axiom
annotated source: in neoteny relationship with
annotated property: definition
annotated target: Paedomorphosis that is produced by a retardation of somatic development.
database_cross_reference: Neoteny
database_cross_reference: HOM_0000032
database_cross_reference: ISBN:978-0674639416

in mimicry relationship with
type: ObjectProperty
sub property of: in convergence relationship with
type: SymmetricProperty
definition: Convergence that results from co-evolution usually involving an evolutionary arms race.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: mimicrous to

Axiom
annotated source: in mimicry relationship with
annotated property: definition
annotated target: Convergence that results from co-evolution usually involving an evolutionary arms race.
database_cross_reference: Mimicry
database_cross_reference: HOM_0000033

in 1 to many orthology relationship with
type: ObjectProperty
sub property of: in orthology relationship with
sub property of: in 1 to many homology relationship with
type: SymmetricProperty
definition: Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: 1 to many orthologous to
has_exact_synonym: 1:many orthology
has_exact_synonym: one-to-many orthology
has_related_synonym: co-orthology
has_related_synonym: many to 1 orthology

Axiom
annotated source: in 1 to many orthology relationship with
annotated property: definition
annotated target: Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
database_cross_reference: 415741a
database_cross_reference: HOM_0000034
database_cross_reference: homology method.html

in many to many homology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that involves two members of a larger set of homologs.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: many to many homologous to
has_exact_synonym: many-to-many homology
has_exact_synonym: many:many homology

Axiom
annotated source: in many to many homology relationship with
annotated property: definition
annotated target: Historical homology that involves two members of a larger set of homologs.
database_cross_reference: msp002
database_cross_reference: HOM_0000036

in 1 to many homology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: 1 to many homologous to
has_exact_synonym: one-to-many homology
has_related_synonym: 1:many homology

Axiom
annotated source: in 1 to many homology relationship with
annotated property: definition
annotated target: Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
database_cross_reference: HOM_0000037
database_cross_reference: BGEE:curator

in apomorphy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
property disjoint with: in plesiomorphy relationship with
definition: Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: apomorphous to
has_related_synonym: synapomorphy

Axiom
annotated source: in apomorphy relationship with
annotated property: definition
annotated target: Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
database_cross_reference: HOM_0000042
database_cross_reference: ISBN:978-0252068140

in plesiomorphy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that is based on distant shared ancestry.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: plesiomorphous to
has_related_synonym: symplesiomorphy
comment: This term is usually contrasted to apomorphy.

Axiom
annotated source: in plesiomorphy relationship with
annotated property: definition
annotated target: Historical homology that is based on distant shared ancestry.
database_cross_reference: HOM_0000043
database_cross_reference: ISBN:978-0252068140

in deep homology relationship with
type: ObjectProperty
sub property of: in homocracy relationship with
sub property of: in parallelism relationship with
type: SymmetricProperty
definition: Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: deep genetic homology
has_exact_synonym: deep homologous to
has_related_synonym: generative homology
has_related_synonym: homoiology
comment: Used for structures in distantly related taxa.

Axiom
annotated source: in deep homology relationship with
annotated property: definition
annotated target: Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
database_cross_reference: http://dx.doi.org/10.1007/BF02814485
database_cross_reference: nature07891
database_cross_reference: HOM_0000044

in hemiplasy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: hemiplasous to

Axiom
annotated source: in hemiplasy relationship with
annotated property: definition
annotated target: Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
database_cross_reference: pnas.0807433105
database_cross_reference: HOM_0000045

in gametology relationship with
type: ObjectProperty
sub property of: in chromosomal homology relationship with
type: SymmetricProperty
definition: Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: gametologous to

Axiom
annotated source: in gametology relationship with
annotated property: definition
annotated target: Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
database_cross_reference: HOM_0000046
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/11110898

in chromosomal homology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: MeSH:Chromosome_Pairing
has_exact_synonym: chromosomal homologous to

Axiom
annotated source: in chromosomal homology relationship with
annotated property: definition
annotated target: Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
database_cross_reference: HOM_0000047
database_cross_reference: ISBN:0195307615

in many to many orthology relationship with
type: ObjectProperty
sub property of: in orthology relationship with
sub property of: in many to many homology relationship with
type: SymmetricProperty
definition: Orthology that involves two genes that experienced duplications more recent than the species split that created them.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: many to many orthologous to
has_exact_synonym: many-to-many orthology
has_exact_synonym: many:many orthology
has_exact_synonym: trans-orthology
has_related_synonym: co-orthology
has_related_synonym: trans-homology

Axiom
annotated source: in many to many orthology relationship with
annotated property: definition
annotated target: Orthology that involves two genes that experienced duplications more recent than the species split that created them.
database_cross_reference: 415741a
database_cross_reference: HOM_0000048
database_cross_reference: homology method.html

in within-species paralogy relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
property disjoint with: in between-species paralogy relationship with
definition: Paralogy that involves genes from the same species.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: within-species paralogous to

Axiom
annotated source: in within-species paralogy relationship with
annotated property: definition
annotated target: Paralogy that involves genes from the same species.
database_cross_reference: HOM_0000049
database_cross_reference: homology method.html

in between-species paralogy relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
definition: Paralogy that involves genes from different species.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: between-species paralogous to
comment: The genes have diverged before a speciation event.

Axiom
annotated source: in between-species paralogy relationship with
annotated property: definition
annotated target: Paralogy that involves genes from different species.
database_cross_reference: HOM_0000050
database_cross_reference: homology method.html

in postdisplacement relationship with
type: ObjectProperty
sub property of: in paedomorphorsis relationship with
type: SymmetricProperty
definition: Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: post-displacement

Axiom
annotated source: in postdisplacement relationship with
annotated property: definition
annotated target: Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
database_cross_reference: Pedomorphosis
database_cross_reference: HOM_0000051

in hypermorphosis relationship with
type: ObjectProperty
sub property of: in peramorphosis relationship with
type: SymmetricProperty
definition: Peramorphosis that is produced by a delay in the offset of development.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated source: in hypermorphosis relationship with
annotated property: definition
annotated target: Peramorphosis that is produced by a delay in the offset of development.
database_cross_reference: Peramorphosis
database_cross_reference: HOM_0000052
database_cross_reference: ISBN:978-0674639416

in synology relationship with
type: ObjectProperty
sub property of: in xenology relationship with
type: SymmetricProperty
definition: Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: synologous to

Axiom
annotated source: in synology relationship with
annotated property: definition
annotated target: Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
database_cross_reference: http://dx.doi.org/10.1007/BF00173425
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: HOM_0000053

in isoorthology relationship with
type: ObjectProperty
sub property of: in orthology relationship with
sub property of: in equivalogy relationship with
type: SymmetricProperty
definition: Orthology that involves functional equivalent genes with retention of the ancestral function.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: ECO:0000080
has_exact_synonym: isoorthologous to

Axiom
annotated source: in isoorthology relationship with
annotated property: definition
annotated target: Orthology that involves functional equivalent genes with retention of the ancestral function.
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: HOM_0000054

in tandem paralogy relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
definition: Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: tandem paralogous to
has_related_synonym: iterative paralogy
has_related_synonym: serial paralogy

Axiom
annotated source: in tandem paralogy relationship with
annotated property: definition
annotated target: Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: HOM_0000055
database_cross_reference: ISBN:978-0878932665

in latent homology relationship with
type: ObjectProperty
sub property of: in parallelism relationship with
sub property of: in syngeny relationship with
type: SymmetricProperty
definition: Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: apomorphic tendency
has_exact_synonym: cryptic homology
has_exact_synonym: latent homologous to
has_exact_synonym: underlying synapomorphy
has_related_synonym: homoiology
has_related_synonym: homoplastic tendency
has_related_synonym: re-awakening
comment: Used for structures in closely related taxa.

Axiom
annotated source: in latent homology relationship with
annotated property: definition
annotated target: Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
database_cross_reference: http://dx.doi.org/10.1007/BF02814485
database_cross_reference: j.jhevol.2006.11.010
database_cross_reference: http://dx.doi.org/10.1186/1742-9994-2-15
database_cross_reference: HOM_0000057
database_cross_reference: ISBN:0199141118

in syngeny relationship with
type: ObjectProperty
sub property of: in homocracy relationship with
type: SymmetricProperty
definition: Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: generative homology
has_exact_synonym: syngenous to
comment: Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes.

Axiom
annotated source: in syngeny relationship with
annotated property: definition
annotated target: Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
database_cross_reference: http://dx.doi.org/10.1186/1742-9994-2-15
database_cross_reference: HOM_0000058
database_cross_reference: DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R

in apparent orthology relationship with
type: ObjectProperty
sub property of: in 1 to 1 homology relationship with
sub property of: in between-species paralogy relationship with
type: SymmetricProperty
definition: Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: 1:1 paralogy
has_exact_synonym: apparent 1:1 orthology
has_exact_synonym: apparent orthologous to
has_exact_synonym: pseudoorthology
comment: The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss.

Axiom
annotated source: in apparent orthology relationship with
annotated property: definition
annotated target: Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000060
database_cross_reference: homology method.html

in pseudoparalogy relationship with
type: ObjectProperty
sub property of: in xenology relationship with
type: SymmetricProperty
definition: Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: pseudoparalogous to
comment: These genes may come out as paralogs in a single-genome analysis.

Axiom
annotated source: in pseudoparalogy relationship with
annotated property: definition
annotated target: Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000061

in equivalogy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
sub property of: in functional equivalence relationship with
type: SymmetricProperty
definition: Historical homology that involves functional equivalent genes with retention of the ancestral function.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: equivalogous to
comment: This may include examples of orthology, paralogy and xenology.

Axiom
annotated source: in equivalogy relationship with
annotated property: definition
annotated target: Historical homology that involves functional equivalent genes with retention of the ancestral function.
database_cross_reference: gkl1043
database_cross_reference: HOM_0000062

in interology relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that involves orthologous pairs of interacting molecules in different organisms.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: interologous to

Axiom
annotated source: in interology relationship with
annotated property: definition
annotated target: Historical homology that involves orthologous pairs of interacting molecules in different organisms.
database_cross_reference: gr.1774904
database_cross_reference: science.287.5450.116
database_cross_reference: HOM_0000063

in functional equivalence relationship with
type: ObjectProperty
sub property of: in similarity relationship with
type: SymmetricProperty
definition: Similarity that is characterized by interchangeability in function.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_related_synonym: functional similarity

Axiom
annotated source: in functional equivalence relationship with
annotated property: definition
annotated target: Similarity that is characterized by interchangeability in function.
database_cross_reference: http://dx.doi.org/10.1007/BF02814484
database_cross_reference: 415741a
database_cross_reference: HOM_0000065

in iterative homology relationship with
type: ObjectProperty
sub property of: in biological homology relationship with
type: SymmetricProperty
definition: Biological homology that involves parts of the same organism.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: iterative homologous to

Axiom
annotated source: in iterative homology relationship with
annotated property: definition
annotated target: Biological homology that involves parts of the same organism.
database_cross_reference: annurev.es.20.110189.000411
database_cross_reference: HOM_0000066

in paraxenology relationship with
type: ObjectProperty
sub property of: in xenology relationship with
type: SymmetricProperty
definition: Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: duplicate xenology
has_exact_synonym: multiple xenology
has_exact_synonym: paraxenologous to

Axiom
annotated source: in paraxenology relationship with
annotated property: definition
annotated target: Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
database_cross_reference: HOM_0000068
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/3065587

in plerology relationship with
type: ObjectProperty
sub property of: in paralogy relationship with
type: SymmetricProperty
definition: Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: plerologous to
comment: This phenomenon is usually due to gene conversion process.

Axiom
annotated source: in plerology relationship with
annotated property: definition
annotated target: Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
database_cross_reference: HOM_0000069
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/3065587

in homotopy relationship with
type: ObjectProperty
sub property of: in structural homology relationship with
type: SymmetricProperty
property disjoint with: in homeosis relationship with
definition: Structural homology that involves structures with the same or similar relative positions.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: homotopous to
comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use.

Axiom
annotated source: in homotopy relationship with
annotated property: definition
annotated target: Structural homology that involves structures with the same or similar relative positions.
database_cross_reference: http://dx.doi.org/10.1007/BF02814484
database_cross_reference: http://dx.doi.org/10.1007/BF02814485
database_cross_reference: HOM_0000071
database_cross_reference: ISBN:0123195837

in homeosis relationship with
type: ObjectProperty
sub property of: in biological homology relationship with
type: SymmetricProperty
definition: Biological homology that involves an ectopic structure and the normally positioned structure.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_related_synonym: heterotopy

Axiom
annotated source: in homeosis relationship with
annotated property: definition
annotated target: Biological homology that involves an ectopic structure and the normally positioned structure.
database_cross_reference: http://dx.doi.org/10.1007/BF02814485
database_cross_reference: j.cell.2008.06.030
database_cross_reference: HOM_0000072

in homoeology relationship with
type: ObjectProperty
sub property of: in ohnology relationship with
sub property of: in synology relationship with
type: SymmetricProperty
definition: Synology that results from allopolyploidy.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: homoeologous to
comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication.

Axiom
annotated source: in homoeology relationship with
annotated property: definition
annotated target: Synology that results from allopolyploidy.
database_cross_reference: pnas.0505156102
database_cross_reference: HOM_0000073

in paramorphism relationship with
type: ObjectProperty
sub property of: in homocracy relationship with
sub property of: in iterative homology relationship with
type: SymmetricProperty
definition: Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_related_synonym: axis paramorphism

Axiom
annotated source: in paramorphism relationship with
annotated property: definition
annotated target: Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
database_cross_reference: s10441-007-9023-8
database_cross_reference: j.1525-142x.2000.00054.x
database_cross_reference: HOM_0000074

in regulogy relationship with
type: ObjectProperty
sub property of: in historical homology relationship with
type: SymmetricProperty
definition: Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
creator: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
has_exact_synonym: regulogous to

Axiom
annotated source: in regulogy relationship with
annotated property: definition
annotated target: Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
database_cross_reference: gr.1774904
database_cross_reference: HOM_0000075

has measurement value
type: DatatypeProperty
type: FunctionalProperty
domain: scalar measurement datum
range: double

has x coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

has z coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

has y coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

date
type: DatatypeProperty
domain: one-dimensional temporal region
range: string
comment: The only valid string values for this property are ISO 8601 formatted date strings in extended form. It is allowable specify only the year, e.g. '2016' but only when the 1D temporal region references the entire year. Ditto for month, e.g. 2016-04 is acceptable but only if it references the entire interval of that month.

time of day
type: DatatypeProperty
domain: Class
  union of: one-dimensional temporal region
  union of: zero-dimensional temporal region
range: string
alternative term: time

has increased age-specific mortality rate
type: DatatypeProperty
range: Datatype
  on datatype: short
  with restrictions:
    min inclusive: 0
  with restrictions:
    max inclusive: 100
definition: Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.
creation date: 2018-05-22T16:43:28Z
comment: This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses.
created by: dos

Axiom
annotated source: has increased age-specific mortality rate
annotated property: definition
annotated target: Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.
database_cross_reference: PMID:24138933
database_cross_reference: Wikipedia:Infant_mortality

obsolete International Classification of Diseases
type: Class
subclass of: code set
deprecated: true

obsolete_deontic document act
type: Class
subclass of: Obsolete Class
example of usage: my filling in an immigration form, a judge's signing and stamping a court order
definition: A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document.
definition editor: Mathias Brochhausen
has obsolescence reason: placeholder removed
deprecated: true

software development
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      union of: software
      union of: source code module
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: software
    union of: source code module
definition: A planned process that has specified output a software product and that involves the creation of source code.
definition editor: Mathias Brochhausen
definition editor: William R. Hogan
definition source: http://en.wikipedia.org/wiki/Software_development
elucidation: A planned process resulting in a software product involving the creation of source code.

count
type: Class
equivalent class: Class
  intersection of: data item
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: counting
subclass of: measurement datum
subclass of: Restriction
  on property: is_specified_output_of
  some values from: counting
definition: A measurement datum that is the output of counting.
definition editor: Mathias Brochhausen
elucidation: A measurement datum that is the output of counting.

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
subclass of: Restriction
  on property: has_specified_output
  some values from: count
definition: The planned process of finding the number of elements in a finite set of objects.
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Counting
elucidation: The planned process of finding the number of elements in a finite set of objects.

name of temporal interval
type: Class
subclass of: name of temporal region
definition: A name of temporal region that specifies a time span on a specified time scale by giving a start time and a duration.
definition editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl
elucidation: An information content entity that specifies a time span on a specified time scale by giving a start time and a duration.
Unique Apollo Label: TimeSpanCategoryDefinition

name of a temporal boundary
type: Class
subclass of: name of temporal region
definition: A name of temporal region that designates a temporal boundary
definition editor: Matthew Diller
definition editor: William R. Hogan
imported from: http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl
elucidation: An information content entity that designates a temporal boundary
Unique Apollo Label: RealTimePointCategoryDefinition

name of temporal region
type: Class
subclass of: identifier
imported from: http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl

date
type: Class
subclass of: name of temporal region
definition: A name of a temporal region that is systematized according to a particular calendar system, such as the Gregorian calendar.
definition editor: Matthew Diller
definition editor: William R. Hogan
imported from: http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl
elucidation: A name of a temporal region that is systematized according to a particular calendar system, such as the Gregorian calendar.
Unique Apollo Label: date

geographical migration of organism
type: Class
subclass of: behavior
definition: A behavior of one or more organisms that is characterized by the displacement from one geographic region to some target geographic region, and is the realization of either a biological function or (a concretization of) an objective specification.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A behavior of one or more organisms that is characterized by the displacement from one geographic region to some target geographic region, and is the realization of either a biological function or (a concretization of) an objective specification.

source code repository
type: Class
subclass of: document
subclass of: Restriction
  on property: has part
  some values from: source code module
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      some values from: source code module
editor preferred term: software source code version control repository
definition: A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc.
definition editor: William R. Hogan
comment: Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based

compiling software
type: Class
subclass of: software development
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      union of: software
      union of: source code module
  intersection of: Restriction
    on property: has_specified_output
    some values from: software
editor preferred term: process of compiling software
definition: A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions.
definition editor: William R. Hogan
comment: It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.).
comment: Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code.

human travel
type: Class
subclass of: geographical migration of organism
definition: A geographical migration of an organism belonging to the species Homo sapiens.
definition editor: Matthew Diller
definition editor: William R. Hogan

dataset creating
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has_specified_output
    some values from: data set
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: data set
editor preferred term: creating a data set
definition: A planned process that has a data set as its specified output.
definition editor: William R. Hogan
alternative term: data set creation
alternative term: dataset creation

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
subclass of: Restriction
  on property: part of
  all values from: continuant
subclass of: Restriction
  on property: in similarity relationship with
  all values from: continuant
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
subclass of: Restriction
  on property: part of
  all values from: occurrent
subclass of: Restriction
  on property: in similarity relationship with
  all values from: occurrent
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
subclass of: Restriction
  on property: part of
  all values from: independent 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

obsolete dependent continuant
type: Class
subclass of: Obsolete Class
definition: A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
deprecated: true

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: 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

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

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)
imported from: ido.owl
imported from: omrse.owl
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.
imported from: ido.owl
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
subclass of: Restriction
  on property: part of
  all values from: realizable entity
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
subclass of: Restriction
  on property: part of
  all values from: quality
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
subclass of: Restriction
  on property: part of
  all values from: specifically dependent continuant
disjoint with: generically dependent continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
editor preferred term: specifically dependent continuant
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 relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
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.
imported from: ido.owl
imported from: omrse.owl
imported from: pato.owl
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.
imported from: omrse.owl
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
subclass of: Restriction
  on property: part of
  all values from: generically dependent 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
disjoint with: Restriction
  on property: part of
  some values from: 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.
imported from: ido.owl
imported from: omrse.owl
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
disjoint with: Restriction
  on property: has part
  some values from: material entity
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 term: 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

temporal interval
type: Class
subclass of: one-dimensional temporal region
imported from: http://purl.obolibrary.org/obo/bfo/2020/bfo.owl
definition: (Elucidation) a temporal interval is a one-dimensional temporal region that is continuous, thus without gaps or breaks
example: The year 2018.
scope note: A one-dimensional temporal region can include as parts not only temporal intervals but also temporal instants separated from other parts by gaps.

temporal instant
type: Class
subclass of: zero-dimensional temporal region
imported from: http://purl.obolibrary.org/obo/bfo/2020/bfo.owl
definition: (Elucidation) a temporal instant is a zero-dimensional temporal region that has no proper temporal part
example: The millennium.

mesoscopic physical object
type: Class
subclass of: object
definition: An environmental feature that is, or can be, contained and is predominantly composed of one or a few types of stuff.
definition: An object which is large enough to be visible to humans, but small enough that humans can handle the object (i.e. transport it, examine it, etc) in its entirety with little to no technological assistance.
alternative term: mesoscopic physical object
imported from: http://purl.obolibrary.org/obo/envo.owl
database_cross_reference: MA:ma
comment: This is a legacy class from ENVO's early versions. It will be depopulated and filled in by inference using a PATO quality. Not to be confused with "mesoscopic" as defined in physics, which deals with objects typically between 10e-6 and 10-8 meters in diameter.
comment: https://en.oxforddictionaries.com/definition/mesoscopic
label: physical object of mesoscopic geological size

manufactured product
type: Class
subclass of: anthropogenic abiotic mesoscopic feature
definition: A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products.
imported from: http://purl.obolibrary.org/obo/envo.owl
has_exact_synonym: manufactured good
comment: https://en.wikipedia.org/wiki/Manufactured_product

anthropogenic abiotic mesoscopic feature
type: Class
subclass of: abiotic mesoscopic physical object
imported from: http://purl.obolibrary.org/obo/envo.owl
has_obo_namespace: ENVO
id: ENVO:00003075

abiotic mesoscopic physical object
type: Class
subclass of: mesoscopic physical object
imported from: http://purl.obolibrary.org/obo/envo.owl
has_obo_namespace: ENVO
id: ENVO:01000010

environmental system
type: Class
subclass of: system
definition: A system which has the disposition to environ one or more material entities.
imported from: http://purl.obolibrary.org/obo/envo.owl
creation date: 2013-09-23T16:04:08Z
database_cross_reference: DOI:10.1186/2041-1480-4-43
database_cross_reference: EcoLexicon:environment
has_exact_synonym: environment
comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.

vehicle
type: Class
subclass of: manufactured product
definition: A vehicle is a mobile machine which transports people or cargo.
imported from: http://purl.obolibrary.org/obo/envo.owl
database_cross_reference: https://en.wikipedia.org/wiki/Vehicle

Anatomical cluster
type: Class
subclass of: Anatomical structure

vocal fold
type: Class
subclass of: Subdivision of larynx

Subdivision of larynx
type: Class
subclass of: Heterogeneous cluster

Heterogeneous cluster
type: Class
subclass of: Anatomical cluster

Anatomical structure
type: Class
subclass of: Material anatomical entity

Material anatomical entity
type: Class
subclass of: material entity

geographic location
type: Class
subclass of: site
type: NamedIndividual
definition: A reference to a place on the Earth, by its name or by its geographical location.
imported from: gaz.owl

molecular_function
type: Class
subclass of: process
OBO foundry unique label: molecular process

catalytic activity
type: Class
subclass of: molecular_function

behavior
type: Class
subclass of: response to stimulus
definition: The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
database_cross_reference: Wikipedia:Behavior
comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).

Axiom
annotated source: behavior
annotated property: definition
annotated target: The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
database_cross_reference: GOC:ems
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0395448956
database_cross_reference: PMID:20160973

biological_process
type: Class
subclass of: process
disjoint with: planned process
definition: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
database_cross_reference: Wikipedia:Biological_process
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.

Axiom
annotated source: biological_process
annotated property: definition
annotated target: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
database_cross_reference: GOC:pdt

kinase activity
type: Class
subclass of: transferase activity, transferring phosphorus-containing groups
subclass of: Restriction
  on property: is kinase activity
  has self: true

transferase activity
type: Class
subclass of: catalytic activity

transferase activity, transferring phosphorus-containing groups
type: Class
subclass of: transferase activity

response to stimulus
type: Class
subclass of: biological_process

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.
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
definition source: OBI_0000349

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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot

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?
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Barry Smith
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
alternative term: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217

narrative object
type: Class
subclass of: information content entity
editor preferred term: narrative object
example of usage: Examples of narrative objects are reports, journal articles, and patents submission.
has curation status: metadata incomplete
definition: A narrative object is an information content entity that is a set of propositions.
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
editor note: agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
definition editor: person:Chris Stoeckert
definition source: OBI_0000013
definition source: group:OBI

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.
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch

obsolete_artifact
type: Class
subclass of: Obsolete Class
has obsolescence reason: failed exploratory term
deprecated: true

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
definition 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.

software
type: Class
subclass of: plan specification
editor preferred term: software
has curation status: metadata complete
definition: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
editor note: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Melanie Courtot
definition source: GROUP: OBI

obsolete2_digital entity
type: Class
subclass of: Obsolete Class
editor preferred term: obsolete_digital entity
definition: A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality'
definition editor: person:Chris Stoeckert
definition source: OBI_0000261
definition source: group:OBI
has obsolescence reason: failed exploratory term
deprecated: true

journal article
type: Class
subclass of: report
subclass of: publication
subclass of: Restriction
  on property: is_specified_output_of
  some values from: publishing process
subclass of: Restriction
  on property: is_specified_output_of
  all values from: publishing process
editor preferred term: journal article
example of usage: Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
has curation status: metadata complete
definition: A report that is published in a journal.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition source: OBI_0000159
definition source: group:OBI

information carrier
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: concretizes
    some values from: information content entity
subclass of: quality
subclass of: Restriction
  on property: concretizes
  some values from: information content entity
editor preferred term: information carrier
example of usage: In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
has curation status: pending final vetting
definition: A quality of an information bearer that imparts the information content
editor note: 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
editor note: 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
definition editor: PERSON: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

model number
type: Class
subclass of: symbol
editor preferred term: model number
has curation status: pending final vetting
definition: A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
editor note: manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
definition editor: Person: Alan Ruttenberg

obsolete_material_entity
type: Class
subclass of: Obsolete Class
has obsolescence reason: placeholder removed
deprecated: true

obsolete2_binary digital entity
type: Class
subclass of: Obsolete Class
editor preferred term: binary digital entity
example of usage: MS Word document, ZIP file, DICOM file, JPEG file
definition: A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity'
editor note: digital_entity
definition editor: person:Chris Stoeckert
definition source: OBI_0000244
definition source: group:OBI
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_unit of measure
type: Class
subclass of: Obsolete Class
example of usage: The length of a ruler.
definition: a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
definition editor: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
has obsolescence reason: failed exploratory term
deprecated: true

programming language
type: Class
subclass of: plan specification
editor preferred term: programming language
example of usage: R, Perl, Java
has curation status: metadata complete
definition: A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
definition source: OBI_0000058
definition source: group:OBI

data item
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: Homo sapiens
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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
alternative term: data

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).
definition editor: PERSON: James A. Overton
definition editor: PERSON: Jonathan Rees
definition source: based on Oxford English Dictionary

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

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
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.
definition editor: PERSON: Chris Stoeckert
definition source: OBI_0000142

integer numeral
type: Class
subclass of: numeral
editor preferred term: integer numeral
has curation status: metadata incomplete
definition: A numeral that denotes an integer
definition editor: PERSON: Jonathan Rees

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable 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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters

time trigger
type: Class
subclass of: conditional specification
editor preferred term: time trigger
has curation status: uncurated
definition editor: PlanAndPlannedProcess Branch

obsolete_study interpretation
type: Class
subclass of: Obsolete Class
editor preferred term: obsolete_study interpretation
has curation status: pending final vetting
definition: A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses
editor note: 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application."
editor note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
editor note: The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead.
definition editor: Lawrence Hunter
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Jennifer Fostel
definition editor: PERSON: Melanie Courtot
alternative term: conclusion
definition source: OBI_0000005
has obsolescence reason: failed exploratory term
deprecated: true

dot plot
type: Class
subclass of: graph
editor preferred term: dot plot
example of usage: Dot plot of SSC-H and FSC-H.
has curation status: example to be eventually removed
definition: A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
definition source: OBI_0000123
definition source: group:OBI

graph
type: Class
subclass of: diagram
editor preferred term: graph
has curation status: pending final vetting
definition: A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
definition editor: PERSON: Lawrence Hunter
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson Lister
definition source: OBI_0000240
definition source: group:OBI

obsolete2_text based digital entity
type: Class
subclass of: Obsolete Class
editor preferred term: text based digital entity
example of usage: XML file, C++ source code file
definition: A text based digital entity is a digital entity that is encoded so that it only contains text characters.
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document'
editor note: digital_entity
definition editor: person:Chris Stoeckert
definition source: OBI_0000132
definition source: group:OBI
has obsolescence reason: failed exploratory term
deprecated: true

rule
type: Class
subclass of: conditional specification
editor preferred term: rule
example of usage: example to be added
has curation status: metadata incomplete
definition: A rule is an executable which guides, defines, restricts actions.
editor note: MSI
definition editor: PRS
definition source: OBI_0500021
definition source: PRS

contour plot
type: Class
subclass of: graph
editor preferred term: contour plot
example of usage: Contour plot of SSC-H, FSC-H, and FL1-H.
has curation status: example to be eventually removed
editor note: generically_dependent_continuants
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
definition source: OBI_0000246
definition source: group:Flow Cytometry community

obsolete2_report figure
type: Class
subclass of: Obsolete Class
editor preferred term: report figure
has curation status: uncurated
definition: A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
editor note: I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report
editor note: Replaced by defined version of figure
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson Lister
definition source: OBI_0000027
definition source: group:OBI
has obsolescence reason: failed exploratory term
deprecated: true

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.
definition editor: Philippe Rocca-Serra
definition editor: PlanAndPlannedProcess Branch
definition source: OBI_0000270
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)

software interpreter
type: Class
subclass of: algorithm
editor preferred term: software interpreter
example of usage: R program, Perl interpreter, Java virtual machine
has curation status: metadata complete
definition: A software interpreter is a software application that executes some specified input software.
editor note: Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
definition source: OBI_0000199
definition source: group:OBI

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)
definition editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266

density plot
type: Class
subclass of: graph
editor preferred term: density plot
example of usage: Density plot of SSC-H and FSC-H.
has curation status: example to be eventually removed
definition: A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
definition source: OBI_0000179
definition source: group:Flow Cytometry community

report
type: Class
subclass of: document
editor preferred term: report
example of usage: Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
has curation status: pending final vetting
definition: A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record).
editor note: 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.
editor note: 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
editor note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
editor note: disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Melanie Courtot
definition source: GROUP: OBI
definition source: OBI_0000099

obsolete_report element
type: Class
subclass of: Obsolete Class
editor preferred term: report element
has curation status: metadata complete
definition: A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page).
editor note: 2009-03-16: needs some more work (clarify relations).
editor note: 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.
editor note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
editor note: Replaced by textual entity and figure
editor note: There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Allyson Lister
definition editor: PERSON: Melanie Courtot
definition source: GROUP:OBI
definition source: OBI_0000001
has obsolescence reason: failed exploratory term
deprecated: true

obsolete2_binary executable
type: Class
subclass of: Obsolete Class
editor preferred term: binary executable
definition: Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity'
definition editor: person:Jennifer Fostel
definition source: OBI_0000222
definition source: group:OBI
has obsolescence reason: failed exploratory term
deprecated: true

source code module
type: Class
subclass of: directive information entity
editor preferred term: source code module
example of usage: The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
has curation status: metadata incomplete
definition: A source code module is a directive information entity that specifies, using a programming language, some algorithm.
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
definition source: OBI_0000039
definition source: group:OBI

obsolete_report table
type: Class
subclass of: Obsolete Class
editor preferred term: report table
has curation status: example to be eventually removed
definition: A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson Lister
definition source: OBI_0000265
definition source: group:OBI
has obsolescence reason: failed exploratory term
deprecated: true

data format specification
type: Class
subclass of: directive information entity
editor preferred term: data format specification
has curation status: metadata incomplete
definition: A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
editor note: 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
definition editor: PERSON: Alan Ruttenberg
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
definition source: OBI_0000187

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.
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
definition source: OBI_0000042
definition source: group:OBI

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.
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson
definition editor: person:Chris Stoeckert
definition source: OBI_0000030
definition source: group:OBI

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
definition editor: Person:Alan Ruttenberg

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: objective specification
subclass of: Restriction
  on property: has part
  some values from: action specification
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 that, when concretized, 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: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
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

obsolete2_digital document
type: Class
subclass of: Obsolete Class
editor preferred term: digital document
definition: A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'
definition editor: person:Jennifer Fostel
definition source: OBI_0000195
definition source: group:OBI
has obsolescence reason: failed exploratory term
deprecated: true

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?
definition editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI

obsolete_identifier
type: Class
subclass of: Obsolete Class
has curation status: organizational term
editor note: _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.
has obsolescence reason: placeholder removed
deprecated: true

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
definition editor: GROUP: IAO

serial number
type: Class
subclass of: symbol
editor preferred term: serial number
has curation status: metadata incomplete
definition: A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
editor note: Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
definition editor: GROUP: IAO

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.
definition editor: GROUP: IAO
alternative term: batch number

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.

obsolete_digital quality
type: Class
subclass of: Obsolete Class
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
editor note: Need to rework digital entity. Digital quality was suggested by Barry.
has obsolescence reason: failed exploratory term
deprecated: true

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
definition editor: Person:Alan Ruttenberg

material information bearer
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: bearer of
    some values from: Restriction
      on property: concretizes
      some values from: information content entity
subclass of: material entity
subclass of: Restriction
  on property: bearer of
  some values from: Restriction
    on property: concretizes
    some values from: information content 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.
definition editor: GROUP: IAO

histogram
type: Class
subclass of: graph
editor preferred term: histogram
has curation status: ready for release
definition: A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBI

heatmap
type: Class
subclass of: graph
editor preferred term: heatmap
has curation status: ready for release
definition: A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBI

Venn diagram
type: Class
subclass of: graph
editor preferred term: Venn diagram
has curation status: ready for release
definition: A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Venn_diagram

obsolete_survival curve
type: Class
subclass of: Obsolete Class
editor preferred term: obsolete_survival curve
has curation status: ready for release
definition: A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://www.graphpad.com/www/book/survive.htm
has obsolescence reason: failed exploratory term
deprecated: true

dendrogram
type: Class
subclass of: graph
editor preferred term: dendrogram
example of usage: Dendrograms are often used in computational biology to illustrate the clustering of genes.
has curation status: ready for release
definition: A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Dendrogram

scatter plot
type: Class
subclass of: graph
editor preferred term: scatter plot
example of usage: Comparison of gene expression values in two samples can be displayed in a scatter plot
has curation status: ready for release
definition: A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
alternative term: scattergraph
definition source: WEB: http://en.wikipedia.org/wiki/Scatterplot

photograph
type: Class
subclass of: image
has curation status: ready for release
definition: A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Joanne Luciano
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wiktionary.org/wiki/photograph

photographic print
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: bearer of
    some values from: Restriction
      on property: concretizes
      some values from: photograph
subclass of: material information bearer
subclass of: Restriction
  on property: bearer of
  some values from: Restriction
    on property: concretizes
    some values from: photograph
editor preferred term: photographic print
has curation status: pending final vetting
definition: A photographic print is a material entity upon which a photograph generically depends.
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot

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
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.
definition editor: PERSON: Alan Ruttenberg
definition 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.
definition editor: PERSON: Lawrence Hunter
alternative term: text

citation
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: document
editor preferred term: citation
example of usage: Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
has curation status: pending final vetting
definition: A textual entity intended to identify a particular publication.
definition editor: PERSON: Lawrence Hunter

author identification
type: Class
subclass of: written name
editor preferred term: author identification
example of usage: L. Hunter
has curation status: pending final vetting
definition: A textual entity intended to identify a particular author
definition editor: PERSON: Lawrence Hunter

institutional identification
type: Class
subclass of: textual entity
editor preferred term: institutional identification
example of usage: University of Colorado Denver School of Medicine
has curation status: pending final vetting
definition: A textual entity intended to identify a particular institution
definition editor: PERSON: Lawrence Hunter

caption
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: figure
editor preferred term: caption
example of usage: Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
has curation status: pending final vetting
definition: A textual entity that describes a figure
definition editor: PERSON: Lawrence Hunter

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
definition editor: PERSON: Lawrence Hunter

table
type: Class
subclass of: textual entity
editor preferred term: table
example of usage: | T F --+----- T | T F F | F F
has curation status: pending final vetting
definition: A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
definition editor: PERSON: Lawrence Hunter

table of abbreviations
type: Class
subclass of: table
editor preferred term: table of abbreviations
example of usage: IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
has curation status: pending final vetting
definition: A table where the constituent texts are abbreviations and their expansions
definition editor: PERSON: Lawrence Hunter

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.
definition editor: PERSON: Lawrence Hunter

diagram
type: Class
subclass of: figure
editor preferred term: diagram
example of usage: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
has curation status: metadata complete
definition: A figure that expresses one or more propositions
definition editor: PERSON: Lawrence Hunter

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
definition editor: PERSON: Lawrence Hunter

publication
type: Class
equivalent class: Class
  intersection of: document
  intersection of: Restriction
    on property: is_specified_output_of
    all values from: publishing process
subclass of: document
editor preferred term: publication
example of usage: journal article, newspaper story, book, etc.
has curation status: metadata complete
definition: A document that is the output of a publishing process.
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
definition editor: PERSON: Lawrence Hunter
alternative term: published document
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/232
comment: Revisit the term in Octorber 2020. Improve the defintion.

publication about an investigation
type: Class
subclass of: publication
subclass of: Restriction
  on property: is about
  some values from: investigation
editor preferred term: publication about an investigation
example of usage: Most scientific journal articles
has curation status: metadata complete
definition: A publication that is about an investigation
definition editor: PERSON: Lawrence Hunter
alternative term: scientific publication

patent
type: Class
subclass of: document
editor preferred term: patent
example of usage: US Patent 6,449,603
has curation status: metadata complete
definition: A document that has been accepted by a patent authority
definition editor: PERSON: Lawrence Hunter

document part
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: part of
  some values from: document
editor preferred term: document part
example of usage: An abstract, introduction, method or results section.
has curation status: metadata complete
definition: An information content entity that is part of a document.
definition editor: PERSON: Lawrence Hunter

abstract
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document
editor preferred term: abstract
example of usage: The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.
has curation status: metadata complete
definition: A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
definition editor: PERSON: Lawrence Hunter
alternative term: precis
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

introduction to a publication about an investigation
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: objective specification
editor preferred term: introduction to a publication about an investigation
example of usage: Section labelled 'introduction' of a typical scientific journal article
has curation status: metadata complete
definition: A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
definition editor: PERSON: Lawrence Hunter
alternative term: background
alternative term: introduction
alternative term: overview
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

methods section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: study design
editor preferred term: methods section
example of usage: The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
has curation status: metadata complete
definition: A part of a publication about an investigation that is about the study design of the investigation
definition editor: PERSON: Lawrence Hunter
alternative term: experimental
alternative term: experimental methods
alternative term: experimental procedures
alternative term: experimental section
alternative term: method
alternative term: methodology
alternative term: methods
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

results section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: study design execution
editor preferred term: results section
example of usage: The section labelled 'results' in a typical scientific journal article
has curation status: metadata complete
definition: A part of a publication about an investigation that is about a study design execution
definition editor: PERSON: Lawrence Hunter
alternative term: results

discussion section of a publication about an investigation
type: Class
subclass of: document part
editor preferred term: discussion section of a publication about an investigation
has curation status: metadata complete
definition: A part of a publication about an investigation that is about the study interpretation of the investigation
definition editor: PERSON: Lawrence Hunter
alternative term: discussion
alternative term: discussion section
alternative term: discussions
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

references section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: citation
editor preferred term: references section
example of usage: The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
has curation status: metadata complete
definition: A part of a document that has citations as parts
definition editor: PERSON: Lawrence Hunter
alternative term: literature cited
alternative term: reference
alternative term: reference list
alternative term: references
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

author list
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: author identification
editor preferred term: author list
example of usage: Lawrence Hunter and Kevin Brettonel Cohen
has curation status: metadata complete
definition: A part of a document that enumerates the authors of the document
definition editor: PERSON: Lawrence Hunter

institution list
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: institutional identification
editor preferred term: institution list
example of usage: The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
has curation status: metadata complete
definition: A part of a document that has parts that are institution identifications associated with the authors of the document
definition editor: PERSON: Lawrence Hunter

author contributions section
type: Class
subclass of: document part
editor preferred term: author contributions section
example of usage: LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript.
has curation status: metadata complete
definition: A part of a publication that is about the specific contributions of each author
definition editor: PERSON: Lawrence Hunter
alternative term: author contributions
alternative term: authors' contribution
alternative term: authors' contributions
alternative term: authors' roles
alternative term: contributions by the authors
alternative term: contributorship
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

acknowledgements section
type: Class
subclass of: document part
editor preferred term: acknowledgements section
example of usage: The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
has curation status: metadata complete
definition: Part of a publication that is about the contributions of people or institutions other than the authors.
definition editor: PERSON: Lawrence Hunter
alternative term: acknowledgement
alternative term: acknowledgements
alternative term: acknowledgment
alternative term: acknowledgments
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

footnote
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document part
editor preferred term: footnote
example of usage: The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.
has curation status: metadata complete
definition: A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.
definition editor: PERSON: Lawrence Hunter
alternative term: endnote
alternative term: footnotes
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

supplementary material to a document
type: Class
subclass of: document part
editor preferred term: supplementary material to a document
has curation status: metadata complete
definition: A part of a document that is segregated from the rest of the document due to its size
definition editor: PERSON: Lawrence Hunter
alternative term: additional file
alternative term: additional files
alternative term: additional information
alternative term: appendix
alternative term: electronic supplementary material
alternative term: electronic supplementary materials
alternative term: supplemental data
alternative term: supplemental information
alternative term: supplemental material
alternative term: supplementary data
alternative term: supplementary files
alternative term: supplementary information
alternative term: supplementary material
alternative term: supplementary materials
alternative term: supporting information
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

table of contents
type: Class
subclass of: table
editor preferred term: table of contents
has curation status: pending final vetting
definition: A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred).
definition editor: PERSON: Lawrence Hunter

table of figures
type: Class
subclass of: table
editor preferred term: table of figures
has curation status: pending final vetting
definition: A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred).
definition editor: PERSON: Lawrence Hunter

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
definition editor: PERSON: Lawrence Hunter

copyright section
type: Class
subclass of: document part
editor preferred term: copyright section
example of usage: This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
has curation status: metadata complete
definition: A document part that describes legal restrictions on making or distributing copies of the document
definition editor: PERSON: Lawrence Hunter

cartesian spatial coordinate datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: denotes
  some values from: zero-dimensional spatial region
subclass of: Restriction
  on property: has coordinate unit label
  cardinality: 1
has curation status: metadata complete
definition: A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
editor note: 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
definition editor: Alan Ruttenberg
curator note: AR notes: We need to discuss whether it should include site.

one dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero-dimensional spatial region
    intersection of: Restriction
      on property: part of
      some values from: one-dimensional spatial region
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
has curation status: metadata incomplete
definition: A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
definition editor: Alan Ruttenberg

two dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero-dimensional spatial region
    intersection of: Restriction
      on property: part of
      some values from: two-dimensional spatial region
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
has curation status: metadata incomplete
definition: A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
definition editor: Alan Ruttenberg

three dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero-dimensional spatial region
    intersection of: Restriction
      on property: part of
      some values from: three-dimensional spatial region
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has z coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
has curation status: metadata incomplete
definition: A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
definition editor: Alan Ruttenberg

length measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: length unit
subclass of: Restriction
  on property: is quality measurement of
  some values from: length
has curation status: metadata incomplete
definition: A scalar measurement datum that is the result of measurement of length quality
definition editor: Alan Ruttenberg

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.
definition editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters

mass measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: mass unit
  intersection of: Restriction
    on property: is quality measurement of
    all values from: mass
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
definition editor: Person:Alan Ruttenberg

hypothesis textual entity
type: Class
subclass of: textual entity
editor preferred term: hypothesis 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 an assertion that is intended to be tested.
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition editor: Person:Alan Ruttenberg

time measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: time unit
  intersection of: Restriction
    on property: is duration of
    all values from: process
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
definition editor: Person:Alan Ruttenberg

postal address
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: geographic location
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

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
definition editor: Person:Alan Ruttenberg
definition editor: Person:Chris Stoeckart

author role
type: Class
subclass of: role
editor preferred term: author role
has curation status: pending final vetting
definition: A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot

data item extraction from journal article
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: journal article
subclass of: Restriction
  on property: has_specified_output
  some values from: data item
has curation status: metadata complete
definition: A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
definition editor: Person:Alan Ruttenberg

publishing process
type: Class
subclass of: planned process
has curation status: metadata complete
definition: A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free.
definition editor: Person: Jie Zheng
definition source: https://en.wikipedia.org/wiki/Publishing
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/232
ontology term requester: VEuPathDB

document in preparation for publication
type: Class
subclass of: document
has curation status: metadata complete
definition: A document that is in preparation for submission to be published.
definition editor: PERSON: Jie Zheng
definition source: EFO_0001795 in preparation
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/232
ontology term requester: VEuPathDB

documenting
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
subclass of: Restriction
  on property: has_specified_output
  some values from: document
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
definition editor: Bjoern Peters
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting

line graph
type: Class
subclass of: graph
editor preferred term: line graph
has curation status: ready for release
definition: A line graph is a type of graph created by connecting a series of data points together with a line.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:Melanie Courtot
alternative term: line chart
definition source: GROUP:OBI
definition source: WEB: http://en.wikipedia.org/wiki/Line_chart

assigning a centrally registered identifier
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has_participant
  some values from: centrally registered identifier registry
example of usage: A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
has curation status: metadata complete
definition: A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
editor note: 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
definition editor: Person:Alan Ruttenberg
definition editor: Person:Bjoern Peters
definition editor: Person:Melanie Courtot
alternative term: assigning a CRID

associating information with a centrally registered identifier in its registry
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has_participant
  some values from: centrally registered identifier registry
example of usage: Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them.
has curation status: metadata complete
definition: A planned process in which a CRID registry associates an information content entity with a CRID symbol
definition editor: PERSON:Alan Ruttenberg
alternative term: associating information with a CRID in the CRID registry

obsolete_establishing a CRID registry
type: Class
subclass of: Obsolete Class
definition: a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
editor note: MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.
has obsolescence reason: failed exploratory term
deprecated: true

centrally registered identifier symbol
type: Class
subclass of: symbol
subclass of: Restriction
  on property: part of
  some values from: centrally registered identifier
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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: CRID symbol
definition source: Original proposal from Bjoern, discussions at IAO calls

centrally registered identifier
type: Class
subclass of: identifier
subclass of: Restriction
  on property: has part
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: denotes
    some values from: centrally registered identifier registry
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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: CRID
definition source: Original proposal from Bjoern, discussions at IAO calls

centrally registered identifier registry
type: Class
subclass of: data set
example of usage: PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
has curation status: metadata complete
definition: A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: CRID registry
definition source: Original proposal from Bjoern, discussions at IAO calls

looking up a centrally registered identifier
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has_specified_output
  some values from: information content entity
subclass of: Restriction
  on property: has_participant
  some values from: centrally registered identifier registry
example of usage: Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID.
has curation status: metadata complete
definition: A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: looking up a CRID

time stamped measurement datum
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has time stamp
    some values from: time measurement datum
  intersection of: Restriction
    on property: has measurement datum
    some values from: measurement datum
has curation status: metadata incomplete

time sampled measurement data set
type: Class
subclass of: data set
subclass of: Restriction
  on property: has part
  some values from: time stamped measurement datum
example of usage: pmid:20604925 - time-lapse live cell microscopy
has curation status: metadata complete
definition: A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
definition editor: Alan Ruttenberg
alternative term: experimental time series

written name
type: Class
subclass of: textual entity
editor preferred term: written name
example of usage: "Bill Clinton"
example of usage: "The Eiffel Tower"
example of usage: "United States of America"
has curation status: pending final vetting
definition: A textual entity that denotes a particular in reality.
definition editor: PERSON: Bill Hogan
definition source: https://github.com/information-artifact-ontology/IAO/issues/114
curator note: The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.

software method
type: Class
subclass of: software
has curation status: metadata incomplete
definition: A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

software module
type: Class
subclass of: software
has curation status: metadata incomplete
definition: A software module is software composed of a collection of software methods.
definition editor: PERSON: Melanei Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

software library
type: Class
subclass of: software
has curation status: metadata incomplete
definition: A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

software application
type: Class
subclass of: software
has curation status: metadata incomplete
definition: A software application is software that can be directly executed by some processing unit.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

software script
type: Class
subclass of: software
has curation status: metadata incomplete
definition: A software script is software whose instructions can be executed using a software interpreter.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80

abbreviation textual entity
type: Class
subclass of: textual entity
editor preferred term: abbreviation textual entity
example of usage: From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect.
definition: A textual entity listing abbreviations and their expansions that are used in a document.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

abbreviations section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: abbreviation textual entity
editor preferred term: abbreviations section
example of usage: The section labelled 'abbreviations' in a typical scientific journal article.
definition: A part of a document where abbreviations and their long-forms used within the document are listed.
definition editor: PERSON: Bill Baumgartner
alternative term: abbreviation and acronyms
alternative term: abbreviation list
alternative term: abbreviations
alternative term: abbreviations and acronyms
alternative term: abbreviations list
alternative term: abbreviations used
alternative term: definitions for abbreviations
alternative term: list of abbreviations
alternative term: list of abbreviations used
alternative term: non-standard abbreviations
alternative term: nonstandard abbreviations
alternative term: nonstandard abbreviations and acronyms
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

author information section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: author information textual entity
editor preferred term: author information section
example of usage: The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/)
definition: A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
definition editor: PERSON: Bill Baumgartner
alternative term: author information
alternative term: authors’ information
alternative term: biographies
alternative term: contributor information
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

author information textual entity
type: Class
subclass of: textual entity
editor preferred term: author information textual entity
example of usage: From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD.
definition: A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

author summary section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: author summary textual entity
editor preferred term: author summary section
example of usage: The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/)
definition: A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers.
definition editor: PERSON: Bill Baumgartner
alternative term: author summary
alternative term: summary
alternative term: synopsis
definition source: Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

author summary textual entity
type: Class
subclass of: textual entity
editor preferred term: author summary textual entity
example of usage: From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX.
definition: A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).
definition editor: PERSON: Bill Baumgartner
definition source: Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

availability section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: availability textual entity
editor preferred term: availability section
example of usage: The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
definition: A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained.
definition editor: PERSON: Bill Baumgartner
alternative term: availability
alternative term: availability of data
alternative term: data archiving
alternative term: data availability
alternative term: data availability statement
alternative term: data sharing statement
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

availability textual entity
type: Class
subclass of: textual entity
editor preferred term: availability textual entity
example of usage: From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): Project home page:http://krux.googlecode.com
definition: A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

case report section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: case report textual entity
editor preferred term: case report section
example of usage: The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/)
definition: A part of a document about the medical history of a specific patient as it relates to the topic of the document.
definition editor: PERSON: Bill Baumgartner
alternative term: case presentation
alternative term: case report
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

case report textual entity
type: Class
subclass of: textual entity
editor preferred term: case report textual entity
example of usage: Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension.
definition: A textual entity that expresses a detailed account of a portion of the medical history for a specific patient.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

conclusion section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: conclusion textual entity
editor preferred term: conclusion section
example of usage: The section labelled 'conclusion' in a typical scientific journal article.
definition: A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document.
definition editor: PERSON: Bill Baumgartner
alternative term: concluding remarks
alternative term: conclusion
alternative term: conclusions
alternative term: findings
alternative term: summary
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

conflict of interest section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: conflict of interest textual entity
editor preferred term: conflict of interest section
example of usage: The section labelled 'conflict of interest statement' in a typical scientific journal article.
definition: A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document.
definition editor: PERSON: Bill Baumgartner
alternative term: authors' disclosures of potential conflicts of interest
alternative term: competing financial interests
alternative term: competing interests
alternative term: conflict of interest
alternative term: conflict of interest statement
alternative term: conflict of interests
alternative term: conflicts of interest
alternative term: declaration of competing interest
alternative term: declaration of competing interests
alternative term: declaration of interest
alternative term: declaration of interests
alternative term: disclosure of conflict of interest
alternative term: disclosure of potential conflicts of interest
alternative term: duality of interest
alternative term: statement of interest
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

conflict of interest textual entity
type: Class
subclass of: textual entity
editor preferred term: conflict of interest statement
example of usage: SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)]
definition: A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

consent section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: consent textual entity
editor preferred term: consent section
example of usage: The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)
definition: A part of a document about the consent process that was used to enroll patients in a study.
definition editor: PERSON: Bill Baumgartner
alternative term: consent
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

consent textual entity
type: Class
subclass of: textual entity
editor preferred term: consent textual entity
example of usage: From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal.
definition: A textual entity that documents the consenting process used to enroll patients in a study.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

ethical approval section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: ethical approval textual entity
editor preferred term: ethical approval section
example of usage: The section labelled 'ethical approval' in a typical scientific journal article.
definition: A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis.
definition editor: PERSON: Bill Baumgartner
alternative term: ethical approval
alternative term: ethical requirements
alternative term: ethics
alternative term: ethics statement
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

ethical approval textual entity
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: study design
editor preferred term: ethical approval textual entity
example of usage: From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review.
definition: A textual entity that documents the ethical approval of some study design.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

figures section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: figure
editor preferred term: figures section
example of usage: The section labelled 'figures' in a typical scientific journal article.
definition: A part of a document that contains one or more figures.
definition editor: PERSON: Bill Baumgartner
alternative term: figures
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

funding source declaration section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: funding source declaration textual entity
editor preferred term: funding source declaration section
example of usage: The section labelled 'funding' in a typical scientific journal article.
definition: A part of a document used to detail information regarding the source of funding used in support of the generation of the document content.
definition editor: PERSON: Bill Baumgartner
alternative term: financial support
alternative term: funding
alternative term: funding information
alternative term: funding sources
alternative term: funding statement
alternative term: funding/support
alternative term: grants
alternative term: role of the funding source
alternative term: source of funding
alternative term: sources of funding
alternative term: study funding
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

funding source declaration textual entity
type: Class
subclass of: textual entity
editor preferred term: funding souce declaration textual entity
example of usage: From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication.
definition: A textual entity documenting the source of funding that supported some study.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

future directions section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: future directions textual entity
editor preferred term: future directions section
example of usage: The section labelled 'future directions' in a typical scientific journal article.
definition: A part of a document detailing extensions of the described work that may be implemented at some future point in time.
definition editor: PERSON: Bill Baumgartner
alternative term: future challenges
alternative term: future considerations
alternative term: future developments
alternative term: future directions
alternative term: future outlook
alternative term: future perspectives
alternative term: future plans
alternative term: future prospects
alternative term: future research
alternative term: future research directions
alternative term: future studies
alternative term: future work
alternative term: outlook
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

future directions textual entity
type: Class
subclass of: textual entity
editor preferred term: future directions textual entity
example of usage: Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members.
definition: A textual entity expressing ideas regarding future work relevant to work described in a document that could be done.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

genome announcement section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: genome announcement textual entity
editor preferred term: genome announcement section
example of usage: The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/)
definition: A document part announcing the publication of a novel draft genome sequence.
definition editor: PERSON: Bill Baumgartner
alternative term: genome announcement
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

genome announcement textual entity
type: Class
subclass of: textual entity
editor preferred term: genome announcement textual entity
example of usage: Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB).
definition: A textual entity that describes the generation and public release of a novel, draft genome sequence.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

keyword textual entity
type: Class
subclass of: textual entity
editor preferred term: keyword textual entity
example of usage: From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): Exon orthology; alternative splicing; exon duplication; intron-exon structure.
definition: A textual entity listing keywords indicating the major theme(s) of a document.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

keywords section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: keyword textual entity
editor preferred term: keywords section
example of usage: The section labelled 'keywords' in a typical scientific journal article.
definition: A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed.
definition editor: PERSON: Bill Baumgartner
alternative term: keywords
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

study limitations section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: study limitations textual entity
subclass of: Restriction
  on property: is about
  some values from: study design
editor preferred term: study limitations section
example of usage: The section labelled 'limitations' in a typical scientific journal article.
definition: A part of a document about biases or short comings related to the study design and execution.
definition editor: PERSON: Bill Baumgartner
alternative term: limitations
alternative term: study limitations
definition source: Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

study limitations textual entity
type: Class
subclass of: textual entity
editor preferred term: study limitations textual entity
example of usage: Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out.
definition: A textual entity addressing a shortcoming or bias of a study design or execution.
definition editor: PERSON: Bill Baumgartner
definition source: Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

materials section
type: Class
subclass of: document part
editor preferred term: materials section
example of usage: The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)
definition: A part of a document about the materials required to reproduce the content of the document.
definition editor: PERSON: Bill Baumgartner
alternative term: materials
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

notes section
type: Class
subclass of: document part
editor preferred term: notes section
example of usage: The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):
definition: A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc.
definition editor: PERSON: Bill Baumgartner
alternative term: notes
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

patients section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: patients textual entity
editor preferred term: patients section
example of usage: The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/)
definition: A part of a document about the patients that participated in a study.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

patients textual entity
type: Class
subclass of: textual entity
editor preferred term: patients textual entity
example of usage: Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred.
definition: A textual entity expressing information regarding the patients used in a study.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

pre-publication history section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: pre-publication history textual entity
editor preferred term: pre-publication history section
example of usage: The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/)
definition: A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors.
definition editor: PERSON: Bill Baumgartner
alternative term: notice of republication
alternative term: pre-publication history
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

pre-publication history textual entity
type: Class
subclass of: textual entity
editor preferred term: pre-publication history textual entity
example of usage: From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): The pre-publication history for this paper can be accessed here: http://www.biomedcentral.com/1471-2253/13/33/prepub
definition: A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

related work section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: related work textual entity
editor preferred term: related work section
example of usage: The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/)
definition: A part of a document about work in other publications that is relevant to the content of the document.
definition editor: PERSON: Bill Baumgartner
alternative term: related literature
alternative term: related work
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

related work textual entity
type: Class
subclass of: textual entity
editor preferred term: related work textual entity
example of usage: Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).
definition: A textual entity that discusses work from other publications and expresses their relevancy to the content of a document.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

requirements section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: requirements textual entity
editor preferred term: requirements section
example of usage: The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
definition: A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource.
definition editor: PERSON: Bill Baumgartner
alternative term: requirements
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

requirements textual entity
type: Class
subclass of: textual entity
editor preferred term: requirements textual entity
example of usage: From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): • Operating systems: Platform independent • Programming language: Matlab, R, Python • Other requirements: None • License: GNU GPL v3 • Any restrictions to use by non-academics: None
definition: A textual entity that expresses the requirements necessary to use a resource, e.g. software.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

statistical analysis textual entity
type: Class
subclass of: textual entity
editor preferred term: statistical analysis textual entity
example of usage: From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant.
definition: A textual entity documenting statistical analysis tools and techniques employed.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

statistical analysis section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: statistical analysis textual entity
editor preferred term: statistical analysis section
example of usage: The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)
definition: A part of the document used to describe the statistical methodologies employed in the work presented in the document.
definition editor: PERSON: Bill Baumgartner
alternative term: statistical analysis
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

tables section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: table
editor preferred term: tables section
example of usage: The section labelled 'tables' in a typical scientific journal article.
definition: A part of a document that contains one or more tables.
definition editor: PERSON: Bill Baumgartner
alternative term: tables
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

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.
definition editor: Mathias Brochhausen

Postal delivery route
type: Class
subclass of: plan specification
definition: A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region.
definition editor: Mathias Brochhausen

zone improvement plan code
type: Class
subclass of: postal code
definition: A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes.
definition editor: Mathias Brochhausen
alternative term: ZIP code

database extract, transform, and load process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
subclass of: Restriction
  on property: has_specified_output
  some values from: information content entity
editor preferred term: database extract, transform, and load process
definition: A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second.
editor note: Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second
editor note: Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output.
definition editor: PERSON:Alan Ruttenberg
alternative term: ETL
definition source: WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/187

descriptive data section
type: Class
subclass of: document part
editor preferred term: descriptive data section
has curation status: metadata complete
definition: A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made.
definition editor: PERSON: Chen Yang
definition editor: PERSON: Jie Zheng
definition source: https://www.equator-network.org/reporting-guidelines/prisma/
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/235
ontology term requester: ONE ontology

additional results section
type: Class
subclass of: results section
editor preferred term: additional results section
has curation status: metadata complete
definition: A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.)
definition editor: PERSON: Chen Yang
definition editor: PERSON: Jie Zheng
definition source: https://www.equator-network.org/reporting-guidelines/consort/
definition source: https://www.equator-network.org/reporting-guidelines/prisma/
definition source: https://www.equator-network.org/reporting-guidelines/strobe/
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/235
ontology term requester: ONE ontology

research participants section
type: Class
subclass of: document part
editor preferred term: research participants section
has curation status: metadata complete
definition: A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.).
definition editor: PERSON: Chen Yang
definition editor: PERSON: Jie Zheng
definition source: https://www.equator-network.org/reporting-guidelines/consort/
definition source: https://www.equator-network.org/reporting-guidelines/prisma/
definition source: https://www.equator-network.org/reporting-guidelines/strobe-nut/
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/235
ontology term requester: ONE ontology

measurement methods section
type: Class
subclass of: methods section
editor preferred term: measurement methods section
has curation status: metadata complete
definition: A methods section that describes details of data assessment methods (data measurement).
definition editor: PERSON: Chen Yang
definition editor: PERSON: Jie Zheng
definition source: https://www.equator-network.org/reporting-guidelines/strobe/
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/235
ontology term requester: ONE ontology

research settings section
type: Class
subclass of: document part
editor preferred term: research settings section
has curation status: metadata complete
definition: A document part that describes the physical/social/cultural conditions around a research trial.
definition editor: PERSON: Chen Yang
definition editor: PERSON: Jie Zheng
definition source: https://www.ncbi.nlm.nih.gov/books/NBK262175/
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/235
ontology term requester: ONE ontology

study bias section
type: Class
subclass of: study limitations section
editor preferred term: study bias section
has curation status: metadata complete
definition: A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others.
definition editor: PERSON: Chen Yang
definition editor: PERSON: Jie Zheng
definition source: DOI: 10.1097/PRS.0b013e3181de24bc
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/235
ontology term requester: ONE ontology

graphical abstract
type: Class
subclass of: abstract
editor preferred term: graphical abstract
has curation status: metadata complete
definition: An abstract that is pictorial summary of the main findings described in the document.
definition editor: PERSON: Jie Zheng
definition editor: PERSON: Tim Beck
alternative term: visual abstract
definition source: https://www.elsevier.com/authors/journal-authors/graphical-abstract
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234
ontology term requester: Biomedical literature NLP project

identifier
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: denotes
    some values from: entity
  intersection of: Restriction
    on property: is_specified_output_of
    all values from: dubbing process
subclass of: information content entity
subclass of: Restriction
  on property: denotes
  some values from: entity
editor preferred term: identifier
definition: An identifier 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.
definition editor: Mathias Brochhausen
alternative term: proper name
imported from: pno.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)

grapheme
type: Class
subclass of: information content entity
example of usage: alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems
definition: A grapheme is an information content entity that is a fundamental unit in a written language.
definition source: http://en.wikipedia.org/wiki/Grapheme
creator: Mathias Brochhausen

utterance
type: Class
subclass of: information content entity
definition: An utterance is an information content entity that is a complete unit of speech in spoken language.
definition editor: Mathias Brochhausen
definition source: Wikipedia: http://en.wikipedia.org/wiki/Utterance
creator: Mathias Brochhausen

mechanical wave quality
type: Class
subclass of: quality
definition: An attributive collection of qualities inhering in energy when transported through a medium in a wave.
creator: Mathias Brochhausen

writing quality
type: Class
subclass of: quality
definition: is a quality that is the concretization of graphemes and inheres in a material object.
definition editor: Mathias Brochhausen
creator: Mathias Brochhausen

writing bearer
type: Class
equivalent class: Class
  intersection of: material information bearer
  intersection of: Restriction
    on property: bearer of
    some values from: Restriction
      on property: concretizes
      some values from: grapheme
subclass of: material information bearer
subclass of: Restriction
  on property: bearer of
  some values from: Restriction
    on property: concretizes
    some values from: grapheme
example of usage: pieces of paper, tables, walls, floors, driveways, highway signs, computer screens, skin, tablets of clay, rocks, sheets of metal (license plates), sheets of papyrus, etc. clouds of smoke in skywriting,
definition: is a material information bearer that bears the concretization of graphemes.
definition editor: Mathias Brochhausen
creator: Mathias Brochhausen

portion of energy
type: Class
subclass of: independent continuant

sound energy
type: Class
equivalent class: Class
  intersection of: portion of energy
  intersection of: Restriction
    on property: bearer of
    some values from: mechanical wave quality
  intersection of: Restriction
    on property: participates in
    some values from: Class
      intersection of: oscillating
      intersection of: Restriction
        on property: has_participant
        some values from: Class
subclass of: portion of energy
subclass of: Restriction
  on property: bearer of
  some values from: mechanical wave quality
subclass of: Restriction
  on property: participates in
  some values from: Class
    intersection of: oscillating
    intersection of: Restriction
      on property: has_participant
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
definition: Energy that is transported in a sound wave.
creator: Mathias Brochhausen

utterance energy
type: Class
equivalent class: Class
  intersection of: sound energy
  intersection of: Restriction
    on property: bearer of
    some values from: Restriction
      on property: concretizes
      some values from: utterance
  intersection of: Restriction
    on property: is_specified_output_of
    all values from: utterance process
subclass of: sound energy
subclass of: Restriction
  on property: bearer of
  some values from: Restriction
    on property: concretizes
    some values from: utterance
definition: Sound energy bearing the concretization of an utterance and being the output of an uttering process.

oscillating
type: Class
subclass of: process
definition: Oscillating is a processual that shows repetitive variation, typically in time, of some measured quality about a central value (often a point of equilibrium) or between two or more different states.
definition source: http://en.wikipedia.org/wiki/Oscillation
creator: Mathias Brochhausen

dubbing process
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: identifier
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: identifier
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.
definition editor: Mathias Brochhausen
creator: Mathias Brochhausen

utterance process
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: utterance energy
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: utterance energy
definition: is a planned process of making speech sounds which may or may not have an actual language involved.
definition editor: Mathias Brochhausen
definition source: http://en.wiktionary.org/wiki/utter
creator: Mathias Brochhausen

personal name
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: denotes
    all values from: Homo sapiens
subclass of: identifier
definition: A personal name is a proper name identifying an individual person.
definition 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)
comment: Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB)

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
definition 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.
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Family_name

code set
type: Class
subclass of: document
subclass of: Restriction
  on property: has part
  some values from: identifier
definition: A document that is a collection of identifiers that has been created to identify and annotate core ideas of a specified domain, and where the intention of its creators is that the identifiers have a one-to-one correspondence with entities in reality outside the aggregate.
definition editor: Mathias Brochhausen
alternative term: code system
alternative term: codeset
alternative term: coding system
alternative term: controlled vocabulary
contributor: Clint Dowland
contributor: Matt Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: Does not imply absence vs. presence of any taxonomy.
comment: Does not imply that identifiers denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities (e.g., SNOMED and even various OBO ontologies have identifiers that identify entities in all three categories).
comment: Each identifier is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. When there is no such string, it is almost always because the identifiers take the form of human language words. For example, a “sex” or “gender” code set could have identifiers “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).
comment: For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).
comment: For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.
comment: Many code sets are created for a specific purpose in addition to merely identifying and annotating core ideas of a specified domain.
comment: The identifiers do not denote each other.

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: inheres in
        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: inheres in
        some values from: Restriction
subclass of: document
subclass of: Restriction
  on property: is about
  some values from: documented identity
subclass of: Restriction
  on property: is concretized as
  some values from: Class
    intersection of: specifically dependent continuant
    intersection of: Restriction
      on property: inheres in
      some values from: Restriction
        on property: bearer of
        some values from: credential role
definition: A document that denotes some identity and is concretized by the bearer of some credential role.
definition 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.
definition 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).
definition 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: inheres in
    some values from: Restriction
      on property: bearer of
      some values from: Restriction
        on property: concretizes
        some values from: identity document
subclass of: role
subclass of: Restriction
  on property: realized in
  some values from: authentication
subclass of: Restriction
  on property: inheres in
  some values from: Restriction
    on property: bearer of
    some values from: Restriction
      on property: concretizes
      some values from: identity document
definition: A role that inheres in a concretization of an identity document and is realized by an authentication process.
definition editor: Amanda Hicks

obligor role
type: Class
subclass of: deontic role
editor preferred term: obligor role
example of usage: Sam's obligor role realized by him taking Nigel to lunch after promising to do so; Sarah's obligor role realized by paying the purchase price to Layla after signing the contract specifying that she is buying a piece of land from Layla.
definition: A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements.
definition editor: Mathias Brochhausen
definition editor: Sarah Bost

obligee role
type: Class
subclass of: deontic role
editor preferred term: obligee role
example of usage: Nigel's obligee role realized by Sam taking him out for lunch after Sam so promised; Layla's obligee role realized by receiving the money after signing a contract in which Sarah obtained a piece of land in exchange for a specified sum of money.
definition: A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements.
definition editor: Mathias Brochhausen
definition editor: Sarah Bost

owner role
type: Class
subclass of: role in human social processes
example of usage: Tammy's owner role with regards to the house on 234 Evergreen Terrace; Walter's owner role with regards to the intellectual property on his movie script
definition: A role in a human social process that is based on a social act and whose bearer exercises exclusive control over a property, where this control is permitted by one or more deontic roles, which are parts of the owner role.
definition editor: Mathias Brochhausen
definition source: OBIB/ICO community
definition source: https://github.com/d-acts/d-acts/issues/29

obsolete_claim
type: Class
subclass of: Obsolete Class
has obsolescence reason: placeholder removed
deprecated: true

deontic document act
type: Class
equivalent class: Class
  intersection of: deontic declaration
  intersection of: Restriction
    on property: has_specified_input
    some values from: document act input document
  intersection of: Restriction
    on property: has_specified_output
    some values from: document
subclass of: deontic declaration
subclass of: Restriction
  on property: has_specified_input
  some values from: document act input document
subclass of: Restriction
  on property: has_specified_output
  some values from: document
example of usage: my filling in an immigration form, a judge's signing and stamping a court order
definition: A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document.
definition editor: Mathias Brochhausen

obsolete_document act
type: Class
subclass of: Obsolete Class
example of usage: my filling in an immigration form, a judge's signing and stamping a court order
definition: A social act creating, revoking or transferring a socio-legal generically dependent continuant or a role by validating (signing, stamping, publishing) a document.
definition editor: Mathias Brochhausen
has obsolescence reason: failed exploratory term
term replaced by: obsolete_deontic document act
deprecated: true

social act
type: Class
subclass of: planned process
example of usage: Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom
definition: A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived.
definition editor: Mathias Brochhausen
comment: The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012). Reinach clearly does not imply that a command that does not fulfill its prupose would not be a command. Thanks to W.R. Hogan for finding the Reinach quote.

obsolete_socio-legal generically dependent continuant
type: Class
subclass of: Obsolete Class
example of usage: the claim of a piece of land, the obligation to pay rent to the owner of a rental property
definition: Socio-legal generically dependent continuants are generically dependent continuants that come into existence through social acts and that if they get concretized are concretized as realizable entities.
definition editor: Mathias Brochhausen
deprecated: true

obsolete_deontic declaration
type: Class
subclass of: Obsolete Class
editor preferred term: deontic declaration
example of usage: my consenting verbally to buy a used TV set for $ 500, John Robie's taking of Mrs. Steven's jewels, Jane Doe's revoking of informed consent over the phone, John Doe signing an employment contract.
definition: A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or transforms a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document.
definition editor: Mathias Brochhausen
alternative term: declaration
alternative term: status function declaration
has obsolescence reason: failed exploratory term
deprecated: true

obsolete obligee role
type: Class
subclass of: Obsolete Class
definition: A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements.
definition editor: Mathias Brochhausen
deprecated: true

document act input document
type: Class
subclass of: document
definition: A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification).
definition editor: Mathias Brochhausen

deontic role
type: Class
subclass of: role
definition: A role that inheres in an agent and which is externally grounded in the normative expectations that other agents within a social context have concerning how that agent should behave.
definition editor: Mathias Brochhausen
definition editor: Neil Otte

deontic declaration
type: Class
equivalent class: Class
  union of: Restriction
    on property: legally revokes
    some values from: deontic role
  union of: Restriction
    on property: has_specified_output
    some values from: deontic role
subclass of: social act
definition: A social act that creates or revokes a deontic role.
definition editor: Mathias Brochhausen

obsolete_obligation
type: Class
subclass of: Obsolete Class
has obsolescence reason: placeholder removed
deprecated: true

obsolete_declaration executive role
type: Class
subclass of: Obsolete Class
definition: The role borne by a human being, an organization or an aggregate of either of both that is realized by being the active participant in a declaration.
definition editor: Mathias Brochhausen
has obsolescence reason: placeholder removed
deprecated: true

obsolete_document template creator role
type: Class
subclass of: Obsolete Class
example of usage: the role borne by the US Citizen and Immigration Service realized by providing the template form for entering the US as a non-resident alien, the role of a guideline committee in putting together a clinical guideline
definition: The role of a human being or an aggregate of human beings preparing the initial document to undergo a document act, thus creating a socio-legal generically dependent continuant.
definition editor: Mathias Brochhausen
has obsolescence reason: placeholder removed
comment: not that the "template" does not need to be a template at all. It can be a document that is getting stamped and signed and by these acts creating some socio-legal generically dependent continuants.
deprecated: true

obsolete_claimant role
type: Class
subclass of: Obsolete Class
definition: The role of a human being or an aggregate of human beings concretizing a claim.
definition editor: Mathias Brochhausen
has obsolescence reason: placeholder removed
deprecated: true

obsolete_obligator role
type: Class
subclass of: Obsolete Class
definition: The role of a human being or an aggregate of human beings concretizing an obligation.
definition editor: Mathias Brochhausen
has obsolescence reason: placeholder removed
deprecated: true

obsolete_declaration target
type: Class
subclass of: Obsolete Class
example of usage: me as a bearer of a spouse role, which participates in a document act, John Doe as bearer of a debtor role, which participates in a document act
definition: The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act.
definition editor: Mathias Brochhausen
has obsolescence reason: failed exploratory term
deprecated: true

document act template creator role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: Class
      union of: Homo sapiens
      union of: organization
      union of: collection of humans
      union of: aggregate of organizations
    intersection of: Restriction
      on property: realized in
      all values from: Class
        intersection of: planned process
        intersection of: Restriction
example of usage: The role of the U.S. Citizenship and Immigration Service realized by the creation of an immigration form that is being filled in, the role of a national professional association realized by the creation of a clinical guideline that is to be certified
definition: A role that inheres in a human being or organization or aggregate of any of the aforementioned that prepares a document that is the specified input to a document act and is the input document of a document act.
definition editor: Mathias Brochhausen

deontic declaration performer role
type: Class
subclass of: role
definition: A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration.
definition editor: Mathias Brochhausen
alternative term: declaration performer role

obsoleted_document act target
type: Class
subclass of: Obsolete Class
definition: The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act.
definition editor: Mathias Brochhausen
deprecated: true

document act performer role
type: Class
subclass of: role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      union of: Homo sapiens
      union of: organization
      union of: collection of humans
      union of: aggregate of organizations
  intersection of: Restriction
    on property: realized in
    all values from: deontic document act
example of usage: a judge's role of signing a court order
definition: A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a document act.
definition editor: Mathias Brochhausen

obsolete_obligee role
type: Class
subclass of: Obsolete Class
definition: A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements.
definition editor: Sarah Bost
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_obligor role
type: Class
subclass of: Obsolete Class
definition: A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements.
definition editor: Sarah Bost
has obsolescence reason: failed exploratory term
deprecated: true

standing declaration
type: Class
subclass of: social act
definition: A social act that postulates a socio-legal fact for a specified group of people or organizations.
definition editor: Mathias Brochhausen
alternative term: enactment

obsolete obligor role
type: Class
subclass of: Obsolete Class
definition: A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements.
definition editor: John Judkins
definition editor: Mathias Brochhausen
deprecated: true

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 term: 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 term: 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 term: 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 term: ontology slim
alternative term: 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 term: 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 term: 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 term: 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 term: 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

Homo sapiens
type: Class
subclass of: organism
editor preferred term: Homo sapiens
alternative term: human being
imported from: ncbitaxon.owl

obsolete Systematized Nomenclature of Medicine
type: Class
subclass of: code set
deprecated: true

medical intervention
type: Class
subclass of: planned process
definition: medical intervention is a planned process that has the goal of diagnosing, preventing or relieving illness or injury.
editor note: The act of intervening, interfering or interceding with the intent of modifying the outcome. In medicine, an intervention is usually undertaken to help treat or cure a condition. For example, "Acupuncture as a therapeutic intervention is widely practiced in the United States," Reference: http://www.medterms.com/script/main/art.asp?articlekey=34214 . Some interventions can be used for diagnosis.
definition editor: YH
definition source: WEB: http://wiki.answers.com/Q/What_is_medical_intervention

surgery
type: Class
subclass of: medical procedure
definition: Surgery is a medical procedure that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury, to help improve bodily function or appearance. The key difference between a surgery and a general procedure is the need for an incision. Making an incision, or cutting into the skin to gain access to the body’s deeper tissues or organs, is a defining characteristic of surgery.
definition editor: YH, SS
alternative term: surgical procedure
definition source: WEB: http://en.wikipedia.org/wiki/Surgery
definition source: WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm
has_MedDRA_id: 10042609

medical procedure
type: Class
subclass of: medical intervention
definition: a medical intervention that refers to any series of pre-defined steps that should be followed to achieve a desired result.
definition editor: YH, SS
definition source: WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm

planned process
type: Class
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.
definition: A processual entity 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.
definition 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

investigation
type: Class
subclass of: planned process
editor preferred term: investigation
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
imported from: obi.owl

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.
definition: An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Philippe Rocca-Serra
definition editor: PERSON: Susanna Sansone
definition source: GROUP: OBI

study design execution
type: Class
subclass of: planned process
editor preferred term: study design execution
definition: a planned process that carries out a study design
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: organizational term
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.
definition editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism

data transformation
type: Class
subclass of: planned process
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.
definition editor: Elisabetta Manduchi
definition editor: Helen Parkinson
definition editor: James Malone
definition editor: Melanie Courtot
definition editor: Philippe Rocca-Serra
definition editor: Richard Scheuermann
definition editor: Ryan Brinkman
definition editor: Tina Hernandez-Boussard
alternative term: data analysis
alternative term: data processing
definition source: Branch editors
imported from: obi.owl

study design
type: Class
subclass of: plan specification
editor preferred term: study design
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.
imported from: obi.owl

dialysis
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
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
definition editor: PERSON:Kevin Clancy
definition source: OBI branch derived

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.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:21:20Z
imported from: https://github.com/OGMS/ogms/releases/tag/v2019-04-30

diagnosis
type: Class
subclass of: clinical data item
subclass of: Restriction
  on property: mentions
  some values from: Restriction
    on property: bearer of
    some values from: patient role
subclass of: Restriction
  on property: is_specified_output_of
  some values from: diagnostic process
definition: The representation of a conclusion of a diagnostic process.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T12:42:23Z
imported from: https://github.com/OGMS/ogms/releases/tag/v2019-04-30

health care process
type: Class
subclass of: planned process
definition: A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient
definition editor: Albert Goldfain Sagar Jain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z editor date: 2017-04-18
imported from: https://github.com/OGMS/ogms/releases/tag/v2019-04-30

health care encounter
type: Class
subclass of: planned 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
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z

outpatient encounter
type: Class
subclass of: health care encounter
definition: TODO
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
imported from: https://github.com/OGMS/ogms/releases/tag/v2019-04-30

inpatient encounter
type: Class
subclass of: health care encounter
definition: TODO
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
imported from: https://github.com/OGMS/ogms/releases/tag/v2019-04-30

injury
type: Class
subclass of: material entity
definition: A disorder that involves some structural damage that is immediately caused by a catastrophic external force.
editor note: At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level.
definition editor: Albert Goldfain Sagar Jain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5 OGMS call adoption- 16 SEPT 2015 https://docs.google.com/document/d/1iiV1-fTS7BUUSzDw3N_Afx42698YWf54-FOTY2NkAxo/edit
curator note: creation date: 2011-09-20T09:57:44Z edited date: 30 SEPT 2015

diagnostic process
type: Class
subclass of: health care process
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: health care provider role
    intersection of: Restriction
      on property: inheres in
      some values from: Homo sapiens
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).
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e
curator note: creation date: 2011-09-20T09:57:44Z
imported from: https://github.com/OGMS/ogms/releases/tag/v2019-04-30

clinical data item
type: Class
subclass of: data item
definition: a data item that is about a patient and is the specified output of a health care process assay or diagnostic process
curator note: creation date: 2018-11-27
imported from: https://github.com/OGMS/ogms/releases/tag/v2019-04-30

survey data
type: Class
subclass of: data item
definition: A data item that contains the outcome of a survey.
definition editor: Alice Nzinga
definition editor: Mathias Brochhausen

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).
definition editor: Alice Nzinga
definition editor: Mathias Brochhausen

survey execution
type: Class
subclass of: planned process
definition: A planned process that realizes the concretization of a survey to generate an output(survey data.)

social security number
type: Class
subclass of: centrally registered identifier
definition: Social Security Number(SSN) is a Centrally Registered IDentifier that is a nine-digit number issued to U.S. citizens, permanent residents, and temporary (working) residents under section 205(c) of the Social Security Act, codified as 42 U.S.C. § 405(c). The number is issued to an individual by the Social Security Administration, an independent agency of the United States government. Its primary purpose is to track individuals for Social Security purposes.
alternative term: SSN
definition source: http://en.wikipedia.org/wiki/Social_Security_number
creator: Cheng Chen(cxchen1@ualr.edu)

human social role
type: Class
subclass of: organism social role
subclass of: Homo sapiens role
definition: A social role inhering in a human being.
definition editor: Mathias Brochhausen
definition editor: William R. Hogan

party to a legal entity
type: Class
subclass of: role in human social processes
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      union of: Homo sapiens
      union of: organization
  intersection of: Restriction
    on property: inheres in
    all values from: Class
      union of: Homo sapiens
      union of: organization

party to a legal proceeding
type: Class
subclass of: party to a legal entity

party to a legal agreement
type: Class
subclass of: party to a legal entity

party to a marriage contract
type: Class
subclass of: party to a legal agreement
subclass of: Homo sapiens role

party to a power of attorney
type: Class
subclass of: party to a legal entity

gender role
type: Class
subclass of: organism role
definition: A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture.
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Gender_role

male gender role
type: Class
subclass of: gender role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: inheres in
    all values from: organism
definition: A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question.
definition editor: Mathias Brochhausen
alternative term: male gender

female gender role
type: Class
subclass of: gender role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: inheres in
    all values from: organism
definition: A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question.
definition editor: Mathias Brochhausen
alternative term: female gender

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.
definition editor: William R. Hogan
alternative term: health care role
comment: Mathias Brochhausen

patient role
type: Class
subclass of: human health care role
subclass of: organism role
definition: A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.
definition editor: Amanda Hicks
definition editor: Mathias Brochhausen
alternative term: patient
definition source: CAFE domain expert working group.
comment: In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications.

health care provider role
type: Class
subclass of: human health care role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      union of: Homo sapiens
      union of: organization
  intersection of: Restriction
    on property: inheres in
    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.
definition editor: Mathias Brochhausen
comment: William R. Hogan

physician 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 promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments.
definition editor: Mathias Brochhausen
alternative term: physician
definition source: http://en.wikipedia.org/wiki/Physician

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.
definition editor: Mathias Brochhausen
alternative term: nurse
definition source: based on: http://en.wikipedia.org/wiki/Nursing

health care provider organization role
type: Class
subclass of: organization health care role
subclass of: Restriction
  on property: realized in
  some values from: health care encounter
definition: A role that inheres in an organization and that is realized by the providing of services in a health care encounter.
contributor: Mathias Brochhausen
creator: Amanda Hicks

person health care provider role
type: Class
subclass of: human social role

physician practice
type: Class
subclass of: health care provider organization role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: organization
    intersection of: Restriction
      on property: has organization member
      min qualified cardinality: 2
      on class: Restriction
        on property: bearer of
        some values from: physician role
definition: A health care provider organization role that inheres in an organization consisting of two or more physicians.
definition editor: Amanda Hicks

obsolete_hospital role
type: Class
subclass of: Obsolete Class
definition: A role borne by an organization and realized by providing healthcare services by healthcare professionals of multiple different disciplines of medicine and enabling stationary treatment.
definition editor: Mathias Brochhausen
alternative term: hospital
deprecated: true

integrated delivery network
type: Class
subclass of: health care provider organization role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: organization
    intersection of: Restriction
      on property: has organization member
      all values from: organization
definition: A health care provider organization role that inheres in an organization that is comprised of other organizations.
definition editor: Amanda Hicks

aggregate of objectual organisms
type: Class
subclass of: object aggregate
subclass of: Restriction
  on property: has member
  all values from: Class
    intersection of: object
    intersection of: organism
definition: An object aggregate of objectual organisms.
imported from: http://purl.obolibrary.org/obo/omrse.owl
comment: Any arbitrary collection of organisms. They need not be of the same taxonomic class.

collection of humans
type: Class
subclass of: aggregate of objectual organisms
subclass of: Restriction
  on property: has member
  all values from: Homo sapiens
definition: An object aggregate all of whose components are human beings.
imported from: http://purl.obolibrary.org/obo/omrse.owl

role in human social processes
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    union of: organization
    union of: organism
subclass of: Restriction
  on property: inheres in
  all values from: Class
    union of: organization
    union of: organism
definition: A role inhering in an entity realized by social interactions in human society.
definition editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/omrse.owl
comment: Previous definition: A role played by an entity in human social processes.

organization social role
type: Class
subclass of: role in human social processes
subclass of: organization role
definition: A role in human social processes that inheres in an organization.
definition editor: William R. Hogan
comment: Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants.

organism social role
type: Class
subclass of: role in human social processes
subclass of: organism role
definition: A role in human social processes that inheres in an organism.
definition editor: William R. Hogan Mathias Brochhausen
comment: Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants.
comment: Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc.
comment: Previous definition: A role in human social processes played by an organism.

organization health care role
type: Class
subclass of: organization social role
definition: An organization social role that, if realized, is realized by either a health care process or an ancillary health care process
comment: Previous definition: An organization social role played by an organization in health care processes.

obsolete geopolitical organization
type: Class
subclass of: Obsolete Class
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).
definition editor: William R. Hogan
alternative term: geopolitical organization
deprecated: true

obsolete geopoli organization
type: Class
subclass of: Obsolete Class
alternative term: geopoli organization
deprecated: true

human patient role
type: Class
equivalent class: Class
  intersection of: patient role
  intersection of: Restriction
    on property: inheres in
    some values from: Homo sapiens
subclass of: patient role
subclass of: Homo sapiens role
definition: A patient role that inheres in a human being.

obsolete major administrative subdivision
type: Class
subclass of: Obsolete Class
definition: A subnational entity that is the primary organizational member of a nation, is subject to the full set of laws of the nation, enjoys all the privileges established under the laws of the nation, is not a member of any other geopolitical entity, and itself governs a part of the geographical region governed by the nation.
alternative term: major administrative subdivision
comment: example: Northern Ireland
deprecated: true

obsolete geopolitical dependency
type: Class
subclass of: Obsolete Class
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.
alternative term: geopolitical dependency
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).
deprecated: true

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 aggregate of organizations that have some feature in common, but is not itself an organization.
definition: An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common
definition editor: William R. Hogan
definition editor: William R. Hogan Amanda Hicks
imported from: http://purl.obolibrary.org/obo/omrse.owl
comment: It is often convenient to group organizations together that otherwise might not even interact with one another.

obsolete aggregate of sovereign states
type: Class
subclass of: Obsolete Class
definition: An aggregate of sovereign states that share some feature in common, but is not an organization nor necessarily the outcome of some treaty among them.
definition editor: An aggregate of geopoli organizations that is not itself a sovereign state and whose members are only sovereign states that have some feature in common
definition editor: William R. Hogan
alternative term: aggregate of sovereign states
deprecated: true

obsolete aggregate of geopoli organizations
type: Class
subclass of: Obsolete Class
definition: An object aggregate that is not itself a geopolitical organization and whose members are only geopolitical organizations that have some feature in common
definition editor: Amanda Hicks
definition editor: William R. Hogan
alternative term: aggregate of geopoli organizations
deprecated: true

obsolete aggregate of dependencies
type: Class
subclass of: Obsolete Class
definition: An aggregate of geopoli organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common.
definition editor: Amanda Hicks
alternative term: aggregate of dependencies
deprecated: true

obsolete aggregate of major administrative subdivisions
type: Class
subclass of: Obsolete Class
definition: An aggregate of geopoli organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common
definition editor: Amanda Hicks
alternative term: aggregate of major administrative subdivisions
deprecated: true

legal person role
type: Class
subclass of: role in human social processes
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      union of: Homo sapiens
      union of: collection of humans
  intersection of: Restriction
    on property: inheres in
    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.
definition editor: Mathias Brochhausen
definition source: Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
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.

smoker role
type: Class
subclass of: Homo sapiens role
definition: A role that inheres in an organism and is realized by habitually smoking tobacco products.

intravenous drug user
type: Class
subclass of: Homo sapiens role

obsolete intergovernmental organization
type: Class
subclass of: Obsolete Class
definition: an intergovernmental organization that has at least three member states, that has activies in at least three states, and that is unified by some formal intergovernmental agreement
definition editor: Amanda Hicks
alternative term: intergovernmental organization
definition source: "IGOs are organizations whose memebers include at lesat three states, that have activities in several states, and whose members are held together by a formal intergovernmental agreement ... These organizations range in size from three members (North American Free Trade Argreement [NAFTA]) to more than 190 memembers (Universal Postal Union (UPU)]. Memebers may come from primarily one georgraphic regioni (Oragnaization of American States [OAS]) or from all geographic regions (World Bank). although soem IGOs are designed to achieve a single purpose (Organization of Petroleum exporting countries [OPEC]), others have been developed for multiple tasks (United Nations [UN}). ... IGOs are recognized subjects of international law with separate standing fromt heir member states." Karns and Mingst I(2004) p. 7
contributor: Katrina Donovan
comment: examples: North American Free Trade Argreement [NAFTA] , Universal Postal Union [UPU], Oragnaization of American States [OAS], World Bank), Organization of Petroleum exporting countries [OPEC] United Nations [UN[, The World Trade Organization [WTO], The World Health Organization [WHO], UNICEF
deprecated: true

obsolete nongovernmental organization
type: Class
subclass of: Obsolete Class
definition: a geopolitical organization that is voluntary and private, whose members are individual persons or organizations that come together to acheive a common purpose.
alternative term: nongovernmental organizations
definition source: NGOs are private voluntary organizations whose members are individuals or associations that come together to acheive a common purpose. Some organizations are formed to advocate a particular cause such as human rights, peace, or envirnomental projetion. Others are established to provide services such as disaster relief, humantarian aid in war-torn socieities, or development assistance. ... National level groups are often called interest or pressure groups, and many of them are now linked to counterpart groups in other countries through transnational networks or federations. International NGOs, like IGOs, may draw their members from one region or several regions, and they may have very specific functions or be multi-functional. Karns and Mingst (2004) p. 10f.
contributor: Katrina Donovan
comment: Examples: Internaltion Federation of Red Cross and Red Crescent Societies, Oxfam, CARE, Doctors Without Borders, World Wildlife Fund, Transparency International, Human Rights Watch, Amnesty International, and Save the Children.
deprecated: true

obsolete private governance organizations
type: Class
subclass of: Obsolete Class
definition editor: Amanda Hicks
alternative term: private governance organizations
definition source: "Although the very meaning of the term is controversial, it involves authoritative decsionmaking in areas that once were part of national legal frameworks, the government, the sovereign state, or the public sector." Karns and Mingst (2004) p. 14.
contributor: Katrina Donovan
comment: Examples: private bond-rating agencies such as Moody's Investors Service, International Chamber of Commerce, Worldwide Responsible Apparel Manufacturing Principles, Forest Stewardship
deprecated: true

obsolete governmental organization
type: Class
subclass of: Obsolete Class
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".
definition editor: Amanda Hicks
alternative term: governmental organization
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.
deprecated: true

obsolete sovereign state
type: Class
subclass of: Obsolete Class
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.
definition editor: William R. Hogan
alternative term: nation
alternative term: nation state
alternative term: sovereign state
definition source: http://en.wikipedia.org/wiki/Sovereign_state
comment: Per Wikipedia, the word 'nation' does not always refer to soverign states. For example, the "nation of Islam".
deprecated: true

obsolete subnational entity
type: Class
subclass of: Obsolete Class
definition: a governmental organization that has a local, regional, or territorial government that recognizes a sovereign state as its higher political authority
definition editor: Amanda Hicks
definition editor: William R. Hogan
alternative term: subnational entity
deprecated: true

obsolete supranational entity
type: Class
subclass of: Obsolete Class
definition editor: Amanda Hicks
alternative term: supranational entity
comment: e.g., the EU
deprecated: true

material entity role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: inheres in
    some values from: material entity
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
subclass of: Restriction
  on property: inheres in
  all values from: material entity

organism role
type: Class
equivalent class: Class
  intersection of: material entity role
  intersection of: Restriction
    on property: inheres in
    some values from: organism
subclass of: material entity role
subclass of: Restriction
  on property: inheres in
  some values from: organism
subclass of: Restriction
  on property: inheres in
  all values from: organism

Homo sapiens role
type: Class
equivalent class: Class
  intersection of: organism role
  intersection of: Restriction
    on property: inheres in
    some values from: Homo sapiens
subclass of: organism role
subclass of: Restriction
  on property: inheres in
  some values from: Homo sapiens
subclass of: Restriction
  on property: inheres in
  all values from: Homo sapiens

organization role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: inheres in
    some values from: organization
subclass of: material entity role
subclass of: Restriction
  on property: inheres in
  some values from: organization
subclass of: Restriction
  on property: inheres in
  all values from: organization

hospital function
type: Class
subclass of: function
definition: A function inhering in a material entity that, if realized, is realized by the material entity being the site at which inpatient and outpatient healthcare is provided to a patient population.
definition editor: Mathias Brochhausen

school function
type: Class
subclass of: function
definition: A function inhering in a material entity that, if realized, is realized by that material entity being the site at which formal education is provided to a student population.
definition editor: Mathias Brochhausen

hospital role
type: Class
subclass of: health care provider organization role
definition: A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care.
definition editor: Mathias Brochhausen

school role
type: Class
subclass of: organization social role
definition editor: An organization social role that inheres in an organization and is realized by providing formal education to students.
definition editor: Mathias Brochhausen

hospital organization
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: bearer of
    some values from: hospital role
subclass of: organization
subclass of: Restriction
  on property: bearer of
  some values from: hospital role
definition: An organization that is the bearer of a hospital role.
definition editor: Mathias Brochhausen

school organization
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: bearer of
    some values from: school role
subclass of: organization
subclass of: Restriction
  on property: bearer of
  some values from: school role
definition: An organization that is the bearer of a school role.
definition editor: Mathias Brochhausen

student role
type: Class
subclass of: Class
  intersection of: human role within an organization
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: deontic declaration
      intersection of: Restriction
        on property: obsolete has active participant
        some values from: school organization
definition: A human social role that, if realized, is realized by the process of formal education that the bearer undergoes.
definition editor: Mathias Brochhausen

nursery school role
type: Class
subclass of: school role
definition editor: Mathias Brochhausen

primary school role
type: Class
subclass of: school role
definition editor: Mathias Brochhausen

architectural structure
type: Class
subclass of: material entity
definition: A material entity that is a human made strcuture with firm connection between its foundation and the ground.
definition editor: Mathias Brochhausen
definition source: http://de.wikipedia.org/wiki/Bauwerk
comment: "Building" is a subclass of this.
comment: This type of entity is referred to as "Bauwerk" or "Bauliche Anlage".

facility
type: Class
equivalent class: Class
  intersection of: architectural structure
  intersection of: Restriction
    on property: bearer of
    some values from: function
subclass of: architectural structure
subclass of: Restriction
  on property: is administered by
  some values from: organization
subclass of: Restriction
  on property: bearer of
  some values from: function
definition: An architectural structure that bears some function.
definition editor: Mathias Brochhausen

Axiom
annotated source: facility
annotated property: subClassOf
annotated target: Restriction
  on property: is administered by
  some values from: organization
version info: 09/09/2017

hospital facility
type: Class
equivalent class: Class
  intersection of: Class
    union of: Restriction
      on property: is owned by
      some values from: hospital organization
    union of: Restriction
      on property: is administered by
      some values from: hospital organization
  intersection of: Restriction
    on property: bearer of
    some values from: hospital function
subclass of: health care facility
subclass of: Restriction
  on property: contains process
  some values from: acute care encounter
subclass of: Restriction
  on property: bearer of
  some values from: hospital function
definition: A health care facility that bears the function to provide acute and intensive healthcare services and that is run by a hospital organization and is the bearer of a hospital function.
definition editor: Mathias Brochhausen
definition editor: William Hogan

school facility
type: Class
equivalent class: Class
  intersection of: facility
  intersection of: Class
    union of: Restriction
      on property: is owned by
      some values from: school organization
    union of: Restriction
      on property: is administered by
      some values from: school organization
  intersection of: Restriction
    on property: bearer of
    some values from: school function
subclass of: facility
subclass of: Restriction
  on property: bearer of
  some values from: school function
definition: A facility that is run by a school organization and is the bearer of a school function.
definition editor: Mathias Brochhausen

secondary school role
type: Class
subclass of: school role
definition editor: Mathias Brochhausen

pediatric trauma patient role
type: Class
subclass of: human patient role
definition: A trauma patient role that inheres in a homo sapiens who is under the age of 15 years.
definition editor: Amanda Hicks
alternative term: pediatric trauma patient
definition source: The following definition for 'pediatric trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. "A trauma patient who is under the age of 15 years."

injured patient role
type: Class
equivalent class: Class
  intersection of: patient role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: has part
        some values from: injury
subclass of: patient role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: has part
      some values from: injury
definition: A patient role that inheres an organism suffering one or more injuries.
definition editor: Amanda Hicks
alternative term: injured patient
definition source: The following definition for 'injured patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient suffering one or more injuries.

burn patient role
type: Class
subclass of: injured patient role
definition: A patient role that inheres in an organism suffering a thermal, electrical, chemical or radiation burn.
definition editor: Amanda Hicks
definition editor: The following definition for 'burn patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient suffering a thermal, electrical, chemical or radiation burn.
definition editor: burn patient

physiatrist role
type: Class
subclass of: physician role
definition: A physician role that is created by training and certification in rehabilitation/physical medicine and that is realized by the provision of or supervising of the provision of rehabilitation or physical therapy to a patient.
definition editor: Amanda Hicks
alternative term: physiatrist
definition source: The following definition for 'physiatrist' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A physician with training and certification in rehabilitation/physical medicine.
comment: Definition updated May 5, 2016. Original definitions was, a health care role borne by a human being and realized by training and certification in rehabilitation medicine.

trauma patient role
type: Class
subclass of: patient role
definition: A patient role that inheres in an organism with some non-superficial traumatic injury. The role is realized by admision to a hospital, transfer from one hospital to another for the purpose of trauma care, or has death as a result of the traumatic injury.
definition editor: Amanda Hicks
alternative term: trauma patient
definition source: The following definition for 'trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient sustaining an injury who has been admitted to the hospital, transferred from one hospital to another for the purpose of trauma care, or has died as a result of the traumatic injury.

housing unit
type: Class
subclass of: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has part
    some values from: site
  intersection of: Restriction
    on property: has part
    some values from: material entity
  intersection of: Restriction
    on property: bearer of
    qualified cardinality: 1
    on class: residence function
definition: A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function.
definition editor: Amanda Hicks
definition source: https://github.com/ufbmi/OMRSE/wiki/Housing-unit-and-Household
comment: Housing units are individuated by their residence functions.

residence function
type: Class
subclass of: function
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has part
      some values from: site
definition: A function that inheres in a material entity and, if realized, is realized by protecting persons and their possessions from weather and by some person or group of persons habitually sleeping in at least one site that is contained by that material entity.
definition editor: Amanda Hicks

household
type: Class
equivalent class: Class
  intersection of: Class
    union of: Homo sapiens
    union of: collection of humans
  intersection of: Restriction
    on property: participates in
    some values from: Class
      intersection of: process
      intersection of: Restriction
        on property: realizes
        some values from: residence function
      intersection of: Restriction
        on property: occurs in
        some values from: housing unit
subclass of: material entity
subclass of: Restriction
  on property: participates in
  some values from: Class
    intersection of: process
    intersection of: Restriction
      on property: realizes
      some values from: residence function
    intersection of: Restriction
      on property: occurs in
      some values from: housing unit
definition: A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of that housing unit's residence function.
definition editor: Amanda Hicks
comment: Note in OMRSE it is the housing unit, not the people living there, that are the bearers of a "residence function". Note the distinction between being a residence and a resident.
comment: Note that it is not possible in OWL 2, at least that we have yet found, to say that the housing unit in which the process occurs is the same one that is the bearer of the residence function (that the process realizes).

job role
type: Class
subclass of: Class
  intersection of: role in human social processes
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: deontic declaration
      intersection of: Restriction
        on property: obsolete has active participant
        some values from: Class
subclass of: Restriction
  on property: realized in
  some values from: employment process
definition: A role in human social processes that, if realized, is realized when the bearer provides labor or services in exchange for a wage or salary as specified by some deontic declaration.
definition editor: Amanda hicks
alternative term: employee

workplace facility
type: Class
subclass of: facility
subclass of: Restriction
  on property: bearer of
  some values from: workplace function
definition editor: Amanda Hicks

workplace function
type: Class
subclass of: function
definition: a function inhering in a material entity that, if realized, is realized by that material entity being the site where the work of some organization is carried out
definition editor: Amanda Hicks

US census householder role
type: Class
subclass of: human social role
definition: A US Census householder role is a human social role that, if realized, is realized by that person being a member of a household and either owning or renting the housing unit in which that household resides and being designated as the householder. If there is only one member of the household who owns or rents the housing unit, that person is designated the householder by default.
definition editor: Amanda Hicks
definition source: http://www.census.gov/cps/about/cpsdef.html last accessed on June 30, 2015

US Census reference person role
type: Class
subclass of: human social role
subclass of: Restriction
  on property: realized in
  some values from: documenting
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: member of
      some values from: household
definition: A US cenus reference person role is a human social role that inheres in a Homo sapiens who is a member of a household and is realized by other persons in the household being recorded in the US census in relation to that person.
definition editor: Amanda Hicks
definition source: http://www.census.gov/cps/about/cpsdef.html last accessed June 30, 2015

obsolete OMB ethnic identity datum
type: Class
subclass of: obsolete ethnic identity datum
definition: An ethnic identity datum that is the output of an ethnic identification process that uses OMB terminology for ethnicity or terminology that is mapped the OMB ethnicity terms.
definition editor: Amanda Hicks
term replaced by: OMB ethnic identity information content entity
deprecated: true

enrollment end date
type: Class
subclass of: one-dimensional temporal region

obsolete socio-legal human social role
type: Class
subclass of: human social role
subclass of: Obsolete Class
definition editor: A role that concretizes a socio-lega generically dependent continuant
definition editor: Amanda Hicks
deprecated: true

human role within an organization
type: Class
subclass of: Class
  intersection of: human social role
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: deontic declaration
      intersection of: Restriction
        on property: obsolete has active participant
        some values from: Class
definition: A human social role that is created by a deontic declaration performed by an organization.
definition editor: Amanda Hicks
alternative term: human organizational role

employer role
type: Class
subclass of: role in human social processes
subclass of: Restriction
  on property: realized in
  some values from: employment process
definition: a role in human social processes that is realized when the bearer provides a wage or salary in exchange for some labour or services as specified by some declaration

age measurement datum
type: Class
subclass of: time measurement datum

contract
type: Class
subclass of: document
definition: A document that records a legally binding agreement between two or more parties.
editor note: A contract is a document that is the specified output of a legally binding document act and records a legally binding agreement between two or more parties.

indemnity contract
type: Class
subclass of: Class
  intersection of: contract
  intersection of: Restriction
    on property: has part
    some values from: conditional specification
  intersection of: Restriction
    on property: has part
    some values from: objective specification
  intersection of: Restriction
    on property: has part
    some values from: action specification
  intersection of: Restriction
    on property: has part
    some values from: plan specification
definition: A contract by which one party secures the other against pecuniary loss by payment of a sum of money if a specified event occurs.
definition editor: Amanda Hicks

insurance policy
type: Class
subclass of: indemnity contract
subclass of: Class
  intersection of: indemnity contract
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: deontic document act
      intersection of: Restriction
        on property: obsolete has active participant
        some values from: insurance company
      intersection of: Restriction
        on property: obsolete has active participant
        some values from: Class
definition: An indemnity contract that distributes risk among a group of people
definition editor: Amanda Hicks

insured party role
type: Class
subclass of: role in human social processes
subclass of: Class
  intersection of: role in human social processes
  intersection of: Restriction
    on property: participates in
    some values from: Class
      intersection of: deontic document act
      intersection of: Restriction
        on property: has_specified_output
        some values from: insurance policy
  intersection of: Restriction
    on property:
      inverse of: is about
    some values from: Class
      intersection of: conditional specification
      intersection of: Restriction
        on property: part of
        some values from: insurance policy
definition: A role that inheres in an organism that is able to receive benefits from an insurance policy. The role, if realized, is realized by receiving benefits that are covered by the insurance policy.
definition editor: Amanda Hicks

insurance company
type: Class
subclass of: organization
subclass of: Class
  intersection of: organization
  intersection of: Restriction
    on property: bearer of
    some values from: party to an insurance policy
  intersection of: Restriction
    on property: bearer of
    some values from: Class
      intersection of: payer role
      intersection of: Restriction
        on property: is_specified_output_of
        some values from: deontic document act
  intersection of: Restriction
    on property:
      inverse of: is about
    some values from: Class
      intersection of: action specification
      intersection of: Restriction
        on property: part of
        some values from: insurance policy
definition: An organization that secures a group of people against pecuniary loss by payment of a sum of money if a a specified event occurs.
definition editor: Amanda Hicks

policy holder role
type: Class
subclass of: Class
  intersection of: insured party role
  intersection of: Restriction
    on property: inheres in
    some values from: Restriction
      on property: bearer of
      some values from: party to an insurance policy
definition: An insured party role that inheres in a person who participates in the creation of the insurance contract and is eligible to receive benefits as specified by the insurance contract.
definition editor: Amanda Hicks

payer role
type: Class
subclass of: role in human social processes

party to an insurance policy
type: Class
subclass of: party to a legal agreement

enrollment start date
type: Class
subclass of: one-dimensional temporal region

obsolete racial identity datum
type: Class
equivalent class: Class
  intersection of: obsolete identity datum
  intersection of: Restriction
    on property: part of
    some values from: documented identity
  intersection of: Restriction
    on property: has part
    some values from: Restriction
      on property: is_specified_output_of
      some values from: racial identification process
  intersection of: Restriction
    on property: is about
    some values from: Homo sapiens
subclass of: obsolete identity datum
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: is_specified_output_of
    some values from: racial identification process
definition: A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
term replaced by: racial identity information content entity
deprecated: true

racial identification process
type: Class
subclass of: Class
  intersection of: identification process
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: part of
      some values from: obsolete racial identity datum

obsolete ethnic identity datum
type: Class
equivalent class: Class
  intersection of: obsolete identity datum
  intersection of: Restriction
    on property: part of
    some values from: documented identity
  intersection of: Restriction
    on property: has part
    some values from: Restriction
      on property: is_specified_output_of
      some values from: ethnic identification process
  intersection of: Restriction
    on property: is about
    some values from: Homo sapiens
subclass of: obsolete identity datum
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: is_specified_output_of
    some values from: ethnic identification process
definition: An ethnic identity datum is an information content entity that is the output of some ethnic identitification process and is intended to be a truthful statement about the cultural or national heritage of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
definition editor: Amanda Hicks
term replaced by: ethnic identity information content entity
deprecated: true

ethnic identification process
type: Class
subclass of: Class
  intersection of: identification process
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: part of
      some values from: obsolete ethnic identity datum

health care facility
type: Class
subclass of: facility
subclass of: Class
  union of: Class
    intersection of: facility
    intersection of: Restriction
      on property: is owned by
      some values from: Restriction
        on property: bearer of
        some values from: health care provider organization role
  union of: Restriction
    on property: is administered by
    some values from: Restriction
      on property: bearer of
      some values from: health care provider organization role
definition editor: A facility bearing the function to provide healthcare and that is administered by a health care organization for the purpose of providing health care to a patient or patient population.
definition editor: William Hogan

US Census unemployed role
type: Class
subclass of: human social role
definition: A human social role that inheres in a human who is legally eligible to work, is conferred by the U.S. Census Bureau, and is realized by the bearer not working and either making active efforts to find employment in the four weeks prior to the reference week or waiting to be recalled from temporary layoff.
definition editor: Amanda Hicks

hospice facility
type: Class
subclass of: health care facility
subclass of: Restriction
  on property: contains process
  some values from: skilled nursing encounter
subclass of: Restriction
  on property: bearer of
  some values from: hospice function
definition: A health care facility that bears a function to provide healthcare to the sick or terminally ill
definition editor: Amanda Hicks
definition editor: Emma Norris
definition editor: William Hogan
definition source: Human Behaviour Change Project

skilled nursing facility
type: Class
subclass of: community living health care facility
subclass of: Restriction
  on property: contains process
  some values from: skilled nursing encounter
subclass of: Restriction
  on property: bearer of
  some values from: skilled nursing function
definition editor: Amanda Hicks

rehabilitation facility
type: Class
subclass of: community living health care facility
subclass of: Restriction
  on property: contains process
  some values from: skilled nursing encounter
subclass of: Restriction
  on property: bearer of
  some values from: rehabilitation function
definition: A facility to assist in physical or addiction recovery
definition editor: Amanda Hicks
definition editor: Emma Norris
definition editor: William Hogan
definition source: Human Behaviour Change Project

nursing home facility
type: Class
subclass of: community living health care facility
subclass of: Restriction
  on property: contains process
  some values from: skilled nursing encounter
subclass of: Restriction
  on property: bearer of
  some values from: nursing home function
definition: A facility that is run by a nursing home organization and is the bearer of a nursing home function.
definition editor: Amanda Hicks

residential health care facility
type: Class
subclass of: community living health care facility
subclass of: Restriction
  on property: bearer of
  some values from: residential function
definition: A community living health care facility that provides health care services in a home-like setting
definition editor: Amanda Hicks
definition editor: William Hogan

overnight dialysis facility
type: Class
subclass of: health care facility
subclass of: Restriction
  on property: contains process
  some values from: dialysis
subclass of: Restriction
  on property: contains process
  some values from: skilled nursing encounter
subclass of: Restriction
  on property: bearer of
  some values from: overnight dialysis function
definition editor: Amanda Hicks

outpatient clinic facility
type: Class
subclass of: health care facility
subclass of: Restriction
  on property: bearer of
  some values from: outpatient clinic function
definition: A health care facility that bears a function to provide low intensity healthcare services to patients on a short-term basis, with patients leaving on the same date as arriving (i.e., without them staying overnight)
definition editor: Amanda Hicks
definition editor: Emma Norris
definition editor: William Hogan
definition source: Human Behaviour Change Project
comment: Broadened from treatment to healthcare services generally. "Low intensity" is not defined at the moment, but is needed to differentiate from same-day surgery centers or observation stays in hospitals that last <24 hours. The idea is that few invasive procedures are performed, and the ones that are invasive are not typically much worse than a blood draw. Maybe bone marrow biopsy is as aggressive as it gets. I wonder if hematologists do that on an outpatient basis.

physician office facility
type: Class
subclass of: health care facility
subclass of: Restriction
  on property: bearer of
  some values from: physician office function
definition editor: Amanda Hicks

ambulatory surgery facility
type: Class
subclass of: health care facility
subclass of: Restriction
  on property: contains process
  some values from: surgery
subclass of: Restriction
  on property: bearer of
  some values from: ambulatory surgery function
definition editor: Amanda Hicks

urgent care facility
type: Class
subclass of: health care facility
subclass of: Restriction
  on property: bearer of
  some values from: urgent care function
definition editor: Amanda Hicks

emergency department facility
type: Class
subclass of: health care facility
subclass of: Restriction
  on property: contains process
  some values from: acute care encounter
subclass of: Restriction
  on property: bearer of
  some values from: emergency department function
definition: A health care facility that bears a function to provide emergency healthcare services and the acute care of patients who present without prior appointment, having arrived either by their own means or by ambulance
definition editor: Amanda Hicks
definition editor: Emma Norris
definition editor: William Hogan
definition source: Adapted from Human Behaviour Change Project

urgent care function
type: Class
subclass of: function

ambulatory surgery function
type: Class
subclass of: function
subclass of: Restriction
  on property: realized in
  some values from: surgery
definition editor: Amanda Hicks

hospice function
type: Class
subclass of: palliative function

emergency department function
type: Class
subclass of: function

physician office function
type: Class
subclass of: function

outpatient clinic function
type: Class
subclass of: function

overnight dialysis function
type: Class
subclass of: function
subclass of: Restriction
  on property: realized in
  some values from: dialysis

rehabilitation function
type: Class
subclass of: function

skilled nursing function
type: Class
subclass of: function

residential function
type: Class
subclass of: function

nursing home function
type: Class
subclass of: function

patient discharge
type: Class
subclass of: deontic document act
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: document
      intersection of: Restriction
        on property: has part
        some values from: plan specification
  intersection of: Restriction
    on property: obsolete has active participant
    some values from: Class
      intersection of: Homo sapiens
      intersection of: Restriction
        on property: bearer of
        some values from: health care provider role
subclass of: Restriction
  on property: ends
  some values from: inpatient encounter
subclass of: Restriction
  on property:
    inverse of: before
  some values from: admission process
definition: A deontic document act that concludes an inpatient encounter.
definition editor: Amanda Hicks
alternative term: discharge process

obsolete hispanic or latino identity datum
type: Class
subclass of: obsolete OMB ethnic identity datum
definition: An OMB ethnic identity datum that indicates the person identified is of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race.
definition editor: Amanda Hicks
term replaced by: OMB Hispanic or Latino identity information content entity
deprecated: true

obsolete not hispanic or latino identity datum
type: Class
subclass of: obsolete OMB ethnic identity datum
definition: An OMB ethnic identity datum that indicates the person identified is not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race.
definition editor: Amanda Hicks
term replaced by: OMB not Hispanic or Latino identity information content entity
deprecated: true

US physician assistant role
type: Class
subclass of: health care provider role
subclass of: Homo sapiens role
definition: A human health care provider role that inheres in a human being that is created by state licensing and that is realized by taking patient histories, performing physical exams, diagnosing illnesses, developing treatment plans, ordering lab tests, prescribing medications, counselling and educating patients, suturing wounds, and assisting in surgery under the supervision of a physician or a surgeon.

anesthesiologist role
type: Class
subclass of: physician role
definition: A physician role that inheres a human being and, if it is realized, is realized either by administering medication for the temporary general or local suppression of sensory or motor nerve function during some health care encounter or by making decisions independently of a supervising physician regarding the adminstration of such medication.

OMB racial identification process
type: Class
subclass of: racial identification process
subclass of: Restriction
  on property: has_specified_output
  some values from: obsolete OMB racial identity datum

obsolete identity datum
type: Class
equivalent class: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: part of
    some values from: documented identity
  intersection of: Restriction
    on property: has part
    some values from: Restriction
      on property: is_specified_output_of
      some values from: identification process
  intersection of: Restriction
    on property: is about
    some values from: Homo sapiens
subclass of: answer to identity question
subclass of: Restriction
  on property: part of
  some values from: documented identity
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: is_specified_output_of
    some values from: identification process
subclass of: Restriction
  on property: is about
  some values from: Homo sapiens
definition: An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method.
term replaced by: social identity information content entity
creator: Amanda Hicks
deprecated: true

obsolete gender identity datum
type: Class
equivalent class: Class
  intersection of: obsolete identity datum
  intersection of: Restriction
    on property: part of
    some values from: documented identity
  intersection of: Restriction
    on property: has part
    some values from: Restriction
      on property: is_specified_output_of
      some values from: gender identification process
  intersection of: Restriction
    on property: is about
    some values from: Homo sapiens
subclass of: obsolete identity datum
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: is_specified_output_of
    some values from: gender identification process
definition: A gender identity is an information content entity that is the output of some gender identitification process and is intended to be a truthful statement about a person's subjective sense of their gender. Unlike data items they are not necessilary contributed or acquired by a reliable method.
term replaced by: gender identity information content entity
creator: Amanda Hicks
deprecated: true

identification process
type: Class
subclass of: social act
creator: Amanda Hicks

gender identification process
type: Class
subclass of: Class
  intersection of: identification process
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: part of
      some values from: obsolete gender identity datum

obsolete female gender identity datum
type: Class
subclass of: obsolete gender identity datum
definition: a gender identity datum resulting from a gender identification process in which ‘female’ is selected based on the participant's subjective sense of gender
definition editor: Amanda Hicks
term replaced by: female gender identity information content entity
deprecated: true

surgeon role
type: Class
subclass of: physician role
subclass of: Restriction
  on property: realized in
  some values from: surgery

neurosurgeon role
type: Class
subclass of: surgeon role
definition: A surgeon role realized by its bearer using performing neurosurgery.

obsolete male gender identity datum
type: Class
subclass of: obsolete gender identity datum
definition: a gender identity datum resulting from a gender identification process in which ‘male’ is selected based on the participant's subjective sense of gender
definition editor: Amanda Hicks
term replaced by: male gender identity information content entity
deprecated: true

human traveling information
type: Class
equivalent class: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: is about
    some values from: human travel
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: human travel
definition: An information content entity that is about human travel.
definition source: https://github.com/ufbmi/OMRSE/issues/79
contributor: Jie Zheng
creator: Amanda Hicks

household identifier
type: Class
equivalent class: Class
  intersection of: symbol
  intersection of: Restriction
    on property: denotes
    some values from: household
subclass of: symbol
subclass of: Restriction
  on property: denotes
  some values from: household
contributor: A symbol that denotes a specific household
contributor: Jie Zheng
creator: Amanda Hicks

family identifier
type: Class
equivalent class: Class
  intersection of: symbol
  intersection of: Restriction
    on property: denotes
    some values from: family
subclass of: symbol
subclass of: Restriction
  on property: denotes
  some values from: family
definition: A symbol that denotes a family.
contributor: Jie Zheng
creator: Amanda Hicks

obsolete self-identity data item
type: Class
subclass of: obsolete identity datum
definition: an identity datum that has been asserted by the person whom it is about
definition editor: Amanda Hicks
deprecated: true

employment process
type: Class
subclass of: planned process
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: job role
  intersection of: Restriction
    on property: realizes
    some values from: employer role
definition: A planned process in which the bearer of an employer role provides wages or salary to the bearer of an employee roll in fullfillment of the arrangements specified in some declaration

pediatric surgeon role
type: Class
subclass of: surgeon role
definition: A surgeon role borne by a human being and that, if realized, is realized by its bearer using operative manual and instrumental techniques on preadult patients to investigate and/or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas.
definition editor: Amanda Hicks

adult foster home facility
type: Class
subclass of: community living health care facility
subclass of: Restriction
  on property: bearer of
  some values from: adult foster home function
definition: a facility that is run by an adult foster home organization and is the bearer of an adult foster home organization
definition editor: Amanda Hicks

adult foster home function
type: Class
subclass of: function

community living health care facility
type: Class
subclass of: health care facility
subclass of: Restriction
  on property: contains process
  some values from: assistance with activities of daily living care encounter
subclass of: Restriction
  on property: contains process
  some values from: assistance with instrumental activities of daily living encounter
subclass of: Restriction
  on property: bearer of
  some values from: residence function
definition: a health care facility that also bears a residence function and thus one in which the patients are also residents of the facility

registered nurse role
type: Class
subclass of: nurse role

skilled nursing encounter
type: Class
subclass of: health care encounter
subclass of: Restriction
  on property: realizes
  some values from: registered nurse role

assistive care encounter
type: Class
subclass of: planned process
definition: They include assistance with activities of daily living, assistance with instrumental activities of daily living, medication assistance, and health support http://ahca.myflorida.com/Medicaid/acs/index.shtml
definition editor: Amanda Hicks

assistance with activities of daily living care encounter
type: Class
subclass of: assistive care encounter

assistance with instrumental activities of daily living encounter
type: Class
subclass of: assistive care encounter

medication assistance care encounter
type: Class
subclass of: assistive care encounter

assisted living facility
type: Class
subclass of: community living health care facility
definition: A facility that is run by an assisted living facility organization and is the bearer of an assisted living facility function.

assisted living function
type: Class
subclass of: function

post-acute health care encounter
type: Class
subclass of: health care encounter
subclass of: Restriction
  on property: occurs in
  some values from: community living health care facility
disjoint with: acute care encounter
definition: temporally located after some acute care encounter Somehow involves skilled nursing encounters

acute care encounter
type: Class
subclass of: health care encounter

leaving a health care facility after receiving care
type: Class
subclass of: process
subclass of: Restriction
  on property: has_participant
  some values from: Restriction
    on property: bearer of
    some values from: patient role

obsolete medical advice
type: Class
subclass of: social act
deprecated: true

response to a question asking process
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: participates in
  some values from: questions asking process
comment: Note that not all responses to a question asking process are answers. For example, a refusal to answer is not an answer. A refusal to answer is also not a specified output of the question asking process since it does not acheive the objective of asking the question, which is to get an answer.

home health care organization
type: Class
subclass of: organization
subclass of: Restriction
  on property: bearer of
  some values from: function

home health care function
type: Class
subclass of: health care function
subclass of: Restriction
  on property: realized in
  some values from: assistance with activities of daily living care encounter
subclass of: Restriction
  on property: realized in
  some values from: assistance with instrumental activities of daily living encounter
subclass of: Restriction
  on property: realized in
  some values from: home health care encounter

home health care encounter
type: Class
subclass of: health care encounter
subclass of: Restriction
  on property: occurs in
  some values from: housing unit

questions asking process
type: Class
subclass of: occurrent
subclass of: Obsolete Class
subclass of: Restriction
  on property: has_participant
  some values from: Homo sapiens
subclass of: Restriction
  on property: has_participant
  some values from: material information bearer of question text plus answer set
term replaced by: information content entity-request process
deprecated: true

palliative function
type: Class
subclass of: health care function
subclass of: Restriction
  on property: realized in
  some values from: assistance with activities of daily living care encounter
subclass of: Restriction
  on property: realized in
  some values from: assistance with instrumental activities of daily living encounter
subclass of: Restriction
  on property: realized in
  some values from: palliative care encounter

palliative care encounter
type: Class
subclass of: health care encounter

hospice organization
type: Class
subclass of: organization
subclass of: Restriction
  on property: bearer of
  some values from: hospice function

health care function
type: Class
equivalent class: Class
  intersection of: function
  intersection of: Restriction
    on property: realized in
    some values from: health care encounter
subclass of: function
subclass of: Restriction
  on property: realized in
  some values from: health care encounter

material information bearer of question text plus answer set
type: Class
subclass of: material entity
deprecated: true

refusal to answer datum
type: Class
subclass of: response to a question asking process

response to an identity question asking process
type: Class
subclass of: response to a question asking process

identity question asking process
type: Class
subclass of: questions asking process
deprecated: true

ethnic identity question asking process
type: Class
subclass of: identity question asking process
term replaced by: information content entity request about ethnic identity
deprecated: true

race identity question asking process
type: Class
subclass of: identity question asking process
term replaced by: information content entity request about racial identity
deprecated: true

answer to identity question
type: Class
subclass of: response to an identity question asking process

obsolete American Indian or Alaska Native identity datum
type: Class
subclass of: obsolete OMB racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment.
definition editor: Amanda Hicks
term replaced by: OMB American Indian or Alaska Native identity information content entity
deprecated: true

obsolete Asian identity datum
type: Class
subclass of: obsolete OMB racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent.
definition editor: Amanda Hicks
term replaced by: OMB Asian identity information content entity
deprecated: true

obsolete black or African American identity datum
type: Class
subclass of: obsolete OMB racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the black racial groups of Africa.
definition editor: Amanda Hicks
term replaced by: OMB black or African American identity information content entity
deprecated: true

obsolete Native Hawaiian or other Pacific Islander identity datum
type: Class
subclass of: obsolete OMB racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands.
definition editor: Amanda Hicks
term replaced by: OMB Native Hawaiian or other Pacific Islander identity information content entity
deprecated: true

obsolete white identity datum
type: Class
subclass of: obsolete OMB racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Europe, the Middle East, or North Africa.
definition editor: Amanda Hicks
term replaced by: OMB white identity information content entity
deprecated: true

obsolete OMB racial identity datum
type: Class
subclass of: obsolete racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms.
definition editor: Amanda Hicks
term replaced by: OMB racial identity information content entity
deprecated: true

heavy smoker role
type: Class
subclass of: smoker role
definition: A role that inheres in an organism and is realized by habitually smoking 10 or more tobacco cigerettes a day or the equivalent in other tobacco products.

light smoker role
type: Class
subclass of: smoker role
definition: A role that inheres in an organism and is realized by habitually smoking 1>10 tobacco cigerettes a day or the equivalent in other tobacco products.

answer set
type: Class
subclass of: information content entity

question text
type: Class
subclass of: information content entity

option as member of some answer set
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: member of
  some values from: answer set

residential facility
type: Class
subclass of: facility
editor preferred term: residential facility
definition: A facility that has at least one housing unit as part in which a person or persons live
definition editor: Emma Norris
definition editor: William Hogan
definition source: Modified version of definition provided by Human Behaviour Change Project

communication
type: Class
subclass of: process
subclass of: Restriction
  on property: has_participant
  some values from: material entity
subclass of: Restriction
  on property: has_participant
  some values from: information content entity
definition: A process in which some participant shares some information content entity about some state of that participant with some other participant.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: William R. Hogan
comment: The term 'participant' in the definition need not refer to a human agent.

linguistic competence
type: Class
subclass of: disposition
subclass of: Restriction
  on property: realized in
  some values from: communication
subclass of: Restriction
  on property: inheres in
  some values from: material entity
definition: A disposition inhering in a material entity that, if realized, is realized by that material entity’s communicating via some linguistic concretization.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: William R. Hogan

language
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: has member
    some values from: linguistic competence
  intersection of: Restriction
    on property: has member
    all values from: linguistic competence
subclass of: Restriction
  on property: realized in
  some values from: communication
definition: A disposition inhering in a linguistic community that (i) is a maximal aggregate of communicatively compatible linguistic competences, and (ii) if realized, is realized by any and all realizations of those linguistic competences.
definition editor: William R. Hogan
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: S. Clint Dowland

linguistic community
type: Class
subclass of: material entity
subclass of: Class
  intersection of: Restriction
    on property: has member
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: bearer of
        some values from: linguistic competence
  intersection of: Restriction
    on property: has member
    all values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: bearer of
        some values from: linguistic competence
subclass of: Restriction
  on property: bearer of
  some values from: language
definition: A maximal aggregate of material entities such that each member bears a linguistic competence for the same language.
definition editor: Matthew Diller
contributor: Mathias Brochhausen
contributor: S. Clint Dowland
contributor: William R. Hogan

expression of preferred language
type: Class
subclass of: planned process
subclass of: communication
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: specifically dependent continuant
    intersection of: Restriction
      on property: concretizes
      some values from: preferred language information content entity
definition: A communication in which some participant states a preference for some communicative process to be in a certain language, and that has a concretization of a preferred language information content entity as its specified output.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: William R. Hogan

preferred language information content entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: linguistic competence
subclass of: Restriction
  on property: is about
  some values from: language
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: bearer of
      some values from: linguistic competence
definition: An information content entity that (i) is about some person, some language, and some linguistic competence; and (ii) conveys the language with which that person prefers to communicate within some given context.
definition editor: Mathias Brochhausen
contributor: Matthew Diller
contributor: S. Clint Dowland
contributor: William R. Hogan

information content entity-request process
type: Class
subclass of: communication
definition: a communication in which some participant requests of some other participant an information content entity about some portion of reality
definition editor: S. Clint Dowland
comment: As with the parent class, 'participant' in the definition need not refer to a human agent.
comment: The medium and grammatical form are irrelevant. For example, the request may be written or spoken, and while it may be in the form of a question, it need not be.

information content entity request about ethnic identity
type: Class
subclass of: information content entity-request process
definition: an information content entity-request process in which some participant requests of some other participant an information content entity that indicates the ethnic identity of that other participant
definition editor: S. Clint Dowland

information content entity request about racial identity
type: Class
subclass of: information content entity-request process
definition: an information content entity-request process in which some participant requests of some other participant an information content entity that indicates the racial identity of that other participant
definition editor: S. Clint Dowland

admission process
type: Class
subclass of: deontic document act
subclass of: Restriction
  on property: before
  some values from: patient discharge
subclass of: Restriction
  on property: starts
  some values from: inpatient encounter
definition: A deontic document act in which a patient is registered with a health care provider for the purpose of receiving care in an inpatient encounter.
definition editor: Amanda Hicks

cancer summary staging
type: Class
subclass of: planned process
editor preferred term: cancer summary staging
example of usage: The cancer summary staging performed on patient John Doe's clinical picture.
definition: A planned process of determining the extent to which a cancer disease has developed by growing and spreading throughout an organism.
definition editor: Mathias Brochhausen
alternative term: tumor summary staging

cancer summary staging code
type: Class
subclass of: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: cancer summary staging
editor preferred term: cancer summary staging code
example of usage: The cancer summary staging code that is the outcome of the cancer summary staging performed on patient John Doe's clinical picture.
definition: An information content entity that is the specified output of cancer summary staging.
definition editor: Mathias Brochhausen
alternative term: tumor summary staging code

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.
definition editor: S. Clint Dowland
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.
definition editor: S. Clint Dowland
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.
definition editor: S. Clint Dowland
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.
definition editor: S. Clint Dowland
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.
definition editor: S. Clint Dowland
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.
definition editor: S. Clint Dowland
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.
definition editor: S. Clint Dowland
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.
definition editor: S. Clint Dowland
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.
definition editor: S. Clint Dowland
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.
definition editor: S. Clint Dowland
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.
definition editor: S. Clint Dowland
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.
definition editor: S. Clint Dowland
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.
definition editor: S. Clint Dowland
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.
definition editor: S. Clint Dowland
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.
definition editor: S. Clint Dowland
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.
definition editor: S. Clint Dowland
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

sexual orientation 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 having some sexual orientation.
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

residence ZIP code information content entity
type: Class
subclass of: information content entity
definition: An information content entity that is about some geographical region, in which a postal delivery route denoted by a particular ZIP code is realized, and that is the specified output of a disclosure of residence.
definition editor: Matthew Diller
contributor: Hansi Zhang
contributor: Mathias Brochhausen
contributor: S. Clint Dowland
contributor: Sarah Bost
contributor: William R. Hogan

disclosure of residence
type: Class
subclass of: social act
definition: A social act that creates an information content entity that is about some geographical region in which a human being dwells.
definition editor: Matthew Diller
contributor: Hansi Zhang
contributor: Mathias Brochhausen
contributor: S. Clint Dowland
contributor: Sarah Bost
contributor: William R. Hogan

electronic health record data set
type: Class
subclass of: data set
definition: A data set whose members are obtained from one or more electronic health records.
definition editor: Matthew Diller
alternative term: EHR data set
contributor: Alan Ruttenberg
contributor: Mathias Brocchausen
contributor: S. Clint Dowland
contributor: Sarah Bost
contributor: William R. Hogan

health care claim data set
type: Class
subclass of: data set
definition: A data set whose members are the specified output of some process of adjudicating health care insurance claims (and whose inputs are at least partly some members of a health care billing data set).
definition editor: William R. Hogan
contributor: Alan Ruttenberg
contributor: Mathias Brocchausen
contributor: Matthew Diller
contributor: S. Clint Dowland
contributor: Sarah Bost
comment: It covers prescription claims because pharmacies bill insurance companies for patients’ prescriptions via submitting insurance claims.
comment: The insurance claim is submitted to the insurance company by either the patient or the provider. It is not necessarily always the provider, although in the United States, it typically is.
comment: The outcome of the adjudication of a claim in the claims dataset could be favorable or unfavorable for the healthcare provider, the patient, or both. The idea is just that they’ve been adjudicated, one way or the other (or anything in between if that’s a possibility).
comment: The reason we say billing data are only part of the input is because we are not conflating the insurance claim with the bill. It is our understanding that the provider’s bill of services is either part of the claim or “attached” to it in some manner, but doesn’t constitute the entire claim itself.
comment: The sources of these data are held by insurers or other health plan providers.

health care billing data set
type: Class
subclass of: data set
definition: A data set whose members are obtained from billing-related data sources that (i) are generated by a health care organization as a result of internal administrative processes, and (ii) are about services rendered or materials used during some health care encounter.
definition editor: S. Clint Dowland
contributor: Alan Ruttenberg
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

health care administrative process
type: Class
subclass of: planned process
example of usage: Recording data in an EHR. Financial tasks for a healthcare organization. Scheduling shifts for health care workers.
definition: A planned process (i) that is neither a health care process nor an ancillary health care process, and (ii) in which some employee of a health care organization manages, or helps to manage, the performance of tasks that realize the functions of that organization.
definition editor: Matthew Diller
contributor: S. Clint Dowland

principal diagnosis-assignment process
type: Class
subclass of: health care administrative process
definition: A health care administrative process that has as input a diagnosis, and has as output a value indicating that diagnosis is about the condition that prompts the admission process that starts the encounter during which the diagnostic process that outputs that diagnosis begins.
definition editor: S. Clint Dowland
contributor: Matthew Diller

secondary diagnosis-assignment process
type: Class
subclass of: health care administrative process
definition: A health care administrative process that has as input a diagnosis, and has as output a value indicating that diagnosis is about an underlying condition that is distinct from the condition that prompts the admission process that starts the encounter during which the diagnostic process that outputs that diagnosis begins.
definition editor: S. Clint Dowland
contributor: Matthew Diller

county smoking survey plan specification
type: Class
subclass of: survey plan specification
example of usage: The Alachua county smoking survey plan specification.
definition: A survey plan specification that aims to collect information about the smoking behavior or lack thereof of a population on a county level. Concretization of a smoking survey plan that is stratified by county.
definition editor: Mathias Brochhausen
contributor: Hansi Zhang
contributor: Jiang Bian
contributor: Matthew Diller
contributor: S. Clint Dowland
contributor: Sarah Bost
contributor: William R. Hogan

county smoking survey execution
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: county smoking survey plan specification
subclass of: survey execution
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: county smoking survey plan specification
example of usage: The Alachua county smoking survey execution.
definition: A survey execution that realizes the concretization of a smoking survey plan specification that is stratified by county.
definition editor: Mathias Brochhausen
contributor: Hansi Zhang
contributor: Jiang Bian
contributor: Matthew Diller
contributor: S. Clint Dowland
contributor: Sarah Bost
contributor: William R. Hogan

county smoking survey data
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: county smoking survey execution
subclass of: survey data
subclass of: Restriction
  on property: is_specified_output_of
  some values from: county smoking survey execution
example of usage: The Alachua county smoking survey data.
definition: Survey data that is the specified output of a county smoking survey execution.
definition editor: Mathias Brochhausen
contributor: Hansi Zhang
contributor: Jiang Bian
contributor: Matthew Diller
contributor: S. Clint Dowland
contributor: Sarah Bost
contributor: William R. Hogan

smoking rate calculation
type: Class
subclass of: data transformation
example of usage: Calculating the Alachua County smoking rate from Alachua County smoking data.
definition: A data transformation that has data about the smoking status of a population as its specified input and a percentage or ratio of smokers in that population as a specified output.
definition editor: Mathias Brochhausen

county smoking rate data
type: Class
subclass of: data item
example of usage: The Alachua County smoking rate.
definition: A data item that is the specified output of a smoking rate calculation that has data about smoking behavior or lack there of on a county level.
definition editor: Mathias Brochhausen

job role data item
type: Class
equivalent class: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: Class
      union of: job role
      union of: Class
        intersection of: process
        intersection of: Restriction
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: Class
    union of: job role
    union of: Class
      intersection of: process
      intersection of: Restriction
        on property: realizes
        some values from: job role
example of usage: Can be about any aspect of employment, such as salary, work location, or employer.
definition: A data item that is about a person's job role and/or its realization.
definition editor: Matthew Diller
alternative term: employment data item
contributor: Chris Stoeckert
contributor: S. Clint. Dowland
contributor: William R. Hogan

income data item
type: Class
subclass of: socio-economic data item

government assistance health care plan data item
type: Class
subclass of: socio-economic data item

health care plan data item
type: Class
subclass of: socio-economic data item

government assistance income data item
type: Class
subclass of: socio-economic data item

WIC data item
type: Class
subclass of: socio-economic data item

socio-economic data item
type: Class
subclass of: data item

obsolete non-binary gender identity datum
type: Class
subclass of: obsolete gender identity datum
editor preferred term: non-binary gender identity datum
definition: A gender identity datum resulting from a gender identification process in which ‘non binary’ is selected based on the participant's subjective sense of gender.
definition editor: Paul Fabry
definition editor: William Hogan
term replaced by: non-binary gender identity information content entity
comment: Alternatively: A gender identity datum stating that a person's subjective sense of gender is non-binary.) Examples of usage: ‘Non-binary’, ‘Trigender’, ‘Agender’, ‘Genderfluid’, ‘2’ (intended to refer to a non-binary gender role)
deprecated: true

education process
type: Class
subclass of: planned process
editor preferred term: educating
definition: A planned process with an active participant who acquires mental representations of information content entities (ICEs), which had no previous mental representation in the cognitive system, and through repeated use or application of these ICEs becomes the bearer of a new instance of some type of capability, and the participant was not previously the bearer of that instance of that type of capability.
definition editor: William R. Hogan
elucidation: An act of acquiring new information and repeatedly applying that information to develop a new skill.
comment: An interesting question is whether there must be another participant who is the "educator". Some might object that many people are "self taught". A real case of being self taught is the first person who learned to play a stringed instrument, or to spin a ball on the top of a finger. There was no previous information about that. The ICEs acquired are via one's sensory systems (vision, proprioception, auditory, etc.). On the other hand, in the case of those who are self-taught by reading books or watching videos, or acquiring some other form of ICEs concretized outside their brain, one argument might be that the author of those ICEs somehow "plays a role" in the education, although they cannot participate in the education process itself (If I read Aristotle, and through repeated application of the information I acquire through doing so, develop the ability to write better ontology definitions, surely Aristotle did not actively participate in my particular education process, although he did influence it in a very real way).

educational objective
type: Class
equivalent class: Class
  intersection of: objective specification
  intersection of: Restriction
    on property: is about
    some values from: Restriction
      on property: realized in
      some values from: education process
subclass of: objective specification
subclass of: Restriction
  on property: is about
  some values from: Restriction
    on property: realized in
    some values from: education process
editor preferred term: educational objective specification
definition: An objective specification that describes the type of capability or capabilities to be imparted by its realization, which is an educating (education process).
definition editor: William R. Hogan
elucidation: An objective specification that describes the new knowledge & skill(s) to be obtained via an education process.

educational program
type: Class
equivalent class: Class
  intersection of: plan specification
  intersection of: Restriction
    on property: has part
    some values from: educational objective
subclass of: plan specification
subclass of: Restriction
  on property: has part
  some values from: educational objective
editor preferred term: educational plan specification
definition: A plan specification with an educational objective specification as part.
definition editor: William R. Hogan
elucidation: A plan specification with one or more educational objectives.
comment: Very broad. Covers everything from grade school to high school to college to graduate education, a MOOC, an individual course, a tutorial at a conference, a continuing education course or program, an informed consent video, etc, etc.

completing a program of education
type: Class
equivalent class: Class
  intersection of: education process
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes
      some values from: educational program
subclass of: education process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: educational program
editor preferred term: completing a program of eduction
definition: An educating that realizes a concretization of some program of education.
definition editor: William R. Hogan
comment: Note that parent class 'educating' and referenced class 'program of education' are defined elsewhere in this education module of OMRSE.
comment: This class refers extremely broadly to the successful realization of any program of education: a single course, first grade, MD, PhD, high school, the ninth grade, getting a black belt in karate, getting a master mechanic certification, a bachelor's degree, a masters degree, a graduate certificate, early childhood education program, and even getting a certificate at the end of some week-long workshop, summer camp, a certifcate from a cooking class, an actuarial certification.

early childhood education plan specification
type: Class
subclass of: educational program
subclass of: Class
  intersection of: educational program
  intersection of: Restriction
    on property: is concretized as
    some values from: Restriction
      on property: realized in
      all values from: Class
        intersection of: education process
        intersection of: Restriction
editor preferred term: early childhood education program
definition: An educational program whose intended active participant, when a concretization of it is realized, is a human child of age birth to 8 years or a human fetus prior to birth.
definition editor: William R. Hogan
alternative term: pre-K education program
alternative term: prekindergarten education program
alternative term: preschool education program
definition source: https://apps.who.int/iris/bitstream/handle/10665/69729/a91213.pdf

primary education program
type: Class
equivalent class: Class
  intersection of: educational program
  intersection of: Class
    complement of: Restriction
      on property: has part
      some values from: Class
        complement of: primary education objective
  intersection of: Restriction
    on property: has part
    some values from: primary education objective
subclass of: educational program
subclass of: Restriction
  on property: has part
  some values from: primary education objective
editor preferred term: primary education plan specification
definition: An education plan specification with one or more primary education objective specifications as parts, and these are the only objective specifications it has as parts.
definition editor: William R. Hogan
alternative term: elementary education
comment: In the united states, also called "elementary education"
comment: It can still have action specifications as parts, and possibly other ICEs as parts. That's why we cannot say it has only primary education objectives as parts, and we have to introduce the double negative in the class axiom.
comment: Primary education provides learning and educational activities typically designed to provide students with fundamental skills in reading, writing and mathematics (i.e. literacy and numeracy), and to establish a sound foundation for learning and solid understanding of core areas of knowledge and personal development, preparing for lower secondary education. It aims at learning at a basic level of complexity with little if any specialisation.

primary education objective
type: Class
subclass of: educational objective
editor preferred term: primary education objective specification
definition: An education objective specification that has a concretization that, when realized, results in the active participant's acquisition and development of fundamental skills in reading, writing and mathematics (i.e. literacy and numeracy).
definition editor: William R. Hogan
definition source: http://uis.unesco.org/en/glossary-term/primary-education-isced-1
comment: By the end of primary education, the student has established a sound foundation for learning and solid understanding of core areas of knowledge and personal development, preparing for lower secondary education. It aims at learning at a basic level of complexity with little if any specialisation.

lower secondary education objective
type: Class
subclass of: educational objective
editor preferred term: lower secondary education objective specification
definition: An education objective specification that has a concretization that, when realized, confers to the active participant skills and knowledge in subject areas more specialized than basic reading, writing, and mathematics, with the overall goal of laying the foundation for lifelong learning and human development on which education systems may systematically expand further educational opportunities.
definition editor: William R. Hogan
definition source: http://uis.unesco.org/en/glossary-term/lower-secondary-education-isced-2
comment: Examples of specific subjects could--but are not necessarily required to--include biology, history, science, literature, music, art. Programs at this level are usually organized around a more subject-oriented curriculum, introducing theoretical concepts across a broad range of subjects.
comment: Programmes at ISCED level 2, or ‘lower secondary’ education, are typically designed to build upon the fundamental teaching and learning processes which begin at ISCED level 1. Usually, the educational aim is to lay the foundation for lifelong learning and human development on which education systems may systematically expand further educational opportunities. Programmes at this level are usually organized around a more subject-oriented curriculum, introducing theoretical concepts across a broad range of subjects.

awarding an academic degree
type: Class
equivalent class: Class
  intersection of: deontic document act
  intersection of: Restriction
    on property: has_specified_output
    some values from: academic degree
subclass of: deontic document act
subclass of: Restriction
  on property: has_specified_output
  some values from: academic degree
editor preferred term: awarding of an academic degree
definition: A deontic document act that has as specified output an academic degree and that confers on recipient of the academic degree the recognition and the claims and obligations that accompany the degree.
definition editor: William R. Hogan
comment: Different degrees have different claims and obligations associated with them. For example, having a medical degree (either M.D. or D.O.) entitles a person to sit for stage 3 of the US Medical Licensing Exam (otherwise one may not take the exam).

basic education program
type: Class
equivalent class: Class
  intersection of: educational program
  intersection of: Restriction
    on property: has part
    some values from: primary education objective
  intersection of: Restriction
    on property: has part
    some values from: lower secondary education objective
subclass of: educational program
subclass of: Restriction
  on property: has part
  some values from: primary education objective
subclass of: Restriction
  on property: has part
  some values from: lower secondary education objective
editor preferred term: basic education plan specification
definition: An education plan specification that has as part both a primary educational objective specification and a lower secondary educational objective specification.
definition editor: William R. Hogan
definition source: http://uis.unesco.org/en/glossary-term/basic-education
comment: Most nations in the world mandate that children complete at least a basic education program. Some nations go further and include upper secondary education after basic education.
comment: Whole range of educational activities, taking place in various settings, that aim to meet basic learning needs as defined in the World Declaration on Education for All (Jomtien, Thailand, 1990). According to ISCED standard, basic education comprises primary education (first stage of basic education) and lower secondary education (second stage). It also covers a wide variety of non-formal and informal public and private activities intended to meet the basic learning needs of people of all ages.

lower secondary education program
type: Class
equivalent class: Class
  intersection of: educational program
  intersection of: Class
    complement of: Restriction
      on property: has part
      some values from: Class
        intersection of: educational objective
        intersection of: Class
  intersection of: Restriction
    on property: has part
    some values from: lower secondary education objective
  intersection of: Restriction
    on property: is concretized as
    some values from: Restriction
      on property: realized in
      some values from: completing a program of education
subclass of: educational program
subclass of: Restriction
  on property: has part
  some values from: lower secondary education objective
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: completing a program of education
editor preferred term: lower secondary education plan specification
definition: An education plan specification with one or more lower secondary education objective specifications as parts, and these are the only objective specifications it has as parts.
definition editor: William R. Hogan
comment: It can still have action specifications as parts, and possibly other ICEs as parts. That's why we cannot say it has only lower secondary education objectives as parts, and we have to introduce the double negative in the class axiom.
comment: Programmes at ISCED level 2, or ‘lower secondary’ education, are typically designed to build upon the fundamental teaching and learning processes which begin at ISCED level 1. Usually, the educational aim is to lay the foundation for lifelong learning and human development on which education systems may systematically expand further educational opportunities. Programmes at this level are usually organized around a more subject-oriented curriculum, introducing theoretical concepts across a broad range of subjects.
comment: Requires successful completion of a primary education program as a pre-requisite.

upper secondary education objective
type: Class
subclass of: educational objective
editor preferred term: upper secondary education objective specification
definition: An educational objective specification that has a concretization that, when realized, confers on the active participant skills and knowledge that prepare them for tertiary education, or employment, or both.
definition editor: William R. Hogan
definition source: http://uis.unesco.org/en/glossary-term/upper-secondary-education-isced-3
comment: Programmes at ISCED level 3, or ‘upper secondary’ education, are typically designed to complete secondary education in preparation for tertiary education, or to provide skills relevant to employment, or both. Programmes at this level offer students more varied, specialised and in-depth instruction than programmes at lower secondary education (ISCED level 2). They are more differentiated, with an increased range of options and streams available.

upper secondary education program
type: Class
equivalent class: Class
  intersection of: educational program
  intersection of: Class
    complement of: Restriction
      on property: has part
      some values from: Class
        intersection of: educational objective
        intersection of: Class
  intersection of: Restriction
    on property: has part
    some values from: upper secondary education objective
  intersection of: Restriction
    on property: is concretized as
    some values from: Restriction
      on property: realized in
      some values from: completing a program of education
subclass of: educational program
subclass of: Restriction
  on property: has part
  some values from: upper secondary education objective
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: completing a program of education
editor preferred term: upper secondary education plan specification
definition: An education plan specification with one or more upper secondary education objective specifications as parts, and these are the only objective specifications it has as parts.
definition editor: William R. Hogan
comment: It can still have action specifications as parts, and possibly other ICEs as parts. That's why we cannot say it has only lower secondary education objectives as parts, and we have to introduce the double negative in the class axiom.
comment: Programmes at ISCED level 3, or ‘upper secondary’ education, are typically designed to complete secondary education in preparation for tertiary education, or to provide skills relevant to employment, or both. Programmes at this level offer students more varied, specialised and in-depth instruction than programmes at lower secondary education (ISCED level 2). They are more differentiated, with an increased range of options and streams available.
comment: Requires successful completion of a lower secondary education program as a pre-requisite.

higher education program
type: Class
equivalent class: Class
  intersection of: educational program
  intersection of: Class
    complement of: Restriction
      on property: has part
      some values from: Class
        intersection of: educational objective
        intersection of: Class
  intersection of: Restriction
    on property: has part
    some values from: higher education objective
  intersection of: Restriction
    on property: is concretized as
    some values from: Restriction
      on property: realized in
      some values from: completing a program of education
subclass of: educational program
subclass of: Restriction
  on property: has part
  some values from: higher education objective
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: completing a program of education
editor preferred term: higher education plan specification
definition editor: William R. Hogan
alternative term: post-secondary education plan specification
alternative term: post-secondary education program
comment: Includes college, university, community college, professional schools (MD, RN, PharmD, PT, OT, DDS, dental hygienist, etc.), and so on.
comment: Refers to all higher education beyond secondary education, and thus encompasses ISCED levels 5 and above, which will eventually be subclasses of this one.
comment: Requires successful completion of a secondary education program as a pre-requisite.

higher education objective
type: Class
subclass of: educational objective
editor preferred term: higher education objective specification
definition: An educational objective specification that has a concretization that, when realized, confers on the active participant skills and knowledge in a specialized discipline, and culminates in the awarding of an academic degree.
definition editor: William R. Hogan
alternative term: post-secondary education objective
comment: Refers to all education beyond secondary education that leads to the awarding of an academic degree.

vocational education objective
type: Class
subclass of: educational objective
editor preferred term: vocational education objective specification
definition: An educational objective specification that has a concretization that, when realized, is realized by a process that confers on the active participant knowledge and skills required to realize a particular type of employee role for a given occupation or trade.
definition editor: William R. Hogan
definition source: http://uis.unesco.org/sites/default/files/documents/international-standard-classification-of-education-isced-2011-en.pdf
comment: Usually the skills are a major focus moreso than in other types of education. For example, auto mechanics, plumbers, and electricians.

highest level of education data item
type: Class
subclass of: socio-economic data item
editor preferred term: highest level of education socio-economic data item
definition: A socio-economic data item that is about a person and their completion of an education program (and its type), where that education progam is the last one in a sequence (of education programs) that the person has completed, where each education program completed except the last one is a pre-requisite to the education program completed after it.
definition editor: William R. Hogan
comment: This data item in a typical attribute-value system such as table, XML, JSON takes values like "secondary education", "Associate Degree", "Bachelor Degree", "High School", and so on.

OMRSE_00002046
type: Class
equivalent class: Class
  intersection of: educational program
  intersection of: Restriction
    on property: has part
    some values from: vocational education objective
subclass of: educational program
subclass of: Restriction
  on property: has part
  some values from: vocational education objective
editor preferred term: vocational education plan specification
definition: An educational plan specification that has a vocational objective specification as part.
definition editor: William R. Hogan
definition source: http://uis.unesco.org/sites/default/files/documents/international-standard-classification-of-education-isced-2011-en.pdf
comment: Vocational education programs are designed for learners to acquire the knowledge, skills and competencies specific to a particular occupation, trade, or class of occupations or trades. Such programs may have work-based components (e.g. apprenticeships, dual-system education programmes). Successful completion of such programs leads to labor market-relevant, vocational qualifications acknowledged as occupationally-oriented by the relevant national authorities and/or the labor market.
comment: vocational education program

OMRSE_00002047
type: Class
subclass of: primary education program
editor preferred term: kindergarten education plan specification
definition: A primary education plan specification that specifies the competencies and information content entities that should be acquired by students in the first year of primary education in the United States.
definition editor: William R. Hogan
definition editor: kindergarten education program
creator: http://orcid.org/0000-0002-9881-1017
date: 2020-09-02T12:38:43Z

undergraduate higher education program
type: Class
subclass of: higher education program
editor preferred term: undergraduate higher education plan specification
definition: A higher education plan specification that specifies the awarding of an associates or bachelors degree in the United States or equivalent degrees in other nations, and specifies as a pre-requisite the completion of some secondary education program.
definition editor: William R. Hogan
alternative term: undergraduate education program
creator: http://orcid.org/0000-0002-9881-1017
date: 2020-09-02T12:52:46Z

graduate higher education program
type: Class
subclass of: higher education program
editor preferred term: graduate higher education plan specification
definition: A higher education plan specification that specifies the awarding of a graduate certificate or degree, and specifies as a pre-requisite the awarding of an undergraduate degree.
alternative term: graduate education program
creator: http://orcid.org/0000-0002-9881-1017
date: 2020-09-02T13:01:34Z
comment: Graduate degrees include masters, PhD, MD, PharmD, and other post-graduate professional degrees. To distinguish MS/PhD from the professional ones, subclass this class.
comment: The prerequisite degree is at the bachelors level or equivalent. An associates degree is almost never sufficient for entry into graduate education programs.

highest level of education is grades 1 through 6 data item
type: Class
subclass of: highest level of education data item
editor preferred term: highest level of education is completion of grades one through six socio-economic data item
definition: A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is in the range of first through sixth grade.
definition editor: William R. Hogan
creator: http://orcid.org/0000-0002-9881-1017
date: 2020-09-02T13:23:46Z
comment: Note: this broad, very loose level of grouping emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI. It indicates completion of some to all of primary education in the United States.

highest level of education is grades 7 through 9 data item
type: Class
subclass of: highest level of education data item
editor preferred term: highest level of education is completion of grades seven through nine socio-economic data item
definition: A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is in the range of seventh (7th) through ninth (9th) grade.
definition editor: William R. Hogan
creator: http://orcid.org/0000-0002-9881-1017
date: 2020-09-02T13:27:15Z
comment: Note: this broad, very loose level of grouping emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI. It indicates completion of some to all of lower secondary education in the United States.

highest level of education is grades 10 through 12 data item
type: Class
subclass of: highest level of education data item
editor preferred term: highest level of education is completion of grades ten through twelve socio-economic data item
definition: A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is in the range of tenth (10th) through twelfth (12th) grade.
definition editor: William R. Hogan
creator: http://orcid.org/0000-0002-9881-1017
date: 2020-09-02T13:27:50Z
comment: Note: this broad, very loose level of grouping emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI. It indicates completion of some to all of upper secondary education in the United States.

highest level of education is completion of undergraduate degree data item
type: Class
subclass of: highest level of education data item
editor preferred term: highest level of education is completion of some undergraduate degree socio-economic data item
definition: A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some undergraduate degree.
definition editor: William R. Hogan
creator: http://orcid.org/0000-0002-9881-1017
date: 2020-09-02T13:28:27Z
comment: Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.

highest level of education is completion of graduate certificate or degree data item
type: Class
subclass of: highest level of education data item
editor preferred term: highest level of education is completion of some graduate degree socio-economic data item
definition: A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some graduate certificate or degree.
definition editor: William R. Hogan
creator: http://orcid.org/0000-0002-9881-1017
date: 2020-09-02T13:28:49Z
comment: Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.

highest level of education is completion of vocaational education program data item
type: Class
subclass of: highest level of education data item
editor preferred term: highest level of education is completion of some vocational education program socio-economic data item
definition: A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some vocational education program.
definition editor: William R. Hogan
creator: http://orcid.org/0000-0002-9881-1017
date: 2020-09-02T13:29:28Z
comment: Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.

highest level of education is completion of kindergarten data item
type: Class
subclass of: highest level of education data item
editor preferred term: highest level of education is completion of kindergarten socio-economic data item
definition: A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is pre-kindergarten.
definition editor: William R. Hogan
creator: http://orcid.org/0000-0002-9881-1017
date: 2020-09-02T13:47:38Z
comment: Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI. It indicates that a person has completed only early childhood education and nothing more.

highest level of education is completion of pre-kindergarten data item
type: Class
subclass of: highest level of education data item
editor preferred term: highest level of education is completion of pre-kindergarten socio-economic data item
definition: A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is kindergarten.
definition editor: William R. Hogan
creator: http://orcid.org/0000-0002-9881-1017
date: 2020-09-02T13:48:10Z
comment: Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.

linguistic literacy competence
type: Class
subclass of: disposition
editor preferred term: language literacy competence
definition: A disposition borne by a human being that (1) has a linguistic competence as a dispositional part and (2) if realized, is realized by the bearer's achievement of some personal goal.
definition editor: William R. Hogan
alternative term: human literacy
alternative term: linguistic literacy
contributor: Jiang Bian
contributor: Xi Yang
contributor: Yonghui Wu
comment: Other dispositions that it can and likely does have as dispositional parts include cultural competencies, interpersonal competencies, competencies for navigating a society's systems of laws, claims, obligations, deontic declarations, and norms of financial and other economic exchange.
comment: The realization of this disposition by definition realizes the bearer's linguistic competence that is a dispositional part of this disposition. The realization of the linguistic competence would be an occurrent part of the realization of this disposition (and not a temporal part).
comment: Whereas linguistic competence may be afforded to non-human agents, literacy is nearly always considered in the context of human beings.

caregiver role
type: Class
subclass of: human social role
definition: A human social role that, if realized, is realized in providing assistance in the activities of daily living of another human being who possesses reduced capability to complete some of these activities alone.
definition editor: Matthew Diller
contributor: John Judkins
contributor: S. Clint Dowland
contributor: William R. Hogan

family relationship
type: Class
subclass of: relational quality
definition: A relational quality that inheres within two or more persons related as members of a domestic group, or a number of domestic groups linked through descent from a common ancestor, marriage, or adoption.
definition source: http://purl.obolibrary.org/obo/ERO_0002033
contributor: John Judkins
contributor: S. Clint Dowland
contributor: William R. Hogan
comment: We are also intending on including other family arrangements. This is something we are working on.

academic degree
type: Class
subclass of: information content entity
definition: An information content entity that is the specified outcome of and documents the sucessful completion of a tertiary education program.
definition editor: John Judkins
definition editor: Mathias Brochhausen
OOSTT user-centered description: Recognized degree awarded after successful completion of a college or post-graduate porgram.

associate degree
type: Class
subclass of: academic degree
definition: An academic degree awarded by colleges and universities upon completion of a program of study lasting two years.
definition editor: John Judkins
definition editor: Mathias Brochhausen
definition source: https://en.wikipedia.org/w/index.php
OOSTT user-centered description: Recognition awarded after completion of a specific curriculum from an accredited tertiary education provider that falls between high school and bachelor's degree program.

master's degree
type: Class
subclass of: academic degree
definition: An academic degree awarded by universities upon completion of a course of study demonstrating a mastery or high-order overview of a specific field of study or area of professional practice.[1] Within the area studied, graduates are posited to possess advanced knowledge of a specialized body of theoretical and applied topics; high order skills in analysis, critical evaluation, or professional application; and the ability to solve complex problems and think rigorously and independently.
definition editor: John Judkins
definition editor: Mathias Brochhausen
definition source: https://en.wikipedia.org/w/index.php

bachelor's degree
type: Class
subclass of: academic degree
definition: An academic degree awarded by colleges and universities upon completion of a course of study lasting three to seven years.
definition editor: John Judkins
definition editor: Mathias Brochhausen
definition source: https://en.wikipedia.org/w/index.php

bachelor's of nursing degree
type: Class
subclass of: bachelor's degree
definition: An academic degree in the science and principles of nursing, granted by an accredited tertiary education provider after the successful completion of a bachelor's of nursing program.
definition editor: John Judkins
definition editor: Mathias Brochhausen
definition source: https://en.wikipedia.org/w/index.php

master's in the science of nursing degree
type: Class
subclass of: master's degree
definition: An academic degree in the science and principles of nursing, granted by an accredited tertiary education provider after the successful completion of a master's of nursing program.
definition editor: John Judkins
definition editor: Mathias Brochhausen
OOSTT user-centered description: An advanced academic degree in the principles and practices of nursing, with a focus on administration, education, or advanced nursing practice, granted by an accredited college or university after the successful completion of a master's of nursing program.

admitting diagnosis
type: Class
subclass of: diagnosis
subclass of: Restriction
  on property: denotes
  some values from: diagnosis
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: diagnostic process
    intersection of: Restriction
      on property: before or simultaneous with
      some values from: admission process
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: diagnostic process
    intersection of: Restriction
      on property: happens during
      some values from: inpatient encounter
disjoint with: interim diagnosis
definition: a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs before or during the admission of that patient
definition editor: Amanda Hicks
definition editor: S. Clint Dowland
definition source: PCORnet CDM 4.1

obsolete PCORnet racial identity datum
type: Class
subclass of: obsolete racial identity datum
definition editor: Amanda Hicks
term replaced by: 'PCORnet racial identity information content entity'
comment: A racial identity that is the output of a racial identification process that uses the PCORnet CDM race or terminology. PCORnet CDM claims to use the OMB racial classification, but the crucial difference is that PCORnet CDM requires persons to identify with only one category whereas the OMB allows for multiple racial identities as outputs of an identification process.
deprecated: true

obsolete PCORnet American Indian or Alaska Native identity datum
type: Class
subclass of: obsolete PCORnet racial identity datum
definition editor: Amanda Hicks
term replaced by: 'PCORnet American Indian or Alaska Native identity information content entity'
deprecated: true

obsolete PCORnet Asian identity datum
type: Class
subclass of: obsolete PCORnet racial identity datum
definition editor: Amanda Hicks
term replaced by: 'PCORnet Asian identity information content entity'
deprecated: true

obsolete PCORnet black or African American identity datum
type: Class
subclass of: obsolete PCORnet racial identity datum
definition editor: Amanda Hicks
term replaced by: 'PCORnet black or African American identity information content entity'
label: obsolete PCORnet item
deprecated: true

obsolete PCORnet CDM item identifier
type: Class
subclass of: information content entity
deprecated: true

obsolete PCORnet item
type: Class
subclass of: information content entity
deprecated: true

obsolete PCORnet Native Hawaiian or other Pacific Islander identity datum
type: Class
subclass of: obsolete PCORnet racial identity datum
definition editor: Amanda Hicks
term replaced by: 'PCORnet Native Hawaiian or other Pacific Islander identity information content entity'
deprecated: true

obsolete PCORnet white identity datum
type: Class
subclass of: obsolete PCORnet racial identity datum
definition editor: Amanda Hicks
term replaced by: 'PCORnet white identity information content entity'
deprecated: true

obsolete PCORnet multiple race identity datum
type: Class
subclass of: obsolete PCORnet racial identity datum
definition editor: Amanda Hicks
term replaced by: 'PCORnet multiple race identity information content entity'
deprecated: true

obsolete PCORnet Hispanic identity datum
type: Class
subclass of: obsolete hispanic or latino identity datum
definition editor: Amanda Hicks
term replaced by: 'PCORnet Hispanic identity information content entity'
comment: From PCORnet CDM "A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race."
deprecated: true

obsolete PCORnet not Hispanic identity datum
type: Class
subclass of: obsolete not hispanic or latino identity datum
definition editor: Amanda Hicks
term replaced by: 'PCORnet non-Hispanic identity information content entity'
deprecated: true

obsolete PCORnet ethnic identity datum
type: Class
subclass of: obsolete ethnic identity datum
definition editor: Amanda Hicks
term replaced by: 'PCORnet ethnic identity information content entity'
deprecated: true

PCORnet patient identifier
type: Class
subclass of: identifier
definition: A centrally registered identifier that denotes a person in a PCORnet data mart and is used to link across tables. This identifier is not necessarily unique within PCORnet.
definition editor: Amanda Hicks

obsolete admission process
type: Class
subclass of: obsolete_document act
definition: a social act in which a patient is registered with a health care provider for the purposes of recieving care in an inpatient encounter
definition editor: Amanda Hicks
term replaced by: 'admission process' http://purl.obolibrary.org/obo/OMRSE_00000201
deprecated: true

discharge diagnosis
type: Class
subclass of: diagnosis
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: diagnostic process
    intersection of: Restriction
      on property: before or simultaneous with
      some values from: patient discharge
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: diagnostic process
    intersection of: Restriction
      on property: happens during
      some values from: inpatient encounter
disjoint with: interim diagnosis
definition: a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs before or simultaneously with the discharge of that patient
definition editor: Amanda Hicks
definition editor: S. Clint Dowland
definition source: PCORnet CDM 4.1

final diagnosis
type: Class
subclass of: diagnosis
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: diagnostic process
    intersection of: Restriction
      on property: happens during
      some values from: outpatient encounter
definition: a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs during an outpatient encounter
definition editor: Amanda Hicks
definition editor: S. Clint Dowland
definition source: PCORnet CDM 4.1

interim diagnosis
type: Class
subclass of: diagnosis
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: diagnostic process
    intersection of: Restriction
      on property: happens during
      some values from: inpatient encounter
definition: a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs during an inpatient encounter, after admission, and before discharge of that patient
definition editor: Amanda Hicks
definition editor: S. Clint Dowland
definition source: PCORnet CDM 4.1

PCORnet racial identification process
type: Class
subclass of: racial identification process

obsolete PCORnet sexual orientation identity datum
type: Class
subclass of: obsolete sexual orientation identity datum
term replaced by: 'PCORnet sexual orientation identity information content entity'
deprecated: true

ambulatory visit
type: Class
subclass of: outpatient encounter
subclass of: Class
  intersection of: Class
    complement of: Restriction
      on property: has temporal part
      some values from: patient discharge
  intersection of: Class
    complement of: Restriction
      on property: has temporal part
      some values from: admission process
disjoint with: deprecated emergency department encounter
definition: An outpatient encounter that occurs in an outpatient clinic, physician office, ambulatory surgery facility, urgent care facilitu, or a hospital encounters and that does not occur in an emergency department facillity.
definition editor: Amanda Hicks
definition source: PCORnet CDM 4.1
ORCS_00000090: Includes visits at outpatient clinics, physician offices, same day/ambulatory surgery centers, urgent care facilities, and other same-day ambulatory hospital encounters, but excludes emergency department encounters

deprecated emergency department encounter
type: Class
subclass of: health care encounter
definition: A health care encounter that occurs in an emergency department facillity and realizes the health care provider role of an organization and the emergency department function of the facility.
definition editor: Amanda Hicks
definition source: PCORnet CDM 4.1
ORCS_00000090: Includes ED encounters that become inpatient stays (in which case inpatient stays would be a separate encounter). Excludes urgent care facility visits. ED claims should be pulled before hospitalization claims to ensure that ED with subsequent admission won't be rolled up in the hospital event. Does not include observation stays, where known.
deprecated: true

obsolete sexual orientation identity datum
type: Class
subclass of: obsolete identity datum
definition editor: Amanda Hicks
term replaced by: 'sexual orientation identity information content entity'
comment: A sexual orientation identity datum sis an information content entity that is the output of some sexual orientation identitification process and is intended to be a truthful statement about the subjective feelings of sexual attration, emotional attraction, and romantic attatchments of the person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
deprecated: true

obsolete PCORnet asexual identity datum
type: Class
subclass of: obsolete PCORnet sexual orientation identity datum
term replaced by: 'PCORnet asexual identity information content entity'
label: obsolete inpatient hospital encounter
deprecated: true

obsolete PCORnet gay identity datum
type: Class
subclass of: obsolete PCORnet sexual orientation identity datum
term replaced by: 'PCORnet gay identity information content entity'
deprecated: true

obsolete PCORnet lesbian identity datum
type: Class
subclass of: obsolete PCORnet sexual orientation identity datum
term replaced by: 'PCORnet lesbian identity information content entity'
deprecated: true

obsolete PCORnet multiple sexual orientations identity datum
type: Class
subclass of: obsolete PCORnet sexual orientation identity datum
term replaced by: 'PCORnet multiple sexual orientations identity information content entity'
deprecated: true

obsolete PCORnet queer identity datum
type: Class
subclass of: obsolete PCORnet sexual orientation identity datum
term replaced by: 'PCORnet queer identity information content entity'
deprecated: true

obsolete PCORnet questioning identity datum
type: Class
subclass of: obsolete PCORnet sexual orientation identity datum
term replaced by: 'PCORnet questioning sexual orientation identity information content entity'
deprecated: true

obsolete PCORnet something else identity datum
type: Class
subclass of: obsolete PCORnet sexual orientation identity datum
term replaced by: 'PCORnet something else sexual orientation identity information content entity'
deprecated: true

obsolete PCORnet straight identity datum
type: Class
subclass of: obsolete PCORnet sexual orientation identity datum
term replaced by: 'PCORnet straight identity information content entity'
deprecated: true

obsolete PCORnet gender identity datum
type: Class
subclass of: obsolete gender identity datum
term replaced by: 'PCORnet gender identity information content entity'
comment: A gender identity that is the output of a racial identification process that uses the PCORnet CDM race or terminology. PCORnet CDM claims to use the 2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, but the crucial difference is that PCORnet CDM requires persons to identify with only one category whereas the other does not have a multiple gender option, which changes the meaning of the values in the value set.
deprecated: true

obsolete PCORnet genderqueer identity datum
type: Class
subclass of: obsolete PCORnet gender identity datum
term replaced by: 'PCORnet genderqueer/non-binary identity information content entity'
deprecated: true

obsolete PCORnet man identity datum
type: Class
subclass of: obsolete PCORnet gender identity datum
term replaced by: 'PCORnet man identity information content entity'
deprecated: true

obsolete PCORnet multiple genders datum
type: Class
subclass of: obsolete PCORnet gender identity datum
term replaced by: 'PCORnet multiple gender categories identity information content entity'
deprecated: true

obsolete PCORnet something else identity datum
type: Class
subclass of: obsolete PCORnet gender identity datum
term replaced by: 'PCORnet something else gender identity information content entity'
deprecated: true

obsolete PCORnet transgenderfemale/transwoman/male-to-female identity datum
type: Class
subclass of: obsolete PCORnet gender identity datum
term replaced by: 'PCORnet transgender female/trans woman/male-to-female identity information content entity'
deprecated: true

obsolete PCORnet transgendermale/transman/female-to-male identity datum
type: Class
subclass of: obsolete PCORnet gender identity datum
term replaced by: 'PCORnet transgender male/trans man/female-to-male identity information content entity'
deprecated: true

obsolete PCORnet woman identity datum
type: Class
subclass of: obsolete PCORnet gender identity datum
term replaced by: 'PCORnet woman identity information content entity'
deprecated: true

PCORnet diagnosis identifier
type: Class
subclass of: identifier
definition: An identifier that denotes a diagnosis.

DEPRECATED obsolete code set
type: Class
comment: This class is superfluous, given the addition of PNO: code set.
deprecated: true

PCORnet discharge status data item
type: Class
subclass of: data item
definition: A data item that is about a documentation activity that records either (i) that some healthcare encounter ends with a patient discharge; (ii) that some healthcare encounter is terminated by a patient without any patient discharge; or (iii) that some healthcare encounter continues while the patient remains in the same hospital and while the hospital is billing a healthcare payor for services after a specified period.
editor note: If the healthcare encounter ends with a patient discharge, then the status might also indicate the type of facility or organization, if any, to which the patient is discharged.
definition editor: Mathias Brochhausen
definition editor: Matthew Diller
definition editor: S. Clint Dowland
definition editor: William R. Hogan

PCORnet skilled nursing facility discharge status data item
type: Class
subclass of: PCORnet discharge status data item
definition: A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to a skilled nursing facility.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet adult foster home facility discharge status data item
type: Class
subclass of: PCORnet discharge status data item
definition: A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to an adult foster home facility.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet assisted living facility discharge status data item
type: Class
subclass of: PCORnet discharge status data item
definition: A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to an assisted living facility.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet other acute inpatient hospital discharge status data item
type: Class
subclass of: PCORnet discharge status data item
definition: A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to another hospital.
definition editor: Amanda Hicks
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet nursing home facility discharge status data item
type: Class
subclass of: PCORnet discharge status data item
definition: A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to a nursing home facility.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet rehabilitation facility discharge status data item
type: Class
subclass of: PCORnet discharge status data item
definition: A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to a rehabilitation facility.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet residential facility discharge status data item
type: Class
subclass of: PCORnet discharge status data item
definition: A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to a residential facility.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet hospice discharge status data item
type: Class
subclass of: PCORnet discharge status data item
definition: A PCORnet discharge status data item that is about a discharge process in which a patient is discharged under the care of a hospice organization.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet against medical advice discharge status data item
type: Class
subclass of: PCORnet discharge status data item
definition: A PCORnet discharge status data item that is about a discharge process in which a patient is discharged upon deciding to end the encounter against the advice of a healthcare provider.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet still in hospital discharge status data item
type: Class
subclass of: PCORnet discharge status data item
definition: A PCORnet discharge status data item that is about a healthcare encounter that continues while the patient remains in the same hospital, and while the hospital is billing a healthcare payor for services after a specified period (typically 90 days).
definition editor: Matthew Diller
definition editor: S. Clint Dowland
definition editor: William R. Hogan

PCORnet home health discharge status data item
type: Class
subclass of: PCORnet discharge status data item
definition: A PCORnet discharge status data item that is about a discharge process in which a patient is discharged (i) to a housing unit, and (ii) under the care of a home healthcare organization.
definition editor: Matthew Diller
definition editor: S. Clint Dowland
definition editor: William R. Hogan

PCORnet admitting source data item
type: Class
subclass of: data item
definition: A data item that is about a patient admission and the type of facility from which a patient was discharged prior to admission.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet home health admitting source data item
type: Class
subclass of: PCORnet admitting source data item
definition: A PCORnet data item that is about a home healthcare organization and the household from which a patient was discharged prior to admission.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet skilled nursing facility admitting source data item
type: Class
subclass of: PCORnet admitting source data item
definition: A PCORnet data item that is about a skilled nursing facility from which a patient was discharged prior to admission.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet ethnic identity information content entity
type: Class
subclass of: ethnic identity information content entity
definition: An ethnic identity information content entity that uses PCORnet CDM terminology for ethnicity, where this terminology corresponds to values for the "Hispanic" field of the Demographic Table.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

PCORnet Hispanic identity information content entity
type: Class
subclass of: PCORnet ethnic identity information content entity
definition: A PCORnet ethnic identity information content entity that is about some person's identifying as Hispanic, which is intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race.
definition editor: S. Clint Dowland
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

PCORnet non-Hispanic identity information content entity
type: Class
subclass of: PCORnet ethnic identity information content entity
definition: A PCORnet ethnic identity information content entity that is about some person's identifying as not Hispanic, where "Hispanic" is intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

PCORnet gender identity information content entity
type: Class
subclass of: gender identity information content entity
definition: A gender identity information content entity that uses the PCORnet CDM terminology for gender, where this terminology corresponds to values for the "gender identity" field of the Demographic Table.
definition editor: S. Clint Dowland
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: The PCORnet CDM cites the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services as the source for its terminology, but the two differ in that the PCORnet CDM allows one to select only one value for gender and includes 'multiple gender' as an option, while the other lacks a 'multiple gender' option and allows multiple options to be selected. For that source used by PCORnet, see here: https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base

PCORnet genderqueer/non-binary identity information content entity
type: Class
subclass of: PCORnet gender identity information content entity
definition: A PCORnet gender identity information content entity that is about some person's identifying as neither exclusively male nor exclusively female in gender.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

PCORnet man identity information content entity
type: Class
subclass of: PCORnet gender identity information content entity
definition: A PCORnet gender identity information content entity that is about some person's identifying as a man.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

PCORnet multiple gender categories identity information content entity
type: Class
subclass of: PCORnet gender identity information content entity
definition: A PCORnet gender identity information content entity that is about some person's identifying as more than one gender.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

PCORnet something else gender identity information content entity
type: Class
subclass of: PCORnet gender identity information content entity
definition: A PCORnet gender identity information content entity that is about some person's identifying as some gender that is not referred to or described by the other value options for the "gender identity" field of the PCORnet Demographic Table.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

PCORnet transgender female/trans woman/male-to-female identity information content entity
type: Class
subclass of: PCORnet gender identity information content entity
definition: A PCORnet gender identity information content entity that is about some person's identifying as transgender female, a trans woman, or male-to-female.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

PCORnet transgender male/trans man/female-to-male identity information content entity
type: Class
subclass of: PCORnet gender identity information content entity
definition: A PCORnet gender identity information content entity that is about some person's identifying as transgender male, a trans man, or female-to-male.
definition editor: Mathias Brochhausen
definition editor: Matthew Diller
definition editor: S. Clint Dowland
definition editor: William R. Hogan
contributor: Sarah Bost

PCORnet woman identity information content entity
type: Class
subclass of: PCORnet gender identity information content entity
definition: A PCORnet gender identity information content entity that is about some person's identifying as a woman.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

PCORnet racial identity information content entity
type: Class
subclass of: racial identity information content entity
definition: A racial identity information content entity that uses the PCORnet CDM terminology for race, where this terminology corresponds to the values for the "race" field of the Demographic Table.
definition editor: S. Clint Dowland
contributor: Amanda Hicks
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: The PCORnet CDM's values for the race field are based on the OMB racial classification, but differ in that the PCORnet CDM allows one to select only one value for race and includes "multiple race" as an option, while OMB lacks a 'multiple race' option and allows multiple options to be selected.

PCORnet American Indian or Alaska Native identity information content entity
type: Class
subclass of: PCORnet racial identity information content entity
definition: A PCORnet 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.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: This definition corresponds to that used by OMB, which is PCORnet's source for the terminology used for the value options of the 'race' field. 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.

PCORnet Asian identity information content entity
type: Class
subclass of: PCORnet racial identity information content entity
definition: A PCORnet 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.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

PCORnet black or African American identity information content entity
type: Class
subclass of: PCORnet racial identity information content entity
definition: A PCORnet 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.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

PCORnet multiple race identity information content entity
type: Class
subclass of: PCORnet racial identity information content entity
definition: A PCORnet racial identity information content entity that is about some person's identifying as more than one race.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

PCORnet Native Hawaiian or other Pacific Islander identity information content entity
type: Class
subclass of: PCORnet racial identity information content entity
definition: A PCORnet 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.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

PCORnet white identity information content entity
type: Class
subclass of: PCORnet racial identity information content entity
definition: A PCORnet 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.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan

PCORnet sexual orientation identity information content entity
type: Class
subclass of: sexual orientation identity information content entity
definition: A sexual orientation identity information content entity that uses the PCORnet terminology for sexual orientation, where this terminology corresponds to the permitted values for the "sexual orientation" field of the Demographic Table.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.

PCORnet asexual identity information content entity
type: Class
subclass of: PCORnet sexual orientation identity information content entity
definition: A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "asexual."
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.

PCORnet bisexual identity information content entity
type: Class
subclass of: PCORnet sexual orientation identity information content entity
definition: A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "bisexual."
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.

PCORnet gay identity information content entity
type: Class
subclass of: PCORnet sexual orientation identity information content entity
definition: A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "gay."
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.

PCORnet lesbian identity information content entity
type: Class
subclass of: PCORnet sexual orientation identity information content entity
type: NamedIndividual
contributor: Mathias Brochhausen
contributor: William R. Hogan
contributor: Matthew Diller
contributor: Sarah Bost
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
definition editor: S. Clint Dowland
definition: A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "lesbian."

Internationalized Resource Identifier
type: Class
subclass of: identifier
editor preferred term: Internationalized Resource Identifier
definition: An identifier that is the specified output of a planned process that realizes the Internet standard RFC 3987 which is available from http://www.ietf.org/rfc/rfc3987.txt.
alternative term: IRI
comment: RFC 3987 has the title "Internationalized Resource Identifiers (IRIs)". It was published in 2005.

PCORnet emergency department admitting source data item
type: Class
subclass of: PCORnet admitting source data item
definition: A PCORnet data item that is about an emergency department from which a patient was discharged prior to admission.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet intra-hospital admitting source data item
type: Class
subclass of: PCORnet admitting source data item
definition: A PCORnet data item that is about another department in the same hospital from which a patient was discharged prior to admission.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet ambulatory visit admitting source data item
type: Class
subclass of: PCORnet admitting source data item
definition: A PCORnet data item that is about a patient admission that is causally upstream of an outpatient encounter.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet health care encounter identifier
type: Class
subclass of: identifier
definition: An identifier that denotes a health care encounter and has part some symbol.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet facility identifier
type: Class
subclass of: identifier
definition: An identifier that denotes a health care facility and has part some symbol.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

institutional professional consult
type: Class
subclass of: health care encounter
definition: A health care encounter that realizes some health care provider role that inheres in some Homo sapiens.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

non-acute institutional stay
type: Class
subclass of: health care encounter
definition: A health care encounter that occurs in some hospice facility, skilled nursing facility, rehabilitation facility, nursing home facility, residential home facility, overnight non-hospital dialysis facility, adult foster home facility, or assisted living facility.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet absent without leave discharge status data item
type: Class
subclass of: PCORnet discharge status data item
definition: A PCORnet discharge status data item that is about a termination of an inpatient encounter, initiated by the patient, that lacks a discharge process as a proper part.
definition editor: Mathias Brochhausen
definition editor: Matthew Diller
definition editor: S. Clint Dowland
definition editor: William R. Hogan

observation stay
type: Class
subclass of: health care encounter
definition: A health care encounter that occurs in some hospital facility or emergency department and that realizes some healthcare provider role that inheres in some organization.
definition editor: Matthew Diller

PCORnet provider identifier
type: Class
subclass of: identifier
definition: An identifier that denotes a human being who is a bearer of a person healthcare provider role.
definition editor: Matthew Diller
definition editor: S. Clint Dowland

PCORnet multiple sexual orientations identity information content entity
type: Class
subclass of: PCORnet sexual orientation identity information content entity
definition: A PCORnet sexual orientation identity information content entity that is about some person's identifying as having multiple sexual orientations.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.

PCORnet queer identity information content entity
type: Class
subclass of: PCORnet sexual orientation identity information content entity
definition: A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "queer."
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.

PCORnet questioning sexual orientation identity information content entity
type: Class
subclass of: PCORnet sexual orientation identity information content entity
definition: A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "queer."
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.
comment: While this is not about one's identifying as having or not having some sexual orientation, we regard it as a 'sexual orientation identity information content entity,' which is defined as being about "whether one identifies as having some sexual orientation." For example, if one is uncertain whether one is bisexual or heterosexual, one might be in a state of questioning one's sexuality, and an information content entity about that would seem to qualify as being about whether one identifies as having some sexual orientations. Indeed, there would be two sexual orientations in that example, and the information content entity could be both about whether one identifies as bisexual and about whether one identifies as heterosexual.

PCORnet something else sexual orientation identity information content entity
type: Class
subclass of: PCORnet sexual orientation identity information content entity
definition: A PCORnet sexual orientation identity information content entity that is about some person's identifying as some sexual orientation that is not represented by the other value set options for the "sexual orientation" field of the PCORnet Demographic Table.
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.

PCORnet straight identity information content entity
type: Class
subclass of: PCORnet sexual orientation identity information content entity
definition: A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "straight."
definition editor: S. Clint Dowland
contributor: Mathias Brochhausen
contributor: Matthew Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two.

patient PCORnet specimen source value name
type: Class
subclass of: PCORnet specimen source value name
definition: A PCORnet specimen source value name that is about a patient.
definition editor: Matthew Diller
contributor: William R. Hogan
comment: The LOINC codes that this value name applies to are 59768-2 (Procedure indications [Interpretation] Narrative), 32624-9 (Race), 56850-1 (Interpretation and review of laboratory results), and 56794-1 (Internal identifier).
comment: This value name is not about an actual specimen.

provider PCORnet specimen source value name
type: Class
subclass of: PCORnet specimen source value name
definition: A PCORnet specimen source value name that is about some identifier that denotes a physician.
definition editor: Matthew Diller
contributor: William R. Hogan
comment: The PROVIDER value name might denote something other than a physician identifier, like a telephone number, depending on the data source. We limit it to being about an identifier that denotes a physician because this is what our data sources apply the value name to.
comment: This value name is not about an actual specimen.

emergency department admit to inpatient hospital stay
type: Class
subclass of: health care encounter
definition: A health care encounter that first occurs as an emergency department visit and then becomes an inpatient hospital stay
definition editor: Amanda Hicks
definition source: PCORnet CDM 4.1
ORCS_00000090: Permissible substitution for preferred state of separate ED and IP records. Only for use with data sources where the individual records for ED and IP cannot be distinguished.

PCORnet medical procedure
type: Class
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: patient role
definition: A planned process that realizes a patient role.
definition editor: William R. Hogan
contributor: Matthew Diller
contributor: S. Clint Dowland
contributor: Sarah Bost

PCORnet specimen source value name
type: Class
subclass of: identifier
definition: An identifier that denotes a LOINC information content entity that itself is about some material entity that is the bearer of a specimen role.
definition editor: Matthew Diller
definition source: PCORnet Common Data Model Specification v5.1
contributor: William R. Hogan
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."

serum, plasma, or urine PCORnet specimen source value name
type: Class
subclass of: PCORnet specimen source value name
definition: A PCORnet specimen source value name that is about some blood serum, blood plasma, or urine samples.
definition editor: Matthew Diller
contributor: William R. Hogan
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
comment: This class, while not ideal in that it doesn’t refer to an actual universal, is a consequence of LOINC system identifiers that consist of disjunctions (e.g., ‘Serum or plasma’).

serum or plasma PCORnet specimen source value name
type: Class
subclass of: PCORnet specimen source value name
definition: A PCORnet specimen source value name that is about some blood serum or blood plasma samples.
definition editor: Matthew Diller
contributor: William R. Hogan
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
comment: This class, while not ideal in that it doesn’t refer to an actual universal, is a consequence of LOINC system identifiers that consist of disjunctions (e.g., ‘Serum or plasma’).

serum, plasma, or blood PCORnet specimen source value name
type: Class
subclass of: PCORnet specimen source value name
definition: A PCORnet specimen source value name that is about some blood serum, blood plasma, or whole blood samples.
definition editor: Matthew Diller
contributor: William R. Hogan
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
comment: This class, while not ideal in that it doesn’t refer to an actual universal, is a consequence of LOINC system identifiers that consist of disjunctions (e.g., ‘Serum or plasma’).

blood or tissue PCORnet specimen source value name
type: Class
subclass of: PCORnet specimen source value name
definition: A PCORnet specimen source value name that is about some blood plasma or tissue samples.
definition editor: Matthew Diller
contributor: William R. Hogan
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."
comment: This class, while not ideal in that it doesn’t refer to an actual universal, is a consequence of LOINC system identifiers that consist of disjunctions (e.g., ‘Serum or plasma’).

blood plasma PCORnet specimen source value name
type: Class
subclass of: PCORnet specimen source value name
definition: A PCORnet specimen source value name that is about some specimen of blood plasma.
definition editor: Matthew Diller
contributor: William R. Hogan
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."

cerebrospinal fluid PCORnet specimen source value name
type: Class
subclass of: PCORnet specimen source value name
definition: A PCORnet specimen source value name that is about some specimen of cerebrospinal fluid.
definition editor: Matthew Diller
contributor: William R. Hogan
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."

vagina PCORnet specimen source value name
type: Class
subclass of: PCORnet specimen source value name
definition: A PCORnet specimen source value name that is about some vaginal specimen.
definition editor: Matthew Diller
contributor: William R. Hogan
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."

cervix PCORnet specimen source value name
type: Class
subclass of: PCORnet specimen source value name
definition: A PCORnet specimen source value name that is about some cervical specimen.
definition editor: Matthew Diller
contributor: William R. Hogan
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."

pericardial fluid PCORnet specimen source value name
type: Class
subclass of: PCORnet specimen source value name
definition: A PCORnet specimen source value name that is about some specimen of pericardial fluid.
definition editor: Matthew Diller
contributor: William R. Hogan
comment: The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names."

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: http://purl.obolibrary.org/obo/pato.owl
has_obo_namespace: quality
id: PATO:0000047
in_subset: attribute slim

morphology
type: Class
subclass of: physical object quality
editor preferred term: morphology
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

length
type: Class
subclass of: morphology
editor preferred term: length
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
editor preferred term: mass
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

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: http://purl.obolibrary.org/obo/pato.owl
has_obo_namespace: quality
id: PATO:0000169
in_subset: attribute slim
in_subset: disposition slim

female
type: Class
subclass of: phenotypic sex
definition: A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
imported from: http://purl.obolibrary.org/obo/pato.owl
has_obo_namespace: quality
id: PATO:0000383
in_subset: mpath slim
in_subset: value slim

male
type: Class
subclass of: phenotypic sex
definition: A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
imported from: http://purl.obolibrary.org/obo/pato.owl
has_obo_namespace: quality
id: PATO:0000384
in_subset: mpath slim
in_subset: value slim

physical quality
type: Class
subclass of: physical object quality
editor preferred term: physical 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
editor preferred term: physical object 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: http://purl.obolibrary.org/obo/pato.owl
has_obo_namespace: quality
id: PATO:0001421
in_subset: value slim

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: http://purl.obolibrary.org/obo/pato.owl
has_obo_namespace: quality
id: PATO:0001422
in_subset: value slim

phenotypic sex
type: Class
subclass of: biological sex
imported from: http://purl.obolibrary.org/obo/pato.owl
has_obo_namespace: quality
id: PATO:0001894
in_subset: attribute slim

organismal quality
type: Class
subclass of: quality
definition: A quality that inheres in an entire organism or part of an organism.
imported from: http://purl.obolibrary.org/obo/pato.owl
has_obo_namespace: quality
id: PATO:0001995

family
type: Class
subclass of: aggregate of objectual organisms
has curation status: metadata incomplete
definition: A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.
editor note: Needs axioms for family relationships.
definition source: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173
comment: Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry.

system
type: Class
subclass of: material entity
definition: A material entity consisting of multiple components that are causally integrated.
editor note: May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
definition editor: Chris Mungall
definition source: http://www.jbiomedsem.com/content/4/1/43

uterine cervix
type: Class
subclass of: neck of organ
definition: Lower, narrow portion of the uterus where it joins with the top end of the vagina.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
external_definition: The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]
homology_notes: The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG]
has_relational_adjective: cervical
date retrieved: 2012-09-17
external class: VHOG:0001359
has_broad_synonym: cervix
database_cross_reference: Cervix
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0007874
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181453009
database_cross_reference: BTO:0001421
database_cross_reference: BTO:0002249
database_cross_reference: CALOHA:TS-0134
database_cross_reference: EFO:0000979
database_cross_reference: EMAPA:29927
database_cross_reference: EV:0100114
database_cross_reference: FMA:17740
database_cross_reference: FMA:TA
database_cross_reference: GAID:376
database_cross_reference: MA:0000392
database_cross_reference: MAT:0000292
database_cross_reference: MESH:D002584
database_cross_reference: NCIT:C12311
database_cross_reference: OpenCyc:Mx4rvVipEJwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0007874
database_cross_reference: VHOG:0001359
database_cross_reference: galen:CervixUteri
has_exact_synonym: canalis cervicis uteri
has_exact_synonym: caudal segment of uterus
has_exact_synonym: cervical canal of uterus
has_exact_synonym: cervix uteri
has_exact_synonym: neck of uterus
has_exact_synonym: uterine cervix
has_obo_namespace: uberon
has_related_synonym: cervical canal
has_related_synonym: cervix of uterus
has_synonym_type: LATIN
id: UBERON:0000002
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim
ontology: VHOG
source: bgee.unil.ch
source: uterine+cervix
source: DOI:10.1098/rspb.2004.2848 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004)
source: ncithesaurus:Cervix

nose
type: Class
subclass of: olfactory organ
definition: The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047].
external_definition: a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose].
external_definition: the organ that is specialized for smell and is part of the respiratory system
taxon_notes: the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359]
database_cross_reference: Nose
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0028429
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181195007
database_cross_reference: BTO:0000840
database_cross_reference: CALOHA:TS-2037
database_cross_reference: EHDAA2:0001274
database_cross_reference: EHDAA:1502
database_cross_reference: EMAPA:16542
database_cross_reference: EV:0100037
database_cross_reference: EV:0100370
database_cross_reference: FMA:46472
database_cross_reference: GAID:77
database_cross_reference: MA:0000281
database_cross_reference: MAT:0000139
database_cross_reference: MESH:D009666
database_cross_reference: MIAA:0000139
database_cross_reference: NCIT:C12756
database_cross_reference: OpenCyc:Mx4rvViCbJwpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000047
database_cross_reference: UBERON:cjm
database_cross_reference: UMLS:C0028429
database_cross_reference: ZFA:0000047
database_cross_reference: galen:Nose
has_exact_synonym: nasal sac
has_exact_synonym: nose
has_exact_synonym: peripheral olfactory organ
has_obo_namespace: uberon
has_related_synonym: nasus
has_related_synonym: olfactory apparatus
has_related_synonym: proboscis
has_synonym_type: HUMAN PREFERRED
has_synonym_type: LATIN
has_synonym_type: SENSU
id: UBERON:0000004
in_subset: efo slim
in_subset: major organ
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
source: Nose
source: MP:0002233
source: ZFA:0000047
source: ncithesaurus:Nose

zone of skin
type: Class
subclass of: zone of organ
definition: Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
curator note: Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
homology_notes: (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
external_ontology_notes: we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
date retrieved: 2012-09-17
external class: VHOG:0000860
database_cross_reference: Skin
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/20795001
database_cross_reference: EHDAA2:0001844
database_cross_reference: EHDAA:6530
database_cross_reference: EMAPA:17525
database_cross_reference: EV:0100152
database_cross_reference: FMA:86166
database_cross_reference: GAID:933
database_cross_reference: MA:0000151
database_cross_reference: MAT:0000284
database_cross_reference: MESH:D012867
database_cross_reference: MIAA:0000284
database_cross_reference: OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA
database_cross_reference: VHOG:0000860
has_exact_synonym: portion of skin
has_exact_synonym: region of skin
has_exact_synonym: skin
has_exact_synonym: skin region
has_exact_synonym: skin zone
has_obo_namespace: uberon
id: UBERON:0000014
in_subset: pheno slim
ontology: VHOG
source: bgee.unil.ch
source: DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)

sense organ
type: Class
subclass of: organ
definition: An organ that is capable of transducing sensory stimulus to the nervous system.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
contributor: cmungall
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0935626
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/244485009
database_cross_reference: https://github.com/obophenotype/uberon/issues/549
database_cross_reference: https://orcid.org/0000-0002-6601-2165
database_cross_reference: AEO:0000094
database_cross_reference: BSA:0000121
database_cross_reference: BTO:0000202
database_cross_reference: CALOHA:TS-2043
database_cross_reference: EHDAA2:0001824
database_cross_reference: EHDAA:500
database_cross_reference: EMAPA:35955
database_cross_reference: FBbt:00005155
database_cross_reference: GAID:63
database_cross_reference: HAO:0000930
database_cross_reference: MA:0000017
database_cross_reference: MESH:D012679
database_cross_reference: NCIT:C33224
database_cross_reference: OBOL:accepted
database_cross_reference: OBOL:automatic
database_cross_reference: UMLS:C0935626
database_cross_reference: VHOG:0001407
database_cross_reference: WBbt:0006929
has_exact_synonym: organ of sense organ system
has_exact_synonym: organ of sensory organ system
has_exact_synonym: organ of sensory system
has_exact_synonym: sense organ system organ
has_exact_synonym: sensory organ
has_exact_synonym: sensory organ system organ
has_exact_synonym: sensory system organ
has_narrow_synonym: sensillum
has_obo_namespace: uberon
has_related_synonym: Sinnesorgan
has_related_synonym: sensor
id: UBERON:0000020
in_subset: uberon slim
source: ncithesaurus:Organ_of_the_Special_Sense

cutaneous appendage
type: Class
subclass of: integumentary projection
definition: Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales.
editor note: Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20484386), but these structures do not fit the current definition (lactiferous glands are part of the integumentary system in FMA). Note the FMA class is a subdivision of epidermis, which may be too restrictive for our purposes here.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/276160000
database_cross_reference: https://orcid.org/0000-0002-6601-2165
database_cross_reference: CALOHA:TS-0051
database_cross_reference: FMA:71012
has_exact_synonym: skin appendage
has_narrow_synonym: epidermal appendage
has_obo_namespace: uberon
has_related_synonym: epidermal growth
id: UBERON:0000021
in_subset: uberon slim

feather
type: Class
subclass of: cutaneous appendage
definition: one of the epidermal growths that form the distinctive outer covering, or plumage, on birds. Feathers are formed in tiny follicles in the epidermis, or outer skin layer, that produce keratin proteins.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
taxon_notes: Among the characteristics that distinguish the extant Aves from other living groups. Feathers have also been noticed in those Theropoda which have been termed feathered dinosaurs. Although feathers cover most parts of the body of birds, they arise only from certain well-defined tracts on the skin. They aid in flight, thermal insulation, waterproofing and coloration that helps in communication and protection
structure_notes: The beta-keratins in feathers, beaks and claws - and the claws, scales and shells of reptiles - are composed of protein strands hydrogen-bonded into beta-pleated sheets, which are then further twisted and crosslinked by disulfide bridges into structures even tougher than the alpha-keratins of mammalian hair, horns and hoof.
database_cross_reference: Feather
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/410027006
database_cross_reference: BTO:0000447
database_cross_reference: EFO:0000955
database_cross_reference: GAID:1214
database_cross_reference: MAT:0000156
database_cross_reference: MESH:D005241
database_cross_reference: OpenCyc:Mx4rvVjW-5wpEbGdrcN5Y29ycA
has_obo_namespace: uberon
id: UBERON:0000022
in_subset: efo slim
in_subset: uberon slim

serous membrane
type: Class
subclass of: multi-tissue structure
definition: multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
external_definition: a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
external_ontology_notes: in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
contributor: cmungall
date retrieved: 2012-08-14
external class: TAO:0005425
external ontology: FMA
database_cross_reference: Serous membrane
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0036760
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/362878009
database_cross_reference: https://github.com/obophenotype/uberon/issues/86
database_cross_reference: FMA:9581
database_cross_reference: GAID:19
database_cross_reference: MESH:D012704
database_cross_reference: NCIT:C13169
database_cross_reference: TAO:0005425
database_cross_reference: UMLS:C0036760
database_cross_reference: ZFA:0005425
has_exact_synonym: tunica serosa
has_exact_synonym: wall of serous sac
has_obo_namespace: uberon
has_related_synonym: serosa
has_synonym_type: LATIN
id: UBERON:0000042
in_subset: uberon slim
in_subset: vertebrate core
ontology: TAO
source: Serous membrane
source: ncithesaurus:Serosa

urethra
type: Class
subclass of: organ
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: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
has_relational_adjective: urethral
taxon_notes: In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening.
database_cross_reference: Urethra
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0041967
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/302513006
database_cross_reference: BTO:0001426
database_cross_reference: CALOHA:TS-1132
database_cross_reference: EFO:0000931
database_cross_reference: EMAPA:30901
database_cross_reference: EV:0100099
database_cross_reference: FMA:19667
database_cross_reference: GAID:390
database_cross_reference: MA:0000379
database_cross_reference: MAT:0000121
database_cross_reference: MESH:D014521
database_cross_reference: MGI:anna
database_cross_reference: MIAA:0000121
database_cross_reference: MP:0000537
database_cross_reference: NCIT:C12417
database_cross_reference: OpenCyc:Mx4rvVjkypwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0041967
database_cross_reference: VHOG:0001264
database_cross_reference: XAO:0000153
database_cross_reference: galen:Urethra
has_obo_namespace: uberon
id: UBERON:0000057
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
source: ncithesaurus:Urethra

anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: AnatomicalStructure
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/362889002
database_cross_reference: AAO:0010825
database_cross_reference: AEO:0000003
database_cross_reference: BILA:0000003
database_cross_reference: CARO:0000003
database_cross_reference: EHDAA2:0003003
database_cross_reference: EMAPA:0
database_cross_reference: FBbt:00007001
database_cross_reference: FMA:305751
database_cross_reference: FMA:67135
database_cross_reference: GAID:781
database_cross_reference: HAO:0000003
database_cross_reference: MA:0003000
database_cross_reference: MESH:D000825
database_cross_reference: TAO:0000037
database_cross_reference: TGMA:0001823
database_cross_reference: VHOG:0001759
database_cross_reference: XAO:0003000
database_cross_reference: ZFA:0000037
has_exact_synonym: biological structure
has_exact_synonym: connected biological structure
has_obo_namespace: uberon
id: UBERON:0000061
in_subset: upper level

organ
type: Class
subclass of: multicellular anatomical structure
definition: Anatomical structure that performs a specific function or group of functions [WP].
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
external_ontology_notes: CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
database_cross_reference: Organ (anatomy)
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0178784
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: birnlex 4
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/272625005
database_cross_reference: CARO:0020004
database_cross_reference: EFO:0000634
database_cross_reference: EMAPA:35949
database_cross_reference: ENVO:01000162
database_cross_reference: FMA:67498
database_cross_reference: MA:0003001
database_cross_reference: NCIT:C13018
database_cross_reference: OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA
database_cross_reference: OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0178784
database_cross_reference: WBbt:0003760
has_obo_namespace: uberon
has_related_synonym: anatomical unit
has_related_synonym: body organ
has_related_synonym: element
id: UBERON:0000062
in_subset: upper level
source: GO:0048513
source: ncithesaurus:Organ

organ part
type: Class
subclass of: multicellular anatomical structure
definition: A multicellular structure that is a part of an organ.
curator note: currently defined in a very broad sense, may be replaced by more specific classes in the future
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: birnlex 16
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/113343008
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/91717005
database_cross_reference: AAO:0011124
database_cross_reference: EFO:0000635
database_cross_reference: FMA:82472
database_cross_reference: NIFSTD:birnlex_16
has_exact_synonym: cardinal organ part
has_obo_namespace: uberon
has_related_synonym: regional part of organ
id: UBERON:0000064
in_subset: efo slim
in_subset: non informative
in_subset: upper level

death stage
type: Class
subclass of: life cycle stage
definition: End of the life of an organism.
imported from: http://purl.obolibrary.org/obo/uberon.owl
external_ontology_notes: ncit:Death is an outcome
database_cross_reference: XAO:0000437
database_cross_reference: XtroDO:0000085
has_obo_namespace: uberon
has_related_synonym: death
id: UBERON:0000071

male reproductive system
type: Class
subclass of: reproductive organ
definition: The organs associated with producing offspring in the gender that produces spermatozoa.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
homology_notes: By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0000725
database_cross_reference: Male reproductive system (human)
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0017422
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1963704
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/361340001
database_cross_reference: BTO:0000082
database_cross_reference: CALOHA:TS-1310
database_cross_reference: EFO:0000970
database_cross_reference: EHDAA2:0001054
database_cross_reference: EHDAA:8136
database_cross_reference: EMAPA:17968
database_cross_reference: EV:0100101
database_cross_reference: FBbt:00004927
database_cross_reference: FMA:45664
database_cross_reference: GAID:386
database_cross_reference: HAO:0000505
database_cross_reference: MA:0000396
database_cross_reference: MESH:D005837
database_cross_reference: MP:0001145
database_cross_reference: NCIT:C12722
database_cross_reference: OBOL:automatic
database_cross_reference: OpenCyc:Mx4rvViCepwpEbGdrcN5Y29ycA
database_cross_reference: TGMA:0000634
database_cross_reference: UMLS:C0017422
database_cross_reference: UMLS:C1963704
database_cross_reference: VHOG:0000725
database_cross_reference: WBbt:0008423
database_cross_reference: XAO:0000155
has_exact_synonym: genitalia of male organism
has_exact_synonym: male genital system
has_exact_synonym: male genitalia
has_exact_synonym: male genitals
has_exact_synonym: male organism genitalia
has_exact_synonym: male organism reproductive system
has_exact_synonym: reproductive system of male organism
has_obo_namespace: uberon
has_related_synonym: male genital organ
has_related_synonym: male genital tract
has_related_synonym: male reproductive tract
has_related_synonym: systema genitale masculinum
id: UBERON:0000079
in_subset: efo slim
in_subset: pheno slim
ontology: VHOG
source: bgee.unil.ch
source: ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43
source: ncithesaurus:Male_Genitalia
source: ncithesaurus:Male_Reproductive_System

life cycle
type: Class
subclass of: history
definition: An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
imported from: http://purl.obolibrary.org/obo/uberon.owl
database_cross_reference: FBdv:00000000
database_cross_reference: HsapDv:0000001
database_cross_reference: MmusDv:0000001
database_cross_reference: OGES:000011
database_cross_reference: ncithesaurus:Life
has_exact_synonym: entire life cycle
has_exact_synonym: entire lifespan
has_exact_synonym: life
has_exact_synonym: lifespan
has_obo_namespace: uberon
id: UBERON:0000104
in_subset: upper level

life cycle stage
type: Class
subclass of: spatiotemporal region
definition: A spatiotemporal region encompassing some part of the life cycle of an organism.
editor note: this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
imported from: http://purl.obolibrary.org/obo/uberon.owl
external_ontology_notes: the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
external_ontology_notes: we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
database_cross_reference: BILS:0000105
database_cross_reference: EFO:0000399
database_cross_reference: FBdv:00007012
database_cross_reference: FMA:24120
database_cross_reference: HsapDv:0000000
database_cross_reference: MmusDv:0000000
database_cross_reference: OlatDv:0000010
database_cross_reference: PdumDv:0000090
database_cross_reference: WBls:0000002
database_cross_reference: XAO:1000000
database_cross_reference: ZFS:0000000
database_cross_reference: ZFS:0100000
database_cross_reference: ncithesaurus:Developmental_Stage
has_narrow_synonym: developmental stage
has_narrow_synonym: stage
has_obo_namespace: uberon
id: UBERON:0000105
in_subset: efo slim
in_subset: upper level

mouth
type: Class
subclass of: subdivision of digestive tract
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).
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
homology_notes: Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
has_relational_adjective: oral
development_notes: some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
external_ontology_notes: in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
date retrieved: 2012-06-20
date retrieved: 2012-09-17
external class: AAO:0010355
external class: VHOG:0000812
external ontology: FMA
database_cross_reference: Mouth
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/21082005
database_cross_reference: The-digestive-tract
database_cross_reference: AAO:0010355
database_cross_reference: BTO:0001090
database_cross_reference: BTO:0004698
database_cross_reference: CALOHA:TS-1315
database_cross_reference: EFO:0000825
database_cross_reference: EHDAA2:0001326
database_cross_reference: EHDAA:542
database_cross_reference: EMAPA:16262
database_cross_reference: FBbt:00003126
database_cross_reference: FMA:49184
database_cross_reference: FMA:TA
database_cross_reference: GAID:75
database_cross_reference: MA:0000341
database_cross_reference: MA:0002474
database_cross_reference: MAT:0000038
database_cross_reference: MESH:D009055
database_cross_reference: MIAA:0000038
database_cross_reference: OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA
database_cross_reference: TADS:0000040
database_cross_reference: TAO:0000547
database_cross_reference: TAO:0000590
database_cross_reference: TGMA:0000131
database_cross_reference: VHOG:0000280
database_cross_reference: VHOG:0000812
database_cross_reference: XAO:0003029
database_cross_reference: ZFA:0000547
database_cross_reference: ZFA:0000590
database_cross_reference: galen:Mouth
has_exact_synonym: regio oralis
has_narrow_synonym: adult mouth
has_obo_namespace: uberon
has_related_synonym: cavital oralis
has_related_synonym: cavitas oris
has_related_synonym: cavum oris
has_related_synonym: mouth cavity
has_related_synonym: oral region
has_related_synonym: oral vestibule
has_related_synonym: rima oris
has_related_synonym: stoma
has_related_synonym: stomatodaeum
has_related_synonym: trophic apparatus
has_related_synonym: vestibule of mouth
has_related_synonym: vestibulum oris
has_synonym_type: LATIN
id: UBERON:0000165
in_subset: efo slim
in_subset: major organ
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
ontology: AAO
ontology: VHOG
source: bgee.unil.ch
source: AAO:BJB
source: DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)

vomit
type: Class
subclass of: regurgitated substance
definition: A bodily fluid consisting of the expulsed contents of the stomach disgorged through the mouth or nose that happens as a result of a vomit reflex.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: Vomiting
database_cross_reference: ENVO:00000338
database_cross_reference: NCIT:C77666
database_cross_reference: OpenCyc:Mx4rvViQTJwpEbGdrcN5Y29ycA
database_cross_reference: UBERON:cjm
database_cross_reference: galen:Vomitus
has_exact_synonym: vomitus
has_obo_namespace: uberon
has_synonym_type: LATIN
id: UBERON:0000172

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: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0002638
database_cross_reference: BTO:0000068
database_cross_reference: CALOHA:TS-0034
database_cross_reference: EMAPA:36771
database_cross_reference: ENVO:02000021
database_cross_reference: EV:0100123
database_cross_reference: FMA:305905
database_cross_reference: GAID:1155
database_cross_reference: MA:0002893
database_cross_reference: MESH:D000653
database_cross_reference: MP:MP
database_cross_reference: NCIT:C13188
database_cross_reference: UMLS:C0002638
database_cross_reference: VHOG:0001267
has_obo_namespace: uberon
has_related_synonym: acqua amnii
has_related_synonym: liquor amnii
has_synonym_type: LATIN
id: UBERON:0000173
in_subset: pheno slim
source: ncithesaurus:Amniotic_Fluid

excreta
type: Class
subclass of: organism substance
definition: A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
has_alternative_id: UBERON:0000324
has_alternative_id: UBERON:0007550
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: AEO:0000184
database_cross_reference: BTO:0000491
database_cross_reference: EHDAA2_RETIRED:0003184
database_cross_reference: ENVO:02000022
database_cross_reference: FMA:9674
database_cross_reference: GO:0007588
database_cross_reference: galen:Excretion
has_exact_synonym: excreted substance
has_exact_synonym: portion of excreted substance
has_exact_synonym: waste substance
has_obo_namespace: uberon
has_related_synonym: excretion
id: UBERON:0000174

pus
type: Class
subclass of: organism substance
definition: Pus is a bodily fluid consisting of a whitish-yellow or yellow substance produced during inflammatory responses of the body that can be found in regions of pyogenic bacterial infections. Pus is produced from the dead and living cells which travel into the intercellular spaces around the affected cells.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_ontology_notes: biospecimen in NCIT
external ontology: NCIT
database_cross_reference: Pus
database_cross_reference: ENVO:02000038
database_cross_reference: OpenCyc:Mx4rvVjG6ZwpEbGdrcN5Y29ycA
database_cross_reference: galen:Pus
database_cross_reference: ncithesaurus:Pus
has_obo_namespace: uberon
has_related_synonym: purulent exudate
id: UBERON:0000177

blood
type: Class
subclass of: haemolymphatic fluid
definition: A fluid that is composed of blood plasma and erythrocytes.
curator note: This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
external_definition: Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
axiom_lost_from_external_ontology: relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
homology_notes: Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
contributor: cmungall
contributor: tmeehan
date retrieved: 2012-06-20
date retrieved: 2012-08-14
date retrieved: 2012-09-17
external class: AAO:0000046
external class: TAO:0000007
external class: VHOG:0000224
database_cross_reference: Blood
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0005767
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: https://github.com/obophenotype/uberon/issues/9
database_cross_reference: AAO:0000046
database_cross_reference: BTO:0000089
database_cross_reference: CALOHA:TS-0079
database_cross_reference: EFO:0000296
database_cross_reference: EHDAA2:0000176
database_cross_reference: EHDAA:418
database_cross_reference: EMAPA:16332
database_cross_reference: ENVO:02000027
database_cross_reference: EV:0100047
database_cross_reference: FMA:9670
database_cross_reference: GAID:965
database_cross_reference: MA:0000059
database_cross_reference: MESH:D001769
database_cross_reference: MIAA:0000315
database_cross_reference: NCIT:C12434
database_cross_reference: OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000007
database_cross_reference: UMLS:C0005767
database_cross_reference: VHOG:0000224
database_cross_reference: XAO:0000124
database_cross_reference: ZFA:0000007
database_cross_reference: galen:Blood
has_exact_synonym: portion of blood
has_exact_synonym: vertebrate blood
has_obo_namespace: uberon
has_related_synonym: whole blood
id: UBERON:0000178
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
ontology: AAO
ontology: TAO
ontology: VHOG
source: bgee.unil.ch
source: AAO:LAP
source: DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006)
source: ZFIN:curator
source: ncithesaurus:Blood

haemolymphatic fluid
type: Class
subclass of: bodily fluid
definition: Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
created by: cjm
creation date: 2009-04-08T04:38:19Z
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: CARO:0000081
has_obo_namespace: uberon
has_related_synonym: blood or blood analog
has_related_synonym: circulating fluid
id: UBERON:0000179

breast
type: Class
subclass of: external soft tissue zone
definition: The upper ventral region of the torso of an organism.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
taxon_notes: The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's.
database_cross_reference: Breast
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0006141
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181131000
database_cross_reference: BTO:0000149
database_cross_reference: CALOHA:TS-2083
database_cross_reference: EV:0100124
database_cross_reference: FMA:9601
database_cross_reference: GAID:33
database_cross_reference: MESH:D001940
database_cross_reference: NCIT:C12971
database_cross_reference: OpenCyc:Mx4rvVjV7ZwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0006141
database_cross_reference: galen:Breast
has_exact_synonym: mammary part of chest
has_exact_synonym: mammary region
has_obo_namespace: uberon
has_related_synonym: mamma
has_synonym_type: LATIN
id: UBERON:0000310
in_subset: pheno slim
source: WP,unvetted
source: ncithesaurus:Breast

secretion of exocrine gland
type: Class
subclass of: organism substance
definition: A portion of organism substance that is produced by exocrine glands.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_ontology_notes: BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
external ontology: BTO
has_alternative_id: UBERON:0006540
has_broad_synonym: secretion
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1516992
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: AEO:0001005
database_cross_reference: BTO:0002977
database_cross_reference: BTO:0002979
database_cross_reference: EMAPA:36535
database_cross_reference: FMA:9675
database_cross_reference: MA:0002504
database_cross_reference: MESH:D012634
database_cross_reference: NCIT:C34062
database_cross_reference: UMLS:C1516992
database_cross_reference: galen:Secretion
has_exact_synonym: bodily secretion
has_exact_synonym: exocrine gland fluid/secretion
has_exact_synonym: secreted substance
has_obo_namespace: uberon
has_related_synonym: exocrine gland fluid
has_related_synonym: exocrine gland fluid or secretion
has_related_synonym: exocrine gland secretion
has_related_synonym: external secretion
id: UBERON:0000456
source: ncithesaurus:Exocrine_Gland_Fluid_or_Secretion

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.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://orcid.org/0000-0001-9114-8737
database_cross_reference: AAO:0010839
database_cross_reference: AEO:0000004
database_cross_reference: BILA:0000004
database_cross_reference: CALOHA:TS-2101
database_cross_reference: CARO:0000004
database_cross_reference: EHDAA2:0003004
database_cross_reference: EMAPA:35178
database_cross_reference: FBbt:00007019
database_cross_reference: FMA:9669
database_cross_reference: HAO:0000004
database_cross_reference: MA:0002450
database_cross_reference: NCIT:C13236
database_cross_reference: SPD:0000008
database_cross_reference: TAO:0001487
database_cross_reference: TGMA:0001824
database_cross_reference: VHOG:0001726
database_cross_reference: XAO:0004001
database_cross_reference: ZFA:0001487
database_cross_reference: galen:BodySubstance
has_exact_synonym: body fluid or substance
has_exact_synonym: body substance
has_exact_synonym: organism substance
has_exact_synonym: portion of body substance
has_exact_synonym: portion of organism substance
has_obo_namespace: uberon
id: UBERON:0000463
in_subset: pheno slim
in_subset: upper level

material anatomical entity
type: Class
subclass of: anatomical entity
definition: Anatomical entity that has mass.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://orcid.org/0000-0001-9114-8737
database_cross_reference: AAO:0010264
database_cross_reference: AEO:0000006
database_cross_reference: BILA:0000006
database_cross_reference: CARO:0000006
database_cross_reference: EHDAA2:0003006
database_cross_reference: FBbt:00007016
database_cross_reference: FMA:67165
database_cross_reference: HAO:0000006
database_cross_reference: TAO:0001836
database_cross_reference: TGMA:0001826
database_cross_reference: VHOG:0001721
has_obo_namespace: uberon
id: UBERON:0000465
in_subset: upper level

testis
type: Class
subclass of: gonad
definition: A gonad of a male animal. A gonad produces and releases sperm.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: Male reproductive organ.[TAO]
homology_notes: (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]
has_relational_adjective: testicular
taxon_notes: The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally
date retrieved: 2012-08-14
date retrieved: 2012-09-17
external class: TAO:0000598
external class: VHOG:0000252
has_alternative_id: UBERON:0002117
database_cross_reference: Testis
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0039597
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181431007
database_cross_reference: AAO:0000606
database_cross_reference: BILA:0000124
database_cross_reference: BSA:0000085
database_cross_reference: BTO:0001363
database_cross_reference: CALOHA:TS-1030
database_cross_reference: EFO:0000984
database_cross_reference: EHDAA2:0002007
database_cross_reference: EHDAA:8146
database_cross_reference: EMAPA:17972
database_cross_reference: EV:0100102
database_cross_reference: FBbt:00004928
database_cross_reference: FMA:7210
database_cross_reference: GAID:396
database_cross_reference: HAO:0001007
database_cross_reference: MA:0000411
database_cross_reference: MAT:0000132
database_cross_reference: MESH:D013737
database_cross_reference: MIAA:0000132
database_cross_reference: NCIT:C12412
database_cross_reference: OBOL:automatic
database_cross_reference: OpenCyc:Mx4rvVjM25wpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000598
database_cross_reference: UMLS:C0039597
database_cross_reference: VHOG:0000252
database_cross_reference: WBbt:0006794
database_cross_reference: XAO:0000157
database_cross_reference: ZFA:0000598
database_cross_reference: galen:Testis
has_exact_synonym: gonad of male genitalia
has_exact_synonym: gonad of male reproductive system
has_exact_synonym: male gonad
has_exact_synonym: testicle
has_obo_namespace: uberon
has_related_synonym: orchis
has_related_synonym: testes
has_related_synonym: testiculus
has_synonym_type: LATIN
has_synonym_type: PLURAL
id: UBERON:0000473
in_subset: efo slim
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
ontology: TAO
ontology: VHOG
source: bgee.unil.ch
source: DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
source: ISBN-10:0123971756
source: ZFIN:curator
source: ncithesaurus:Testis
taxon: NCBITaxon:40674

tissue
type: Class
subclass of: multicellular anatomical structure
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.
editor note: changed label and definition to reflect CARO2
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0040300
database_cross_reference: birnlex 19
database_cross_reference: AAO:0000607
database_cross_reference: AAO:0010054
database_cross_reference: AEO:0000043
database_cross_reference: BILA:0000043
database_cross_reference: CALOHA:TS-2090
database_cross_reference: CARO:0000043
database_cross_reference: EHDAA2:0003043
database_cross_reference: EMAPA:35868
database_cross_reference: FBbt:00007003
database_cross_reference: FMA:9637
database_cross_reference: HAO:0000043
database_cross_reference: MA:0003002
database_cross_reference: MESH:D014024
database_cross_reference: NCIT:C12801
database_cross_reference: TAO:0001477
database_cross_reference: TGMA:0001844
database_cross_reference: UMLS:C0040300
database_cross_reference: VHOG:0001757
database_cross_reference: WBbt:0005729
database_cross_reference: XAO:0003040
database_cross_reference: ZFA:0001477
database_cross_reference: galen:Tissue
has_exact_synonym: portion of tissue
has_exact_synonym: tissue portion
has_narrow_synonym: simple tissue
has_obo_namespace: uberon
id: UBERON:0000479
in_subset: pheno slim
in_subset: upper level
source: ncithesaurus:Tissue

multi-tissue structure
type: Class
subclass of: multicellular anatomical structure
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: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://orcid.org/0000-0001-9114-8737
database_cross_reference: AAO:0010048
database_cross_reference: AEO:0000055
database_cross_reference: BILA:0000055
database_cross_reference: CARO:0000055
database_cross_reference: EHDAA2:0003055
database_cross_reference: FBbt:00007010
database_cross_reference: HAO:0000055
database_cross_reference: TAO:0001488
database_cross_reference: TGMA:0001847
database_cross_reference: VHOG:0001762
database_cross_reference: XAO:0003037
database_cross_reference: ZFA:0001488
has_obo_namespace: uberon
has_related_synonym: multi-tissue structures
has_synonym_type: PLURAL
id: UBERON:0000481
in_subset: upper level

stomach
type: Class
subclass of: subdivision of digestive tract
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: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
homology_notes: It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]
taxon_notes: We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa
date retrieved: 2012-06-20
date retrieved: 2012-09-17
external class: AAO:0000579
external class: VHOG:0000408
database_cross_reference: Stomach
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0038351
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181246003
database_cross_reference: https://orcid.org/0000-0002-6601-2165
database_cross_reference: AAO:0000579
database_cross_reference: ANISEED:1235297
database_cross_reference: BTO:0001307
database_cross_reference: CALOHA:TS-0980
database_cross_reference: EFO:0000837
database_cross_reference: EHDAA2:0001915
database_cross_reference: EHDAA:2993
database_cross_reference: EMAPA:17021
database_cross_reference: EV:0100070
database_cross_reference: FMA:7148
database_cross_reference: GAID:293
database_cross_reference: ISBN10:0073040584
database_cross_reference: MA:0000353
database_cross_reference: MAT:0000051
database_cross_reference: MESH:A03.492.766
database_cross_reference: MIAA:0000051
database_cross_reference: NCIT:C12391
database_cross_reference: OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA
database_cross_reference: TAO:0002121
database_cross_reference: UMLS:C0038351
database_cross_reference: VHOG:0000408
database_cross_reference: XAO:0000128
database_cross_reference: galen:Stomach
has_narrow_synonym: stomach chamber
has_obo_namespace: uberon
has_related_synonym: anterior intestine
has_related_synonym: gaster
has_related_synonym: mesenteron
has_related_synonym: ventriculus
has_synonym_type: LATIN
id: UBERON:0000945
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
ontology: AAO
ontology: VHOG
source: bgee.unil.ch
source: AAO:EJS
source: DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)
source: WP:Stomach#In_other_animals
source: ncithesaurus:Stomach

brain
type: Class
subclass of: organ
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].
editor note: requires review for applicability to invertebrate structures, e.g. synganglion
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
external_definition: Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
external_definition: The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
homology_notes: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
contributor: cmungall
date retrieved: 2012-06-20
date retrieved: 2012-08-14
date retrieved: 2012-09-17
external class: AAO:0010478
external class: TAO:0000008
external class: VHOG:0000157
database_cross_reference: http://braininfo.rprc.washington.edu/centraldirectory.aspx
database_cross_reference: Brain
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0006104
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1269537
database_cross_reference: birnlex 796
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/258335003
database_cross_reference: https://github.com/obophenotype/uberon/issues/300
database_cross_reference: AAO:0010478
database_cross_reference: ABA:Brain
database_cross_reference: BAMS:Br
database_cross_reference: BAMS:Brain
database_cross_reference: BILA:0000135
database_cross_reference: BTO:0000142
database_cross_reference: CALOHA:TS-0095
database_cross_reference: DHBA:10155
database_cross_reference: EFO:0000302
database_cross_reference: EHDAA2:0000183
database_cross_reference: EHDAA:2641
database_cross_reference: EHDAA:6485
database_cross_reference: EMAPA:16894
database_cross_reference: EV:0100164
database_cross_reference: FBbt:00005095
database_cross_reference: FMA:50801
database_cross_reference: GAID:571
database_cross_reference: HBA:4005
database_cross_reference: MA:0000168
database_cross_reference: MAT:0000098
database_cross_reference: MBA:8
database_cross_reference: MBA:997
database_cross_reference: MESH:D001921
database_cross_reference: MIAA:0000098
database_cross_reference: NCIT:C12439
database_cross_reference: NeuroNames:21
database_cross_reference: OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA
database_cross_reference: PBA:3999
database_cross_reference: TAO:0000008
database_cross_reference: UMLS:C0006104
database_cross_reference: UMLS:C1269537
database_cross_reference: VHOG:0000157
database_cross_reference: XAO:0000010
database_cross_reference: ZFA:0000008
database_cross_reference: galen:Brain
has_obo_namespace: uberon
has_related_synonym: encephalon
has_related_synonym: suprasegmental levels of nervous system
has_related_synonym: suprasegmental structures
has_related_synonym: synganglion
has_related_synonym: the brain
id: UBERON:0000955
in_subset: cumbo
in_subset: efo slim
in_subset: major organ
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
ontology: AAO
ontology: TAO
ontology: VHOG
source: bgee.unil.ch
source: Cumbo terms
source: AAO:BJB
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165
source: NIFSTD:birnlex_796
source: ZFIN:curator

eye
type: Class
subclass of: sense organ
definition: An organ that detects light.
curator note: This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
has_relational_adjective: ocular
has_relational_adjective: optic
structure_notes: Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva,
database_cross_reference: Eye
database_cross_reference: https://orcid.org/0000-0002-6601-2165
database_cross_reference: BILA:0000017
database_cross_reference: BTO:0000439
database_cross_reference: CALOHA:TS-0309
database_cross_reference: EFO:0000827
database_cross_reference: EV:0100336
database_cross_reference: FBbt:00005162
database_cross_reference: GAID:69
database_cross_reference: MAT:0000140
database_cross_reference: MESH:D005123
database_cross_reference: MIAA:0000140
database_cross_reference: OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA
has_obo_namespace: uberon
has_related_synonym: light-detecting organ
has_related_synonym: visual apparatus
id: UBERON:0000970
in_subset: efo slim
in_subset: functional classification
in_subset: major organ
in_subset: organ slim
in_subset: uberon slim

pleura
type: Class
subclass of: serous membrane
definition: The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion).
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
present_in_taxon: NCBITaxon 8782
external_definition: The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG]
has_relational_adjective: pleural
external_ontology_notes: In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86
date retrieved: 2012-09-17
external class: VHOG:0000394
database_cross_reference: Pleura
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0032225
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181609007
database_cross_reference: Pulmonary pleurae
database_cross_reference: https://github.com/obophenotype/uberon/issues/1231
database_cross_reference: BTO:0001791
database_cross_reference: CALOHA:TS-2081
database_cross_reference: EFO:0001980
database_cross_reference: EMAPA:16775
database_cross_reference: EV:0100044
database_cross_reference: FMA:9583
database_cross_reference: GAID:360
database_cross_reference: ISBN:0-683-40008-8
database_cross_reference: MA:0000433
database_cross_reference: MESH:D010994
database_cross_reference: MP:0010820
database_cross_reference: NCIT:C12469
database_cross_reference: OpenCyc:Mx4rv3zwLZwpEbGdrcN5Y29ycA
database_cross_reference: UBERON:cjm
database_cross_reference: UMLS:C0032225
database_cross_reference: VHOG:0000394
has_exact_synonym: wall of pleural sac
has_obo_namespace: uberon
has_related_synonym: pleura
has_related_synonym: pleural tissue
id: UBERON:0000977
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim
ontology: VHOG
source: bgee.unil.ch
source: BGEE:AN
source: ISBN10:0124020607
source: ISBN:978-0030223693
source: ncithesaurus:Pleural_Tissue

penis
type: Class
subclass of: intromittent organ
definition: A intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
has_relational_adjective: penile
has_relational_adjective: phallic
taxon_notes: Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca
database_cross_reference: Penis
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0030851
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/265793009
database_cross_reference: BTO:0000405
database_cross_reference: CALOHA:TS-0758
database_cross_reference: EFO:0000987
database_cross_reference: EHDAA2:0001433
database_cross_reference: EHDAA:9380
database_cross_reference: EMAPA:18682
database_cross_reference: EMAPA_RETIRED:18996
database_cross_reference: EV:0100107
database_cross_reference: FMA:9707
database_cross_reference: GAID:389
database_cross_reference: ISBN:0-683-40008-8
database_cross_reference: MA:0000408
database_cross_reference: MAT:0000186
database_cross_reference: MESH:D010413
database_cross_reference: MIAA:0000186
database_cross_reference: MP:0005187
database_cross_reference: NCIT:C12409
database_cross_reference: OpenCyc:Mx4rvVjkCZwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0030851
database_cross_reference: VHOG:0000727
database_cross_reference: galen:Penis
has_obo_namespace: uberon
has_related_synonym: penes
has_related_synonym: phallus
has_synonym_type: PLURAL
id: UBERON:0000989
in_subset: efo slim
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
source: WP
source: ncithesaurus:Penis

gonad
type: Class
subclass of: reproductive organ
definition: Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]
external_definition: The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]
homology_notes: Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]
has_relational_adjective: gonadal
external_ontology_notes: FMA xref is a 'general anatomical term'
date retrieved: 2012-06-20
date retrieved: 2012-08-14
date retrieved: 2012-09-17
external class: AAO:0000213
external class: TAO:0000413
external class: VHOG:0000397
external ontology: FMA
database_cross_reference: Gonad
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0018067
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/304623008
database_cross_reference: AAO:0000213
database_cross_reference: BILA:0000123
database_cross_reference: BSA:0000079
database_cross_reference: BTO:0000534
database_cross_reference: EMAPA:17383
database_cross_reference: FBbt:00004858
database_cross_reference: FMA:18250
database_cross_reference: GAID:368
database_cross_reference: HAO:0000379
database_cross_reference: ISBN:0140512888
database_cross_reference: MA:0002420
database_cross_reference: MESH:D006066
database_cross_reference: NCIT:C12725
database_cross_reference: OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000413
database_cross_reference: UMLS:C0018067
database_cross_reference: VHOG:0000397
database_cross_reference: WBbt:0005175
database_cross_reference: XAO:0003146
database_cross_reference: ZFA:0000413
database_cross_reference: ZFIN:curator
has_exact_synonym: gonada
has_obo_namespace: uberon
has_related_synonym: gonads
has_synonym_type: PLURAL
id: UBERON:0000991
in_subset: major organ
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
ontology: AAO
ontology: TAO
ontology: VHOG
source: bgee.unil.ch
source: AAO:BJB
source: DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
source: ZFIN:curator
source: ncithesaurus:Gonad

ovary
type: Class
subclass of: gonad
definition: the gonad of a female organism which contains germ cells
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]
external_definition: Female reproductive organ.[TAO]
homology_notes: (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]
has_relational_adjective: ovarian
taxon_notes: Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo
date retrieved: 2012-06-20
date retrieved: 2012-08-14
date retrieved: 2012-09-17
external class: AAO:0000371
external class: TAO:0000403
external class: VHOG:0000251
database_cross_reference: Ovary
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0029939
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181464007
database_cross_reference: AAO:0000371
database_cross_reference: BILA:0000125
database_cross_reference: BSA:0000080
database_cross_reference: BTO:0000975
database_cross_reference: CALOHA:TS-0730
database_cross_reference: EFO:0000973
database_cross_reference: EHDAA2:0001360
database_cross_reference: EHDAA:8124
database_cross_reference: EMAPA:17962
database_cross_reference: EV:0100111
database_cross_reference: FBbt:00004865
database_cross_reference: FMA:7209
database_cross_reference: GAID:367
database_cross_reference: GO:0061039
database_cross_reference: ISBN:0-683-40008-8
database_cross_reference: MA:0000384
database_cross_reference: MESH:D010053
database_cross_reference: MIAA:0000125
database_cross_reference: MP:0001126
database_cross_reference: NCIT:C12404
database_cross_reference: OBOL:automatic
database_cross_reference: OpenCyc:Mx4rvVi9QJwpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000403
database_cross_reference: UMLS:C0029939
database_cross_reference: VHOG:0000251
database_cross_reference: XAO:0000258
database_cross_reference: ZFA:0000403
has_exact_synonym: animal ovary
has_exact_synonym: female gonad
has_exact_synonym: female organism genitalia gonad
has_exact_synonym: female organism genitalia gonada
has_exact_synonym: female organism reproductive system gonad
has_exact_synonym: female organism reproductive system gonada
has_exact_synonym: female reproductive system gonad
has_exact_synonym: female reproductive system gonada
has_exact_synonym: genitalia of female organism gonad
has_exact_synonym: genitalia of female organism gonada
has_exact_synonym: gonad of female organism genitalia
has_exact_synonym: gonad of female organism reproductive system
has_exact_synonym: gonad of female reproductive system
has_exact_synonym: gonad of genitalia of female organism
has_exact_synonym: gonad of reproductive system of female organism
has_exact_synonym: gonada of female organism genitalia
has_exact_synonym: gonada of female organism reproductive system
has_exact_synonym: gonada of female reproductive system
has_exact_synonym: gonada of genitalia of female organism
has_exact_synonym: gonada of reproductive system of female organism
has_exact_synonym: ovum-producing ovary
has_exact_synonym: reproductive system of female organism gonad
has_exact_synonym: reproductive system of female organism gonada
has_obo_namespace: uberon
has_related_synonym: ovaries
has_related_synonym: ovarium
has_synonym_type: LATIN
has_synonym_type: PLURAL
has_synonym_type: SENSU
id: UBERON:0000992
in_subset: efo slim
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core

uterus
type: Class
subclass of: subdivision of oviduct
definition: the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG]
homology_notes: An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]
has_relational_adjective: uterine
taxon_notes: Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream.
development_notes: Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus]
date retrieved: 2012-09-17
external class: VHOG:0001137
database_cross_reference: Uterus
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0042149
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181452004
database_cross_reference: BTO:0001424
database_cross_reference: CALOHA:TS-1102
database_cross_reference: EFO:0000975
database_cross_reference: EMAPA:29915
database_cross_reference: EV:0100113
database_cross_reference: FMA:17558
database_cross_reference: GAID:172
database_cross_reference: MA:0000389
database_cross_reference: MAT:0000127
database_cross_reference: MESH:D014599
database_cross_reference: MGI:csmith
database_cross_reference: MIAA:0000127
database_cross_reference: MP:0001120
database_cross_reference: NCIT:C12405
database_cross_reference: OpenCyc:Mx4rvViojJwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0042149
database_cross_reference: VHOG:0001137
database_cross_reference: galen:Uterus
has_obo_namespace: uberon
id: UBERON:0000995
in_subset: efo slim
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
ontology: VHOG
source: bgee.unil.ch
source: uterus
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678
source: ncithesaurus:Uterus

vagina
type: Class
subclass of: subdivision of oviduct
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: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
external_definition: Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA]
external_definition: The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG]
homology_notes: The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG]
has_relational_adjective: vaginal
development_notes: 'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688
date retrieved: 2012-09-17
date retrieved: 2012-11-29
external class: FMA:19949
external class: VHOG:0001138
database_cross_reference: Vagina
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0042232
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181441005
database_cross_reference: BTO:0000243
database_cross_reference: CALOHA:TS-1103
database_cross_reference: EFO:0000976
database_cross_reference: EMAPA:18986
database_cross_reference: EV:0100117
database_cross_reference: FMA:19949
database_cross_reference: GAID:381
database_cross_reference: MA:0000394
database_cross_reference: MAT:0000128
database_cross_reference: MESH:D014621
database_cross_reference: MIAA:0000128
database_cross_reference: NCIT:C12407
database_cross_reference: OpenCyc:Mx4rvVj1B5wpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0042232
database_cross_reference: VHOG:0001138
database_cross_reference: galen:Vagina
has_obo_namespace: uberon
has_related_synonym: distal oviductal region
has_related_synonym: distal portion of oviduct
has_related_synonym: vaginae
has_synonym_type: PLURAL
id: UBERON:0000996
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim
ontology: FMA
ontology: VHOG
source: bgee.unil.ch
source: vagina
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688
source: ncithesaurus:Vagina

strand of hair
type: Class
subclass of: cutaneous appendage
definition: A filament, mostly protein, that grows from follicles found in the dermis[WP].
editor note: TODO for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales)
curator note: this class defines an individual hair
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: Hair
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0018494
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/361702001
database_cross_reference: BTO:0001501
database_cross_reference: CALOHA:TS-0430
database_cross_reference: EFO:0000958
database_cross_reference: EMAPA:18769
database_cross_reference: EV:0100157
database_cross_reference: FMA:53667
database_cross_reference: GAID:71
database_cross_reference: MA:0000155
database_cross_reference: MAT:0000160
database_cross_reference: MESH:D006197
database_cross_reference: MIAA:0000160
database_cross_reference: NCIT:C32705
database_cross_reference: UMLS:C0018494
database_cross_reference: VHOG:0001191
has_exact_synonym: hair
has_obo_namespace: uberon
has_related_synonym: coat hair
has_related_synonym: coat/ hair
has_related_synonym: fur
has_related_synonym: microchaeta
has_related_synonym: quill
has_related_synonym: setulae
has_related_synonym: vibrissa
has_related_synonym: whisker
has_synonym_type: SENSU
id: UBERON:0001037
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim
source: ncithesaurus:Hair

rectum
type: Class
subclass of: subdivision of digestive tract
definition: the terminal portion of the intestinal tube, terminating with the anus
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
has_relational_adjective: rectal
taxon_notes: In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html
date retrieved: 2012-09-17
external class: VHOG:0001751
database_cross_reference: Rectum
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0034896
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181261002
database_cross_reference: AAO:0010401
database_cross_reference: BTO:0001158
database_cross_reference: CALOHA:TS-1180
database_cross_reference: EFO:0000848
database_cross_reference: EHDAA2:0001592
database_cross_reference: EHDAA:5836
database_cross_reference: EMAPA:17896
database_cross_reference: EV:0100081
database_cross_reference: FMA:14544
database_cross_reference: GAID:311
database_cross_reference: ISBN:0-683-40008-8
database_cross_reference: MA:0000336
database_cross_reference: MAT:0000050
database_cross_reference: MESH:A03.492.411.495.767
database_cross_reference: MIAA:0000050
database_cross_reference: MP:0000492
database_cross_reference: NCIT:C12390
database_cross_reference: OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0034896
database_cross_reference: VHOG:0001751
database_cross_reference: XAO:0000238
database_cross_reference: galen:Rectum
has_exact_synonym: terminal portion of intestine
has_obo_namespace: uberon
has_related_synonym: intestinum rectum
has_related_synonym: rectal sac
has_related_synonym: terminal portion of large intestine
id: UBERON:0001052
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim
ontology: VHOG
source: bgee.unil.ch
source: ncithesaurus:Rectum

anatomical entity
type: Class
subclass of: independent continuant
definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1515976
database_cross_reference: http://orcid.org/0000-0001-9114-8737
database_cross_reference: birnlex 6
database_cross_reference: AAO:0010841
database_cross_reference: AEO:0000000
database_cross_reference: BILA:0000000
database_cross_reference: CARO:0000000
database_cross_reference: EHDAA2:0002229
database_cross_reference: FBbt:10000000
database_cross_reference: FBbt_root:00000000
database_cross_reference: FMA:62955
database_cross_reference: HAO:0000000
database_cross_reference: MA:0000001
database_cross_reference: NCIT:C12219
database_cross_reference: TAO:0100000
database_cross_reference: TGMA:0001822
database_cross_reference: UMLS:C1515976
database_cross_reference: WBbt:0000100
database_cross_reference: XAO:0000000
database_cross_reference: ZFA:0100000
has_obo_namespace: uberon
id: UBERON:0001062
in_subset: upper level
source: ncithesaurus:Anatomic_Structure_System_or_Substance

urine
type: Class
subclass of: excreta
definition: Excretion that is the output of a kidney
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
taxon_notes: kidney excreta from some taxa (e.g. in aves) may not be liquid
database_cross_reference: Urine
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0042036
database_cross_reference: https://github.com/geneontology/go-ontology/issues/11025
database_cross_reference: BTO:0001419
database_cross_reference: CALOHA:TS-1092
database_cross_reference: EFO:0001939
database_cross_reference: EMAPA:36554
database_cross_reference: ENVO:00002047
database_cross_reference: FMA:12274
database_cross_reference: GAID:1189
database_cross_reference: MA:0002545
database_cross_reference: MAT:0000058
database_cross_reference: MESH:D014556
database_cross_reference: MIAA:0000058
database_cross_reference: NCIT:C13283
database_cross_reference: OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0042036
database_cross_reference: galen:Urine
has_obo_namespace: uberon
id: UBERON:0001088
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim
source: ncithesaurus:Urine

sweat
type: Class
subclass of: secretion of exocrine gland
definition: Secretion produced by a sweat gland.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: Sweat
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0038984
database_cross_reference: BTO:0001254
database_cross_reference: ENVO:02000025
database_cross_reference: FMA:12275
database_cross_reference: GAID:1172
database_cross_reference: MA:0002539
database_cross_reference: MESH:D013542
database_cross_reference: NCIT:C13280
database_cross_reference: OpenCyc:Mx4rvVjJtZwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0038984
has_obo_namespace: uberon
has_related_synonym: skin exudate
id: UBERON:0001089
in_subset: pheno slim
in_subset: uberon slim
source: ncithesaurus:Sweat

colon
type: Class
subclass of: subdivision of digestive tract
definition: Last portion of the large intestine before it becomes the rectum.
editor note: TODO - abstract this such that it legitimately covers all vertebrates
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]
external_definition: The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]
homology_notes: Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
has_relational_adjective: colonic
taxon_notes: In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]
taxon_notes: In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]
function_notes: it extracts water and salt from solid wastes before they are eliminated from the body[WP]
date retrieved: 2012-06-20
date retrieved: 2012-08-14
date retrieved: 2012-09-17
external class: AAO:0010400
external class: TAO:0000706
external class: VHOG:0000648
database_cross_reference: Colon (anatomy)
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0009368
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/302508007
database_cross_reference: AAO:0010400
database_cross_reference: BTO:0000269
database_cross_reference: CALOHA:TS-0158
database_cross_reference: EFO:0000361
database_cross_reference: EMAPA:18939
database_cross_reference: EV:0100079
database_cross_reference: FMA:14543
database_cross_reference: GAID:309
database_cross_reference: MA:0000335
database_cross_reference: MAP:0000001
database_cross_reference: MAT:0000526
database_cross_reference: MESH:A03.492.411.495.356
database_cross_reference: NCIT:C12382
database_cross_reference: OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000706
database_cross_reference: UMLS:C0009368
database_cross_reference: VHOG:0000648
database_cross_reference: XAO:0000243
database_cross_reference: ZFA:0000706
database_cross_reference: ZFIN:curator
database_cross_reference: galen:Colon
has_exact_synonym: large bowel
has_narrow_synonym: posterior intestine
has_obo_namespace: uberon
has_related_synonym: hindgut
id: UBERON:0001155
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
ontology: AAO
ontology: TAO
ontology: VHOG
source: bgee.unil.ch
source: ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
source: UBERON:0001155
source: ZFIN:curator
source: ncithesaurus:Colon

pancreas
type: Class
subclass of: viscus
definition: An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO].
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]
homology_notes: In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]
has_relational_adjective: pancreatic
taxon_notes: As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52)
taxon_notes: The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm
function_notes: The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans
date retrieved: 2012-06-20
date retrieved: 2012-09-17
external class: AAO:0010112
external class: VHOG:0000050
database_cross_reference: Pancreas
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0030274
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181277001
database_cross_reference: AAO:0010112
database_cross_reference: BTO:0000988
database_cross_reference: CALOHA:TS-0736
database_cross_reference: EFO:0000855
database_cross_reference: EHDAA2:0001367
database_cross_reference: EHDAA:6893
database_cross_reference: EMAPA:17503
database_cross_reference: EV:0100092
database_cross_reference: FMA:7198
database_cross_reference: GAID:334
database_cross_reference: GO:0031016
database_cross_reference: MA:0000120
database_cross_reference: MAT:0000075
database_cross_reference: MESH:D010179
database_cross_reference: MIAA:0000075
database_cross_reference: NCIT:C12393
database_cross_reference: OpenCyc:Mx4rvVimZZwpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000140
database_cross_reference: UMLS:C0030274
database_cross_reference: VHOG:0000050
database_cross_reference: XAO:0000136
database_cross_reference: ZFA:0000140
database_cross_reference: galen:Pancreas
has_obo_namespace: uberon
id: UBERON:0001264
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
ontology: AAO
ontology: VHOG
source: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/16417468
source: http://www.ncbi.nlm.nih.gov/pubmed/20959416
source: AAO:BJB
source: DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)
source: ncithesaurus:Pancreas

cerebrospinal fluid
type: Class
subclass of: transudate
definition: A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
editor note: many sources state the CP as sole producer of CSF, but this is disputed [DOI:10.1007/s11064-015-1581-6]
imported from: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
external_definition: Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO]
homology_notes: In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG]
external_ontology_notes: EHDAA2 models this as developing from CP, which is wrong
external_ontology_notes: the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations.
date retrieved: 2012-08-14
date retrieved: 2012-09-17
external class: TAO:0002184
external class: VHOG:0001278
external ontology: EHDAA2
external ontology: FMA
database_cross_reference: Cerebrospinal fluid
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0007806
database_cross_reference: BIRNLEX:1798
database_cross_reference: BTO:0000237
database_cross_reference: CALOHA:TS-0130
database_cross_reference: EFO:0000329
database_cross_reference: EHDAA2:0004441
database_cross_reference: ENVO:02000029
database_cross_reference: EV:0100311
database_cross_reference: FMA:20935
database_cross_reference: GAID:1181
database_cross_reference: MA:0002503
database_cross_reference: MAT:0000499
database_cross_reference: MESH:A12.207.268
database_cross_reference: NCIT:C12692
database_cross_reference: TAO:0002184
database_cross_reference: UMLS:C0007806
database_cross_reference: VHOG:0001278
database_cross_reference: ZFA:0001626
has_exact_synonym: CSF
has_exact_synonym: cerebral spinal fluid
has_obo_namespace: uberon
has_related_synonym: liquor cerebrospinalis
has_related_synonym: spinal fluid
id: UBERON:0001359
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
ontology: TAO
ontology: VHOG
source: bgee.unil.ch
source: BIRNLEX:1798
source: DOI:10.1021/pr050213t Parada C, Gato A, Bueno D, Mammalian embryonic cerebrospinal fluid proteome has greater apolipoprotein and enzyme pattern complexity than the avian proteome. Journal of Proteome Research (2005)
source: ZFIN:curator
source: ncithesaurus:Cerebrospinal_Fluid

neck of organ
type: Class
subclass of: zone of organ
imported from: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
database_cross_reference: FMA:45733
has_exact_synonym: organ neck
has_obo_namespace: uberon
id: UBERON:0001560
in_subset: non informative

ear
type: Class
subclass of: sense organ
definition: Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: The organ of hearing and of equilibrium. [TFD][VHOG]
homology_notes: Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG]
has_relational_adjective: auricular
date retrieved: 2012-09-17
external class: VHOG:0000330
database_cross_reference: Ear
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0013443
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0521421
database_cross_reference: birnlex 1062
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/1910005
database_cross_reference: AAO:0011014
database_cross_reference: BTO:0000368
database_cross_reference: CALOHA:TS-1165
database_cross_reference: EFO:0000826
database_cross_reference: EHDAA2:0000423
database_cross_reference: EHDAA:502
database_cross_reference: EMAPA:16193
database_cross_reference: EV:0100353
database_cross_reference: FMA:52780
database_cross_reference: GAID:62
database_cross_reference: GO:0042471
database_cross_reference: MA:0000236
database_cross_reference: MAT:0000138
database_cross_reference: MESH:D004423
database_cross_reference: MIAA:0000138
database_cross_reference: NCIT:C12394
database_cross_reference: OpenCyc:Mx4rvViXS5wpEbGdrcN5Y29ycA
database_cross_reference: OpenCyc:Mx4rvVjL05wpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0013443
database_cross_reference: UMLS:C0521421
database_cross_reference: VHOG:0000330
database_cross_reference: XAO:0000189
database_cross_reference: galen:Ear
has_obo_namespace: uberon
has_related_synonym: auditory apparatus
has_related_synonym: auris
id: UBERON:0001690
in_subset: efo slim
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
ontology: VHOG
source: bgee.unil.ch
source: ear
source: DOI:10.1002/dvdy.20207 Boekhoff-Falk G, Hearing in Drosophila: Development of Johnston's organ and emerging parallels to vertebrate ear development. Developmental Dynamics (2005)
source: NIFSTD:birnlex_1062
source: ncithesaurus:Ear

nail
type: Class
subclass of: distal limb integumentary appendage
definition: A horn-like keratin structure covering the dorsal aspect of the terminal phalanges of fingers and toes[WP].
curator note: Use this class for both the nails of primates and the homologous claws of mammals such as mouse.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
taxon_notes: A primate's nail consists of the unguis alone; the subunguis has disappeared
contributor: cmungall
contributor: mellybelly
database_cross_reference: Claw
database_cross_reference: Nail (anatomy)
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0027342
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/72651009
database_cross_reference: https://github.com/obophenotype/uberon/issues/120
database_cross_reference: BTO:0001719
database_cross_reference: CALOHA:TS-2034
database_cross_reference: EFO:0000956
database_cross_reference: EMAPA:35580
database_cross_reference: EV:0100159
database_cross_reference: FMA:54326
database_cross_reference: GAID:1320
database_cross_reference: MA:0002703
database_cross_reference: MAT:0000158
database_cross_reference: MESH:D009262
database_cross_reference: MIAA:0000158
database_cross_reference: NCIT:C33156
database_cross_reference: OpenCyc:Mx4rvVjJv5wpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0027342
database_cross_reference: VHOG:0001361
database_cross_reference: XAO:0003103
database_cross_reference: galen:Nail
has_exact_synonym: nail/claw
has_narrow_synonym: claw
has_obo_namespace: uberon
has_related_synonym: talon
has_synonym_type: SENSU
id: UBERON:0001705
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim
source: ncithesaurus:Nail
comment: The nails of humans and the claws are moth are highly similar. Both species have a proximal nail fold, cuticle, nail matrix, nail bed, nail plate, and hyponychium. Distinguishing features are the shape of the nail and the presence of an extended hyponychium in the mouse [PMC3579226]

secretion of lacrimal gland
type: Class
subclass of: secretion of exocrine gland
definition: Aqueous substance secreted by the lacrimal gland.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: Tear
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0039409
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: BTO:0001499
database_cross_reference: CALOHA:TS-1016
database_cross_reference: EMAPA:36537
database_cross_reference: ENVO:02000034
database_cross_reference: FMA:59756
database_cross_reference: GAID:1173
database_cross_reference: MA:0002508
database_cross_reference: MESH:D013666
database_cross_reference: NCIT:C33739
database_cross_reference: UMLS:C0039409
database_cross_reference: galen:Tear
database_cross_reference: galen:Tears
has_exact_synonym: lacrimal fluid
has_exact_synonym: lacrimal gland secretion
has_exact_synonym: lacrimal secretion
has_exact_synonym: tear
has_exact_synonym: tears
has_obo_namespace: uberon
has_related_synonym: tear fluid
has_synonym_type: PLURAL
id: UBERON:0001827
in_subset: uberon slim
source: ncithesaurus:Tear

saliva
type: Class
subclass of: secretion of exocrine gland
definition: A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
has_relational_adjective: salivary
taxon_notes: We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin
database_cross_reference: Saliva
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0036087
database_cross_reference: BTO:0001202
database_cross_reference: CALOHA:TS-0891
database_cross_reference: EMAPA:36536
database_cross_reference: ENVO:02000036
database_cross_reference: FMA:59862
database_cross_reference: GAID:1167
database_cross_reference: GO:0046541
database_cross_reference: MA:0002507
database_cross_reference: MAT:0000444
database_cross_reference: MESH:D012463
database_cross_reference: NCIT:C13275
database_cross_reference: OpenCyc:Mx4rvVjJ95wpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0036087
database_cross_reference: galen:Saliva
has_exact_synonym: salivary gland secretion
has_obo_namespace: uberon
has_related_synonym: sailva normalis
has_related_synonym: saliva atomaris
has_related_synonym: saliva molecularis
has_synonym_type: LATIN
id: UBERON:0001836
in_subset: uberon slim
source: GO
source: ncithesaurus:Saliva

milk
type: Class
subclass of: mammary gland fluid/secretion
definition: An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.
editor note: to axiomatize the different forms of mammary gland secretion an ontology of the phases of pregnancy/lactation is required. Using the existing GO def of lactation is circular.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
homology_notes: The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]
external_ontology_notes: ncit:Milk refers specifically to cow milk
date retrieved: 2012-09-17
external class: VHOG:0001263
external ontology: ncit
database_cross_reference: Breast milk
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1511310
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: BTO:0000868
database_cross_reference: CALOHA:TS-0636
database_cross_reference: EMAPA:36540
database_cross_reference: ENVO:02000031
database_cross_reference: EV:0100126
database_cross_reference: FMA:62100
database_cross_reference: GAID:1230
database_cross_reference: MA:0002552
database_cross_reference: MAT:0000056
database_cross_reference: MESH:A13.622
database_cross_reference: MIAA:0000056
database_cross_reference: NCIT:C13401
database_cross_reference: OpenCyc:Mx4rvVjGZJwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C1511310
database_cross_reference: VHOG:0001263
database_cross_reference: galen:Milk
has_exact_synonym: mammary gland milk
has_obo_namespace: uberon
id: UBERON:0001913
in_subset: pheno slim
in_subset: uberon slim
ontology: VHOG
source: bgee.unil.ch
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224
source: ncithesaurus:Breast_Fluid_or_Secretion

semen
type: Class
subclass of: organism substance
definition: Organism substance that is composed of sperm cells suspended in seminal fluid.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
has_relational_adjective: seminal
taxon_notes: Note that in this ontology, semen is defined as the sum of sperm and seminal fluid, where seminal fluid is defined in taxonomically generic way (see comments for UBERON:0006530).
database_cross_reference: Semen
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1518159
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C2756969
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: BTO:0001230
database_cross_reference: CALOHA:TS-0917
database_cross_reference: EMAPA:31488
database_cross_reference: FMA:62966
database_cross_reference: GAID:1169
database_cross_reference: MA:0002522
database_cross_reference: MESH:D012661
database_cross_reference: NCIT:C13277
database_cross_reference: NCIT:C13713
database_cross_reference: OpenCyc:Mx4rvgC-zpwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C1518159
database_cross_reference: UMLS:C2756969
has_obo_namespace: uberon
has_related_synonym: ejaculate
has_related_synonym: sperm
id: UBERON:0001968
in_subset: pheno slim
in_subset: uberon slim
source: ncithesaurus:Male_Genital_System_Fluid_or_Secretion
source: ncithesaurus:Semen

blood plasma
type: Class
subclass of: haemolymphatic fluid
definition: The liquid component of blood, in which erythrocytes are suspended.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
has_broad_synonym: plasma
has_broad_synonym: portion of plasma
database_cross_reference: Blood plasma
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0032105
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: BTO:0000131
database_cross_reference: CALOHA:TS-0800
database_cross_reference: EFO:0001905
database_cross_reference: EMAPA:35690
database_cross_reference: FMA:62970
database_cross_reference: GAID:1178
database_cross_reference: MA:0002501
database_cross_reference: MAT:0000052
database_cross_reference: MESH:D010949
database_cross_reference: MIAA:0000052
database_cross_reference: NCIT:C13356
database_cross_reference: OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw
database_cross_reference: UMLS:C0032105
has_exact_synonym: blood plasm
has_exact_synonym: portion of blood plasma
has_obo_namespace: uberon
id: UBERON:0001969
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim
source: ncithesaurus:Plasma

bile
type: Class
subclass of: secretion of exocrine gland
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: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
taxon_notes: In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum.
function_notes: aids the process of digestion of lipids in the small intestine
function_notes: bile salts function to emulsify dietary fats and facilitate their intestinal absorption
function_notes: elimination of cholesterol
function_notes: major excretory route for potentially harmful exogenous lipophilic substances
function_notes: many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates
function_notes: protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine
database_cross_reference: Bile
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0005388
database_cross_reference: cphy.c120027
database_cross_reference: BTO:0000121
database_cross_reference: CALOHA:TS-1172
database_cross_reference: ENVO:02000023
database_cross_reference: FMA:62971
database_cross_reference: GAID:1157
database_cross_reference: MA:0002513
database_cross_reference: MESH:D001646
database_cross_reference: NCIT:C13192
database_cross_reference: UMLS:C0005388
database_cross_reference: ZFA:0005857
database_cross_reference: galen:Bile
has_obo_namespace: uberon
has_related_synonym: fel
has_related_synonym: gall
id: UBERON:0001970
in_subset: pheno slim
in_subset: uberon slim
source: ncithesaurus:Bile

blood serum
type: Class
subclass of: haemolymphatic fluid
definition: The portion of blood plasma that excludes clotting factors.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: Serum (blood)
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0229671
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: BTO:0000133
database_cross_reference: BTO:0001239
database_cross_reference: CALOHA:TS-0923
database_cross_reference: EHDAA2:0004728
database_cross_reference: EMAPA:35770
database_cross_reference: FMA:63083
database_cross_reference: MA:0002502
database_cross_reference: NCIT:C13325
database_cross_reference: UMLS:C0229671
has_exact_synonym: serum
has_obo_namespace: uberon
id: UBERON:0001977
in_subset: pheno slim
in_subset: uberon slim
source: ncithesaurus:Serum

feces
type: Class
subclass of: excreta
definition: Portion of semisolid bodily waste discharged through the anus[MW,modified]
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: Excretion in semisolid state processed by the intestine.[FMA]
has_relational_adjective: fecal
has_broad_synonym: excreta
database_cross_reference: Cow dung
database_cross_reference: Feces
database_cross_reference: Fewmet
database_cross_reference: Frass
database_cross_reference: Guano
database_cross_reference: Spraint
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0015733
database_cross_reference: feces
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/23285307
database_cross_reference: BTO:0000440
database_cross_reference: CALOHA:TS-2345
database_cross_reference: ENVO:00002003
database_cross_reference: FMA:64183
database_cross_reference: GAID:1199
database_cross_reference: MA:0002509
database_cross_reference: MAT:0000053
database_cross_reference: MESH:D005243
database_cross_reference: MIAA:0000053
database_cross_reference: NCIT:C13234
database_cross_reference: OpenCyc:Mx4rvVjJMZwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0015733
database_cross_reference: galen:Feces
has_exact_synonym: faeces
has_exact_synonym: fecal material
has_exact_synonym: fecal matter
has_exact_synonym: matières fécales@fr
has_exact_synonym: merde@fr
has_exact_synonym: partie de la merde@fr
has_exact_synonym: piece of shit
has_exact_synonym: porción de mierda@es
has_exact_synonym: portion of excrement
has_exact_synonym: portion of faeces
has_exact_synonym: portion of fecal material
has_exact_synonym: portion of fecal matter
has_exact_synonym: portion of feces
has_exact_synonym: portionem cacas
has_exact_synonym: stool
has_exact_synonym: teil der fäkalien@de
has_narrow_synonym: cow dung
has_narrow_synonym: cow pat
has_narrow_synonym: dung
has_narrow_synonym: fewmet
has_narrow_synonym: frass
has_narrow_synonym: guano
has_narrow_synonym: portion of dung
has_narrow_synonym: portion of guano
has_narrow_synonym: portion of scat
has_narrow_synonym: scat
has_narrow_synonym: spraint
has_obo_namespace: uberon
has_related_synonym: droppings
has_related_synonym: excrement
has_related_synonym: ordure
has_related_synonym: spoor
has_synonym_type: LATIN
id: UBERON:0001988
in_subset: pheno slim
in_subset: uberon slim
source: FMA:64183
source: ncithesaurus:Feces

thyroid gland
type: Class
subclass of: endocrine gland
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].
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO]
homology_notes: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG]
taxon_notes: In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes
taxon_notes: In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine)
taxon_notes: In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species
date retrieved: 2012-06-20
date retrieved: 2012-09-17
external class: AAO:0010544
external class: VHOG:0000418
database_cross_reference: Thyroid
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0040132
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181117000
database_cross_reference: AAO:0010544
database_cross_reference: BTO:0001379
database_cross_reference: CALOHA:TS-1047
database_cross_reference: EFO:0000861
database_cross_reference: EHDAA2:0002028
database_cross_reference: EHDAA:2148
database_cross_reference: EHDAA:2975
database_cross_reference: EMAPA:17068
database_cross_reference: EV:0100133
database_cross_reference: FMA:9603
database_cross_reference: GAID:465
database_cross_reference: MA:0000129
database_cross_reference: MAT:0000081
database_cross_reference: MESH:D013961
database_cross_reference: MIAA:0000081
database_cross_reference: NCIT:C12400
database_cross_reference: OpenCyc:Mx4rvVjLT5wpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0040132
database_cross_reference: VHOG:0000418
database_cross_reference: XAO:0000162
database_cross_reference: galen:ThyroidGland
has_exact_synonym: thyroid
has_obo_namespace: uberon
has_related_synonym: glandula thyroidea
has_scope: NCBITaxon:32443
has_scope: NCBITaxon:32523
has_scope: NCBITaxon:7746
has_synonym_type: LATIN
id: UBERON:0002046
in_subset: efo slim
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
ontology: AAO
ontology: VHOG
source: bgee.unil.ch
source: Other animals
source: AAO:BJB
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
source: Romer
source: ncithesaurus:Thyroid_Gland

lung
type: Class
subclass of: thoracic cavity element
definition: Respiration organ that develops as an oupocketing of the esophagus.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
homology_notes: Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]
has_relational_adjective: pulmonary
taxon_notes: respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi
date retrieved: 2012-06-20
date retrieved: 2012-09-17
external class: AAO:0010567
external class: VHOG:0000310
database_cross_reference: Lung
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0024109
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181216001
database_cross_reference: AAO:0000275
database_cross_reference: AAO:0010567
database_cross_reference: BTO:0000763
database_cross_reference: CALOHA:TS-0568
database_cross_reference: EFO:0000934
database_cross_reference: EHDAA2:0001042
database_cross_reference: EHDAA:1554
database_cross_reference: EHDAA:2205
database_cross_reference: EMAPA:16728
database_cross_reference: EV:0100042
database_cross_reference: FMA:7195
database_cross_reference: GAID:345
database_cross_reference: MA:0000415
database_cross_reference: MAT:0000135
database_cross_reference: MESH:D008168
database_cross_reference: MIAA:0000135
database_cross_reference: NCIT:C12468
database_cross_reference: OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0024109
database_cross_reference: VHOG:0000310
database_cross_reference: XAO:0000119
database_cross_reference: galen:Lung
has_exact_synonym: pulmo
has_obo_namespace: uberon
has_synonym_type: LATIN
id: UBERON:0002048
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
ontology: AAO
ontology: VHOG
source: bgee.unil.ch
source: AAO:SBH
source: ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011)
source: ncithesaurus:Lung
comment: Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]

viscus
type: Class
subclass of: trunk region element
definition: An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
external_ontology_notes: general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.
date retrieved: 2012-06-20
external class: AAO:0010386
external ontology: FMA
database_cross_reference: Viscus
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0042779
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/118760003
database_cross_reference: https://github.com/obophenotype/mouse-anatomy-ontology/issues/14
database_cross_reference: AAO:0010386
database_cross_reference: BTO:0001491
database_cross_reference: EHDAA:512
database_cross_reference: EMAPA:16245
database_cross_reference: FMA:7085
database_cross_reference: MA:0000019
database_cross_reference: MESH:D014781
database_cross_reference: NCIT:C28287
database_cross_reference: RETIRED_EHDAA2:0002201
database_cross_reference: UMLS:C0042779
database_cross_reference: XAO:0003034
has_exact_synonym: visceral organ
has_exact_synonym: visceral organ system
has_obo_namespace: uberon
has_related_synonym: Organsystem@de
has_related_synonym: splanchnic tissue
has_related_synonym: viscera
has_related_synonym: visceral tissue
id: UBERON:0002075
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: upper level
ontology: AAO
source: BTO:0001491
source: ncithesaurus:Viscera

spleen
type: Class
subclass of: abdominal viscera
definition: the organ that functions to filter blood and to store red corpuscles and platelets
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: An organ involved in red blood cell filtration and immune response.[AAO]
homology_notes: With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG]
has_relational_adjective: lienal
has_relational_adjective: splenic
taxon_notes: In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron
taxon_notes: Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96)
function_notes: It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells
date retrieved: 2012-06-20
date retrieved: 2012-09-17
external class: AAO:0010395
external class: VHOG:0000120
database_cross_reference: Spleen
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0037993
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181279003
database_cross_reference: AAO:0010395
database_cross_reference: BTO:0001281
database_cross_reference: CALOHA:TS-0956
database_cross_reference: EFO:0000869
database_cross_reference: EMAPA:18767
database_cross_reference: EV:0100055
database_cross_reference: FMA:7196
database_cross_reference: GAID:1289
database_cross_reference: ISBN:0-683-40008-8
database_cross_reference: MA:0000141
database_cross_reference: MAT:0000085
database_cross_reference: MESH:A15.382.520.604.713
database_cross_reference: MIAA:0000085
database_cross_reference: MP:0000689
database_cross_reference: NCIT:C12432
database_cross_reference: OpenCyc:Mx4rvVjgw5wpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000436
database_cross_reference: UMLS:C0037993
database_cross_reference: VHOG:0000120
database_cross_reference: XAO:0000328
database_cross_reference: ZFA:0000436
database_cross_reference: galen:Spleen
has_obo_namespace: uberon
has_related_synonym: lien
has_synonym_type: LATIN
id: UBERON:0002106
in_subset: efo slim
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
ontology: AAO
ontology: VHOG
source: bgee.unil.ch
source: http://www.ncbi.nlm.nih.gov/pubmed/20959416
source: AAO:BMZ
source: ISBN:978-0781765190 Paul WE, Fundamental Immunology (2008) p.94
source: ncithesaurus:Spleen

liver
type: Class
subclass of: digestive system gland
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: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
axiom_lost_from_external_ontology: relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
homology_notes: All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]
has_relational_adjective: hepatic
taxon_notes: An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).
taxon_notes: The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.
function_notes: 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].
external_ontology_notes: Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function.
date retrieved: 2012-06-20
date retrieved: 2012-09-17
external class: AAO:0010111
external class: VHOG:0000257
external ontology: ZFA
database_cross_reference: Liver
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0023884
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181268008
database_cross_reference: AAO:0010111
database_cross_reference: BTO:0000759
database_cross_reference: CALOHA:TS-0564
database_cross_reference: EFO:0000887
database_cross_reference: EHDAA2:0000997
database_cross_reference: EHDAA:2197
database_cross_reference: EMAPA:16846
database_cross_reference: EV:0100089
database_cross_reference: FMA:7197
database_cross_reference: GAID:288
database_cross_reference: MA:0000358
database_cross_reference: MAT:0000097
database_cross_reference: MESH:D008099
database_cross_reference: MIAA:0000097
database_cross_reference: NCIT:C12392
database_cross_reference: OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA
database_cross_reference: TAO:0000123
database_cross_reference: UMLS:C0023884
database_cross_reference: VHOG:0000257
database_cross_reference: XAO:0000133
database_cross_reference: ZFA:0000123
database_cross_reference: galen:Liver
has_obo_namespace: uberon
has_related_synonym: iecur
has_related_synonym: jecur
has_synonym_type: LATIN
id: UBERON:0002107
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
ontology: AAO
ontology: VHOG
source: bgee.unil.ch
source: AAO:BJB
source: ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.526, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
source: ncithesaurus:Liver

kidney
type: Class
subclass of: abdomen element
definition: A paired organ of the urinary tract which has the production of urine as its primary function.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]
has_relational_adjective: renal
fma_set_term: FMA_264815
date retrieved: 2012-06-20
external class: AAO:0000250
database_cross_reference: kidney.html
database_cross_reference: Kidney
database_cross_reference: Reniculate kidney
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0022646
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181414000
database_cross_reference: AAO:0000250
database_cross_reference: BTO:0000671
database_cross_reference: CALOHA:TS-0510
database_cross_reference: EFO:0000929
database_cross_reference: EMAPA:17373
database_cross_reference: EV:0100096
database_cross_reference: FMA:7203
database_cross_reference: GAID:423
database_cross_reference: MA:0000368
database_cross_reference: MAT:0000119
database_cross_reference: MESH:D007668
database_cross_reference: MIAA:0000119
database_cross_reference: NCIT:C12415
database_cross_reference: OpenCyc:Mx4rvVjlYpwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0022646
database_cross_reference: XAO:0003267
database_cross_reference: galen:Kidney
has_narrow_synonym: reniculate kidney
has_obo_namespace: uberon
has_synonym_type: SENSU
id: UBERON:0002113
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
ontology: AAO
source: AAO:BJB
source: ncithesaurus:Kidney

olfactory organ
type: Class
subclass of: sense organ
definition: An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ.
editor note: An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_ontology_notes: fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
database_cross_reference: AAO:0010180
database_cross_reference: BTO:0001772
database_cross_reference: FBbt:00005158
database_cross_reference: FMA:77659
database_cross_reference: UBERON:cjm
database_cross_reference: VHOG:0000287
database_cross_reference: XAO:0000273
has_exact_synonym: olfactory organ
has_exact_synonym: olfactory sense organ
has_exact_synonym: olfactory sensory organ
has_narrow_synonym: main olfactory organ
has_narrow_synonym: primary olfactory organ
has_obo_namespace: uberon
has_related_synonym: olfactory neuroepithelium
has_related_synonym: organ olfactus
has_related_synonym: organum olfactorium
id: UBERON:0002268
in_subset: functional classification

peritoneum
type: Class
subclass of: serous membrane
definition: A serous membrane that lines the peritoneal cavity[VHOG,modified].
editor note: TODO - in ZFA is_a epithelium
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: An epithelium that lines the peritoneal cavity.[TAO]
external_definition: Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO]
has_relational_adjective: peritoneal
external_ontology_notes: todo: check MA/EMAPA.
date retrieved: 2012-06-20
date retrieved: 2012-08-14
external class: AAO:0010814
external class: TAO:0005120
external ontology: MA
database_cross_reference: Peritoneum
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0031153
database_cross_reference: AAO:0010814
database_cross_reference: BTO:0001472
database_cross_reference: CALOHA:TS-2072
database_cross_reference: EV:0100087
database_cross_reference: FMA:9584
database_cross_reference: GAID:18
database_cross_reference: MA:0000449
database_cross_reference: MESH:A01.047.025.600
database_cross_reference: NCIT:C12770
database_cross_reference: OpenCyc:Mx4rvjJ72ZwpEbGdrcN5Y29ycA
database_cross_reference: TAO:0005120
database_cross_reference: UMLS:C0031153
database_cross_reference: VHOG:0001257
database_cross_reference: XAO:0000139
database_cross_reference: ZFA:0005120
database_cross_reference: galen:Peritoneum
has_obo_namespace: uberon
has_related_synonym: peritonaeum
id: UBERON:0002358
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core
ontology: AAO
ontology: TAO
source: AAO:JMG
source: ZFIN:curator
source: ncithesaurus:Peritoneum

prostate gland
type: Class
subclass of: male accessory sex gland
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.
editor note: TODO - FMA treats the gland as part of the prostate - see also FMA:74119.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
has_relational_adjective: prostatic
database_cross_reference: Prostate
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0033572
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/10668204
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181422007
database_cross_reference: BTO:0001129
database_cross_reference: CALOHA:TS-0828
database_cross_reference: EFO:0000858
database_cross_reference: EMAPA:19287
database_cross_reference: EV:0100104
database_cross_reference: FMA:9600
database_cross_reference: GAID:392
database_cross_reference: GO:0030850
database_cross_reference: MA:0000404
database_cross_reference: MAT:0000078
database_cross_reference: MESH:D011467
database_cross_reference: MIAA:0000078
database_cross_reference: NCIT:C12410
database_cross_reference: OpenCyc:Mx4rv6trqZwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0033572
database_cross_reference: VHOG:0001261
database_cross_reference: galen:ProstateGland
has_exact_synonym: male prostate
has_exact_synonym: prostate
has_obo_namespace: uberon
has_related_synonym: prostata
has_synonym_type: LATIN
id: UBERON:0002367
in_subset: efo slim
in_subset: major organ
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
source: ncithesaurus:Prostate_Gland

endocrine gland
type: Class
subclass of: gland
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].
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: Ductless gland
database_cross_reference: Endocrine gland
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0014133
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/40818001
database_cross_reference: AEO:0000098
database_cross_reference: BTO:0001488
database_cross_reference: CALOHA:TS-1300
database_cross_reference: EHDAA2:0003098
database_cross_reference: EMAPA:35999
database_cross_reference: FMA:9602
database_cross_reference: GAID:335
database_cross_reference: MA:0002563
database_cross_reference: MESH:D004702
database_cross_reference: NCIT:C12704
database_cross_reference: OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0014133
has_exact_synonym: ductless gland
has_exact_synonym: glandula endocrina
has_obo_namespace: uberon
has_related_synonym: ductless gland
has_related_synonym: glandulae endocrinae
has_synonym_type: LATIN
id: UBERON:0002368
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
source: ncithesaurus:Endocrine_Gland

adrenal gland
type: Class
subclass of: adrenal/interrenal gland
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].
imported from: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
external_definition: Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO]
homology_notes: All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]
taxon_notes: The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole
function_notes: suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n.
date retrieved: 2012-06-20
date retrieved: 2012-09-17
external class: AAO:0010551
external class: VHOG:0001141
database_cross_reference: Adrenal gland
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0001625
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/181127006
database_cross_reference: AAO:0010551
database_cross_reference: BTO:0000047
database_cross_reference: CALOHA:TS-0016
database_cross_reference: EFO:0000238
database_cross_reference: EMAPA:18426
database_cross_reference: EV:0100135
database_cross_reference: FMA:9604
database_cross_reference: GAID:446
database_cross_reference: GO:0030325
database_cross_reference: MA:0000116
database_cross_reference: MAT:0000071
database_cross_reference: MESH:D000311
database_cross_reference: MIAA:0000071
database_cross_reference: NCIT:C12666
database_cross_reference: OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0001625
database_cross_reference: VHOG:0001141
database_cross_reference: XAO:0000164
database_cross_reference: galen:AdrenalGland
has_exact_synonym: glandula adrenalis
has_exact_synonym: glandula suprarenalis
has_obo_namespace: uberon
has_related_synonym: adrenal
has_related_synonym: adrenal capsule
has_related_synonym: adrenal medulla cell
has_related_synonym: atrabiliary capsule
has_related_synonym: epinephric gland
has_related_synonym: epinephros
has_related_synonym: glandula suprarenalis
has_related_synonym: interrenal gland
has_related_synonym: suprarenal capsule
has_related_synonym: suprarenal gland
has_synonym_type: HOMOLOGY
has_synonym_type: LATIN
id: UBERON:0002369
in_subset: organ slim
in_subset: pheno slim
in_subset: uberon slim
ontology: AAO
ontology: VHOG
source: bgee.unil.ch
source: AAO:BJB
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9
source: ncithesaurus:Adrenal_Gland

bone marrow
type: Class
subclass of: tissue
definition: the soft tissue that fills the cavities of bones
editor note: TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs
editor note: consider placement of NCIT:C53466 medullary bone
imported from: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
homology_notes: The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]
function_notes: In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]
date retrieved: 2012-09-17
external class: VHOG:0001218
database_cross_reference: Bone marrow
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0005953
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/421320006
database_cross_reference: AAO:0011007
database_cross_reference: BTO:0000141
database_cross_reference: BTO:0000829
database_cross_reference: CALOHA:TS-0087
database_cross_reference: EFO:0000868
database_cross_reference: EMAPA:32760
database_cross_reference: EV:0100046
database_cross_reference: FMA:9608
database_cross_reference: GAID:1287
database_cross_reference: MA:0000134
database_cross_reference: MAT:0000084
database_cross_reference: MESH:D001853
database_cross_reference: MGI:cwg
database_cross_reference: MIAA:0000084
database_cross_reference: MP:0002397
database_cross_reference: NCIT:C12431
database_cross_reference: OpenCyc:Mx4rvVm-FpwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0005953
database_cross_reference: VHOG:0001218
database_cross_reference: XAO:0000123
database_cross_reference: galen:BoneMarrow
has_exact_synonym: medulla ossea
has_exact_synonym: medulla ossium
has_obo_namespace: uberon
has_related_synonym: medulla of bone
has_related_synonym: medullary bone
has_synonym_type: LATIN
id: UBERON:0002371
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim
ontology: VHOG
source: bgee.unil.ch
source: DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006)
source: ncithesaurus:Bone_Marrow

pericardial fluid
type: Class
subclass of: secretion of serous gland
definition: Transudate contained in the pericardial cavity.[FMA]
imported from: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
database_cross_reference: Pericardial fluid
database_cross_reference: BTO:0001016
database_cross_reference: FMA:9887
database_cross_reference: MA:0002530
has_obo_namespace: uberon
id: UBERON:0002409
in_subset: uberon slim

gland
type: Class
subclass of: organ
definition: an organ that functions as a secretory or excretory organ
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
has_relational_adjective: glandular
has_alternative_id: UBERON:MIAA_0000021
database_cross_reference: Gland
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1285092
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/134358001
database_cross_reference: AAO:0000212
database_cross_reference: AEO:0000096
database_cross_reference: BTO:0000522
database_cross_reference: EFO:0000797
database_cross_reference: EHDAA2:0003096
database_cross_reference: EHDAA:2161
database_cross_reference: EHDAA:4475
database_cross_reference: EHDAA:6522
database_cross_reference: EMAPA:18425
database_cross_reference: FBbt:00100317
database_cross_reference: FMA:7146
database_cross_reference: FMA:86294
database_cross_reference: HAO:0000375
database_cross_reference: MA:0003038
database_cross_reference: MAT:0000021
database_cross_reference: MGI:csmith
database_cross_reference: MIAA:0000021
database_cross_reference: MP:0002163
database_cross_reference: NCIT:C13319
database_cross_reference: OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C1285092
database_cross_reference: WikipediaCategory:Glands
database_cross_reference: galen:Gland
has_exact_synonym: glandular organ
has_obo_namespace: uberon
has_related_synonym: Druese
has_related_synonym: glandula
has_synonym_type: LATIN
id: UBERON:0002530
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim
source: ncithesaurus:Gland

reproductive organ
type: Class
subclass of: organ
definition: An organ involved in reproduction
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_ontology_notes: GO uses genitalia for the singular organ
external ontology: GO
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0017420
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/128181006
database_cross_reference: EMAPA:17381
database_cross_reference: EMAPA:37731
database_cross_reference: MA:0001752
database_cross_reference: MESH:D005835
database_cross_reference: NCIT:C25177
database_cross_reference: OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA
database_cross_reference: TGMA:0000591
database_cross_reference: UBERON:xp
database_cross_reference: UMLS:C0017420
database_cross_reference: WBbt:0008422
has_exact_synonym: genital organ
has_exact_synonym: reproductive system organ
has_exact_synonym: sex organ
has_obo_namespace: uberon
has_related_synonym: genitalia
has_synonym_type: PLURAL
id: UBERON:0003133
in_subset: functional classification
in_subset: organ slim
in_subset: pheno slim
source: MA:th
source: ncithesaurus:Genitalia

reproductive gland
type: Class
subclass of: gland
definition: Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: MA:0001751
database_cross_reference: MP:0000653
database_cross_reference: OBOL:automatic
has_exact_synonym: genitalia gland
has_exact_synonym: gland of genitalia
has_exact_synonym: gland of reproductive system
has_exact_synonym: reproductive gland
has_exact_synonym: reproductive system gland
has_exact_synonym: sex gland
has_obo_namespace: uberon
id: UBERON:0003937
in_subset: organ slim
in_subset: pheno slim

subdivision of digestive tract
type: Class
subclass of: subdivision of tube
definition: A proximal-distal subdivision of the digestive tract.
curator note: intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: FBbt:00100315
database_cross_reference: FMA:71131
has_obo_namespace: uberon
has_related_synonym: alimentary system subdivision
has_related_synonym: intestinal tract
has_related_synonym: segment of intestinal tract
has_related_synonym: subdivision of alimentary system
id: UBERON:0004921
in_subset: non informative

abdomen element
type: Class
subclass of: abdominal segment element
definition: An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/272631008
database_cross_reference: MA:0000522
has_exact_synonym: abdomen organ
has_obo_namespace: uberon
id: UBERON:0005172
in_subset: non informative

abdominal segment element
type: Class
subclass of: trunk region element
definition: An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: EMAPA:37062
database_cross_reference: MA:0000529
has_exact_synonym: abdominal segment organ
has_obo_namespace: uberon
id: UBERON:0005173
in_subset: non informative
source: MA:th

trunk region element
type: Class
subclass of: organ
definition: An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: EMAPA:37270
database_cross_reference: MA:0000516
has_exact_synonym: trunk organ
has_obo_namespace: uberon
id: UBERON:0005177
in_subset: non informative
in_subset: organ slim
source: MA:th

thoracic cavity element
type: Class
subclass of: thoracic segment organ
definition: An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: EMAPA:37273
database_cross_reference: MA:0000557
has_exact_synonym: thoracic cavity organ
has_obo_namespace: uberon
id: UBERON:0005178
in_subset: non informative
in_subset: pheno slim
source: MA:th

thoracic segment organ
type: Class
subclass of: trunk region element
definition: An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: EMAPA:37271
database_cross_reference: MA:0000563
has_obo_namespace: uberon
has_related_synonym: upper body organ
id: UBERON:0005181
in_subset: non informative
source: MA:th

male reproductive gland
type: Class
subclass of: reproductive gland
definition: A sex gland that is part of a male reproductive system.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: BTO:0000080
database_cross_reference: EMAPA:19285
database_cross_reference: MA:0000399
database_cross_reference: OBOL:automatic
has_obo_namespace: uberon
has_related_synonym: accessory sex gland
id: UBERON:0005399
in_subset: organ slim
in_subset: pheno slim

integumentary adnexa
type: Class
subclass of: organ part
definition: Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers.
editor note: add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678]
database_cross_reference: http://code.google.com/p/caro2/issues/detail
database_cross_reference: Skin appendage
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: EMAPA:37883
database_cross_reference: GO:GO
has_narrow_synonym: body hair or bristle
has_obo_namespace: uberon
has_related_synonym: adnexae cutis
has_related_synonym: skin adnexa
has_related_synonym: skin adnexal structure
has_related_synonym: skin appendage
has_synonym_type: LATIN
id: UBERON:0006003
in_subset: pheno slim
source: MA:th
source: MP:0010678

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.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
has_broad_synonym: fluid
database_cross_reference: Body fluid
database_cross_reference: birnlex 20
database_cross_reference: EMAPA:37441
database_cross_reference: FMA:280556
database_cross_reference: GAID:266
database_cross_reference: MESH:A12.207
database_cross_reference: MESH:D001826
database_cross_reference: galen:BodyFluid
has_exact_synonym: body fluid
has_obo_namespace: uberon
id: UBERON:0006314
in_subset: pheno slim
source: MA:th

respiratory system fluid/secretion
type: Class
subclass of: organism substance
definition: A portion of organism substance that secreted_by a respiratory system.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1514899
database_cross_reference: EMAPA:36550
database_cross_reference: MA:0002533
database_cross_reference: NCIT:C13722
database_cross_reference: OBOL:automatic
database_cross_reference: UMLS:C1514899
has_obo_namespace: uberon
has_related_synonym: respiratory system fluid
has_related_synonym: respiratory system secretion
id: UBERON:0006538
source: ncithesaurus:Respiratory_System_Fluid_or_Secretion

mammary gland fluid/secretion
type: Class
subclass of: secretion of exocrine gland
definition: A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: EMAPA:36538
database_cross_reference: MA:0002505
has_obo_namespace: uberon
has_related_synonym: lactiferous gland fluid
has_related_synonym: lactiferous gland secretion
has_related_synonym: mammary gland fluid
has_related_synonym: mammary gland secreted fluid
has_related_synonym: mammary gland secretion
has_related_synonym: secretion of mammary gland
id: UBERON:0006539

pharynx
type: Class
subclass of: subdivision of digestive tract
definition: The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
curator note: currently this is an extremely generic class, encompassing both protostomes and deuterostomes.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
has_relational_adjective: branchial
has_relational_adjective: pharyngeal
database_cross_reference: FBbt:00005380
database_cross_reference: GO:0060465
database_cross_reference: MAT:0000049
database_cross_reference: MIAA:0000049
has_obo_namespace: uberon
has_related_synonym: anterior part of foregut
has_related_synonym: pharyngeal tube
id: UBERON:0006562
in_subset: grouping class
in_subset: uberon slim

adrenal/interrenal gland
type: Class
subclass of: endocrine gland
definition: This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO]
editor note: keep this grouping class so long as it is required for GO
imported from: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
homology_notes: All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]
date retrieved: 2012-09-17
external class: VHOG:0001141
database_cross_reference: GO:0030325
database_cross_reference: VHOG:0001141
has_exact_synonym: adrenal gland - interrenal gland
has_exact_synonym: adrenal gland/interrenal tissue
has_obo_namespace: uberon
has_related_synonym: adrenal - interrenal gland
has_related_synonym: suprarenal gland - interrenal gland
id: UBERON:0006858
in_subset: homology grouping
in_subset: organ slim
ontology: VHOG
source: bgee.unil.ch
source: ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9

digestive system gland
type: Class
subclass of: endocrine gland
definition: Any gland that is part of the digestive system.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: AAO:0000130
database_cross_reference: BTO:0000345
database_cross_reference: UBERON:cjm
has_obo_namespace: uberon
has_related_synonym: digestive gland
id: UBERON:0006925
in_subset: organ slim

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: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: BTO:0000838
database_cross_reference: ncithesaurus:Meconium
has_obo_namespace: uberon
id: UBERON:0007109

neonate stage
type: Class
subclass of: life cycle stage
definition: Of or pertaining to the period of time immediately following birth, or to the newborn.
editor note: consider splitting infant/newborn
imported from: http://purl.obolibrary.org/obo/uberon.owl
database_cross_reference: Infant
database_cross_reference: Category:Infant organism
database_cross_reference: Category:Newborn organism
database_cross_reference: BTO:0001762
database_cross_reference: EV:0300037
database_cross_reference: HsapDv:0000082
database_cross_reference: MmusDv:0000096
database_cross_reference: NIF_Organism:birnlex_695
database_cross_reference: OGES:000025
has_exact_synonym: neonatal stage
has_narrow_synonym: fledgling stage
has_narrow_synonym: hatchling
has_narrow_synonym: hatchling stage
has_narrow_synonym: infant stage
has_narrow_synonym: nestling stage
has_narrow_synonym: pouch stage
has_narrow_synonym: puggle
has_narrow_synonym: puggle stage
has_obo_namespace: uberon
has_related_synonym: newborn stage
id: UBERON:0007221

sputum
type: Class
subclass of: respiratory system fluid/secretion
definition: Matter ejected from the lungs, bronchi, and trachea, through the mouth.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0038056
database_cross_reference: BTO:0001297
database_cross_reference: CALOHA:TS-0963
database_cross_reference: Dorlands_Medical_Dictionary:MerckSource
database_cross_reference: EMAPA:36553
database_cross_reference: FMA:312401
database_cross_reference: GAID:1171
database_cross_reference: MA:0002536
database_cross_reference: MESH:D013183
database_cross_reference: NCIT:C13278
database_cross_reference: UMLS:C0038056
has_obo_namespace: uberon
has_related_synonym: expectoration
id: UBERON:0007311
source: ncithesaurus:Sputum

transudate
type: Class
subclass of: bodily fluid
definition: Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces
imported from: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
has_relational_adjective: transudative
structure_notes: characteristically low in protein and cellular content (unless there has been secondary concentration)
database_cross_reference: transudate
database_cross_reference: FMA:12276
database_cross_reference: GAID:1195
database_cross_reference: MESH:D005122
database_cross_reference: ncithesaurus:Transudate
has_obo_namespace: uberon
has_related_synonym: plasma ultrafiltrate
id: UBERON:0007779

secretion of serous gland
type: Class
subclass of: bodily fluid
definition: Any fluid produced by a serous gland.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
has_broad_synonym: serous fluid
database_cross_reference: Serous fluid
database_cross_reference: UBERON:cjm
has_exact_synonym: serosal fluid
has_exact_synonym: serous gland fluid
has_obo_namespace: uberon
id: UBERON:0007794

intromittent organ
type: Class
subclass of: male reproductive system
definition: An external organ of a male organism that is specialized to deliver sperm during copulation. Intromittent organs are found most often in terrestrial species, as most aquatic species fertilize their eggs externally, although there are exceptions[WP].
curator note: this is a broad grouping class connecting a number of different analagous organs by their function. We place the insect aedeagus here rather than penis, although this is somewhat arbitrary given the broadness of the current definition
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_definition: Surface structure that is an external structure of a male organism through which sperm is transferred to a female organism during mating.[TAO]
date retrieved: 2012-08-14
external class: TAO:0002036
database_cross_reference: Intromittent organ
database_cross_reference: AAO:0010255
database_cross_reference: FBbt:00004850
database_cross_reference: HAO:0000091
database_cross_reference: TAO:0002036
database_cross_reference: TGMA:0000585
has_narrow_synonym: aedeagus
has_narrow_synonym: penis
has_obo_namespace: uberon
has_related_synonym: copulatory organ
has_synonym_type: SENSU
id: UBERON:0008811
in_subset: grouping class
in_subset: organ slim
ontology: TAO
source: TAO:wd

distal limb integumentary appendage
type: Class
subclass of: integumentary projection
definition: A nail, hoof or claw.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/11710767
database_cross_reference: MESH:D006724
has_obo_namespace: uberon
has_related_synonym: hoof or claw
has_related_synonym: hoof, claw or nail
has_related_synonym: keratin plate
has_related_synonym: keratin sheath
has_related_synonym: unguis
id: UBERON:0009564

multicellular anatomical structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that has more than one cell as a part.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: CARO:0010000
database_cross_reference: FBbt:00100313
has_exact_synonym: multicellular structure
has_obo_namespace: uberon
id: UBERON:0010000
in_subset: upper level

male accessory sex gland
type: Class
subclass of: male reproductive gland
definition: Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: BTO:0004798
has_obo_namespace: uberon
has_related_synonym: male accessory gland
has_related_synonym: male accessory reproductive gland
id: UBERON:0010147
in_subset: pheno slim

bulb of aorta
type: Class
subclass of: organ part
definition: The portion of the left ventricular outflow tract delineated by the sinotubular ridge superiorly and the bases of the valve leaflets inferiorly; it comprises the aortic sinuses, the aortic valve leaflets, the commissures, and the interleaflet triangles
imported from: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
external_definition: The dilated first part of the aorta containing the aortic semilunar valves and the aortic sinuses.
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/362032000
database_cross_reference: BTO:0004695
database_cross_reference: FMA:3740
database_cross_reference: FMA:TA
database_cross_reference: MP:0011572
database_cross_reference: MP:0011575
has_exact_synonym: aorta bulb
has_exact_synonym: aortic bulb
has_exact_synonym: aortic root
has_exact_synonym: bulb of ascending aorta
has_exact_synonym: bulbus aortae
has_exact_synonym: root of aorta
has_exact_synonym: supraaortic valve area
has_obo_namespace: uberon
has_synonym_type: LATIN
id: UBERON:0010172
in_subset: pheno slim
source: aortic+bulb

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: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
database_cross_reference: Cord blood
database_cross_reference: BTO:0004053
database_cross_reference: CALOHA:TS-1079
database_cross_reference: EFO:0001942
database_cross_reference: MESH:A12.207.152.200
database_cross_reference: MESH:D005312
has_obo_namespace: uberon
has_related_synonym: cord blood
has_related_synonym: fetal blood
has_related_synonym: umbilical cord blood
id: UBERON:0012168
in_subset: efo slim
comment: Cord blood is collected because it contains stem cells, which can be used to treat hematopoietic and genetic disorders.[WP]

subdivision of oviduct
type: Class
subclass of: subdivision of tube
definition: A section through the tube or network of tubes that connects the ovaries to the outside of the body.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
external_ontology_notes: FMA class may only represent the uterine portion
external ontology: FMA
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: FMA:18302
has_exact_synonym: subdivision of oviduct
has_exact_synonym: subdivision of uterine tube
has_exact_synonym: uterine tube zone
has_exact_synonym: zone of uterine tube
has_narrow_synonym: subdivision of fallopian tube
has_obo_namespace: uberon
id: UBERON:0013515
in_subset: non informative

subdivision of tube
type: Class
subclass of: organ part
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
has_obo_namespace: uberon
id: UBERON:0013522

integumentary projection
type: Class
subclass of: integumentary adnexa
definition: Anatomical projection that is part of the integumentl system.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://orcid.org/0000-0002-6601-2165
has_narrow_synonym: skin projection
has_obo_namespace: uberon
id: UBERON:0013703

arterial blood
type: Class
subclass of: blood
definition: A blood that is part of a artery.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
database_cross_reference: FMA:83066
database_cross_reference: OBOL:automatic
has_exact_synonym: arterial blood
has_exact_synonym: blood in artery
has_exact_synonym: portion of arterial blood
has_obo_namespace: uberon
id: UBERON:0013755
in_subset: pheno slim

venous blood
type: Class
subclass of: blood
definition: A blood that is part of a vein.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
database_cross_reference: FMA:83067
database_cross_reference: OBOL:automatic
has_exact_synonym: blood in vein
has_exact_synonym: portion of venous blood
has_exact_synonym: venous blood
has_obo_namespace: uberon
id: UBERON:0013756

abdominal viscera
type: Class
subclass of: abdomen element
definition: A viscus that is part of a abdomen.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: FMA:32413
database_cross_reference: FMA:67355
database_cross_reference: OBOL:automatic
has_exact_synonym: abdominal viscera
has_exact_synonym: abdominal viscera set
has_exact_synonym: set of abdominal viscera
has_obo_namespace: uberon
id: UBERON:0017672
in_subset: pheno slim

bodily gas
type: Class
subclass of: organism substance
definition: Any substance in the body or expelled from the body that is in a gaseous state.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: FMA:84580
has_exact_synonym: gas in anatomical space
has_exact_synonym: portion of gas in anatomical space
has_obo_namespace: uberon
id: UBERON:0034873

external soft tissue zone
type: Class
subclass of: multicellular anatomical structure
definition: A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: http://orcid.org/0000-0002-6601-2165
has_obo_namespace: uberon
id: UBERON:0034929

zone of organ
type: Class
subclass of: organ part
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: FMA:55268
has_exact_synonym: organ sector
has_exact_synonym: organ zonal region
has_exact_synonym: organ zone
has_obo_namespace: uberon
has_related_synonym: organ region with floating fiat boundary
id: UBERON:0034944

gas in respiratory system
type: Class
subclass of: bodily gas
definition: Any portion of gas located in a part of the respiratory system.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl
database_cross_reference: http://orcid.org/0000-0002-6601-2165
has_exact_synonym: respiratory gas
has_exact_synonym: respiratory system gas
has_obo_namespace: uberon
id: UBERON:0034947

life cycle temporal boundary
type: Class
subclass of: process boundary
definition: A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.
has_obo_namespace: uberon
id: UBERON:0035943
in_subset: upper level

life-death temporal boundary
type: Class
subclass of: life cycle temporal boundary
definition: A life cycle temporal boundary that marks the end of the life cycle of the organism.
has_exact_synonym: end of life cycle
has_exact_synonym: moment of death
has_exact_synonym: time of death
has_obo_namespace: uberon
has_related_synonym: death
has_related_synonym: end of life
id: UBERON:0035944

start of neonate stage
type: Class
subclass of: life cycle temporal boundary
definition: A life cycle temporal boundary that marks the start of the neonate stage of the organism.
has_exact_synonym: moment of birth
has_exact_synonym: time of birth
has_obo_namespace: uberon
has_related_synonym: birth
id: UBERON:0035946

regurgitated substance
type: Class
subclass of: organism substance
definition: A bodily fluid consisting of the contents of the digestive tract expulsed through the anterior portion of the digestive tract.
imported from: http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl
database_cross_reference: UBERON:cjm
has_obo_namespace: uberon
has_related_synonym: regurgitate
id: UBERON:0036017

length unit
type: Class
subclass of: measurement unit label
editor preferred term: length unit
definition: A unit which is a standard measure of the distance between two points.
imported from: uo.owl

mass unit
type: Class
subclass of: measurement unit label
editor preferred term: mass unit
definition: A unit which is a standard measure of the amount of matter/energy of a physical object.
imported from: uo.owl

time unit
type: Class
subclass of: measurement unit label
editor preferred term: time unit
definition: A unit which is a standard measure of the dimension in which events occur in sequence.
imported from: uo.owl

obsolete obligee role
type: Class
subclass of: Obsolete Class
definition: A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements.
definition editor: Sarah Bost
deprecated: true

obsolete obligor role
type: Class
subclass of: Obsolete Class
definition: A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements.
definition editor: Sarah Bost
deprecated: true

pressure
type: Class
subclass of: quality
has_obo_namespace: quality
in_subset: attribute slim

Obsolete Class
type: Class

example to be eventually removed
type: NamedIndividual
type: curation status specification
editor preferred term: example to be eventually removed

failed exploratory term
type: Thing
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
definition 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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
has obsolescence reason: placeholder removed
deprecated: true

placeholder removed
type: Thing
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.

obsolete_other
type: NamedIndividual
editor note: This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
editor note: We expect to be able to mine these new reasons and add instances as required.
deprecated: true

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.
definition 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.
definition 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
definition 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.
definition 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.
definition editor: Alan Ruttenberg
definition source: group:OBI

International Classification of Diseases, Tenth Revision, Clinical Modification
type: NamedIndividual
type: code set
definition: An extension of the ICD-10 created by the U.S. National Center for Health Statistics so that the system could be used to capture more morbidity data. This extension included a section of procedure codes.
alternative term: ICD-10-CM
definition source: NCI

Systematized Nomenclature of Medicine Clinical Terms
type: NamedIndividual
type: code set
definition: Published by the College of American Pathologists, the Systematized Nomenclature of Medicine Clinical Terms is a combination of content of SNOMED Reference Terminology and READ codes.
alternative term: SNOMED CT
definition source: NCI

International Classification of Diseases, Ninth Revision, Clinical Modification
type: NamedIndividual
type: code set
definition: An extension of the ICD-9 created by the U.S. National Center for Health Statistics so that the system could be used to capture more morbidity data. This extension included a section of procedure codes.
alternative term: ICD-9-CM
definition source: NCI

John Doe
type: NamedIndividual
type: Homo sapiens
participates in: John Doe's neonate stage

John Doe's birth
type: NamedIndividual
type: start of neonate stage
temporal part of: John Doe's neonate stage
occupies temporal region: 23:59

23:59
type: NamedIndividual
type: zero-dimensional temporal region
temporal part of: John Doe's neonate stage
temporal part of: 2000-02-02

John Doe's neonate stage
type: NamedIndividual
type: neonate stage
occupies temporal region: 1D temporal interval occuped by John Doe's neonate stage

1D temporal interval occuped by John Doe's neonate stage
type: NamedIndividual
type: one-dimensional temporal region

2000-02-02
type: NamedIndividual
type: one-dimensional temporal region

rta1
type: NamedIndividual
is about: ORCS_00000085
participates in: eiqap1

eiqap1
type: NamedIndividual
type: ethnic identity question asking process

Jane Doe
type: NamedIndividual
type: Homo sapiens
participates in: eiqap1

g
type: NamedIndividual
type: identifier
obsolete_designates: John Doe

p4
type: NamedIndividual
type: Homo sapiens

f1
type: NamedIndividual
type: female
inheres in: PCORnet multiple race identity information content entity

p5
type: NamedIndividual
type: Homo sapiens

John Doe's patient role
type: NamedIndividual
type: patient role
inheres in: ORCS_00000084
label: m1

ridqap1
type: NamedIndividual
type: race identity question asking process

Jane Doe's American Indian or Alaska Native identity datum
type: NamedIndividual
type: obsolete American Indian or Alaska Native identity datum

p6
type: NamedIndividual
type: Homo sapiens
participates in: ridqap1

rta2
type: NamedIndividual
is about: PCORnet lesbian identity information content entity
participates in: ridqap1

Jane Doe's racial identification process
type: NamedIndividual
type: racial identification process

ETL process of Jane Doe’s racial identity datum
type: NamedIndividual
type: database extract, transform, and load process

John Doe's Hispanic or Latino identity datum
type: NamedIndividual
type: obsolete hispanic or latino identity datum
is about: ORCS_00000084
is_specified_input_of: ETL process of John Doe’s ethnic identity datum
is_specified_output_of: John Doe’s ethnic identification process

John Doe’s ethnic identification process
type: NamedIndividual
type: ethnic identification process

John Doe’s PCORnet Hispanic identity datum
type: NamedIndividual
type: obsolete PCORnet Hispanic identity datum
is about: ORCS_00000084
is_specified_output_of: ETL process of John Doe’s ethnic identity datum

ETL process of John Doe’s ethnic identity datum
type: NamedIndividual
type: database extract, transform, and load process

Jane Doe's not Hispanic or Latino identity datum
type: NamedIndividual
type: obsolete not hispanic or latino identity datum
is about: ORCS_00000085
is_specified_input_of: ETL process of Jane Doe’s ethnic identity datum
is_specified_output_of: Jane Doe’s ethnic identification process

Jane Doe’s ethnic identification process
type: NamedIndividual
type: ethnic identification process

Jane Doe’s PCORnet not Hispanic identity datum
type: NamedIndividual
type: obsolete PCORnet not Hispanic identity datum
is about: ORCS_00000085
is_specified_output_of: ETL process of Jane Doe’s ethnic identity datum

ETL process of John Doe’s ethnic identity datum
type: NamedIndividual
type: database extract, transform, and load process

ETL process of Jane Doe’s ethnic identity datum
type: NamedIndividual
type: database extract, transform, and load process

John Doe's patient role
type: NamedIndividual
type: patient role
inheres in: ORCS_00000084

1234
type: NamedIndividual
type: symbol

International Classification of Diseases, Tenth Revision, Procedure Coding System
type: NamedIndividual
type: code set
alternative term: ICD-10-PCS

Current Procedural Terminology
type: NamedIndividual
type: code set
alternative term: CPT

Healthcare Common Procedural Coding System
type: NamedIndividual
type: code set
alternative term: HCPCS

Uniform Billing 04 Form Locator 42 Revenue Codes
type: NamedIndividual
type: code set
alternative term: UB-04 FL 42 Revenue Codes

axiom holds for all times
type: NamedIndividual
definition: ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation

relation has no temporal argument
type: NamedIndividual
definition: ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y)

OGMS_0000101
definition: A health care encounter that occurs in an emergency department facillity and realizes the health care provider role of an organization and the emergency department function of the facility.
definition source: PCORnet CDM 4.1
editor preferred term: emergency department encounter
ORCS_00000090: Includes ED encounters that become inpatient stays (in which case inpatient stays would be a separate encounter). Excludes urgent care facility visits. ED claims should be pulled before hospitalization claims to ensure that ED with subsequent admission won't be rolled up in the hospital event. Does not include observation stays, where known.
definition editor: Amanda Hicks

infer input from direct reg
is rule enabled: true
comment: MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
type: Imp
body: IndividualPropertyAtom
  property predicate: enables
  argument1: http://purl.obolibrary.org/obo/ro.owl#z
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#y
head: IndividualPropertyAtom
  property predicate: has input
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#z

enabling an MF enables its parts
comment: GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
type: Imp
body: ClassAtom
  class predicate: molecular_function
  argument1: y
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: has part
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: z

involved in BP
is rule enabled: true
comment: GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
type: Imp
body: ClassAtom
  class predicate: biological_process
  argument1: z
body: IndividualPropertyAtom
  property predicate: part of
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
head: IndividualPropertyAtom
  property predicate: involved in
  argument1: x
  argument2: z

Imp
comment: This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps"
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: occurs in
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: part of
  argument1: x
  argument2: z

inferring direct reg edge from input to regulatory subfunction
comment: If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: A
  argument2: D

inferring direct neg reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has negative regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: A
  argument2: D

inferring direct positive reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has positive regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: A
  argument2: D

effector input is compound function input
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in
head: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in

Input of effector is input of its parent MF
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in
head: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in

Imp
comment: if effector directly regulates X, its parent MF directly regulates X
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: eff
  argument2: mf2

Imp
comment: if effector directly positively regulates X, its parent MF directly positively regulates X
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: mf
  argument2: mf2
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: eff
  argument2: mf2

if effector directly negatively regulates X, its parent MF directly negatively regulates X
type: Imp
body: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: eff
  argument2: mf2

'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally downstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x

'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally upstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x