pco.owl
type: Ontology
version IRI: pco.owl
contributor: http://orcid.org/0000-0002-4366-3088
contributor: https://orcid.org/0000-0001-8815-0078
creator: David Osumi-Sutherland
creator: Jie Zheng
creator: Pier Luigi Buttigieg
creator: Ramona Walls
license: http://creativecommons.org/publicdomain/zero/1.0/
comment: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators.

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

example of usage
type: AnnotationProperty
editor preferred term: example
has curation status: ready for release
definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

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

has curation status
type: AnnotationProperty
editor preferred term: has curation status
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bill Bug
term editor: PERSON:Melanie Courtot
definition source: OBI_0000281

definition
type: AnnotationProperty
editor preferred term: definition
has curation status: ready for release
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

editor note
type: AnnotationProperty
editor preferred term: editor note
has curation status: ready for release
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>

term editor
type: AnnotationProperty
editor preferred term: term editor
has curation status: ready for release
definition: Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

alternative 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)
term 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
term editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has obsolescence reason
type: AnnotationProperty
editor preferred term: has obsolescence reason
definition: Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot

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

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

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

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

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

expand expression to
type: AnnotationProperty
editor preferred term: expand expression to
example of usage: ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
definition: A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
term editor: Chris Mungall

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

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

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

OBO foundry unique label
type: AnnotationProperty
editor preferred term: OBO foundry unique label
has curation status: pending final vetting
definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

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

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

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

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

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

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

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

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

may be identical to
type: AnnotationProperty
definition: A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
term editor: David Osumi-Sutherland
term tracker item: #40
ontology term requester: VFB
creation date: 2018-09-21T16:43:39Z
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
definition: Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
term editor: Chris Mungall, Jie Zheng
term tracker item: https://github.com/geneontology/go-ontology/issues/15532
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/32
ontology term requester: GO ontology
range: dateTime

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

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

has_alternative_id
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

in_subset
type: AnnotationProperty

entity
type: Class
BFO_0000179: entity
BFO_0000180: Entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
editor note: BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
editor note: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

Axiom
annotated source: entity
annotated property: editor note
annotated target: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith

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

continuant
type: Class
subclass of: entity
disjoint with: occurrent
BFO_0000179: continuant
BFO_0000180: Continuant
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: 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

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

occurrent
type: Class
subclass of: entity
BFO_0000179: occurrent
BFO_0000180: Occurrent
editor note: BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
editor note: BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
editor note: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
editor note: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
elucidation: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000012

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

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

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

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

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

independent continuant
type: Class
subclass of: continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
BFO_0000179: ic
BFO_0000180: 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: 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

process
type: Class
subclass of: occurrent
BFO_0000179: process
BFO_0000180: 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: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
editor note: BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
has associated axiom(fol): (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]

Axiom
annotated source: process
annotated property: definition
annotated target: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
annotated source: process
annotated property: has associated axiom(fol)
annotated target: (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

realizable entity
type: Class
subclass of: specifically dependent continuant
BFO_0000179: realizable
BFO_0000180: 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
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

specifically dependent continuant
type: Class
subclass of: continuant
disjoint with: generically dependent continuant
BFO_0000179: sdc
BFO_0000180: SpecificallyDependentContinuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
editor note: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: specifically dependent continuant
annotated property: editor note
annotated target: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

role
type: Class
subclass of: realizable entity
BFO_0000179: role
BFO_0000180: 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
editor note: BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
elucidation: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

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

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

object aggregate
type: Class
subclass of: material entity
BFO_0000179: object-aggregate
BFO_0000180: 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

site
type: Class
subclass of: immaterial entity
BFO_0000179: site
BFO_0000180: 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

generically dependent continuant
type: Class
subclass of: continuant
BFO_0000179: gdc
BFO_0000180: 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: 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

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
BFO_0000179: material
BFO_0000180: 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
editor note: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
editor note: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
editor note: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
elucidation: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]

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

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

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

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

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

immaterial entity
type: Class
subclass of: independent continuant
BFO_0000179: immaterial
BFO_0000180: 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

organism or virus or viroid
type: Class
subclass of: organismal entity
definition: Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
OBO foundry unique label: organism or virus
IAO created by: Melissa Haendel
IAO creation date: 9/18/11

organism
type: Class
subclass of: organism or virus or viroid
definition: An individual member of a clade.
OBO foundry unique label: organism
IAO created by: mah
IAO creation date: 7.16.2011
comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms.

construction
type: Class
subclass of: astronomical body part
definition: A feature that has been constructed by deliberate human effort.
editor note: "constructed" should probably be made something like a quality and this class obsoleted or filled only by inference
has_exact_synonym: constructed feature

Axiom
annotated source: construction
annotated property: definition
annotated target: A feature that has been constructed by deliberate human effort.
has db xref: MA:ma

environmental feature
type: Class
subclass of: material entity
definition: A material entity which determines an environmental system.
has_obo_namespace: ENVO
id: ENVO:00002297
comment: A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised.

Axiom
annotated source: environmental feature
annotated property: definition
annotated target: A material entity which determines an environmental system.
has db xref: DOI:10.1186/2041-1480-4-43
has db xref: NM:nm
has db xref: ORCID:0000-0002-4366-3088

environmental system
type: Class
subclass of: material entity
definition: A system which has the disposition to environ one or more material entities.
creation date: 2013-09-23T16:04:08Z
has db xref: 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.

Axiom
annotated source: environmental system
annotated property: definition
annotated target: A system which has the disposition to environ one or more material entities.
has db xref: DOI:10.1186/2041-1480-4-43

human dwelling
type: Class
subclass of: construction
definition: A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning.
editor note: See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work.
editor note: Subclasses will be added by inference.

Axiom
annotated source: human dwelling
annotated property: definition
annotated target: A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning.
has db xref: https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015

astronomical body part
type: Class
subclass of: environmental feature
definition: A material part of an astronomical body.
in_subset: envoAstro
in_subset: envoPolar

tidal mangrove shrubland
type: Class
subclass of: environmental system
definition: A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas.
created by: http://orcid.org/0000-0002-4366-3088
has_alternative_id: CMECS:577
has db xref: https://cmecscatalog.org/cmecs/classification/unit/577.html
in_subset: envoCmecs
in_subset: envoMarine
comment: This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions. CMECS provides the following notes: "Commonly found on intertidal mud flats along the shores of estuaries. Tidal mangrove shrublands may include immature stands or stunted mature trees that indicate a harsh growing environment. Areas characterized by tall mangroves (> 6 meters) are placed in the Tidal Mangrove Forest Biotic Group. Where tidal amplitude is relatively low, the vegetation forms narrow bands along the coastal plains, and it rarely penetrates inland more than several kilometers along rivers. Where tidal amplitude is greater, mangroves extend further inland along river courses, forming extensive stands in the major river deltas. Also, mangrove cays may occur within the lagoon complex of barrier reefs. The list of biotic communities for this group is long: a few examples are provided below, and the complete list is available in Appendix F"

behavior
type: Class
subclass of: biological_process
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.
created by: janelomax
creation date: 2012-09-20T14:06:08Z
has_alternative_id: GO:0044708
has db xref: Wikipedia:Behavior
has_exact_synonym: behavioral response to stimulus
has_exact_synonym: behaviour
has_exact_synonym: behavioural response to stimulus
has_obo_namespace: biological_process
has_related_synonym: single-organism behavior
id: GO:0007610
in_subset: gocheck do not manually annotate
in_subset: goslim agr
in_subset: goslim flybase ribbon
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.
has db xref: GOC:ems
has db xref: GOC:jl
has db xref: ISBN:0395448956
has db xref: PMID:20160973

biological_process
type: Class
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.
created by: janelomax
creation date: 2012-09-19T15:05:24Z
has_alternative_id: GO:0000004
has_alternative_id: GO:0007582
has_alternative_id: GO:0044699
has db xref: Wikipedia:Biological_process
has_exact_synonym: biological process
has_exact_synonym: physiological process
has_obo_namespace: biological_process
has_related_synonym: single organism process
has_related_synonym: single-organism process
id: GO:0008150
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim pombe
in_subset: goslim yeast
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.
has db xref: GOC:pdt

social behavior
type: Class
subclass of: intraspecies interaction between organisms
subclass of: multi-organism behavior
definition: Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group.
has db xref: Wikipedia:Social_behavior
has_exact_synonym: social behaviour
has_obo_namespace: biological_process
has_related_synonym: cooperative behavior
id: GO:0035176
comment: Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior.

Axiom
annotated source: social behavior
annotated property: definition
annotated target: Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group.
has db xref: GOC:jh2
has db xref: PMID:12848939
has db xref: Wikipedia:Social_behavior

interspecies interaction between organisms
type: Class
subclass of: multi-organism process
definition: Any process in which an organism has an effect on an organism of a different species.
has_exact_synonym: interaction with another species
has_exact_synonym: interspecies interaction
has_exact_synonym: interspecies interaction with other organisms
has_obo_namespace: biological_process
id: GO:0044419
in_subset: goslim candida
in_subset: goslim pir

Axiom
annotated source: interspecies interaction between organisms
annotated property: definition
annotated target: Any process in which an organism has an effect on an organism of a different species.
has db xref: GOC:cc

intraspecies interaction between organisms
type: Class
subclass of: multi-organism process
definition: Any process in which an organism has an effect on an organism of the same species.
has_exact_synonym: intraspecies interaction with other organisms
has_obo_namespace: biological_process
id: GO:0051703
in_subset: goslim pir

Axiom
annotated source: intraspecies interaction between organisms
annotated property: definition
annotated target: Any process in which an organism has an effect on an organism of the same species.
has db xref: GOC:ai

multi-organism process
type: Class
subclass of: process
subclass of: biological_process
definition: A biological process which involves another organism of the same or different species.
has_alternative_id: GO:0051706
has_exact_synonym: interaction between organisms
has_exact_synonym: physiological interaction between organisms
has_exact_synonym: physiological interaction with other organism
has_obo_namespace: biological_process
id: GO:0051704
in_subset: gocheck do not annotate
in_subset: goslim pir

Axiom
annotated source: multi-organism process
annotated property: definition
annotated target: A biological process which involves another organism of the same or different species.
has db xref: GOC:jl

multi-organism behavior
type: Class
subclass of: behavior
subclass of: multi-organism process
definition: Any process in which an organism has a behavioral effect on another organism of the same or different species.
has_alternative_id: GO:0023032
has_alternative_id: GO:0044709
has_exact_synonym: behavioral interaction between organisms
has_exact_synonym: behavioral interaction with other organism
has_exact_synonym: behavioural interaction between organisms
has_exact_synonym: behavioural interaction with other organism
has narrow synonym: behavioral signaling
has narrow synonym: behavioral signalling
has_obo_namespace: biological_process
id: GO:0051705
in_subset: goslim pir

Axiom
annotated source: multi-organism behavior
annotated property: definition
annotated target: Any process in which an organism has a behavioral effect on another organism of the same or different species.
has db xref: GOC:ai

Axiom
annotated source: multi-organism behavior
annotated property: hasNarrowSynonym
annotated target: behavioral signalling
has db xref: GOC:mah

data item
type: Class
subclass of: information content entity

information content entity
type: Class
subclass of: generically dependent continuant

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

data about an ontology part
type: Class
subclass of: data item
definition: data about an ontology part is a data item about a part of an ontology, for example a term
term editor: Person:Alan Ruttenberg

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

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

ontology module
type: Class
subclass of: data about an ontology part
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.
created by: cjm
creation date: 2018-05-20T20:55:03Z

base ontology module
type: Class
subclass of: 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.
created by: cjm
creation date: 2018-05-20T20:55:30Z

editors ontology module
type: Class
subclass of: 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
created by: cjm
creation date: 2018-05-20T20:55:47Z

main release ontology module
type: Class
subclass of: 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
created by: cjm
creation date: 2018-05-20T20:56:13Z

bridge ontology module
type: Class
subclass of: 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.
created by: cjm
creation date: 2018-05-20T20:56:23Z

import ontology module
type: Class
subclass of: subset 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
created by: cjm
creation date: 2018-05-20T20:56:47Z

subset ontology module
type: Class
subclass of: 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
created by: cjm
creation date: 2018-05-20T20:58:11Z

curation subset ontology module
type: Class
subclass of: 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.
created by: cjm
creation date: 2018-05-20T20:58:38Z

analysis subset ontology module
type: Class
subclass of: subset ontology module
definition: An ontology module that is intended for usage in analysis or discovery applications.
created by: cjm
creation date: 2018-05-20T20:58:49Z

single layer subset ontology module
type: Class
subclass of: subset 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
created by: cjm
creation date: 2018-05-20T20:59:19Z

exclusion subset ontology module
type: Class
subclass of: 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
created by: cjm
creation date: 2018-05-20T20:59:57Z

external import ontology module
type: Class
subclass of: 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
created by: cjm
creation date: 2018-05-20T21:00:14Z

species subset ontology module
type: Class
subclass of: subset ontology module
definition: A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
alternative term: taxon subset
created by: cjm
creation date: 2018-05-20T21:14:16Z

reasoned ontology module
type: Class
subclass of: 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.
created by: cjm
creation date: 2018-05-20T21:20:33Z

generated ontology module
type: Class
subclass of: 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
created by: cjm
creation date: 2018-05-20T21:21:12Z

template generated ontology module
type: Class
subclass of: generated ontology module
definition: An ontology module that is automatically generated from a template specification and fillers for slots in that template.
created by: cjm
creation date: 2018-05-20T21:21:21Z

taxonomic bridge ontology module
type: Class
subclass of: bridge ontology module
created by: cjm
creation date: 2018-05-20T21:28:15Z

ontology module subsetted by expressivity
type: Class
subclass of: subset ontology module
created by: cjm
creation date: 2018-05-22T04:15:54Z

obo basic subset ontology module
type: Class
subclass of: ontology module subsetted by expressivity
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
created by: cjm
creation date: 2018-05-22T04:16:10Z

ontology module subsetted by OWL profile
type: Class
subclass of: ontology module subsetted by expressivity
created by: cjm
creation date: 2018-05-22T04:16:28Z

EL++ ontology module
type: Class
subclass of: ontology module subsetted by OWL profile
created by: cjm
creation date: 2018-05-22T04:16:48Z

Viruses
type: Class
has rank: NCBITaxon superkingdom
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Vira
has_related_synonym: Viridae
has_related_synonym: viruses

Axiom
annotated source: Viruses
annotated property: has_related_synonym
annotated target: Vira
has synonym type: synonym

Axiom
annotated source: Viruses
annotated property: has_related_synonym
annotated target: Viridae
has synonym type: synonym

Axiom
annotated source: Viruses
annotated property: has_related_synonym
annotated target: viruses
has synonym type: blast name

Teleostomi
type: Class
subclass of: Gnathostomata <vertebrate>
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Euteleostomi
type: Class
subclass of: Teleostomi
has_alternative_id: NCBITaxon:40673
has db xref: GC_ID:1
has_exact_synonym: bony vertebrates
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Euteleostomi
annotated property: has_exact_synonym
annotated target: bony vertebrates
has synonym type: genbank common name

Viroids
type: Class
has rank: NCBITaxon superkingdom
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Viroid
has_related_synonym: viroids

Axiom
annotated source: Viroids
annotated property: has_related_synonym
annotated target: Viroid
has synonym type: synonym

Axiom
annotated source: Viroids
annotated property: has_related_synonym
annotated target: viroids
has synonym type: blast name

Streptophytina
type: Class
subclass of: Streptophyta
has rank: NCBITaxon subphylum
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Charophyta/Embryophyta group
has_related_synonym: charophyte/embryophyte group

Axiom
annotated source: Streptophytina
annotated property: has_related_synonym
annotated target: Charophyta/Embryophyta group
has synonym type: synonym

Axiom
annotated source: Streptophytina
annotated property: has_related_synonym
annotated target: charophyte/embryophyte group
has synonym type: synonym

cellular organisms
type: Class
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: biota

Axiom
annotated source: cellular organisms
annotated property: has_related_synonym
annotated target: biota
has synonym type: synonym

Dipnotetrapodomorpha
type: Class
subclass of: Sarcopterygii
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Boreoeutheria
type: Class
subclass of: Eutheria
has db xref: GC_ID:1
has db xref: PMID:11743200
has db xref: PMID:11791233
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Boreotheria

Axiom
annotated source: Boreoeutheria
annotated property: has_related_synonym
annotated target: Boreotheria
has synonym type: synonym

Acrogymnospermae
type: Class
subclass of: Spermatophyta
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Bacteria
type: Class
subclass of: cellular organisms
has rank: NCBITaxon superkingdom
has db xref: GC_ID:11
has db xref: PMID:10425795
has db xref: PMID:10425796
has db xref: PMID:10425797
has db xref: PMID:10490293
has db xref: PMID:10843050
has db xref: PMID:10939651
has db xref: PMID:10939673
has db xref: PMID:10939677
has db xref: PMID:11211268
has db xref: PMID:11321083
has db xref: PMID:11321113
has db xref: PMID:11411719
has db xref: PMID:11540071
has db xref: PMID:11542017
has db xref: PMID:11542087
has db xref: PMID:11760965
has db xref: PMID:12054223
has db xref: PMID:2112744
has db xref: PMID:270744
has db xref: PMID:8123559
has db xref: PMID:8590690
has db xref: PMID:9103655
has db xref: PMID:9336922
has_exact_synonym: eubacteria
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Monera
has_related_synonym: Procaryotae
has_related_synonym: Prokaryota
has_related_synonym: Prokaryotae
has_related_synonym: bacteria
has_related_synonym: prokaryote
has_related_synonym: prokaryotes

Axiom
annotated source: Bacteria
annotated property: has_related_synonym
annotated target: prokaryotes
has synonym type: in part

Axiom
annotated source: Bacteria
annotated property: has_exact_synonym
annotated target: eubacteria
has synonym type: genbank common name

Axiom
annotated source: Bacteria
annotated property: has_related_synonym
annotated target: Monera
has synonym type: in part

Axiom
annotated source: Bacteria
annotated property: has_related_synonym
annotated target: Procaryotae
has synonym type: in part

Axiom
annotated source: Bacteria
annotated property: has_related_synonym
annotated target: Prokaryota
has synonym type: in part

Axiom
annotated source: Bacteria
annotated property: has_related_synonym
annotated target: Prokaryotae
has synonym type: in part

Axiom
annotated source: Bacteria
annotated property: has_related_synonym
annotated target: bacteria
has synonym type: blast name

Axiom
annotated source: Bacteria
annotated property: has_related_synonym
annotated target: prokaryote
has synonym type: in part

Homininae
type: Class
subclass of: Hominidae
has rank: NCBITaxon subfamily
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Homo/Pan/Gorilla group

Axiom
annotated source: Homininae
annotated property: has_related_synonym
annotated target: Homo/Pan/Gorilla group
has synonym type: synonym

Archaea
type: Class
subclass of: cellular organisms
has rank: NCBITaxon superkingdom
has db xref: GC_ID:11
has db xref: PMID:10425795
has db xref: PMID:10425796
has db xref: PMID:10425797
has db xref: PMID:10490293
has db xref: PMID:10843050
has db xref: PMID:10939651
has db xref: PMID:10939673
has db xref: PMID:10939677
has db xref: PMID:11211268
has db xref: PMID:11321083
has db xref: PMID:11321113
has db xref: PMID:11411719
has db xref: PMID:11540071
has db xref: PMID:11541975
has db xref: PMID:11542064
has db xref: PMID:11542149
has db xref: PMID:11760965
has db xref: PMID:12054223
has db xref: PMID:2112744
has db xref: PMID:25527841
has db xref: PMID:270744
has db xref: PMID:8123559
has db xref: PMID:8590690
has db xref: PMID:9103655
has db xref: PMID:9336922
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Archaebacteria
has_related_synonym: Mendosicutes
has_related_synonym: Metabacteria
has_related_synonym: Monera
has_related_synonym: Procaryotae
has_related_synonym: Prokaryota
has_related_synonym: Prokaryotae
has_related_synonym: archaea
has_related_synonym: prokaryote
has_related_synonym: prokaryotes

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: Archaebacteria
has synonym type: synonym

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: Mendosicutes
has synonym type: synonym

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: Metabacteria
has synonym type: synonym

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: Monera
has synonym type: in part

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: Procaryotae
has synonym type: in part

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: Prokaryota
has synonym type: in part

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: Prokaryotae
has synonym type: in part

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: archaea
has synonym type: blast name

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: prokaryote
has synonym type: in part

Axiom
annotated source: Archaea
annotated property: has_related_synonym
annotated target: prokaryotes
has synonym type: in part

Eukaryota
type: Class
subclass of: cellular organisms
has rank: NCBITaxon superkingdom
has db xref: GC_ID:1
has db xref: PMID:23020233
has_exact_synonym: eucaryotes
has_exact_synonym: eukaryotes
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Eucarya
has_related_synonym: Eucaryotae
has_related_synonym: Eukarya
has_related_synonym: Eukaryotae
has_related_synonym: eukaryotes

Axiom
annotated source: Eukaryota
annotated property: has_exact_synonym
annotated target: eucaryotes
has synonym type: genbank common name

Axiom
annotated source: Eukaryota
annotated property: has_exact_synonym
annotated target: eukaryotes
has synonym type: common name

Axiom
annotated source: Eukaryota
annotated property: has_related_synonym
annotated target: Eucarya
has synonym type: synonym

Axiom
annotated source: Eukaryota
annotated property: has_related_synonym
annotated target: Eucaryotae
has synonym type: synonym

Axiom
annotated source: Eukaryota
annotated property: has_related_synonym
annotated target: Eukarya
has synonym type: synonym

Axiom
annotated source: Eukaryota
annotated property: has_related_synonym
annotated target: Eukaryotae
has synonym type: synonym

Axiom
annotated source: Eukaryota
annotated property: has_related_synonym
annotated target: eukaryotes
has synonym type: blast name

Chlorophyta
type: Class
subclass of: Viridiplantae
has rank: NCBITaxon phylum
has db xref: GC_ID:1
has db xref: PMID:23020233
has_exact_synonym: green algae
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Chlorophycota
has_related_synonym: Chlorophyta sensu Bremer 1985
has_related_synonym: algae
has_related_synonym: green algae

Axiom
annotated source: Chlorophyta
annotated property: has_exact_synonym
annotated target: green algae
has synonym type: genbank common name

Axiom
annotated source: Chlorophyta
annotated property: has_related_synonym
annotated target: Chlorophycota
has synonym type: synonym

Axiom
annotated source: Chlorophyta
annotated property: has_related_synonym
annotated target: Chlorophyta sensu Bremer 1985
has synonym type: synonym

Axiom
annotated source: Chlorophyta
annotated property: has_related_synonym
annotated target: algae
has synonym type: in part

Axiom
annotated source: Chlorophyta
annotated property: has_related_synonym
annotated target: green algae
has synonym type: blast name

Euarchontoglires
type: Class
subclass of: Boreoeutheria
has rank: NCBITaxon superorder
has db xref: GC_ID:1
has db xref: PMID:11214319
has db xref: PMID:12082125
has db xref: PMID:12878460
has db xref: PMID:15522813
has_obo_namespace: ncbi_taxonomy

Simiiformes
type: Class
subclass of: Haplorrhini
has rank: NCBITaxon infraorder
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Anthropoidea

Axiom
annotated source: Simiiformes
annotated property: has_related_synonym
annotated target: Anthropoidea
has synonym type: synonym

Hominoidea
type: Class
subclass of: Catarrhini
has rank: NCBITaxon superfamily
has db xref: GC_ID:1
has_exact_synonym: ape
has_exact_synonym: apes
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Hominoidea
annotated property: has_exact_synonym
annotated target: ape
has synonym type: common name

Axiom
annotated source: Hominoidea
annotated property: has_exact_synonym
annotated target: apes
has synonym type: genbank common name

Embryophyta
type: Class
subclass of: Streptophytina
has db xref: GC_ID:1
has_exact_synonym: higher plants
has_exact_synonym: land plants
has_exact_synonym: plants
has_obo_namespace: ncbi_taxonomy
has_related_synonym: land plants

Axiom
annotated source: Embryophyta
annotated property: has_exact_synonym
annotated target: higher plants
has synonym type: common name

Axiom
annotated source: Embryophyta
annotated property: has_exact_synonym
annotated target: land plants
has synonym type: common name

Axiom
annotated source: Embryophyta
annotated property: has_exact_synonym
annotated target: plants
has synonym type: common name

Axiom
annotated source: Embryophyta
annotated property: has_related_synonym
annotated target: land plants
has synonym type: blast name

Tetrapoda
type: Class
subclass of: Dipnotetrapodomorpha
has db xref: GC_ID:1
has_exact_synonym: tetrapods
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Tetrapoda
annotated property: has_exact_synonym
annotated target: tetrapods
has synonym type: genbank common name

Amniota
type: Class
subclass of: Tetrapoda
has db xref: GC_ID:1
has_exact_synonym: amniotes
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Amniota
annotated property: has_exact_synonym
annotated target: amniotes
has synonym type: genbank common name

Theria <Mammalia>
type: Class
subclass of: Mammalia
has db xref: GC_ID:1
has_exact_synonym: Theria
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Theria <Mammalia>
annotated property: has_exact_synonym
annotated target: Theria
has synonym type: scientific name

Viridiplantae
type: Class
subclass of: Eukaryota
has rank: NCBITaxon kingdom
has db xref: GC_ID:1
has_exact_synonym: green plants
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Chlorobionta
has_related_synonym: Chlorophyta/Embryophyta group
has_related_synonym: chlorophyte/embryophyte group
has_related_synonym: green plants

Axiom
annotated source: Viridiplantae
annotated property: has_exact_synonym
annotated target: green plants
has synonym type: common name

Axiom
annotated source: Viridiplantae
annotated property: has_related_synonym
annotated target: Chlorobionta
has synonym type: synonym

Axiom
annotated source: Viridiplantae
annotated property: has_related_synonym
annotated target: Chlorophyta/Embryophyta group
has synonym type: synonym

Axiom
annotated source: Viridiplantae
annotated property: has_related_synonym
annotated target: chlorophyte/embryophyte group
has synonym type: synonym

Axiom
annotated source: Viridiplantae
annotated property: has_related_synonym
annotated target: green plants
has synonym type: blast name

Opisthokonta
type: Class
subclass of: Eukaryota
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Fungi/Metazoa group
has_related_synonym: opisthokonts

Axiom
annotated source: Opisthokonta
annotated property: has_related_synonym
annotated target: Fungi/Metazoa group
has synonym type: synonym

Axiom
annotated source: Opisthokonta
annotated property: has_related_synonym
annotated target: opisthokonts
has synonym type: synonym

Metazoa
type: Class
subclass of: Opisthokonta
has rank: NCBITaxon kingdom
has db xref: GC_ID:1
has_exact_synonym: metazoans
has_exact_synonym: multicellular animals
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Animalia
has_related_synonym: animals

Axiom
annotated source: Metazoa
annotated property: has_exact_synonym
annotated target: metazoans
has synonym type: genbank common name

Axiom
annotated source: Metazoa
annotated property: has_exact_synonym
annotated target: multicellular animals
has synonym type: common name

Axiom
annotated source: Metazoa
annotated property: has_related_synonym
annotated target: Animalia
has synonym type: synonym

Axiom
annotated source: Metazoa
annotated property: has_related_synonym
annotated target: animals
has synonym type: blast name

Bilateria
type: Class
subclass of: Eumetazoa
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Deuterostomia
type: Class
subclass of: Bilateria
has db xref: GC_ID:1
has_exact_synonym: deuterostomes
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Deuterostomia
annotated property: has_exact_synonym
annotated target: deuterostomes
has synonym type: common name

Magnoliophyta
type: Class
subclass of: Spermatophyta
has db xref: GC_ID:1
has db xref: PMID:25249442
has_exact_synonym: angiosperms
has_exact_synonym: flowering plants
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Angiospermae
has_related_synonym: flowering plants

Axiom
annotated source: Magnoliophyta
annotated property: has_exact_synonym
annotated target: angiosperms
has synonym type: common name

Axiom
annotated source: Magnoliophyta
annotated property: has_exact_synonym
annotated target: flowering plants
has synonym type: genbank common name

Axiom
annotated source: Magnoliophyta
annotated property: has_related_synonym
annotated target: Angiospermae
has synonym type: synonym

Axiom
annotated source: Magnoliophyta
annotated property: has_related_synonym
annotated target: flowering plants
has synonym type: blast name

Streptophyta
type: Class
subclass of: Viridiplantae
has rank: NCBITaxon phylum
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Haplorrhini
type: Class
subclass of: Primates
has rank: NCBITaxon suborder
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Mammalia
type: Class
subclass of: Amniota
has rank: NCBITaxon class
has db xref: GC_ID:1
has_exact_synonym: mammals
has_obo_namespace: ncbi_taxonomy
has_related_synonym: mammals

Axiom
annotated source: Mammalia
annotated property: has_exact_synonym
annotated target: mammals
has synonym type: genbank common name

Axiom
annotated source: Mammalia
annotated property: has_related_synonym
annotated target: mammals
has synonym type: blast name

Tracheophyta
type: Class
subclass of: Embryophyta
has db xref: GC_ID:1
has_exact_synonym: vascular plants
has_obo_namespace: ncbi_taxonomy
has_related_synonym: vascular plants

Axiom
annotated source: Tracheophyta
annotated property: has_exact_synonym
annotated target: vascular plants
has synonym type: common name

Axiom
annotated source: Tracheophyta
annotated property: has_related_synonym
annotated target: vascular plants
has synonym type: blast name

Spermatophyta
type: Class
subclass of: Euphyllophyta
has db xref: GC_ID:1
has_exact_synonym: seed plants
has_obo_namespace: ncbi_taxonomy
has_related_synonym: seed plants

Axiom
annotated source: Spermatophyta
annotated property: has_exact_synonym
annotated target: seed plants
has synonym type: common name

Axiom
annotated source: Spermatophyta
annotated property: has_related_synonym
annotated target: seed plants
has synonym type: blast name

Eumetazoa
type: Class
subclass of: Metazoa
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Chordata
type: Class
subclass of: Deuterostomia
has rank: NCBITaxon phylum
has db xref: GC_ID:1
has_exact_synonym: chordates
has_obo_namespace: ncbi_taxonomy
has_related_synonym: chordates

Axiom
annotated source: Chordata
annotated property: has_exact_synonym
annotated target: chordates
has synonym type: genbank common name

Axiom
annotated source: Chordata
annotated property: has_related_synonym
annotated target: chordates
has synonym type: blast name

Vertebrata <Metazoa>
type: Class
subclass of: Craniata <chordata>
has db xref: GC_ID:1
has_exact_synonym: Vertebrata
has_exact_synonym: vertebrates
has_obo_namespace: ncbi_taxonomy
has_related_synonym: vertebrates

Axiom
annotated source: Vertebrata <Metazoa>
annotated property: has_exact_synonym
annotated target: Vertebrata
has synonym type: scientific name

Axiom
annotated source: Vertebrata <Metazoa>
annotated property: has_exact_synonym
annotated target: vertebrates
has synonym type: genbank common name

Axiom
annotated source: Vertebrata <Metazoa>
annotated property: has_related_synonym
annotated target: vertebrates
has synonym type: blast name

Gnathostomata <vertebrate>
type: Class
subclass of: Vertebrata <Metazoa>
has db xref: GC_ID:1
has_exact_synonym: Gnathostomata
has_exact_synonym: jawed vertebrates
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Gnathostomata <vertebrate>
annotated property: has_exact_synonym
annotated target: Gnathostomata
has synonym type: scientific name

Axiom
annotated source: Gnathostomata <vertebrate>
annotated property: has_exact_synonym
annotated target: jawed vertebrates
has synonym type: genbank common name

Euphyllophyta
type: Class
subclass of: Tracheophyta
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: euphyllophytes

Axiom
annotated source: Euphyllophyta
annotated property: has_related_synonym
annotated target: euphyllophytes
has synonym type: synonym

Sarcopterygii
type: Class
subclass of: Euteleostomi
has rank: NCBITaxon superclass
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Craniata <chordata>
type: Class
subclass of: Chordata
has rank: NCBITaxon subphylum
has db xref: GC_ID:1
has_exact_synonym: Craniata
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Craniata <chordata>
annotated property: has_exact_synonym
annotated target: Craniata
has synonym type: scientific name

Eutheria
type: Class
subclass of: Theria <Mammalia>
has db xref: GC_ID:1
has_exact_synonym: eutherian mammals
has_exact_synonym: placental mammals
has_exact_synonym: placentals
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Placentalia
has_related_synonym: placentals

Axiom
annotated source: Eutheria
annotated property: has_exact_synonym
annotated target: eutherian mammals
has synonym type: common name

Axiom
annotated source: Eutheria
annotated property: has_exact_synonym
annotated target: placental mammals
has synonym type: common name

Axiom
annotated source: Eutheria
annotated property: has_exact_synonym
annotated target: placentals
has synonym type: genbank common name

Axiom
annotated source: Eutheria
annotated property: has_related_synonym
annotated target: Placentalia
has synonym type: synonym

Axiom
annotated source: Eutheria
annotated property: has_related_synonym
annotated target: placentals
has synonym type: blast name

Primates
type: Class
subclass of: Euarchontoglires
has rank: NCBITaxon order
has db xref: GC_ID:1
has_exact_synonym: primate
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Primata
has_related_synonym: primates

Axiom
annotated source: Primates
annotated property: has_exact_synonym
annotated target: primate
has synonym type: equivalent name

Axiom
annotated source: Primates
annotated property: has_related_synonym
annotated target: Primata
has synonym type: synonym

Axiom
annotated source: Primates
annotated property: has_related_synonym
annotated target: primates
has synonym type: blast name

Catarrhini
type: Class
subclass of: Simiiformes
has rank: NCBITaxon parvorder
has db xref: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Hominidae
type: Class
subclass of: Hominoidea
has rank: NCBITaxon family
has db xref: GC_ID:1
has_exact_synonym: great apes
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Pongidae

Axiom
annotated source: Hominidae
annotated property: has_exact_synonym
annotated target: great apes
has synonym type: genbank common name

Axiom
annotated source: Hominidae
annotated property: has_related_synonym
annotated target: Pongidae
has synonym type: synonym

Homo
type: Class
subclass of: Homininae
has rank: NCBITaxon genus
has db xref: GC_ID:1
has_exact_synonym: humans
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Homo
annotated property: has_exact_synonym
annotated target: humans
has synonym type: common name

Homo sapiens
type: Class
subclass of: Homo
has rank: NCBITaxon species
has db xref: GC_ID:1
has_exact_synonym: human
has_exact_synonym: man
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Home sapiens
has_related_synonym: Homo sampiens
has_related_synonym: Homo sapeins
has_related_synonym: Homo sapian
has_related_synonym: Homo sapians
has_related_synonym: Homo sapien
has_related_synonym: Homo sapience
has_related_synonym: Homo sapiense
has_related_synonym: Homo sapients
has_related_synonym: Homo sapines
has_related_synonym: Homo spaiens
has_related_synonym: Homo spiens
has_related_synonym: Humo sapiens

Axiom
annotated source: Homo sapiens
annotated property: has_exact_synonym
annotated target: human
has synonym type: genbank common name

Axiom
annotated source: Homo sapiens
annotated property: has_exact_synonym
annotated target: man
has synonym type: common name

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Home sapiens
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sampiens
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sapeins
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sapian
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sapians
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sapien
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sapience
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sapiense
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sapients
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo sapines
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo spaiens
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Homo spiens
has synonym type: misspelling

Axiom
annotated source: Homo sapiens
annotated property: has_related_synonym
annotated target: Humo sapiens
has synonym type: misspelling

quality
type: Class
definition: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
has_alternative_id: PATO:0000072
has_exact_synonym: trait
has_obo_namespace: quality
id: PATO:0000001

Axiom
annotated source: quality
annotated property: definition
annotated target: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
has db xref: PATOC:GVG

rate
type: Class
subclass of: physical quality of a process
definition: A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time.
has_obo_namespace: quality
id: PATO:0000161
in_subset: attribute slim
in_subset: scalar slim

Axiom
annotated source: rate
annotated property: definition
annotated target: A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time.
has db xref: PATOC:melissa

process quality
type: Class
subclass of: quality
definition: A quality which inheres in an process.
has_alternative_id: PATO:0001239
has_alternative_id: PATO:0001240
has_exact_synonym: quality of a process
has_exact_synonym: quality of occurrent
has_exact_synonym: quality of process
has_exact_synonym: relational quality of occurrent
has_obo_namespace: quality
id: PATO:0001236
comment: See comments of relational quality of a physical entity.

Axiom
annotated source: process quality
annotated property: definition
annotated target: A quality which inheres in an process.
has db xref: PATOC:GVG

physical object quality
type: Class
subclass of: quality
definition: A quality which inheres in a continuant.
has_alternative_id: PATO:0001237
has_alternative_id: PATO:0001238
has db xref: snap:Quality
has_exact_synonym: monadic quality of a continuant
has_exact_synonym: multiply inhering quality of a physical entity
has_exact_synonym: quality of a continuant
has_exact_synonym: quality of a single physical entity
has_exact_synonym: quality of an object
has_exact_synonym: quality of continuant
has narrow synonym: monadic quality of an object
has narrow synonym: monadic quality of continuant
has_obo_namespace: quality
id: PATO:0001241
comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.

Axiom
annotated source: physical object quality
annotated property: definition
annotated target: A quality which inheres in a continuant.
has db xref: PATOC:GVG

mixed sex
type: Class
subclass of: population quality
definition: A biological sex quality inhering in a population of multiple sexes.
has_obo_namespace: quality
id: PATO:0001338
in_subset: value slim
comment: For example a mixture of females and male or males and hermaphrodites.

Axiom
annotated source: mixed sex
annotated property: definition
annotated target: A biological sex quality inhering in a population of multiple sexes.
has db xref: MGED:MGED

morbidity
type: Class
subclass of: population quality
definition: A quality inhering in a population by virtue of the proportion of its members that are ill at a given time.
has_obo_namespace: quality
id: PATO:0001415
in_subset: attribute slim
in_subset: scalar slim

Axiom
annotated source: morbidity
annotated property: definition
annotated target: A quality inhering in a population by virtue of the proportion of its members that are ill at a given time.
has db xref: PATOC:GVG

population quality
type: Class
subclass of: physical object quality
definition: A quality that inheres in an entire population or part of a population.
has_obo_namespace: quality
id: PATO:0002003
in_subset: attribute slim

Axiom
annotated source: population quality
annotated property: definition
annotated target: A quality that inheres in an entire population or part of a population.
has db xref: PATOC:GVG

physical quality of a process
type: Class
subclass of: process quality
created by: george
creation date: 2009-06-05T09:16:46Z
has_obo_namespace: quality
id: PATO:0002062
in_subset: attribute slim

collection of organisms
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: RO_0002351
    all values from: organism or virus or viroid
  intersection of: Restriction
    on property: RO_0002351
    min qualified cardinality: 2
    on class: organism or virus or viroid
subclass of: object aggregate
subclass of: organismal entity
subclass of: Restriction
  on property: RO_0002351
  some values from: organism or virus or viroid
example of usage: Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
has curation status: pending final vetting
definition: A material entity that consists of two or more organisms, viruses, or viroids.
alternative term: group of organism
alternative term: organism collection
comment: May be of the same or different species.

population of organisms
type: Class
subclass of: single-species collection of organisms
example of usage: This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed.
has curation status: pending final vetting
definition: A collection of organisms, all of the same species, that live in the same place.
definition source: ISBN:0878932739
comment: It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used.

ecological community
type: Class
subclass of: Class
  intersection of: multi-species collection of organisms
  intersection of: Restriction
    on property: RO_0002351
    min qualified cardinality: 2
    on class: population of organisms
definition: A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members.
alternative term: multispecies community
definition source: ISBN:0865423504
comment: Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community.

quality of a population
type: Class
equivalent class: Class
  intersection of: population quality
  intersection of: Restriction
    on property: RO_0000052
    some values from: population of organisms
subclass of: population quality
subclass of: Restriction
  on property: RO_0000052
  some values from: population of organisms
has curation status: requires discussion
definition: A quality that inheres in a biological population.
editor note: See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2.
comment: Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term.

quality of an ecological community
type: Class
equivalent class: Class
  intersection of: population quality
  intersection of: Restriction
    on property: RO_0000052
    some values from: ecological community
subclass of: population quality
subclass of: Restriction
  on property: RO_0000052
  some values from: ecological community
has curation status: requires discussion
definition: A quality that inheres in a community.
editor note: These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2.
comment: Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual.

population process
type: Class
subclass of: process
subclass of: Restriction
  on property: RO_0000057
  some values from: population of organisms
has curation status: metadata incomplete
definition: A process that has as primary participant a population.
comment: Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes.

population birth rate
type: Class
subclass of: quality of a population
has curation status: metadata incomplete

population death rate
type: Class
subclass of: quality of a population
has curation status: metadata incomplete

population growth rate
type: Class
subclass of: quality of a population
has curation status: metadata incomplete
editor note: Is a rate a quality? Population growth rate may be better classified as a process profile.

obsolete carrying capacity
type: Class
subclass of: ObsoleteClass
definition: The maximum number of individuals that can be supported in a population that is growing according to logistic growth.
editor note: Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE.
definition source: ISBN:0878932739
has obsolescence reason: to be replaced with external ontology term
deprecated: true

community species richness
type: Class
subclass of: quality of an ecological community
has curation status: metadata complete
definition: The number of different species represented in an ecological community.
editor note: This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019).
definition source: adapted from http://en.wikipedia.org/wiki/Species_richness

population growth
type: Class
subclass of: population process
has curation status: metadata incomplete
definition: A process that leads to a change in the number of individuals (positive or negative) in a population.

logistic population growth
type: Class
subclass of: population growth
has curation status: metadata incomplete
definition: A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat.

exponential population growth
type: Class
subclass of: population growth
has curation status: metadata incomplete
definition: A population growth process that leads to an exponential increase in the number of individuals in a population.

predator role
type: Class
subclass of: role
has curation status: uncurated

prey role
type: Class
subclass of: role
has curation status: uncurated

symbiont role
type: Class
subclass of: role
has curation status: uncurated

species as a collection of organisms
type: Class
subclass of: single-species collection of organisms
has curation status: metadata complete
definition: A collection of organisms that has as parts every organism of given species and no organisms of any other species.
editor note: At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible.
comment: This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user.

single-species collection of organisms
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: RO_0002351
    all values from: organism or virus or viroid
  intersection of: Restriction
    on property: RO_0002351
    all values from: Restriction
      on property: RO_0002350
      qualified cardinality: 1
      on class: species as a collection of organisms
  intersection of: Restriction
    on property: RO_0002351
    min qualified cardinality: 2
    on class: organism or virus or viroid
subclass of: collection of organisms
has curation status: metadata complete
definition: A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species.
alternative term: collection of organisms of the same species

community species diversity
type: Class
subclass of: quality of an ecological community
has curation status: metadata complete
definition: The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness.
editor note: If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity.
definition source: adapted from http://en.wikipedia.org/wiki/Species_diversity
comment: The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified.

family
type: Class
subclass of: single-species collection of 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.

population extinction
type: Class
subclass of: population process
has curation status: metadata incomplete
definition: A population process that ultimately leads to the death of all individuals in a population.

species extinction
type: Class
subclass of: process
has curation status: metadata incomplete
definition: A process that ultimately leads to the death of all individuals in a population.

community species evenness
type: Class
subclass of: quality of an ecological community
example of usage: If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even.
has curation status: metadata complete
definition: A quality of a community that reflects how close in abundance all species in a community are.
definition source: adapted from http://en.wikipedia.org/wiki/Species_evenness

household
type: Class
subclass of: organismal entity
subclass of: Class
  intersection of: Restriction
    on property: RO_0002351
    all values from: Homo sapiens
  intersection of: Restriction
    on property: RO_0002351
    min qualified cardinality: 1
    on class: Homo sapiens
subclass of: Restriction
  on property: RO_0002321
  some values from: human dwelling
has curation status: metadata incomplete
definition: An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people.
term editor: Person: Jie Zheng
definition source: WEB: http://en.wikipedia.org/wiki/Household

red population
type: Class
subclass of: ObsoleteClass
has obsolescence reason: example to be eventually removed
comment: This is an example population added to demonstrate the modeling pattern for collections of organisms.
deprecated: true

red organism
type: Class
subclass of: ObsoleteClass
has obsolescence reason: example to be eventually removed
comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query.
deprecated: true

collection of humans
type: Class
equivalent class: Class
  intersection of: single-species collection of organisms
  intersection of: Restriction
    on property: RO_0002351
    all values from: Homo sapiens
  intersection of: Restriction
    on property: RO_0002351
    min qualified cardinality: 2
    on class: Homo sapiens
subclass of: single-species collection of organisms
subclass of: Restriction
  on property: RO_0002351
  some values from: Homo sapiens
has curation status: pending final vetting
definition: A collection of organisms of the same species that has as members only humans.
alternative term: human community
alternative term: human population

community
type: Class
subclass of: ObsoleteClass
definition: A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other.
editor note: Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete.
has obsolescence reason: failed exploratory term
comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community).
deprecated: true

multi-species collection of organisms
type: Class
subclass of: collection of organisms
has curation status: metadata incomplete
definition: A collection of organisms that consists of two or more organisms from at least two species.
editor note: Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))".

agricultural household
type: Class
subclass of: household
has curation status: metadata incomplete
definition: A household in which the majority of the income of its members is derived from agricultural activities.
editor note: This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term.

organismal entity
type: Class
equivalent class: Class
  union of: organism or virus or viroid
  union of: collection of organisms
subclass of: material entity
has curation status: metadata complete
definition: A material entity that is one or more organisms, viruses or viroids.

biological family
type: Class
subclass of: family
definition: A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other.
alternative term: genealogical family
definition source: Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/

human social gathering activity
type: Class
subclass of: social behavior
subclass of: Restriction
  on property: RO_0000057
  some values from: collection of humans
definition: A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially.
editor note: Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029
definition source: GenEpiO curators

human community event
type: Class
subclass of: human social gathering activity
definition: A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area.
editor note: Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034
definition source: GenEpio curators

party
type: Class
subclass of: human social gathering activity
definition: A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose.
editor note: Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030
definition source: GenEpiO curators

potluck
type: Class
subclass of: human social gathering activity
editor note: Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033
definition source: A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering.
definition source: GenEpio curators

wedding
type: Class
subclass of: human social gathering activity
definition: A human social gathering at which two people are married. May include a legal or social ceremony.
editor note: Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031
definition source: GenEpio curators

baby shower
type: Class
subclass of: human social gathering activity
definition: A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby.
editor note: Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032
definition source: GenEpiO curators

pair of interacting organisms
type: Class
subclass of: collection of organisms
subclass of: Restriction
  on property: RO_0002351
  all values from: organism or virus or viroid
subclass of: Restriction
  on property: RO_0002351
  qualified cardinality: 2
  on class: organism or virus or viroid
definition: A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other.

pair of interacting organisms of the same species
type: Class
equivalent class: Class
  intersection of: pair of interacting organisms
  intersection of: Restriction
    on property: RO_0002351
    all values from: Restriction
      on property: RO_0002350
      qualified cardinality: 1
      on class: species as a collection of organisms
subclass of: single-species collection of organisms
subclass of: pair of interacting organisms

migratory population
type: Class
subclass of: population of organisms
subclass of: Restriction
  on property: RO_0000056
  some values from: population migration
has curation status: metadata incomplete
definition: A population which is participating in a migration process.

population migration
type: Class
subclass of: population process
has curation status: metadata incomplete
definition: A population process during which a population moves from one area to another.
definition source: https://en.wikipedia.org/wiki/Migration
comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations.

human population migration
type: Class
subclass of: population migration
subclass of: Restriction
  on property: RO_0000057
  some values from: collection of humans
has curation status: metadata incomplete
definition: A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location.
definition source: https://en.wikipedia.org/wiki/Human_migration
comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration

human migratory population
type: Class
subclass of: collection of humans
subclass of: Restriction
  on property: RO_0000056
  some values from: human population migration
has curation status: metadata incomplete
definition: A migratory population of humans, travelling with the intention of settling in a new area.
definition source: https://en.wikipedia.org/wiki/Human_migration

microbial community
type: Class
subclass of: ecological community
subclass of: multi-species collection of microbes
has curation status: pending final vetting
definition: An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness.
editor note: A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22
term editor: http://orcid.org/0000-0002-4366-3088
definition source: http://dx.doi.org/10.1038/ismej.2009.88
has broad synonym: microbiota
comment: The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another.

obsolete organismal entity
type: Class
subclass of: ObsoleteClass
definition: A material entity that is one or more organisms, viruses or viroids.
has obsolescence reason: wrong IRI form
term replaced by: organismal entity
deprecated: true

tidal mangrove shrubland community
type: Class
subclass of: ecological community
subclass of: Restriction
  on property: BFO_0000050
  some values from: tidal mangrove shrubland
definition: An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima.
contributor: https://orcid.org/0000-0002-4366-3088
has db xref: https://cmecscatalog.org/cmecs/classification/unit/577.html
has_related_synonym: mangrove community
has_related_synonym: tidal shrubland community

invisible to unaided eye
type: Class
subclass of: physical object quality
definition: A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye.
comment: should move to PATO

microbe
type: Class
subclass of: organism or virus or viroid
subclass of: Restriction
  on property: RO_0000086
  some values from: invisible to unaided eye
has_exact_synonym: microbial organism

collection of microbial organisms
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: RO_0002351
    all values from: microbe
  intersection of: Restriction
    on property: RO_0002351
    min qualified cardinality: 2
    on class: microbe
subclass of: collection of organisms
subclass of: Restriction
  on property: RO_0002351
  some values from: microbe
definition: A collection of organisms consisting of two or more microbes.
creator: https://orcid.org/0000-0001-8815-0078

multi-species collection of microbes
type: Class
subclass of: multi-species collection of organisms
subclass of: collection of microbial organisms
definition: A multi-species collection of organisms that consists of two or more microbes from at least two species.
creator: https://orcid.org/0000-0001-8815-0078

single species collection of microbes
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: RO_0002351
    all values from: microbe
  intersection of: Restriction
    on property: RO_0002351
    all values from: Restriction
      on property: RO_0002350
      qualified cardinality: 1
      on class: species as a collection of organisms
  intersection of: Restriction
    on property: RO_0002351
    min qualified cardinality: 2
    on class: microbe
subclass of: single-species collection of organisms
subclass of: collection of microbial organisms
definition: A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species.
creator: https://orcid.org/0000-0001-8815-0078

microbial population
type: Class
subclass of: population of organisms
subclass of: single species collection of microbes
subclass of: Restriction
  on property: RO_0002351
  all values from: microbe
definition: A population of organisms consisting of only microbes of the same species, that live in the same place.
creator: https://orcid.org/0000-0001-8815-0078
has broad synonym: microbiota

example to be eventually removed
type: NamedIndividual
type: curation status specification

failed exploratory term
type: NamedIndividual
type: obsolescence reason specification
definition: The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
term editor: Person:Alan Ruttenberg

metadata complete
type: NamedIndividual
type: curation status specification
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
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
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
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
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: NamedIndividual
type: curation status specification
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.

core
type: NamedIndividual
type: Subset
definition: Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

placeholder removed
type: NamedIndividual
type: obsolescence reason specification

terms merged
type: NamedIndividual
type: obsolescence reason specification
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 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 note: This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.

universal
type: NamedIndividual
type: denotator type
editor note: Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
term editor: Alan Ruttenberg
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf

defined class
type: NamedIndividual
type: denotator type
definition: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
editor note: "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
term editor: Alan Ruttenberg

named class expression
type: NamedIndividual
type: denotator type
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
editor note: named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
term editor: Alan Ruttenberg

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification
definition: Terms with this status should eventually replaced with a term from another ontology.
term editor: Alan Ruttenberg
definition source: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
definition: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
term editor: Alan Ruttenberg
definition source: group:OBI