Population and Community Ontology
type: Ontology
version IRI: pco-full.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
description: The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology.
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 label
type: AnnotationProperty
editor preferred label: editor preferred label
editor preferred label: editor preferred term
editor preferred label: editor preferred term~editor preferred label
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>
label: editor preferred term
label: editor preferred term~editor preferred label

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

in branch
type: AnnotationProperty
editor preferred label: 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 label: 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 label: definition
editor preferred label: textual definition
has curation status: ready for release
definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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>
label: textual definition

editor note
type: AnnotationProperty
editor preferred label: 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>
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
database_cross_reference: IAO:0000116
has OBO namespace: uberon
id: editor_note
is metadata tag: true
shorthand: editor_note

term editor
type: AnnotationProperty
editor preferred label: 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 label: 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 label: definition source
has curation status: ready for release
definition: Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
definition: 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 label: 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 label: 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 label: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
has curation status: pending final vetting
definition: An IRI or similar locator for a request or discussion of an ontology term.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

STATO alternative term
type: AnnotationProperty
definition: an alternative term used for STATO statistical ontology and ISA team
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

has_alternative_id
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

in_subset
type: AnnotationProperty

label
type: AnnotationProperty
editor preferred label: label

part of
type: ObjectProperty
inverse of: has part
type: TransitiveProperty
editor preferred label: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
alternative term: part_of
RO_0001900: RO_0001901

has part
type: ObjectProperty
type: TransitiveProperty
editor preferred label: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
alternative term: has_part
RO_0001900: RO_0001901

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

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

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

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: occurrent
range: occurrent
editor preferred label: precedes
definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
in_subset: ro-eco

occurs in
type: ObjectProperty
inverse of: contains process
domain: occurrent
range: independent continuant
property chain axiom: part of
editor preferred label: occurs in
definition: b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
alternative term: occurs_in
alternative term: unfolds in
alternative term: unfolds_in
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

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

is about
type: ObjectProperty
example of usage: This document is about information artifacts and their representations
has curation status: pending final vetting
definition: A (currently) primitive relation that relates an information artifact to an entity.
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
term editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

obsolete has member of
type: ObjectProperty
has obsolescence reason: failed exploratory term
deprecated: true

inheres in
type: ObjectProperty
inverse of: bearer of
editor preferred label: inheres in
example of usage: this fragility inheres in this vase
example of usage: this red color inheres in this apple
definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
alternative term: inheres_in
RO_0001900: RO_0001901

bearer of
type: ObjectProperty
range: specifically dependent continuant
editor preferred label: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
editor note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
alternative term: bearer_of
alternative term: is bearer of
RO_0001900: RO_0001901

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

has participant
type: ObjectProperty
domain: occurrent
range: continuant
editor preferred label: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
alternative term: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

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

concretizes
type: ObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.

function of
type: ObjectProperty
sub property of: inheres in
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative term: function_of
alternative term: is function of

quality of
type: ObjectProperty
sub property of: inheres in
inverse of: has quality
example of usage: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
alternative term: is quality of
alternative term: quality_of

role of
type: ObjectProperty
sub property of: inheres in
inverse of: has role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
alternative term: is role of
alternative term: role_of

has function
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
alternative term: has_function

has quality
type: ObjectProperty
sub property of: bearer of
range: quality
example of usage: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
alternative term: has_quality

has role
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
alternative term: has_role

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

disposition of
type: ObjectProperty
sub property of: inheres in

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

derives into
type: ObjectProperty
example of usage: this parent cell derives into this cell (cell division)
example of usage: this parent nucleus derives into this nucleus (nuclear division)
has curation status: pending final vetting
definition: a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
alternative term: derives_into

location of
type: ObjectProperty
inverse of: located in
type: TransitiveProperty
editor preferred label: is location of
example of usage: my head is the location of my brain
example of usage: this cage is the location of this rat
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
alternative term: location_of
RO_0001900: RO_0001901

located in
type: ObjectProperty
type: TransitiveProperty
domain: independent continuant
domain: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
range: independent continuant
range: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
editor preferred label: located in
example of usage: my brain is located in my head
example of usage: this rat is located in this cage
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
editor note: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
alternative term: located_in
RO_0001900: RO_0001901
source: http://www.obofoundry.org/ro/#OBO_REL:located_in

Axiom
annotated source: located in
annotated property: range
annotated target: independent continuant
editor note: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

Axiom
annotated source: located in
annotated property: domain
annotated target: independent continuant
editor note: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

2D boundary of
type: ObjectProperty
inverse of: has 2D boundary
example of usage: the surface of my skin is a 2D boundary of my body
definition: a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative term: 2D_boundary_of
alternative term: boundary of
alternative term: is 2D boundary of
alternative term: is boundary of
RO_0001900: RO_0001901

has 2D boundary
type: ObjectProperty
domain: material entity
range: immaterial entity
example of usage: my body has 2D boundary the surface of my skin
definition: a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative term: has boundary
alternative term: has_2D_boundary
RO_0001900: RO_0001901

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

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

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

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

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

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

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
term editor: David Osumi-Sutherland
in_subset: ro-eco
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

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

immediately precedes
type: ObjectProperty
sub property of: precedes
term editor: David Osumi-Sutherland
alternative term: ends_at_start_of
alternative term: meets
RO_0002575: precedes
in_subset: ro-eco
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
has curation status: pending final vetting
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO_0001900: RO_0001901
in_subset: valid for go annotation extension
in_subset: valid for gocam
in_subset: ro-eco

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

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
definition: Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
term editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: negatively regulates (process to process)
RO_0004050: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
definition: Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
term editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: positively regulates (process to process)
RO_0004049: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

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

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
term editor: Chris Mungall
alternative term: has function in

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

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: process
has curation status: pending final vetting
definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
term editor: Chris Mungall
alternative term: consumes
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: ro-eco

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

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

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
RO_0004049: causally upstream of
creator: cjm
in_subset: valid for go annotation extension
in_subset: valid for gocam
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
RO_0004050: causally upstream of
creator: cjm
comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y

ecologically related to
type: ObjectProperty
definition: A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
editor note: Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
term editor: Chris Mungall
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
in_subset: ro-eco

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
term editor: Chris Mungall
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO_0001900: RO_0001901

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

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

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

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

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

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
definition: inverse of regulates
term editor: Chris Mungall
OBO foundry unique label: regulated by (processual)
in_subset: RO_0002259

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
term editor: Chris Mungall
in_subset: RO_0002259

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
term editor: Chris Mungall
in_subset: RO_0002259

member of
type: ObjectProperty
sub property of: part of
inverse of: has member
example of usage: An organism that is a member of a population of organisms
definition: is member of is a mereological relation between a item and a collection.
alternative term: is member of
alternative term: member part of
definition source: SIO
RO_0001900: RO_0001901

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
definition: has member is a mereological relation between a collection and an item.
definition source: SIO
RO_0001900: RO_0001901

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has input
term editor: Chris Mungall
in_subset: RO_0002259
in_subset: ro-eco

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

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

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

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

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
has curation status: requires discussion
definition: p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
term editor: Chris Mungall
RO_0002575: causally upstream of

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

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
term editor: Chris Mungall
definition source: causal-relations
in_subset: RO_0002259

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

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
term editor: Chris Mungall
RO_0004049: involved in regulation of

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
term editor: Chris Mungall
RO_0004050: involved in regulation of

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

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

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

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

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

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

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

directly regulates activity of
type: ObjectProperty
sub property of: molecularly interacts with
sub property of: regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
term editor: Chris Mungall
term editor: Vasundra Touré
has_exact_synonym: molecularly controls

directly negatively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly negatively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
term editor: Chris Mungall
term editor: Vasundra Touré
alternative term: directly inhibits
has_exact_synonym: molecularly decreases activity of

directly positively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly positively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
term editor: Chris Mungall
term editor: Vasundra Touré
alternative term: directly activates
has_exact_synonym: molecularly increases activity of

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

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

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

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

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

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

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

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

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

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

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
definition: Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
term editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: directly regulates (processual)
RO_0002575: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

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

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

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

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

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

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

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
definition: Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
definition source: causal-relations
OBO foundry unique label: directly positively regulates (process to process)
RO_0004049: directly regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
definition: Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
definition source: causal-relations
OBO foundry unique label: directly negatively regulates (process to process)
RO_0004050: directly regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

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

acts upstream of or within, positive effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, positive effect
RO_0004049: acts upstream of or within
created by: cjm
creation date: 2018-01-26T23:49:30Z
in_subset: valid for go gp2term

acts upstream of or within, negative effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, negative effect
RO_0004050: acts upstream of or within
created by: cjm
creation date: 2018-01-26T23:49:51Z
in_subset: valid for go gp2term

acts upstream of, positive effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, positive effect
property chain axiom: enables
property chain axiom: causally upstream of, positive effect
definition: c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
RO_0004049: acts upstream of
created by: cjm
creation date: 2018-01-26T23:53:14Z
in_subset: valid for go gp2term

acts upstream of, negative effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, negative effect
property chain axiom: enables
property chain axiom: causally upstream of, negative effect
definition: c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
RO_0004050: acts upstream of
created by: cjm
creation date: 2018-01-26T23:53:22Z
in_subset: valid for go gp2term

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004050: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004049: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:19Z

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

decreased_in_magnitude_relative_to
type: ObjectProperty
sub property of: different_in_magnitude_relative_to
type: TransitiveProperty
domain: quality
range: quality
definition: q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
has OBO namespace: quality
id: decreased_in_magnitude_relative_to
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.

Axiom
annotated source: decreased_in_magnitude_relative_to
annotated property: definition
annotated target: q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
database_cross_reference: PATOC:CJM

different_in_magnitude_relative_to
type: ObjectProperty
domain: quality
range: quality
definition: q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
has OBO namespace: quality
id: different_in_magnitude_relative_to

Axiom
annotated source: different_in_magnitude_relative_to
annotated property: definition
annotated target: q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
database_cross_reference: PATOC:CJM

increased_in_magnitude_relative_to
type: ObjectProperty
sub property of: different_in_magnitude_relative_to
type: TransitiveProperty
domain: quality
range: quality
definition: q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
has OBO namespace: quality
id: increased_in_magnitude_relative_to
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.

Axiom
annotated source: increased_in_magnitude_relative_to
annotated property: definition
annotated target: q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
database_cross_reference: PATOC:CJM

reciprocal_of
type: ObjectProperty
definition: q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
has OBO namespace: quality
id: reciprocal_of
comment: There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.

Axiom
annotated source: reciprocal_of
annotated property: definition
annotated target: q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
database_cross_reference: PATOC:CJM

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
disjoint with: Restriction
  on property: part of
  some values from: occurrent
BFO_0000179: continuant
BFO_0000180: Continuant
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
editor note: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
editor note: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has associated axiom(nl): if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has associated axiom(nl): if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has associated axiom(nl): if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

Axiom
annotated source: continuant
annotated property: editor note
annotated target: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000007

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

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

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

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

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

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

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

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

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

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

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

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

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

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

independent continuant
type: Class
subclass of: continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
BFO_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: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
has associated axiom(nl): For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has associated axiom(nl): For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

Axiom
annotated source: independent continuant
annotated property: 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

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

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

spatial region
type: Class
subclass of: immaterial entity

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

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

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

disposition
type: Class
subclass of: realizable entity
disjoint with: role

realizable entity
type: Class
subclass of: specifically dependent continuant
disjoint with: quality
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
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
term editor: https://orcid.org/0000-0001-8815-0078
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

quality
type: Class
subclass of: specifically dependent continuant

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: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
editor note: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]

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

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

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

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

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

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

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: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
definition: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

Axiom
annotated source: generically dependent continuant
annotated property: definition
annotated target: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

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

function
type: Class
subclass of: disposition

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

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

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

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

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

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

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

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

multicellular organism
type: Class
subclass of: organism
definition: Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell.
OBO foundry unique label: multicellular organism
IAO created by: Melissa Haendel
IAO creation date: 9/18/11
comment: MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history.
comment: MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities.

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.

symbiotroph
type: Class
subclass of: organism or virus or viroid
definition: heterotroph that acquires nutrition from a symbiont
term editor: http://orcid.org/0000-0002-2908-3327

parasite
type: Class
subclass of: symbiotroph
definition: A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host
term editor: http://orcid.org/0000-0002-2908-3327
database_cross_reference: https://www.wikidata.org/entity/Q10253316

human dwelling
type: Class
subclass of: material entity
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.
database_cross_reference: https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015

tidal mangrove shrubland
type: Class
subclass of: material entity
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
database_cross_reference: 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"

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

catalytic activity
type: Class
subclass of: molecular_function

behavior
type: Class
subclass of: 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: jl
creation date: 2012-09-20T14:06:08Z
has_alternative_id: GO:0023032
has_alternative_id: GO:0044708
has_alternative_id: GO:0044709
database_cross_reference: 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.
database_cross_reference: GOC:ems
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0395448956
database_cross_reference: PMID:20160973

biological_process
type: Class
subclass of: process
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: jl
creation date: 2012-09-19T15:05:24Z
has_alternative_id: GO:0000004
has_alternative_id: GO:0007582
has_alternative_id: GO:0044699
database_cross_reference: 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.
database_cross_reference: GOC:pdt

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

transferase activity
type: Class
subclass of: catalytic activity

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

social behavior
type: Class
subclass of: behavior
subclass of: biological process involved in intraspecies interaction between organisms
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.
database_cross_reference: 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.
database_cross_reference: GOC:jh2
database_cross_reference: PMID:12848939
database_cross_reference: Wikipedia:Social_behavior

biological process involved in interspecies interaction between organisms
type: Class
subclass of: biological_process
definition: Any process evolved to enable an interaction with an organism of a different species.
term tracker item: https://github.com/geneontology/go-ontology/issues/20191
RO_0002161: NCBITaxon 4895
has_exact_synonym: interaction with another species
has_exact_synonym: interspecies interaction
has_exact_synonym: interspecies interaction between organisms
has_exact_synonym: interspecies interaction with other organisms
has OBO namespace: biological_process
id: GO:0044419
in_subset: gocheck do not annotate
in_subset: goslim candida
in_subset: goslim pir

Axiom
annotated source: biological process involved in interspecies interaction between organisms
annotated property: definition
annotated target: Any process evolved to enable an interaction with an organism of a different species.
database_cross_reference: GOC:cc

biological process involved in intraspecies interaction between organisms
type: Class
subclass of: biological_process
definition: Any process in which an organism has an effect on an organism of the same species.
term tracker item: https://github.com/geneontology/go-ontology/issues/20191
has_exact_synonym: intraspecies interaction between organisms
has_exact_synonym: intraspecies interaction with other organisms
has OBO namespace: biological_process
id: GO:0051703
in_subset: gocheck do not annotate
in_subset: goslim pir

Axiom
annotated source: biological process involved in 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.
database_cross_reference: GOC:ai

multi-organism process
type: Class
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.
database_cross_reference: GOC:jl

data item
type: Class
subclass of: information content entity
editor preferred label: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: pending final vetting
definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
alternative term: data
imported from: obi.owl

information content entity
type: Class
subclass of: generically dependent continuant
editor preferred label: information content entity

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 label: 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
editor preferred label: data about an ontology part
definition: Data about an ontology part is a data item about a part of an ontology, for example a term
term editor: Person:Alan Ruttenberg

measurement datum
type: Class
subclass of: data item
editor preferred label: measurement datum
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
has curation status: pending final vetting
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
editor note: 2/2/2009 is_specified_output of some assay?
term editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI
imported from: obi.owl

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Viruses
type: Class
has rank: NCBITaxon superkingdom
database_cross_reference: 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 <vertebrates>
database_cross_reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Euteleostomi
type: Class
subclass of: Teleostomi
has_alternative_id: NCBITaxon:40673
database_cross_reference: 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

Streptophytina
type: Class
subclass of: Streptophyta
has rank: NCBITaxon subphylum
database_cross_reference: GC_ID:1
has_exact_synonym: charophyte/embryophyte group
has OBO namespace: ncbi_taxonomy
has_related_synonym: Charophyta/Embryophyta group

Axiom
annotated source: Streptophytina
annotated property: has_exact_synonym
annotated target: charophyte/embryophyte group
has synonym type: equivalent name

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

cellular organisms
type: Class
database_cross_reference: 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
database_cross_reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Boreoeutheria
type: Class
subclass of: Eutheria
database_cross_reference: GC_ID:1
database_cross_reference: PMID:11743200
database_cross_reference: 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
database_cross_reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Bacteria
type: Class
subclass of: cellular organisms
has rank: NCBITaxon superkingdom
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10425795
database_cross_reference: PMID:10425796
database_cross_reference: PMID:10425797
database_cross_reference: PMID:10490293
database_cross_reference: PMID:10843050
database_cross_reference: PMID:10939651
database_cross_reference: PMID:10939673
database_cross_reference: PMID:10939677
database_cross_reference: PMID:11211268
database_cross_reference: PMID:11321083
database_cross_reference: PMID:11321113
database_cross_reference: PMID:11411719
database_cross_reference: PMID:11540071
database_cross_reference: PMID:11542017
database_cross_reference: PMID:11542087
database_cross_reference: PMID:11760965
database_cross_reference: PMID:12054223
database_cross_reference: PMID:2112744
database_cross_reference: PMID:270744
database_cross_reference: PMID:7520741
database_cross_reference: PMID:8123559
database_cross_reference: PMID:8186100
database_cross_reference: PMID:8590690
database_cross_reference: PMID:9103655
database_cross_reference: 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_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

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

Homininae
type: Class
subclass of: Hominidae
has rank: NCBITaxon subfamily
database_cross_reference: 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
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10425795
database_cross_reference: PMID:10425796
database_cross_reference: PMID:10425797
database_cross_reference: PMID:10490293
database_cross_reference: PMID:10843050
database_cross_reference: PMID:10939651
database_cross_reference: PMID:10939673
database_cross_reference: PMID:10939677
database_cross_reference: PMID:11211268
database_cross_reference: PMID:11321083
database_cross_reference: PMID:11321113
database_cross_reference: PMID:11411719
database_cross_reference: PMID:11540071
database_cross_reference: PMID:11541975
database_cross_reference: PMID:11542064
database_cross_reference: PMID:11542149
database_cross_reference: PMID:11760965
database_cross_reference: PMID:12054223
database_cross_reference: PMID:2112744
database_cross_reference: PMID:25527841
database_cross_reference: PMID:270744
database_cross_reference: PMID:8123559
database_cross_reference: PMID:8590690
database_cross_reference: PMID:9103655
database_cross_reference: 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
database_cross_reference: GC_ID:1
database_cross_reference: PMID:23020233
database_cross_reference: PMID:30257078
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
database_cross_reference: GC_ID:1
database_cross_reference: 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
database_cross_reference: GC_ID:1
database_cross_reference: PMID:11214319
database_cross_reference: PMID:12082125
database_cross_reference: PMID:12878460
database_cross_reference: PMID:15522813
has OBO namespace: ncbi_taxonomy

Simiiformes
type: Class
subclass of: Haplorrhini
has rank: NCBITaxon infraorder
database_cross_reference: 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
database_cross_reference: 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
database_cross_reference: 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
database_cross_reference: 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
database_cross_reference: 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 <mammals>
type: Class
subclass of: Mammalia
database_cross_reference: GC_ID:1
has_exact_synonym: Theria
has OBO namespace: ncbi_taxonomy

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

Viridiplantae
type: Class
subclass of: Eukaryota
has rank: NCBITaxon kingdom
database_cross_reference: GC_ID:1
database_cross_reference: PMID:16248873
database_cross_reference: PMID:30257078
has_exact_synonym: Chlorophyta/Embryophyta group
has_exact_synonym: chlorophyte/embryophyte group
has_exact_synonym: green plants
has OBO namespace: ncbi_taxonomy
has_related_synonym: Chlorobionta
has_related_synonym: Chloroplastida
has_related_synonym: green plants

Axiom
annotated source: Viridiplantae
annotated property: has_exact_synonym
annotated target: Chlorophyta/Embryophyta group
has synonym type: equivalent name

Axiom
annotated source: Viridiplantae
annotated property: has_exact_synonym
annotated target: chlorophyte/embryophyte group
has synonym type: equivalent name

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: Chloroplastida
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
database_cross_reference: 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
database_cross_reference: 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
database_cross_reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Deuterostomia
type: Class
subclass of: Bilateria
database_cross_reference: 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

Magnoliopsida
type: Class
subclass of: Spermatophyta
has rank: NCBITaxon class
database_cross_reference: GC_ID:1
database_cross_reference: PMID:25249442
has_exact_synonym: angiosperms
has_exact_synonym: flowering plants
has OBO namespace: ncbi_taxonomy
has_related_synonym: Angiospermae
has_related_synonym: Magnoliophyta
has_related_synonym: flowering plants

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

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

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

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

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

Streptophyta
type: Class
subclass of: Viridiplantae
has rank: NCBITaxon phylum
database_cross_reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Haplorrhini
type: Class
subclass of: Primates
has rank: NCBITaxon suborder
database_cross_reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Mammalia
type: Class
subclass of: Amniota
has rank: NCBITaxon class
database_cross_reference: 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

Fungi
type: Class
subclass of: Opisthokonta
has rank: NCBITaxon kingdom
database_cross_reference: GC_ID:1
database_cross_reference: PMID:11062127
database_cross_reference: PMID:12684019
has OBO namespace: ncbi_taxonomy
has_related_synonym: Mycota
has_related_synonym: fungi

Axiom
annotated source: Fungi
annotated property: has_related_synonym
annotated target: Mycota
has synonym type: genbank synonym

Axiom
annotated source: Fungi
annotated property: has_related_synonym
annotated target: fungi
has synonym type: blast name

Axiom
annotated source: Fungi
annotated property: has_related_synonym
annotated target: fungi
has synonym type: in part

Tracheophyta
type: Class
subclass of: Embryophyta
database_cross_reference: 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
database_cross_reference: 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
database_cross_reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Chordata
type: Class
subclass of: Deuterostomia
has rank: NCBITaxon phylum
database_cross_reference: 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 <vertebrates>
type: Class
subclass of: Craniata <chordates>
database_cross_reference: GC_ID:1
has_exact_synonym: Vertebrata
has_exact_synonym: vertebrates
has OBO namespace: ncbi_taxonomy
has_related_synonym: vertebrates

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

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

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

Gnathostomata <vertebrates>
type: Class
subclass of: Vertebrata <vertebrates>
database_cross_reference: GC_ID:1
has_exact_synonym: Gnathostomata
has_exact_synonym: jawed vertebrates
has OBO namespace: ncbi_taxonomy

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

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

Euphyllophyta
type: Class
subclass of: Tracheophyta
database_cross_reference: GC_ID:1
has_exact_synonym: euphyllophytes
has OBO namespace: ncbi_taxonomy

Axiom
annotated source: Euphyllophyta
annotated property: has_exact_synonym
annotated target: euphyllophytes
has synonym type: equivalent name

Sarcopterygii
type: Class
subclass of: Euteleostomi
has rank: NCBITaxon superclass
database_cross_reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Craniata <chordates>
type: Class
subclass of: Chordata
has rank: NCBITaxon subphylum
database_cross_reference: GC_ID:1
has_exact_synonym: Craniata
has OBO namespace: ncbi_taxonomy

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

Eutheria
type: Class
subclass of: Theria <mammals>
database_cross_reference: 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
database_cross_reference: 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
database_cross_reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Hominidae
type: Class
subclass of: Hominoidea
has rank: NCBITaxon family
database_cross_reference: 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
database_cross_reference: 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
database_cross_reference: GC_ID:1
has_exact_synonym: human
has_exact_synonym: man
has OBO namespace: ncbi_taxonomy

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

quality
type: Class
subclass of: specifically dependent continuant
definition: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
OBO foundry unique label: quality (PATO)
has_alternative_id: PATO:0000072
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
database_cross_reference: PATOC:GVG

qualitative
type: Class
subclass of: quality
has OBO namespace: quality
id: PATO:0000068
comment: TODO: define this or obsolete it and move children somewhere else.

deviation (from_normal)
type: Class
subclass of: qualitative
definition: A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
has OBO namespace: quality
id: PATO:0000069
in_subset: attribute slim

Axiom
annotated source: deviation (from_normal)
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
database_cross_reference: PATOC:GVG

amount
type: Class
subclass of: qualitative
subclass of: Restriction
  on property: reciprocal_of
  some values from: has number of
definition: The number of entities of this type that are part of the whole organism.
has_alternative_id: PATO:0000053
has_alternative_id: PATO:0000071
has_alternative_id: PATO:0001169
has_alternative_id: PATO:0001226
has_exact_synonym: presence or absence in organism
has_exact_synonym: quantitative
has OBO namespace: quality
has_related_synonym: count in organism
has_related_synonym: number
has_related_synonym: presence
id: PATO:0000070
in_subset: attribute slim
comment: This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10.

Axiom
annotated source: amount
annotated property: definition
annotated target: The number of entities of this type that are part of the whole organism.
database_cross_reference: 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.
database_cross_reference: PATOC:melissa

normal
type: Class
subclass of: qualitative
definition: A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.
RO_0002604: PATO_0000460
has OBO namespace: quality
has_related_synonym: average
id: PATO:0000461
in_subset: abnormal slim
in_subset: mpath slim
in_subset: value slim

Axiom
annotated source: normal
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.
database_cross_reference: PATOC:GVG

present
type: Class
subclass of: amount
definition: A quality inhering in a bearer by virtue of the bearer's existence.
RO_0002604: PATO_0000462
has OBO namespace: quality
has_related_synonym: present in organism
id: PATO:0000467
in_subset: absent slim
in_subset: value slim

Axiom
annotated source: present
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of the bearer's existence.
database_cross_reference: PATOC:GVG

increased amount
type: Class
equivalent class: Class
  intersection of: amount
  intersection of: Restriction
    on property: increased_in_magnitude_relative_to
    some values from: normal
subclass of: present
subclass of: increased quality
definition: An amount which is relatively high.
RO_0002604: decreased amount
has_alternative_id: PATO:0000420
has_alternative_id: PATO:0000650
has_exact_synonym: increased number
has_exact_synonym: present in greater numbers in organism
has_exact_synonym: supernumerary
has OBO namespace: quality
has_related_synonym: accessory
has_related_synonym: increased
id: PATO:0000470
in_subset: value slim

Axiom
annotated source: increased amount
annotated property: definition
annotated target: An amount which is relatively high.
database_cross_reference: PATOC:GVG

decreased rate
type: Class
equivalent class: Class
  intersection of: rate
  intersection of: Restriction
    on property: decreased_in_magnitude_relative_to
    some values from: normal
subclass of: rate
subclass of: decreased process quality
definition: A rate which is relatively low.
RO_0002604: increased rate
has_exact_synonym: slow rate
has OBO namespace: quality
id: PATO:0000911
in_subset: mpath slim
in_subset: value slim

Axiom
annotated source: decreased rate
annotated property: definition
annotated target: A rate which is relatively low.
database_cross_reference: PATO:GVG

increased rate
type: Class
equivalent class: Class
  intersection of: rate
  intersection of: Restriction
    on property: increased_in_magnitude_relative_to
    some values from: normal
subclass of: rate
subclass of: increased process quality
definition: A rate which is relatively high.
RO_0002604: decreased rate
has_exact_synonym: fast rate
has_exact_synonym: high rate
has OBO namespace: quality
id: PATO:0000912
in_subset: mpath slim
in_subset: value slim

Axiom
annotated source: increased rate
annotated property: definition
annotated target: A rate which is relatively high.
database_cross_reference: PATO:GVG

physical quality
type: Class
subclass of: physical object quality
definition: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
has_alternative_id: PATO:0002079
database_cross_reference: Wikipedia:Physical_property
has_exact_synonym: relational physical quality
has OBO namespace: quality
id: PATO:0001018
in_subset: attribute slim

Axiom
annotated source: physical quality
annotated property: definition
annotated target: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
database_cross_reference: PATOC:GVG

mass density
type: Class
subclass of: physical quality
definition: A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size.
has OBO namespace: quality
has_related_synonym: density
id: PATO:0001019
in_subset: attribute slim
in_subset: scalar slim

Axiom
annotated source: mass density
annotated property: definition
annotated target: A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size.
database_cross_reference: WordNet:WordNet

dense
type: Class
subclass of: mass density
definition: A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density.
has OBO namespace: quality
id: PATO:0001164
in_subset: mpath slim
in_subset: value slim

Axiom
annotated source: dense
annotated property: definition
annotated target: A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density.
database_cross_reference: PATOC:GVG

process quality
type: Class
subclass of: quality
disjoint with: physical object 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.
database_cross_reference: 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
database_cross_reference: 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.
database_cross_reference: 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.
database_cross_reference: 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.
database_cross_reference: PATOC:GVG

has number of
type: Class
subclass of: physical object quality
subclass of: Restriction
  on property: reciprocal_of
  some values from: amount
definition: The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts.
database_cross_reference: OBO_REL:has_part
has_exact_synonym: extra or missing physical or functional parts
has_exact_synonym: has or lacks parts of type
has_exact_synonym: mereological quality
has_exact_synonym: number of
has OBO namespace: quality
has_related_synonym: cardinality
has_related_synonym: number
id: PATO:0001555
in_subset: attribute slim
in_subset: relational slim

Axiom
annotated source: has number of
annotated property: definition
annotated target: The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts.
database_cross_reference: PATOC:CJM

increased mass density
type: Class
equivalent class: Class
  intersection of: dense
  intersection of: Restriction
    on property: increased_in_magnitude_relative_to
    some values from: normal
subclass of: dense
subclass of: increased object quality
definition: A density which is higher relative to the normal or average.
RO_0002604: decreased mass density
has_exact_synonym: high density
has OBO namespace: quality
id: PATO:0001788
in_subset: value slim

Axiom
annotated source: increased mass density
annotated property: definition
annotated target: A density which is higher relative to the normal or average.
database_cross_reference: PATOC:GVG

decreased mass density
type: Class
equivalent class: Class
  intersection of: dense
  intersection of: Restriction
    on property: decreased_in_magnitude_relative_to
    some values from: normal
subclass of: dense
subclass of: decreased object quality
definition: A density which is lower relative to the normal or average.
RO_0002604: increased mass density
has_exact_synonym: low density
has OBO namespace: quality
id: PATO:0001790
in_subset: value slim

Axiom
annotated source: decreased mass density
annotated property: definition
annotated target: A density which is lower relative to the normal or average.
database_cross_reference: PATOC:GVG

decreased amount
type: Class
equivalent class: Class
  intersection of: amount
  intersection of: Restriction
    on property: decreased_in_magnitude_relative_to
    some values from: normal
subclass of: present
subclass of: decreased quality
definition: An amount which is relatively low.
RO_0002604: increased amount
has_alternative_id: PATO:0000419
has_alternative_id: PATO:0000468
has_exact_synonym: decreased number
has_exact_synonym: present in fewer numbers in organism
has OBO namespace: quality
has_related_synonym: decreased
has_related_synonym: reduced
has_related_synonym: subnumerary
id: PATO:0001997
in_subset: value slim

Axiom
annotated source: decreased amount
annotated property: definition
annotated target: An amount which is relatively low.
database_cross_reference: 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.
database_cross_reference: 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

increased quality
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: increased_in_magnitude_relative_to
    some values from: normal
subclass of: deviation (from_normal)
subclass of: Restriction
  on property: increased_in_magnitude_relative_to
  some values from: normal
definition: A quality that has a value that is increased compared to normal or average.
RO_0002604: decreased quality
created by: George Gkoutos
creation date: 2011-06-16T06:39:43Z
has OBO namespace: quality
id: PATO:0002300

Axiom
annotated source: increased quality
annotated property: definition
annotated target: A quality that has a value that is increased compared to normal or average.
database_cross_reference: PATOC:GVG

decreased quality
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: decreased_in_magnitude_relative_to
    some values from: normal
subclass of: deviation (from_normal)
subclass of: Restriction
  on property: decreased_in_magnitude_relative_to
  some values from: normal
definition: A quality that has a value that is decreased compared to normal or average.
RO_0002604: increased quality
created by: George Gkoutos
creation date: 2011-06-16T06:40:15Z
has OBO namespace: quality
id: PATO:0002301

Axiom
annotated source: decreased quality
annotated property: definition
annotated target: A quality that has a value that is decreased compared to normal or average.
database_cross_reference: PATOC:GVG

decreased process quality
type: Class
equivalent class: Class
  intersection of: process quality
  intersection of: Restriction
    on property: decreased_in_magnitude_relative_to
    some values from: normal
subclass of: process quality
subclass of: decreased quality
definition: A quality of a process that has a value that is decreased compared to normal or average.
RO_0002604: increased process quality
created by: George Gkoutos
creation date: 2011-06-16T06:50:59Z
has OBO namespace: quality
id: PATO:0002302

Axiom
annotated source: decreased process quality
annotated property: definition
annotated target: A quality of a process that has a value that is decreased compared to normal or average.
database_cross_reference: PATOC:GVG

decreased object quality
type: Class
equivalent class: Class
  intersection of: physical object quality
  intersection of: Restriction
    on property: decreased_in_magnitude_relative_to
    some values from: normal
subclass of: physical object quality
subclass of: decreased quality
definition: A quality of an object that has a value that is decreased compared to normal or average.
RO_0002604: increased object quality
created by: George Gkoutos
creation date: 2011-06-16T06:51:54Z
has OBO namespace: quality
id: PATO:0002303

Axiom
annotated source: decreased object quality
annotated property: definition
annotated target: A quality of an object that has a value that is decreased compared to normal or average.
database_cross_reference: PATOC:GVG

increased process quality
type: Class
equivalent class: Class
  intersection of: process quality
  intersection of: Restriction
    on property: increased_in_magnitude_relative_to
    some values from: normal
subclass of: process quality
subclass of: increased quality
definition: A quality of a process that has a value that is increased compared to normal or average.
RO_0002604: decreased process quality
created by: George Gkoutos
creation date: 2011-06-16T06:53:08Z
has OBO namespace: quality
id: PATO:0002304

Axiom
annotated source: increased process quality
annotated property: definition
annotated target: A quality of a process that has a value that is increased compared to normal or average.
database_cross_reference: PATOC:GVG

increased object quality
type: Class
equivalent class: Class
  intersection of: physical object quality
  intersection of: Restriction
    on property: increased_in_magnitude_relative_to
    some values from: normal
subclass of: physical object quality
subclass of: increased quality
definition: A quality of an object that has a value that is increased compared to normal or average.
RO_0002604: decreased object quality
created by: George Gkoutos
creation date: 2011-06-16T06:54:01Z
has OBO namespace: quality
id: PATO:0002305

Axiom
annotated source: increased object quality
annotated property: definition
annotated target: A quality of an object that has a value that is increased compared to normal or average.
database_cross_reference: PATOC:GVG

collection of organisms
type: Class
equivalent class: Class
  intersection of: object aggregate
  intersection of: Restriction
    on property: has member
    all values from: organism or virus or viroid
  intersection of: Restriction
    on property: has member
    min qualified cardinality: 2
    on class: organism or virus or viroid
subclass of: object aggregate
subclass of: organismal entity
subclass of: Restriction
  on property: has member
  some values from: organism or virus or viroid
subclass of: Restriction
  on property: has member
  all 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: multi-species collection 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: inheres in
    some values from: population of organisms
subclass of: population quality
subclass of: Restriction
  on property: inheres in
  some values from: population of organisms
has curation status: requires discussion
definition: A quality that inheres in a population of organisms.
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.
editor note: This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community.
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: inheres in
    some values from: ecological community
subclass of: population quality
subclass of: Restriction
  on property: inheres in
  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: has participant
  some values from: population of organisms
has curation status: metadata incomplete
definition: A process that has as primary participant a population. 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.
comment: The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these 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: rate
has curation status: metadata incomplete
definition: The rate of birth of a population of organisms.

population death rate
type: Class
subclass of: rate
has curation status: metadata incomplete
definition: The rate of death of a population of organsisms.

population growth rate
type: Class
subclass of: rate
has curation status: metadata incomplete
definition: The rate of growth of a population.

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.

obsolete predator role
type: Class
subclass of: ObsoleteClass
editor note: Interactions are now covered in EcoCore ontology.
deprecated: true

Axiom
annotated source: obsolete predator role
annotated property: deprecated
annotated target: true
has obsolescence reason: failed exploratory term

obsolete prey role
type: Class
subclass of: ObsoleteClass
editor note: Interactions are now covered in EcoCore ontology.
deprecated: true

Axiom
annotated source: obsolete prey role
annotated property: deprecated
annotated target: true
has obsolescence reason: failed exploratory term

obsolete symbiont role
type: Class
subclass of: ObsoleteClass
editor note: Interactions are now covered in EcoCore ontology.
deprecated: true

Axiom
annotated source: obsolete symbiont role
annotated property: deprecated
annotated target: true
has obsolescence reason: failed exploratory term

species as a collection of organisms
type: Class
subclass of: single-species collection of organisms
subclass of: taxon as collection of organisms
has curation status: metadata complete
definition: A collection of organisms that has as members every organism of given species and no organisms of any other species.
definition: A collection of organisms that has as parts every organism of a 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.
database_cross_reference: GENO_0000113
database_cross_reference: TAXRANK_0000006
database_cross_reference: Species
has_exact_synonym: taxonomic group
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
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 an ecological 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: has member
    all values from: Homo sapiens
  intersection of: Restriction
    on property: has member
    min qualified cardinality: 1
    on class: Homo sapiens
subclass of: Restriction
  on property: ecologically related to
  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: https://orcid.org/0000-0002-2999-0103
definition source: WEB: http://en.wikipedia.org/wiki/Household

obsolete 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

obsolete 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: has member
    all values from: Homo sapiens
  intersection of: Restriction
    on property: has member
    min qualified cardinality: 2
    on class: Homo sapiens
subclass of: single-species collection of organisms
subclass of: Restriction
  on property: has member
  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

obsolete 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
subclass of: Restriction
  on property: has member
  min qualified cardinality: 2
  on class: population 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: has participant
  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
definition: 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.
editor note: Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033
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

tidal mangrove shrubland community
type: Class
subclass of: ecological community
subclass of: Restriction
  on property: part of
  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
database_cross_reference: 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
has_exact_synonym: microbial organism

collection of microbial organisms
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has member
    all values from: microbe
  intersection of: Restriction
    on property: has member
    min qualified cardinality: 2
    on class: microbe
subclass of: Restriction
  on property: has member
  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
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: has member
    all values from: microbe
  intersection of: Restriction
    on property: has member
    all values from: Restriction
      on property: member of
      qualified cardinality: 1
      on class: species as a collection of organisms
  intersection of: Restriction
    on property: has member
    min qualified cardinality: 2
    on class: microbe
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
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

number of generations of multicellular organism
type: Class
subclass of: count
subclass of: Restriction
  on property: is about
  all values from: multicellular organism
has curation status: pending final vetting
definition: A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism.
term editor: https://orcid.org/0000-0002-2999-0103
has broad synonym: number of generations

Axiom
annotated source: number of generations of multicellular organism
annotated property: definition
annotated target: A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism.
comment: NCIT C88214
comment: EFO_0000507

overcrowded population
type: Class
subclass of: quality of a population
subclass of: Class
  intersection of: increased mass density
  intersection of: Restriction
    on property: inheres in
    some values from: population of organisms
has curation status: pending final vetting
definition: An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels.
term editor: https://orcid.org/0000-0001-8815-0078
has_exact_synonym: increased density of population

overcrowded human population
type: Class
equivalent class: Class
  intersection of: overcrowded population
  intersection of: Restriction
    on property: inheres in
    some values from: collection of humans
subclass of: overcrowded population
subclass of: Restriction
  on property: inheres in
  some values from: collection of humans
has curation status: pending final vetting
definition: A quality of a human population such that the density humans in an area is increased beyond sustainable levels.
term editor: https://orcid.org/0000-0001-8815-0078

taxon as collection of organisms
type: Class
subclass of: collection of organisms
has curation status: requires discussion
definition: A collection of organisms that has as members every organism of a taxon and no organisms of any other equal or higher ranked taxon. The taxon may be at any level. If the taxon is species, then this is the same as the class species as a collection of organisms. When defining a taxon, it is generally understood that members include both living organisms and dead organisms that are known through specimens or observations.
term editor: https://orcid.org/0000-0001-8815-0078
database_cross_reference: data 1868
comment: This term is neutral with respect to which organisms are included in a taxon. Membership will depend on the taxon concept and the assertions used to define the taxon. These criteria must be specified by the user. The best practice is to refer to a formal taxon description, rather than informal names "Genus species" without an authority.

microbial parasite
type: Class
subclass of: parasite
subclass of: microbe
has curation status: pending final vetting
definition: An organism or virus or viroid that is a microbe and a parasite.
term editor: https://orcid.org/0000-0001-8815-0078

parasite isolate population
type: Class
subclass of: collection of microbial organisms
subclass of: microbial population
subclass of: Restriction
  on property: has member
  all values from: microbial parasite
example of usage: PMC4811772
has curation status: pending final vetting
definition: A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations.
term editor: https://orcid.org/0000-0001-8815-0078
term editor: VEuPathDB

Shannon diversity index
type: Class
subclass of: community species diversity
has curation status: pending final vetting
definition: A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi).
definition source: shannonDI.html
definition source: Shannon index
has_exact_synonym: Shannon entropy
has_exact_synonym: Shannon's diversity index
has_exact_synonym: Shannon-Wiener index

Simpson diversity index
type: Class
subclass of: community species diversity
has curation status: pending final vetting
definition: A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi).
definition source: simpsonDI.html
definition source: Simpson index
has_exact_synonym: Simpson index

inverse Simpson diversity index
type: Class
subclass of: community species diversity
has curation status: pending final vetting
definition: A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi).
definition source: simpsonDI.html
definition source: Inverse Simpson index

alga excluding Cyanobacteria
type: Class
subclass of: organism
definition: An organism that is part of a polyphyletic group of mostly photosynthetic Eukaryotes encompassing green plants excluding Embriophyta (land plants). Included organisms range from unicellular microalgae, such as Chlorella and diatoms to multicellular forms such as giant kelp.
definition source: Algae
has_exact_synonym: alga
has_exact_synonym: algae
has narrow synonym: seaweed

alpha diversity
type: Class
subclass of: community species diversity
definition: A community species diversity that is the mean species diversity at a site or within a specific habitat.
term editor: https://orcid.org/0000-0001-8815-0078
definition source: Alpha diversity
has_exact_synonym: α-diversity

beta diversity
type: Class
subclass of: community species diversity
definition: A community species diversity that is the ratio between regional and local species diversity.
term editor: https://orcid.org/0000-0001-8815-0078
definition source: Beta diversity
has_exact_synonym: true beta diversity
has_exact_synonym: β-diversity

gamma diversity
type: Class
subclass of: community species diversity
definition: A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity.
term editor: https://orcid.org/0000-0001-8815-0078
definition source: Gamma diversity
has_exact_synonym: γ-diversity

plant density
type: Class
subclass of: mass density
editor note: TBD: add logical definition
term editor: https://orcid.org/0000-0001-6284-4821
term editor: https://orcid.org/0000-0001-8815-0078
term editor: The density of plants in an ecological community or population, often measured as the number of plants per area.

seedling density
type: Class
subclass of: plant density
definition: The density of seedlings in an ecological community or population, often measured as the number of seedlings per area.
editor note: TBD: add logical definition
term editor: https://orcid.org/0000-0001-6284-4821
term editor: https://orcid.org/0000-0001-8815-0078

plant density of a population
type: Class
subclass of: quality of a population
subclass of: plant density
definition: The density of plants in a population or organisms (a single species), often measured as the number of plants per area.
editor note: TBD: add logical definition
term editor: https://orcid.org/0000-0001-6284-4821
term editor: https://orcid.org/0000-0001-8815-0078

plant density of an ecological community
type: Class
subclass of: quality of an ecological community
subclass of: plant density
definition: The density of plants in an ecological community (multiple species), often measured as the number of plants per area.
editor note: TBD: add logical definition
term editor: https://orcid.org/0000-0001-6284-4821
term editor: https://orcid.org/0000-0001-8815-0078

seedling density of a population
type: Class
subclass of: quality of a population
subclass of: seedling density
definition: The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area.
editor note: TBD: add logical definition
term editor: https://orcid.org/0000-0001-6284-4821
term editor: https://orcid.org/0000-0001-8815-0078

seedling density of an ecological community
type: Class
subclass of: quality of an ecological community
subclass of: seedling density
definition: The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area.
editor note: TBD: add logical definition
term editor: https://orcid.org/0000-0001-6284-4821
term editor: https://orcid.org/0000-0001-8815-0078

pair of interacting organisms
type: Class
equivalent class: Class
  intersection of: collection of organisms
  intersection of: Restriction
    on property: has member
    qualified cardinality: 2
    on class: organism or virus or viroid
subclass of: collection of organisms
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
subclass of: single-species collection of organisms
subclass of: pair of interacting organisms
has curation status: requires discussion
definition: A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other.

migratory population
type: Class
subclass of: population of organisms
subclass of: Restriction
  on property: participates in
  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: has participant
  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: participates in
  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.

count
type: Class
subclass of: measurement datum
example of usage: a count of 4 resulting from counting limbs in humans
has curation status: ready for release
definition: a count is a data item denoted by an integer and represented the number of instances or occurences of an entity
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

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

obsolete tidal mangrove shrubland community
type: Class
subclass of: ObsoleteClass
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.
has obsolescence reason: failed exploratory term
contributor: https://orcid.org/0000-0002-4366-3088
database_cross_reference: https://cmecscatalog.org/cmecs/classification/unit/577.html
has_related_synonym: mangrove community
has_related_synonym: tidal shrubland community
deprecated: true

obsolete invisible to unaided eye
type: Class
subclass of: ObsoleteClass
definition: A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye.
has obsolescence reason: failed exploratory term
comment: should move to PATO
deprecated: true

obsolete microbe
type: Class
subclass of: ObsoleteClass
has obsolescence reason: failed exploratory term
has_exact_synonym: microbial organism
deprecated: true

obsolete collection of microbial organisms
type: Class
subclass of: ObsoleteClass
definition: A collection of organisms consisting of two or more microbes.
has obsolescence reason: failed exploratory term
creator: https://orcid.org/0000-0001-8815-0078
deprecated: true

obsolete multi-species collection of microbes
type: Class
subclass of: ObsoleteClass
definition: A multi-species collection of organisms that consists of two or more microbes from at least two species.
has obsolescence reason: failed exploratory term
creator: https://orcid.org/0000-0001-8815-0078
deprecated: true

obsolete single species collection of microbes
type: Class
subclass of: ObsoleteClass
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.
has obsolescence reason: failed exploratory term
creator: https://orcid.org/0000-0001-8815-0078
deprecated: true

obsolete microbial population
type: Class
subclass of: ObsoleteClass
definition: A population of organisms consisting of only microbes of the same species, that live in the same place.
has obsolescence reason: failed exploratory term
creator: https://orcid.org/0000-0001-8815-0078
has broad synonym: microbiota
deprecated: true

example to be eventually removed
type: NamedIndividual
type: curation status specification
editor preferred label: example to be eventually removed

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

metadata complete
type: NamedIndividual
type: curation status specification
editor preferred label: metadata complete
definition: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.

organizational term
type: NamedIndividual
type: curation status specification
editor preferred label: organizational term
definition: Term created to ease viewing/sort terms for development purpose, and will not be included in a release

ready for release
type: NamedIndividual
type: curation status specification
editor preferred label: ready for release
definition: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."

metadata incomplete
type: NamedIndividual
type: curation status specification
editor preferred label: metadata incomplete
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

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

pending final vetting
type: NamedIndividual
type: curation status specification
editor preferred label: pending final vetting
definition: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.

obsolete_core
type: NamedIndividual
definition: Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
has obsolescence reason: placeholder removed
deprecated: true

placeholder removed
type: NamedIndividual
type: obsolescence reason specification
editor preferred label: placeholder removed

terms merged
type: NamedIndividual
type: obsolescence reason specification
editor preferred label: terms merged
editor note: An editor note should explain what were the merged terms and the reason for the merge.

term imported
type: NamedIndividual
type: obsolescence reason specification
editor preferred label: term imported
editor note: This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.

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

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

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

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

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

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

infer input from direct reg
is rule enabled: true
comment: MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
type: Imp
body: IndividualPropertyAtom
  property predicate: enables
  argument1: http://purl.obolibrary.org/obo/ro.owl#z
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#y
head: IndividualPropertyAtom
  property predicate: has input
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#z

'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally downstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x

'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally upstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x