format-version: 1.2
data-version: releases/2021-05-03
remark: 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.
ontology: pco
property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0001-8815-0078 xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "David Osumi-Sutherland" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "Jie Zheng" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "Pier Luigi Buttigieg" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "Ramona Walls" xsd:string
property_value: http://purl.org/dc/elements/1.1/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." xsd:string
property_value: http://purl.org/dc/elements/1.1/title "Population and Community Ontology" xsd:string
property_value: http://purl.org/dc/terms/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string

[Term]
id: BFO:0000001
name: entity
property_value: BFO:0000179 "entity" xsd:string
property_value: BFO:0000180 "Entity" xsd:string
property_value: 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" xsd:string
property_value: 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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"}
property_value: IAO:0000112 "Julius Caesar" xsd:string
property_value: IAO:0000112 "the Second World War" xsd:string
property_value: IAO:0000112 "Verdi’s Requiem" xsd:string
property_value: IAO:0000112 "your body mass index" xsd:string
property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000002
name: continuant
def: "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." []
is_a: BFO:0000001 ! entity
disjoint_from: BFO:0000003 ! occurrent
property_value: BFO:0000179 "continuant" xsd:string
property_value: BFO:0000180 "Continuant" xsd:string
property_value: 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" xsd:string
property_value: 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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"}
property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"}
property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"}
property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"}
property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"}
property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"}
property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"}
property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"}
property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000003
name: occurrent
def: "An entity that has temporal parts and that happens, unfolds or develops through time." []
is_a: BFO:0000001 ! entity
property_value: BFO:0000179 "occurrent" xsd:string
property_value: BFO:0000180 "Occurrent" xsd:string
property_value: 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" xsd:string
property_value: 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." xsd:string
property_value: 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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"}
property_value: 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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"}
property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"}
property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"}
property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"}
property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"}
property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000004
name: independent continuant
def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." []
def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"}
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000020 ! specifically dependent continuant
disjoint_from: BFO:0000031 ! generically dependent continuant
property_value: BFO:0000179 "ic" xsd:string
property_value: BFO:0000180 "IndependentContinuant" xsd:string
property_value: IAO:0000112 "a chair" xsd:string
property_value: IAO:0000112 "a heart" xsd:string
property_value: IAO:0000112 "a leg" xsd:string
property_value: IAO:0000112 "a molecule" xsd:string
property_value: IAO:0000112 "a spatial region" xsd:string
property_value: IAO:0000112 "an atom" xsd:string
property_value: IAO:0000112 "an orchestra." xsd:string
property_value: IAO:0000112 "an organism" xsd:string
property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string
property_value: IAO:0000112 "the interior of your mouth" xsd:string
property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"}
property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"}
property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"}
property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"}
property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000005
name: obsolete dependent continuant
def: "A continuant  that is either dependent on one or other independent continuant  bearers or inheres in or is borne by other entities." []
is_a: ObsoleteClass
is_obsolete: true

[Term]
id: BFO:0000006
name: spatial region
is_a: BFO:0000141 ! immaterial entity

[Term]
id: BFO:0000015
name: process
def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." []
def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"}
is_a: BFO:0000003 ! occurrent
property_value: BFO:0000179 "process" xsd:string
property_value: BFO:0000180 "Process" xsd:string
property_value: 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)" xsd:string
property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string
property_value: IAO:0000112 "a process of meiosis" xsd:string
property_value: IAO:0000112 "a process of sleeping" xsd:string
property_value: IAO:0000112 "the course of a disease" xsd:string
property_value: IAO:0000112 "the flight of a bird" xsd:string
property_value: IAO:0000112 "the life of an organism" xsd:string
property_value: IAO:0000112 "your process of aging." xsd:string
property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000016
name: disposition
is_a: BFO:0000017 ! realizable entity
disjoint_from: BFO:0000023 ! role

[Term]
id: BFO:0000017
name: realizable entity
def: "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." []
is_a: BFO:0000020 ! specifically dependent continuant
disjoint_from: BFO:0000019 ! quality
property_value: BFO:0000179 "realizable" xsd:string
property_value: BFO:0000180 "RealizableEntity" xsd:string
property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string
property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string
property_value: IAO:0000112 "the function of your reproductive organs" xsd:string
property_value: IAO:0000112 "the role of being a doctor" xsd:string
property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 xsd:string
property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"}
property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"}
property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"}
property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000019
name: quality
is_a: BFO:0000020 ! specifically dependent continuant

[Term]
id: BFO:0000020
name: specifically dependent continuant
def: "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." []
def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"}
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000031 ! generically dependent continuant
property_value: BFO:0000179 "sdc" xsd:string
property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string
property_value: 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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"}
property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string
property_value: IAO:0000112 "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." xsd:string
property_value: IAO:0000112 "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" xsd:string
property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string
property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string
property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string
property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string
property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string
property_value: IAO:0000112 "the role of being a doctor" xsd:string
property_value: IAO:0000112 "the shape of this hole." xsd:string
property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string
property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000023
name: role
def: "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." []
is_a: BFO:0000017 ! realizable entity
property_value: BFO:0000179 "role" xsd:string
property_value: BFO:0000180 "Role" xsd:string
property_value: 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." xsd:string
property_value: IAO:0000112 "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." xsd:string
property_value: IAO:0000112 "the priest role" xsd:string
property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string
property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string
property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string
property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string
property_value: IAO:0000112 "the student role" xsd:string
property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"}
property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000027
name: object aggregate
is_a: BFO:0000040 ! material entity
property_value: BFO:0000179 "object-aggregate" xsd:string
property_value: BFO:0000180 "ObjectAggregate" xsd:string
property_value: 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 " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"}
property_value: 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 " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"}
property_value: 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)." xsd:string
property_value: IAO:0000112 "a collection of cells in a blood biobank." xsd:string
property_value: IAO:0000112 "a swarm of bees is an aggregate of members who are linked together through natural bonds" xsd:string
property_value: IAO:0000112 "a symphony orchestra" xsd:string
property_value: IAO:0000112 "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)" xsd:string
property_value: IAO:0000112 "defined by fiat: the aggregate of members of an organization" xsd:string
property_value: IAO:0000112 "defined through physical attachment: the aggregate of atoms in a lump of granite" xsd:string
property_value: IAO:0000112 "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container" xsd:string
property_value: IAO:0000112 "defined via attributive delimitations such as: the patients in this hospital" xsd:string
property_value: IAO:0000112 "the aggregate of bearings in a constant velocity axle joint" xsd:string
property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:string
property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string
property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string
property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string
property_value: IAO:0000119 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"}
property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"}
property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000029
name: site
is_a: BFO:0000141 ! immaterial entity
property_value: BFO:0000179 "site" xsd:string
property_value: BFO:0000180 "Site" xsd:string
property_value: IAO:0000112 "a hole in the interior of a portion of cheese" xsd:string
property_value: IAO:0000112 "a rabbit hole" xsd:string
property_value: IAO:0000112 "an air traffic control region defined in the airspace above an airport" xsd:string
property_value: IAO:0000112 "Manhattan Canyon)" xsd:string
property_value: IAO:0000112 "the cockpit of an aircraft" xsd:string
property_value: IAO:0000112 "the Grand Canyon" xsd:string
property_value: IAO:0000112 "the hold of a ship" xsd:string
property_value: IAO:0000112 "the interior of a kangaroo pouch" xsd:string
property_value: IAO:0000112 "the interior of the trunk of your car" xsd:string
property_value: IAO:0000112 "the interior of your bedroom" xsd:string
property_value: IAO:0000112 "the interior of your office" xsd:string
property_value: IAO:0000112 "the interior of your refrigerator" xsd:string
property_value: IAO:0000112 "the lumen of your gut" xsd:string
property_value: IAO:0000112 "the Piazza San Marco" xsd:string
property_value: IAO:0000112 "your left nostril (a fiat part – the opening – of your left nasal cavity)" xsd:string
property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"}
property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000031
name: generically dependent continuant
def: "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." []
def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"}
is_a: BFO:0000002 ! continuant
property_value: BFO:0000179 "gdc" xsd:string
property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string
property_value: IAO:0000112 "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." xsd:string
property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string
property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string
property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000034
name: function
is_a: BFO:0000016 ! disposition

[Term]
id: BFO:0000040
name: material entity
def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." []
is_a: BFO:0000004 ! independent continuant
disjoint_from: BFO:0000141 ! immaterial entity
property_value: BFO:0000179 "material" xsd:string
property_value: BFO:0000180 "MaterialEntity" xsd:string
property_value: 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" xsd:string
property_value: 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." xsd:string
property_value: 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." xsd:string
property_value: IAO:0000112 "a flame" xsd:string
property_value: IAO:0000112 "a forest fire" xsd:string
property_value: IAO:0000112 "a human being" xsd:string
property_value: IAO:0000112 "a hurricane" xsd:string
property_value: IAO:0000112 "a photon" xsd:string
property_value: IAO:0000112 "a puff of smoke" xsd:string
property_value: IAO:0000112 "a sea wave" xsd:string
property_value: IAO:0000112 "a tornado" xsd:string
property_value: IAO:0000112 "an aggregate of human beings." xsd:string
property_value: IAO:0000112 "an energy wave" xsd:string
property_value: IAO:0000112 "an epidemic" xsd:string
property_value: IAO:0000112 "the undetached arm of a human being" xsd:string
property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"}
property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"}
property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"}
property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"}
property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"}
property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000141
name: immaterial entity
is_a: BFO:0000004 ! independent continuant
property_value: BFO:0000179 "immaterial" xsd:string
property_value: BFO:0000180 "ImmaterialEntity" xsd:string
property_value: 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" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: CARO:0000012
name: multicellular organism
def: "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." []
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.
is_a: CARO:0010004 ! organism
property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string
property_value: IAO:0000589 "multicellular organism" xsd:string

[Term]
id: CARO:0001010
name: organism or virus or viroid
def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." []
is_a: PCO:0000031 ! organismal entity
property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string
property_value: IAO:0000589 "organism or virus" xsd:string

[Term]
id: CARO:0010004
name: organism
def: "An individual member of a clade." []
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.
is_a: CARO:0001010 ! organism or virus or viroid
property_value: http://purl.obolibrary.org/obo/IAO_created_by "mah" xsd:string
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string
property_value: IAO:0000589 "organism" xsd:string

[Term]
id: ECOCORE:00000045
name: symbiotroph
def: "heterotroph that acquires nutrition from a symbiont" []
is_a: CARO:0001010 ! organism or virus or viroid
property_value: IAO:0000117 http://orcid.org/0000-0002-2908-3327 xsd:string

[Term]
id: ECOCORE:00000146
name: parasite
def: "A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host" []
xref: https://www.wikidata.org/entity/Q10253316
is_a: ECOCORE:00000045 ! symbiotroph
property_value: IAO:0000117 http://orcid.org/0000-0002-2908-3327 xsd:string

[Term]
id: ENVO:01000744
name: human dwelling
def: "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." [https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015]
is_a: BFO:0000040 ! material entity
property_value: 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." xsd:string
property_value: editor_note "Subclasses will be added by inference." xsd:string

[Term]
id: ENVO:01001369
name: tidal mangrove shrubland
alt_id: CMECS:577
def: "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." []
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"
subset: envoCmecs
subset: envoMarine
xref: https://cmecscatalog.org/cmecs/classification/unit/577.html
is_a: BFO:0000040 ! material entity
created_by: http://orcid.org/0000-0002-4366-3088

[Term]
id: GO:0003674
name: molecular_function
is_a: BFO:0000015 ! process
property_value: IAO:0000589 "molecular process" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl

[Term]
id: GO:0003824
name: catalytic activity
is_a: GO:0003674 ! molecular_function
property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl

[Term]
id: GO:0007610
name: behavior
namespace: biological_process
alt_id: GO:0023032
alt_id: GO:0044708
alt_id: GO:0044709
def: "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." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973]
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.\n2. 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).
subset: gocheck_do_not_manually_annotate
subset: goslim_agr
subset: goslim_flybase_ribbon
synonym: "behavioral response to stimulus" EXACT []
synonym: "behaviour" EXACT []
synonym: "behavioural response to stimulus" EXACT []
synonym: "single-organism behavior" RELATED []
xref: Wikipedia:Behavior
is_a: GO:0008150 ! biological_process
property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl
created_by: jl
creation_date: 2012-09-20T14:06:08Z

[Term]
id: GO:0008150
name: biological_process
namespace: biological_process
alt_id: GO:0000004
alt_id: GO:0007582
alt_id: GO:0044699
def: "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." [GOC:pdt]
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.
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_yeast
synonym: "biological process" EXACT []
synonym: "physiological process" EXACT []
synonym: "single organism process" RELATED []
synonym: "single-organism process" RELATED []
xref: Wikipedia:Biological_process
is_a: BFO:0000015 ! process
property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl
created_by: jl
creation_date: 2012-09-19T15:05:24Z

[Term]
id: GO:0016301
name: kinase activity
is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups
property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl

[Term]
id: GO:0016740
name: transferase activity
is_a: GO:0003824 ! catalytic activity
property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl

[Term]
id: GO:0016772
name: transferase activity, transferring phosphorus-containing groups
is_a: GO:0016740 ! transferase activity
property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl

[Term]
id: GO:0035176
name: social behavior
namespace: biological_process
def: "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." [GOC:jh2, PMID:12848939, Wikipedia:Social_behavior]
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.
synonym: "cooperative behavior" RELATED []
synonym: "social behaviour" EXACT []
xref: Wikipedia:Social_behavior
is_a: GO:0007610 ! behavior
is_a: GO:0051703 ! biological process involved in intraspecies interaction between organisms
property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl

[Term]
id: GO:0044419
name: biological process involved in interspecies interaction between organisms
namespace: biological_process
def: "Any process evolved to enable an interaction with an organism of a different species." [GOC:cc]
subset: gocheck_do_not_annotate
subset: goslim_candida
subset: goslim_pir
synonym: "interaction with another species" EXACT []
synonym: "interspecies interaction" EXACT []
synonym: "interspecies interaction between organisms" EXACT []
synonym: "interspecies interaction with other organisms" EXACT []
is_a: GO:0008150 ! biological_process
property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/20191 xsd:anyURI
property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl
property_value: RO:0002161 NCBITaxon:4895

[Term]
id: GO:0051703
name: biological process involved in intraspecies interaction between organisms
namespace: biological_process
def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai]
subset: gocheck_do_not_annotate
subset: goslim_pir
synonym: "intraspecies interaction between organisms" EXACT []
synonym: "intraspecies interaction with other organisms" EXACT []
is_a: GO:0008150 ! biological_process
property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/20191 xsd:anyURI
property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl

[Term]
id: GO:0051704
name: multi-organism process
namespace: biological_process
alt_id: GO:0051706
def: "A biological process which involves another organism of the same or different species." [GOC:jl]
subset: gocheck_do_not_annotate
subset: goslim_pir
synonym: "interaction between organisms" EXACT []
synonym: "physiological interaction between organisms" EXACT []
synonym: "physiological interaction with other organism" EXACT []
is_a: GO:0008150 ! biological_process
property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl

[Term]
id: IAO:0000027
name: data item
def: "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." []
is_a: IAO:0000030 ! information content entity
property_value: 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." xsd:string
property_value: 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." xsd:string
property_value: editor_note "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string
property_value: editor_note "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string
property_value: editor_note "JAR: datum     -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string
property_value: IAO:0000111 "data item" xsd:string
property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string
property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string
property_value: IAO:0000118 "data" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: IAO:0000030
name: information content entity
is_a: BFO:0000031 ! generically dependent continuant
property_value: IAO:0000111 "information content entity" xsd:string

[Term]
id: IAO:0000078
name: curation status specification
def: "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." []
is_a: IAO:0000102 ! data about an ontology part
property_value: editor_note "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string
property_value: IAO:0000111 "curation status specification" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string
property_value: IAO:0000119 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> xsd:string
property_value: IAO:0000119 "OBI_0000266" xsd:string

[Term]
id: IAO:0000102
name: data about an ontology part
def: "Data about an ontology part is a data item about a part of an ontology, for example a term" []
is_a: IAO:0000027 ! data item
property_value: IAO:0000111 "data about an ontology part" xsd:string
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string

[Term]
id: IAO:0000109
name: measurement datum
def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." []
is_a: IAO:0000027 ! data item
property_value: editor_note "2/2/2009 is_specified_output of some assay?" xsd:string
property_value: IAO:0000111 "measurement datum" xsd:string
property_value: IAO:0000112 "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,}." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000305" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: IAO:0000225
name: obsolescence reason specification
def: "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." []
is_a: IAO:0000102 ! data about an ontology part
property_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." xsd:string
property_value: IAO:0000111 "obsolescence reason specification" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string

[Term]
id: IAO:0000409
name: denotator type
def: "A denotator type indicates how a term should be interpreted from an ontological perspective." []
is_a: IAO:0000102 ! data about an ontology part
property_value: IAO:0000111 "denotator type" xsd:string
property_value: IAO:0000112 "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." xsd:string
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string

[Term]
id: IAO:8000000
name: ontology module
is_a: IAO:0000102 ! data about an ontology part
property_value: 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." xsd:string
property_value: IAO:0000111 "ontology module" xsd:string
property_value: IAO:0000118 "ontology file" xsd:string
property_value: IAO:0000232 "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." xsd:string

[Term]
id: IAO:8000001
name: base ontology module
def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "base ontology module" xsd:string
property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50

[Term]
id: IAO:8000002
name: editors ontology module
def: "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." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "editors ontology module" xsd:string
property_value: IAO:0000118 "source ontology module" xsd:string

[Term]
id: IAO:8000003
name: main release ontology module
def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." []
is_a: IAO:8000000 ! ontology module
property_value: editor_note "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string
property_value: IAO:0000111 "main release ontology module" xsd:string

[Term]
id: IAO:8000004
name: bridge ontology module
def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "bridge ontology module" xsd:string
property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies

[Term]
id: IAO:8000005
name: import ontology module
def: "A subset ontology module that is intended to be imported from another ontology." []
is_a: IAO:8000006 ! subset ontology module
property_value: editor_note "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string
property_value: IAO:0000111 "import ontology module" xsd:string
property_value: IAO:0000118 "import file" xsd:string
property_value: seeAlso http://robot.obolibrary.org/extract

[Term]
id: IAO:8000006
name: subset ontology module
def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "subset ontology module" xsd:string
property_value: IAO:0000118 "ontology slim" xsd:string
property_value: IAO:0000118 "subset ontology" xsd:string
property_value: seeAlso http://robot.obolibrary.org/filter
property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide

[Term]
id: IAO:8000007
name: curation subset ontology module
def: "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." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "curation subset ontology module" xsd:string

[Term]
id: IAO:8000008
name: analysis subset ontology module
def: "An ontology module that is intended for usage in analysis or discovery applications." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "analysis ontology module" xsd:string

[Term]
id: IAO:8000009
name: single layer subset ontology module
def: "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." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "single layer ontology module" xsd:string
property_value: IAO:0000118 "ribbon subset" xsd:string

[Term]
id: IAO:8000010
name: exclusion subset ontology module
def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "exclusion subset ontology module" xsd:string
property_value: IAO:0000118 "antislim" xsd:string

[Term]
id: IAO:8000011
name: external import ontology module
def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." []
is_a: IAO:8000005 ! import ontology module
property_value: IAO:0000111 "external import ontology module" xsd:string
property_value: IAO:0000118 "external import" xsd:string

[Term]
id: IAO:8000012
name: species subset ontology module
def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." []
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "species subset ontology module" xsd:string
property_value: IAO:0000118 "taxon subset" xsd:string
property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints

[Term]
id: IAO:8000013
name: reasoned ontology module
def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." []
is_a: IAO:8000000 ! ontology module
property_value: IAO:0000111 "reasoned ontology module" xsd:string
property_value: seeAlso http://robot.obolibrary.org/reason

[Term]
id: IAO:8000014
name: generated ontology module
def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." []
is_a: IAO:8000000 ! ontology module
property_value: editor_note "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string
property_value: IAO:0000111 "generated ontology module" xsd:string

[Term]
id: IAO:8000015
name: template generated ontology module
def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." []
is_a: IAO:8000014 ! generated ontology module
property_value: IAO:0000111 "template generated ontology module" xsd:string
property_value: seeAlso http://robot.obolibrary.org/template
property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0
property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/

[Term]
id: IAO:8000016
name: taxonomic bridge ontology module
is_a: IAO:8000004 ! bridge ontology module
property_value: IAO:0000111 "taxonomic bridge ontology module" xsd:string

[Term]
id: IAO:8000017
name: ontology module subsetted by expressivity
is_a: IAO:8000006 ! subset ontology module
property_value: IAO:0000111 "ontology module subsetted by expressivity" xsd:string

[Term]
id: IAO:8000018
name: obo basic subset ontology module
def: "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.\n\nExamples 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).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" []
is_a: IAO:8000017 ! ontology module subsetted by expressivity
property_value: IAO:0000111 "obo basic subset ontology module" xsd:string
property_value: seeAlso "6.2"

[Term]
id: IAO:8000019
name: ontology module subsetted by OWL profile
is_a: IAO:8000017 ! ontology module subsetted by expressivity
property_value: IAO:0000111 "ontology module subsetted by OWL profile" xsd:string

[Term]
id: IAO:8000020
name: EL++ ontology module
is_a: IAO:8000019 ! ontology module subsetted by OWL profile
property_value: IAO:0000111 "EL++ ontology module" xsd:string

[Term]
id: NCBITaxon:10239
name: Viruses
namespace: ncbi_taxonomy
synonym: "Vira" RELATED synonym []
synonym: "Viridae" RELATED synonym []
synonym: "viruses" RELATED blast_name []
xref: GC_ID:1
property_value: has_rank NCBITaxon:superkingdom
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:117570
name: Teleostomi
namespace: ncbi_taxonomy
xref: GC_ID:1
is_a: NCBITaxon:7776 ! Gnathostomata <vertebrates>
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:117571
name: Euteleostomi
namespace: ncbi_taxonomy
alt_id: NCBITaxon:40673
synonym: "bony vertebrates" EXACT genbank_common_name []
xref: GC_ID:1
is_a: NCBITaxon:117570 ! Teleostomi
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:131221
name: Streptophytina
namespace: ncbi_taxonomy
synonym: "Charophyta/Embryophyta group" RELATED synonym []
synonym: "charophyte/embryophyte group" EXACT equivalent_name []
xref: GC_ID:1
is_a: NCBITaxon:35493 ! Streptophyta
property_value: has_rank NCBITaxon:subphylum
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:131567
name: cellular organisms
namespace: ncbi_taxonomy
synonym: "biota" RELATED synonym []
xref: GC_ID:1
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:1338369
name: Dipnotetrapodomorpha
namespace: ncbi_taxonomy
xref: GC_ID:1
is_a: NCBITaxon:8287 ! Sarcopterygii
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:1437010
name: Boreoeutheria
namespace: ncbi_taxonomy
synonym: "Boreotheria" RELATED synonym []
xref: GC_ID:1
xref: PMID:11743200
xref: PMID:11791233
is_a: NCBITaxon:9347 ! Eutheria
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:1437180
name: Acrogymnospermae
namespace: ncbi_taxonomy
xref: GC_ID:1
is_a: NCBITaxon:58024 ! Spermatophyta
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:2
name: Bacteria
namespace: ncbi_taxonomy
synonym: "bacteria" RELATED blast_name []
synonym: "eubacteria" EXACT genbank_common_name []
synonym: "Monera" RELATED in_part []
synonym: "Procaryotae" RELATED in_part []
synonym: "Prokaryota" RELATED in_part []
synonym: "Prokaryotae" RELATED in_part []
synonym: "prokaryote" RELATED in_part []
synonym: "prokaryotes" RELATED in_part []
xref: GC_ID:11
xref: PMID:10425795
xref: PMID:10425796
xref: PMID:10425797
xref: PMID:10490293
xref: PMID:10843050
xref: PMID:10939651
xref: PMID:10939673
xref: PMID:10939677
xref: PMID:11211268
xref: PMID:11321083
xref: PMID:11321113
xref: PMID:11411719
xref: PMID:11540071
xref: PMID:11542017
xref: PMID:11542087
xref: PMID:11760965
xref: PMID:12054223
xref: PMID:2112744
xref: PMID:270744
xref: PMID:7520741
xref: PMID:8123559
xref: PMID:8186100
xref: PMID:8590690
xref: PMID:9103655
xref: PMID:9336922
is_a: NCBITaxon:131567 ! cellular organisms
property_value: has_rank NCBITaxon:superkingdom
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:207598
name: Homininae
namespace: ncbi_taxonomy
synonym: "Homo/Pan/Gorilla group" RELATED synonym []
xref: GC_ID:1
is_a: NCBITaxon:9604 ! Hominidae
property_value: has_rank NCBITaxon:subfamily
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:2157
name: Archaea
namespace: ncbi_taxonomy
synonym: "archaea" RELATED blast_name []
synonym: "Archaebacteria" RELATED synonym []
synonym: "Mendosicutes" RELATED synonym []
synonym: "Metabacteria" RELATED synonym []
synonym: "Monera" RELATED in_part []
synonym: "Procaryotae" RELATED in_part []
synonym: "Prokaryota" RELATED in_part []
synonym: "Prokaryotae" RELATED in_part []
synonym: "prokaryote" RELATED in_part []
synonym: "prokaryotes" RELATED in_part []
xref: GC_ID:11
xref: PMID:10425795
xref: PMID:10425796
xref: PMID:10425797
xref: PMID:10490293
xref: PMID:10843050
xref: PMID:10939651
xref: PMID:10939673
xref: PMID:10939677
xref: PMID:11211268
xref: PMID:11321083
xref: PMID:11321113
xref: PMID:11411719
xref: PMID:11540071
xref: PMID:11541975
xref: PMID:11542064
xref: PMID:11542149
xref: PMID:11760965
xref: PMID:12054223
xref: PMID:2112744
xref: PMID:25527841
xref: PMID:270744
xref: PMID:8123559
xref: PMID:8590690
xref: PMID:9103655
xref: PMID:9336922
is_a: NCBITaxon:131567 ! cellular organisms
property_value: has_rank NCBITaxon:superkingdom
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:2759
name: Eukaryota
namespace: ncbi_taxonomy
synonym: "Eucarya" RELATED synonym []
synonym: "Eucaryotae" RELATED synonym []
synonym: "eucaryotes" EXACT genbank_common_name []
synonym: "Eukarya" RELATED synonym []
synonym: "Eukaryotae" RELATED synonym []
synonym: "eukaryotes" EXACT common_name []
synonym: "eukaryotes" RELATED blast_name []
xref: GC_ID:1
xref: PMID:23020233
xref: PMID:30257078
is_a: NCBITaxon:131567 ! cellular organisms
property_value: has_rank NCBITaxon:superkingdom
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:3041
name: Chlorophyta
namespace: ncbi_taxonomy
synonym: "algae" RELATED in_part []
synonym: "Chlorophycota" RELATED synonym []
synonym: "Chlorophyta sensu Bremer 1985" RELATED synonym []
synonym: "green algae" EXACT genbank_common_name []
synonym: "green algae" RELATED blast_name []
xref: GC_ID:1
xref: PMID:23020233
is_a: NCBITaxon:33090 ! Viridiplantae
property_value: has_rank NCBITaxon:phylum
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:314146
name: Euarchontoglires
namespace: ncbi_taxonomy
xref: GC_ID:1
xref: PMID:11214319
xref: PMID:12082125
xref: PMID:12878460
xref: PMID:15522813
is_a: NCBITaxon:1437010 ! Boreoeutheria
property_value: has_rank NCBITaxon:superorder
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:314293
name: Simiiformes
namespace: ncbi_taxonomy
synonym: "Anthropoidea" RELATED synonym []
xref: GC_ID:1
is_a: NCBITaxon:376913 ! Haplorrhini
property_value: has_rank NCBITaxon:infraorder
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:314295
name: Hominoidea
namespace: ncbi_taxonomy
synonym: "ape" EXACT common_name []
synonym: "apes" EXACT genbank_common_name []
xref: GC_ID:1
is_a: NCBITaxon:9526 ! Catarrhini
property_value: has_rank NCBITaxon:superfamily
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:3193
name: Embryophyta
namespace: ncbi_taxonomy
synonym: "higher plants" EXACT common_name []
synonym: "land plants" EXACT common_name []
synonym: "land plants" RELATED blast_name []
synonym: "plants" EXACT common_name []
xref: GC_ID:1
is_a: NCBITaxon:131221 ! Streptophytina
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:32523
name: Tetrapoda
namespace: ncbi_taxonomy
synonym: "tetrapods" EXACT genbank_common_name []
xref: GC_ID:1
is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:32524
name: Amniota
namespace: ncbi_taxonomy
synonym: "amniotes" EXACT genbank_common_name []
xref: GC_ID:1
is_a: NCBITaxon:32523 ! Tetrapoda
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:32525
name: Theria <mammals>
namespace: ncbi_taxonomy
synonym: "Theria" EXACT scientific_name []
xref: GC_ID:1
is_a: NCBITaxon:40674 ! Mammalia
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:33090
name: Viridiplantae
namespace: ncbi_taxonomy
synonym: "Chlorobionta" RELATED synonym []
synonym: "Chlorophyta/Embryophyta group" EXACT equivalent_name []
synonym: "chlorophyte/embryophyte group" EXACT equivalent_name []
synonym: "Chloroplastida" RELATED synonym []
synonym: "green plants" EXACT common_name []
synonym: "green plants" RELATED blast_name []
xref: GC_ID:1
xref: PMID:16248873
xref: PMID:30257078
is_a: NCBITaxon:2759 ! Eukaryota
property_value: has_rank NCBITaxon:kingdom
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:33154
name: Opisthokonta
namespace: ncbi_taxonomy
synonym: "Fungi/Metazoa group" RELATED synonym []
synonym: "opisthokonts" RELATED synonym []
xref: GC_ID:1
is_a: NCBITaxon:2759 ! Eukaryota
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:33208
name: Metazoa
namespace: ncbi_taxonomy
synonym: "Animalia" RELATED synonym []
synonym: "animals" RELATED blast_name []
synonym: "metazoans" EXACT genbank_common_name []
synonym: "multicellular animals" EXACT common_name []
xref: GC_ID:1
is_a: NCBITaxon:33154 ! Opisthokonta
property_value: has_rank NCBITaxon:kingdom
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:33213
name: Bilateria
namespace: ncbi_taxonomy
xref: GC_ID:1
is_a: NCBITaxon:6072 ! Eumetazoa
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:33511
name: Deuterostomia
namespace: ncbi_taxonomy
synonym: "deuterostomes" EXACT common_name []
xref: GC_ID:1
is_a: NCBITaxon:33213 ! Bilateria
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:3398
name: Magnoliopsida
namespace: ncbi_taxonomy
synonym: "Angiospermae" RELATED synonym []
synonym: "angiosperms" EXACT common_name []
synonym: "flowering plants" EXACT genbank_common_name []
synonym: "flowering plants" RELATED blast_name []
synonym: "Magnoliophyta" RELATED synonym []
xref: GC_ID:1
xref: PMID:25249442
is_a: NCBITaxon:58024 ! Spermatophyta
property_value: has_rank NCBITaxon:class
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:35493
name: Streptophyta
namespace: ncbi_taxonomy
xref: GC_ID:1
is_a: NCBITaxon:33090 ! Viridiplantae
property_value: has_rank NCBITaxon:phylum
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:376913
name: Haplorrhini
namespace: ncbi_taxonomy
xref: GC_ID:1
is_a: NCBITaxon:9443 ! Primates
property_value: has_rank NCBITaxon:suborder
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:40674
name: Mammalia
namespace: ncbi_taxonomy
synonym: "mammals" EXACT genbank_common_name []
synonym: "mammals" RELATED blast_name []
xref: GC_ID:1
is_a: NCBITaxon:32524 ! Amniota
property_value: has_rank NCBITaxon:class
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:4751
name: Fungi
namespace: ncbi_taxonomy
synonym: "fungi" RELATED in_part []
synonym: "fungi" RELATED blast_name []
synonym: "Mycota" RELATED genbank_synonym []
xref: GC_ID:1
xref: PMID:11062127
xref: PMID:12684019
is_a: NCBITaxon:33154 ! Opisthokonta
property_value: has_rank NCBITaxon:kingdom
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:58023
name: Tracheophyta
namespace: ncbi_taxonomy
synonym: "vascular plants" EXACT common_name []
synonym: "vascular plants" RELATED blast_name []
xref: GC_ID:1
is_a: NCBITaxon:3193 ! Embryophyta
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:58024
name: Spermatophyta
namespace: ncbi_taxonomy
synonym: "seed plants" EXACT common_name []
synonym: "seed plants" RELATED blast_name []
xref: GC_ID:1
is_a: NCBITaxon:78536 ! Euphyllophyta
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:6072
name: Eumetazoa
namespace: ncbi_taxonomy
xref: GC_ID:1
is_a: NCBITaxon:33208 ! Metazoa
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:7711
name: Chordata
namespace: ncbi_taxonomy
synonym: "chordates" EXACT genbank_common_name []
synonym: "chordates" RELATED blast_name []
xref: GC_ID:1
is_a: NCBITaxon:33511 ! Deuterostomia
property_value: has_rank NCBITaxon:phylum
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:7742
name: Vertebrata <vertebrates>
namespace: ncbi_taxonomy
synonym: "Vertebrata" EXACT scientific_name []
synonym: "vertebrates" EXACT genbank_common_name []
synonym: "vertebrates" RELATED blast_name []
xref: GC_ID:1
is_a: NCBITaxon:89593 ! Craniata <chordates>
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:7776
name: Gnathostomata <vertebrates>
namespace: ncbi_taxonomy
synonym: "Gnathostomata" EXACT scientific_name []
synonym: "jawed vertebrates" EXACT genbank_common_name []
xref: GC_ID:1
is_a: NCBITaxon:7742 ! Vertebrata <vertebrates>
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:78536
name: Euphyllophyta
namespace: ncbi_taxonomy
synonym: "euphyllophytes" EXACT equivalent_name []
xref: GC_ID:1
is_a: NCBITaxon:58023 ! Tracheophyta
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:8287
name: Sarcopterygii
namespace: ncbi_taxonomy
xref: GC_ID:1
is_a: NCBITaxon:117571 ! Euteleostomi
property_value: has_rank NCBITaxon:superclass
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:89593
name: Craniata <chordates>
namespace: ncbi_taxonomy
synonym: "Craniata" EXACT scientific_name []
xref: GC_ID:1
is_a: NCBITaxon:7711 ! Chordata
property_value: has_rank NCBITaxon:subphylum
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:9347
name: Eutheria
namespace: ncbi_taxonomy
synonym: "eutherian mammals" EXACT common_name []
synonym: "placental mammals" EXACT common_name []
synonym: "Placentalia" RELATED synonym []
synonym: "placentals" EXACT genbank_common_name []
synonym: "placentals" RELATED blast_name []
xref: GC_ID:1
is_a: NCBITaxon:32525 ! Theria <mammals>
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:9443
name: Primates
namespace: ncbi_taxonomy
synonym: "Primata" RELATED synonym []
synonym: "primate" EXACT equivalent_name []
synonym: "primates" RELATED blast_name []
xref: GC_ID:1
is_a: NCBITaxon:314146 ! Euarchontoglires
property_value: has_rank NCBITaxon:order
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:9526
name: Catarrhini
namespace: ncbi_taxonomy
xref: GC_ID:1
is_a: NCBITaxon:314293 ! Simiiformes
property_value: has_rank NCBITaxon:parvorder
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:9604
name: Hominidae
namespace: ncbi_taxonomy
synonym: "great apes" EXACT genbank_common_name []
synonym: "Pongidae" RELATED synonym []
xref: GC_ID:1
is_a: NCBITaxon:314295 ! Hominoidea
property_value: has_rank NCBITaxon:family
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:9605
name: Homo
namespace: ncbi_taxonomy
synonym: "humans" EXACT common_name []
xref: GC_ID:1
is_a: NCBITaxon:207598 ! Homininae
property_value: has_rank NCBITaxon:genus
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:9606
name: Homo sapiens
namespace: ncbi_taxonomy
synonym: "human" EXACT genbank_common_name []
synonym: "man" EXACT common_name []
xref: GC_ID:1
is_a: NCBITaxon:9605 ! Homo
property_value: has_rank NCBITaxon:species
property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: PATO:0000001
name: quality
namespace: quality
alt_id: PATO:0000072
def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG]
is_a: BFO:0000020 ! specifically dependent continuant
property_value: IAO:0000589 "quality (PATO)" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0000068
name: qualitative
namespace: quality
comment: TODO: define this or obsolete it and move children somewhere else.
is_a: PATO:0000001 ! quality
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0000069
name: deviation (from_normal)
namespace: quality
def: "A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average." [PATOC:GVG]
subset: attribute_slim
is_a: PATO:0000068 ! qualitative
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0000070
name: amount
namespace: quality
alt_id: PATO:0000053
alt_id: PATO:0000071
alt_id: PATO:0001169
alt_id: PATO:0001226
def: "The number of entities of this type that are part of the whole organism." [PATOC:GVG]
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.
subset: attribute_slim
synonym: "count in organism" RELATED []
synonym: "number" RELATED []
synonym: "presence" RELATED []
synonym: "presence or absence in organism" EXACT []
synonym: "quantitative" EXACT []
is_a: PATO:0000068 ! qualitative
relationship: reciprocal_of PATO:0001555 ! has number of
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0000161
name: rate
namespace: quality
def: "A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time." [PATOC:melissa]
subset: attribute_slim
subset: scalar_slim
is_a: PATO:0002062 ! physical quality of a process
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0000461
name: normal
namespace: quality
def: "A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average." [PATOC:GVG]
subset: abnormal_slim
subset: mpath_slim
subset: value_slim
synonym: "average" RELATED []
is_a: PATO:0000068 ! qualitative
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
property_value: RO:0002604 PATO:0000460

[Term]
id: PATO:0000467
name: present
namespace: quality
def: "A quality inhering in a bearer by virtue of the bearer's existence." [PATOC:GVG]
subset: absent_slim
subset: value_slim
synonym: "present in organism" RELATED []
is_a: PATO:0000070 ! amount
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
property_value: RO:0002604 PATO:0000462

[Term]
id: PATO:0000470
name: increased amount
namespace: quality
alt_id: PATO:0000420
alt_id: PATO:0000650
def: "An amount which is relatively high." [PATOC:GVG]
subset: value_slim
synonym: "accessory" RELATED []
synonym: "increased" RELATED []
synonym: "increased number" EXACT []
synonym: "present in greater numbers in organism" EXACT []
synonym: "supernumerary" EXACT []
is_a: PATO:0000467 ! present
is_a: PATO:0002300 ! increased quality
intersection_of: PATO:0000070 ! amount
intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
property_value: RO:0002604 PATO:0001997

[Term]
id: PATO:0000911
name: decreased rate
namespace: quality
def: "A rate which is relatively low." [PATO:GVG]
subset: mpath_slim
subset: value_slim
synonym: "slow rate" EXACT []
is_a: PATO:0000161 ! rate
is_a: PATO:0002302 ! decreased process quality
intersection_of: PATO:0000161 ! rate
intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
property_value: RO:0002604 PATO:0000912

[Term]
id: PATO:0000912
name: increased rate
namespace: quality
def: "A rate which is relatively high." [PATO:GVG]
subset: mpath_slim
subset: value_slim
synonym: "fast rate" EXACT []
synonym: "high rate" EXACT []
is_a: PATO:0000161 ! rate
is_a: PATO:0002304 ! increased process quality
intersection_of: PATO:0000161 ! rate
intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
property_value: RO:0002604 PATO:0000911

[Term]
id: PATO:0001018
name: physical quality
namespace: quality
alt_id: PATO:0002079
def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG]
subset: attribute_slim
synonym: "relational physical quality" EXACT []
xref: Wikipedia:Physical_property
is_a: PATO:0001241 ! physical object quality
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0001019
name: mass density
namespace: quality
def: "A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size." [WordNet:WordNet]
subset: attribute_slim
subset: scalar_slim
synonym: "density" RELATED []
is_a: PATO:0001018 ! physical quality
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0001164
name: dense
namespace: quality
def: "A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density." [PATOC:GVG]
subset: mpath_slim
subset: value_slim
is_a: PATO:0001019 ! mass density
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0001236
name: process quality
namespace: quality
alt_id: PATO:0001239
alt_id: PATO:0001240
def: "A quality which inheres in an process." [PATOC:GVG]
comment: See comments of relational quality of a physical entity.
synonym: "quality of a process" EXACT []
synonym: "quality of occurrent" EXACT []
synonym: "quality of process" EXACT []
synonym: "relational quality of occurrent" EXACT []
is_a: PATO:0000001 ! quality
disjoint_from: PATO:0001241 ! physical object quality
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0001241
name: physical object quality
namespace: quality
alt_id: PATO:0001237
alt_id: PATO:0001238
def: "A quality which inheres in a continuant." [PATOC:GVG]
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.
synonym: "monadic quality of a continuant" EXACT []
synonym: "monadic quality of an object" NARROW []
synonym: "monadic quality of continuant" NARROW []
synonym: "multiply inhering quality of a physical entity" EXACT []
synonym: "quality of a continuant" EXACT []
synonym: "quality of a single physical entity" EXACT []
synonym: "quality of an object" EXACT []
synonym: "quality of continuant" EXACT []
xref: snap:Quality
is_a: PATO:0000001 ! quality
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0001338
name: mixed sex
namespace: quality
def: "A biological sex quality inhering in a population of multiple sexes." [MGED:MGED]
comment: For example a mixture of females and male or males and hermaphrodites.
subset: value_slim
is_a: PATO:0002003 ! population quality
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0001415
name: morbidity
namespace: quality
def: "A quality inhering in a population by virtue of the proportion of its members that are ill at a given time." [PATOC:GVG]
subset: attribute_slim
subset: scalar_slim
is_a: PATO:0002003 ! population quality
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0001555
name: has number of
namespace: quality
def: "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." [PATOC:CJM]
subset: attribute_slim
subset: relational_slim
synonym: "cardinality" RELATED []
synonym: "extra or missing physical or functional parts" EXACT []
synonym: "has or lacks parts of type" EXACT []
synonym: "mereological quality" EXACT []
synonym: "number" RELATED []
synonym: "number of" EXACT []
xref: OBO_REL:has_part
is_a: PATO:0001241 ! physical object quality
relationship: reciprocal_of PATO:0000070 ! amount
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0001788
name: increased mass density
namespace: quality
def: "A density which is higher relative to the normal or average." [PATOC:GVG]
subset: value_slim
synonym: "high density" EXACT []
is_a: PATO:0001164 ! dense
is_a: PATO:0002305 ! increased object quality
intersection_of: PATO:0001164 ! dense
intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
property_value: RO:0002604 PATO:0001790

[Term]
id: PATO:0001790
name: decreased mass density
namespace: quality
def: "A density which is lower relative to the normal or average." [PATOC:GVG]
subset: value_slim
synonym: "low density" EXACT []
is_a: PATO:0001164 ! dense
is_a: PATO:0002303 ! decreased object quality
intersection_of: PATO:0001164 ! dense
intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
property_value: RO:0002604 PATO:0001788

[Term]
id: PATO:0001997
name: decreased amount
namespace: quality
alt_id: PATO:0000419
alt_id: PATO:0000468
def: "An amount which is relatively low." [PATOC:GVG]
subset: value_slim
synonym: "decreased" RELATED []
synonym: "decreased number" EXACT []
synonym: "present in fewer numbers in organism" EXACT []
synonym: "reduced" RELATED []
synonym: "subnumerary" RELATED []
is_a: PATO:0000467 ! present
is_a: PATO:0002301 ! decreased quality
intersection_of: PATO:0000070 ! amount
intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
property_value: RO:0002604 PATO:0000470

[Term]
id: PATO:0002003
name: population quality
namespace: quality
def: "A quality that inheres in an entire population or part of a population." [PATOC:GVG]
subset: attribute_slim
is_a: PATO:0001241 ! physical object quality
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl

[Term]
id: PATO:0002062
name: physical quality of a process
namespace: quality
subset: attribute_slim
is_a: PATO:0001236 ! process quality
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
created_by: george
creation_date: 2009-06-05T09:16:46Z

[Term]
id: PATO:0002300
name: increased quality
namespace: quality
def: "A quality that has a value that is increased compared to normal or average." [PATOC:GVG]
is_a: PATO:0000069 ! deviation (from_normal)
intersection_of: PATO:0000001 ! quality
intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal
relationship: increased_in_magnitude_relative_to PATO:0000461 ! normal
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
property_value: RO:0002604 PATO:0002301
created_by: George Gkoutos
creation_date: 2011-06-16T06:39:43Z

[Term]
id: PATO:0002301
name: decreased quality
namespace: quality
def: "A quality that has a value that is decreased compared to normal or average." [PATOC:GVG]
is_a: PATO:0000069 ! deviation (from_normal)
intersection_of: PATO:0000001 ! quality
intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal
relationship: decreased_in_magnitude_relative_to PATO:0000461 ! normal
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
property_value: RO:0002604 PATO:0002300
created_by: George Gkoutos
creation_date: 2011-06-16T06:40:15Z

[Term]
id: PATO:0002302
name: decreased process quality
namespace: quality
def: "A quality of a process that has a value that is decreased compared to normal or average." [PATOC:GVG]
is_a: PATO:0001236 ! process quality
is_a: PATO:0002301 ! decreased quality
intersection_of: PATO:0001236 ! process quality
intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
property_value: RO:0002604 PATO:0002304
created_by: George Gkoutos
creation_date: 2011-06-16T06:50:59Z

[Term]
id: PATO:0002303
name: decreased object quality
namespace: quality
def: "A quality of an object that has a value that is decreased compared to normal or average." [PATOC:GVG]
is_a: PATO:0001241 ! physical object quality
is_a: PATO:0002301 ! decreased quality
intersection_of: PATO:0001241 ! physical object quality
intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
property_value: RO:0002604 PATO:0002305
created_by: George Gkoutos
creation_date: 2011-06-16T06:51:54Z

[Term]
id: PATO:0002304
name: increased process quality
namespace: quality
def: "A quality of a process that has a value that is increased compared to normal or average." [PATOC:GVG]
is_a: PATO:0001236 ! process quality
is_a: PATO:0002300 ! increased quality
intersection_of: PATO:0001236 ! process quality
intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
property_value: RO:0002604 PATO:0002302
created_by: George Gkoutos
creation_date: 2011-06-16T06:53:08Z

[Term]
id: PATO:0002305
name: increased object quality
namespace: quality
def: "A quality of an object that has a value that is increased compared to normal or average." [PATOC:GVG]
is_a: PATO:0001241 ! physical object quality
is_a: PATO:0002300 ! increased quality
intersection_of: PATO:0001241 ! physical object quality
intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
property_value: RO:0002604 PATO:0002303
created_by: George Gkoutos
creation_date: 2011-06-16T06:54:01Z

[Term]
id: PCO:0000000
name: collection of organisms
def: "A material entity that consists of two or more organisms, viruses, or viroids." []
comment: May be of the same or different species.
is_a: BFO:0000027 ! object aggregate
is_a: PCO:0000031 ! organismal entity
intersection_of: BFO:0000027 ! object aggregate
intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid
intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid
relationship: RO:0002351 CARO:0001010 ! has member organism or virus or viroid
relationship: RO:0002351 CARO:0001010 ! has member organism or virus or viroid
property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000118 "group of organism" xsd:string
property_value: IAO:0000118 "organism collection" xsd:string

[Term]
id: PCO:0000001
name: population of organisms
def: "A collection of organisms, all of the same species, that live in the same place." []
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. \n\nClasses 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.
is_a: PCO:0000018 ! single-species collection of organisms
property_value: IAO:0000112 "" xsd:string
property_value: IAO:0000112 "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." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000119 ISBN:0878932739 xsd:string

[Term]
id: PCO:0000002
name: ecological community
def: "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." []
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.
is_a: PCO:0000029 ! multi-species collection of organisms
property_value: IAO:0000118 "multispecies community" xsd:string
property_value: IAO:0000119 ISBN:0865423504 xsd:string

[Term]
id: PCO:0000003
name: quality of a population
def: "A quality that inheres in a population of organisms." []
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.
is_a: PATO:0002003 ! population quality
intersection_of: PATO:0002003 ! population quality
intersection_of: RO:0000052 PCO:0000001 ! inheres in population of organisms
relationship: RO:0000052 PCO:0000001 ! inheres in population of organisms
property_value: 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." xsd:string
property_value: 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." xsd:string
property_value: IAO:0000114 IAO:0000428

[Term]
id: PCO:0000004
name: quality of an ecological community
def: "A quality that inheres in a community." []
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.
is_a: PATO:0002003 ! population quality
intersection_of: PATO:0002003 ! population quality
intersection_of: RO:0000052 PCO:0000002 ! inheres in ecological community
relationship: RO:0000052 PCO:0000002 ! inheres in ecological community
property_value: 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." xsd:string
property_value: IAO:0000114 IAO:0000428

[Term]
id: PCO:0000005
name: population process
def: "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.
is_a: BFO:0000015 ! process
relationship: RO:0000057 PCO:0000001 ! has participant population of organisms
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000006
name: population birth rate
def: "The rate of birth of a population of organisms." []
is_a: PATO:0000161 ! rate
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000007
name: population death rate
def: "The rate of death of a population of organsisms." []
is_a: PATO:0000161 ! rate
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000008
name: population growth rate
def: "The rate of growth of a population." []
is_a: PATO:0000161 ! rate
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000009
name: obsolete carrying capacity
def: "The maximum number of individuals that can be supported in  a population that is growing according to logistic growth." []
is_a: ObsoleteClass
property_value: 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." xsd:string
property_value: IAO:0000119 ISBN:0878932739 xsd:string
property_value: IAO:0000231 IAO:0000423
is_obsolete: true

[Term]
id: PCO:0000010
name: community species richness
def: "The number of different species represented in an ecological community." []
is_a: PCO:0000004 ! quality of an ecological community
property_value: 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)." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_richness" xsd:string

[Term]
id: PCO:0000011
name: population growth
def: "A process that leads to a change in the number of individuals (positive or negative) in a population." []
is_a: PCO:0000005 ! population process
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000012
name: logistic population growth
def: "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." []
is_a: PCO:0000011 ! population growth
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000013
name: exponential population growth
def: "A population growth process that leads to an exponential increase in the number of individuals in a population." []
is_a: PCO:0000011 ! population growth
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000014
name: obsolete predator role
is_a: ObsoleteClass
property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string
is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"}

[Term]
id: PCO:0000015
name: obsolete prey role
is_a: ObsoleteClass
property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string
is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"}

[Term]
id: PCO:0000016
name: obsolete symbiont role
is_a: ObsoleteClass
property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string
is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"}

[Term]
id: PCO:0000017
name: species as a collection of organisms
def: "A collection of organisms that has as members every organism of given species and no organisms of any other species." []
def: "A collection of organisms that has as parts every organism of a species and no organisms of any other species." []
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.
synonym: "taxonomic group" EXACT []
xref: GENO:0000113
xref: Species
xref: TAXRANK:0000006
is_a: PCO:0000018 ! single-species collection of organisms
is_a: PCO:0000059 ! taxon as collection of organisms
property_value: 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." xsd:string
property_value: IAO:0000114 IAO:0000120

[Term]
id: PCO:0000018
name: single-species collection of organisms
def: "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." []
is_a: PCO:0000000 ! collection of organisms
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000118 "collection of organisms of the same species" xsd:string

[Term]
id: PCO:0000019
name: community species diversity
def: "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." []
comment: The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified.
is_a: PCO:0000004 ! quality of an ecological community
property_value: 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." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_diversity" xsd:string

[Term]
id: PCO:0000020
name: family
def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." []
comment: Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry.
is_a: PCO:0000018 ! single-species collection of organisms
property_value: editor_note "Needs axioms for family relationships." xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000119 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 xsd:string

[Term]
id: PCO:0000021
name: population extinction
def: "A population process that ultimately leads to the death of all individuals in a population." []
is_a: PCO:0000005 ! population process
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000022
name: species extinction
def: "A process that ultimately leads to the death of all individuals in a population." []
is_a: BFO:0000015 ! process
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000023
name: community species evenness
def: "A quality of an ecological community that reflects how close in abundance all species in a community are." []
is_a: PCO:0000004 ! quality of an ecological community
property_value: IAO:0000112 "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." xsd:string
property_value: IAO:0000114 IAO:0000120
property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_evenness" xsd:string

[Term]
id: PCO:0000024
name: household
def: "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." []
is_a: PCO:0000031 ! organismal entity
relationship: RO:0002321 ENVO:01000744 ! ecologically related to human dwelling
relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! has member Homo sapiens
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000117 https://orcid.org/0000-0002-2999-0103
property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:string

[Term]
id: PCO:0000025
name: obsolete red population
comment: This is an example population added to demonstrate the modeling pattern for collections of organisms.
is_a: ObsoleteClass
property_value: IAO:0000231 IAO:0000002
is_obsolete: true

[Term]
id: PCO:0000026
name: obsolete red organism
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.
is_a: ObsoleteClass
property_value: IAO:0000231 IAO:0000002
is_obsolete: true

[Term]
id: PCO:0000027
name: collection of humans
def: "A collection of organisms of the same species that has as members only humans." []
is_a: PCO:0000018 ! single-species collection of organisms
intersection_of: PCO:0000018 ! single-species collection of organisms
intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} ! has member Homo sapiens
intersection_of: RO:0002351 NCBITaxon:9606 {minCardinality="2"} ! has member Homo sapiens
relationship: RO:0002351 NCBITaxon:9606 ! has member Homo sapiens
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000118 "human community" xsd:string
property_value: IAO:0000118 "human population" xsd:string

[Term]
id: PCO:0000028
name: obsolete community
def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." []
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).
is_a: ObsoleteClass
property_value: 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." xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: PCO:0000029
name: multi-species collection of organisms
def: "A collection of organisms that consists of two or more organisms from at least two species." []
is_a: PCO:0000000 ! collection of organisms
relationship: RO:0002351 PCO:0000001 {minCardinality="2"} ! has member population of organisms
property_value: 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'))\"." xsd:string
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:0000030
name: agricultural household
name: obsolete organismal entity
def: "A household in which the majority of the income of its members is derived from agricultural activities." []
def: "A material entity that is one or more organisms, viruses or viroids." []
is_a: ObsoleteClass
is_a: PCO:0000024 ! household
property_value: 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." xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000231 "wrong IRI form" xsd:string
is_obsolete: true
replaced_by: http://purl.obolibrary.org/obo/PCO_0000031

[Term]
id: PCO:0000031
name: organismal entity
def: "A material entity that is one or more organisms, viruses or viroids." []
is_a: BFO:0000040 ! material entity
union_of: CARO:0001010 ! organism or virus or viroid
union_of: PCO:0000000 ! collection of organisms
property_value: IAO:0000114 IAO:0000120

[Term]
id: PCO:0000032
name: biological family
def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." []
is_a: PCO:0000020 ! family
property_value: IAO:0000118 "genealogical family" xsd:string
property_value: IAO:0000119 "Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/" xsd:string

[Term]
id: PCO:0000033
name: human social gathering activity
def: "A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially." []
is_a: GO:0035176 ! social behavior
relationship: RO:0000057 PCO:0000027 ! has participant collection of humans
property_value: editor_note "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029" xsd:string
property_value: IAO:0000119 "GenEpiO curators" xsd:string

[Term]
id: PCO:0000034
name: human community event
def: "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." []
is_a: PCO:0000033 ! human social gathering activity
property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034" xsd:string
property_value: IAO:0000119 "GenEpio curators" xsd:string

[Term]
id: PCO:0000035
name: party
def: "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." []
is_a: PCO:0000033 ! human social gathering activity
property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030" xsd:string
property_value: IAO:0000119 "GenEpiO curators" xsd:string

[Term]
id: PCO:0000037
name: potluck
def: "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." []
is_a: PCO:0000033 ! human social gathering activity
property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string
property_value: IAO:0000119 "GenEpio curators" xsd:string

[Term]
id: PCO:0000038
name: wedding
def: "A human social gathering at which two people are married. May include a legal or social ceremony." []
is_a: PCO:0000033 ! human social gathering activity
property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031" xsd:string
property_value: IAO:0000119 "GenEpio curators" xsd:string

[Term]
id: PCO:0000039
name: baby shower
def: "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." []
is_a: PCO:0000033 ! human social gathering activity
property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032" xsd:string
property_value: IAO:0000119 "GenEpiO curators" xsd:string

[Term]
id: PCO:0000040
name: obsolete tidal mangrove shrubland community
def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." []
synonym: "mangrove community" RELATED []
synonym: "tidal shrubland community" RELATED []
xref: https://cmecscatalog.org/cmecs/classification/unit/577.html
is_a: ObsoleteClass
property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: PCO:0000041
name: obsolete invisible to unaided eye
def: "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
is_a: ObsoleteClass
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: PCO:0000042
name: obsolete microbe
synonym: "microbial organism" EXACT []
is_a: ObsoleteClass
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: PCO:0000043
name: obsolete collection of microbial organisms
def: "A collection of organisms consisting of two or more microbes." []
is_a: ObsoleteClass
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: PCO:0000044
name: obsolete multi-species collection of microbes
def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." []
is_a: ObsoleteClass
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: PCO:0000045
name: obsolete single species collection of microbes
def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." []
is_a: ObsoleteClass
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: PCO:0000046
name: obsolete microbial population
def: "A population of organisms consisting of only microbes of the same species, that live in the same place." []
synonym: "microbiota" BROAD []
is_a: ObsoleteClass
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Term]
id: PCO:0000047
name: tidal mangrove shrubland community
def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." []
synonym: "mangrove community" RELATED []
synonym: "tidal shrubland community" RELATED []
xref: https://cmecscatalog.org/cmecs/classification/unit/577.html
is_a: PCO:0000002 ! ecological community
relationship: BFO:0000050 ENVO:01001369 ! part of tidal mangrove shrubland
property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string

[Term]
id: PCO:0000048
name: invisible to unaided eye
def: "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
is_a: PATO:0001241 ! physical object quality

[Term]
id: PCO:0000049
name: microbe
synonym: "microbial organism" EXACT []
is_a: CARO:0001010 ! organism or virus or viroid

[Term]
id: PCO:0000050
name: collection of microbial organisms
def: "A collection of organisms consisting of two or more microbes." []
intersection_of: RO:0002351 PCO:0000049 {all_only="true"} ! has member microbe
intersection_of: RO:0002351 PCO:0000049 {minCardinality="2"} ! has member microbe
relationship: RO:0002351 PCO:0000049 ! has member microbe
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string

[Term]
id: PCO:0000051
name: multi-species collection of microbes
def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." []
is_a: PCO:0000029 ! multi-species collection of organisms
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string

[Term]
id: PCO:0000052
name: single species collection of microbes
def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." []
is_a: PCO:0000050 ! collection of microbial organisms
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string

[Term]
id: PCO:0000053
name: microbial population
def: "A population of organisms consisting of only microbes of the same species, that live in the same place." []
synonym: "microbiota" BROAD []
is_a: PCO:0000001 ! population of organisms
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string

[Term]
id: PCO:0000054
name: number of generations of multicellular organism
def: "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"}
synonym: "number of generations" BROAD []
is_a: STATO:0000047 ! count
relationship: IAO:0000136 CARO:0000012 ! is about multicellular organism
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-2999-0103

[Term]
id: PCO:0000057
name: overcrowded population
def: "An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels." []
synonym: "increased density of population" EXACT []
is_a: PCO:0000003 ! quality of a population
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0000058
name: overcrowded human population
def: "A quality of a human population such that the density humans in an area is increased beyond sustainable levels." []
is_a: PCO:0000057 ! overcrowded population
intersection_of: PCO:0000057 ! overcrowded population
intersection_of: RO:0000052 PCO:0000027 ! inheres in collection of humans
relationship: RO:0000052 PCO:0000027 ! inheres in collection of humans
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0000059
name: taxon as collection of organisms
def: "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." []
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.
xref: data:1868
is_a: PCO:0000000 ! collection of organisms
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0000060
name: microbial parasite
def: "An organism or virus or viroid that is a microbe and a parasite." []
is_a: ECOCORE:00000146 ! parasite
is_a: PCO:0000049 ! microbe
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0000061
name: parasite isolate population
def: "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." []
is_a: PCO:0000050 ! collection of microbial organisms
is_a: PCO:0000053 ! microbial population
relationship: RO:0002351 PCO:0000060 ! has member microbial parasite
property_value: IAO:0000112 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811772/
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078
property_value: IAO:0000117 "VEuPathDB" xsd:string

[Term]
id: PCO:0000062
name: Shannon diversity index
def: "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)." []
synonym: "Shannon entropy" EXACT []
synonym: "Shannon's diversity index" EXACT []
synonym: "Shannon-Wiener index" EXACT []
is_a: PCO:0000019 ! community species diversity
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/shannonDI.html
property_value: IAO:0000119 "Shannon_index"

[Term]
id: PCO:0000063
name: Simpson diversity index
def: "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)." []
synonym: "Simpson index" EXACT []
is_a: PCO:0000019 ! community species diversity
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html
property_value: IAO:0000119 "Simpson_index"

[Term]
id: PCO:0000064
name: inverse Simpson diversity index
def: "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)." []
is_a: PCO:0000019 ! community species diversity
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html
property_value: IAO:0000119 "Inverse_Simpson_index"

[Term]
id: PCO:0000073
name: alga excluding Cyanobacteria
def: "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." []
synonym: "alga" EXACT []
synonym: "algae" EXACT []
synonym: "seaweed" NARROW []
is_a: CARO:0010004 ! organism
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Algae

[Term]
id: PCO:0000074
name: alpha diversity
def: "A community species diversity that is the mean species diversity at a site or within a specific habitat." []
synonym: "α-diversity" EXACT []
is_a: PCO:0000019 ! community species diversity
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078
property_value: IAO:0000119 Alpha:diversity

[Term]
id: PCO:0000075
name: beta diversity
def: "A community species diversity that is the ratio between regional and local species diversity." []
synonym: "true beta diversity" EXACT []
synonym: "β-diversity" EXACT []
is_a: PCO:0000019 ! community species diversity
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078
property_value: IAO:0000119 Beta:diversity

[Term]
id: PCO:0000076
name: gamma diversity
def: "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." []
synonym: "γ-diversity" EXACT []
is_a: PCO:0000019 ! community species diversity
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078
property_value: IAO:0000119 Gamma:diversity

[Term]
id: PCO:0000077
name: plant density
is_a: PATO:0001019 ! mass density
property_value: editor_note "TBD: add logical definition" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078
property_value: IAO:0000117 "The density of plants in an ecological community or population, often measured as the number of plants per area." xsd:string

[Term]
id: PCO:0000078
name: seedling density
def: "The density of seedlings in an ecological community or population, often measured as the number of seedlings per area." []
is_a: PCO:0000077 ! plant density
property_value: editor_note "TBD: add logical definition" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0000079
name: plant density of a population
def: "The density of plants in a population or organisms (a single species), often measured as the number of plants per area." []
is_a: PCO:0000003 ! quality of a population
is_a: PCO:0000077 ! plant density
property_value: editor_note "TBD: add logical definition" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0000080
name: plant density of an ecological community
def: "The density of plants in an ecological community (multiple species), often measured as the number of plants per area." []
is_a: PCO:0000004 ! quality of an ecological community
is_a: PCO:0000077 ! plant density
property_value: editor_note "TBD: add logical definition" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0000081
name: seedling density of a population
def: "The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area." []
is_a: PCO:0000003 ! quality of a population
is_a: PCO:0000078 ! seedling density
property_value: editor_note "TBD: add logical definition" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0000082
name: seedling density of an ecological community
def: "The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area." []
is_a: PCO:0000004 ! quality of an ecological community
is_a: PCO:0000078 ! seedling density
property_value: editor_note "TBD: add logical definition" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821
property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078

[Term]
id: PCO:0001000
name: pair of interacting organisms
def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." []
is_a: PCO:0000000 ! collection of organisms
intersection_of: PCO:0000000 ! collection of organisms
intersection_of: RO:0002351 CARO:0001010 {cardinality="2"} ! has member organism or virus or viroid

[Term]
id: PCO:0001001
name: pair of interacting organisms of the same species
def: "A pair of interacting  organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other." []
is_a: PCO:0000018 ! single-species collection of organisms
is_a: PCO:0001000 ! pair of interacting organisms
property_value: IAO:0000114 IAO:0000428

[Term]
id: PCO:1000000
name: migratory population
def: "A population which is participating in a migration process." []
is_a: PCO:0000001 ! population of organisms
relationship: RO:0000056 PCO:1000001 ! participates in population migration
property_value: IAO:0000114 IAO:0000123

[Term]
id: PCO:1000001
name: population migration
def: "A population process during which a population moves from one area to another." []
comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations.
is_a: PCO:0000005 ! population process
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Migration xsd:string

[Term]
id: PCO:1000002
name: human population migration
def: "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." []
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
is_a: PCO:1000001 ! population migration
relationship: RO:0000057 PCO:0000027 ! has participant collection of humans
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string

[Term]
id: PCO:1000003
name: human migratory population
def: "A migratory population of humans, travelling with the intention of settling in a new area." []
is_a: PCO:0000027 ! collection of humans
relationship: RO:0000056 PCO:1000002 ! participates in human population migration
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string

[Term]
id: PCO:1000004
name: microbial community
def: "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." []
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.
synonym: "microbiota" BROAD []
is_a: PCO:0000002 ! ecological community
is_a: PCO:0000051 ! multi-species collection of microbes
property_value: 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" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 xsd:string
property_value: IAO:0000119 http://dx.doi.org/10.1038/ismej.2009.88 xsd:string

[Term]
id: STATO:0000047
name: count
def: "a count is a data item denoted by an integer and represented the number of instances or occurences of an entity" []
is_a: IAO:0000109 ! measurement datum
property_value: IAO:0000112 "a count of 4 resulting from counting limbs in humans" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string
property_value: IAO:0000117 "Orlaith Burke" xsd:string
property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string
property_value: IAO:0000119 "STATO" xsd:string
property_value: STATO:0000032 "" xsd:string

[Typedef]
id: BFO:0000050
name: part of
def: "a core relation that holds between a part and its whole" []
property_value: 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." xsd:string
property_value: 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" xsd:string
property_value: 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.)\n\nA 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'." xsd:string
property_value: IAO:0000111 "is part of" xsd:string
property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string
property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string
property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string
property_value: IAO:0000118 "part_of" xsd:string
property_value: RO:0001900 RO:0001901
property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string
is_transitive: true
inverse_of: BFO:0000051 ! has part

[Typedef]
id: BFO:0000051
name: has part
def: "a core relation that holds between a whole and its part" []
property_value: 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." xsd:string
property_value: 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" xsd:string
property_value: 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.)\n\nA 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'." xsd:string
property_value: IAO:0000111 "has part" xsd:string
property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string
property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string
property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string
property_value: IAO:0000118 "has_part" xsd:string
property_value: RO:0001900 RO:0001901
is_transitive: true

[Typedef]
id: BFO:0000054
name: realized in
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
property_value: IAO:0000111 "realized in" xsd:string
property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string
property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string
property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string
property_value: IAO:0000118 "is realized by" xsd:string
property_value: IAO:0000118 "realized_in" xsd:string
property_value: IAO:0000600 "[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])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000017 ! realizable entity
range: BFO:0000015 ! process
inverse_of: BFO:0000055 ! realizes

[Typedef]
id: BFO:0000055
name: realizes
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
property_value: IAO:0000111 "realizes" xsd:string
property_value: IAO:0000112 "this disease course realizes this disease" xsd:string
property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string
property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string
property_value: IAO:0000600 "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])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl
domain: BFO:0000015 ! process
range: BFO:0000017 ! realizable entity

[Typedef]
id: BFO:0000062
name: preceded by
def: "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." []
subset: ro-eco
property_value: 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." xsd:string
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string
property_value: IAO:0000111 "preceded by" xsd:string
property_value: IAO:0000118 "is preceded by" xsd:string
property_value: IAO:0000118 "preceded_by" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
is_transitive: true
is_a: RO:0002086 ! ends after
inverse_of: BFO:0000063 ! precedes

[Typedef]
id: BFO:0000063
name: precedes
def: "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." []
subset: ro-eco
property_value: IAO:0000111 "precedes" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
is_transitive: true
is_a: RO:0002222 ! temporally related to

[Typedef]
id: BFO:0000066
name: occurs in
def: "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 a process and an independent continuant, in which the process takes place entirely within the independent continuant
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000111 "occurs in" xsd:string
property_value: IAO:0000118 "occurs_in" xsd:string
property_value: IAO:0000118 "unfolds in" xsd:string
property_value: IAO:0000118 "unfolds_in" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000003 ! occurrent
range: BFO:0000004 ! independent continuant
holds_over_chain: BFO:0000050 BFO:0000066
inverse_of: BFO:0000067 ! contains process
transitive_over: BFO:0000050 ! part of

[Typedef]
id: BFO:0000067
name: contains process
def: "[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
property_value: IAO:0000111 "site of" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Typedef]
id: IAO:0000136
name: is about
def: "A (currently) primitive relation that relates an information artifact to an entity." []
property_value: 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. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome 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." xsd:string
property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string

[Typedef]
id: PCO:0000055
name: obsolete has member of
property_value: IAO:0000231 IAO:0000103
is_obsolete: true

[Typedef]
id: RO:0000052
name: inheres in
def: "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" []
property_value: editor_note "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string
property_value: IAO:0000111 "inheres in" xsd:string
property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string
property_value: IAO:0000112 "this red color inheres in this apple" xsd:string
property_value: IAO:0000118 "inheres_in" xsd:string
property_value: RO:0001900 RO:0001901
inverse_of: RO:0000053 ! bearer of

[Typedef]
id: RO:0000053
name: bearer of
def: "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" []
property_value: 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." xsd:string
property_value: IAO:0000111 "bearer of" xsd:string
property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string
property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string
property_value: IAO:0000118 "bearer_of" xsd:string
property_value: IAO:0000118 "is bearer of" xsd:string
property_value: RO:0001900 RO:0001901
range: BFO:0000020 ! specifically dependent continuant

[Typedef]
id: RO:0000056
name: participates in
def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" []
property_value: IAO:0000111 "participates in" xsd:string
property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string
property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string
property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string
property_value: IAO:0000118 "participates_in" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
domain: BFO:0000002 ! continuant
range: BFO:0000003 ! occurrent
inverse_of: RO:0000057 ! has participant

[Typedef]
id: RO:0000057
name: has participant
def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" []
property_value: 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." xsd:string
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string
property_value: IAO:0000111 "has participant" xsd:string
property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string
property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string
property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string
property_value: IAO:0000118 "has_participant" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
domain: BFO:0000003 ! occurrent
range: BFO:0000002 ! continuant

[Typedef]
id: RO:0000058
name: is concretized as
def: "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." []
property_value: IAO:0000112 "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)." xsd:string
property_value: IAO:0000112 "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)." xsd:string
domain: BFO:0000031 ! generically dependent continuant
range: BFO:0000020 ! specifically dependent continuant
inverse_of: RO:0000059 ! concretizes

[Typedef]
id: RO:0000059
name: concretizes
def: "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." []
property_value: IAO:0000112 "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)." xsd:string
property_value: IAO:0000112 "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)." xsd:string
domain: BFO:0000020 ! specifically dependent continuant
range: BFO:0000031 ! generically dependent continuant

[Typedef]
id: RO:0000079
name: function of
def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" []
property_value: 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." xsd:string
property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string
property_value: IAO:0000118 "function_of" xsd:string
property_value: IAO:0000118 "is function of" xsd:string
domain: BFO:0000034 ! function
is_a: RO:0000052 ! inheres in
inverse_of: RO:0000085 ! has function

[Typedef]
id: RO:0000080
name: quality of
def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" []
property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string
property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string
property_value: IAO:0000118 "is quality of" xsd:string
property_value: IAO:0000118 "quality_of" xsd:string
is_a: RO:0000052 ! inheres in
inverse_of: RO:0000086 ! has quality

[Typedef]
id: RO:0000081
name: role of
def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" []
property_value: 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." xsd:string
property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string
property_value: IAO:0000118 "is role of" xsd:string
property_value: IAO:0000118 "role_of" xsd:string
is_a: RO:0000052 ! inheres in
inverse_of: RO:0000087 ! has role

[Typedef]
id: RO:0000085
name: has function
def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" []
property_value: 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." xsd:string
property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string
property_value: IAO:0000118 "has_function" xsd:string
domain: BFO:0000004 ! independent continuant
range: BFO:0000034 ! function
is_a: RO:0000053 ! bearer of

[Typedef]
id: RO:0000086
name: has quality
def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" []
property_value: 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." xsd:string
property_value: IAO:0000112 "this apple has quality this red color" xsd:string
property_value: IAO:0000118 "has_quality" xsd:string
range: BFO:0000019 ! quality
is_a: RO:0000053 ! bearer of

[Typedef]
id: RO:0000087
name: has role
def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" []
property_value: 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." xsd:string
property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string
property_value: IAO:0000118 "has_role" xsd:string
domain: BFO:0000004 ! independent continuant
range: BFO:0000023 ! role
is_a: RO:0000053 ! bearer of

[Typedef]
id: RO:0000091
name: has disposition
def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" []
domain: BFO:0000004 ! independent continuant
range: BFO:0000016 ! disposition
is_a: RO:0000053 ! bearer of
inverse_of: RO:0000092 ! disposition of

[Typedef]
id: RO:0000092
name: disposition of
is_a: RO:0000052 ! inheres in

[Typedef]
id: RO:0001000
name: derives from
def: "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" []
property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string
property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string
property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000118 "derives_from" xsd:string
inverse_of: RO:0001001 ! derives into

[Typedef]
id: RO:0001001
name: derives into
def: "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" []
property_value: 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'." xsd:string
property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string
property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000118 "derives_into" xsd:string

[Typedef]
id: RO:0001015
name: location of
def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" []
property_value: 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" xsd:string
property_value: IAO:0000111 "is location of" xsd:string
property_value: IAO:0000112 "my head is the location of my brain" xsd:string
property_value: IAO:0000112 "this cage is the location of this rat" xsd:string
property_value: IAO:0000118 "location_of" xsd:string
property_value: RO:0001900 RO:0001901
is_transitive: true
inverse_of: RO:0001025 ! located in

[Typedef]
id: RO:0001025
name: located in
def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" []
property_value: 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" xsd:string
property_value: 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" xsd:string
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string
property_value: IAO:0000111 "located in" xsd:string
property_value: IAO:0000112 "my brain is located in my head" xsd:string
property_value: IAO:0000112 "this rat is located in this cage" xsd:string
property_value: IAO:0000118 "located_in" xsd:string
property_value: RO:0001900 RO:0001901
domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="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."} ! independent continuant
range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="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."} ! independent continuant
is_transitive: true

[Typedef]
id: RO:0002000
name: 2D boundary of
def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" []
property_value: 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." xsd:string
property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string
property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string
property_value: IAO:0000118 "2D_boundary_of" xsd:string
property_value: IAO:0000118 "boundary of" xsd:string
property_value: IAO:0000118 "is 2D boundary of" xsd:string
property_value: IAO:0000118 "is boundary of" xsd:string
property_value: RO:0001900 RO:0001901
inverse_of: RO:0002002 ! has 2D boundary

[Typedef]
id: RO:0002002
name: has 2D boundary
def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" []
property_value: 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." xsd:string
property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string
property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string
property_value: IAO:0000118 "has boundary" xsd:string
property_value: IAO:0000118 "has_2D_boundary" xsd:string
property_value: RO:0001900 RO:0001901
domain: BFO:0000040 ! material entity
range: BFO:0000141 ! immaterial entity

[Typedef]
id: RO:0002022
name: directly regulated by
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. {xref="GOC:dos"}
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002334 ! regulated by
inverse_of: RO:0002578 ! directly regulates
created_by: dos
creation_date: 2017-09-17T13:52:24Z

[Typedef]
id: RO:0002023
name: directly negatively regulated by
def: "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." [GOC:dos]
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002022 ! directly regulated by
inverse_of: RO:0002630 ! directly negatively regulates
created_by: dos
creation_date: 2017-09-17T13:52:38Z

[Typedef]
id: RO:0002024
name: directly positively regulated by
def: "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." [GOC:dos]
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002022 ! directly regulated by
inverse_of: RO:0002629 ! directly positively regulates
created_by: dos
creation_date: 2017-09-17T13:52:47Z

[Typedef]
id: RO:0002086
name: ends after
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_transitive: true
is_a: RO:0002222 ! temporally related to

[Typedef]
id: RO:0002087
name: immediately preceded by
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "starts_at_end_of" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: BFO:0000062 ! preceded by
inverse_of: RO:0002090 ! immediately precedes

[Typedef]
id: RO:0002090
name: immediately precedes
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "ends_at_start_of" xsd:string
property_value: IAO:0000118 "meets" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0002575 BFO:0000063
is_a: BFO:0000063 ! precedes

[Typedef]
id: RO:0002131
name: overlaps
def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_gocam
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0001900 RO:0001901
is_a: RO:0002323 ! mereotopologically related to
expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" []

[Typedef]
id: RO:0002211
name: regulates
def: "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." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: 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" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "David Hill" xsd:string
property_value: IAO:0000117 "Tanya Berardini" xsd:string
property_value: IAO:0000119 "GO" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string
property_value: IAO:0000589 "regulates (processual)" xsd:string
property_value: IAO:0000600 "false" xsd:boolean
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
domain: BFO:0000015 ! process
range: BFO:0000015 ! process
holds_over_chain: RO:0002578 RO:0002578
is_transitive: true
is_a: RO:0002411 ! causally upstream of
inverse_of: RO:0002334 ! regulated by

[Typedef]
id: RO:0002212
name: negatively regulates
def: "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." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0004050 RO:0002211
is_a: RO:0002211 ! regulates
is_a: RO:0002305 ! causally upstream of, negative effect
inverse_of: RO:0002335 ! negatively regulated by

[Typedef]
id: RO:0002213
name: positively regulates
def: "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." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "positively regulates (process to process)" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0004049 RO:0002211
holds_over_chain: RO:0002212 RO:0002212
is_transitive: true
is_a: RO:0002211 ! regulates
is_a: RO:0002304 ! causally upstream of, positive effect
inverse_of: RO:0002336 ! positively regulated by

[Typedef]
id: RO:0002215
name: capable of
def: "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. " []
subset: ro-eco
property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string
property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has function realized in" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450
property_value: IAO:0000232 "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)\"." xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
domain: BFO:0000004 ! independent continuant
range: BFO:0000015 ! process
is_a: RO:0002216 ! capable of part of

[Typedef]
id: RO:0002216
name: capable of part of
def: "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." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has function in" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: seeAlso "defining-property-chains-involving-reflexivity"
is_a: RO:0002328 ! functionally related to
is_a: RO:0002500 ! causal agent in process

[Typedef]
id: RO:0002222
name: temporally related to
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
subset: ro-eco
property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra
property_value: IAO:0000232 "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." xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent

[Typedef]
id: RO:0002233
name: has input
def: "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." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "consumes" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
domain: BFO:0000015 ! process
is_a: RO:0000057 ! has participant
inverse_of: RO:0002352 ! input of

[Typedef]
id: RO:0002263
name: acts upstream of
def: "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." []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: IAO:0000112 "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." xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of
holds_over_chain: RO:0002327 RO:0002411
is_a: RO:0002264 ! acts upstream of or within

[Typedef]
id: RO:0002264
name: acts upstream of or within
def: "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." []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
synonym: "affects" RELATED []
property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within
holds_over_chain: RO:0002327 RO:0002418
is_a: RO:0002500 ! causal agent in process

[Typedef]
id: RO:0002304
name: causally upstream of, positive effect
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
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: http://purl.org/dc/terms/creator "cjm" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0004049 RO:0002411
is_a: RO:0002411 ! causally upstream of
is_a: RO:0004047 ! causally upstream of or within, positive effect

[Typedef]
id: RO:0002305
name: causally upstream of, negative effect
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
property_value: http://purl.org/dc/terms/creator "cjm" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0004050 RO:0002411
is_a: RO:0002411 ! causally upstream of
is_a: RO:0004046 ! causally upstream of or within, negative effect

[Typedef]
id: RO:0002321
name: ecologically related to
def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" []
subset: ro-eco
property_value: editor_note "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string

[Typedef]
id: RO:0002323
name: mereotopologically related to
def: "A mereological relationship or a topological relationship" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0001900 RO:0001901

[Typedef]
id: RO:0002327
name: enables
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "catalyzes" xsd:string
property_value: IAO:0000118 "executes" xsd:string
property_value: IAO:0000118 "has" xsd:string
property_value: IAO:0000118 "is catalyzing" xsd:string
property_value: IAO:0000118 "is executing" xsd:string
property_value: IAO:0000232 "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." xsd:string
property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002215 ! capable of
inverse_of: RO:0002333 ! enabled by

[Typedef]
id: RO:0002328
name: functionally related to
def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl

[Typedef]
id: RO:0002329
name: part of structure that is capable of
def: "this relation holds between c and p when c is part of some c', and c' is capable of p." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "false" xsd:boolean
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002331
name: involved in
def: "c involved_in p if and only if c enables some process p', and p' is part of p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "actively involved in" xsd:string
property_value: IAO:0000118 "enables part of" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: seeAlso Involved:in
is_a: RO:0000056 ! participates in
is_a: RO:0002431 ! involved in or involved in regulation of

[Typedef]
id: RO:0002333
name: enabled by
def: "inverse of enables" []
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0000057 ! has participant
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002334
name: regulated by
def: "inverse of regulates" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000589 "regulated by (processual)" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
domain: BFO:0000015 ! process
range: BFO:0000015 ! process
is_transitive: true
is_a: RO:0002427 ! causally downstream of or within

[Typedef]
id: RO:0002335
name: negatively regulated by
def: "inverse of negatively regulates" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002334 ! regulated by

[Typedef]
id: RO:0002336
name: positively regulated by
def: "inverse of positively regulates" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002334 ! regulated by

[Typedef]
id: RO:0002350
name: member of
def: "is member of is a mereological relation between a item and a collection." []
property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string
property_value: IAO:0000118 "is member of" xsd:string
property_value: IAO:0000118 "member part of" xsd:string
property_value: IAO:0000119 "SIO" xsd:string
property_value: RO:0001900 RO:0001901
is_a: BFO:0000050 ! part of
inverse_of: RO:0002351 ! has member

[Typedef]
id: RO:0002351
name: has member
def: "has member is a mereological relation between a collection and an item." []
property_value: IAO:0000119 "SIO" xsd:string
property_value: RO:0001900 RO:0001901
is_a: BFO:0000051 ! has part

[Typedef]
id: RO:0002352
name: input of
def: "inverse of has input" []
subset: ro-eco
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0000056 ! participates in
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002404
name: causally downstream of
def: "inverse of upstream of" []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: BFO:0000062 ! preceded by
is_a: RO:0002427 ! causally downstream of or within
inverse_of: RO:0002411 ! causally upstream of

[Typedef]
id: RO:0002405
name: immediately causally downstream of
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002087 ! immediately preceded by
is_a: RO:0002404 ! causally downstream of
inverse_of: RO:0002412 ! immediately causally upstream of

[Typedef]
id: RO:0002410
name: causally related to
def: "This relation groups causal relations between material entities and causal relations between processes" []
property_value: 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.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe 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.\n\nFor 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.\n\nFor 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.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl

[Typedef]
id: RO:0002411
name: causally upstream of
def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_transitive: true
is_a: BFO:0000063 ! precedes
is_a: RO:0002418 ! causally upstream of or within

[Typedef]
id: RO:0002412
name: immediately causally upstream of
def: "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." []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0002575 RO:0002411
is_a: RO:0002090 ! immediately precedes
is_a: RO:0002411 ! causally upstream of

[Typedef]
id: RO:0002418
name: causally upstream of or within
def: "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." []
synonym: "affects" RELATED []
property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "influences (processual)" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_transitive: true
is_a: RO:0002501 ! causal relation between processes
inverse_of: RO:0002427 ! causally downstream of or within

[Typedef]
id: RO:0002427
name: causally downstream of or within
def: "inverse of causally upstream of or within" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_transitive: true
is_a: RO:0002501 ! causal relation between processes

[Typedef]
id: RO:0002428
name: involved in regulation of
def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
holds_over_chain: RO:0002327 RO:0002211
holds_over_chain: RO:0002331 RO:0002211
is_a: RO:0002263 ! acts upstream of
is_a: RO:0002431 ! involved in or involved in regulation of

[Typedef]
id: RO:0002429
name: involved in positive regulation of
def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0004049 RO:0002428
holds_over_chain: RO:0002327 RO:0002213
holds_over_chain: RO:0002331 RO:0002213
is_a: RO:0002428 ! involved in regulation of

[Typedef]
id: RO:0002430
name: involved in negative regulation of
def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0004050 RO:0002428
holds_over_chain: RO:0002327 RO:0002212
holds_over_chain: RO:0002331 RO:0002212
is_a: RO:0002428 ! involved in regulation of

[Typedef]
id: RO:0002431
name: involved in or involved in regulation of
def: "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" []
property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "involved in or reguates" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002264 ! acts upstream of or within
is_a: RO:0002328 ! functionally related to
is_a: RO:0002500 ! causal agent in process

[Typedef]
id: RO:0002432
name: is active in
def: "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." [GOC:cjm, GOC:dos]
synonym: "enables activity in" EXACT []
property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "executes activity in" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"}
is_a: RO:0002131 ! overlaps
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002434
name: interacts with
def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." []
subset: ro-eco
synonym: "in pairwise interaction with" EXACT []
property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI
property_value: 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." xsd:string
property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "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." xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_symmetric: true

[Typedef]
id: RO:0002436
name: molecularly interacts with
def: "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." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "binds" xsd:string
property_value: IAO:0000118 "molecularly binds with" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: seeAlso ECO:0000353
property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI
is_symmetric: true
is_a: RO:0002434 ! interacts with

[Typedef]
id: RO:0002447
name: phosphorylates
property_value: editor_note "Axiomatization to GO to be added later" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002436 ! molecularly interacts with

[Typedef]
id: RO:0002448
name: directly regulates activity of
def: "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.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." []
synonym: "molecularly controls" EXACT []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "Vasundra Touré" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: RO:0002436 ! molecularly interacts with
is_a: RO:0011002 ! regulates activity of

[Typedef]
id: RO:0002449
name: directly negatively regulates activity of
def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." []
synonym: "molecularly decreases activity of" EXACT []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "Vasundra Touré" xsd:string
property_value: IAO:0000118 "directly inhibits" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: RO:0002448 ! directly regulates activity of

[Typedef]
id: RO:0002450
name: directly positively regulates activity of
def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." []
synonym: "molecularly increases activity of" EXACT []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "Vasundra Touré" xsd:string
property_value: IAO:0000118 "directly activates" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: RO:0002448 ! directly regulates activity of

[Typedef]
id: RO:0002464
name: helper property (not for use in curation)
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl

[Typedef]
id: RO:0002479
name: has part that occurs in
def: "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." []
subset: ro-eco
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
domain: BFO:0000003 ! occurrent
range: BFO:0000004 ! independent continuant

[Typedef]
id: RO:0002481
name: is kinase activity
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002564 ! molecular interaction relation helper property

[Typedef]
id: RO:0002500
name: causal agent in process
def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" []
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002595 ! causal relation between material entity and a process
inverse_of: RO:0002608 ! process has causal agent

[Typedef]
id: RO:0002501
name: causal relation between processes
def: "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." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002506
name: causal relation between entities
property_value: 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" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
domain: BFO:0000002 ! continuant
range: BFO:0000002 ! continuant
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002559
name: causally influenced by
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002506 ! causal relation between entities
inverse_of: RO:0002566 ! causally influences

[Typedef]
id: RO:0002563
name: interaction relation helper property
property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29
is_a: RO:0002464 ! helper property (not for use in curation)

[Typedef]
id: RO:0002564
name: molecular interaction relation helper property
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002563 ! interaction relation helper property

[Typedef]
id: RO:0002566
name: causally influences
def: "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)." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "Vasundra Touré" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
domain: BFO:0000002 ! continuant
range: BFO:0000002 ! continuant
is_a: RO:0002506 ! causal relation between entities

[Typedef]
id: RO:0002578
name: directly regulates
def: "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." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly regulates (processual)" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0002575 RO:0002211
is_a: RO:0002211 ! regulates
is_a: RO:0002412 ! immediately causally upstream of

[Typedef]
id: RO:0002584
name: has part structure that is capable of
def: "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" []
property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002328 ! functionally related to
is_a: RO:0002595 ! causal relation between material entity and a process

[Typedef]
id: RO:0002595
name: causal relation between material entity and a process
def: "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." []
property_value: 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." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
domain: BFO:0000040 ! material entity
range: BFO:0000015 ! process
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002596
name: capable of regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." []
property_value: IAO:0000112 "pyrethroid -> growth" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
holds_over_chain: RO:0002215 RO:0002211
is_a: RO:0002500 ! causal agent in process

[Typedef]
id: RO:0002597
name: capable of negatively regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." []
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
holds_over_chain: RO:0002215 RO:0002212
is_a: RO:0002596 ! capable of regulating

[Typedef]
id: RO:0002598
name: capable of positively regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." []
property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
holds_over_chain: RO:0002215 RO:0002213
is_a: RO:0002596 ! capable of regulating

[Typedef]
id: RO:0002608
name: process has causal agent
def: "Inverse of 'causal agent in process'" []
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002629
name: directly positively regulates
def: "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." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0004049 RO:0002578
is_a: RO:0002213 ! positively regulates
is_a: RO:0002578 ! directly regulates

[Typedef]
id: RO:0002630
name: directly negatively regulates
def: "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." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0004050 RO:0002578
is_a: RO:0002212 ! negatively regulates
is_a: RO:0002578 ! directly regulates

[Typedef]
id: RO:0004031
name: enables subfunction
def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." []
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002328 ! functionally related to
created_by: cjm
creation_date: 2018-01-25T23:20:13Z

[Typedef]
id: RO:0004032
name: acts upstream of or within, positive effect
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0004049 RO:0002264
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect
holds_over_chain: RO:0002327 RO:0004047
is_a: RO:0002264 ! acts upstream of or within
created_by: cjm
creation_date: 2018-01-26T23:49:30Z

[Typedef]
id: RO:0004033
name: acts upstream of or within, negative effect
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0004050 RO:0002264
holds_over_chain: RO:0002327 RO:0004046
is_a: RO:0002264 ! acts upstream of or within
created_by: cjm
creation_date: 2018-01-26T23:49:51Z

[Typedef]
id: RO:0004034
name: acts upstream of, positive effect
def: "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" []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0004049 RO:0002263
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect
holds_over_chain: RO:0002327 RO:0002304
is_a: RO:0002263 ! acts upstream of
is_a: RO:0004032 ! acts upstream of or within, positive effect
created_by: cjm
creation_date: 2018-01-26T23:53:14Z

[Typedef]
id: RO:0004035
name: acts upstream of, negative effect
def: "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" []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0004050 RO:0002263
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect
holds_over_chain: RO:0002327 RO:0002305
is_a: RO:0002263 ! acts upstream of
is_a: RO:0004033 ! acts upstream of or within, negative effect
created_by: cjm
creation_date: 2018-01-26T23:53:22Z

[Typedef]
id: RO:0004046
name: causally upstream of or within, negative effect
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0004050 RO:0002418
is_a: RO:0002418 ! causally upstream of or within
created_by: cjm
creation_date: 2018-03-13T23:55:05Z

[Typedef]
id: RO:0004047
name: causally upstream of or within, positive effect
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
property_value: RO:0004049 RO:0002418
is_a: RO:0002418 ! causally upstream of or within
created_by: cjm
creation_date: 2018-03-13T23:55:19Z

[Typedef]
id: RO:0011002
name: regulates activity of
def: "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." []
property_value: IAO:0000117 "Vasundra Touré" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: RO:0002566 ! causally influences

[Typedef]
id: decreased_in_magnitude_relative_to
name: decreased_in_magnitude_relative_to
namespace: quality
def: "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." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
domain: PATO:0000001 ! quality
range: PATO:0000001 ! quality
is_transitive: true
is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to

[Typedef]
id: different_in_magnitude_relative_to
name: different_in_magnitude_relative_to
namespace: quality
def: "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." [PATOC:CJM]
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
domain: PATO:0000001 ! quality
range: PATO:0000001 ! quality

[Typedef]
id: editor_note
name: editor note
namespace: uberon
def: "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." []
xref: IAO:0000116
property_value: IAO:0000111 "editor note" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string
property_value: IAO:0000119 GROUP:OBI:<http://purl.obfoundry.org/obo/obi> xsd:string
property_value: IAO:0000119 GROUP:OBI:<http://purl.obofoundry.org/obo/obi> xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl
is_metadata_tag: true

[Typedef]
id: increased_in_magnitude_relative_to
name: increased_in_magnitude_relative_to
namespace: quality
def: "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." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl
domain: PATO:0000001 ! quality
range: PATO:0000001 ! quality
is_transitive: true
is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to

[Typedef]
id: reciprocal_of
name: reciprocal_of
namespace: quality
def: "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." [PATOC:CJM]
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.
property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl