(obolog_version "0.01")
(module ro)
;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; is_a and instance_of
;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(relation is_a)
(label is_a "is_a")
(transitive is_a)
(anti_symmetric is_a)
(reflexive is_a)
(comment is_a "The is_a relationship is considered axiomatic by the obo file format specification. In the representation of obo in OWL, where obo terms are represented as OWL classes, is_a is mapped on to the subClassOf axiom")
(example is_a (is_a "astrocyte" "glial cell") "CL")
(example is_a (is_a "serotonin" "biogenic amine") "CHEBI")
(example is_a (is_a "catabolic process" "metabolic process") "GO")
(exact_synonym is_a "is_subtype_of")
(exact_synonym is_a "subtype_of")
(exact_synonym is_a "is_a_kind_of")
(exact_synonym is_a "kind_of")
(exact_synonym is_a "type_of")
(exported_identifier is_a "OBO_REL_C:0000001")
(alternate_identifier is_a "OBO_REL:is_a")
(xref is_a "rdfs:subClassOf")
(text_definition is_a "For continuants: C is_a C' if and only if: given any c that instantiates C at a time t, c instantiates C' at t. For processes: P is_a P' if and only if: that given any p that instantiates P, then p instantiates P'.")
(text_definition_xref is_a "PMID:15892874")
(type_type is_a)
(atemporal is_a)
(=>
(is_a ?X ?Y)
(=> (instance_of ?i ?X)
(instance_of ?i ?Y)))
(=>
(is_a ?X ?Y)
(=> (instance_of ?i ?X ?t)
(instance_of ?i ?Y ?t)))
(relation instance_of)
(label instance_of "instance_of")
(comment instance_of "The instance_of relationship is considered axiomatic by the obo file format specification; ie it is taken for granted. The is_a relation is still included in this ontology for completeness")
(xref instance_of "rdf:type")
(example instance_of (instance_of "John Doe's heart" "Heart [FMA]"))
(example instance_of (instance_of "Lake Geneva [GAZ:1234567]" "freshwater lake [ENO:98765432]") "GAZ")
(exported_identifier instance_of "OBO_REL_I:0000023")
(text_definition instance_of "A relation between an instance and a class/type. For components: a primitive relation between a component instance and a class which it instantiates at a specific time. For processes: a primitive relation, between a process instance and a class which it instantiates, holding independently of time")
(text_definition_xref instance_of "PMID:15892874")
(instance_type instance_of)
(atemporal_or_temporal instance_of)
(instance_type instance_of)
;(holds_temporally_between instance_of Continuant type)
;(holds_atemporally_between instance_of Occurrent type)
;; @Axiom: continuants temporally instantiate types
(=> (instance_of ?x ?U ?t) (is_a ?U Continuant))
;; @Axiom: occurrents (processes, stages, etc) atemporally instantiate types
(=> (instance_of ?x ?U) (is_a ?U Occurrent))
;; @Axiom:
;; http://www.acsu.buffalo.edu/~bittner3/Theories/BFO/Instantiation.html
;; lemma Inst_IsA_rule: [instantiation]
;; process instantiation: binary
(=>
(and (instance_of ?i ?X)
(is_a ?X ?Y))
(instance_of ?i ?Y))
;; continuant instantiation: time-indexed
(=>
(and (instance_of ?i ?X ?t)
(is_a ?X ?Y))
(instance_of ?i ?Y ?t))
;;(relation identical_to)
;;(instance_instance identical_to)
;;(exported_identifier transformation_of "OBO_REL_I:0000013")
;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; part_of
;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(relation part_of)
(label part_of "part_of")
(exact_synonym part_of "is_part_of")
(inverse_of part_of has_part)
(normative_direction_for part_of "part")
(normative part_of)
(transitive part_of)
(anti_symmetric part_of)
(example part_of (part_of "John Doe's Heart" "John Doe's Body" t1))
(example part_of (part_of "John Doe's childhood" "John Doe's lifespan"))
(comment
(anti_symmetric part_of)
"not included in Bittner and Donnelly / Logical properties of foundational relations: We do not include an axiom of antisymmetry for parthood among objects, since we want to leave open the possibility that there may be distinct objects which have exactly the same parts at a given time. For example, the FMA distinguishes between an anatomical entity and the tissue which constitutes that entity at a given time (Rosse and Mejino, 2003)")
(reflexive part_of)
(exported_identifier part_of "OBO_REL_I:0000002")
(alternate_identifier part_of "OBO_REL:part_of")
(comment part_of "The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t.")
(text_definition part_of "part_of on the instance level is a primitive relation, holding either atemporally between two process instances or temporally between two continuant instances")
(text_definition_xref part_of "PMID:15892874")
(instance_instance part_of)
(homeomorphic_for part_of IndependentContinuant)
(homeomorphic_for part_of DependentContinuant)
(homeomorphic_for part_of Occurrent)
(homeomorphic_for part_of Process)
(homeomorphic_for part_of Role)
(homeomorphic_for part_of Quality)
(homeomorphic_for part_of RealizableEntity)
(homeomorphic_for part_of SpatialRegion)
(homeomorphic_for part_of ProcessualEntity)
(atemporal_or_temporal part_of)
(holds_temporally_between part_of Continuant Continuant)
;;ilc_part(x,y, w) -> (I1r(Continuant, x) & I1r(Continuant, y) & I1o(Timepoint, w)). ;; Neuhaus
(=> (part_of ?x ?y ?w)
(and (instance_of ?x Continuant)
(instance_of ?y Continuant)
(instance_of ?w TemporalInstant)))
(holds_atemporally_between part_of Occurrent Occurrent)
;;ilc_part(x,y, w) -> exists_at(x,w) & exists_at(y,w).
(=> (part_of ?x ?y ?w)
(and (exists_at ?x ?w)
(exists_at ?y ?w)))
(never_holds_between Entity Function)
(never_holds_between Entity Disposition)
(relation part_of_some)
(type_type part_of_some)
(holds_over part_of_some part_of)
(label part_of_some "part_of")
(transitive part_of_some)
(anti_symmetric part_of_some)
(reflexive part_of_some)
(example part_of_some (part_of_some "mitochondrial matrix" "mitochodrion") "GO")
(example part_of_some (part_of_some "transcription" "gene expression") "GO")
(example part_of_some (part_of_some "cell nucleus" "cell") "GO")
(example part_of_some (part_of_some "heart ventricle" "heart") "MA")
(comment part_of_some "To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell.")
(exported_identifier part_of_some "OBO_REL_C:0000002")
(text_definition part_of_some "For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c part_of c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p part_of p' at t. (Here part_of is the instance-level part-relation, @OBO_REL_I:0000002@).")
(text_definition_xref part_of_some "PMID:15892874")
(all_some_all_times part_of_some part_of)
(all_some part_of_some part_of)
(relation has_part)
(instance_instance has_part)
(label has_part "has_part")
(inverse_of has_part part_of)
(transitive has_part)
(anti_symmetric has_part)
(reflexive has_part)
(exported_identifier has_part "OBO_REL_I:0000003")
(comment has_part "primitive instance-level relation, the inverse of *part_of*")
(atemporal_or_temporal has_part)
(relation has_part_some)
(type_type has_part_some)
(holds_over has_part_some has_part)
(all_some_all_times has_part_some has_part)
(label has_part_some "has_part")
(transitive has_part_some)
(anti_symmetric has_part_some)
(reflexive has_part_some)
(example has_part_some (has_part_some "nucleate cell" "nucleus") "CL")
(example has_part_some (has_part_some "cell" "cytoplasm") "GO")
(exported_identifier has_part_some "OBO_REL_C:0000003")
(text_definition has_part_some "C has_part_some C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *has_part* c' at t. For processes: P has_part_some P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *has_part* p' at t. (Here *has_part* is the instance-level part-relation, @OBO_REL_I:0000003@)")
(relation integral_part_of)
(type_type integral_part_of)
(type_level_only integral_part_of)
(label integral_part_of "integral_part_of")
(subrelation integral_part_of part_of_some)
(transitive integral_part_of)
(anti_symmetric integral_part_of)
(reflexive integral_part_of)
(inverse_of integral_part_of has_integral_part)
(inverse_always_true integral_part_of part_of_some)
(holds_bidirectionally_for integral_part_of part_of_some has_part_some)
(normative_direction_for integral_part_of "integral_part")
(exported_identifier integral_part_of "OBO_REL_C:0000004")
(text_definition integral_part_of "C integral_part_of C' if and only if: C part_of C' AND C' has_part C")
(text_definition_xref integral_part_of "PMID:15892874")
(example integral_part_of (integral_part_of "heart morphogenesis" "heart development") "GO")
(<=> (integral_part_of ?X ?Y)
(and (part_of_some ?X ?Y)
(has_part_some ?Y ?X)))
(relation has_integral_part)
(type_type has_integral_part)
(type_level_only has_integral_part)
(label has_integral_part "has_integral_part")
(subrelation has_integral_part has_part_some)
(transitive has_integral_part)
(anti_symmetric has_integral_part)
(reflexive has_integral_part)
(exported_identifier has_integral_part "OBO_REL_C:0000005")
(text_definition has_integral_part "Type level inverse of integral_part_of. C has_integral_part C' if and only if: C has_part C' AND C' part_of C")
(<=> (has_integral_part ?X ?Y)
(and (part_of_some ?Y ?X)
(has_part_some ?X ?Y)))
(relation proper_part_of)
(instance_instance proper_part_of)
(label proper_part_of "proper_part_of")
(subrelation proper_part_of part_of)
(inverse_of proper_part_of has_proper_part)
(normative_direction_for proper_part_of "proper_part")
(transitive proper_part_of)
(proper_subrelation proper_part_of part_of)
(exported_identifier proper_part_of "OBO_REL_I:0000006")
(text_definition proper_part_of "As for part_of, with the additional constraint that subject and object are distinct")
(text_definition_xref proper_part_of "PMID:15892874")
(<=> (proper_part_of ?x ?y)
(and (part_of ?x ?y)
(not (part_of ?y ?x))))
(relation proper_part_of_some)
(type_type proper_part_of_some)
(all_some proper_part_of_some proper_part_of)
(label proper_part_of_some "proper_part_of")
(subrelation proper_part_of_some part_of_some)
(transitive proper_part_of_some)
(exported_identifier proper_part_of_some "OBO_REL_C:0000006")
(text_definition proper_part_of_some "As for part_of_some, with the additional constraint that subject and object are distinct")
(text_definition_xref proper_part_of_some "PMID:15892874")
(relation has_proper_part)
(instance_instance has_proper_part)
(label has_proper_part "has_proper_part")
(subrelation has_proper_part has_part)
(inverse_of has_proper_part proper_part_of)
(transitive has_proper_part)
(text_definition has_proper_part "As for has_part, with the additional constraint that subject and object are distinct")
(exported_identifier has_proper_part "OBO_REL_I:0000007")
(relation has_proper_part_some)
(type_type has_proper_part_some)
(all_some has_proper_part_some has_proper_part)
(label has_proper_part_some "has_proper_part")
(subrelation has_proper_part_some has_part_some)
(transitive has_proper_part_some)
(exported_identifier has_proper_part_some "OBO_REL_C:0000007")
;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; spatial
;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(relation adjacent_to)
(instance_instance adjacent_to)
(label adjacent_to "adjacent_to")
(symmetric adjacent_to)
(comment adjacent_to
"Note that adjacent_to is only symmetric at the instance level")
(exported_identifier adjacent_to "OBO_REL_I:0000012")
(text_definition adjacent_to "c adjacent to c' if and only if: c and c' are in spatial proximity")
(domain adjacent_to IndependentContinuant)
(range adjacent_to IndependentContinuant)
(=> (adjacent_to ?x ?y)
(not (overlaps ?x ?y)))
(relation adjacent_to_some)
(type_type adjacent_to_some)
(all_some_all_times adjacent_to_some adjacent_to)
(label adjacent_to_some "adjacent_to")
(comment adjacent_to_some
"Note that adjacent_to_some as defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to_some cytoplasm; seminal vesicle adjacent_to_some urinary bladder; ovary adjacent_to_some parietal pelvic peritoneum")
(exported_identifier adjacent_to_some "OBO_REL_C:0000012")
(text_definition adjacent_to_some "C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity")
(text_definition_xref adjacent_to_some "PMID:15892874")
(relation contained_in)
(instance_instance contained_in)
(label contained_in "contained_in")
(inverse_of contained_in contains)
(normative_direction_for contained_in "containment")
(comment contained_in "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):")
(exported_identifier contained_in "OBO_REL_I:0000010")
(text_definition contained_in "c contained_in c' at t if and only if: c located_in c' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.)")
(text_definition_xref contained_in "PMID:15892874")
(holds_temporally contained_in)
(domain contained_in IndependentContinuant)
(range contained_in IndependentContinuant)
(<=> (contained_in ?x ?y ?t)
(and (located_in ?x ?y ?t)
(not (overlaps ?x ?y ?t))))
(relation contained_in_some)
(type_type contained_in_some)
(holds_over contained_in_some contained_in)
(all_some_all_times contained_in_some contained_in)
(label contained_in_some "contained_in")
(exported_identifier contained_in_some "OBO_REL_C:0000010")
(text_definition contained_in_some "C contained_in_some C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c located_in c' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.)")
(text_definition_xref contained_in_some "PMID:15892874")
(relation contains)
(instance_instance contains)
(label contains "contains")
(inverse_of contains contained_in)
(exported_identifier contains "OBO_REL_I:0000011")
(relation contains_some)
(type_type contains_some)
(label contains_some "contains")
(exported_identifier contains_some "OBO_REL_C:0000011")
(relation located_in)
(label located_in "located_in")
(domain located_in Continuant)
(range located_in IndependentContinuant)
(inverse_of located_in location_of)
(normative_direction_for located_in "location")
(transitive located_in)
(reflexive located_in)
(transitive_over located_in part_of)
(comment located_in "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")
(exported_identifier located_in "OBO_REL_I:0000008")
(text_definition located_in "Primitive")
(text_definition_xref located_in "PMID:15892874")
(<=> (located_in ?c ?c1)
(part_of (regionFn ?c) (regionFn ?c1)))
(relation located_in_some)
(type_type located_in_some)
(all_some_all_times located_in_some located_in)
(label located_in_some "located_in")
(type_domain located_in_some Continuant)
(type_range located_in_some Continuant)
(transitive located_in_some)
(reflexive located_in_some)
(transitive_over located_in_some part_of_some)
(exported_identifier located_in_some "OBO_REL_C:0000008")
(text_definition located_in_some "C located_in_some C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)")
(text_definition_xref located_in "PMID:15892874")
(relation location_of)
(label location_of "location_of")
(domain location_of Continuant)
(range location_of Continuant)
(inverse_of location_of located_in)
(transitive location_of)
(reflexive location_of)
(exported_identifier location_of "OBO_REL_I:0000009")
(relation location_of_some)
(type_type location_of_some)
(all_some_all_times location_of_some location_of)
(label location_of_some "location_of")
(type_domain location_of_some Continuant)
(type_range location_of_some Continuant)
(transitive location_of_some)
(reflexive location_of_some)
(text_definition location_of_some "C location_of_some C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *location_of* c'. (Here *location_of* is the instance-level location relation, @OBO_REL_I:0000009@.)")
(exported_identifier location_of_some "OBO_REL_C:0000009")
(relation overlaps)
(label overlaps "overlaps")
(domain overlaps IndependentContinuant)
(range overlaps IndependentContinuant)
(symmetric overlaps)
(reflexive overlaps)
(intransitive overlaps)
(text_definition overlaps "x overlaps y if and only if: there is some z such that: z part_of x and z part_of y (i.e. x and y share a part)")
(comment overlaps "note that the definition of overlaps includes the case where x is part_of y - for example, a nucleus overlaps a cell. We also have the *partial_overlaps* relation for those cases where x and y overlap but neither is part of the other")
(exported_identifier overlaps "OBO_REL_I:0000201")
(<=> (overlaps ?x ?y)
(exists (?z) (and (part_of ?z ?x)
(part_of ?z ?y))))
;; AM4 in Bittner and Donnelly / Logical properties of foundational relations
(=> (and (exists_at ?x ?t)
(forall (?z)
(=> (overlaps ?z ?x ?t)
(overlaps ?y ?x ?t))))
(part_of ?x ?y ?t))
(relation overlaps_some)
(type_type overlaps_some)
(label overlaps_some "overlaps")
(comment overlaps_some "Note that overlaps is symmetric on the instance level but not the type level")
(all_some_all_times overlaps_some overlaps)
(reflexive overlaps_some)
(example overlaps_some "uterine tract overlaps urogenital system but NOT urogenital system overlaps uterine tracts")
(exported_identifier overlaps_some "OBO_REL_C:0000201")
(relation partially_overlaps)
(subrelation partially_overlaps overlaps)
(label partially_overlaps "partially_overlaps")
(example partially_overlaps "A National Park whose area is included in two counties would have this relationship to each of the counties." "GAZ")
(domain partially_overlaps IndependentContinuant)
(range partially_overlaps IndependentContinuant)
(intransitive partially_overlap)
(symmetric partially_overlap)
(exported_identifier partially_overlaps "OBO_REL_I:0000202")
(text_definition partially_overlaps "x partially_overlaps y if and only if: x overlaps y and neither x is part_of y not y is part_of x")
(<=> (partially_overlaps ?x ?y)
(and (overlaps ?x ?y)
(not (part_of ?x ?y))
(not (part_of ?y ?x))))
(relation underlaps)
(label underlaps "underlaps")
(domain underlaps IndependentContinuant)
(range underlaps IndependentContinuant)
(symmetric underlaps)
(reflexive underlaps)
(intransitive underlaps)
(exported_identifier underlaps "OBO_REL_I:0000210")
(<=> (underlaps ?x ?y)
(exists (?z) (and (part_of ?x ?z)
(part_of ?y ?z))))
;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; participation
;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(relation has_participant)
(instance_instance has_participant)
(label has_participant "has_participant")
(domain has_participant Occurrent)
(range has_participant IndependentContinuant)
(inverse_of has_participant participates_in)
(normative_direction_for has_participant "participation")
(text_definition has_participant "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.")
(exported_identifier has_participant "OBO_REL_I:0000019")
(text_definition_xref has_participant "PMID:15892874")
(holds_temporally_between has_participant Occurrent Continuant)
(holds_over_chain has_participant realizes inheres_in)
;; @Axiom: has_participant . part_of --> has_participant. See Dumontier OWLED2008
(transitive_over has_participant part_of)
(relation has_participant_some)
(type_type has_participant_some)
(all_some has_participant_some has_participant)
(label has_participant_some "has_participant")
(type_domain has_participant_some Occurrent)
(type_range has_participant_some IndependentContinuant)
(exported_identifier has_participant_some "OBO_REL_C:0000019")
(text_definition has_participant_some "P has_participant_some C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t")
(text_definition_xref has_participant_some "PMID:15892874")
(relation participates_in)
(instance_instance participates_in)
(label participates_in "participates_in")
(domain participates_in IndependentContinuant)
(range participates_in Occurrent)
(inverse_of participates_in has_participant)
(exported_identifier participates_in "OBO_REL_I:0000020")
(holds_temporally_between participates_in Continuant Occurrent)
(holds_over_chain participates_in has_bearer realized_by)
(relation participates_in_some)
(type_type participates_in_some)
(all_some participates_in_some participates_in)
(label participates_in_some "participates_in")
(type_domain participates_in_some IndependentContinuant)
(type_range participates_in_some Occurrent)
(exported_identifier participates_in_some "OBO_REL_C:0000020")
(text_definition participates_in_some "C participates_in_some P if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t")
(relation has_agent)
(instance_instance has_agent)
(label has_agent "has_agent")
(subrelation has_agent has_participant)
(type_domain has_agent Occurrent)
(type_range has_agent IndependentContinuant)
(inverse_of has_agent agent_in)
(normative_direction_for has_agent "agency")
(exported_identifier has_agent "OBO_REL_I:0000021")
(text_definition has_agent "As for has_participant, but with the additional condition that the component instance is causally active in the relevant process")
(text_definition_xref has_agent "PMID:15892874")
(relation has_agent_some)
(type_type has_agent_some)
(all_some has_agent_some has_agent)
(label has_agent_some "has_agent")
(subrelation has_agent_some has_participant_some)
(type_domain has_agent_some Occurrent)
(type_range has_agent_some IndependentContinuant)
(exported_identifier has_agent_some "OBO_REL_C:0000021")
(text_definition has_agent_some "P has_agent_some C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c has_agent p at t")
(text_definition_xref has_agent_some "PMID:15892874")
(relation agent_in)
(instance_instance agent_in)
(label agent_in "agent_in")
(subrelation agent_in participates_in)
(domain agent_in IndependentContinuant)
(range agent_in Occurrent)
(inverse_of agent_in has_agent)
(exported_identifier agent_in "OBO_REL_I:0000022")
(instance_level agent_id)
(relation agent_in_some)
(type_type agent_in_some)
(all_some agent_in_some agent_in)
(label agent_in_some "agent_in")
(subrelation agent_in_some participates_in_some)
(type_domain agent_in_some IndependentContinuant)
(type_range agent_in_some Occurrent)
(exported_identifier agent_in_some "OBO_REL_C:0000022")
;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; dependents
;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; DC
(relation inheres_in)
(instance_instance inheres_in)
(label inheres_in "inheres_in")
(inverse_of inheres_in bearer_of)
(normative_direction_for inheres_in "inherence")
(comment inheres_in "This relation links qualities, functions, dispositions and other dependent continuants to their bearers. Examples: The redness that ineres in a Drosophila eye; Catalytic activity function inheres_in catalytic molecule.")
(exact_synonym inheres_in "has_bearer")
(exported_identifier inheres_in "OBO_REL_I:0000026")
(text_definition inheres_in "A primitive relation that holds between a dependent continuant instance and a bearer")
(domain inheres_in DependentContinuant)
(holds_temporally_between inheres_in DependentContinuant Entity)
;;(text_definition_xref inheres_in "GOC:Neuhaus")
(relation inheres_in_some)
(type_type inheres_in_some)
(label inheres_in_some "inheres_in")
(exported_identifier inheres_in_some "OBO_REL_C:0000026")
(text_definition inheres_in_some "A relation between a dependent continuant D and an entity E. D inheres_in E iff: given any d that instantiates D at t, there exists some e that instantiates E at t and d *inheres_in* e at t. Here *inheres_in* is the primitive instance level relation, OBO_REL_I:0000026.")
(all_some_all_times inheres_in_some inheres_in)
(relation bearer_of)
(instance_instance bearer_of)
(label bearer_of "bearer_of")
(inverse_of bearer_of inheres_in)
(exact_synonym bearer_of "has_inherent")
(exact_synonym bearer_of "has_inherer")
(exact_synonym bearer_of "bears")
(exact_synonym bearer_of "is_bearer_of")
(exported_identifier bearer_of "OBO_REL_I:0000027")
(text_definition bearer_of "A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in")
(range bearer_of DependentContinuant)
(relation bearer_of_some)
(type_type bearer_of_some)
(label bearer_of_some "bearer_of")
(comment bearer_of_some "Examples: red eye bearer_of_some redness")
(exact_synonym bearer_of_some "has_inherent")
(exact_synonym bearer_of_some "has_inherer")
(exported_identifier bearer_of_some "OBO_REL_C:0000027")
(text_definition bearer_of_some "C bearer_of_some DC if and only if : given any continuant c that instantiates C at t, there exists some c that instantiates C at t and d *inheres_in* c at t. Here *inheres_in* is the primitive instance level relation, @OBO_REL_I:0000026@.")
(all_some_all_times bearer_of_some bearer_of)
;; QUALITY
(relation quality_of)
(label quality_of "quality_of")
(equivalent_relation_between quality_of specifically_inheres_in Quality Entity)
(subrelation quality_of inheres_in)
(inverse_of quality_of has_quality)
(functional quality_of)
(normative_direction_for quality_of "quality")
(exact_synonym quality_of "is_quality_of")
(exported_identifier quality_of "OBO_REL_I:0000028")
(text_definition quality_of "A relation between a quality Q and an entity E. Q quality_of E iff: Q inheres_in E and Q is a quality")
(domain quality_of Quality)
(relation quality_of_some)
(type_type quality_of_some)
(label quality_of_some "quality_of")
(subrelation quality_of_some inheres_in_some)
(exact_synonym quality_of_some "is_all_quality_of")
(exported_identifier quality_of_some "OBO_REL_C:0000028")
(text_definition quality_of_some "A relation between a quality Q and an entity E. Q quality_of_some E iff: Q inheres_in E and Q is a quality")
(all_some_all_times quality_of_some quality_of)
(relation has_quality)
(label has_quality "has_quality")
(subrelation has_quality bearer_of)
(inverse_of has_quality quality_of)
(exported_identifier has_quality "OBO_REL_I:0000029")
(text_definition has_quality "A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality")
(range has_quality Quality)
(relation has_quality_some)
(type_type has_quality_some)
(label has_quality_some "has_quality")
(subrelation has_quality_some bearer_of_some)
(exported_identifier has_quality_some "OBO_REL_C:0000029")
(text_definition has_quality_some "A relation between an entity and a quality. For types: E has_quality_some Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality_some q at t iff q inheres_in e at t and q instance-of Quality")
(all_some_all_times has_quality_some has_quality)
;; REALIZABLE
;; FUNCTION
(relation function_of)
(label function_of "function_of")
(subrelation function_of inheres_in)
(equivalent_relation_between function_of inheres_in Function IndependentContinuant)
(inverse_of function_of has_function)
(normative_direction_for function_of "function")
(comment function_of "Example: 'to blood pump' function_of 'heart'")
(exported_identifier function_of "OBO_REL_I:0000030")
(text_definition function_of "f function_of c at t iff : f inheres_in c at t and f instantiates a function")
(domain function_of Function)
(range function_of IndependentContinuant)
(relation function_of_some)
(type_type function_of_some)
(label function_of_some "function_of")
(subrelation function_of_some inheres_in_some)
(comment function_of_some "Example: 'to blood pump' function_of_some 'heart'")
(exported_identifier function_of_some "OBO_REL_C:0000030")
(text_definition function_of_some "F function_of C iff : for any f, t such that f instantiates F at t, there exists some c such that c instantiates C at t and f *function_of* C at t")
(all_some_all_times function_of_some function_of)
(relation has_function)
(label has_function "has_function")
(subrelation has_function bearer_of)
(equivalent_relation_between has_function bearer_of IndependentContinuant Function)
(inverse_of has_function function_of)
(comment has_function "heart has_function to-pump-blood")
(exported_identifier has_function "OBO_REL_I:0000031")
(text_definition has_function "Relation between an independent continuant and a function.")
(domain has_function IndependentContinuant)
(range has_function Function)
(relation has_function_some)
(type_type has_function_some)
(label has_function_some "has_function")
(subrelation has_function_some bearer_of_some)
(comment has_function_some "heart has_function_some to-pump-blood")
(exported_identifier has_function_some "OBO_REL_C:0000031")
(text_definition has_function_some "Relation between an independent continuant and a function.")
(all_some_all_times has_function_some has_function)
;; ROLE
(relation role_of)
(functional role_of)
(label role_of "role_of")
(subrelation role_of inheres_in)
(equivalent_relation_between role_of inheres_in Role IndependentContinuant)
(inverse_of role_of has_role)
(normative_direction_for role_of "role")
(exported_identifier role_of "OBO_REL_I:0000032")
(text_definition role_of "A relation between a role r and a continuant c. r role_of c at t iff: r inheres_in c at t and r instance_of Role at t")
(domain role_of Role)
;; weaken to Continuant?
(range role_of IndependentContinuant)
(relation role_of_some)
(type_type role_of_some)
(label role_of_some "role_of")
(subrelation role_of_some inheres_in_some)
(comment role_of_some "Example: 'to blood pump' function_of 'heart'")
(exported_identifier role_of_some "OBO_REL_C:0000032")
(text_definition role_of_some "A relation between a role R and an entity E. R role_of_some E iff: R inheres_in_some E and R is_a role")
(all_some_all_times role_of_some role_of)
(relation has_role)
(label has_role "has_role")
(equivalent_relation_between has_role bearer_of IndependentContinuant Role)
(subrelation has_role bearer_of)
(inverse_of has_role role_of)
(exported_identifier has_role "OBO_REL_I:0000033")
(text_definition has_role "A relation between a continuant C and a role R. The inverse_of role_of.")
(domain has_role IndependentContinuant)
(range has_role Role)
(relation has_role_some)
(type_type has_role_some)
(label has_role_some "has_role")
(subrelation has_role_some bearer_of_some)
(exported_identifier has_role_some "OBO_REL_C:0000033")
(text_definition has_role_some "A relation between a continuant C and a role R. The reciprocal relation of role_of.")
(all_some_all_times has_role_some has_role)
(relation realizes)
(label realizes "realizes")
(inverse_of realizes realized_by)
(comment realizes "in BFO realizable is the parent of function, role and disposition. We should also have realization_of and has_realizable for consistency. Will the terminology get too confusing?")
;; OBI
(narrow_synonym realizes "is_realization_of")
(narrow_synonym realizes "realization_of")
(narrow_synonym realizes "is_functioning_of")
(narrow_synonym realizes "executes")
;(exact_synonym realizes "has_function_part")
(exported_identifier realizes "OBO_REL_I:0000034")
(text_definition realizes "Relation between a process and a realizable entity")
(domain realizes Process)
(range realizes RealizableEntity)
(relation realizes_some)
(type_type realizes_some)
(label realizes_some "realizes")
(comment realizes_some "The process of 'histidine catabolism' (GO:0006548) realizes_some the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes_some (as bewteen a function and it's functioning) and indirectly_realizes")
;; OBI
(narrow_synonym realizes_some "is_realization_of")
(narrow_synonym realizes_some "realization_of")
(narrow_synonym realizes_some "has_function_part")
(exported_identifier realizes_some "OBO_REL_C:0000034")
(text_definition realizes_some "Relation between a process and a realizable entity. P /realizes_some/ F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation")
(all_some realizes_some realizes)
(relation realized_by)
(label realized_by "realized_by")
(inverse_of realized_by realizes)
(transitive_over realized_by part_of)
(normative_direction_for realized_by "realization")
(related_synonym realized_by "executed_during")
(narrow_synonym realized_by "realized_as")
;; OBI
(narrow_synonym realized_by "is_realized_as")
(narrow_synonym realized_by "executed_by")
(narrow_synonym realized_by "has_realization")
(narrow_synonym realized_by "has_functioning")
(exported_identifier realized_by "OBO_REL_I:0000035")
(text_definition realized_by "Relation between a realizable entity (such as a function or role) and a process.")
(domain realized_by RealizableEntity)
(range realized_by Process)
(relation realized_by_some)
(type_type realized_by_some)
(label realized_by_some "realized_by")
(related_synonym realized_by_some "executed_during")
(narrow_synonym realized_by_some "has_realization")
(exported_identifier realized_by_some "OBO_REL_C:0000035")
(text_definition realized_by_some "F realized_by P iff every instance of F is realized_by some instance of P")
(all_some realized_by_some realized_by)
;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; development and change
;; ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(relation derives_from)
(label derives_from "derives_from")
(label derives_from "derives_from")
(domain derives_from Continuant)
(range derives_from Continuant)
(inverse_of derives_from derived_into)
(transitive derives_from)
(normative_direction_for derives_from "derives")
(comment derives_from "Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.")
(exact_synonym derives_from "derived_from")
(exported_identifier derives_from "OBO_REL_I:0000015")
(text_definition derives_from "Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later.")
(text_definition_xref derives_from "PMID:15892874")
(=> (derives_from ?c ?c1)
(exists (?t)
(and (only_exists_prior_to ?c1 ?t)
(only_exists_subsequent_to ?c ?t))))
;; the following axioms are introduced in order to define derives_from
(<=> (only_exists_prior_to ?c ?t)
(and (exists (?t1)
(and (exists_at ?c ?t1)
(earlier_than ?t1 ?t)))
(=> (exists_at ?c ?t2)
(earlier_than ?t ?t2))))
(<=> (only_exists_subsequent_to ?c ?t)
(and (exists (?t1)
(and (exists_at ?c ?t1)
(earlier_than ?t ?t1)))
(=> (exists_at ?c ?t2)
(earlier_than ?t2 ?t))))
(relation derives_from_some)
(type_type derives_from_some)
(label derives_from_some "derives_from")
;;(subrelation derives_from_some develops_from_some)
(transitive derives_from_some)
(comment derives_from_some "C derives_from_some class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from_some osteoblast")
(exact_synonym derives_from_some "derived_from")
(exported_identifier derives_from_some "OBO_REL_C:0000015")
(text_definition derives_from_some "C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from_some C' if and only if: there is an chain of immediate derivation relations connecting C to C'.")
(text_definition_xref derives_from_some "PMID:15892874")
(image_xref derives_from_some "http://genomebiology.com/content/figures/gb-2005-6-5-r46-3.jpg")
;; no need for ALL-SOME form?
(relation derived_into)
(label derived_into "derived_into")
(domain derived_into Continuant)
(range derived_into Continuant)
(inverse_of derived_into derives_from)
(transitive derived_into)
(exported_identifier derived_into "OBO_REL_I:0000016")
(relation transformation_of)
(type_type transformation_of)
(type_level_only transformation_of)
(label transformation_of "transformation_of")
(instance_domain transformation_of Continuant)
(instance_range transformation_of Continuant)
(transitive transformation_of)
(comment transformation_of "When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.")
(exported_identifier transformation_of "OBO_REL_C:0000013")
(text_definition transformation_of "Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2.")
(text_definition_xref transformation_of "PMID:15892874")
(image_xref transformation_of "http://genomebiology.com/content/figures/gb-2005-6-5-r46-2-l.jpg")
;; @Axiom: C transformation_of C' defined as: if c instantiates C at t, then it must be the case there is some earlier time such that c instantiates C' at that time, and there is no time where c instantiates both C and C'
(<=> (transformation_of ?C ?C1)
(=> (instance_of ?c ?C ?t)
(exists (?t1)
(and (instance_of ?c ?C1 ?t1)
(earlier_than ?t1 ?t)
(not (exists (?t2)
(and (instance_of ?c ?C ?t2)
(instance_of ?c ?C1 ?t2))))))))
;; TODO: shoukd these relations be moved out into a separate "background" ontology?
(relation exists_at)
(text_definition exists_at "A primitive relation between a continuant and an instant of time.")
(label exists_at "exists_at")
(domain exists_at Continuant)
(range exists_at TemporalInstant)
(exported_identifier exists_at "OBO_REL_I:0000040")
;; @Axiom: something exists at a time iff it is an instance of something at that time
(<=>
(exists_at ?i ?t)
(exists (?U) (instance_of ?i ?U ?t)))
;; @Axiom: something exists at a time iff it is participating in something at that time
(<=> (exists_at ?c ?t)
(exists (?p)
(has_participant ?p ?c ?t)))
(relation occurs_at)
(label occurs_at "occurs_at")
(domain occurs_at Occurrent)
(range occurs_at TemporalInstant)
(exported_identifier occurs_at "OBO_REL_I:0000041")
(<=> (occurs_at ?p ?t)
(exists (?c)
(has_participant ?p ?c ?t)))
(relation preceded_by)
(label preceded_by "preceded_by")
(domain preceded_by Occurrent)
(range preceded_by Occurrent)
(inverse_of preceded_by precedes)
(transitive preceded_by)
(comment preceded_by "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.")
(exported_identifier preceded_by "OBO_REL_I:0000017")
(text_definition preceded_by "P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. ")
(text_definition_xref preceded_by "PMID:15892874")
(<=> (preceded_by ?p ?p1)
(=> (and (occurs_at ?p ?t)
(occurs_at ?p1 ?t1))
(earlier_than ?t1 ?t)))
(relation first_instant_of)
(label first_instant_of "first_instant_of")
(exported_identifier first_instant_of "OBO_REL_I:0000042")
(<=> (first_instant_of ?t ?p)
(and (occurs_at ?p ?t)
(=> (earlier_than ?t1 ?t)
(not (occurs_at ?p ?t1)))))
(relation last_instant_of)
(label last_instant_of "last_instant_of")
(exported_identifier last_instant_of "OBO_REL_I:0000043")
(<=> (last_instant_of ?t ?p)
(and (occurs_at ?p ?t)
(=> (earlier_than ?t ?t1)
(not (occurs_at ?p ?t1)))))
;; see also ro-development
(relation immediately_preceded_by)
(label immediately_preceded_by "immediately_preceded_by")
(exported_identifier immediately_preceded_by "OBO_REL_I:0000044")
(<=> (immediately_preceded_by ?p ?p1)
(exists (?t) (and (first_instant_of ?t ?p)
(last_instant_of ?t ?p1))))
(relation has_duration)
(label has_duration "has_duration")
(domain has_duration Occurrent)
(range has_duration TemporalInterval)
(text_definition has_duration "Instance level relation between an occurrent and a temporal interval, such that the two temporally coincide. The interval is defined by the start and end of the process.")
(exported_identifier has_duration "OBO_REL_I:0000045")
;; @Axiom: p has_duration y iff p is an occurrent, and for any t such that t is bound by the start and end of p, it is the case that p occurs_at t, and y is the interval with those boundaries
(<=> (has_duration ?p ?y)
(and (instance_of ?p Occurrent)
(exists (?t1) (first_instant_of ?t1 ?p))
(exists (?t2) (last_instant_of ?t2 ?p))
(=> (and (earlier_than ?t1 ?t)
(earlier_than ?t ?t2))
(occurs_at ?p ?t))
(= ?y (interval ?t1 ?t2))))
;; Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.
(relation preceded_by_some)
(type_type preceded_by_some)
(label preceded_by_some "preceded_by")
(type_domain preceded_by_some Occurrent)
(type_range preceded_by_some Occurrent)
(transitive preceded_by_some)
(comment preceded_by_some "An example is: translation preceded_by_some transcription; aging preceded_by_some development (not however death preceded_by_some 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.")
(exported_identifier preceded_by_some "OBO_REL_C:0000017")
(text_definition preceded_by_some "P preceded_by_some P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. ")
(text_definition_xref preceded_by_some "PMID:15892874")
(relation precedes)
(label precedes "precedes")
(domain precedes Occurrent)
(range precedes Occurrent)
(inverse_of precedes preceded_by)
(transitive precedes)
(exported_identifier precedes "OBO_REL_I:0000018")
;; imported IDs
;;(exported_identifier IndependentContinuant "bfo:IndependentContinuant")
(relation earlier_than)
(label earlier_than "earlier_than")
(broad_synonym earlier_than "<")
(exact_synonym earlier_than "earlier")
(exact_synonym earlier_than "before")
(domain earlier_than TemporalInstant)
(range earlier_than TemporalInstant)
(transitive earlier_than)
(comment earlier_than "earlier_than is treated as a primitive in RO. Neuhaus & Osumi-Sutherland treat befsim as the primitive")
(text_definition_xref earlier_than "PMID:15892874")
(relation occurs_in)
(label occurs_in "occurs_in")
(exact_synonym occurs_in "unfolds_in")
(exact_synonym occurs_in "process_located_in")
(holds_over_chain occurs_in has_participant located_in)
(exported_identifier occurs_in "OBO_REL_I:0000064")
(text_definition occurs_in "p occurs_in s at t : the participants of of p are spatially contained by s at t.")
;; @Axiom: p occurs_in s at t iff forall c such that c participates_in p at t, c located_in s at t
(<=> (occurs_in ?p ?s ?t)
(forall (?c)
(=> (has_participant ?p ?c ?t)
(located_in ?c ?s ?t))))
(relation occurs_in_some)
(type_type occurs_in_some)
(all_some_all_times occurs_in_some occurs_in)
(comment occurs_in_some "Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process occurs_in the oocyte")
(holds_over_chain occurs_in_some has_participant_some located_in_some)
(exported_identifier occurs_in_some "OBO_REL_C:0000064")
(label occurs_in_some "occurs_in_some")