ogms-full.obo

format-version: 1.2
data-version: ogms/releases/2025-07-02/ogms-full.owl
idspace: dce http://purl.org/dc/elements/1.1/ 
idspace: dcterms http://purl.org/dc/terms/ 
idspace: swrl http://www.w3.org/2003/11/swrl# 
idspace: swrlb http://www.w3.org/2003/11/swrlb# 
ontology: ogms/ogms-full
property_value: dcterms:description "None" xsd:string
property_value: dcterms:license https://creativecommons.org/licenses/unspecified
property_value: dcterms:title "The Ontology for General Medical Science" xsd:string
property_value: owl:versionInfo "2025-07-02" xsd:string

[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." []
disjoint_from: BFO:0000003 ! occurrent
relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part of continuant

[Term]
id: BFO:0000003
name: occurrent
def: "An entity that has temporal parts and that happens, unfolds or develops through time." []
relationship: BFO:0000050 BFO:0000003 {all_only="true"} ! part of occurrent

[Term]
id: BFO:0000004
name: independent continuant
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])" []
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000020 ! specifically dependent continuant
relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant

[Term]
id: BFO:0000015
name: process
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])" []
is_a: BFO:0000003 ! occurrent

[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
relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity

[Term]
id: BFO:0000019
name: quality
is_a: BFO:0000020 ! specifically dependent continuant
relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality

[Term]
id: BFO:0000020
name: specifically dependent continuant
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])" []
is_a: BFO:0000002 ! continuant
relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant

[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

[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

[Term]
id: GO:0003674
name: molecular_function
is_a: BFO:0000015 ! process

[Term]
id: GO:0008150
name: biological_process
is_a: BFO:0000015 ! process

[Term]
id: GO:0016301
name: kinase activity
is_a: GO:0003674 ! molecular_function

[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." []

[Term]
id: OGMS:0000000
name: root node

[Term]
id: PATO:0000001
name: quality
is_a: BFO:0000020 ! specifically dependent continuant

[Typedef]
id: BFO:0000050
name: part of
def: "a core relation that holds between a part and its whole" []
is_transitive: true
is_a: RO:0002131 ! overlaps
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" []
is_transitive: true
is_a: RO:0002131 ! overlaps

[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." []
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
holds_over_chain: BFO:0000050 BFO:0000062
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." []
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
holds_over_chain: BFO:0000050 BFO:0000063
is_transitive: true
is_a: RO:0002222 ! temporally related to

[Typedef]
id: RO:0000052
name: characteristic of
def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." []
is_functional: true
is_a: RO:0002314 ! characteristic of part of
inverse_of: RO:0000053 ! has characteristic

[Typedef]
id: RO:0000053
name: has characteristic
def: "Inverse of characteristic_of" []
range: BFO:0000020 ! specifically dependent continuant
is_inverse_functional: true

[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" []
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" []
domain: BFO:0000003 ! occurrent
range: BFO:0000002 ! continuant
holds_over_chain: BFO:0000051 RO:0000057

[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" []
domain: BFO:0000034 ! function
is_a: RO:0000052 ! characteristic of
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" []
is_a: RO:0000052 ! characteristic of
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" []
is_a: RO:0000052 ! characteristic of
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" []
domain: BFO:0000004 ! independent continuant
range: BFO:0000034 ! function
is_a: RO:0000053 ! has characteristic

[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" []
range: BFO:0000019 ! quality
is_a: RO:0000053 ! has characteristic

[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" []
domain: BFO:0000004 ! independent continuant
range: BFO:0000023 ! role
is_a: RO:0000053 ! has characteristic

[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 ! has characteristic
inverse_of: RO:0000092 ! disposition of

[Typedef]
id: RO:0000092
name: disposition of
def: "inverse of has disposition" []
is_a: RO:0000052 ! characteristic of

[Typedef]
id: RO:0002013
name: has regulatory component activity
def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." []
is_a: RO:0002017 ! has component activity
is_a: RO:0002334 ! regulated by

[Typedef]
id: RO:0002014
name: has negative regulatory component activity
def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole.  More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." []
is_a: RO:0002013 ! has regulatory component activity
is_a: RO:0002335 ! negatively regulated by

[Typedef]
id: RO:0002015
name: has positive regulatory component activity
def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole.  More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." []
is_a: RO:0002013 ! has regulatory component activity
is_a: RO:0002336 ! positively regulated by

[Typedef]
id: RO:0002017
name: has component activity
is_a: RO:0002018 ! has component process

[Typedef]
id: RO:0002018
name: has component process
def: "w 'has process component' p if p and w are processes,  w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." []
domain: BFO:0000015 ! process
range: BFO:0000015 ! process
is_a: RO:0002180 ! has component

[Typedef]
id: RO:0002022
name: directly regulated by
is_a: RO:0002334 ! regulated by
inverse_of: RO:0002578 ! directly regulates

[Typedef]
id: RO:0002023
name: directly negatively regulated by
is_a: RO:0002022 ! directly regulated by
inverse_of: RO:0002630 ! directly negatively regulates

[Typedef]
id: RO:0002024
name: directly positively regulated by
is_a: RO:0002022 ! directly regulated by
inverse_of: RO:0002629 ! directly positively regulates

[Typedef]
id: RO:0002025
name: has effector activity
is_functional: true
is_a: RO:0002017 ! has component activity

[Typedef]
id: RO:0002086
name: ends after
is_transitive: true
is_a: RO:0002222 ! temporally related to

[Typedef]
id: RO:0002087
name: immediately preceded by
is_a: BFO:0000062 ! preceded by
inverse_of: RO:0002090 ! immediately precedes

[Typedef]
id: RO:0002090
name: immediately precedes
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" []
holds_over_chain: BFO:0000050 BFO:0000050
holds_over_chain: BFO:0000051 RO:0002131
is_symmetric: true
is_a: RO:0002323 ! mereotopologically related to
transitive_over: BFO:0000050 ! part of

[Typedef]
id: RO:0002180
name: has component
def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." []
is_a: BFO:0000051 ! has part

[Typedef]
id: RO:0002211
name: regulates
def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." []
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
transitive_over: RO:0002025 ! has effector activity

[Typedef]
id: RO:0002212
name: negatively regulates
def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." []
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: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." []
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. " []
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." []
is_a: RO:0002328 ! functionally related to
is_a: RO:0002500 ! causal agent in process

[Typedef]
id: RO:0002222
name: temporally related to
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." []
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." []
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." []
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
def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." []
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
def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." []
is_a: RO:0002411 ! causally upstream of
is_a: RO:0004046 ! causally upstream of or within, negative effect

[Typedef]
id: RO:0002314
name: characteristic of part of
def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." []
is_a: RO:0002502 ! depends on
transitive_over: BFO:0000050 ! part of

[Typedef]
id: RO:0002323
name: mereotopologically related to
def: "A mereological relationship or a topological relationship" []

[Typedef]
id: RO:0002327
name: enables
def: "c enables p iff c is capable of p and c acts to execute p." []
is_a: RO:0002215 ! capable of
inverse_of: RO:0002333 ! enabled by
transitive_over: BFO:0000051 ! has part
transitive_over: RO:0002017 ! has component activity

[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." []

[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." []
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" []
holds_over_chain: RO:0002327 BFO:0000050
is_a: RO:0000056 ! participates in
is_a: RO:0002431 ! involved in or involved in regulation of
transitive_over: BFO:0000050 ! part of

[Typedef]
id: RO:0002333
name: enabled by
def: "inverse of enables" []
is_a: RO:0000057 ! has participant
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002334
name: regulated by
def: "inverse of regulates" []
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" []
is_a: RO:0002334 ! regulated by

[Typedef]
id: RO:0002336
name: positively regulated by
def: "inverse of positively regulates" []
is_a: RO:0002334 ! regulated by

[Typedef]
id: RO:0002352
name: input of
def: "inverse of has input" []
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" []
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
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:0002407
name: indirectly positively regulates
def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." []
holds_over_chain: RO:0002409 RO:0002409
holds_over_chain: RO:0002629 RO:0002407
holds_over_chain: RO:0002629 RO:0002629
is_transitive: true
is_a: RO:0002213 ! positively regulates
is_a: RO:0012012 ! indirectly regulates
transitive_over: RO:0002629 ! directly positively regulates

[Typedef]
id: RO:0002409
name: indirectly negatively regulates
def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." []
holds_over_chain: RO:0002630 RO:0002409
holds_over_chain: RO:0002630 RO:0002630
is_transitive: true
is_a: RO:0002212 ! negatively regulates
is_a: RO:0012012 ! indirectly regulates
transitive_over: RO:0002630 ! directly negatively regulates

[Typedef]
id: RO:0002410
name: causally related to

[Typedef]
id: RO:0002411
name: causally upstream of
def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." []
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 p is causally upstream of q, and the end of p is coincident with the beginning of q." []
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 is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." []
is_transitive: true
is_a: RO:0002501 ! causal relation between processes
inverse_of: RO:0002427 ! causally downstream of or within
transitive_over: BFO:0000050 ! part of

[Typedef]
id: RO:0002427
name: causally downstream of or within
def: "inverse of causally upstream of or within" []
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" []
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" []
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" []
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" []
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:0002434
name: interacts with
def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." []
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." []
is_symmetric: true
is_a: RO:0002434 ! interacts with

[Typedef]
id: RO:0002447
name: phosphorylates
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." []
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." []
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." []
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)

[Typedef]
id: RO:0002481
name: is kinase activity
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" []
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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." []
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002502
name: depends on

[Typedef]
id: RO:0002506
name: causal relation between entities
domain: BFO:0000002 ! continuant
range: BFO:0000002 ! continuant
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002559
name: causally influenced by
is_a: RO:0002506 ! causal relation between entities
inverse_of: RO:0002566 ! causally influences

[Typedef]
id: RO:0002563
name: interaction relation helper property
is_a: RO:0002464 ! helper property (not for use in curation)

[Typedef]
id: RO:0002564
name: molecular interaction relation helper property
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)." []
domain: BFO:0000002 ! continuant
range: BFO:0000002 ! continuant
is_a: RO:0002506 ! causal relation between entities

[Typedef]
id: RO:0002578
name: directly regulates
def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." []
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" []
holds_over_chain: BFO:0000051 RO:0002215
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." []
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." []
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." []
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." []
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'" []
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002629
name: directly positively regulates
def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." []
is_a: RO:0002213 ! positively regulates
is_a: RO:0002578 ! directly regulates

[Typedef]
id: RO:0002630
name: directly negatively regulates
def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." []
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." []
holds_over_chain: RO:0002327 BFO:0000051
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0004032
name: acts upstream of or within, positive effect
holds_over_chain: RO:0002327 RO:0004047
is_a: RO:0002264 ! acts upstream of or within

[Typedef]
id: RO:0004033
name: acts upstream of or within, negative effect
holds_over_chain: RO:0002327 RO:0004046
is_a: RO:0002264 ! acts upstream of or within

[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" []
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

[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" []
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

[Typedef]
id: RO:0004046
name: causally upstream of or within, negative effect
is_a: RO:0002418 ! causally upstream of or within

[Typedef]
id: RO:0004047
name: causally upstream of or within, positive effect
is_a: RO:0002418 ! causally upstream of or within

[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." []
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: RO:0002566 ! causally influences

[Typedef]
id: RO:0012011
name: indirectly causally upstream of
def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." []
is_a: RO:0002411 ! causally upstream of

[Typedef]
id: RO:0012012
name: indirectly regulates
def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." []
is_a: RO:0002211 ! regulates
is_a: RO:0012011 ! indirectly causally upstream of

[Typedef]
id: RO:0017001
name: device utilizes material
def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." []
holds_over_chain: RO:0002215 RO:0002233

[Typedef]
id: RO:0019000
name: regulates characteristic
def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." []
domain: BFO:0000015 ! process
range: PATO:0000001 ! quality
holds_over_chain: RO:0002211 RO:0019000
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0019001
name: positively regulates characteristic
def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." []
holds_over_chain: RO:0002213 RO:0019001
is_a: RO:0019000 ! regulates characteristic

[Typedef]
id: RO:0019002
name: negatively regulates characteristic
def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." []
holds_over_chain: RO:0002212 RO:0019001
holds_over_chain: RO:0002213 RO:0019002
is_a: RO:0019000 ! regulates characteristic