From 189c6c79a6cf8e55aaeac1b398e31c2a12bd8b2d Mon Sep 17 00:00:00 2001 From: Laurel Cooper Date: Wed, 12 Jul 2023 15:51:18 -0600 Subject: [PATCH] updated RO imports --- imports/ro_import.obo | 192 +++++------------ imports/ro_import.owl | 475 ++++++++++++++++++++---------------------- 2 files changed, 279 insertions(+), 388 deletions(-) diff --git a/imports/ro_import.obo b/imports/ro_import.obo index 021505d..2fd919b 100644 --- a/imports/ro_import.obo +++ b/imports/ro_import.obo @@ -17,7 +17,7 @@ relationship: BFO:0000050 BFO:0000003 ! part of occurrent [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])" [] is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant relationship: BFO:0000050 BFO:0000004 ! part of independent continuant @@ -30,7 +30,7 @@ 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])" [] is_a: BFO:0000003 ! occurrent [Term] @@ -56,7 +56,7 @@ relationship: BFO:0000050 BFO:0000019 ! part of quality [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])" [] is_a: BFO:0000002 ! continuant relationship: BFO:0000050 BFO:0000020 ! part of specifically dependent continuant @@ -83,73 +83,55 @@ id: BFO:0000141 name: immaterial entity is_a: BFO:0000004 ! independent continuant -[Term] -id: CARO:0000000 -name: anatomical entity -is_a: CARO:0030000 ! biological entity -property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl - -[Term] -id: CARO:0001010 -name: organism or virus or viroid -is_a: BFO:0000040 ! material entity - -[Term] -id: CARO:0030000 -name: biological entity -is_a: BFO:0000004 ! independent continuant - [Term] id: GO:0003674 name: molecular_function -is_a: BFO:0000015 ! process -property_value: IAO:0000589 "molecular process" xsd:string - -[Term] -id: GO:0003824 -name: catalytic activity -is_a: GO:0003674 ! molecular_function +def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] +synonym: "molecular function" EXACT [] [Term] id: GO:0008150 name: biological_process -is_a: BFO:0000015 ! process +def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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] +synonym: "biological process" EXACT [] +synonym: "physiological process" EXACT [] +synonym: "single organism process" RELATED [] +synonym: "single-organism process" RELATED [] [Term] id: GO:0016301 name: kinase activity -is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups +def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732] +synonym: "phosphokinase activity" EXACT [] +is_a: GO:0003674 ! molecular_function [Term] -id: GO:0016740 -name: transferase activity -is_a: GO:0003824 ! catalytic activity +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: GO:0016772 -name: transferase activity, transferring phosphorus-containing groups -is_a: GO:0016740 ! transferase activity +id: OBI:0100026 +name: organism +def: "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." [] +is_a: BFO:0000040 ! material entity [Term] id: PATO:0000001 name: quality +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 + +[Term] +id: UBERON:0001062 +name: anatomical entity +def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." [FMA:62955, http://orcid.org/0000-0001-9114-8737] +is_a: BFO:0000004 ! independent continuant [Typedef] id: BFO:0000050 name: part of def: "a core relation that holds between a part and its whole" [] -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:0000116 "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: IAO:0000116 "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: IAO:0000116 "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: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 is_a: RO:0002131 ! overlaps inverse_of: BFO:0000051 ! has part @@ -158,15 +140,6 @@ inverse_of: BFO:0000051 ! has part id: BFO:0000051 name: has part def: "a core relation that holds between a whole and its part" [] -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:0000116 "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: IAO:0000116 "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: IAO:0000116 "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:0000118 "has_part" xsd:string -property_value: RO:0001900 RO:0001901 is_transitive: true is_a: RO:0002131 ! overlaps @@ -174,11 +147,6 @@ is_a: RO:0002131 ! overlaps 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." [] -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:0000116 "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: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: BFO:0000050 BFO:0000062 @@ -190,7 +158,6 @@ inverse_of: BFO:0000063 ! precedes 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." [] -property_value: IAO:0000111 "precedes" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: BFO:0000050 BFO:0000063 @@ -201,12 +168,6 @@ is_a: RO:0002222 ! temporally related to 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." [] -comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. -property_value: IAO:0000111 "inheres in" xsd:string -property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string -property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string -property_value: IAO:0000118 "inheres_in" xsd:string -property_value: RO:0001900 RO:0001901 is_functional: true is_a: RO:0002314 ! characteristic of part of inverse_of: RO:0000053 ! has characteristic @@ -215,13 +176,6 @@ inverse_of: RO:0000053 ! has characteristic id: RO:0000053 name: has characteristic def: "Inverse of characteristic_of" [] -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:0000116 "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: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 is_inverse_functional: true @@ -229,11 +183,6 @@ is_inverse_functional: true 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 domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: RO:0000057 ! has participant @@ -242,13 +191,6 @@ inverse_of: RO:0000057 ! has participant 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: 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:0000116 "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: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant holds_over_chain: BFO:0000051 RO:0000057 @@ -257,11 +199,6 @@ holds_over_chain: BFO:0000051 RO:0000057 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" [] -comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string -property_value: IAO:0000116 "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:0000118 "function_of" xsd:string -property_value: IAO:0000118 "is function of" xsd:string domain: BFO:0000034 ! function is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function @@ -270,11 +207,6 @@ inverse_of: RO:0000085 ! has function 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" [] -comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string -property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string -property_value: IAO:0000118 "is quality of" xsd:string -property_value: IAO:0000118 "quality_of" xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000086 ! has quality @@ -282,11 +214,6 @@ inverse_of: RO:0000086 ! has quality 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" [] -comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string -property_value: IAO:0000116 "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:0000118 "is role of" xsd:string -property_value: IAO:0000118 "role_of" xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role @@ -294,9 +221,6 @@ inverse_of: RO:0000087 ! has role 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: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string -property_value: IAO:0000116 "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:0000118 "has_function" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function is_a: RO:0000053 ! has characteristic @@ -305,9 +229,6 @@ is_a: RO:0000053 ! has characteristic 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: IAO:0000112 "this apple has quality this red color" xsd:string -property_value: IAO:0000116 "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:0000118 "has_quality" xsd:string range: BFO:0000019 ! quality is_a: RO:0000053 ! has characteristic @@ -315,9 +236,6 @@ is_a: RO:0000053 ! has characteristic 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: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string -property_value: IAO:0000116 "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:0000118 "has_role" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role is_a: RO:0000053 ! has characteristic @@ -335,19 +253,12 @@ inverse_of: RO:0000092 ! disposition of id: RO:0000092 name: disposition of def: "inverse of has disposition" [] -comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. is_a: RO:0000052 ! characteristic of [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: 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:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" 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 @@ -367,14 +278,6 @@ name: contains 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: 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:0000116 "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: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" 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 @@ -423,48 +326,39 @@ inverse_of: RO:0002578 ! directly regulates [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] +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." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002630 ! directly negatively regulates [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] +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." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002629 ! directly positively regulates [Typedef] id: RO:0002025 name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] is_functional: true is_a: RO:0002017 ! has component activity [Typedef] id: RO:0002086 name: ends after -comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string 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 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) -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 is_a: BFO:0000063 ! precedes [Typedef] @@ -488,7 +382,7 @@ is_a: RO:0002162 ! in taxon id: RO:0002162 name: in taxon def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] -range: CARO:0001010 ! organism or virus or viroid +range: OBI:0100026 ! organism holds_over_chain: BFO:0000050 RO:0002162 holds_over_chain: BFO:0000051 RO:0002162 holds_over_chain: RO:0002202 RO:0002162 @@ -584,9 +478,6 @@ is_a: RO:0002163 ! spatially disjoint from [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. -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent @@ -602,8 +493,8 @@ inverse_of: RO:0002352 ! input of id: RO:0002254 name: has developmental contribution from def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] -domain: CARO:0000000 ! anatomical entity -range: CARO:0000000 ! anatomical entity +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0001062 ! anatomical entity holds_over_chain: BFO:0000051 RO:0002202 is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002255 ! developmentally contributes to @@ -758,8 +649,8 @@ is_a: RO:0002131 ! overlaps id: RO:0002384 name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] -domain: CARO:0000000 ! anatomical entity -range: CARO:0000000 ! anatomical entity +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to [Typedef] @@ -1045,6 +936,11 @@ name: process has causal agent def: "Inverse of 'causal agent in process'" [] is_a: RO:0002410 ! causally related to +[Typedef] +id: RO:0002610 +name: correlated with +def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] + [Typedef] id: RO:0002629 name: directly positively regulates @@ -1132,6 +1028,14 @@ def: "X device utilizes material Y means X and Y are material entities, and X is synonym: "utilizes" BROAD [] holds_over_chain: RO:0002215 RO:0002233 +[Typedef] +id: RO:0017003 +name: positively correlated with +def: "A relation between entities in which one increases or decreases as the other does the same." [] +is_reflexive: true +is_symmetric: true +is_a: RO:0002610 ! correlated with + [Typedef] id: RO:0019000 name: regulates characteristic diff --git a/imports/ro_import.owl b/imports/ro_import.owl index 3a07755..6796197 100644 --- a/imports/ro_import.owl +++ b/imports/ro_import.owl @@ -1,17 +1,16 @@ + xmlns:obo="http://purl.obolibrary.org/obo/" + xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#"> @@ -27,24 +26,6 @@ - - - - - - - - - - - - - - - - - - @@ -54,48 +35,12 @@ - + 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. editor note - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -114,12 +59,6 @@ - - - - - - @@ -179,20 +118,8 @@ - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole - 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. - 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - part of - http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -202,18 +129,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) a core relation that holds between a whole and its part - 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. - 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - has part @@ -231,12 +147,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - preceded by 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. - 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. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by @@ -253,7 +164,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - precedes 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. precedes @@ -266,13 +176,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple 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. - inheres_in - - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -283,14 +187,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility Inverse of characteristic_of - 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. - bearer_of - is bearer of - has characteristic @@ -302,12 +199,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in participates in @@ -322,14 +214,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process - 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. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -341,12 +226,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - 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. - function_of - is function of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of @@ -357,12 +237,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of @@ -373,12 +248,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - 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. - is role of - role_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of @@ -390,10 +260,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - 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. - has_function has function @@ -404,10 +271,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - 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. - has_quality has quality @@ -419,10 +283,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - 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. - has_role has role @@ -446,7 +307,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. inverse of has disposition - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of @@ -457,13 +317,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is location of - my head is the location of my brain - this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - location of @@ -522,15 +376,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - located in - my brain is located in my head - this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location - 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 - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in located in @@ -624,7 +470,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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 + @@ -641,7 +487,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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 + @@ -658,7 +504,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -668,8 +514,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - David Osumi-Sutherland - X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after @@ -680,9 +524,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by @@ -692,10 +533,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - David Osumi-Sutherland - ends_at_start_of - meets - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes @@ -742,7 +579,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. - only in taxon + only in taxon @@ -751,7 +588,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + @@ -773,7 +610,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - in taxon + in taxon @@ -783,7 +620,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. A is spatially_disjoint_from B if and only if they have no parts in common - spatially disjoint from + spatially disjoint from @@ -929,9 +766,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to @@ -954,8 +788,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - + + @@ -1254,8 +1088,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). has developmental potential involving @@ -1787,6 +1621,15 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + correlated with + + + + @@ -1944,6 +1787,18 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + A relation between entities in which one increases or decreases as the other does the same. + positively correlated with + + + + @@ -2057,7 +1912,7 @@ For example, A and B may be gene products and binding of B by A positively regul - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + 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]) independent continuant @@ -2076,7 +1931,7 @@ For example, A and B may be gene products and binding of B by A positively regul - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + 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]) process @@ -2134,7 +1989,7 @@ For example, A and B may be gene products and binding of B by A positively regul - 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. + 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]) specifically dependent continuant @@ -2191,102 +2046,221 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - - - anatomical entity + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. + molecular function + molecular_function + + + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. + GOC:pdt + - + - - - organism or virus or viroid + + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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. + biological process + physiological process + single organism process + single-organism process + biological_process + + + + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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 + - + - - - biological entity + + + + + + true + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + phosphokinase activity + kinase activity + + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + ISBN:0198506732 + - + - - - molecular process - molecular_function + + + + + + + + + + + + + + + + + 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. + curation status specification - + - - - catalytic activity + + + A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. + organism - + - - - biological_process + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + quality + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATOC:GVG + - + - - - - - - true - - - kinase activity + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + anatomical entity + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + FMA:62955 + http://orcid.org/0000-0001-9114-8737 + + + + + + - + - - - transferase activity - + + example to be eventually removed + - + - - - transferase activity, transferring phosphorus-containing groups - + + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + - + - - - quality (PATO) - quality - + + Term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + Terms with this status should eventually replaced with a term from another ontology. + to be replaced with external ontology term + + + + + + + + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + requires discussion + @@ -2331,6 +2305,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + @@ -2655,8 +2642,8 @@ For example, A and B may be gene products and binding of B by A positively regul true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg @@ -2785,8 +2772,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP @@ -3691,5 +3678,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - +