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2024-04-24 Release #795

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May 1, 2024
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2024-04-24 Release #795

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c5595ef
2024-04-04 release
anitacaron Apr 4, 2024
9b1b63a
update orcidio import
anitacaron Apr 4, 2024
2178d7d
update release artefacts
anitacaron Apr 4, 2024
e43dcf9
Merge branch 'master' into release-april
anitacaron Apr 4, 2024
c786f99
update orcidio import
anitacaron Apr 4, 2024
cb60247
update release artefacts after merge
anitacaron Apr 4, 2024
f292592
Merge branch 'master' into release-april
Apr 22, 2024
e970914
release 2024-04-24
anitacaron Apr 24, 2024
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4 changes: 2 additions & 2 deletions core.json
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Expand Up @@ -7,12 +7,12 @@
"val" : "https://creativecommons.org/publicdomain/zero/1.0/"
}, {
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
"val" : "2024-02-13"
"val" : "2024-04-04"
}, {
"pred" : "http://xmlns.com/foaf/0.1/homepage",
"val" : "https://github.com/oborel/obo-relations/wiki/ROCore"
} ],
"version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/core.json"
"version" : "http://purl.obolibrary.org/obo/ro/releases/2024-04-04/core.json"
},
"nodes" : [ {
"id" : "http://purl.obolibrary.org/obo/BFO_0000002",
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4 changes: 2 additions & 2 deletions core.obo
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@@ -1,9 +1,9 @@
format-version: 1.2
data-version: ro/releases/2024-02-13/core.owl
data-version: ro/releases/2024-04-04/core.owl
ontology: ro/core
property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/
property_value: http://xmlns.com/foaf/0.1/homepage "https://github.com/oborel/obo-relations/wiki/ROCore" xsd:anyURI
property_value: owl:versionInfo "2024-02-13" xsd:string
property_value: owl:versionInfo "2024-04-04" xsd:string

[Term]
id: BFO:0000002
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4 changes: 2 additions & 2 deletions core.owl
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Expand Up @@ -13,9 +13,9 @@
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ro/core.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2024-02-13/core.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2024-04-04/core.owl"/>
<terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
<owl:versionInfo>2024-02-13</owl:versionInfo>
<owl:versionInfo>2024-04-04</owl:versionInfo>
<foaf:homepage rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/oborel/obo-relations/wiki/ROCore</foaf:homepage>
</owl:Ontology>

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579 changes: 222 additions & 357 deletions ro-base.json
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560 changes: 263 additions & 297 deletions ro-base.obo
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1,870 changes: 160 additions & 1,710 deletions ro-base.owl
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385 changes: 367 additions & 18 deletions ro-full.json
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142 changes: 132 additions & 10 deletions ro-full.obo
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@@ -1,5 +1,5 @@
format-version: 1.2
data-version: ro/releases/2024-02-13/ro-full.owl
data-version: ro/releases/2024-04-04/ro-full.owl
subsetdef: common_anatomy ""
subsetdef: efo_slim ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
Expand All @@ -18,7 +18,7 @@ property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology
property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/
property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string
property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI
property_value: owl:versionInfo "2024-02-13" xsd:string
property_value: owl:versionInfo "2024-04-04" xsd:string

[Term]
id: BFO:0000002
Expand Down Expand Up @@ -384,6 +384,7 @@ synonym: "single organism process" RELATED []
synonym: "single-organism process" RELATED []
xref: Wikipedia:Biological_process
is_a: BFO:0000015 ! process
disjoint_from: OBI:0000011 ! planned process
relationship: BFO:0000051 GO:0003674 ! has part molecular_function
created_by: jl
creation_date: 2012-09-19T15:05:24Z
Expand Down Expand Up @@ -423,6 +424,20 @@ property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string
property_value: IAO:0000119 "GROUP:OBI:<http://purl.obolibrary.org/obo/obi>" xsd:string
property_value: IAO:0000119 "OBI_0000266" xsd:string

[Term]
id: OBI:0000011
name: planned process
def: "A process that realizes a plan which is the concretization of a plan specification." []
is_a: BFO:0000015 ! process
property_value: IAO:0000111 "planned process" xsd:string
property_value: IAO:0000111 "planned process" xsd:string
property_value: IAO:0000112 "Injecting mice with a vaccine in order to test its efficacy" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000116 "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" xsd:string
property_value: IAO:0000116 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." xsd:string
property_value: IAO:0000117 "Bjoern Peters" xsd:string
property_value: IAO:0000119 "branch derived" xsd:string

[Term]
id: OBI:0000047
name: processed material
Expand All @@ -433,6 +448,20 @@ property_value: IAO:0000112 "Examples include gel matrices, filter paper, parafi
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string

[Term]
id: OBI:0000070
name: assay
def: "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies." []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000111 "assay" xsd:string
property_value: IAO:0000112 "Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house." xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000116 "12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation." xsd:string
property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string
property_value: IAO:0000118 "measuring" xsd:string
property_value: IAO:0000118 "scientific observation" xsd:string
property_value: IAO:0000119 "OBI branch derived" xsd:string

[Term]
id: OBI:0000967
name: container
Expand Down Expand Up @@ -500,6 +529,18 @@ name: linear
def: "A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel." [ISBN:0881923214]
is_a: PATO:0000001 ! quality

[Term]
id: PATO:0001470
name: proportionality to
def: "A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity." [PATOC:nw]
comment: Examples: height to weight; brain size to body size. These could all be children of proportionality. Proportions can be measured as ratios. Some measures may be dimensionless. Not all ratios measure proportionality, eg m/s measures velocity which is not a proportion in the sense defined above, it is a quality in its own right.
synonym: "proportion" EXACT []
synonym: "proportionality" EXACT []
synonym: "quotient" EXACT []
synonym: "rate" RELATED []
synonym: "ratio" EXACT []
is_a: PATO:0000001 ! quality

[Term]
id: PATO:0002124
name: laminar
Expand Down Expand Up @@ -932,7 +973,6 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen
property_value: IAO:0000118 "bearer_of" xsd:string
property_value: IAO:0000118 "is bearer of" xsd:string
property_value: RO:0001900 RO:0001901
property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string
range: BFO:0000020 ! characteristic
is_inverse_functional: true

Expand Down Expand Up @@ -2537,7 +2577,7 @@ is_a: RO:0002444 ! parasite of
id: RO:0002238
name: has component participant
def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." []
property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899
property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string
is_a: RO:0000057 ! has participant

Expand Down Expand Up @@ -3917,6 +3957,7 @@ is_a: RO:0002440 ! symbiotically interacts with
[Typedef]
id: RO:0002444
name: parasite of
def: "A parasite-host relationship where an organism benefits at the expense of another." []
subset: ro-eco
synonym: "direct parasite of" EXACT []
property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string
Expand All @@ -3930,6 +3971,7 @@ inverse_of: RO:0002445 ! parasitized by
[Typedef]
id: RO:0002445
name: parasitized by
def: "Inverse of parasite of" []
subset: ro-eco
synonym: "directly parasitized by" EXACT []
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
Expand Down Expand Up @@ -4053,10 +4095,11 @@ is_a: RO:0002442 ! mutualistically interacts with
[Typedef]
id: RO:0002457
name: acquires nutrients from
def: "Inverse of provides nutrients for" []
subset: ro-eco
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string
is_a: RO:0002438 ! trophically interacts with
is_a: RO:0002437 ! biotically interacts with
inverse_of: RO:0002469 ! provides nutrients for

[Typedef]
Expand Down Expand Up @@ -4143,26 +4186,29 @@ is_a: RO:0002465 ! is symbiosis
[Typedef]
id: RO:0002469
name: provides nutrients for
def: "A biotic interaction where a material entity provides nutrition for an organism." []
subset: ro-eco
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
is_a: RO:0002438 ! trophically interacts with
is_a: RO:0002437 ! biotically interacts with

[Typedef]
id: RO:0002470
name: eats
def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." []
subset: ro-eco
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000118 "is subject of eating interaction with" xsd:string
is_a: RO:0002438 ! trophically interacts with
is_a: RO:0002437 ! biotically interacts with

[Typedef]
id: RO:0002471
name: is eaten by
def: "Inverse of eats" []
subset: ro-eco
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000118 "eaten by" xsd:string
property_value: IAO:0000118 "is target of eating interaction with" xsd:string
is_a: RO:0002438 ! trophically interacts with
is_a: RO:0002437 ! biotically interacts with

[Typedef]
id: RO:0002472
Expand Down Expand Up @@ -4758,6 +4804,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with
[Typedef]
id: RO:0002556
name: pathogen of
def: "Inverse of has pathogen" []
subset: ro-eco
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
is_a: RO:0002454 ! has host
Expand All @@ -4766,6 +4813,7 @@ inverse_of: RO:0002557 ! has pathogen
[Typedef]
id: RO:0002557
name: has pathogen
def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" []
subset: ro-eco
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
is_a: RO:0002453 ! host of
Expand Down Expand Up @@ -5929,6 +5977,26 @@ property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165
is_a: RO:0009001 ! has substance added

[Typedef]
id: RO:0009006
name: assay measures characteristic
def: "A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic." []
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8844-9165
property_value: http://purl.org/dc/terms/date "2023-05-23T15:24:15Z" xsd:dateTime
property_value: IAO:0000112 "A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material." xsd:string
domain: OBI:0000070 ! assay
range: BFO:0000020 ! characteristic
inverse_of: RO:0009007 ! characteristic measured by assay

[Typedef]
id: RO:0009007
name: characteristic measured by assay
def: "Inverse of 'assay measures characteristic'" []
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8844-9165
property_value: http://purl.org/dc/terms/date "2023-05-23T15:29:50Z" xsd:dateTime
domain: BFO:0000020 ! characteristic
range: OBI:0000070 ! assay

[Typedef]
id: RO:0009501
name: realized in response to
Expand Down Expand Up @@ -6479,9 +6547,9 @@ 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." []
synonym: "utilizes" BROAD []
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2620-0345
property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899
property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345
property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string
property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string
holds_over_chain: RO:0002215 RO:0002233
Expand Down Expand Up @@ -6515,6 +6583,40 @@ property_value: IAO:0000112 "anticoagulant-containing test tube contains measure
domain: OBI:0000967 ! container
range: COB:0000121 ! measurement datum

[Typedef]
id: RO:0017006
name: has maximum capacity
def: "A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume." []
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2999-0103
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-5714-991X
property_value: IAO:0000112 "anticoagulant-containing test tube has maximum capacity 10 ml." xsd:string
domain: OBI:0000967 ! container
range: COB:0000121 ! measurement datum

[Typedef]
id: RO:0017008
name: owns
def: "A primitive relation that holds between entities x and y in which y is at x’s full disposal." []
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1834-3856
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269
property_value: http://purl.org/dc/terms/description "This primitive relation is the foundation of the owner’s right to have the owned entity at his/her full disposal." xsd:string
property_value: IAO:0000112 "biobank organization owns a specimen" xsd:string
property_value: IAO:0000112 "hospital owns a laboratory facility" xsd:string
inverse_of: RO:0017009 ! is owned by
creation_date: 2023-03-29T16:57:03Z

[Typedef]
id: RO:0017009
name: is owned by
def: "Inverse of the owns relation." []
subset: RO:0002259
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1834-3856
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269
property_value: IAO:0000112 "freezer is owned by a biobank organization" xsd:string
creation_date: 2023-03-29T17:06:06Z

[Typedef]
id: RO:0018001
name: is myristoyltransferase activity
Expand Down Expand Up @@ -6753,6 +6855,26 @@ range: UBERON:0000061 ! anatomical structure
is_a: RO:0002178 ! supplies
is_a: RO:0002179 ! drains

[Typedef]
id: RO:0020202
name: has numerator
def: "A relationship between a ratio or proportion and its dividend." [] {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0002-8280-0487"}
synonym: "has dividend" EXACT []
domain: PATO:0001470 ! proportionality to
range: PATO:0000001 ! quality
is_a: BFO:0000051 ! has part
created_by: https://orcid.org/0000-0001-8314-2140

[Typedef]
id: RO:0020203
name: has denominator
def: "A relationship between a ratio or proportion and its divisor." [] {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0002-8280-0487"}
synonym: "has divisor" EXACT []
domain: PATO:0001470 ! proportionality to
range: PATO:0000001 ! quality
is_a: BFO:0000051 ! has part
created_by: https://orcid.org/0000-0001-8314-2140

[Typedef]
id: RO:0040035
name: disease relationship
Expand Down
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