From bf9a48f19828228eab22e960f981bc4dc9262ebf Mon Sep 17 00:00:00 2001 From: Bill Duncan Date: Mon, 4 Mar 2024 11:57:28 -0500 Subject: [PATCH] NTR: owns; is owned by (#705) * add individual "Bill Duncan" * add owns/is owned by relations * add 'defined by inverse' annotation to 'is owned by' * add examples of usage * add inverse of axiom for is owned by * fix typo in defintion of owns * add defintion source to "is owned by" * add OBIB:0000735 as source for "owns" * remove complex example of usage * change conflicting IRIs * Fixes contributor annotations for NTR: owns; is owned by (#772) * Update ro-edit.owl Changed dc:contributor to terms:contributor. * Replacing more "dc" with "terms" * For NTR: owns; is owned by; replaces other "dc" with "terms" (#773) * Update ro-edit.owl Changed dc:contributor to terms:contributor. * Replacing more "dc" with "terms" * add Bill Duncan to orcidio_import.owl * remove individual Bill Duncan from ro-edit * remove individual "Bill Duncan" * run update for orcidio * add "William D Duncan" to orcidio_import.owl * add "William D Duncan" as contributor * add "William D Duncan" as contributor * remove dcterms:source from definition of is owned by * remove dcterms:source from definition of owns --------- Co-authored-by: Anita Caron Co-authored-by: Clint Dowland <52045818+CDowland@users.noreply.github.com> Co-authored-by: Anita Caron --- src/ontology/imports/orcidio_import.owl | 13 ++++++ src/ontology/ro-edit.owl | 60 ++++++++++++++++++------- 2 files changed, 56 insertions(+), 17 deletions(-) diff --git a/src/ontology/imports/orcidio_import.owl b/src/ontology/imports/orcidio_import.owl index 1044bba3..507a3345 100644 --- a/src/ontology/imports/orcidio_import.owl +++ b/src/ontology/imports/orcidio_import.owl @@ -14,6 +14,7 @@ Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) @@ -25,6 +26,8 @@ Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) + +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) @@ -60,6 +63,11 @@ AnnotationAssertion(Annotation( ) "researcher, metadata, diseases, University of Maryland") AnnotationAssertion(Annotation( ) rdfs:label "Lynn Schriml") +# Individual: (William D Duncan) + +AnnotationAssertion(Annotation( ) "researcher") +AnnotationAssertion(Annotation( ) rdfs:label "William D Duncan") + # Individual: (Anne Thessen) AnnotationAssertion(Annotation( ) "data scientist") @@ -115,6 +123,11 @@ AnnotationAssertion(Annotation( ) "Canadian biocurator") AnnotationAssertion(Annotation( ) rdfs:label "Pascale Gaudet") + +# Individual: (Mathias Brochhausen) + +AnnotationAssertion(Annotation( ) "researcher") +AnnotationAssertion(Annotation( ) rdfs:label "Mathias Brochhausen") # Individual: (S. Clint Dowland) AnnotationAssertion(Annotation( ) "Researcher ORCID=0000-0003-1909-9269") diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index 3514946b..84fb6809 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -579,6 +579,8 @@ Declaration(ObjectProperty(obo:RO_0017001)) Declaration(ObjectProperty(obo:RO_0017003)) Declaration(ObjectProperty(obo:RO_0017004)) Declaration(ObjectProperty(obo:RO_0017005)) +Declaration(ObjectProperty(obo:RO_0017008)) +Declaration(ObjectProperty(obo:RO_0017009)) Declaration(ObjectProperty(obo:RO_0018001)) Declaration(ObjectProperty(obo:RO_0018002)) Declaration(ObjectProperty(obo:RO_0018003)) @@ -2634,10 +2636,10 @@ SubObjectPropertyOf(obo:RO_0002237 obo:RO_0002444) # Object Property: obo:RO_0002238 (has component participant) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002238 "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys.") -AnnotationAssertion(obo:IAO_0000117 obo:RO_0002238 ) AnnotationAssertion(obo:IAO_0000232 obo:RO_0002238 "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). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'.") +AnnotationAssertion(terms:contributor obo:RO_0002238 ) AnnotationAssertion(rdfs:label obo:RO_0002238 "has component participant"@en) SubObjectPropertyOf(obo:RO_0002238 obo:RO_0000057) @@ -3879,8 +3881,8 @@ SubObjectPropertyOf(obo:RO_0002433 obo:RO_0002131) # Object Property: obo:RO_0002434 (interacts with) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002434 "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") -AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") +AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002434 ) AnnotationAssertion(obo:IAO_0000232 obo:RO_0002434 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002434 "in pairwise interaction with") @@ -6549,10 +6551,10 @@ SubObjectPropertyOf(obo:RO_0016004 obo:RO_0002244) AnnotationAssertion(obo:IAO_0000112 obo:RO_0017001 "A diagnostic testing device utilizes a specimen.") AnnotationAssertion(obo:IAO_0000115 obo:RO_0017001 "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") -AnnotationAssertion(obo:IAO_0000117 obo:RO_0017001 ) -AnnotationAssertion(obo:IAO_0000117 obo:RO_0017001 ) AnnotationAssertion(obo:IAO_0000232 obo:RO_0017001 "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.") AnnotationAssertion(obo:IAO_0000232 obo:RO_0017001 "See github ticket https://github.com/oborel/obo-relations/issues/497") +AnnotationAssertion(terms:contributor obo:RO_0017001 ) +AnnotationAssertion(terms:contributor obo:RO_0017001 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0017001 "2021-11-08T12:00:00Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasBroadSynonym obo:RO_0017001 "utilizes") AnnotationAssertion(rdfs:label obo:RO_0017001 "device utilizes material"@en) @@ -6586,6 +6588,30 @@ AnnotationAssertion(rdfs:label obo:RO_0017005 "contains measured amount"@en) ObjectPropertyDomain(obo:RO_0017005 obo:OBI_0000967) ObjectPropertyRange(obo:RO_0017005 obo:COB_0000121) +# Object Property: obo:RO_0017008 (owns) + +AnnotationAssertion(obo:IAO_0000112 obo:RO_0017008 "biobank organization owns a specimen") +AnnotationAssertion(obo:IAO_0000112 obo:RO_0017008 "hospital owns a laboratory facility") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0017008 "A primitive relation that holds between entities x and y in which y is at x’s full disposal.") +AnnotationAssertion(terms:contributor obo:RO_0017008 ) +AnnotationAssertion(terms:contributor obo:RO_0017008 ) +AnnotationAssertion(terms:contributor obo:RO_0017008 ) +AnnotationAssertion(terms:description obo:RO_0017008 "This primitive relation is the foundation of the owner’s right to have the owned entity at his/her full disposal.") +AnnotationAssertion(oboInOwl:creation_date obo:RO_0017008 "2023-03-29T16:57:03Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label obo:RO_0017008 "owns"@en) +InverseObjectProperties(obo:RO_0017008 obo:RO_0017009) + +# Object Property: obo:RO_0017009 (is owned by) + +AnnotationAssertion(obo:IAO_0000112 obo:RO_0017009 "freezer is owned by a biobank organization") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0017009 "Inverse of the owns relation.") +AnnotationAssertion(terms:contributor obo:RO_0017009 ) +AnnotationAssertion(terms:contributor obo:RO_0017009 ) +AnnotationAssertion(terms:contributor obo:RO_0017009 ) +AnnotationAssertion(oboInOwl:creation_date obo:RO_0017009 "2023-03-29T17:06:06Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:inSubset obo:RO_0017009 obo:RO_0002259) +AnnotationAssertion(rdfs:label obo:RO_0017009 "is owned by"@en) + # Object Property: obo:RO_0018001 (is myristoyltransferase activity) AnnotationAssertion(obo:IAO_0000115 obo:RO_0018001 "Helper relation for OWL definition of RO:0018002 myristoylates") @@ -7190,19 +7216,19 @@ DLSafeRule(Annotation(rdfs:seeAlso ) Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002013 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002014 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002015 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002404 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002131 Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002131 Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0012011 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002211 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0012012 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002213 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0019002 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0019001 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002213 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002264 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002263 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0012011 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002131 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002404 Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002131 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002211 Variable() Variable()) ObjectPropertyAtom(obo:RO_0012011 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0012012 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002213 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()) ObjectPropertyAtom(obo:RO_0019002 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0019001 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002213 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002264 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002263 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0012011 Variable() Variable()))) AnnotationAssertion(owl:deprecated obo:BFO_0000060 "true"^^xsd:boolean) AnnotationAssertion(obo:IAO_0000115 obo:RO_0000092 "inverse of has disposition") AnnotationAssertion(oboInOwl:inSubset obo:RO_0000092 obo:RO_0002259)