From e8696f229f78c2fa3cede2d8c4e79f39617bce99 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 2 Oct 2023 09:11:16 -0700 Subject: [PATCH 1/6] collected during relation --- src/ontology/ro-edit.owl | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index 0fbdb4d5..52740d9f 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -573,6 +573,7 @@ Declaration(ObjectProperty(obo:RO_0016004)) Declaration(ObjectProperty(obo:RO_0017001)) Declaration(ObjectProperty(obo:RO_0017003)) Declaration(ObjectProperty(obo:RO_0017004)) +Declaration(ObjectProperty(obo:RO_0017502)) Declaration(ObjectProperty(obo:RO_0018001)) Declaration(ObjectProperty(obo:RO_0018002)) Declaration(ObjectProperty(obo:RO_0018003)) @@ -1233,7 +1234,7 @@ SubAnnotationPropertyOf(subsets:ro-eco oboInOwl:SubsetProperty) AnnotationAssertion(rdfs:label oboInOwl:SubsetProperty "subset_property") -# Annotation Property: oboInOwl:hasNarrowSynonym (has narrow synonym) +# Annotation Property: oboInOwl:hasNarrowSynonym (has_narrow_synonym) AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym") @@ -1334,7 +1335,6 @@ AnnotationAssertion(rdfs:label obo:RO_0001018 "obsolete contained in") AnnotationAssertion(rdfs:seeAlso obo:RO_0001018 ) AnnotationAssertion(owl:deprecated obo:RO_0001018 "true"^^xsd:boolean) - # Object Property: obo:RO_0001019 (obsolete contains) AnnotationAssertion(obo:IAO_0000111 obo:RO_0001019 "contains"@en) @@ -6513,6 +6513,17 @@ SubObjectPropertyOf(obo:RO_0017004 obo:RO_0002610) SymmetricObjectProperty(obo:RO_0017004) IrreflexiveObjectProperty(obo:RO_0017004) +# Object Property: obo:RO_0017502 (collected during) + +AnnotationAssertion(obo:IAO_0000112 obo:RO_0017502 "A thorax specimen was collected during the larval stage."@en) +AnnotationAssertion(obo:IAO_0000112 obo:RO_0017502 "An oyster was collected during low tide."@en) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0017502 "A relation between a material entity and an occurent in which the specimen is collected during the existence of the occurent."@en) +AnnotationAssertion(terms:contributor obo:RO_0017502 ) +AnnotationAssertion(terms:date obo:RO_0017502 "2023-09-13T04:12:32Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label obo:RO_0017502 "collected during"@en) +ObjectPropertyDomain(obo:RO_0017502 obo:BFO_0000040) +ObjectPropertyRange(obo:RO_0017502 obo:BFO_0000003) + # Object Property: obo:RO_0018001 (is myristoyltransferase activity) AnnotationAssertion(obo:IAO_0000115 obo:RO_0018001 "Helper relation for OWL definition of RO:0018002 myristoylates") From b17d8377cd513d2df55f7c35225b2a72f3b11187 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Sun, 21 Jan 2024 19:05:30 -0800 Subject: [PATCH 2/6] definition tweak. --- src/ontology/ro-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index 52740d9f..8754faad 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -6517,7 +6517,7 @@ IrreflexiveObjectProperty(obo:RO_0017004) AnnotationAssertion(obo:IAO_0000112 obo:RO_0017502 "A thorax specimen was collected during the larval stage."@en) AnnotationAssertion(obo:IAO_0000112 obo:RO_0017502 "An oyster was collected during low tide."@en) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0017502 "A relation between a material entity and an occurent in which the specimen is collected during the existence of the occurent."@en) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0017502 "A relation between a material entity and an occurrent in which the material entity is collected during the existence of the occurrent. The material entity is a specimen that is collected for scientific purposes."@en) AnnotationAssertion(terms:contributor obo:RO_0017502 ) AnnotationAssertion(terms:date obo:RO_0017502 "2023-09-13T04:12:32Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0017502 "collected during"@en) From 4ca19e746ee79ad541a8f4bc34c5a4957ff5d393 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Mon, 22 Jan 2024 16:51:53 -0300 Subject: [PATCH 3/6] update `orcidio_import` --- src/ontology/imports/orcidio_import.owl | 40 +++++++++++++++++++++++-- 1 file changed, 38 insertions(+), 2 deletions(-) diff --git a/src/ontology/imports/orcidio_import.owl b/src/ontology/imports/orcidio_import.owl index 46124dcd..3e58ae12 100644 --- a/src/ontology/imports/orcidio_import.owl +++ b/src/ontology/imports/orcidio_import.owl @@ -7,21 +7,27 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-08-16") + +Annotation(owl:versionInfo "2024-01-22") Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -54,11 +60,21 @@ AnnotationAssertion(Annotation( ) "data scientist") AnnotationAssertion(Annotation( ) rdfs:label "Anne Thessen") +# Individual: (Jie Zheng) + +AnnotationAssertion(Annotation( ) "researcher (ORCID 0000-0002-2999-0103)") +AnnotationAssertion(Annotation( ) rdfs:label "Jie Zheng") + # Individual: (Pier Luigi Buttigieg) AnnotationAssertion(Annotation( ) "researcher") AnnotationAssertion(Annotation( ) rdfs:label "Pier Luigi Buttigieg") +# Individual: (Christian J Stoeckert) + +AnnotationAssertion(Annotation( ) "researcher") +AnnotationAssertion(Annotation( ) rdfs:label "Christian J Stoeckert") + # Individual: (Christopher J. Mungall) AnnotationAssertion(Annotation( ) "bioinformatics researcher") @@ -84,16 +100,36 @@ AnnotationAssertion(Annotation( ) "researcher") AnnotationAssertion(Annotation( ) rdfs:label "James P. Balhoff") +# Individual: (Damion M Dooley) + +AnnotationAssertion(Annotation( ) "researcher (ORCID 0000-0002-8844-9165)") +AnnotationAssertion(Annotation( ) rdfs:label "Damion M Dooley") + # Individual: (Lindsay G Cowell) AnnotationAssertion(Annotation( ) "researcher") AnnotationAssertion(Annotation( ) rdfs:label "Lindsay G Cowell") +# Individual: (Pascale Gaudet) + +AnnotationAssertion(Annotation( ) "Canadian biocurator") +AnnotationAssertion(Annotation( ) rdfs:label "Pascale Gaudet") + +# Individual: (S. Clint Dowland) + +AnnotationAssertion(Annotation( ) "Researcher ORCID=0000-0003-1909-9269") +AnnotationAssertion(Annotation( ) rdfs:label "S. Clint Dowland") + # Individual: (Anna Maria Masci) AnnotationAssertion(Annotation( ) "researcher") AnnotationAssertion(Annotation( ) rdfs:label "Anna Maria Masci") +# Individual: (Jorrit Poelen) + +AnnotationAssertion(Annotation( ) "software/data engineer") +AnnotationAssertion(Annotation( ) rdfs:label "Jorrit Poelen") + # Individual: (Charles Tapley Hoyt) AnnotationAssertion(Annotation( ) "American chemist") From 1380b7786029131714267e8ab15a4f66ce0f7586 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Fri, 9 Feb 2024 10:24:13 +0000 Subject: [PATCH 4/6] normalize ro-edit file --- src/ontology/ro-edit.owl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index bf7596b4..3bbeed88 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -6575,6 +6575,7 @@ AnnotationAssertion(terms:contributor obo:RO_0017005 Date: Tue, 7 May 2024 22:18:00 -0700 Subject: [PATCH 5/6] collected during relation defn simplification --- src/ontology/ro-edit.owl | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index 1efaccc4..ece13d27 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -44,6 +44,7 @@ Declaration(Class(obo:BFO_0000031)) Declaration(Class(obo:CHEBI_50906)) Declaration(Class(obo:COB_0001000)) Declaration(Class(obo:OGMS_0000031)) +Declaration(Class(obo:PATO_0001470)) Declaration(Class(obo:RO_0002310)) Declaration(Class(obo:RO_0002532)) Declaration(Class(obo:RO_0002533)) @@ -6650,7 +6651,7 @@ AnnotationAssertion(rdfs:label obo:RO_0017009 "is owned by"@en) AnnotationAssertion(obo:IAO_0000112 obo:RO_0017502 "A thorax specimen was collected during the larval stage."@en) AnnotationAssertion(obo:IAO_0000112 obo:RO_0017502 "An oyster was collected during low tide."@en) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0017502 "A relation between a material entity and an occurrent in which the material entity is collected during the existence of the occurrent. The material entity is a specimen that is collected for scientific purposes."@en) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0017502 "A relation between a material entity and an occurrent in which the material entity is collected during the existence of the occurrent."@en) AnnotationAssertion(terms:contributor obo:RO_0017502 ) AnnotationAssertion(terms:date obo:RO_0017502 "2023-09-13T04:12:32Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0017502 "collected during"@en) @@ -7287,4 +7288,4 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002086 subsets:ro-eco) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002089 subsets:ro-eco) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002093 subsets:ro-eco) AnnotationAssertion(Annotation(rdfs:comment "This is an experimental annotation") obo:IAO_0000589 rdfs:isDefinedBy "is defined by") -) +) \ No newline at end of file From f6b503b9a5debe3b9299174a6bbe1e744b17914e Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Mon, 15 Jul 2024 10:05:34 +0100 Subject: [PATCH 6/6] remove misplaced pato term from ro-edit --- src/ontology/ro-edit.owl | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index ece13d27..ab3a9686 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -44,7 +44,6 @@ Declaration(Class(obo:BFO_0000031)) Declaration(Class(obo:CHEBI_50906)) Declaration(Class(obo:COB_0001000)) Declaration(Class(obo:OGMS_0000031)) -Declaration(Class(obo:PATO_0001470)) Declaration(Class(obo:RO_0002310)) Declaration(Class(obo:RO_0002532)) Declaration(Class(obo:RO_0002533))