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NTR "has life cycle stage" relation #742

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NTR "has life cycle stage" relation #742

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2cd3d1f
new "has life cycle stage" relation
ddooley Aug 10, 2023
9f8af24
Merge branch 'master' into issue-#598
Aug 11, 2023
af171d3
Changing this pull request to focus on "has life cycle stage" and its…
ddooley Aug 29, 2023
e93cbf0
extra example
ddooley Aug 29, 2023
04af402
Merge branch 'master' into issue-#598
ddooley Aug 29, 2023
ad9dce7
dc prefix update
ddooley Aug 29, 2023
6d86800
undo spurious diff
ddooley Oct 2, 2023
6778732
Merge branch 'master' into issue-#598
anitacaron Jan 22, 2024
d2041b4
Merge branch 'master' into issue-#598
anitacaron Mar 28, 2024
b68b569
removed domain, range on inverse
ddooley May 8, 2024
ec84f1a
Merge branch 'master' into issue-#598
ddooley May 8, 2024
00a385a
remove misplaced pato term from edit file
anitacaron Jul 15, 2024
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19 changes: 16 additions & 3 deletions src/ontology/imports/obi_import.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,12 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/ro/imports/obi_import.owl>
<http://purl.obolibrary.org/obo/ro/releases/2023-06-28/imports/obi_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl>)
Annotation(owl:versionInfo "2023-06-28")
<http://purl.obolibrary.org/obo/ro/releases/2023-08-10/imports/obi_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/obi/2023-07-25/obi.owl>)
Annotation(owl:versionInfo "2023-08-10")

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000040>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0001479>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0100026>))
Declaration(AnnotationProperty(<http://protege.stanford.edu/plugins/owl/protege#defaultLanguage>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000111>))
Expand All @@ -20,6 +21,7 @@ Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000114>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000116>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000117>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000118>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000119>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000589>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/contributor>))
Expand All @@ -38,6 +40,17 @@ Declaration(Datatype(xsd:date))
# Classes
############################

# Class: <http://purl.obolibrary.org/obo/OBI_0001479> (specimen from organism)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/OBI_0001479> "specimen from organism"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/OBI_0001479> <http://purl.obolibrary.org/obo/IAO_0000122>)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBI_0001479> "A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/OBI_0001479> "PERSON: Chris Stoeckert, Jie Zheng")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/OBI_0001479> "tissue specimen"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/OBI_0001479> "MO_954 organism_part")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBI_0001479> "specimen from organism"@en)
SubClassOf(<http://purl.obolibrary.org/obo/OBI_0001479> <http://purl.obolibrary.org/obo/BFO_0000040>)

# Class: <http://purl.obolibrary.org/obo/OBI_0100026> (organism)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/OBI_0100026> "organism"@en)
Expand Down
3 changes: 2 additions & 1 deletion src/ontology/imports/obi_terms.txt
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Original file line number Diff line number Diff line change
@@ -1 +1,2 @@
OBI:0100026
OBI:0100026
OBI:0001479
42 changes: 39 additions & 3 deletions src/ontology/imports/uberon_import.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/ro/imports/uberon_import.owl>
<http://purl.obolibrary.org/obo/ro/releases/2023-06-28/imports/uberon_import.owl>
<http://purl.obolibrary.org/obo/ro/releases/2023-08-10/imports/uberon_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://dbpedia.org>)
Annotation(<http://purl.org/dc/elements/1.1/source> <http://palaeos.com>)
Annotation(<http://purl.org/dc/elements/1.1/source> <http://www.brain-map.org>)
Expand Down Expand Up @@ -36,7 +36,7 @@ Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/wbbt.owl>)
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/xao.owl>)
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/zfa.owl>)
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/uberon/releases/2023-06-27/uberon.owl>)
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/uberon/releases/2023-07-25/uberon.owl>)
Annotation(<http://purl.org/dc/elements/1.1/source> <http://uri.neuinfo.org/nif/nifstd>)
Annotation(<http://purl.org/dc/elements/1.1/source> <http://www.e-lico.eu/public/kupo/kupo.owl>)
Annotation(<http://purl.org/dc/elements/1.1/source> <http://www.ebi.ac.uk/efo/efo.owl>)
Expand Down Expand Up @@ -68,21 +68,24 @@ Annotation(<http://purl.org/dc/elements/1.1/source> "PMID:16417468 Forgotten and
Annotation(<http://purl.org/dc/elements/1.1/source> "aggregates AAO from 13:04:2012")
Annotation(<http://purl.org/dc/elements/1.1/source> "aggregates TAO from 09:08:2012")
Annotation(<http://purl.org/dc/elements/1.1/source> "aggregates VSAO from 16:07:2012")
Annotation(owl:versionInfo "2023-06-28")
Annotation(owl:versionInfo "2023-08-10")

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000004>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000040>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000141>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000061>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000105>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000122>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000465>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000466>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001062>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0010000>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000116>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000700>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002175>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#common_anatomy>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#efo_slim>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#upper_level>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/creator>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/description>))
Expand All @@ -100,6 +103,7 @@ Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#Sub
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#default-namespace>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasDbXref>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#id>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#inSubset>))
Expand All @@ -117,6 +121,10 @@ Declaration(AnnotationProperty(<http://xmlns.com/foaf/0.1/homepage>))

SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/uberon/core#common_anatomy> <http://www.geneontology.org/formats/oboInOwl#SubsetProperty>)

# Annotation Property: <http://purl.obolibrary.org/obo/uberon/core#efo_slim> (<http://purl.obolibrary.org/obo/uberon/core#efo_slim>)

SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/uberon/core#efo_slim> <http://www.geneontology.org/formats/oboInOwl#SubsetProperty>)

# Annotation Property: <http://purl.obolibrary.org/obo/uberon/core#upper_level> (<http://purl.obolibrary.org/obo/uberon/core#upper_level>)

SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/uberon/core#upper_level> <http://www.geneontology.org/formats/oboInOwl#SubsetProperty>)
Expand Down Expand Up @@ -160,6 +168,34 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <htt
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0000061> "anatomical structure")
SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0000061> <http://purl.obolibrary.org/obo/UBERON_0000465>)

# Class: <http://purl.obolibrary.org/obo/UBERON_0000105> (life cycle stage)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://orcid.org/0000-0002-6601-2165") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/UBERON_0000105> "A spatiotemporal region encompassing some part of the life cycle of an organism.")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/UBERON_0000105> "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here")
AnnotationAssertion(<http://purl.obolibrary.org/obo/RO_0002175> <http://purl.obolibrary.org/obo/UBERON_0000105> <http://purl.obolibrary.org/obo/NCBITaxon_33090>)
AnnotationAssertion(<http://purl.obolibrary.org/obo/RO_0002175> <http://purl.obolibrary.org/obo/UBERON_0000105> <http://purl.obolibrary.org/obo/NCBITaxon_4751>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_0000105> "BILS:0000105")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_0000105> "EFO:0000399")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_0000105> "FBdv:00007012")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_0000105> "FMA:24120")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_0000105> "HsapDv:0000000")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_0000105> "MESH:D008018")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_0000105> "MmusDv:0000000")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_0000105> "OlatDv:0000010")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_0000105> "PdumDv:0000090")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_0000105> "WBls:0000002")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_0000105> "XAO:1000000")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_0000105> "ZFS:0000000")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_0000105> "ZFS:0100000")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/UBERON_0000105> "ncithesaurus:Developmental_Stage")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://purl.obolibrary.org/obo/UBERON_0000105> "developmental stage")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://purl.obolibrary.org/obo/UBERON_0000105> "stage")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/UBERON_0000105> "UBERON:0000105")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/UBERON_0000105> <http://purl.obolibrary.org/obo/uberon/core#common_anatomy>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/UBERON_0000105> <http://purl.obolibrary.org/obo/uberon/core#efo_slim>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/UBERON_0000105> <http://purl.obolibrary.org/obo/uberon/core#upper_level>)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0000105> "life cycle stage")

# Class: <http://purl.obolibrary.org/obo/UBERON_0000122> (neuron projection bundle)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "CARO:0001001") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FBC:DOS") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FBbt:00005099") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/UBERON_0000122> "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.")
Expand Down
1 change: 1 addition & 0 deletions src/ontology/imports/uberon_terms.txt
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Expand Up @@ -4,3 +4,4 @@ UBERON:0000466
UBERON:0000465
UBERON:0010000
UBERON:0000122
UBERON:0000105
24 changes: 24 additions & 0 deletions src/ontology/ro-edit.owl
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Expand Up @@ -573,6 +573,8 @@ Declaration(ObjectProperty(obo:RO_0016004))
Declaration(ObjectProperty(obo:RO_0017001))
Declaration(ObjectProperty(obo:RO_0017003))
Declaration(ObjectProperty(obo:RO_0017004))
Declaration(ObjectProperty(obo:RO_0017500))
Declaration(ObjectProperty(obo:RO_0017501))
Declaration(ObjectProperty(obo:RO_0018001))
Declaration(ObjectProperty(obo:RO_0018002))
Declaration(ObjectProperty(obo:RO_0018003))
Expand Down Expand Up @@ -6523,6 +6525,28 @@ SubObjectPropertyOf(obo:RO_0017004 obo:RO_0002610)
SymmetricObjectProperty(obo:RO_0017004)
IrreflexiveObjectProperty(obo:RO_0017004)

# Object Property: obo:RO_0017500 (has life cycle stage)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0017500 "A relationship between an organism and a stage it undergoes within its full life cycle."@en)
AnnotationAssertion(dc:contributor obo:RO_0017500 <https://orcid.org/0000-0002-1373-1705>)
AnnotationAssertion(dc:contributor obo:RO_0017500 <https://orcid.org/0000-0002-8844-9165>)
AnnotationAssertion(dc:date obo:RO_0017500 "2023-08-09T18:37:32Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:comment obo:RO_0017500 "This relation accommodates social, behavioural and biological (developmental) stages."@en)
AnnotationAssertion(rdfs:label obo:RO_0017500 "has life cycle stage"@en)
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SubObjectPropertyOf(obo:RO_0017500 obo:RO_0000056)
ObjectPropertyDomain(obo:RO_0017500 obo:OBI_0100026)
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ObjectPropertyRange(obo:RO_0017500 obo:UBERON_0000105)

# Object Property: obo:RO_0017501 (collected during life cycle stage)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0017501 "A relationship between an organism specimen and the organism's life cycle stage during which specimen collection occurred."@en)
AnnotationAssertion(dc:contributor obo:RO_0017501 <https://orcid.org/0000-0002-8844-9165>)
AnnotationAssertion(dc:date obo:RO_0017501 "2023-08-09T18:40:21Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0017501 "collected during life cycle stage"@en)
SubObjectPropertyOf(obo:RO_0017501 obo:RO_0000056)
ObjectPropertyDomain(obo:RO_0017501 obo:OBI_0001479)
ObjectPropertyRange(obo:RO_0017501 obo:UBERON_0000105)

# Object Property: obo:RO_0018001 (is myristoyltransferase activity)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0018001 "Helper relation for OWL definition of RO:0018002 myristoylates")
Expand Down
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