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Merge pull request #3106 from obophenotype/3088_update_connecting_bra…
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Addresses #3088 change vascular object property
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@aleixpuigb
aleixpuigb authored Nov 30, 2023
2 parents b51b4a0 + 50ab1af commit 5c9edfb
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Showing 6 changed files with 410 additions and 171 deletions.
291 changes: 147 additions & 144 deletions src/ontology/uberon-edit.obo
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4 changes: 4 additions & 0 deletions src/patterns/data/default/vessel_connecting_branch_of_vessel_pattern.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
defined_class defined_class_label stem_vessel stem_vessel_label
UBERON:0001394 axillary artery UBERON:0001394 subclavian artery
UBERON:0001312 superior vesical artery UBERON:0001310 umbilical artery
UBERON:0013137 external pudendal artery UBERON:0002060 femoral artery
22 changes: 20 additions & 2 deletions src/patterns/definitions.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,16 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/uberon/patterns/definitions.owl>
<http://purl.obolibrary.org/obo/uberon/releases/2023-07-24/patterns/definitions.owl>
Annotation(owl:versionInfo "2023-07-24")
<http://purl.obolibrary.org/obo/uberon/releases/2023-11-21/patterns/definitions.owl>
Annotation(owl:versionInfo "2023-11-21")

Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001310>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001312>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001394>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001709>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001710>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0002060>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0013137>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0016454>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0016455>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0018561>))
Expand Down Expand Up @@ -92,6 +97,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_8490050>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_8490051>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BSPO_0000120>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BSPO_0000121>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002252>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002175>))
Declaration(AnnotationProperty(<http://purl.org/dc/terms/contributor>))
Expand All @@ -106,6 +112,18 @@ Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#has
# Classes
############################

# Class: <http://purl.obolibrary.org/obo/UBERON_0001312> (<http://purl.obolibrary.org/obo/UBERON_0001312>)

SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0001312> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002252> <http://purl.obolibrary.org/obo/UBERON_0001310>))

# Class: <http://purl.obolibrary.org/obo/UBERON_0001394> (<http://purl.obolibrary.org/obo/UBERON_0001394>)

SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0001394> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002252> <http://purl.obolibrary.org/obo/UBERON_0001394>))

# Class: <http://purl.obolibrary.org/obo/UBERON_0013137> (<http://purl.obolibrary.org/obo/UBERON_0013137>)

SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0013137> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002252> <http://purl.obolibrary.org/obo/UBERON_0002060>))

# Class: <http://purl.obolibrary.org/obo/UBERON_8490000> (right upper third secondary molar tooth)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/UBERON_8490000> "A upper third secondary molar tooth that is in the right side of the upper jaw region.")
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22 changes: 22 additions & 0 deletions src/patterns/dosdp-patterns/vessel_connecting_branch_of_vessel_pattern.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
pattern_name: vessel_connecting_branch_of_vessel_pattern
pattern_iri: http://purl.obolibrary.org/obo/uberon/src/patterns/vessel_connecting_branch_of_vessel_pattern.yaml

description: A vessel that is branching from another vessel (stem vessel), and it is NOT part of it, it is a 'connecting branch of' the stem vessel.
#examples: vertebral artery(UBERON:0001535) is a connecting branch of subclavian artery(UBERON:0001533)

contributors:
- https://orcid.org/0000-0001-6677-8489

classes:
vessel: "UBERON:0000055"

relations:
connecting_branch_of: "RO:0002252"

vars:
stem_vessel: "'vessel'"

subClassOf:
text: "'connecting_branch_of' some %s"
vars:
- stem_vessel
55 changes: 30 additions & 25 deletions src/patterns/pattern.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -8,36 +8,40 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)

Ontology(<urn:unnamed:ontology#ont1>

Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000055>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001021>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001062>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001091>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001638>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0003672>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0010000>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0010912>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0011595>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0012360>))
Declaration(Class(<http://purl.obolibrary.org/obo/uberon/nerve_by_structure_innervated>))
Declaration(Class(<http://purl.obolibrary.org/obo/uberon/patterns/anatomyPartOfAnatomy.yaml>))
Declaration(Class(<http://purl.obolibrary.org/obo/uberon/patterns/left_teeth.yaml>))
Declaration(Class(<http://purl.obolibrary.org/obo/uberon/patterns/lower_teeth.yaml>))
Declaration(Class(<http://purl.obolibrary.org/obo/uberon/patterns/right_left_teeth.yaml>))
Declaration(Class(<http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml>))
Declaration(Class(<http://purl.obolibrary.org/obo/uberon/patterns/skeleton_of_body_part.yaml>))
Declaration(Class(<http://purl.obolibrary.org/obo/uberon/patterns/upper_teeth.yaml>))
Declaration(Class(<http://purl.obolibrary.org/obo/uberon/patterns/vein_by_drainage.yaml>))
Declaration(Class(<http://purl.obolibrary.org/obo/uberon/src/patterns/vessel_connecting_branch_of_vessel_pattern.yaml>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BSPO_0000120>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BSPO_0000121>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BSPO_0000126>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002134>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002179>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002252>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002576>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002175>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/contributor>))
Declaration(AnnotationProperty(<http://purl.org/dc/terms/contributor>))
Declaration(AnnotationProperty(<http://purl.org/dc/terms/title>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#creation_date>))
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#hasRelatedSynonym>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType>))



Expand All @@ -61,6 +65,17 @@ AnnotationAssertion(<http://purl.org/dc/terms/title> <http://purl.obolibrary.org
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/uberon/patterns/anatomyPartOfAnatomy.yaml> "'anatomical entity' of 'anatomical entity'"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/uberon/patterns/anatomyPartOfAnatomy.yaml> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0001062> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001062>)))

# Class: <http://purl.obolibrary.org/obo/uberon/patterns/left_teeth.yaml> (xsd:string calcareous tooth)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/uberon/patterns/left_teeth.yaml> "A calcareous tooth that is in the left side of the jaw region."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/uberon/patterns/left_teeth.yaml> <https://orcid.org/0000-0001-9625-1899>)
AnnotationAssertion(<http://purl.org/dc/terms/title> <http://purl.obolibrary.org/obo/uberon/patterns/left_teeth.yaml> "left_teeth"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/uberon/patterns/left_teeth.yaml> "xsd:dateTime"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/uberon/patterns/left_teeth.yaml> "xsd:string"^^xsd:string)
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "xsd:string"^^xsd:string) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/uberon/core#HUMAN_PREFERRED>) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/uberon/patterns/left_teeth.yaml> "xsd:string"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/uberon/patterns/left_teeth.yaml> "xsd:string calcareous tooth"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/uberon/patterns/left_teeth.yaml> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0001091> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BSPO_0000120> <http://purl.obolibrary.org/obo/UBERON_0011595>)))

# Class: <http://purl.obolibrary.org/obo/uberon/patterns/lower_teeth.yaml> (dentition_type lower calcareous_tooth)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "'xref'"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/uberon/patterns/lower_teeth.yaml> "A dentition_type calcareous_tooth that is part of a lower jaw region."^^xsd:string)
Expand All @@ -69,31 +84,16 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynony
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/uberon/patterns/lower_teeth.yaml> "dentition_type lower calcareous_tooth"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/uberon/patterns/lower_teeth.yaml> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0001091> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0003672>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0012360>)))

# Class: <http://purl.obolibrary.org/obo/uberon/patterns/right_left_teeth.yaml> (xsd:string calcareous tooth)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/uberon/patterns/right_left_teeth.yaml> "A calcareous tooth that is in the right side of the bone of jaw."^^xsd:string)
AnnotationAssertion(<http://purl.obolibrary.org/obo/RO_0002175> <http://purl.obolibrary.org/obo/uberon/patterns/right_left_teeth.yaml> "xsd:string"^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/uberon/patterns/right_left_teeth.yaml> "xsd:string"^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/title> <http://purl.obolibrary.org/obo/uberon/patterns/right_left_teeth.yaml> "right__left_teeth"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/uberon/patterns/right_left_teeth.yaml> "xsd:dateTime"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/uberon/patterns/right_left_teeth.yaml> "xsd:string"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/uberon/patterns/right_left_teeth.yaml> "xsd:string"^^xsd:string)
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "xsd:string"^^xsd:string) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/uberon/patterns/right_left_teeth.yaml> "xsd:string"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/uberon/patterns/right_left_teeth.yaml> "xsd:string calcareous tooth"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/uberon/patterns/right_left_teeth.yaml> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0001091> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BSPO_0000126> <http://purl.obolibrary.org/obo/UBERON_0012360>)))
# Class: <http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> (xsd:string calcareous tooth)

# Class: <http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> (right calcareous tooth)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> "A calcareous tooth that is in the right side of the bone of jaw."^^xsd:string)
AnnotationAssertion(<http://purl.obolibrary.org/obo/RO_0002175> <http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> "xsd:string"^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> "xsd:string"^^xsd:string)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> "A calcareous tooth that is in the right side of the jaw region."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> <https://orcid.org/0000-0001-9625-1899>)
AnnotationAssertion(<http://purl.org/dc/terms/title> <http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> "right_teeth"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> "xsd:dateTime"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> "xsd:string"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> "xsd:string"^^xsd:string)
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "xsd:string"^^xsd:string) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> "xsd:string"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> "right calcareous tooth"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0001091> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BSPO_0000121> <http://purl.obolibrary.org/obo/UBERON_0012360>)))
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "xsd:string"^^xsd:string) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/uberon/core#HUMAN_PREFERRED>) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> "xsd:string"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> "xsd:string calcareous tooth"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/uberon/patterns/right_teeth.yaml> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0001091> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BSPO_0000121> <http://purl.obolibrary.org/obo/UBERON_0011595>)))

# Class: <http://purl.obolibrary.org/obo/uberon/patterns/skeleton_of_body_part.yaml> (skeleton of 'multicellular anatomical structure')

Expand All @@ -120,5 +120,10 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynony
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/uberon/patterns/vein_by_drainage.yaml> "'multicellular anatomical structure' vein"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/uberon/patterns/vein_by_drainage.yaml> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0001638> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002179> <http://purl.obolibrary.org/obo/UBERON_0010000>)))

# Class: <http://purl.obolibrary.org/obo/uberon/src/patterns/vessel_connecting_branch_of_vessel_pattern.yaml> (<http://purl.obolibrary.org/obo/uberon/src/patterns/vessel_connecting_branch_of_vessel_pattern.yaml>)

AnnotationAssertion(<http://purl.org/dc/terms/title> <http://purl.obolibrary.org/obo/uberon/src/patterns/vessel_connecting_branch_of_vessel_pattern.yaml> "vessel_connecting_branch_of_vessel_pattern"^^xsd:string)
SubClassOf(<http://purl.obolibrary.org/obo/uberon/src/patterns/vessel_connecting_branch_of_vessel_pattern.yaml> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002252> <http://purl.obolibrary.org/obo/UBERON_0000055>))


)
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