Skip to content

Commit

Permalink
updated errors to self refernce
Browse files Browse the repository at this point in the history
  • Loading branch information
Leigh Carmody committed Oct 19, 2023
1 parent 272582c commit 04b8995
Show file tree
Hide file tree
Showing 8 changed files with 42 additions and 11 deletions.
2 changes: 1 addition & 1 deletion src/ontology/maxo-edit.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1217,6 +1217,7 @@ AnnotationAssertion(dce:date <http://purl.obolibrary.org/obo/MAXO_0000012> <2023
AnnotationAssertion(dcterms:creator <http://purl.obolibrary.org/obo/MAXO_0000012> <http://orcid.org/0000-0001-7941-2961>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MAXO_0000012> "surgical procedure on body region")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MAXO_0000012> "surgery by body site")
EquivalentClasses(<http://purl.obolibrary.org/obo/MAXO_0000012> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/MAXO_0000004> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002233> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000467>))))
SubClassOf(<http://purl.obolibrary.org/obo/MAXO_0000012> <http://purl.obolibrary.org/obo/MAXO_0000004>)

# Class: <http://purl.obolibrary.org/obo/MAXO_0000013> (complementary and alternative medical therapy)
Expand Down Expand Up @@ -1358,7 +1359,6 @@ SubClassOf(<http://purl.obolibrary.org/obo/MAXO_0000023> <http://purl.obolibrary
# Class: <http://purl.obolibrary.org/obo/MAXO_0000024> (surgical procedure on the eye)

AnnotationAssertion(dcterms:creator <http://purl.obolibrary.org/obo/MAXO_0000024> <https://orcid.org/0000-0001-7941-2961>)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MAXO_0000024> "surgical procedure on the eye"@en)
SubClassOf(<http://purl.obolibrary.org/obo/MAXO_0000024> <http://purl.obolibrary.org/obo/MAXO_0000012>)

# Class: <http://purl.obolibrary.org/obo/MAXO_0000025> (end-of life care)
Expand Down
11 changes: 11 additions & 0 deletions src/ontology/reports/maxo-base.owl-obo-report.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -539,6 +539,17 @@ WARN missing_superclass MAXO:0001498 rdfs:subClassOf
WARN missing_superclass MAXO:0001499 rdfs:subClassOf
WARN missing_superclass MAXO:0001500 rdfs:subClassOf
WARN missing_superclass MAXO:0001501 rdfs:subClassOf
WARN missing_superclass MAXO:0001503 rdfs:subClassOf
WARN missing_superclass MAXO:0001504 rdfs:subClassOf
WARN missing_superclass MAXO:0001506 rdfs:subClassOf
WARN missing_superclass MAXO:0001507 rdfs:subClassOf
WARN missing_superclass MAXO:0001508 rdfs:subClassOf
WARN missing_superclass MAXO:0001510 rdfs:subClassOf
WARN missing_superclass MAXO:0001511 rdfs:subClassOf
WARN missing_superclass MAXO:0001512 rdfs:subClassOf
WARN missing_superclass MAXO:0001513 rdfs:subClassOf
WARN missing_superclass MAXO:0001514 rdfs:subClassOf
WARN missing_superclass MAXO:0001515 rdfs:subClassOf
WARN missing_superclass MAXO:0010004 rdfs:subClassOf
WARN missing_superclass MAXO:0010005 rdfs:subClassOf
WARN missing_superclass MAXO:0010006 rdfs:subClassOf
Expand Down
11 changes: 11 additions & 0 deletions src/ontology/reports/maxo-edit.owl-obo-report.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -539,6 +539,17 @@ WARN missing_superclass MAXO:0001498 rdfs:subClassOf
WARN missing_superclass MAXO:0001499 rdfs:subClassOf
WARN missing_superclass MAXO:0001500 rdfs:subClassOf
WARN missing_superclass MAXO:0001501 rdfs:subClassOf
WARN missing_superclass MAXO:0001503 rdfs:subClassOf
WARN missing_superclass MAXO:0001504 rdfs:subClassOf
WARN missing_superclass MAXO:0001506 rdfs:subClassOf
WARN missing_superclass MAXO:0001507 rdfs:subClassOf
WARN missing_superclass MAXO:0001508 rdfs:subClassOf
WARN missing_superclass MAXO:0001510 rdfs:subClassOf
WARN missing_superclass MAXO:0001511 rdfs:subClassOf
WARN missing_superclass MAXO:0001512 rdfs:subClassOf
WARN missing_superclass MAXO:0001513 rdfs:subClassOf
WARN missing_superclass MAXO:0001514 rdfs:subClassOf
WARN missing_superclass MAXO:0001515 rdfs:subClassOf
WARN missing_superclass MAXO:0010004 rdfs:subClassOf
WARN missing_superclass MAXO:0010005 rdfs:subClassOf
WARN missing_superclass MAXO:0010006 rdfs:subClassOf
Expand Down
2 changes: 1 addition & 1 deletion src/ontology/reports/owldef-self-reference-violation.csv
View file
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
term
http://purl.obolibrary.org/obo/MAXO_0001269
http://purl.obolibrary.org/obo/MAXO_0000012
3 changes: 1 addition & 2 deletions src/patterns/data/manual/surgery_by_location.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,8 @@ MAXO:0000946 UBERON:0001016 nervous system http://orcid.org/0000-0001-7941-2961
MAXO:0001510 UBERON:2001371 pancreatic system http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z
MAXO:0001511 UBERON:0004100 renal collecting system http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z
MAXO:0001512 UBERON:0000990 reproductive system http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z
MAXO:0000012 surgery by body system UBERON:0000467 anatomical system http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z surgical procedure on body region
MAXO:0001514 UBERON:0001004 respiratory system http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z
MAXO:0001515 UBERON:0007798 vascular system http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z
MAXO:0000479 orthopedic surgery UBERON:0001434 skeletal system 2020-01-20T17:51:02Z orthopedics surgery
MAXO:0000024 surgical procedure on the ey UBERON:0000019 carmera-type eye 2023-02-24T15:25:58Z eye surgery|eye procedure|surgery of the eye
MAXO:0000024 surgical procedure on the eye UBERON:0000019 carmera-type eye 2023-02-24T15:25:58Z eye surgery|eye procedure|surgery of the eye
MAXO:0025005 UBERON:0002392 nasolacrimal duct dacryocystorhinostomy|tear duct surgery
2 changes: 1 addition & 1 deletion src/patterns/data/todo/MAXO_availableIDs.txt
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@

MAXO:0001505

MAXO:0001509
MAXO:0001516
MAXO:0001517
Expand Down
7 changes: 1 addition & 6 deletions src/patterns/definitions.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1409,7 +1409,6 @@ Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000402>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000456>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000458>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000463>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000467>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000468>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000473>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000912>))
Expand Down Expand Up @@ -1639,10 +1638,6 @@ Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#has
# Classes
############################

# Class: <http://purl.obolibrary.org/obo/MAXO_0000012> (surgery by body site)

EquivalentClasses(<http://purl.obolibrary.org/obo/MAXO_0000012> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/MAXO_0000012> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002233> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000467>))))

# Class: <http://purl.obolibrary.org/obo/MAXO_0000024> (surgical procedure on the eye)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/MAXO_0000024> "Any surgical procedure conducted on the camera-type eye.")
Expand All @@ -1651,7 +1646,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynony
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MAXO_0000024> "eye procedure")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MAXO_0000024> "eye surgery")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MAXO_0000024> "surgery of the eye")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MAXO_0000024> "surgical procedure on the ey")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MAXO_0000024> "surgical procedure on the eye")
EquivalentClasses(<http://purl.obolibrary.org/obo/MAXO_0000024> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/MAXO_0000012> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002233> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000019>))))

# Class: <http://purl.obolibrary.org/obo/MAXO_0000045> (dehydration prevention recommendation)
Expand Down
15 changes: 15 additions & 0 deletions src/patterns/pattern.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_52210>))
Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000003>))
Declaration(Class(<http://purl.obolibrary.org/obo/HP_0000118>))
Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000001>))
Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000012>))
Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000033>))
Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000034>))
Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000056>))
Expand Down Expand Up @@ -81,6 +82,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/maxo/patterns/removal_by_locat
Declaration(Class(<http://purl.obolibrary.org/obo/maxo/patterns/removal_by_phenotype.yaml>))
Declaration(Class(<http://purl.obolibrary.org/obo/maxo/patterns/repair_by_location.yaml>))
Declaration(Class(<http://purl.obolibrary.org/obo/maxo/patterns/specimen_collection_by_location.yaml>))
Declaration(Class(<http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml>))
Declaration(Class(<http://purl.obolibrary.org/obo/maxo/patterns/surgical_repair_by_location.yaml>))
Declaration(Class(<http://purl.obolibrary.org/obo/maxo/patterns/swab_by_location.yaml>))
Declaration(Class(<http://purl.obolibrary.org/obo/maxo/patterns/therapeuticprocedure_by_location.yaml>))
Expand Down Expand Up @@ -544,6 +546,19 @@ AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/maxo/patterns/s
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/maxo/patterns/specimen_collection_by_location.yaml> "'location' specimen collection"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/maxo/patterns/specimen_collection_by_location.yaml> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/MAXO_0000547> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002233> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001062>))))

# Class: <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> (surgical procedure on 'location')

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "Any surgical procedure conducted on the 'location'."^^xsd:string)
AnnotationAssertion(<http://purl.obolibrary.org/obo/dcterms_creator> <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "'created_by'"^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "'date'"^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/title> <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "surgery_by_location"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "database cross reference"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "'location' surgical procedure"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "xsd:string"^^xsd:string)
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "'comment'"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "surgical procedure on 'location'"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/MAXO_0000012> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002233> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001062>))))

# Class: <http://purl.obolibrary.org/obo/maxo/patterns/surgical_repair_by_location.yaml> ('location' repair)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/maxo/patterns/surgical_repair_by_location.yaml> "Surgical procedure to repair a 'location'."^^xsd:string)
Expand Down

0 comments on commit 04b8995

Please sign in to comment.