I'm unable to load this ontology using the OWL API due to an invalid def declaration for the term "renal tubulointerstitial score". The def for this term starts with a double quotation mark:
[Term]
id: CMO:0002948
name: renal tubulointerstitial score
def: ""A semiquantitative evaluation of the renal interstitium using a grading system with a score of 0 to 4+, which assesses the tubules and the interstitium for the presence of (1) tubular atrophy, (2) tubular dilatation, (3) interstitial inflammatory cell infiltrates, and (4) interstitial fibrosis. A score of 0 indicates no lesion (normal kidney), 1+ indicates a single, small focal lesion with very minimal tubular alterations and interstitial inflammatory cell infiltration, and 2+ to 4+ indicated increasing severity of tubular lesions, interstitial inflammatory cell infiltration, and/or fibrosis. A score of 4+ indicates involvement of approximately 50% or more of the renal parenchyma or interstitium." [PMID:PMID\:9369281]
...
... which causes a parsing error:
org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing file:/Users/jvendetti/Development/IntelliJ_Projects/owlapi-example-code/src/test/resources/clinical_measurement.obo
Could not parse ontology. Either a suitable parser could not be found, or parsing failed. See parser logs below for explanation.
The following parsers were tried:
1) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@5990e6c5
Detailed logs:
--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@5990e6c5
Stack trace:
LINENO: 26701 - expected newline or end of line but found: A semiquantitative evaluation of the renal interstitium using a grading system with a score of 0 to 4+, which assesses the tubules and the interstitium for the presence of (1) tubular atrophy, (2) tubular dilatation, (3) interstitial inflammatory cell infiltrates, and (4) interstitial fibrosis. A score of 0 indicates no lesion (normal kidney), 1+ indicates a single, small focal lesion with very minimal tubular alterations and interstitial inflammatory cell infiltration, and 2+ to 4+ indicated increasing severity of tubular lesions, interstitial inflammatory cell infiltration, and/or fibrosis. A score of 4+ indicates involvement of approximately 50% or more of the renal parenchyma or interstitium." [PMID:PMID\:9369281]
LINE: def: ""A semiquantitative evaluation of the renal interstitium using a grading system with a score of 0 to 4+, which assesses the tubules and the interstitium for the presence of (1) tubular atrophy, (2) tubular dilatation, (3) interstitial inflammatory cell infiltrates, and (4) interstitial fibrosis. A score of 0 indicates no lesion (normal kidney), 1+ indicates a single, small focal lesion with very minimal tubular alterations and interstitial inflammatory cell infiltration, and 2+ to 4+ indicated increasing severity of tubular lesions, interstitial inflammatory cell infiltration, and/or fibrosis. A score of 4+ indicates involvement of approximately 50% or more of the renal parenchyma or interstitium." [PMID:PMID\:9369281] org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:67)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:221)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1293)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1233)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1184)
edu.stanford.ncbo.bioportal.SimpleLoadTest.testLoadCMOOntology_WithDocumentFormat(SimpleLoadTest.java:415)
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.base/java.lang.reflect.Method.invoke(Method.java:566)
I'm unable to load this ontology using the OWL API due to an invalid def declaration for the term "renal tubulointerstitial score". The def for this term starts with a double quotation mark:
... which causes a parsing error:
Would it be possible to have this corrected? We're currently unable to successfully load this ontology in BioPortal as a result (https://bioportal.bioontology.org/ontologies/CMO).