This may be a problem in OWL API, but just tracking here for now. Run these commands on the latest MONDO release:
curl -L -O 'http://purl.obolibrary.org/obo/mondo/releases/2023-07-03/mondo.owl' riot --validate mondo.owl # outputs some warnings about URN format in SWRL variables, but not fatal robot convert -i mondo.owl -o mondo.ttl riot --validate mondo.ttl # 15:17:40 ERROR riot :: [line: 212732, col: 100] Unrecognized (expected an RDF Term): [SEMICOLON]
The problem section of the file looks like this:
### http://purl.obolibrary.org/obo/MONDO_0000290
obo:MONDO_0000290 rdf:type owl:Class ;
owl:equivalentClass [ owl:intersectionOf ( obo:MONDO_0005550
_:genid24281 rdf:type owl:Restriction ;
owl:onProperty obo:RO_0014001 ;
owl:someValuesFrom obo:NCBITaxon_5763
) ;
rdf:type owl:Class
] ;
rdfs:subClassOf obo:MONDO_0002428 ,
obo:MONDO_0020067 ,
_:genid24281 ;
obo:IAO_0000115 "A infectious disease involving the Naegleria fowleri." ;
terms:conformsTo <http://purl.obolibrary.org/obo/mondo/patterns/infectious_disease_by_agent.yaml> ;
oboInOwl:hasDbXref "DOID:0050242" ,
"GARD:0009554" ,
"MESH:C535275" ,
"SCTID:721816008" ,
"UMLS:C0300934" ,
"UMLS:C4303098" ;
oboInOwl:hasExactSynonym "Naegleria fowleri infection" ;
oboInOwl:hasRelatedSynonym "infections, Naegleria fowleri" ;
oboInOwl:id "MONDO:0000290" ;
oboInOwl:inSubset mondo:mondo_rare ,
mondo:rare ;
rdfs:label "primary amebic meningoencephalitis" ;
skos:exactMatch <http://identifiers.org/mesh/C535275> ,
<http://identifiers.org/snomedct/721816008> ,
<http://linkedlifedata.com/resource/umls/id/C0300934> ,
<http://linkedlifedata.com/resource/umls/id/C4303098> ,
obo:DOID_0050242 .
_:genid24281 rdf:type owl:Restriction ;
owl:onProperty obo:RO_0014001 ;
owl:someValuesFrom obo:NCBITaxon_5763 .
In the intersection list you would expect the existential restriction to be enclosed in [ ], but instead there is a blank node ID _:genid24281 followed by invalid inline properties. The blank node ID is reused twice below, which it should not be (OWL is supposed to use fresh blank nodes for reference to a class expression). That's fine in turtle, but might suggest the source of the error.
Based on the type of expression, it's possible this is somehow related to robot relax.
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