Jim Balhoff
Jim Balhoff
We do still need to address this. I took a look, and we're only avoiding unsatisfiable classes at the moment due to a lack of connections from Uberon into CARO...
The QC check is just checking the ontology for coherency when those classes are present. Generating them as anonymous classes is not an option; anonymous classes wouldn't provide any coherency...
> I guess I meant anon individuals, but that makes debugging harder (inconsistency not unsat). So scratch my comment On Thu, Aug 11, 2022 at 7:09 AM Chris Mungall ***@***.***>...
> Generating them as anonymous classes is not an option; anonymous classes wouldn't provide any coherency violations if the expression was unsatisfiable (but I would love to change the expansion...
@gouttegd it would be something like this: ``` SubClassOf( UBERON:dummy_class ObjectSomeValuesFrom( RO:dummy_property ObjectIntersectionOf( ObjectSomeValuesFrom(RO:0002162 NCBI:Taxon:9681) UBERON:0004187 ) ) ) ``` The same dummy class can be used for every present-in-taxon...
> Unfortunately, it seems like the format data is lost after the ontology is loaded with the OWLAPI OWLOntologyManager. @beckyjackson have you tried this method? http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/model/OWLOntologyManager.html#getOntologyFormat-org.semanticweb.owlapi.model.OWLOntology-
No, sorry, I thought that would work! It's not something I have used before though.
@ramonawalls related discussion: #360
> The main issue I see is that GO allows for a URI to change even when the old term is still valid, and allows the changing of the meaning...
> hard to mentally reason over - logic is separated across ad-hoc filters on OPs, various pre-processing steps, property chains stored centrally in GO The property chains are in RO,...