Open kltm opened 6 years ago
Okay, I'm able to proceed, but I'm now able to see the practical logic behind it as currently all models I've tried have failed so far like:
2018-01-22 13:05:56,437 INFO (ParserWrapper:75) Start loading ontology: file:/home/bbop/local/src/git/noctua-models/models/5459649100000001.ttl from: file:/home/bbop/local/src/git/noctua-models/models/5459649100000001.ttl
2018-01-22 13:05:58,519 INFO (ParserWrapper:82) Finished loading ontology: http://model.geneontology.org/5459649100000001 from: file:/home/bbop/local/src/git/noctua-models/models/5459649100000001.ttl
2018-01-22 13:06:48,213 WARN (SolrCommandRunner:609) Unsatisfiable: 5459649100000001.ttl == [<http://purl.obolibrary.org/obo/EMAPA_36026>, <http://purl.obolibrary.org/obo/EMAPA_25090>, <http://purl.obolibrary.org/obo/EMAPA_16777>, <http://purl.obolibrary.org/obo/EMAPA_16133>, <http://purl.obolibrary.org/obo/EMAPA_17267>, <http://purl.obolibrary.org/obo/EMAPA_18235>, <http://purl.obolibrary.org/obo/EMAPA_17266>, <http://purl.obolibrary.org/obo/EMAPA_17265>, <http://purl.obolibrary.org/obo/EMAPA_17264>, <http://purl.obolibrary.org/obo/EMAPA_16776>, <http://purl.obolibrary.org/obo/EMAPA_16654>, <http://purl.obolibrary.org/obo/EMAPA_16775>, <http://purl.obolibrary.org/obo/EMAPA_17303>, <http://purl.obolibrary.org/obo/EMAPA_18238>, <http://purl.obolibrary.org/obo/EMAPA_19168>, <http://purl.obolibrary.org/obo/EMAPA_17269>, <http://purl.obolibrary.org/obo/EMAPA_17268>, <http://purl.obolibrary.org/obo/EMAPA_18236>, <http://purl.obolibrary.org/obo/EMAPA_36027>, <http://purl.obolibrary.org/obo/EMAPA_17263>, <http://purl.obolibrary.org/obo/EMAPA_18550>, <http://purl.obolibrary.org/obo/EMAPA_18190>, <http://purl.obolibrary.org/obo/EMAPA_18549>, <http://purl.obolibrary.org/obo/EMAPA_17575>, <http://purl.obolibrary.org/obo/EMAPA_17773>, <http://purl.obolibrary.org/obo/EMAPA_18785>, <http://purl.obolibrary.org/obo/EMAPA_17574>, <http://purl.obolibrary.org/obo/EMAPA_17772>, <http://purl.obolibrary.org/obo/EMAPA_18784>, <http://purl.obolibrary.org/obo/EMAPA_17771>, <http://purl.obolibrary.org/obo/EMAPA_18189>, <http://purl.obolibrary.org/obo/EMAPA_17770>, <http://purl.obolibrary.org/obo/EMAPA_18188>, <http://purl.obolibrary.org/obo/EMAPA_18782>, <http://purl.obolibrary.org/obo/EMAPA_17576>, <http://purl.obolibrary.org/obo/EMAPA_19031>, <http://purl.obolibrary.org/obo/EMAPA_19032>, <http://purl.obolibrary.org/obo/EMAPA_18781>, <http://purl.obolibrary.org/obo/EMAPA_18780>, <http://purl.obolibrary.org/obo/EMAPA_35617>, <http://purl.obolibrary.org/obo/EMAPA_19030>, <http://purl.obolibrary.org/obo/EMAPA_17605>, <http://purl.obolibrary.org/obo/EMAPA_17803>, <http://purl.obolibrary.org/obo/EMAPA_17769>, <http://purl.obolibrary.org/obo/EMAPA_17802>, <http://purl.obolibrary.org/obo/EMAPA_17846>, <http://purl.obolibrary.org/obo/EMAPA_17801>, <http://purl.obolibrary.org/obo/EMAPA_16678>, <http://purl.obolibrary.org/obo/EMAPA_17800>, <http://purl.obolibrary.org/obo/EMAPA_18218>, <http://purl.obolibrary.org/obo/EMAPA_18779>, <http://purl.obolibrary.org/obo/EMAPA_16915>, <http://purl.obolibrary.org/obo/EMAPA_16914>, <http://purl.obolibrary.org/obo/EMAPA_17607>, <http://purl.obolibrary.org/obo/EMAPA_17606>, <http://purl.obolibrary.org/obo/EMAPA_19029>, <http://purl.obolibrary.org/obo/EMAPA_17166>, <http://purl.obolibrary.org/obo/EMAPA_16033>, <http://purl.obolibrary.org/obo/EMAPA_18217>, <http://purl.obolibrary.org/obo/EMAPA_16479>, <http://purl.obolibrary.org/obo/EMAPA_18216>, <http://purl.obolibrary.org/obo/EMAPA_35555>, <http://purl.obolibrary.org/obo/EMAPA_17837>, <http://purl.obolibrary.org/obo/EMAPA_16589>, <http://purl.obolibrary.org/obo/EMAPA_17799>, <http://purl.obolibrary.org/obo/EMAPA_16588>, <http://purl.obolibrary.org/obo/EMAPA_17798>, <http://purl.obolibrary.org/obo/EMAPA_17797>, <http://purl.obolibrary.org/obo/EMAPA_35488>, <http://purl.obolibrary.org/obo/EMAPA_17796>, <http://purl.obolibrary.org/obo/EMAPA_35489>, <http://purl.obolibrary.org/obo/GO_0055036>]
tagging @cmungall
@cmungall it looks like we'll get nothing; you mentioned that @balhoff may be able to help out here?
It should be safe to load incoherent consistent models. We should never use the reasoner with inconsistent models
It looks like the only unsatisfiable GO class is virion membrane. This is pretty weird and we should investigate, I assume it's old+new axioms superimposed.
All the rest are EMAPAs, this should only affect MGI annotations that reference these
@ukemi - this is another challenge of allowing EMAPA plus Uberon, it's another thing that can become inconsistent. Uberon has a lot of strict axioms that may be vioated by the EMAPA subclasses. In future I'd like to use uberon for all metazoa in Noctua, and map to ssAOs after the fact
Testing the loader, we now fail with:
This is understandable as (IIRC) it is part of a set of mock-up models--I doubt anything sensible would be loaded even it was satisfiable. I think the best course of action would be to continue on with other models if any single model unsatisfiable. I would like to have something in there soon for demo purposes and this would be the fastest way forward.
Hopefully I'll be able to supply a PR soon...