Unsatisfiable classes in OMIT

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Ontology for MicroRNA Target

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Unsatisfiable classes in OMIT #8

Open matentzn opened 4 years ago

matentzn commented 4 years ago

There are a number of unsats in OMIT (2494), mostly I think due to the fact that miRNA is classified both as small_regulatory_ncRNA (which is is generically dependent continuant), and 'non-coding RNA', which is classified as a molecular entity. Is OMIT still maintained? Would you be able to fix this problem?

Huang-OMIT commented 4 years ago

Hi Nico: Yes, OMIT is still maintained. Any suggestions to solve the issues you identified?

matentzn commented 4 years ago

Unfortunately, this is a bit beyond me; @balhoff do you know what is the appropriate course of action here?

balhoff commented 4 years ago

The problem is conflict between CHEBI material chemical entities (like 'ribonucleic acid') and SO sequence features (like 'miRNA'), which are generically dependent continuants. GO has this problem also (https://github.com/geneontology/go-ontology/issues/15894), currently avoided by just not including the upper level SO axioms about generically dependent continuants. MSO is supposed to clean all this up. It's not ready though I think.

cmungall commented 3 years ago

is this still an issue? SO is no longer GDCs

cmungall commented 3 years ago

Now I look closer, e.g. #10 I see that OMIT does all kinds of strange things such as place all terms from MESH under bfo:quality, so crytpic unsatisfiable classes will be rife