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obophenotype / c-elegans-gross-anatomy-ontology

C. elegans Gross Anatomy Ontology
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OBO fix #4

Closed matentzn closed 5 years ago

matentzn commented 5 years ago
matentzn commented 5 years ago

Test the wbbt.obo to see where this gets you with your ingest errors! Let me know if there are any more.

raymond91125 commented 5 years ago

There are unionof (union_of) relations got filtered out from the simple file. They should be retained. Just a note, unionof in WBbt is the same as owl2 DisjointUnion https://www.w3.org/TR/owl2-new-features/.

matentzn commented 5 years ago

@raymond91125 I will look into this! Out of curiosity, what are you using union_of for?

raymond91125 commented 5 years ago

some worm cells can come from one of two possible lineages (ancestry). thus we need some sort of XOR relationship.

matentzn commented 5 years ago

can this wait till Friday? I think I need to have some discussions about doing this properly with my boss, who is on travelling at the moment..

raymond91125 commented 5 years ago

Sure thing. Just note that I should really fix this type of relations. In Protege, presently, they are represented as (e.g.) 'P1.aaaa nucleus' or 'W.aaa nucleus' But they should be: ('P1.aaaa nucleus' or 'W.aaa nucleus') and not ('P1.aaaa nucleus' and 'W.aaa nucleus') I don't think either of these can be reasoned in Protege, though. HermiT seems to go on forever.

cmungall commented 5 years ago

Contact me so I don't forget about this. I don't think your use case/biology maps onto OWL axioms in exactly the way it may seem on the surface.

matentzn commented 5 years ago

We already took the discussion offline. we are getting rid of the logical axiom for now; see email thread.

matentzn commented 5 years ago

@raymond91125 Sorry for the back and forth here. After some recommendations offline by @cmungall I decided to leave your modelling as it was for now and redefine the OBO export of wbbt as follows: Take the full version of wbbt, remove all non-native (non WBbt) classes, remove redundant subsumptions and export to OBO. Please test wbbt.obo one last time here. I hope the typedefs in the end are not bothering you, else I will get rid of them in a second step.

chris-grove commented 5 years ago

@raymond91125 Have you had a chance to look at this?