import UBERON into BFO based ontology

[wdduncan]

I am trying to use UBERON for an ontology of GYN cancers. My import of UBERON, however, is not aligned with BFO in the sense that UBERON:material anatomical entity is not a subtype of BFO:material entity and UBERON:immaterial anatomical entity is not a subtype of BFO:immaterial anatomical entity.

When I add axioms to align the UBERON and BFO types, UBERON becomes inconsistent (using ELK reasoner). This presents me with interesting choices:

1. Leave the UBERON hierarchy under the class Thing.
2. Try to fix the UBERON axioms/classes so that some basic assertions (such as material and immaterial entities are disjoint) can be reasoned over.

Has anyone else dealt with this?

Thanks,
Bill

[cmungall]

I'm updating the build process to include bridging axioms to BFO then run everything through the test suite. You shouldn't need to make any changes, provided you can wait til the next release, probably next week

[cmungall]

Hmm travis still shows build passing, need to investigate further...

can I confirm the exact combination of purls you are combining?

[cmungall]

Latest on this: a few releases ago we noticed that combing RO with Uberon resulted in Elk hanging. This was resolved by reverting to a previous RO. This is possibly the reason for the difference in our results.

The RO issue will be hard to resolve, there is no axiom that is obviously problematic, and if Elk hangs it makes it very hard to debug the ontology...

[wdduncan]

The PURL I've been using for UBERON is http://purl.obolibrary.org/obo/uberon.owl. The ontology version IRI is http://purl.obolibrary.org/obo/uberon/releases/2016-05-11/uberon.owl.

I tried building UBERON myself from the git repos. But, I can't seem to get it working correctly. Is there a document that explains how to do this and what libraries you need?

[cmungall]

I can provide docs if you really need to do that, but I suspect you don't. Uberon has a very particular and complex development cycle... the PURLs should be fine.

Would you be able to post a screenshot of the explanation of the unsatisfiability? I'm still having trouble reproducing.

[cmungall]

Also if you can post the ELk version too

[wdduncan]

The version of ELk is 0.4.3. The version of Protege is 5-RC-1.

The attached screenshots are:

1. my addition of an subclass axiom showing that an immaterial anatomical
   entity is a subclass of immaterial entity
   2 my addition of an subclass axiom showing that a material anatomical
   entity is a subclass of material entity
2. the resulting inconsistent classes
3. the explanation given for why the class nose is inconsistent

I've also attached the MIREOT of UBERON (as a zip file) that I am using.

Bill

uberon-import-20160603.owl.zip

[cmungall]

Thanks!

[gouttegd]

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