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Remove property chains inferring develops_from over part_of. #1808

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merged 1 commit into from
Apr 12, 2021

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@balhoff balhoff commented Mar 17, 2021

This PR removes two property chains:

  • part_of o develops_from -> develops_from
  • develops_from o part_of -> develops_from

We noticed these causing some unexpected inferences in GO, for example protein-containing complex being inferred to develop from an anatomical entity. These should be in RO anyway, if they were to be accepted.

I also deleted these chains from the cl_import.owl. I looked at the CL source, and I think they got these via Uberon, so hopefully that bit of ontology autophagy will be cleaned up when both have releases.

I computed a reasoned file using this command: robot reason --catalog catalog-v001.xml --exclude-duplicate-axioms true --remove-redundant-subclass-axioms true -i uberon_edit.obo -o reasoned-new.ofn

and compared before and after the changes using robot diff. Somewhat unexpectedly, I didn't see any classification differences.

@balhoff balhoff requested review from cmungall and dosumis March 17, 2021 14:53
@cmungall cmungall merged commit 1b0e17b into master Apr 12, 2021
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dosumis commented Apr 12, 2021

Just spotted this. I think the second of these two property chains is kosher and should be in RO.

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balhoff commented Apr 12, 2021

@dosumis I think that chain leads to weird statements:

'neuron projection bundle' develops_from 'multicellular organism'
'flask cell' develops_from 'organ'
'interrenal gland' develops_from 'abdomen'

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3 participants