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microbiomedata / nmdc-ontology

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Remove inferred equivalences #12

Closed wdduncan closed 3 years ago

wdduncan commented 3 years ago

The relation-graph produce produces classes that are subclasses of each other. Here is the output from nmdco-relation-graph.owl:

fluid astronomical body part is a subclass of compound astronomical body part:

image

And compound astronomical body part is a subclass of fluid astronomical body part:

image

Unfortunately, I can't use robot reason b/c of incoherencies in ENVO. PO uses the domain and range constraints from RO. And the addition of these domains causes unsatisfiable classes, and a DL profile error. A ticket about lack of domain/range constraints has been filed for ENVO: https://github.com/EnvironmentOntology/envo/issues/1182

But, there has not been follow up.

Jim B. suggested I could make a "base" version of PO, using robot like so:

pr-base.ttl: pro_nonreasoned.obo
    $(ROBOT) remove --input $< \
        --base-iri 'http://purl.obolibrary.org/obo/PR_' \
        --axioms external \
        --preserve-structure false \
        --trim false \
        --output $@

cc @cmungall @turbomam

cmungall commented 3 years ago

I have a whole blog post on this issue? :-) https://douroucouli.wordpress.com/2018/09/04/debugging-ontologies-using-owl-reasoning-part-2-unintentional-entailed-equivalence/