unsatisfiability from COB interaction

[balhoff]

I'm trying to resolve unsatisfiable classes found in the Ubergraph build. This issue overlaps OBI, SO, and COB.

genotyping assay EquivalentTo Nothing

• genotyping assay SubClassOf has_specified_output some genotype information
  • genotype information SubClassOf genetic characteristics information
    • genetic characteristics information SubClassOf is about some
      (region and (is concretized as some (characteristic_of some
      (nucleic acid and (part_of some organism)))))
      • region SubClassOf sequence_feature
        • sequence_feature SubClassOf material entity
          • material entity EquivalentTo material entity
            • material entity SubClassOf independent continuant
      • is concretized as Domain generically dependent continuant
• independent continuant DisjointWith generically dependent continuant

The core problem is that OBI is using region as a generically dependent continuant, but COB is asserting it to be a subclass of material entity. Who should change, OBI or COB? Could OBI change the axiom to something like:

• genetic characteristics information SubClassOf is about some (region and (part_of some
  (nucleic acid and (part_of some organism)))

[cmungall]

Slides from COB workshop: https://docs.google.com/presentation/d/1UhWNyZI6_4tc-xR2NXNAIaqBTDgOYLYCAG7emrkGmKY/edit#slide=id.gef3aeb5791_0_630

relevant issue: OBOFoundry/COB#52

[balhoff]

Also want to note this isn't the only unsatisfiable OBI term in Ubergraph, just the only one I've output an explanation for. There are 98; it could be many of them are the same issue.

[cmungall]

looks like this is still an issue?

[jamesaoverton]

Discussed on the OBI call 2023-03-06: OBI would like to follow COB, and so we can put 'region' under 'material entity'. It would be better for SO to clean up their definitions, but that's their problem.

OBI has created two subclasses of 'region':

• http://purl.obolibrary.org/obo/OBI_0000811 'primary structure of DNA macromolecule'
• http://purl.obolibrary.org/obo/OBI_0000845 'primary structure of RNA molecule'

For now at least we will leave these as subclasses of 'region'. We may need to fix that later.

[ddooley]

Update: COB hasn't made commitment to including "region" and some other SO terms yet (ME or ICE discussion). May be discussed in 22/23 Sept 2024 discussion.

[cmungall]

COB has absolutely made the commitment, see

https://github.com/OBOFoundry/COB/blob/master/src/ontology/components/cob-to-external.tsv

SO sf (and this region) are material entities

For full context see the slides from the 2021 workshop where this was agreed on:

https://docs.google.com/presentation/d/1UhWNyZI6_4tc-xR2NXNAIaqBTDgOYLYCAG7emrkGmKY/edit#slide=id.gef3aeb5791_0_572

[cmungall]

the fix here is to change the OBI SO injection to be consistent with COB (this will be fixed when COB imports work smoothly but for now COB should be taken as SOT and we should align with it as far as possible)

[jamesaoverton]

That change to COB hasn't yet been released, but we'll try to get a new COB release soon. Our OBI-to-COB transition PRs do now put 'region' under 'material entity'.