multicellular organism disjoint from organism substance #2421

[ddooley]

Addresses Issue #2421 . This is in external disjoints file though the two terms are native to Uberon though.

[anitacaron]

GitHub action is having issues posting the comment because it comes from a fork, but there're unsats in this PR.

This PR violates some taxon constraints. Here is what the reasoner has to say:

Barley yellow dwarf virus SubClassOf Nothing

• Barley yellow dwarf virus SubClassOf unclassified Luteovirus
  • unclassified Luteovirus SubClassOf Luteovirus
    • Luteovirus SubClassOf Regressovirinae
• Luteovirus DisjointWith Regressovirinae

Luteovirus pavhordei SubClassOf Nothing

• Luteovirus pavhordei SubClassOf Luteovirus
  • Luteovirus SubClassOf Regressovirinae
• Luteovirus DisjointWith Regressovirinae

Barley yellow dwarf virus (ISOLATE MAV-PS1) SubClassOf Nothing

• Barley yellow dwarf virus (ISOLATE MAV-PS1) SubClassOf Barley yellow dwarf virus MAV
  • Barley yellow dwarf virus MAV SubClassOf Luteovirus mavhordei
    • Luteovirus mavhordei SubClassOf Luteovirus
      • Luteovirus SubClassOf Regressovirinae
• Luteovirus DisjointWith Regressovirinae

Histoplasma capsulatum var. duboisii H88 SubClassOf Nothing

• Histoplasma capsulatum var. duboisii H88 SubClassOf Histoplasma capsulatum var. duboisii
• Histoplasma capsulatum var. duboisii DisjointWith Histoplasma capsulatum var. duboisii H88

median vaginal canal SubClassOf Nothing

• median vaginal canal SubClassOf channel for some embryo
  • channel for Range organism substance
  • embryo EquivalentTo multicellular organism and (existence starts with some embryo stage) and (existence ends with some embryo stage)
• organism substance DisjointWith multicellular organism

lateral vaginal canal SubClassOf Nothing

• lateral vaginal canal EquivalentTo vagina and (in lateral side of some internal female genitalia) and (connected to some median vaginal canal)
  • median vaginal canal SubClassOf channel for some embryo
    • channel for Range organism substance
    • embryo EquivalentTo multicellular organism and (existence starts with some embryo stage) and (existence ends with some embryo stage)
• organism substance DisjointWith multicellular organism

Barley yellow dwarf virus (ISOLATE P-PAV) SubClassOf Nothing

• Barley yellow dwarf virus (ISOLATE P-PAV) SubClassOf Barley yellow dwarf virus PAV
  • Barley yellow dwarf virus PAV SubClassOf Luteovirus pavhordei
    • Luteovirus pavhordei SubClassOf Luteovirus
      • Luteovirus SubClassOf Regressovirinae
• Luteovirus DisjointWith Regressovirinae

Barley yellow dwarf virus MAV SubClassOf Nothing

• Barley yellow dwarf virus MAV SubClassOf Luteovirus mavhordei
  • Luteovirus mavhordei SubClassOf Luteovirus
    • Luteovirus SubClassOf Regressovirinae
• Luteovirus DisjointWith Regressovirinae

Luteovirus mavhordei SubClassOf Nothing

• Luteovirus mavhordei SubClassOf Luteovirus
  • Luteovirus SubClassOf Regressovirinae
• Luteovirus DisjointWith Regressovirinae

Bean leafroll virus SubClassOf Nothing

• Bean leafroll virus SubClassOf Luteovirus phaseoli
  • Luteovirus phaseoli SubClassOf Luteovirus
    • Luteovirus SubClassOf Regressovirinae
• Luteovirus DisjointWith Regressovirinae

Luteovirus phaseoli SubClassOf Nothing

• Luteovirus phaseoli SubClassOf Luteovirus
  • Luteovirus SubClassOf Regressovirinae
• Luteovirus DisjointWith Regressovirinae

Barley yellow dwarf virus (ISOLATE NY-RPV) SubClassOf Nothing

• Barley yellow dwarf virus (ISOLATE NY-RPV) SubClassOf Barley yellow dwarf virus
  • Barley yellow dwarf virus SubClassOf unclassified Luteovirus
    • unclassified Luteovirus SubClassOf Luteovirus
      • Luteovirus SubClassOf Regressovirinae
• Luteovirus DisjointWith Regressovirinae

Barley yellow dwarf virus PAV SubClassOf Nothing

• Barley yellow dwarf virus PAV SubClassOf Luteovirus pavhordei
  • Luteovirus pavhordei SubClassOf Luteovirus
    • Luteovirus SubClassOf Regressovirinae
• Luteovirus DisjointWith Regressovirinae

Luteovirus SubClassOf Nothing

• Luteovirus SubClassOf Regressovirinae
• Luteovirus DisjointWith Regressovirinae

unclassified Luteovirus SubClassOf Nothing

• unclassified Luteovirus SubClassOf Luteovirus
  • Luteovirus SubClassOf Regressovirinae
• Luteovirus DisjointWith Regressovirinae

Axiom Impact

Axioms used 12 times

• Luteovirus SubClassOf Regressovirinae [core.owl]
• Luteovirus DisjointWith Regressovirinae [core.owl]

Axioms used 3 times

• Luteovirus mavhordei SubClassOf Luteovirus [core.owl]
• Luteovirus pavhordei SubClassOf Luteovirus [core.owl]
• unclassified Luteovirus SubClassOf Luteovirus [core.owl]

Axioms used 2 times

• embryo EquivalentTo multicellular organism and (existence starts with some embryo stage) and (existence ends with some embryo stage) [core.owl]
• Barley yellow dwarf virus SubClassOf unclassified Luteovirus [core.owl]
• Barley yellow dwarf virus MAV SubClassOf Luteovirus mavhordei [core.owl]
• Barley yellow dwarf virus PAV SubClassOf Luteovirus pavhordei [core.owl]
• Luteovirus phaseoli SubClassOf Luteovirus [core.owl]
• median vaginal canal SubClassOf channel for some embryo [core.owl]
• organism substance DisjointWith multicellular organism [core.owl]
• channel for Range organism substance [core.owl]

Axioms used 1 times

• lateral vaginal canal EquivalentTo vagina and (in lateral side of some internal female genitalia) and (connected to some median vaginal canal) [core.owl]
• Barley yellow dwarf virus (ISOLATE NY-RPV) SubClassOf Barley yellow dwarf virus [core.owl]
• Bean leafroll virus SubClassOf Luteovirus phaseoli [core.owl]
• Barley yellow dwarf virus (ISOLATE MAV-PS1) SubClassOf Barley yellow dwarf virus MAV [core.owl]
• Barley yellow dwarf virus (ISOLATE P-PAV) SubClassOf Barley yellow dwarf virus PAV [core.owl]
• Histoplasma capsulatum var. duboisii H88 SubClassOf Histoplasma capsulatum var. duboisii [core.owl]
• Histoplasma capsulatum var. duboisii DisjointWith Histoplasma capsulatum var. duboisii H88 [core.owl]

Ontologies used:

• core.owl (http://purl.obolibrary.org/obo/uberon/core.owl)

[anitacaron]

Fix unsats.

[gouttegd]

The obvious problem in Uberon is here:

• median vaginal canal SubClassOf channel for some embryo
• channel for Range organism substance

With “channel for” being range-restricted to “organism substances”, it is obviously a mistake to say the vaginal canal is a “channel for” the embryo. Either the range restriction on that relation should be relaxed if the intention is for it to be used for more than just substances, or the relationship between “median vaginal canal” and “embryo” should either be dropped or replaced by a more suitable relation.

[gouttegd]

But I am puzzled by the other unsats, which don’t seem to have anything to do with Uberon at all.

[gouttegd]

I can’t reproduce the other unsats locally. The only unsats I get running the test suite locally are the ones caused by median vaginal canal as explained above.

[github-actions]

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR creator will be allowed to proceed with merging without explicit approval, should they wish to do so.

[cmungall]

The NCBITaxon unsats likely due to superimposition of 2 versions of NCBITaxon (this is one of the key motivations for base files). Difference between local and actions may be due to difference in versions on the network and/or triggering rebuilds of mirrors (but I defer to the Damien with an E who knows ODK better than me)

As for channeling embryos, rococo/vanity axiom, remove it

[gouttegd]

@ddooley Can you remove the “median vaginal canal SubClassOf channel for some embryo“ axiom in Uberon? It makes sense that this should be done as part of this PR, since the incorrectness of this axiom was revealed by the addition of your disjointness axiom between “multicellular organism“ and “organic substance“.

I would also suggest that said disjointness axiom should be added to the main Uberon source file (uberon-edit.obo) rather than the external-disjoints.obo component. That component is only merged at build time, so its axioms are not visible to editors at edit time (e.g. in Protégé). This creates a risk than an editor could later violate the disjointness with no way of realising it until they submit a PR and the violation is caught by the test suite.

[github-actions]

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR creator will be allowed to proceed with merging without explicit approval, should they wish to do so.