There are 6 unsatisfiable classes in the ontology

[anitacaron]

When running prepare_release got this error when generating materialized.owl that uses unreasoned.owl as input.

ERROR There are 6 unsatisfiable classes in the ontology.
ERROR     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0039421
ERROR     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0009046
ERROR     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0009047
ERROR     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0009048
ERROR     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0018253
ERROR     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0009049

The result of robot explain:

inferior external pudendal vein SubClassOf Nothing

• inferior external pudendal vein SubClassOf external pudendal vein
  • external pudendal vein SubClassOf pudendal vein
    • pudendal vein SubClassOf part_of some pelvic region of trunk
      • pelvic region of trunk SubClassOf part_of some abdominal segment of trunk
        • abdominal segment of trunk SubClassOf subdivision of trunk
          • subdivision of trunk SubClassOf part_of some trunk
  • external pudendal vein SubClassOf tributary of some femoral vein
    • tributary of SubPropertyOf: in branching relationship with
      • in branching relationship with SubPropertyOf: part_of
        • Transitive: part_of
    • femoral vein SubClassOf part_of some hindlimb
      • hindlimb EquivalentTo limb and (part_of some pelvic complex)
        • limb SubClassOf paired limb/fin
          • paired limb/fin SubClassOf appendage
• Nothing EquivalentTo (part_of some appendage) and (part_of some trunk)

external pudendal vein SubClassOf Nothing

• external pudendal vein SubClassOf pudendal vein
  • pudendal vein SubClassOf part_of some pelvic region of trunk
    • pelvic region of trunk SubClassOf part_of some abdominal segment of trunk
      • abdominal segment of trunk SubClassOf subdivision of trunk
        • subdivision of trunk SubClassOf part_of some trunk
• external pudendal vein SubClassOf tributary of some femoral vein
  • tributary of SubPropertyOf: in branching relationship with
    • in branching relationship with SubPropertyOf: part_of
      • Transitive: part_of
  • femoral vein SubClassOf part_of some hindlimb
    • hindlimb EquivalentTo limb and (part_of some pelvic complex)
      • limb SubClassOf paired limb/fin
        • paired limb/fin SubClassOf appendage
• Nothing EquivalentTo (part_of some appendage) and (part_of some trunk)

deep external pudendal vein SubClassOf Nothing

• deep external pudendal vein EquivalentTo external pudendal vein and (part_of some deep vasculature)
  • external pudendal vein SubClassOf pudendal vein
    • pudendal vein SubClassOf part_of some pelvic region of trunk
      • pelvic region of trunk SubClassOf part_of some abdominal segment of trunk
        • abdominal segment of trunk SubClassOf subdivision of trunk
          • subdivision of trunk SubClassOf part_of some trunk
  • external pudendal vein SubClassOf tributary of some femoral vein
    • tributary of SubPropertyOf: in branching relationship with
      • in branching relationship with SubPropertyOf: part_of
    • femoral vein SubClassOf part_of some hindlimb
      • hindlimb EquivalentTo limb and (part_of some pelvic complex)
        • limb SubClassOf paired limb/fin
          • paired limb/fin SubClassOf appendage
  • Transitive: part_of
• Nothing EquivalentTo (part_of some appendage) and (part_of some trunk)

superior external pudendal vein SubClassOf Nothing

• superior external pudendal vein SubClassOf external pudendal vein
  • external pudendal vein SubClassOf pudendal vein
    • pudendal vein SubClassOf part_of some pelvic region of trunk
      • pelvic region of trunk SubClassOf part_of some abdominal segment of trunk
        • abdominal segment of trunk SubClassOf subdivision of trunk
          • subdivision of trunk SubClassOf part_of some trunk
  • external pudendal vein SubClassOf tributary of some femoral vein
    • tributary of SubPropertyOf: in branching relationship with
      • in branching relationship with SubPropertyOf: part_of
        • Transitive: part_of
    • femoral vein SubClassOf part_of some hindlimb
      • hindlimb EquivalentTo limb and (part_of some pelvic complex)
        • limb SubClassOf paired limb/fin
          • paired limb/fin SubClassOf appendage
• Nothing EquivalentTo (part_of some appendage) and (part_of some trunk)

superficial external pudendal vein SubClassOf Nothing

• superficial external pudendal vein EquivalentTo external pudendal vein and (part_of some vasculature of integument)
  • external pudendal vein SubClassOf pudendal vein
    • pudendal vein SubClassOf part_of some pelvic region of trunk
      • pelvic region of trunk SubClassOf part_of some abdominal segment of trunk
        • abdominal segment of trunk SubClassOf subdivision of trunk
          • subdivision of trunk SubClassOf part_of some trunk
  • external pudendal vein SubClassOf tributary of some femoral vein
    • tributary of SubPropertyOf: in branching relationship with
      • in branching relationship with SubPropertyOf: part_of
    • femoral vein SubClassOf part_of some hindlimb
      • hindlimb EquivalentTo limb and (part_of some pelvic complex)
        • limb SubClassOf paired limb/fin
          • paired limb/fin SubClassOf appendage
  • Transitive: part_of
• Nothing EquivalentTo (part_of some appendage) and (part_of some trunk)

superficial dorsal vein of penis SubClassOf Nothing

• superficial dorsal vein of penis SubClassOf tributary of some superficial external pudendal vein
  • tributary of SubPropertyOf: in branching relationship with
    • in branching relationship with SubPropertyOf: part_of
      • Transitive: part_of
  • superficial external pudendal vein EquivalentTo external pudendal vein and (part_of some vasculature of integument)
    • external pudendal vein SubClassOf pudendal vein
      • pudendal vein SubClassOf part_of some pelvic region of trunk
        • pelvic region of trunk SubClassOf part_of some abdominal segment of trunk
          • abdominal segment of trunk SubClassOf subdivision of trunk
            • subdivision of trunk SubClassOf part_of some trunk
    • external pudendal vein SubClassOf tributary of some femoral vein
      • femoral vein SubClassOf part_of some hindlimb
        • hindlimb EquivalentTo limb and (part_of some pelvic complex)
          • limb SubClassOf paired limb/fin
            • paired limb/fin SubClassOf appendage
• Nothing EquivalentTo (part_of some appendage) and (part_of some trunk)

Axiom Impact

Axioms used 6 times

• hindlimb EquivalentTo limb and (part_of some pelvic complex) [core.owl]
• Nothing EquivalentTo (part_of some appendage) and (part_of some trunk) [core.owl]
• femoral vein SubClassOf part_of some hindlimb [core.owl]
• limb SubClassOf paired limb/fin [core.owl]
• pelvic region of trunk SubClassOf part_of some abdominal segment of trunk [core.owl]
• abdominal segment of trunk SubClassOf subdivision of trunk [core.owl]
• paired limb/fin SubClassOf appendage [core.owl]
• pudendal vein SubClassOf part_of some pelvic region of trunk [core.owl]
• subdivision of trunk SubClassOf part_of some trunk [core.owl]
• external pudendal vein SubClassOf pudendal vein [core.owl]
• external pudendal vein SubClassOf tributary of some femoral vein [core.owl]
• in branching relationship with SubPropertyOf: part_of [core.owl]
• tributary of SubPropertyOf: in branching relationship with [core.owl]
• Transitive: part_of [core.owl]

Axioms used 2 times

• superficial external pudendal vein EquivalentTo external pudendal vein and (part_of some vasculature of integument) [core.owl]

Axioms used 1 times

• deep external pudendal vein EquivalentTo external pudendal vein and (part_of some deep vasculature) [core.owl]
• inferior external pudendal vein SubClassOf external pudendal vein [core.owl]
• superior external pudendal vein SubClassOf external pudendal vein [core.owl]
• superficial dorsal vein of penis SubClassOf tributary of some superficial external pudendal vein [core.owl]

Ontologies used:

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

[dosumis]

Will look into this as high priority later this afternoon. But wondering why this is not being caught in PRs.

[shawntanzk]

@dosumis - I think this is wrong, as femoral vein extends beyond the limb:

femoral vein SubClassOf part_of some hindlimb

see https://upload.wikimedia.org/wikipedia/commons/thumb/c/cb/Blausen_0609_LegVeins.png/250px-Blausen_0609_LegVeins.png

[dosumis]

femoral vein SubClassOf part_of some hindlimb

Does removing this fix this issue?

(There's a general issue with over-use of partonomy in representing vasculature that seems likely to cause problems for pairwise disjointness which might be cured by switching to connection relationships)

[shawntanzk]

just about to give it a try

[anitacaron]

But wondering why this is not being caught in PRs.

I'm going to include this check now.

[dosumis]

I thought ODK always checked consistency on PRs. Did that change?

[dosumis]

From this #2294 I guess it does check but some axioms missing

[dosumis]

After inference over property & class hierarchy we get:

external pudendal vein part_of some trunk (via pelvic region of trunk)
external pudendal vein part_of some femoral vein. (via tributary_of relation)
femoral vein part_of some hindlimb
part_of some hindlimb disjointWith part_of some trunk

Questions:

• is all of the femoral vein in the limb or is some of it in the pelvic region of the trunk?
• would it be better to use connected_to or some subproperty to relate 'external pudendal vein' to 'femoral vein' ? This will be necessary if all of the femoral vein is in the limb

@shawntanzk - can you investigate a little further?

@GriffinWeber - can you comment on this? More generally, is it possible for editors to look up this type of information in your vasculature DB?

[shawntanzk]

is all of the femoral vein in the limb or is some of it in the pelvic region of the trunk?

Looking at this question, another question I have is if pelvic region of trunk is a part of the pelvic complex - cause that isn't allowed (I don't think this is the case in the ontology, but just wondering in reality). If it is, the disjointness might be not right?

Nothing EquivalentTo (part_of some appendage) and (part_of some trunk)

hindlimb EquivalentTo limb and (part_of some pelvic complex)
limb SubClassOf paired limb/fin
paired limb/fin SubClassOf appendage

pelvic region of trunk SubClassOf part_of some abdominal segment of trunk
abdominal segment of trunk SubClassOf subdivision of trunk
subdivision of trunk SubClassOf part_of some trunk