MP+HP together cause some MP unsats

[matentzn]

absent cochlear hair cells SubClassOf Nothing

• absent cochlear hair cells EquivalentTo has_part some (absent and (inheres in some (sensory hair cell and (part_of some cochlea))) and (has modifier some abnormal))
  • sensory hair cell SubClassOf mechanoreceptor cell
    • mechanoreceptor cell EquivalentTo neuron and (capable_of some detection of mechanical stimulus involved in sensory perception)
    • neuron SubClassOf neural cell
      • neural cell SubClassOf part_of some nervous system
  • cochlea SubClassOf part_of some bony labyrinth
    • bony labyrinth SubClassOf part_of some petrous part of temporal bone
    • petrous part of temporal bone SubClassOf zone of bone organ
      • zone of bone organ SubClassOf part_of some bone element
      • bone element SubClassOf part_of some skeletal system
  • Transitive: part_of
• Nothing EquivalentTo (part_of some nervous system) and (part_of some skeletal system)

absent cochlear outer hair cells SubClassOf Nothing

• absent cochlear outer hair cells EquivalentTo has_part some (absent and (inheres in some (outer hair cell and (part_of some cochlea))) and (has modifier some abnormal))
  • outer hair cell SubClassOf auditory hair cell
    • auditory hair cell SubClassOf ear hair cell
    • ear hair cell SubClassOf sensory hair cell
      • sensory hair cell SubClassOf mechanoreceptor cell
      • mechanoreceptor cell EquivalentTo neuron and (capable_of some detection of mechanical stimulus involved in sensory perception)
        • neuron SubClassOf neural cell
        • neural cell SubClassOf part_of some nervous system
  • cochlea SubClassOf part_of some bony labyrinth
    • bony labyrinth SubClassOf part_of some petrous part of temporal bone
    • petrous part of temporal bone SubClassOf zone of bone organ
      • zone of bone organ SubClassOf part_of some bone element
      • bone element SubClassOf part_of some skeletal system
  • Transitive: part_of
• Nothing EquivalentTo (part_of some nervous system) and (part_of some skeletal system)

absent cochlear inner hair cells SubClassOf Nothing

• absent cochlear inner hair cells SubClassOf absent cochlear hair cells
  • absent cochlear hair cells EquivalentTo has_part some (absent and (inheres in some (sensory hair cell and (part_of some cochlea))) and (has modifier some abnormal))
    • sensory hair cell SubClassOf mechanoreceptor cell
    • mechanoreceptor cell EquivalentTo neuron and (capable_of some detection of mechanical stimulus involved in sensory perception)
      • neuron SubClassOf neural cell
      • neural cell SubClassOf part_of some nervous system
    • cochlea SubClassOf part_of some bony labyrinth
    • bony labyrinth SubClassOf part_of some petrous part of temporal bone
      • petrous part of temporal bone SubClassOf zone of bone organ
      • zone of bone organ SubClassOf part_of some bone element
        • bone element SubClassOf part_of some skeletal system
    • Transitive: part_of
• Nothing EquivalentTo (part_of some nervous system) and (part_of some skeletal system)

Axiom Impact

Axioms used 3 times

• mechanoreceptor cell EquivalentTo neuron and (capable_of some detection of mechanical stimulus involved in sensory perception) [mp.owl]
• Nothing EquivalentTo (part_of some nervous system) and (part_of some skeletal system) [mp.owl]
• neuron SubClassOf neural cell [mp.owl]
• sensory hair cell SubClassOf mechanoreceptor cell [mp.owl]
• neural cell SubClassOf part_of some nervous system [mp.owl]
• bone element SubClassOf part_of some skeletal system [mp.owl]
• petrous part of temporal bone SubClassOf zone of bone organ [mp.owl]
• bony labyrinth SubClassOf part_of some petrous part of temporal bone [mp.owl]
• cochlea SubClassOf part_of some bony labyrinth [mp.owl]
• zone of bone organ SubClassOf part_of some bone element [mp.owl]
• Transitive: part_of [mp.owl]

Axioms used 2 times

• absent cochlear hair cells EquivalentTo has_part some (absent and (inheres in some (sensory hair cell and (part_of some cochlea))) and (has modifier some abnormal)) [mp.owl]

Axioms used 1 times

• absent cochlear outer hair cells EquivalentTo has_part some (absent and (inheres in some (outer hair cell and (part_of some cochlea))) and (has modifier some abnormal)) [mp.owl]
• auditory hair cell SubClassOf ear hair cell [mp.owl]
• outer hair cell SubClassOf auditory hair cell [mp.owl]
• ear hair cell SubClassOf sensory hair cell [mp.owl]
• absent cochlear inner hair cells SubClassOf absent cochlear hair cells [mp.owl]

Ontologies used:

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

@dosumis @balhoff can you pinpoint the problem?

[matentzn]

FYI @viomunoz, this is why the IMPC pipeline currently fails.

[sbello]

@matentzn are you looking at the latest version of the MP file? The eq I see for absent cochlear outer hair cell is: 'has part' some (absent and ('characteristic of' some 'outer hair cell') and ('has modifier' some abnormal))

absent inner hair cells is: 'has part' some (absent and ('characteristic of' some 'inner hair cell') and ('has modifier' some abnormal))

absent cochlear hair cells is 'has part' some (absent and ('characteristic of' some 'auditory hair cell') and ('has modifier' some abnormal))

[dosumis]

This issue has come up in a related context recently:

https://github.com/obophenotype/uberon/issues/1905

The problem is that the cochlea is classified as bone, but the sensory epithelium that lines it ('spiral organ of cochlea' AKA the organ of Corti) has a separate developmental origin (see https://journals.biologists.com/dev/article/147/12/dev162263/224272/Development-of-the-cochlea ). This breaks the spatial disjointness of skeletal system and nervous system.

I suspect that the reason Uberon is not inconsistent is because it breaks the part_of chain with a 'located in' https://github.com/obophenotype/uberon/issues/1513 (although I'm looking in to whether the placement of this is optimal). The phenotype terms add this back with a parthood relationship on the cell type.

Quick fix(ish): change MP/HP patterns. (Update - looks like Sue got there before me).

Agree with this:

cochlear outer hair cell is: 'has part' some (absent and ('characteristic of' some 'outer hair cell') and ('has modifier' some abnormal))

absent inner hair cells is: 'has part' some (absent and ('characteristic of' some 'outer hair cell') and ('has modifier' some abnormal))

For this - I would use:

absent cochlear hair cells is 'has part' some (absent and ('characteristic of' some ('auditory hair cell' and part of some 'spiral organ of cochlea') and ('has modifier' some abnormal))

This is redundant for now but CL is (as usual) much too mammal-centric here. Auditory hair cells exist in other contexts in vertebrates: https://en.wikipedia.org/wiki/Sensory_systems_in_fish. I'll open a ticket on the CL tracker to suggest broadening the definition or auditory hair cell and making a new cochlea subclass of this (following the composition pattern above).

For these two tickets

https://github.com/obophenotype/uberon/issues/1905 https://github.com/obophenotype/uberon/issues/1513

I think it might be sufficient to leave Uberon unchanged - or at most to move the located_in relationship down to 'organ of corti'

[sbello]

I'll make the change to the eq for absent cochlear hair cell and push out a new release ASAP.

[matentzn]

Awesome thank you all! :)

When you are done Sue, in case you have ROBOT installed, you can test like this:

robot merge -i mp.owl -I http://purl.obolibrary.org/obo/hp.owl reason -o x.owl

If not, I can also test it once you have made the changes.