Unsatisfiable classes when combined with Uberon and CL

[balhoff]

There are 3 unsatisfiable classes when MP is used with both Uberon and CL:

• absent cochlear hair cells
• absent cochlear inner hair cells
• absent cochlear outer hair cells

They all have the same cause:

absent cochlear hair cells EquivalentTo 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 EquivalentTo animal cell and (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 part of some basicranium
      • basicranium SubClassOf subdivision of skeletal system
      • subdivision of skeletal system SubClassOf part of some skeletal system
  • Transitive: part of
• Nothing EquivalentTo (part of some nervous system) and (part of some skeletal system)

'sensory hair cell' is a 'neuron' and thus part of the nervous system, and this one is said to be part of the 'cochlea' which is part of the skeletal system. Uberon says these systems don't share parts. I'm not sure what the solution to this is. @cmungall is there a particular relation that should be used instead of 'part of'? Or is Uberon being too strict?

[sbello]

I think Uberon is being too strict, excluding the hair cells and other cell layers of the cochlea from the cochlear term in Uberon does not make biological sense. It may be that the Uberon term should be cochlear bone to make it clear that this is only the bony element but the definition doesn't read that way to me.

[cmungall]

I suspect there is confusion between the skeletal part of the cochlea and the compound structure. The inner and middle ear structures could do with a look at from this perspective

On Mon, Oct 21, 2019, 12:14 Sue Bello notifications@github.com wrote:

I think Uberon is being too strict, excluding the hair cells and other cell layers of the cochlea from the cochlear term in Uberon does not make biological sense. It may be that the Uberon term should be cochlear bone to make it clear that this is only the bony element but the definition doesn't read that way to me.

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