unsats

[shawntanzk]

Looks like unsats are a bit more complicated
will try using robot explain to figure out some stuff
tagging @dosumis

1. no unsats in uberon_slice.owl
2. no unsats in sources_merged.owl
3. unsats when merged the above two

sh run.sh robot merge --input uberon_slice.owl --input sources_merged.owl --output tmp.owl
sh run.sh robot explain -i tmp.owl -M unsatisfiability --unsatisfiable random:10 --explanation unsats.md

olfactory tubercle SubClassOf Nothing

• olfactory tubercle EquivalentTo olfactory tubercle and (part_of some Homo sapiens)
  • Transitive: part_of
  • Homo sapiens SubClassOf Homo
    • Homo SubClassOf Homininae
      • Homininae SubClassOf Hominidae
        • Hominidae SubClassOf Hominoidea
          • Hominoidea SubClassOf Catarrhini
            • Catarrhini SubClassOf Simiiformes
              • Simiiformes SubClassOf Haplorrhini
                • Haplorrhini SubClassOf Primates
• olfactory tubercle SubClassOf part_of some ventral striatum
• Nothing EquivalentTo (part_of some striatum) and (part_of some pallidum)
• ventral striatum SubClassOf part_of some striatum
• substantia innominata SubClassOf part_of some ventral pallidum
• olfactory tubercle, left EquivalentTo olfactory tubercle and (part_of some Homo sapiens)
• olfactory tubercle, left SubClassOf part_of some substantia innominata, left
• olfactory tubercle EquivalentTo olfactory tubercle and (part_of some Primates)
• globus pallidus SubClassOf part_of some pallidum
• substantia innominata EquivalentTo substantia innominata and (part_of some Homo sapiens)
• ventral striatum EquivalentTo ventral striatum and (part_of some Primates)
• substantia innominata, left SubClassOf part_of some substantia innominata
• ventral pallidum SubClassOf part_of some globus pallidus

uncinate fasciculus SubClassOf Nothing

• uncinate fasciculus EquivalentTo uncinate fasciculus and (part_of some Homo sapiens)
  • uncinate fasciculus SubClassOf part_of some forebrain ipsilateral fiber tracts
    • forebrain ipsilateral fiber tracts EquivalentTo forebrain ipsilateral fiber tracts and (part_of some Homo sapiens)
      • forebrain ipsilateral fiber tracts SubClassOf part_of some white matter of forebrain
        • white matter of forebrain EquivalentTo white matter and (part_of some forebrain)
  • uncinate fasciculus SubClassOf part_of some pontine tegmentum
    • pontine tegmentum SubClassOf part_of some pons
      • pons SubClassOf part_of some brainstem
  • Transitive: part_of
• Nothing EquivalentTo (part_of some forebrain) and (part_of some brainstem)

taenia tectum SubClassOf Nothing

• taenia tectum SubClassOf part_of some archicortex
  • archicortex EquivalentTo archicortex and (part_of some Homo sapiens)
    • Homo sapiens SubClassOf Homo
      • Homo SubClassOf Homininae
        • Homininae SubClassOf Hominidae
          • Hominidae SubClassOf Hominoidea
            • Hominoidea SubClassOf Catarrhini
              • Catarrhini SubClassOf Simiiformes
                • Simiiformes SubClassOf Haplorrhini
                  • Haplorrhini SubClassOf Primates
    • archicortex SubClassOf allocortex
• taenia tectum EquivalentTo taenia tectum of brain and (part_of some Homo sapiens)
  • taenia tectum of brain SubClassOf white matter of limbic lobe
    • white matter of limbic lobe EquivalentTo white matter of cerebral lobe and (part_of some limbic lobe)
      • white matter of cerebral lobe EquivalentTo cerebral hemisphere white matter and (part_of some lobe of cerebral hemisphere)
        • cerebral hemisphere white matter SubClassOf white matter of telencephalon
          • white matter of telencephalon SubClassOf white matter of forebrain
            • white matter of forebrain EquivalentTo white matter and (part_of some forebrain)
• white matter SubClassOf part_of some neocortex
• white matter EquivalentTo white matter and (part_of some Primates)
• neocortex EquivalentTo neocortex and (part_of some Primates)
• Nothing EquivalentTo (part_of some neocortex) and (part_of some allocortex)

posterior commissure SubClassOf Nothing

• posterior commissure EquivalentTo posterior commissure and (part_of some Homo sapiens)
  • posterior commissure SubClassOf part_of some white matter of midbrain
    • white matter of midbrain EquivalentTo white matter of midbrain and (part_of some Homo sapiens)
      • white matter of midbrain EquivalentTo white matter and (part_of some midbrain)
  • posterior commissure SubClassOf part_of some diencephalic white matter
    • diencephalic white matter SubClassOf part_of some diencephalon
  • Transitive: part_of
• Nothing EquivalentTo (part_of some midbrain) and (part_of some diencephalon)

islands of Calleja SubClassOf Nothing

• islands of Calleja EquivalentTo island of Calleja and (part_of some Homo sapiens)
  • Transitive: part_of
  • Homo sapiens SubClassOf Homo
    • Homo SubClassOf Homininae
      • Homininae SubClassOf Hominidae
        • Hominidae SubClassOf Hominoidea
          • Hominoidea SubClassOf Catarrhini
            • Catarrhini SubClassOf Simiiformes
              • Simiiformes SubClassOf Haplorrhini
                • Haplorrhini SubClassOf Primates
• islands of Calleja SubClassOf part_of some ventral striatum
• Nothing EquivalentTo (part_of some striatum) and (part_of some pallidum)
• ventral striatum SubClassOf part_of some striatum
• substantia innominata SubClassOf part_of some ventral pallidum
• islands of calleja, left SubClassOf part_of some olfactory tubercle, left
• olfactory tubercle, left SubClassOf part_of some substantia innominata, left
• islands of Calleja EquivalentTo island of Calleja and (part_of some Primates)
• globus pallidus SubClassOf part_of some pallidum
• substantia innominata EquivalentTo substantia innominata and (part_of some Homo sapiens)
• ventral striatum EquivalentTo ventral striatum and (part_of some Primates)
• islands of calleja, left EquivalentTo island of Calleja and (part_of some Homo sapiens)
• substantia innominata, left SubClassOf part_of some substantia innominata
• ventral pallidum SubClassOf part_of some globus pallidus

scattered islands of Calleja SubClassOf Nothing

• scattered islands of Calleja SubClassOf part_of some islands of Calleja
  • Transitive: part_of
  • islands of Calleja EquivalentTo island of Calleja and (part_of some Homo sapiens)
    • Homo sapiens SubClassOf Homo
      • Homo SubClassOf Homininae
        • Homininae SubClassOf Hominidae
          • Hominidae SubClassOf Hominoidea
            • Hominoidea SubClassOf Catarrhini
              • Catarrhini SubClassOf Simiiformes
                • Simiiformes SubClassOf Haplorrhini
                  • Haplorrhini SubClassOf Primates
• islands of Calleja SubClassOf part_of some ventral striatum
• ventral striatum SubClassOf part_of some striatum
• substantia innominata SubClassOf part_of some ventral pallidum
• islands of calleja, left SubClassOf part_of some olfactory tubercle, left
• globus pallidus SubClassOf part_of some pallidum
• substantia innominata EquivalentTo substantia innominata and (part_of some Homo sapiens)
• ventral striatum EquivalentTo ventral striatum and (part_of some Primates)
• Nothing EquivalentTo (part_of some striatum) and (part_of some pallidum)
• olfactory tubercle, left SubClassOf part_of some substantia innominata, left
• islands of Calleja EquivalentTo island of Calleja and (part_of some Primates)
• islands of calleja, left EquivalentTo island of Calleja and (part_of some Homo sapiens)
• substantia innominata, left SubClassOf part_of some substantia innominata
• ventral pallidum SubClassOf part_of some globus pallidus

optic tract SubClassOf Nothing

• optic tract EquivalentTo optic tract and (part_of some Homo sapiens)
  • optic tract SubClassOf tract of diencephalon
    • tract of diencephalon SubClassOf part_of some diencephalon
  • Transitive: part_of
• myelencephalon SubClassOf segmental subdivision of hindbrain
• cranial nerves SubClassOf part_of some myelencephalic white matter
• white matter of myelencephalon SubClassOf part_of some myelencephalon
• optic tract, left SubClassOf part_of some optic nerve, left
• optic nerve, left SubClassOf part_of some optic nerve
• segmental subdivision of hindbrain SubClassOf part_of some hindbrain
• myelencephalic white matter EquivalentTo white matter of myelencephalon and (part_of some Homo sapiens)
• optic tract, left EquivalentTo optic tract and (part_of some Homo sapiens)
• optic nerve SubClassOf part_of some cranial nerves
• Nothing EquivalentTo (part_of some diencephalon) and (part_of some hindbrain)

major island of Calleja SubClassOf Nothing

• major island of Calleja SubClassOf part_of some islands of Calleja
  • Transitive: part_of
  • islands of Calleja EquivalentTo island of Calleja and (part_of some Homo sapiens)
    • Homo sapiens SubClassOf Homo
      • Homo SubClassOf Homininae
        • Homininae SubClassOf Hominidae
          • Hominidae SubClassOf Hominoidea
            • Hominoidea SubClassOf Catarrhini
              • Catarrhini SubClassOf Simiiformes
                • Simiiformes SubClassOf Haplorrhini
                  • Haplorrhini SubClassOf Primates
• islands of Calleja SubClassOf part_of some ventral striatum
• ventral striatum SubClassOf part_of some striatum
• substantia innominata SubClassOf part_of some ventral pallidum
• islands of calleja, left SubClassOf part_of some olfactory tubercle, left
• globus pallidus SubClassOf part_of some pallidum
• substantia innominata EquivalentTo substantia innominata and (part_of some Homo sapiens)
• ventral striatum EquivalentTo ventral striatum and (part_of some Primates)
• Nothing EquivalentTo (part_of some striatum) and (part_of some pallidum)
• olfactory tubercle, left SubClassOf part_of some substantia innominata, left
• islands of Calleja EquivalentTo island of Calleja and (part_of some Primates)
• islands of calleja, left EquivalentTo island of Calleja and (part_of some Homo sapiens)
• substantia innominata, left SubClassOf part_of some substantia innominata
• ventral pallidum SubClassOf part_of some globus pallidus

olfactory bulb SubClassOf Nothing

• olfactory bulb EquivalentTo olfactory bulb and (part_of some Homo sapiens)
  • Transitive: part_of
  • olfactory bulb SubClassOf part_of some paleocortex (semicortex)
    • paleocortex (semicortex) EquivalentTo paleocortex and (part_of some Homo sapiens)
      • Homo sapiens SubClassOf Homo
        • Homo SubClassOf Homininae
          • Homininae SubClassOf Hominidae
            • Hominidae SubClassOf Hominoidea
              • Hominoidea SubClassOf Catarrhini
                • Catarrhini SubClassOf Simiiformes
                  • Simiiformes SubClassOf Haplorrhini
                  • Haplorrhini SubClassOf Primates
      • paleocortex SubClassOf allocortex
• olfactory nerve EquivalentTo olfactory nerve and (part_of some Homo sapiens)
• white matter EquivalentTo white matter and (part_of some Primates)
• myelencephalic white matter SubClassOf part_of some white matter
• olfactory bulb, left SubClassOf part_of some olfactory nerve, left
• cranial nerves EquivalentTo cranial nerve and (part_of some Homo sapiens)
• olfactory nerve SubClassOf cranial nerve
• olfactory bulb, left EquivalentTo olfactory bulb and (part_of some Homo sapiens)
• neocortex EquivalentTo neocortex and (part_of some Primates)
• white matter SubClassOf part_of some neocortex
• cranial nerves SubClassOf part_of some myelencephalic white matter
• white matter EquivalentTo white matter and brain white matter and (part_of some Homo sapiens)
• olfactory nerve, left SubClassOf part_of some olfactory nerve
• Nothing EquivalentTo (part_of some neocortex) and (part_of some allocortex)

indusium griseum SubClassOf Nothing

• indusium griseum EquivalentTo induseum griseum and (part_of some Homo sapiens)
  • induseum griseum SubClassOf white matter of limbic lobe
    • white matter of limbic lobe EquivalentTo white matter of cerebral lobe and (part_of some limbic lobe)
      • white matter of cerebral lobe EquivalentTo cerebral hemisphere white matter and (part_of some lobe of cerebral hemisphere)
        • cerebral hemisphere white matter SubClassOf white matter of telencephalon
          • white matter of telencephalon SubClassOf white matter of forebrain
            • white matter of forebrain EquivalentTo white matter and (part_of some forebrain)
  • indusium griseum SubClassOf part_of some archicortex
    • archicortex SubClassOf part_of some allocortex
      • allocortex EquivalentTo allocortex and (part_of some Homo sapiens)
  • Transitive: part_of
  • Homo sapiens SubClassOf Homo
    • Homo SubClassOf Homininae
      • Homininae SubClassOf Hominidae
        • Hominidae SubClassOf Hominoidea
          • Hominoidea SubClassOf Catarrhini
            • Catarrhini SubClassOf Simiiformes
              • Simiiformes SubClassOf Haplorrhini
                • Haplorrhini SubClassOf Primates
• white matter SubClassOf part_of some neocortex
• white matter EquivalentTo white matter and (part_of some Primates)
• neocortex EquivalentTo neocortex and (part_of some Primates)
• Nothing EquivalentTo (part_of some neocortex) and (part_of some allocortex)

Axiom Impact

Axioms used 9 times

• Transitive: part_of [uberon.owl]

Axioms used 7 times

• Homininae SubClassOf Hominidae [uberon.owl]
• Simiiformes SubClassOf Haplorrhini [uberon.owl]
• Hominoidea SubClassOf Catarrhini [uberon.owl]
• Haplorrhini SubClassOf Primates [uberon.owl]
• Catarrhini SubClassOf Simiiformes [uberon.owl]
• Hominidae SubClassOf Hominoidea [uberon.owl]
• Homo SubClassOf Homininae [uberon.owl]
• Homo sapiens SubClassOf Homo [uberon.owl]

Axioms used 4 times

• substantia innominata EquivalentTo substantia innominata and (part_of some Homo sapiens) [uberon.owl]
• ventral striatum EquivalentTo ventral striatum and (part_of some Primates) [uberon.owl]
• Nothing EquivalentTo (part_of some striatum) and (part_of some pallidum) [uberon.owl]
• olfactory tubercle, left SubClassOf part_of some substantia innominata, left [uberon.owl]
• substantia innominata, left SubClassOf part_of some substantia innominata [uberon.owl]
• globus pallidus SubClassOf part_of some pallidum [uberon.owl]
• ventral pallidum SubClassOf part_of some globus pallidus [uberon.owl]
• substantia innominata SubClassOf part_of some ventral pallidum [uberon.owl]
• ventral striatum SubClassOf part_of some striatum [uberon.owl]

Axioms used 3 times

• islands of Calleja EquivalentTo island of Calleja and (part_of some Homo sapiens) [uberon.owl]
• islands of calleja, left EquivalentTo island of Calleja and (part_of some Homo sapiens) [uberon.owl]
• islands of Calleja EquivalentTo island of Calleja and (part_of some Primates) [uberon.owl]
• neocortex EquivalentTo neocortex and (part_of some Primates) [uberon.owl]
• white matter EquivalentTo white matter and (part_of some Primates) [uberon.owl]
• white matter of forebrain EquivalentTo white matter and (part_of some forebrain) [uberon.owl]
• Nothing EquivalentTo (part_of some neocortex) and (part_of some allocortex) [uberon.owl]
• islands of calleja, left SubClassOf part_of some olfactory tubercle, left [uberon.owl]
• islands of Calleja SubClassOf part_of some ventral striatum [uberon.owl]
• white matter SubClassOf part_of some neocortex [uberon.owl]

Axioms used 2 times

• white matter of cerebral lobe EquivalentTo cerebral hemisphere white matter and (part_of some lobe of cerebral hemisphere) [uberon.owl]
• white matter of limbic lobe EquivalentTo white matter of cerebral lobe and (part_of some limbic lobe) [uberon.owl]
• cranial nerves SubClassOf part_of some myelencephalic white matter [uberon.owl]
• cerebral hemisphere white matter SubClassOf white matter of telencephalon [uberon.owl]
• white matter of telencephalon SubClassOf white matter of forebrain [uberon.owl]

Axioms used 1 times

• allocortex EquivalentTo allocortex and (part_of some Homo sapiens) [uberon.owl]
• archicortex EquivalentTo archicortex and (part_of some Homo sapiens) [uberon.owl]
• indusium griseum EquivalentTo induseum griseum and (part_of some Homo sapiens) [uberon.owl]
• taenia tectum EquivalentTo taenia tectum of brain and (part_of some Homo sapiens) [uberon.owl]
• paleocortex (semicortex) EquivalentTo paleocortex and (part_of some Homo sapiens) [uberon.owl]
• olfactory bulb EquivalentTo olfactory bulb and (part_of some Homo sapiens) [uberon.owl]
• olfactory tubercle EquivalentTo olfactory tubercle and (part_of some Homo sapiens) [uberon.owl]
• posterior commissure EquivalentTo posterior commissure and (part_of some Homo sapiens) [uberon.owl]
• forebrain ipsilateral fiber tracts EquivalentTo forebrain ipsilateral fiber tracts and (part_of some Homo sapiens) [uberon.owl]
• optic tract EquivalentTo optic tract and (part_of some Homo sapiens) [uberon.owl]
• uncinate fasciculus EquivalentTo uncinate fasciculus and (part_of some Homo sapiens) [uberon.owl]
• white matter of midbrain EquivalentTo white matter of midbrain and (part_of some Homo sapiens) [uberon.owl]
• olfactory tubercle, left EquivalentTo olfactory tubercle and (part_of some Homo sapiens) [uberon.owl]
• white matter EquivalentTo white matter and brain white matter and (part_of some Homo sapiens) [uberon.owl]
• myelencephalic white matter EquivalentTo white matter of myelencephalon and (part_of some Homo sapiens) [uberon.owl]
• cranial nerves EquivalentTo cranial nerve and (part_of some Homo sapiens) [uberon.owl]
• olfactory nerve EquivalentTo olfactory nerve and (part_of some Homo sapiens) [uberon.owl]
• olfactory bulb, left EquivalentTo olfactory bulb and (part_of some Homo sapiens) [uberon.owl]
• optic tract, left EquivalentTo optic tract and (part_of some Homo sapiens) [uberon.owl]
• olfactory tubercle EquivalentTo olfactory tubercle and (part_of some Primates) [uberon.owl]
• white matter of midbrain EquivalentTo white matter and (part_of some midbrain) [uberon.owl]
• Nothing EquivalentTo (part_of some forebrain) and (part_of some brainstem) [uberon.owl]
• Nothing EquivalentTo (part_of some midbrain) and (part_of some diencephalon) [uberon.owl]
• Nothing EquivalentTo (part_of some diencephalon) and (part_of some hindbrain) [uberon.owl]
• archicortex SubClassOf part_of some allocortex [uberon.owl]
• indusium griseum SubClassOf part_of some archicortex [uberon.owl]
• taenia tectum SubClassOf part_of some archicortex [uberon.owl]
• olfactory bulb SubClassOf part_of some paleocortex (semicortex) [uberon.owl]
• major island of Calleja SubClassOf part_of some islands of Calleja [uberon.owl]
• scattered islands of Calleja SubClassOf part_of some islands of Calleja [uberon.owl]
• posterior commissure SubClassOf part_of some white matter of midbrain [uberon.owl]
• uncinate fasciculus SubClassOf part_of some forebrain ipsilateral fiber tracts [uberon.owl]
• myelencephalic white matter SubClassOf part_of some white matter [uberon.owl]
• olfactory nerve, left SubClassOf part_of some olfactory nerve [uberon.owl]
• olfactory bulb, left SubClassOf part_of some olfactory nerve, left [uberon.owl]
• optic nerve SubClassOf part_of some cranial nerves [uberon.owl]
• optic nerve, left SubClassOf part_of some optic nerve [uberon.owl]
• optic tract, left SubClassOf part_of some optic nerve, left [uberon.owl]
• olfactory tubercle SubClassOf part_of some ventral striatum [uberon.owl]
• posterior commissure SubClassOf part_of some diencephalic white matter [uberon.owl]
• pons SubClassOf part_of some brainstem [uberon.owl]
• olfactory nerve SubClassOf cranial nerve [uberon.owl]
• optic tract SubClassOf tract of diencephalon [uberon.owl]
• archicortex SubClassOf allocortex [uberon.owl]
• pontine tegmentum SubClassOf part_of some pons [uberon.owl]
• uncinate fasciculus SubClassOf part_of some pontine tegmentum [uberon.owl]
• diencephalic white matter SubClassOf part_of some diencephalon [uberon.owl]
• segmental subdivision of hindbrain SubClassOf part_of some hindbrain [uberon.owl]
• myelencephalon SubClassOf segmental subdivision of hindbrain [uberon.owl]
• tract of diencephalon SubClassOf part_of some diencephalon [uberon.owl]
• paleocortex SubClassOf allocortex [uberon.owl]
• induseum griseum SubClassOf white matter of limbic lobe [uberon.owl]
• taenia tectum of brain SubClassOf white matter of limbic lobe [uberon.owl]
• white matter of myelencephalon SubClassOf part_of some myelencephalon [uberon.owl]
• forebrain ipsilateral fiber tracts SubClassOf part_of some white matter of forebrain [uberon.owl]

[shawntanzk]

wierdly enough when i run
sh run.sh robot explain --input tmp.owl --reasoner ELK --axiom "hindbrain SubClassOf 'part of' some brainstem" --explanation hindbrain-brainstem.md
theres no explanation, not sure where we found that, cause i cant replicate it with aba_uberon too

[shawntanzk]

uncinate fasciculus unsat fixed in uberon

See details here

[uncinate fasciculus](http://purl.obolibrary.org/obo/UBERON_0003044) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pontine tegmentum](http://purl.obolibrary.org/obo/UBERON_0003023) seems wrong

Uncinate fasciculus definition - "Pathway arising from the fastigial nucleus to the vestibular nuclei, reticular formation, motor neurons of brainstem and cervical spinal cord"
but has "part of" pontine tegmentum - which has part of some pons

seems like a legit uberon issue, not sure why this didnt get picked up with uberon? does uberon not have the disjoint Nothing EquivalentTo (part_of some forebrain) and (part_of some brainstem)?

[shawntanzk]

posterior commissure SubClassOf Nothing

error coming from uberon and dhba classifying it differently:

DHBA:
posterior commissure SubClassOf part_of some white matter of midbrain

UBERON:
posterior commissure SubClassOf part_of some diencephalic white matter

On research, hard to say which is actually correct given the commissure connects midbrain and diencephalon structures

[shawntanzk]

Olfactory bulb:

I think this is the issue:
white matter SubClassOf part_of some neocortex

I'm guessing that there is white matter in the allocortex too

but also this seems wrong:
olfactory bulb, left SubClassOf part_of some olfactory nerve, left

[dosumis]

Thinking about this - these inconsistencies must be coming from a clash between the partonomy coming from JSON and spatial disjointness axioms in Uberon expressed above as

Nothing EquivalentTo (part_of some forebrain) and (part_of some brainstem) [uberon.owl]

(I have a vague recollection of having been through this last time I worked on this. Or maybe I was using a version of Uberon that lacked the spatial disjointness.)

I think we need to
(a) strip out disjoints for now so that we can generate accurate reports for review.
(b) Slowly chip away at the reasons for these inconsistencies. They are, I think, likely to indicate that some relationships in ABA JSON files should not be mapped to part_of.

We could also use the approach we developed for HubMap - using UberGraph queries to test the validity and type of each relationship. This would be a lot more work though, so we'd need to consider carefully if we want to take it on.

Note - for ease of reviewing, maybe we should use longer display names for the ABA terms by including species in brackets. The inconsistency reports above are confusing because it's hard to tell ABA and Uberon terms apart - many have the same names.

[dosumis]

These are good examples I think

white matter SubClassOf part_of some neocortex

I'm guessing that there is white matter in the allocortex too

-> overlaps , or we make the term PBA_294022044 'white matter of neocortex'

but also this seems wrong:
olfactory bulb, left SubClassOf part_of some olfactory nerve, left

part_of -> connected_to ?

[shawntanzk]

(a) strip out disjoints for now so that we can generate accurate reports for review.

will do this for now

(b) Slowly chip away at the reasons for these inconsistencies. They are, I think, likely to indicate that some relationships in ABA JSON files should not be mapped to part_of.

This sound a bit too fun and things we can spend too many hours puzzle-solving :p

[dosumis]

Another good example

uncinate fasciculus SubClassOf part_of some pontine tegmentum
seems wrong

Uncinate fasciculus definition - "Pathway arising from the fastigial nucleus to the vestibular nuclei, reticular formation, motor neurons of brainstem and cervical spinal cord"
but has "part of" pontine tegmentum - which has part of some pons

seems like a legit uberon issue, not sure why this didnt get picked up with uberon? does uberon not have the disjoint Nothing EquivalentTo (part_of some forebrain) and (part_of some brainstem)?

->
uncinate fasciculus SubClassOf overlaps some pontine tegmentum

Also we should add the spatial disjointness axiom to Uberon if it's missing.

[dosumis]

These kinds of issues are inevitable in a hierarchy built for annotating an atlas.