Unsats in HCAO caused by Uberon/CL terms

[shawntanzk]

Uberon does not have the following disjoint:

bearer of some maximally connected DisjointWith bearer of some disconnected

which I do not think is problematic, but if you add that in (like HCAO does), a lot of unsats will appear (I assume).

Currently HCAO deals with this by removing the following classes:

http://purl.obolibrary.org/obo/UBERON_0000965 # lens of camera-type eye
http://purl.obolibrary.org/obo/UBERON_0003902 # retinal neural layer
http://purl.obolibrary.org/obo/CL_0000745 # retina horizontal cell (this should be fixed next release, it was using part of instead of has soma location)

However, we should probably look into getting this fixed on Uberons side.

see HumanCellAtlas/ontology#123 for details

I think it might come down to this:

• retinal neural layer SubClassOf developmentally_induced_by some lens vesicle
• developmentally_induced_by Domain connected anatomical structure

and perhaps considering relaxing the domain of developmentally_induced_by would be the solution?

Would appreciate input from @cmungall & @dosumis

Tagging @bvarner-ebi & @anitacaron

[anitacaron]

I just checked, and http://purl.obolibrary.org/obo/CL_0000745 is not causing any unsats in the HCAO pipeline.

[shawntanzk]

From @dosumis

I don’t understand why we’ve ended up with ‘connected’ vs ‘disconnected’ as a distinction we care about for domain and range of anatomical relations. Relaxing these, and probably others to ‘material anatomical entity’ makes sense to me.

[JCGiron]

Piling up on this on unsatisfiable classes:
I added new terms to AISM and tried to run a release using the ODK.
I got errors: 174 unsatisfiable classes where all are from terms imported from UBERON, GO, and CL. Most of the UBERON terms are vertebrate-specific and do not apply to insects, so we don't really need them, but they are there, making thins difficult.

Below is the result from sh run.sh make explain_unsat:

corneal epithelial cell SubClassOf Nothing

• corneal epithelial cell SubClassOf part_of some corneal epithelium
  • corneal epithelium EquivalentTo epithelium and (bounding layer of some cornea)
    • cornea SubClassOf part_of some anterior segment of eyeball
      • anterior segment of eyeball SubClassOf in anterior side of some eyeball of camera-type eye
        • eyeball of camera-type eye SubClassOf contributes to morphology of some camera-type eye
          • camera-type eye SubClassOf has part some lens of camera-type eye
            • lens of camera-type eye SubClassOf developmentally induced by some retinal neural layer
              • developmentally induced by Domain anatomical structure
                • anatomical structure EquivalentTo material anatomical entity and (bearer of some 3-D shape) and (bearer of some maximally connected)
              • retinal neural layer SubClassOf layer of retina
                • layer of retina SubClassOf nervous system cell part layer
                  • nervous system cell part layer SubClassOf multi cell part structure
                  • multi cell part structure SubClassOf anatomical cluster
                  • anatomical cluster SubClassOf disconnected anatomical group
                  • disconnected anatomical group SubClassOf has quality some disconnected
                  • has quality SubPropertyOf: bearer of
              • retinal neural layer SubClassOf developmentally induced by some lens vesicle
• bearer of some maximally connected DisjointWith bearer of some disconnected

smooth muscle cell of sphincter of pupil SubClassOf Nothing

• smooth muscle cell of sphincter of pupil SubClassOf part_of some sphincter pupillae
  • sphincter pupillae SubClassOf iris smooth muscle
    • iris smooth muscle SubClassOf part_of some iris
      • iris SubClassOf part_of some anterior uvea
        • anterior uvea SubClassOf contributes to morphology of some uvea
          • uvea SubClassOf part_of some anterior segment of eyeball
            • anterior segment of eyeball SubClassOf in anterior side of some eyeball of camera-type eye
              • eyeball of camera-type eye SubClassOf contributes to morphology of some camera-type eye
                • camera-type eye SubClassOf has part some lens of camera-type eye
                  • lens of camera-type eye SubClassOf developmentally induced by some retinal neural layer
                  • developmentally induced by Domain anatomical structure
                  • anatomical structure EquivalentTo material anatomical entity and (bearer of some 3-D shape) and (bearer of some maximally connected)
                  • retinal neural layer SubClassOf layer of retina
                  • layer of retina SubClassOf nervous system cell part layer
                  • nervous system cell part layer SubClassOf multi cell part structure
                  • multi cell part structure SubClassOf anatomical cluster
                  • anatomical cluster SubClassOf disconnected anatomical group
                  • disconnected anatomical group SubClassOf has quality some disconnected
                  • has quality SubPropertyOf: bearer of
                  • retinal neural layer SubClassOf developmentally induced by some lens vesicle
• bearer of some maximally connected DisjointWith bearer of some disconnected

keratocyte SubClassOf Nothing

• keratocyte SubClassOf part_of some substantia propria of cornea
  • substantia propria of cornea SubClassOf contributes to morphology of some cornea
    • cornea SubClassOf part_of some tunica fibrosa of eyeball
      • tunica fibrosa of eyeball SubClassOf part_of some eyeball of camera-type eye
        • eyeball of camera-type eye SubClassOf contributes to morphology of some camera-type eye
          • camera-type eye SubClassOf has part some lens of camera-type eye
            • lens of camera-type eye SubClassOf developmentally induced by some retinal neural layer
              • developmentally induced by Domain anatomical structure
                • anatomical structure EquivalentTo material anatomical entity and (bearer of some 3-D shape) and (bearer of some maximally connected)
              • retinal neural layer SubClassOf layer of retina
                • layer of retina SubClassOf nervous system cell part layer
                  • nervous system cell part layer SubClassOf multi cell part structure
                  • multi cell part structure SubClassOf anatomical cluster
                  • anatomical cluster SubClassOf disconnected anatomical group
                  • disconnected anatomical group SubClassOf has quality some disconnected
                  • has quality SubPropertyOf: bearer of
              • retinal neural layer SubClassOf developmentally induced by some lens vesicle
• bearer of some maximally connected DisjointWith bearer of some disconnected

retinal cone cell SubClassOf Nothing

• retinal cone cell SubClassOf camera-type eye photoreceptor cell
  • camera-type eye photoreceptor cell SubClassOf part of some camera-type eye
    • camera-type eye SubClassOf has part some lens of camera-type eye
      • lens of camera-type eye SubClassOf developmentally induced by some retinal neural layer
        • developmentally induced by Domain anatomical structure
          • anatomical structure EquivalentTo material anatomical entity and (has characteristic some 3-D shape) and (has characteristic some maximally connected)
        • retinal neural layer SubClassOf layer of retina
          • layer of retina SubClassOf nervous system cell part layer
            • nervous system cell part layer SubClassOf multi cell part structure
              • multi cell part structure SubClassOf anatomical cluster
                • anatomical cluster SubClassOf disconnected anatomical group
                  • disconnected anatomical group SubClassOf has quality some disconnected
                  • has quality SubPropertyOf: has characteristic
        • retinal neural layer SubClassOf developmentally induced by some lens vesicle
• has characteristic some maximally connected DisjointWith has characteristic some disconnected

vertebrate lens cell SubClassOf Nothing

• vertebrate lens cell SubClassOf part of some lens of camera-type eye
  • lens of camera-type eye SubClassOf developmentally induced by some retinal neural layer
    • developmentally induced by Domain anatomical structure
      • anatomical structure EquivalentTo material anatomical entity and (has characteristic some 3-D shape) and (has characteristic some maximally connected)
    • retinal neural layer SubClassOf layer of retina
      • layer of retina SubClassOf nervous system cell part layer
        • nervous system cell part layer SubClassOf multi cell part structure
          • multi cell part structure SubClassOf anatomical cluster
            • anatomical cluster SubClassOf disconnected anatomical group
              • disconnected anatomical group SubClassOf has quality some disconnected
                • has quality SubPropertyOf: has characteristic
    • retinal neural layer SubClassOf developmentally induced by some lens vesicle
• has characteristic some maximally connected DisjointWith has characteristic some disconnected

choroidal cell of the eye SubClassOf Nothing

• choroidal cell of the eye EquivalentTo structural cell and (part of some optic choroid)
  • optic choroid SubClassOf overlaps some posterior segment of eyeball
    • posterior segment of eyeball SubClassOf in posterior side of some eyeball of camera-type eye
      • eyeball of camera-type eye SubClassOf contributes to morphology of some camera-type eye
        • camera-type eye SubClassOf has part some lens of camera-type eye
          • lens of camera-type eye SubClassOf developmentally induced by some retinal neural layer
            • developmentally induced by Domain anatomical structure
              • anatomical structure EquivalentTo material anatomical entity and (has characteristic some 3-D shape) and (has characteristic some maximally connected)
            • retinal neural layer SubClassOf layer of retina
              • layer of retina SubClassOf nervous system cell part layer
                • nervous system cell part layer SubClassOf multi cell part structure
                  • multi cell part structure SubClassOf anatomical cluster
                  • anatomical cluster SubClassOf disconnected anatomical group
                  • disconnected anatomical group SubClassOf has quality some disconnected
                  • has quality SubPropertyOf: has characteristic
            • retinal neural layer SubClassOf developmentally induced by some lens vesicle
• has characteristic some maximally connected DisjointWith has characteristic some disconnected

scleral cell SubClassOf Nothing

• scleral cell SubClassOf part of some sclera
  • sclera SubClassOf contributes to morphology of some camera-type eye
    • camera-type eye SubClassOf has part some lens of camera-type eye
      • lens of camera-type eye SubClassOf developmentally induced by some retinal neural layer
        • developmentally induced by Domain anatomical structure
          • anatomical structure EquivalentTo material anatomical entity and (has characteristic some 3-D shape) and (has characteristic some maximally connected)
        • retinal neural layer SubClassOf layer of retina
          • layer of retina SubClassOf nervous system cell part layer
            • nervous system cell part layer SubClassOf multi cell part structure
              • multi cell part structure SubClassOf anatomical cluster
                • anatomical cluster SubClassOf disconnected anatomical group
                  • disconnected anatomical group SubClassOf has quality some disconnected
                  • has quality SubPropertyOf: has characteristic
        • retinal neural layer SubClassOf developmentally induced by some lens vesicle
• has characteristic some maximally connected DisjointWith has characteristic some disconnected

retinal ganglion cell SubClassOf Nothing

• retinal ganglion cell SubClassOf has soma location some retina
  • retina SubClassOf part of some posterior segment of eyeball
    • posterior segment of eyeball SubClassOf in posterior side of some eyeball of camera-type eye
      • eyeball of camera-type eye SubClassOf contributes to morphology of some camera-type eye
        • camera-type eye SubClassOf has part some lens of camera-type eye
          • lens of camera-type eye SubClassOf developmentally induced by some retinal neural layer
            • developmentally induced by Domain anatomical structure
              • anatomical structure EquivalentTo material anatomical entity and (has characteristic some 3-D shape) and (has characteristic some maximally connected)
            • retinal neural layer SubClassOf layer of retina
              • layer of retina SubClassOf nervous system cell part layer
                • nervous system cell part layer SubClassOf multi cell part structure
                  • multi cell part structure SubClassOf anatomical cluster
                  • anatomical cluster SubClassOf disconnected anatomical group
                  • disconnected anatomical group SubClassOf has quality some disconnected
                  • has quality SubPropertyOf: has characteristic
            • retinal neural layer SubClassOf developmentally induced by some lens vesicle
• has characteristic some maximally connected DisjointWith has characteristic some disconnected

lens epithelial cell SubClassOf Nothing

• lens epithelial cell SubClassOf part of some epithelium of lens
  • epithelium of lens SubClassOf eye epithelium
    • eye epithelium EquivalentTo epithelium and (part of some camera-type eye)
      • camera-type eye SubClassOf has part some lens of camera-type eye
        • lens of camera-type eye SubClassOf developmentally induced by some retinal neural layer
          • developmentally induced by Domain anatomical structure
            • anatomical structure EquivalentTo material anatomical entity and (has characteristic some 3-D shape) and (has characteristic some maximally connected)
          • retinal neural layer SubClassOf layer of retina
            • layer of retina SubClassOf nervous system cell part layer
              • nervous system cell part layer SubClassOf multi cell part structure
                • multi cell part structure SubClassOf anatomical cluster
                  • anatomical cluster SubClassOf disconnected anatomical group
                  • disconnected anatomical group SubClassOf has quality some disconnected
                  • has quality SubPropertyOf: has characteristic
          • retinal neural layer SubClassOf developmentally induced by some lens vesicle
• has characteristic some maximally connected DisjointWith has characteristic some disconnected

retinal rod cell SubClassOf Nothing

• retinal rod cell SubClassOf camera-type eye photoreceptor cell
  • camera-type eye photoreceptor cell SubClassOf part of some camera-type eye
    • camera-type eye SubClassOf has part some lens of camera-type eye
      • lens of camera-type eye SubClassOf developmentally induced by some retinal neural layer
        • developmentally induced by Domain anatomical structure
          • anatomical structure EquivalentTo material anatomical entity and (has characteristic some 3-D shape) and (has characteristic some maximally connected)
        • retinal neural layer SubClassOf layer of retina
          • layer of retina SubClassOf nervous system cell part layer
            • nervous system cell part layer SubClassOf multi cell part structure
              • multi cell part structure SubClassOf anatomical cluster
                • anatomical cluster SubClassOf disconnected anatomical group
                  • disconnected anatomical group SubClassOf has quality some disconnected
                  • has quality SubPropertyOf: has characteristic
        • retinal neural layer SubClassOf developmentally induced by some lens vesicle
• has characteristic some maximally connected DisjointWith has characteristic some disconnected

Axiom Impact

Axioms used 10 times

• anatomical structure EquivalentTo material anatomical entity and (has characteristic some 3-D shape) and (has characteristic some maximally connected) [cl_import.owl]
• anatomical cluster SubClassOf disconnected anatomical group [cl_import.owl,pato_import.owl]
• lens of camera-type eye SubClassOf developmentally induced by some retinal neural layer [cl_import.owl,pato_import.owl,uberon_import.owl]
• layer of retina SubClassOf nervous system cell part layer [cl_import.owl,pato_import.owl,uberon_import.owl]
• retinal neural layer SubClassOf layer of retina [cl_import.owl,pato_import.owl,uberon_import.owl]
• retinal neural layer SubClassOf developmentally induced by some lens vesicle [cl_import.owl,pato_import.owl,uberon_import.owl]
• multi cell part structure SubClassOf anatomical cluster [uberon_import.owl]
• nervous system cell part layer SubClassOf multi cell part structure [cl_import.owl,pato_import.owl,uberon_import.owl]
• disconnected anatomical group SubClassOf has quality some disconnected [cl_import.owl,pato_import.owl]
• has characteristic some maximally connected DisjointWith has characteristic some disconnected [cl_import.owl]
• has quality SubPropertyOf: has characteristic [ro_import.owl,cl_import.owl,pato_import.owl,bspo_import.owl,uberon_import.owl,iao_import.owl]
• developmentally induced by Domain anatomical structure [uberon_import.owl]

Axioms used 9 times

• camera-type eye SubClassOf has part some lens of camera-type eye [cl_import.owl,pato_import.owl,uberon_import.owl]

Axioms used 5 times

• eyeball of camera-type eye SubClassOf contributes to morphology of some camera-type eye [cl_import.owl,pato_import.owl,uberon_import.owl]

Axioms used 2 times

• camera-type eye photoreceptor cell SubClassOf part of some camera-type eye [cl_import.owl,pato_import.owl]
• anterior segment of eyeball SubClassOf in anterior side of some eyeball of camera-type eye [cl_import.owl,pato_import.owl,uberon_import.owl]
• posterior segment of eyeball SubClassOf in posterior side of some eyeball of camera-type eye [cl_import.owl,pato_import.owl,uberon_import.owl]

Axioms used 1 times

• choroidal cell of the eye EquivalentTo structural cell and (part of some optic choroid) [cl_import.owl,pato_import.owl]
• corneal epithelium EquivalentTo epithelium and (bounding layer of some cornea) [cl_import.owl,pato_import.owl,uberon_import.owl]
• eye epithelium EquivalentTo epithelium and (part of some camera-type eye) [cl_import.owl,pato_import.owl,uberon_import.owl]
• scleral cell SubClassOf part of some sclera [cl_import.owl,pato_import.owl]
• retinal cone cell SubClassOf camera-type eye photoreceptor cell [cl_import.owl,pato_import.owl,uberon_import.owl]
• corneal epithelial cell SubClassOf part of some corneal epithelium [cl_import.owl,pato_import.owl]
• retinal rod cell SubClassOf camera-type eye photoreceptor cell [cl_import.owl,pato_import.owl,uberon_import.owl]
• retinal ganglion cell SubClassOf has soma location some retina [cl_import.owl,pato_import.owl]
• vertebrate lens cell SubClassOf part of some lens of camera-type eye [cl_import.owl,pato_import.owl]
• lens epithelial cell SubClassOf part of some epithelium of lens [cl_import.owl,pato_import.owl]
• smooth muscle cell of sphincter of pupil SubClassOf part of some sphincter pupillae [cl_import.owl,pato_import.owl]
• keratocyte SubClassOf part of some substantia propria of cornea [cl_import.owl,pato_import.owl]
• cornea SubClassOf part of some anterior segment of eyeball [cl_import.owl,pato_import.owl,uberon_import.owl]
• cornea SubClassOf part of some tunica fibrosa of eyeball [cl_import.owl,pato_import.owl,uberon_import.owl]
• retina SubClassOf part of some posterior segment of eyeball [cl_import.owl,pato_import.owl,uberon_import.owl]
• sphincter pupillae SubClassOf iris smooth muscle [cl_import.owl,pato_import.owl,uberon_import.owl]
• uvea SubClassOf part of some anterior segment of eyeball [cl_import.owl,pato_import.owl,uberon_import.owl]
• iris SubClassOf part of some anterior uvea [cl_import.owl,pato_import.owl,uberon_import.owl]
• sclera SubClassOf contributes to morphology of some camera-type eye [cl_import.owl,pato_import.owl,uberon_import.owl]
• optic choroid SubClassOf overlaps some posterior segment of eyeball [cl_import.owl,pato_import.owl,uberon_import.owl]
• substantia propria of cornea SubClassOf contributes to morphology of some cornea [cl_import.owl,pato_import.owl,uberon_import.owl]
• epithelium of lens SubClassOf eye epithelium [cl_import.owl,pato_import.owl,uberon_import.owl]
• iris smooth muscle SubClassOf part of some iris [uberon_import.owl]
• anterior uvea SubClassOf contributes to morphology of some uvea [cl_import.owl,pato_import.owl,uberon_import.owl]
• tunica fibrosa of eyeball SubClassOf part of some eyeball of camera-type eye [cl_import.owl,pato_import.owl,uberon_import.owl]

Ontologies used:

• pato_import.owl (http://purl.obolibrary.org/obo/aism/imports/pato_import.owl)
• bspo_import.owl (http://purl.obolibrary.org/obo/aism/imports/bspo_import.owl)
• ro_import.owl (http://purl.obolibrary.org/obo/aism/imports/ro_import.owl)
• iao_import.owl (http://purl.obolibrary.org/obo/aism/imports/iao_import.owl)
• uberon_import.owl (http://purl.obolibrary.org/obo/aism/imports/uberon_import.owl)
• cl_import.owl (http://purl.obolibrary.org/obo/aism/imports/cl_import.owl)

Please help!
@balhoff @shawntanzk

[shawntanzk]

@JCGiron - I think this should be fixed in RO with this PR oborel/obo-relations#661
Could you try refreshing your RO import and checking again?
I see this:
developmentally induced by Domain anatomical structure
which should have been fixed to having the domain be CARO:0000006

[JCGiron]

It worked!!!
Thank you, @shawntanzk !!

[github-actions]

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

[dosumis]

Looks like this has been fixed. Please re-open if not.