Dangling CARO term and CARO incompatibility with CL

[shawntanzk]

Currently, there is a dangling CARO term (CARO_0010000) that is used by a RO term (directly develops from) that is used in UBERON term (equiv class for maxillary artery) that used by another uberon term (deep auricular artery) that isn't used by any term except itself (I think).
I tried to solve the dangling term by doing and import of that CARO term, however when trying to test a release, CARO seems to be incompatible with CL -> error saying that there are unsatisfiable classes.
I'm not sure if it would be sensible, or for that matter how to, remove some terms in the uberon import?
I'm also not sure if it is an issue that CARO isn't compatible with CL and do we have to chase down a reason?
Or if it's just not worth it and we just leave the dangling term?
Related to obophenotype/uberon#1963

[shawntanzk]

latissimus dorsi muscle SubClassOf Nothing

• latissimus dorsi muscle SubClassOf has muscle antagonist some deltoid
  • deltoid SubClassOf innervated_by some axillary nerve
    • axillary nerve SubClassOf part_of some brachial nerve plexus
      • brachial nerve plexus EquivalentTo spinal nerve plexus and (innervates some forelimb)
        • brachial nerve plexus SubClassOf neuron projection bundle
          • neuron projection bundle SubClassOf multi-cell-part structure
            • multi-cell-part structure SubClassOf connected anatomical structure
        • spinal nerve plexus EquivalentTo nerve plexus and (extends_fibers_into some spinal nerve)
          • nerve plexus SubClassOf neural tissue
            • neural tissue EquivalentTo tissue and (has_part some glial cell) and (has_part some neuron)
              • tissue SubClassOf multicellular anatomical structure
                • multicellular anatomical structure SubClassOf has_quality some multicellular
                  • has_quality SubPropertyOf: bearer of
• multicellular anatomical structure EquivalentTo connected anatomical structure and (bearer of some multicellular)
• multi-cell-part structure DisjointWith multicellular anatomical structure

sciatic nerve SubClassOf Nothing

• sciatic nerve SubClassOf part_of some lumbosacral nerve plexus
  • lumbosacral nerve plexus SubClassOf neuron projection bundle
    • neuron projection bundle SubClassOf multi-cell-part structure
      • multi-cell-part structure SubClassOf connected anatomical structure
  • lumbosacral nerve plexus SubClassOf spinal nerve plexus
    • spinal nerve plexus EquivalentTo nerve plexus and (extends_fibers_into some spinal nerve)
      • nerve plexus SubClassOf neural tissue
        • neural tissue EquivalentTo tissue and (has_part some glial cell) and (has_part some neuron)
          • tissue SubClassOf multicellular anatomical structure
            • multicellular anatomical structure SubClassOf has_quality some multicellular
              • has_quality SubPropertyOf: bearer of
• multicellular anatomical structure EquivalentTo connected anatomical structure and (bearer of some multicellular)
• multi-cell-part structure DisjointWith multicellular anatomical structure

vomeronasal sensory neuron SubClassOf Nothing

• vomeronasal sensory neuron EquivalentTo sensory neuron and (part_of some vomeronasal organ) and (innervates some epithelium of vomeronasal organ)
  • innervates Domain neuron projection bundle
    • neuron projection bundle SubClassOf multi-cell-part structure
  • sensory neuron SubClassOf afferent neuron
    • afferent neuron SubClassOf neuron
      • neuron SubClassOf neural cell
        • neural cell SubClassOf somatic cell
          • somatic cell SubClassOf native cell
            • cell EquivalentTo native cell
• cell DisjointWith multi-cell-part structure

serratus ventralis SubClassOf Nothing

• serratus ventralis SubClassOf has muscle antagonist some trapezius muscle
  • trapezius muscle SubClassOf has muscle antagonist some latissimus dorsi muscle
    • latissimus dorsi muscle SubClassOf has muscle antagonist some deltoid
      • deltoid SubClassOf innervated_by some axillary nerve
        • axillary nerve SubClassOf part_of some brachial nerve plexus
          • brachial nerve plexus EquivalentTo spinal nerve plexus and (innervates some forelimb)
            • brachial nerve plexus SubClassOf neuron projection bundle
              • neuron projection bundle SubClassOf multi-cell-part structure
                • multi-cell-part structure SubClassOf connected anatomical structure
            • spinal nerve plexus EquivalentTo nerve plexus and (extends_fibers_into some spinal nerve)
              • nerve plexus SubClassOf neural tissue
                • neural tissue EquivalentTo tissue and (has_part some glial cell) and (has_part some neuron)
                  • tissue SubClassOf multicellular anatomical structure
                  • multicellular anatomical structure SubClassOf has_quality some multicellular
                  • has_quality SubPropertyOf: has characteristic
• multicellular anatomical structure EquivalentTo connected anatomical structure and (has characteristic some multicellular)
• multi-cell-part structure DisjointWith multicellular anatomical structure

tibial nerve SubClassOf Nothing

• tibial nerve SubClassOf branching_part_of some sciatic nerve
  • sciatic nerve SubClassOf part_of some lumbosacral nerve plexus
    • lumbosacral nerve plexus SubClassOf neuron projection bundle
      • neuron projection bundle SubClassOf multi-cell-part structure
        • multi-cell-part structure SubClassOf connected anatomical structure
    • lumbosacral nerve plexus SubClassOf spinal nerve plexus
      • spinal nerve plexus EquivalentTo nerve plexus and (extends_fibers_into some spinal nerve)
        • nerve plexus SubClassOf neural tissue
          • neural tissue EquivalentTo tissue and (has_part some glial cell) and (has_part some neuron)
            • tissue SubClassOf multicellular anatomical structure
              • multicellular anatomical structure SubClassOf has_quality some multicellular
                • has_quality SubPropertyOf: has characteristic
• multicellular anatomical structure EquivalentTo connected anatomical structure and (has characteristic some multicellular)
• multi-cell-part structure DisjointWith multicellular anatomical structure

microfold cell of epithelium proper of appendix SubClassOf Nothing

• microfold cell of epithelium proper of appendix EquivalentTo M cell of gut and (part_of some vermiform appendix)
  • M cell of gut SubClassOf somatic cell
    • somatic cell SubClassOf native cell
      • cell EquivalentTo native cell
        • cell SubClassOf connected anatomical structure
  • microfold cell of epithelium proper of appendix SubClassOf epithelium of appendix
    • epithelium of appendix SubClassOf epithelium of large intestine
      • epithelium of large intestine EquivalentTo epithelium and (part_of some large intestine)
        • epithelium SubClassOf tissue
          • tissue SubClassOf multicellular anatomical structure
            • multicellular anatomical structure SubClassOf has_quality some multicellular
              • has_quality SubPropertyOf: has characteristic
• cell DisjointWith multicellular anatomical structure
• multicellular anatomical structure EquivalentTo connected anatomical structure and (has characteristic some multicellular)

deltoid SubClassOf Nothing

• deltoid SubClassOf innervated_by some axillary nerve
  • axillary nerve SubClassOf part_of some brachial nerve plexus
    • brachial nerve plexus EquivalentTo spinal nerve plexus and (innervates some forelimb)
      • innervates Domain neuron projection bundle
        • neuron projection bundle SubClassOf multi-cell-part structure
          • multi-cell-part structure SubClassOf connected anatomical structure
      • spinal nerve plexus EquivalentTo nerve plexus and (extends_fibers_into some spinal nerve)
        • nerve plexus SubClassOf neural tissue
          • neural tissue EquivalentTo tissue and (has_part some glial cell) and (has_part some neuron)
            • tissue SubClassOf multicellular anatomical structure
              • multicellular anatomical structure SubClassOf has_quality some multicellular
                • has_quality SubPropertyOf: has characteristic
• multicellular anatomical structure EquivalentTo connected anatomical structure and (has characteristic some multicellular)
• multi-cell-part structure DisjointWith multicellular anatomical structure

brachial nerve plexus SubClassOf Nothing

• brachial nerve plexus EquivalentTo spinal nerve plexus and (innervates some forelimb)
  • innervates Domain neuron projection bundle
    • neuron projection bundle SubClassOf multi-cell-part structure
      • multi-cell-part structure SubClassOf connected anatomical structure
  • spinal nerve plexus EquivalentTo nerve plexus and (extends_fibers_into some spinal nerve)
    • nerve plexus SubClassOf neural tissue
      • neural tissue EquivalentTo tissue and (has_part some glial cell) and (has_part some neuron)
        • tissue SubClassOf multicellular anatomical structure
          • multicellular anatomical structure SubClassOf has_quality some multicellular
            • has_quality SubPropertyOf: has characteristic
• multicellular anatomical structure EquivalentTo connected anatomical structure and (has characteristic some multicellular)
• multi-cell-part structure DisjointWith multicellular anatomical structure

axillary nerve SubClassOf Nothing

• axillary nerve SubClassOf part_of some brachial nerve plexus
  • brachial nerve plexus EquivalentTo spinal nerve plexus and (innervates some forelimb)
    • innervates Domain neuron projection bundle
      • neuron projection bundle SubClassOf multi-cell-part structure
        • multi-cell-part structure SubClassOf connected anatomical structure
    • spinal nerve plexus EquivalentTo nerve plexus and (extends_fibers_into some spinal nerve)
      • nerve plexus SubClassOf neural tissue
        • neural tissue EquivalentTo tissue and (has_part some glial cell) and (has_part some neuron)
          • tissue SubClassOf multicellular anatomical structure
            • multicellular anatomical structure SubClassOf has_quality some multicellular
              • has_quality SubPropertyOf: has characteristic
• multicellular anatomical structure EquivalentTo connected anatomical structure and (has characteristic some multicellular)
• multi-cell-part structure DisjointWith multicellular anatomical structure

lumbosacral nerve plexus SubClassOf Nothing

• lumbosacral nerve plexus SubClassOf neuron projection bundle
  • neuron projection bundle SubClassOf multi-cell-part structure
    • multi-cell-part structure SubClassOf connected anatomical structure
• lumbosacral nerve plexus SubClassOf spinal nerve plexus
  • spinal nerve plexus EquivalentTo nerve plexus and (extends_fibers_into some spinal nerve)
    • nerve plexus SubClassOf neural tissue
      • neural tissue EquivalentTo tissue and (has_part some glial cell) and (has_part some neuron)
        • tissue SubClassOf multicellular anatomical structure
          • multicellular anatomical structure SubClassOf has_quality some multicellular
            • has_quality SubPropertyOf: has characteristic
• multicellular anatomical structure EquivalentTo connected anatomical structure and (has characteristic some multicellular)
• multi-cell-part structure DisjointWith multicellular anatomical structure

Axiom Impact

Axioms used 9 times

• multicellular anatomical structure EquivalentTo connected anatomical structure and (has characteristic some multicellular) [caro_import.owl]
• neuron projection bundle SubClassOf multi-cell-part structure [ro_import.owl]
• tissue SubClassOf multicellular anatomical structure [uberon_import.owl]
• multicellular anatomical structure SubClassOf has_quality some multicellular [uberon_import.owl]
• has_quality SubPropertyOf: has characteristic [caro_import.owl,ro_import.owl,uberon_import.owl]

Axioms used 8 times

• spinal nerve plexus EquivalentTo nerve plexus and (extends_fibers_into some spinal nerve) [uberon_import.owl]
• neural tissue EquivalentTo tissue and (has_part some glial cell) and (has_part some neuron) [uberon_import.owl]
• multi-cell-part structure SubClassOf connected anatomical structure [ro_import.owl]
• nerve plexus SubClassOf neural tissue [uberon_import.owl]
• multi-cell-part structure DisjointWith multicellular anatomical structure [caro_import.owl]

Axioms used 5 times

• brachial nerve plexus EquivalentTo spinal nerve plexus and (innervates some forelimb) [uberon_import.owl]

Axioms used 4 times

• axillary nerve SubClassOf part_of some brachial nerve plexus [uberon_import.owl]
• innervates Domain neuron projection bundle [ro_import.owl,uberon_import.owl]

Axioms used 3 times

• deltoid SubClassOf innervated_by some axillary nerve [uberon_import.owl]
• lumbosacral nerve plexus SubClassOf neuron projection bundle [uberon_import.owl]
• lumbosacral nerve plexus SubClassOf spinal nerve plexus [uberon_import.owl]

Axioms used 2 times

• cell EquivalentTo native cell [caro_import.owl]
• somatic cell SubClassOf native cell [cl.owl,uberon_import.owl]
• latissimus dorsi muscle SubClassOf has muscle antagonist some deltoid [uberon_import.owl]
• sciatic nerve SubClassOf part_of some lumbosacral nerve plexus [uberon_import.owl]
• brachial nerve plexus SubClassOf neuron projection bundle [uberon_import.owl]

Axioms used 1 times

• microfold cell of epithelium proper of appendix EquivalentTo M cell of gut and (part_of some vermiform appendix) [cl.owl]
• vomeronasal sensory neuron EquivalentTo sensory neuron and (part_of some vomeronasal organ) and (innervates some epithelium of vomeronasal organ) [cl.owl]
• epithelium of large intestine EquivalentTo epithelium and (part_of some large intestine) [uberon_import.owl]
• cell SubClassOf connected anatomical structure [caro_import.owl]
• sensory neuron SubClassOf afferent neuron [cl.owl,uberon_import.owl]
• afferent neuron SubClassOf neuron [cl.owl,uberon_import.owl]
• neuron SubClassOf neural cell [cl.owl,uberon_import.owl]
• M cell of gut SubClassOf somatic cell [cl.owl]
• neural cell SubClassOf somatic cell [cl.owl,uberon_import.owl]
• microfold cell of epithelium proper of appendix SubClassOf epithelium of appendix [cl.owl]
• epithelium SubClassOf tissue [uberon_import.owl]
• serratus ventralis SubClassOf has muscle antagonist some trapezius muscle [uberon_import.owl]
• tibial nerve SubClassOf branching_part_of some sciatic nerve [uberon_import.owl]
• trapezius muscle SubClassOf has muscle antagonist some latissimus dorsi muscle [uberon_import.owl]
• epithelium of appendix SubClassOf epithelium of large intestine [uberon_import.owl]
• cell DisjointWith multi-cell-part structure [caro_import.owl]
• cell DisjointWith multicellular anatomical structure [caro_import.owl]

Ontologies used:

• uberon_import.owl (http://purl.obolibrary.org/obo/cl/imports/uberon_import.owl)
• cl.owl (http://purl.obolibrary.org/obo/cl.owl)
• caro_import.owl (http://purl.obolibrary.org/obo/cl/imports/caro_import.owl)
• ro_import.owl (http://purl.obolibrary.org/obo/cl/imports/ro_import.owl)

[shawntanzk]

@cmungall @balhoff @dosumis - Could you help me with the above please? Thanks!

[dosumis]

• multicellular anatomical structure EquivalentTo connected anatomical structure and (has characteristic some multicellular)

• multi-cell-part structure DisjointWith multicellular anatomical structure

• innervates Domain neuron projection bundle

• neuron projection bundle SubClassOf multi-cell-part structure

• nerve plexus SubClassOf neural tissue

• neural tissue EquivalentTo tissue and (has_part some glial cell) and (has_part some neuron)

Suggested fixes: remove domain of innervates. # @shawntanzk to test this fix.

[shawntanzk]

see oborel/obo-relations#527 (comment) for the test on removing domain of innervates and using --unsatisfiable root

[dosumis]

oborel/obo-relations#527 (comment)

[anitacaron]

We'll look this again after base migration.

[shawntanzk]

@shawntanzk to recheck if this is still a problem with basefile

[shawntanzk]

Currently the following are dangling:

Not 100% sure how to handle these with base file merge imports, until then, can't see if CARO imports will cause issues

[dosumis]

Does CARO import still => inconsistency?

[shawntanzk]

Does CARO import still => inconsistency?

Not too sure, actually now that you mention, CARO is not importing cause it isn't declared, let me try fixing and see if there is still issues

[shawntanzk]

Yup there still are incompatibilities:

microfold cell of epithelium proper of appendix SubClassOf Nothing

• microfold cell of epithelium proper of appendix SubClassOf M cell of gut
  • M cell of gut SubClassOf somatic cell
    • somatic cell SubClassOf native cell
      • cell EquivalentTo native cell
        • cell SubClassOf connected anatomical structure
• microfold cell of epithelium proper of appendix SubClassOf epithelium of appendix
  • epithelium of appendix EquivalentTo epithelium and (part_of some vermiform appendix)
    • epithelium EquivalentTo tissue and (composed primarily of some epithelial cell)
      • tissue SubClassOf multicellular anatomical structure
        • multicellular anatomical structure EquivalentTo anatomical structure and (has quality some multicellular)
          • has quality SubPropertyOf: bearer of
• cell DisjointWith multicellular anatomical structure
• multicellular anatomical structure EquivalentTo connected anatomical structure and (bearer of some multicellular)

vomeronasal sensory neuron SubClassOf Nothing

• vomeronasal sensory neuron EquivalentTo sensory neuron and (part_of some vomeronasal organ) and (innervates some epithelium of vomeronasal organ)
  • innervates Domain neuron projection bundle
    • neuron projection bundle SubClassOf multi-cell-part structure
  • sensory neuron SubClassOf afferent neuron
    • afferent neuron SubClassOf neuron
      • neuron SubClassOf neural cell
        • neural cell EquivalentTo animal cell and (part_of some nervous system)
          • animal cell EquivalentTo native cell and (only_in_taxon some Metazoa)
            • cell EquivalentTo native cell
• cell DisjointWith multi-cell-part structure

Axiom Impact

Axioms used 2 times

• cell EquivalentTo native cell [merged_import.owl]

Axioms used 1 times

• multicellular anatomical structure EquivalentTo connected anatomical structure and (bearer of some multicellular) [merged_import.owl]
• animal cell EquivalentTo native cell and (only_in_taxon some Metazoa) [cl.owl]
• neural cell EquivalentTo animal cell and (part_of some nervous system) [cl.owl]
• vomeronasal sensory neuron EquivalentTo sensory neuron and (part_of some vomeronasal organ) and (innervates some epithelium of vomeronasal organ) [cl.owl]
• epithelium EquivalentTo tissue and (composed primarily of some epithelial cell) [merged_import.owl]
• epithelium of appendix EquivalentTo epithelium and (part_of some vermiform appendix) [merged_import.owl]
• multicellular anatomical structure EquivalentTo anatomical structure and (has quality some multicellular) [merged_import.owl]
• cell SubClassOf connected anatomical structure [merged_import.owl]
• neuron projection bundle SubClassOf multi-cell-part structure [merged_import.owl]
• sensory neuron SubClassOf afferent neuron [cl.owl]
• afferent neuron SubClassOf neuron [cl.owl]
• neuron SubClassOf neural cell [cl.owl]
• M cell of gut SubClassOf somatic cell [cl.owl]
• somatic cell SubClassOf native cell [cl.owl]
• microfold cell of epithelium proper of appendix SubClassOf M cell of gut [cl.owl]
• microfold cell of epithelium proper of appendix SubClassOf epithelium of appendix [cl.owl]
• tissue SubClassOf multicellular anatomical structure [merged_import.owl]
• cell DisjointWith multi-cell-part structure [merged_import.owl]
• cell DisjointWith multicellular anatomical structure [merged_import.owl]
• has quality SubPropertyOf: bearer of [merged_import.owl]
• innervates Domain neuron projection bundle [merged_import.owl]

Ontologies used:

• cl.owl (http://purl.obolibrary.org/obo/cl.owl)
• merged_import.owl (http://purl.obolibrary.org/obo/cl/imports/merged_import.owl)

[dosumis]

THese look like genuine errors that should be easy to fix

1. A cell is not an epithelium:

microfold cell of epithelium proper of appendix SubClassOf epithelium of appendix

subClassOf -> part_of (some)

2. vomeronasal sensory neuron EquivalentTo sensory neuron and (part_of some vomeronasal organ) and (innervates some epithelium of vomeronasal organ)

innervates -> 'has sensory dendrite in' http://purl.obolibrary.org/obo/RO_0013007 (see fbbt for precedents)

Also - this should be fixed:
part_of -> has_soma_location

[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5947554/]

[shawntanzk]

Looks like it fixed it :) will make a PR. Thanks!

[shawntanzk]

Currently blocked by obophenotype/caro#23

[cmungall]

I don't see a PR for the simple changes @dosumis requested in #1306 (comment)

[shawntanzk]

@cmungall - I will check up on this