The great base debugging

[anitacaron]

EDIT: these unsats are not the problem anymore, look at my comment below.

neuroblast SubClassOf Nothing

• neuroblast SubClassOf neuronal stem cell
  • neuronal stem cell SubClassOf part of some central nervous system
    • central nervous system SubClassOf part of some nervous system
      • nervous system SubClassOf existence ends during some fully formed stage
        • fully formed stage SubClassOf preceded by some organogenesis stage
          • organogenesis stage SubClassOf preceded by some neurula stage
            • neurula stage SubClassOf simultaneous with some neural tube formation
              • neural tube formation SubClassOf part of some neural tube development
                • neural tube development EquivalentTo anatomical structure development and (results in development of some neural tube)
                  • neural tube SubClassOf develops from some neural rod
                    • develops from SubPropertyOf: has developmental contribution from
                      • has developmental contribution from Domain connected anatomical structure
                        • connected anatomical structure EquivalentTo material anatomical entity and (bearer of some 3-D shape) and (bearer of some maximally connected)
                          • material anatomical entity SubClassOf material entity
                    • neural rod SubClassOf develops from some neural keel
                      • neural keel SubClassOf develops from some neural plate
                        • neural plate SubClassOf developmentally induced by some notochord
                          • notochord SubClassOf part of some axial skeletal system
                            • axial skeletal system SubClassOf has part some axial skeleton plus cranial skeleton
                              • axial skeleton plus cranial skeleton SubClassOf develops from some sclerotome
                                • sclerotome SubClassOf developing mesenchymal condensation
                                  • developing mesenchymal condensation SubClassOf dense mesenchyme tissue
                                    • dense mesenchyme tissue SubClassOf has part some fibroblast
                                      • fibroblast SubClassOf develops from some mesenchymal stem cell
                                        • mesenchymal stem cell EquivalentTo connective tissue cell and (has plasma membrane part some endoglin) and (has plasma membrane part some PR_000001800) and (has plasma membrane part some Thy-1 membrane glycoprotein) and (capable of some osteoblast differentiation) and (capable of some cell migration) and (capable of some neuron differentiation) and (capable of some epithelial cell differentiation) and (capable of some fat cell differentiation) and (capable of some cardiac muscle cell differentiation) and (capable of some chondroblast differentiation) and (lacks_plasma_membrane_part some MHC class II protein complex) and (lacks_plasma_membrane_part some CD34 molecule) and (lacks_plasma_membrane_part some receptor-type tyrosine-protein phosphatase C)
                                          • cardiac muscle cell differentiation SubClassOf part of some cardiac muscle tissue development
                                            • cardiac muscle tissue development EquivalentTo anatomical structure development and (results in development of some cardiac muscle tissue)
                                              • cardiac muscle tissue SubClassOf part of some heart
                                                • heart SubClassOf part of some heart plus pericardium
                                                  • heart plus pericardium SubClassOf thoracic cavity element
                                                    • thoracic cavity element EquivalentTo organ and (located in some thoracic cavity)
                                                      • thoracic cavity EquivalentTo anatomical space and (part of some coelemic cavity lumen) and (luminal space of some thoracic segment of trunk)
                                                        • luminal space of Domain immaterial entity
                                                        • coelemic cavity lumen SubClassOf develops from some future coelemic cavity lumen
                                                        • coelemic cavity lumen SubClassOf luminal space of some coelom
• material entity DisjointWith immaterial entity

Axiom Impact

Axioms used 20 times

• connected anatomical structure EquivalentTo material anatomical entity and (bearer of some 3-D shape) and (bearer of some maximally connected) [merged_import.owl]
• mesenchymal stem cell EquivalentTo connective tissue cell and (has plasma membrane part some endoglin) and (has plasma membrane part some PR_000001800) and (has plasma membrane part some Thy-1 membrane glycoprotein) and (capable of some osteoblast differentiation) and (capable of some cell migration) and (capable of some neuron differentiation) and (capable of some epithelial cell differentiation) and (capable of some fat cell differentiation) and (capable of some cardiac muscle cell differentiation) and (capable of some chondroblast differentiation) and (lacks_plasma_membrane_part some MHC class II protein complex) and (lacks_plasma_membrane_part some CD34 molecule) and (lacks_plasma_membrane_part some receptor-type tyrosine-protein phosphatase C) [merged_import.owl]
• cardiac muscle tissue development EquivalentTo anatomical structure development and (results in development of some cardiac muscle tissue) [merged_import.owl]
• thoracic cavity EquivalentTo anatomical space and (part of some coelemic cavity lumen) and (luminal space of some thoracic segment of trunk) [core.owl]
• thoracic cavity element EquivalentTo organ and (located in some thoracic cavity) [core.owl]
• material anatomical entity SubClassOf material entity [merged_import.owl]
• fibroblast SubClassOf develops from some mesenchymal stem cell [merged_import.owl]
• cardiac muscle cell differentiation SubClassOf part of some cardiac muscle tissue development [merged_import.owl]
• heart SubClassOf part of some heart plus pericardium [core.owl]
• cardiac muscle tissue SubClassOf part of some heart [core.owl]
• coelemic cavity lumen SubClassOf develops from some future coelemic cavity lumen [merged_import.owl]
• coelemic cavity lumen SubClassOf luminal space of some coelom [core.owl]
• heart plus pericardium SubClassOf thoracic cavity element [core.owl]
• material entity DisjointWith immaterial entity [merged_import.owl]
• develops from SubPropertyOf: has developmental contribution from [core.owl]
• has developmental contribution from Domain connected anatomical structure [merged_import.owl]
• luminal space of Domain immaterial entity [merged_import.owl]

Axioms used 19 times

• notochord SubClassOf part of some axial skeletal system [core.owl]
• neural plate SubClassOf developmentally induced by some notochord [core.owl]
• axial skeleton plus cranial skeleton SubClassOf develops from some sclerotome [core.owl]
• dense mesenchyme tissue SubClassOf has part some fibroblast [core.owl]
• axial skeletal system SubClassOf has part some axial skeleton plus cranial skeleton [core.owl]

Axioms used 18 times

• neural tube development EquivalentTo anatomical structure development and (results in development of some neural tube) [merged_import.owl]
• neural tube formation SubClassOf part of some neural tube development [merged_import.owl]
• fully formed stage SubClassOf preceded by some organogenesis stage [core.owl]
• neurula stage SubClassOf simultaneous with some neural tube formation [core.owl]
• organogenesis stage SubClassOf preceded by some neurula stage [core.owl]
• neural tube SubClassOf develops from some neural rod [core.owl]
• neural rod SubClassOf develops from some neural keel [core.owl]
• neural keel SubClassOf develops from some neural plate [core.owl]

Axioms used 16 times

• embryo stage SubClassOf precedes some fully formed stage [core.owl]

Axioms used 15 times

• sclerotome SubClassOf developing mesenchymal condensation [core.owl]
• developing mesenchymal condensation SubClassOf dense mesenchyme tissue [core.owl]

Axioms used 11 times

• anatomical structure SubClassOf existence ends during or before some death stage [core.owl]
• death stage SubClassOf life cycle stage [core.owl]
• life cycle SubClassOf starts with some zygote stage [core.owl]
• life cycle stage SubClassOf part of some life cycle [core.owl,merged_import.owl]
• zygote stage SubClassOf part of some embryo stage [core.owl]

Axioms used 9 times

• epithelial cell SubClassOf part of some epithelium [merged_import.owl]
• animal cell SubClassOf has part some microvillus [merged_import.owl]
• microvillus SubClassOf part of some epithelial cell [merged_import.owl]
• tissue SubClassOf multicellular anatomical structure [core.owl]
• epithelium SubClassOf tissue [merged_import.owl]
• multicellular anatomical structure SubClassOf anatomical structure [merged_import.owl]

Axioms used 7 times

• germ cell SubClassOf germ line cell [merged_import.owl]

Axioms used 4 times

• animal cell EquivalentTo native cell and (only in taxon some Metazoa) [merged_import.owl]
• blastula EquivalentTo multicellular organism and (existence starts and ends during some blastula stage) [core.owl]
• presumptive ectoderm EquivalentTo presumptive structure and (part of some blastula) and (has potential to develop into some ectoderm) [core.owl]
• female germ cell SubClassOf germ cell [merged_import.owl]
• oocyte SubClassOf female germ cell [merged_import.owl]
• oocyte SubClassOf only in taxon some Metazoa [merged_import.owl]
• germ line cell SubClassOf native cell [merged_import.owl]
• germ line cell SubClassOf animal cell [merged_import.owl]
• neurectodermal cell SubClassOf ectodermal cell [merged_import.owl]
• ectodermal cell SubClassOf part of some ectoderm [merged_import.owl]
• migratory neural crest cell SubClassOf develops from some premigratory neural crest cell [merged_import.owl]
• blastula stage SubClassOf part of some embryo stage [core.owl]
• ectoderm SubClassOf develops from some presumptive ectoderm [merged_import.owl]
• somite SubClassOf develops from some presomitic mesoderm [merged_import.owl]
• presomitic mesoderm SubClassOf part of some paraxial mesoderm [core.owl,merged_import.owl]
• paraxial mesoderm SubClassOf dense mesenchyme tissue [merged_import.owl]
• sclerotome SubClassOf develops from some somite [core.owl]

Axioms used 3 times

• male germ cell SubClassOf germ cell [merged_import.owl]
• egg cell SubClassOf develops from some oocyte [merged_import.owl]
• premigratory neural crest cell SubClassOf develops from some neurectodermal cell [merged_import.owl]

Axioms used 2 times

• spermatid EquivalentTo male germ cell and (bearer of some haploid) and (capable of some acrosome assembly) and (capable of some sperm axoneme assembly) and (capable of some spermatid nucleus differentiation) [merged_import.owl]
• anatomical structure development EquivalentTo developmental process and (results in development of some anatomical structure) [merged_import.owl]
• female germ cell SubClassOf capable of some oogenesis [merged_import.owl]
• neuroblast SubClassOf neuronal stem cell [merged_import.owl]
• neuronal stem cell SubClassOf part of some central nervous system [merged_import.owl]
• acrosome assembly SubClassOf cellular component assembly involved in morphogenesis [merged_import.owl]
• anatomical structure morphogenesis SubClassOf part of some anatomical structure development [merged_import.owl]
• cellular component assembly involved in morphogenesis SubClassOf anatomical structure formation involved in morphogenesis [merged_import.owl]
• oogenesis SubClassOf results in development of some egg cell [merged_import.owl]
• anatomical structure formation involved in morphogenesis SubClassOf part of some anatomical structure morphogenesis [merged_import.owl]
• nervous system SubClassOf existence ends during some fully formed stage [core.owl]
• central nervous system SubClassOf part of some nervous system [core.owl,merged_import.owl]

Axioms used 1 times

• germ line stem cell EquivalentTo germ line cell and (capable of some stem cell division) [merged_import.owl]
• spermatogonium EquivalentTo male germ cell and (bearer of some diploid) and (bearer of some immature) [merged_import.owl]
• smooth muscle cell neural crest derived EquivalentTo smooth muscle cell and (develops from some migratory neural crest cell) [merged_import.owl]
• primordial germ cell EquivalentTo germ line cell and (part of some embryo) and (capable of some cell motility) [merged_import.owl]
• embryo EquivalentTo multicellular organism and (existence starts with some embryo stage) and (existence ends with some embryo stage) [core.owl]
• fibroblast neural crest derived SubClassOf fibroblast [merged_import.owl]
• neuronal receptor cell SubClassOf sensory neuron [merged_import.owl]
• early embryonic cell (metazoa) SubClassOf embryonic cell (metazoa) [merged_import.owl]
• migratory cranial neural crest cell SubClassOf migratory neural crest cell [merged_import.owl]
• migratory trunk neural crest cell SubClassOf migratory neural crest cell [merged_import.owl]
• spermatocyte SubClassOf male germ cell [merged_import.owl]
• sperm SubClassOf develops from some spermatid [merged_import.owl]
• female germ line stem cell SubClassOf female germ cell [merged_import.owl]
• oogonial cell SubClassOf develops from some primordial germ cell [merged_import.owl]
• neural crest derived neuron SubClassOf develops from some neural crest derived neuroblast [merged_import.owl]
• glioblast SubClassOf develops from some neurectodermal cell [merged_import.owl]
• sensory neuron SubClassOf afferent neuron [merged_import.owl]
• afferent neuron SubClassOf neuron [merged_import.owl]
• neuron SubClassOf develops from some neuroblast [merged_import.owl]
• embryonic cell (metazoa) SubClassOf animal cell [merged_import.owl]
• neural crest derived neuroblast SubClassOf develops from some migratory neural crest cell [merged_import.owl]
• premigratory neural crest cell SubClassOf part of some neural crest [merged_import.owl]
• neural crest SubClassOf develops from some neural plate [merged_import.owl]

Ontologies used:

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

[shawntanzk]

heart plus pericardium SubClassOf thoracic cavity element thoracic cavity element EquivalentTo organ and (located in some thoracic cavity) thoracic cavity EquivalentTo anatomical space and (part of some coelemic cavity lumen) and (luminal space of some thoracic segment of trunk)

I think this part is the issue: heart which his material, through this chain, ends up being part of a space with is not material. I think the located in from (located in some thoracic cavity) is the main issue, a material entity should be allowed to be located in a immaterial entity - from this example, it doesn't seem so.

[balhoff]

Another problem is 'coelomic cavity lumen' is immaterial but inferred to be material :

• coelemic cavity lumen SubClassOf develops from some future coelemic cavity lumen
• develops from SubPropertyOf: has developmental contribution from
• has developmental contribution from Domain connected anatomical structure
• connected anatomical structure EquivalentTo material anatomical entity and (bearer of some 3-D shape) and (bearer of some maximally connected)

[cmungall]

has developmental contribution from Domain should be weakened in RO

(we can discuss this longer term and implementing a slightly different developmental model but for now it has to be weakened)

@shawntanzk - the located in relation is fine

Domain: 'independent continuant' and (not ('spatial region')) 'independent continuant'

Range: 'independent continuant' and (not ('spatial region')) 'independent continuant'

(don't worry about SR, it's a useless BFO class)

[anitacaron]

New problem after adding CARO back, please could someone check again? @cmungall @balhoff

subarcualis rectus I SubClassOf Nothing

• subarcualis rectus I SubClassOf innervated_by some ramus muscularis of glossopharyngeus nerve
  • ramus muscularis of glossopharyngeus nerve SubClassOf tissue
    • tissue SubClassOf multicellular anatomical structure
      • multicellular anatomical structure EquivalentTo anatomical structure and (has quality some multicellular)
        • has quality SubPropertyOf: bearer of
  • ramus muscularis of glossopharyngeus nerve SubClassOf innervates some subarcualis rectus I
    • innervates Domain neuron projection bundle
      • neuron projection bundle SubClassOf multi-cell-part structure
        • multi-cell-part structure SubClassOf connected anatomical structure
• multicellular anatomical structure EquivalentTo connected anatomical structure and (bearer of some multicellular)
• multi-cell-part structure DisjointWith multicellular anatomical structure

otic ganglion SubClassOf Nothing

• otic ganglion EquivalentTo cranial ganglion and (innervates some parotid gland) and (extends_fibers_into some glossopharyngeal nerve)
  • innervates Domain neuron projection bundle
    • neuron projection bundle SubClassOf multi-cell-part structure
      • multi-cell-part structure SubClassOf connected anatomical structure
  • cranial ganglion EquivalentTo ganglion and (extends_fibers_into some cranial neuron projection bundle)
    • ganglion SubClassOf cell cluster organ
      • cell cluster organ SubClassOf cell cluster
        • cell cluster SubClassOf multicellular anatomical structure
          • multicellular anatomical structure EquivalentTo anatomical structure and (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

ramus muscularis of glossopharyngeus nerve SubClassOf Nothing

• ramus muscularis of glossopharyngeus nerve SubClassOf tissue
  • tissue SubClassOf multicellular anatomical structure
    • multicellular anatomical structure EquivalentTo anatomical structure and (has quality some multicellular)
      • has quality SubPropertyOf: bearer of
• ramus muscularis of glossopharyngeus nerve SubClassOf innervates some subarcualis rectus I
  • innervates Domain neuron projection bundle
    • neuron projection bundle SubClassOf multi-cell-part structure
      • multi-cell-part structure SubClassOf connected anatomical structure
• multicellular anatomical structure EquivalentTo connected anatomical structure and (bearer of some multicellular)
• multi-cell-part structure DisjointWith multicellular anatomical structure

ramus muscularis of vagus nerve SubClassOf Nothing

• ramus muscularis of vagus nerve SubClassOf tissue
  • tissue SubClassOf multicellular anatomical structure
    • multicellular anatomical structure EquivalentTo anatomical structure and (has quality some multicellular)
      • has quality SubPropertyOf: bearer of
• ramus muscularis of vagus nerve SubClassOf innervates some subarcualis rectus I
  • innervates Domain neuron projection bundle
    • neuron projection bundle SubClassOf multi-cell-part structure
      • multi-cell-part structure SubClassOf connected anatomical structure
• multicellular anatomical structure EquivalentTo connected anatomical structure and (bearer of some multicellular)
• multi-cell-part structure DisjointWith multicellular anatomical structure

Axiom Impact

Axioms used 4 times

• multicellular anatomical structure EquivalentTo connected anatomical structure and (bearer of some multicellular) [merged_import.owl]
• multicellular anatomical structure EquivalentTo anatomical structure and (has quality some multicellular) [core.owl]
• multi-cell-part structure SubClassOf connected anatomical structure [merged_import.owl]
• neuron projection bundle SubClassOf multi-cell-part structure [merged_import.owl]
• multi-cell-part structure DisjointWith multicellular anatomical structure [merged_import.owl]
• has quality SubPropertyOf: bearer of [merged_import.owl]
• innervates Domain neuron projection bundle [merged_import.owl]

Axioms used 3 times

• tissue SubClassOf multicellular anatomical structure [core.owl]

Axioms used 2 times

• ramus muscularis of glossopharyngeus nerve SubClassOf tissue [core.owl]
• ramus muscularis of glossopharyngeus nerve SubClassOf innervates some subarcualis rectus I [core.owl]

Axioms used 1 times

• cranial ganglion EquivalentTo ganglion and (extends_fibers_into some cranial neuron projection bundle) [core.owl]
• otic ganglion EquivalentTo cranial ganglion and (innervates some parotid gland) and (extends_fibers_into some glossopharyngeal nerve) [core.owl]
• ganglion SubClassOf cell cluster organ [core.owl]
• cell cluster organ SubClassOf cell cluster [core.owl]
• cell cluster SubClassOf multicellular anatomical structure [core.owl]
• subarcualis rectus I SubClassOf innervated_by some ramus muscularis of glossopharyngeus nerve [core.owl]
• ramus muscularis of vagus nerve SubClassOf tissue [core.owl]
• ramus muscularis of vagus nerve SubClassOf innervates some subarcualis rectus I [core.owl]

Ontologies used:

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

[cmungall]

The explanation makes it easy to see what's going wrong:

id: UBERON:3010726
name: ramus muscularis of glossopharyngeus nerve
def: "Branchiomotor branch of the glossopharyngeus nerve innervating the m. subarcuales rectus I." [AAO:EJS]
is_a: UBERON:0000479 ! tissue
relationship: innervates UBERON:3010659 ! subarcualis rectus I
relationship: part_of UBERON:0001649 ! glossopharyngeal nerve
property_value: provenance_notes "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/aao.owl"}

in uberon, both nerves and branches of nerves should be subclass of nerve not tissue

as an aside, using the inverse innervated_by is not a pattern in uberon

id: UBERON:3010659
name: subarcualis rectus I
def: "Deep, visceral muscle associated with tongue movement." [AAO:BMZ]
is_a: UBERON:3000224 ! hyobranchial muscle
relationship: innervated_by UBERON:3010726 ! ramus muscularis of glossopharyngeus nerve
property_value: provenance_notes "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/aao.owl"}

[cmungall]

we need to get patterns down ASAP. I made a start on this a while ago and did not finish, sorry. Once we have patternization we will see the outliers are the cause of many problems

For {muscle} branch of {nerve} here is an exemplar:

id: UBERON:0022296
name: inferior palpebral branch of infra-orbital nerve
def: "A nerve that innervates a lower eyelid and is a branch of the infra-orbital branch of the maxillary nerve." [http://orcid.org/0000-0002-6601-2165]
synonym: "rami palpebrales inferiores nervi infraorbitalis" EXACT LATIN [Wikipedia:Inferior_palpebral_nerve]
xref: FMA:52983
xref: Wikipedia:Inferior_palpebral_nerve
intersection_of: UBERON:0001021 {source="FMA"} ! nerve
intersection_of: branching_part_of UBERON:0018408 {source="FMA"} ! infra-orbital nerve
intersection_of: innervates UBERON:0001713 {source="FMA"} ! lower eyelid

although we may want to make this even more explicit and have innervates always connect to a muscle

[matentzn]

Thank you @cmungall! I pinged your issue here.

[matentzn]

@anitacaron if you have trouble to figure out what to fix let me know on slack!

[anitacaron]

Ok, I changed the nerves but still have this one:

otic ganglion SubClassOf Nothing

• otic ganglion EquivalentTo cranial ganglion and (innervates some parotid gland) and (extends_fibers_into some glossopharyngeal nerve)
  • innervates Domain neuron projection bundle
    • neuron projection bundle SubClassOf multi-cell-part structure
      • multi-cell-part structure SubClassOf connected anatomical structure
  • cranial ganglion EquivalentTo ganglion and (extends_fibers_into some cranial neuron projection bundle)
    • ganglion SubClassOf cell cluster organ
      • cell cluster organ SubClassOf cell cluster
        • cell cluster SubClassOf multicellular anatomical structure
          • multicellular anatomical structure EquivalentTo anatomical structure and (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

Axiom Impact

Axioms used 1 times

• multicellular anatomical structure EquivalentTo connected anatomical structure and (bearer of some multicellular) [merged_import.owl]
• cranial ganglion EquivalentTo ganglion and (extends_fibers_into some cranial neuron projection bundle) [core.owl]
• otic ganglion EquivalentTo cranial ganglion and (innervates some parotid gland) and (extends_fibers_into some glossopharyngeal nerve) [core.owl]
• multicellular anatomical structure EquivalentTo anatomical structure and (has quality some multicellular) [core.owl]
• multi-cell-part structure SubClassOf connected anatomical structure [merged_import.owl]
• neuron projection bundle SubClassOf multi-cell-part structure [merged_import.owl]
• ganglion SubClassOf cell cluster organ [core.owl]
• cell cluster organ SubClassOf cell cluster [core.owl]
• cell cluster SubClassOf multicellular anatomical structure [core.owl]
• multi-cell-part structure 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:

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

[rays22]

UBERON:0000045 ganglion is currently defined as a subclass of UBERON:0010001 cell cluster organ.

Maybe re-defining UBERON:0000045 ganglion as a subclass of UBERON:0005162 multi-cell-part structure instead of being the subclass of UBERON:0010001 cell cluster organ would solve the logical incoherence?

I am not a nervous system expert, but the text definition of UBERON:0000045 ganglion being a 'A biological tissue mass, most commonly a mass of nerve cell bodies.' would agree with the revision in a biological sense (because cell bodies are cell parts).

• UBERON:0005162 multi-cell-part structure: A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.

[cmungall]

@dosumis may have opinions on the best upper ontology chess moves to make

but this is a pattern outlier. Either more ganglia should innervate or none should (and connection should be 2 hop, ganglion to nerve to innervatee)

[dosumis]

This is an old one! It's been discussed on multiple tickets in the past - some of which have proposed solutions. My take.

• multi cell-part structure would work - or we could just generalise to the parent class (I'm sure very many ganglia also have whole cells). I really think granularity assertions belong on more specific terms, especially in cross-species ontologies - but that's something to discuss another time.
• I think we could we replace the use of innervates for ganglia with 'extends_fibers_into', preserving use of innervates for neuron projection bundles (tracts and nerves) - although I guess that might lose the sense that those fibers synapse to targets in the object of the relationship.

[matentzn]

@anitacaron to try using multi-cell part structure as a first attempt to solve the issue. @anitacaron to make an issue about the extends_fiber_into proposal and disregard here

[anitacaron]

I changed UBERON:0000045 ganglion to be a subclass of UBERON:0005162 multi-cell-part structure, and there isn't any issue with uberon-edit.obo.

However, when I ran the test pipeline, I got an error in the materialized.owl step. In the materialized.owl.LOG There are 122 unsatisfiable classes in ontology. I ran robot explain in that file and got no results.

So I ran robot explain into unreasoned.owl, which is the input in the materialized step, and got many explanations. I'll add some of them in the following comment.

[anitacaron]

neuron of the substantia nigra SubClassOf Nothing

• neuron of the substantia nigra EquivalentTo CNS neuron (sensu Vertebrata) and (has part some (neuronal cell body and (part_of some substantia nigra)))
  • substantia nigra SubClassOf contributes to morphology of some collection of basal ganglia
    • collection of basal ganglia SubClassOf aggregate regional part of brain
      • aggregate regional part of brain EquivalentTo disconnected anatomical group and (part_of some brain) and (has member some regional part of brain)
        • disconnected anatomical group SubClassOf has quality some disconnected
          • has quality SubPropertyOf: has characteristic
        • regional part of brain SubClassOf composed primarily of some neural tissue
          • composed primarily of SubPropertyOf: has part
          • neural tissue EquivalentTo tissue and (has part some glial cell) and (has part some neuron)
            • neuron SubClassOf cell
              • cell SubClassOf connected anatomical structure
                • connected anatomical structure EquivalentTo material anatomical entity and (has characteristic some 3-D shape) and (has characteristic some maximally connected)
                  • material anatomical entity SubClassOf connected anatomical structure
                  • material anatomical entity EquivalentTo anatomical entity and (has characteristic some mass)
            • glial cell SubClassOf neuron associated cell
              • neuron associated cell SubClassOf develops from some neurectodermal cell
        • has member SubPropertyOf: has part
  • Transitive: has part
• has part some (has characteristic some mass) EquivalentTo has characteristic some mass
• has developmental contribution from Domain anatomical entity
• has characteristic some maximally connected DisjointWith has characteristic some disconnected
• has part o develops from SubPropertyOf: has developmental contribution from

globus pallidus SubClassOf Nothing

• globus pallidus SubClassOf contributes to morphology of some collection of basal ganglia
  • collection of basal ganglia SubClassOf aggregate regional part of brain
    • aggregate regional part of brain EquivalentTo disconnected anatomical group and (part_of some brain) and (has member some regional part of brain)
      • has member SubPropertyOf: has part
        • Transitive: has part
      • disconnected anatomical group SubClassOf has quality some disconnected
        • has quality SubPropertyOf: has characteristic
      • regional part of brain SubClassOf composed primarily of some neural tissue
        • composed primarily of SubPropertyOf: has part
        • neural tissue EquivalentTo tissue and (has part some glial cell) and (has part some neuron)
          • neuron SubClassOf cell
            • cell SubClassOf connected anatomical structure
              • connected anatomical structure EquivalentTo material anatomical entity and (has characteristic some 3-D shape) and (has characteristic some maximally connected)
                • material anatomical entity SubClassOf connected anatomical structure
                • material anatomical entity EquivalentTo anatomical entity and (has characteristic some mass)
          • glial cell SubClassOf neuron associated cell
            • neuron associated cell SubClassOf develops from some neurectodermal cell
• has part some (has characteristic some mass) EquivalentTo has characteristic some mass
• has developmental contribution from Domain anatomical entity
• has characteristic some maximally connected DisjointWith has characteristic some disconnected
• has part o develops from SubPropertyOf: has developmental contribution from

Axiom Impact

Axioms used 20 times

• material anatomical entity SubClassOf connected anatomical structure [core.owl]

Axioms used 19 times

• connected anatomical structure EquivalentTo material anatomical entity and (has characteristic some 3-D shape) and (has characteristic some maximally connected) [core.owl]
• material anatomical entity EquivalentTo anatomical entity and (has characteristic some mass) [core.owl]
• neural tissue EquivalentTo tissue and (has part some glial cell) and (has part some neuron) [core.owl]
• aggregate regional part of brain EquivalentTo disconnected anatomical group and (part_of some brain) and (has member some regional part of brain) [core.owl]
• has part some (has characteristic some mass) EquivalentTo has characteristic some mass [core.owl]
• cell SubClassOf connected anatomical structure [core.owl]
• neuron associated cell SubClassOf develops from some neurectodermal cell [core.owl]
• glial cell SubClassOf neuron associated cell [core.owl]
• neuron SubClassOf cell [core.owl]
• regional part of brain SubClassOf composed primarily of some neural tissue [core.owl]
• disconnected anatomical group SubClassOf has quality some disconnected [core.owl]
• has characteristic some maximally connected DisjointWith has characteristic some disconnected [core.owl]
• has quality SubPropertyOf: has characteristic [core.owl]
• has member SubPropertyOf: has part [core.owl]
• composed primarily of SubPropertyOf: has part [core.owl]
• Transitive: has part [core.owl]
• has developmental contribution from Domain anatomical entity [core.owl]
• has part o develops from SubPropertyOf: has developmental contribution from [core.owl]

Axioms used 18 times

• collection of basal ganglia SubClassOf aggregate regional part of brain [core.owl]

Axioms used 14 times

• basal ganglion SubClassOf part_of some collection of basal ganglia [core.owl]

Axioms used 7 times

• striatum SubClassOf part_of some basal ganglion [core.owl]

Axioms used 3 times

• corpus striatum SubClassOf part_of some basal ganglion [core.owl]
• amygdala SubClassOf basal ganglion [core.owl]
• nucleus accumbens SubClassOf contributes to morphology of some ventral striatum [core.owl]
• substantia nigra SubClassOf contributes to morphology of some collection of basal ganglia [core.owl]
• ventral striatum SubClassOf part_of some striatum [core.owl]

Axioms used 2 times

• caudate nucleus SubClassOf part_of some corpus striatum [core.owl]
• putamen SubClassOf part_of some striatum [core.owl]

Axioms used 1 times

• striatum neuron EquivalentTo CNS neuron (sensu Vertebrata) and (has part some (neuronal cell body and (part_of some striatum))) [core.owl]
• neuron of the substantia nigra EquivalentTo CNS neuron (sensu Vertebrata) and (has part some (neuronal cell body and (part_of some substantia nigra))) [core.owl]
• amygdala pyramidal neuron EquivalentTo pyramidal neuron and (has part some (neuronal cell body and (part_of some amygdala))) [core.owl]
• striatum development EquivalentTo anatomical structure development and (RO_0002296 some striatum) [core.owl]
• caudate nucleus development EquivalentTo anatomical structure development and (RO_0002296 some caudate nucleus) [core.owl]
• putamen development EquivalentTo anatomical structure development and (RO_0002296 some putamen) [core.owl]
• globus pallidus development EquivalentTo anatomical structure development and (RO_0002296 some globus pallidus) [core.owl]
• substantia nigra development EquivalentTo anatomical structure development and (RO_0002296 some substantia nigra) [core.owl]
• amygdala development EquivalentTo anatomical structure development and (RO_0002296 some amygdala) [core.owl]
• nucleus accumbens development EquivalentTo anatomical structure development and (RO_0002296 some nucleus accumbens) [core.owl]
• organism substance SubClassOf material anatomical entity [core.owl]
• ventral medial complex of thalamus SubClassOf aggregate regional part of brain [core.owl]
• globus pallidus SubClassOf part_of some basal ganglion [core.owl]
• globus pallidus SubClassOf contributes to morphology of some collection of basal ganglia [core.owl]
• island of Calleja SubClassOf contributes to morphology of some nucleus accumbens [core.owl]
• substantia nigra pars compacta SubClassOf part_of some substantia nigra [core.owl]
• DisjointClasses: connected anatomical structure, organism substance, disconnected anatomical group [core.owl]

Ontologies used:

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

[cmungall]

on reflection, this is a poor grouping class:

id: UBERON:0010009
name: aggregate regional part of brain
def: "A regional part of brain consisting of multiple brain regions that are not related through a simple volummetric part of hierarchy, e.g., basal ganglia[NIF]." [NLXANAT:20090509]
subset: non_informative
synonym: "set of nuclei of neuraxis" RELATED [FMA:256381]
xref: FMA:256381
xref: NLXANAT:20090509
intersection_of: UBERON:0034923 ! disconnected anatomical group
intersection_of: has_member UBERON:0002616 ! regional part of brain
intersection_of: part_of UBERON:0000955 ! brain
property_value: editor_note "May be obsoleted." xsd:string

The over-eager logical definition does not match the textual definition, I am not even sure I understand the textual definition

As a grouping class it doesn't do much work, grouping only 3 regions:

• [] BFO:0000001 ! entity
  • [i] BFO:0000002 ! continuant
    • [i] BFO:0000004 ! independent continuant
      • [i] CARO:0030000 ! biological entity
        • [i] CARO:0000000 ! anatomical entity
          • [i] UBERON:0010009 ! aggregate regional part of brain
            • [i] UBERON:0014370 ! extrastriate cortex
            • [i] UBERON:0010011 ! collection of basal ganglia
              • [i] UBERON:0023920 ! basal ganglia of rodent
            • [i] UBERON:0000431 ! ventral medial complex of thalamus

If there really is something distinct about these then this should be asserted using something like pato characteristics (and it should be done consistently with reasonable completeness)

• Conservative solution: replace the logical definition with is_a regional part of brain
• My preferred solution: obsolete the grouping and rewire the above terms to RPoB

[shawntanzk]

Related to the discussion on innervates and multi-cell-part structure DisjointWith multicellular anatomical structure - please see https://github.com/obophenotype/uberon/pull/2615#issuecomment-1219306915

[rays22]

I think this is the part of the logical definition of CARO:0001000 multi-cell-part structure that causes/will cause disjointness problems in UBERON by being too restrictive:

Subclass of:
'connected anatomical structure' and (
    ('has part' only (not cell)) and
    ('has component' min (2 'cell part'))
    )

It is often the case in the nervous system that some cells have projections (cell parts) that go outside of the boundary (as defined by gross anatomy) of a multicellular anatomical structure. The UBERON:0000045 ganglion example above illustrates that the strict CARO granularity distinction is not an obvious one for the common sense. What is the practical value or use case for the strict separation of the multi cell part structure type anatomical entities from the multicellular anatomical structure types? Can we change the logical definition in CARO?

[matentzn]

What about dropping the disjointness now if that gets everything to pass, and then make an issue and a new PR discussing its reintroduction..

[shawntanzk]

What about dropping the disjointness now if that gets everything to pass, and then make an issue and a new PR discussing its reintroduction..

I think this axiom comes from CARO import - happy to try to write a custom line in uberon.makefile (If I can rmbr/figure out how to lol) to remove that for now and make a draft PR that reverses it?

[matentzn]

Just delete it with protege for now and make an issue for me to deal with it.

[anitacaron]

Thank you to everyone who helped change the UBERON base approach! All the unsats are resolved now.