Replace chebi slim URL and migrate to ODK v1.6

[aleixpuigb]

Replace https://raw.githubusercontent.com/obophenotype/chebi_obo_slim/main/chebi_slim.owl with http://purl.obolibrary.org/obo/upheno/chebi_slim.owl

Migrate ODK from v1.4 to v1.6

[matentzn]

@aleixpuigb can you handle this one? Once QC passes, I think you can merge this but best check with @jamesamcl

[aleixpuigb]

Will do, thanks!

[aleixpuigb]

The ontology is inconsistent because the object property derives from is declared reflexive while also having a range of independent continuant. Reflexivity implies that every entity derives from itself, so anything participating in derives from is inferred to be an independent continuant. This becomes contradictory when roles are involved, since roles are subclasses of specifically dependent continuant, which is explicitly disjoint with independent continuant in BFO. As soon as a role is instantiated, it is inferred to be both dependent and independent, collapsing the ontology to inconsistency. The correct resolution is to remove the reflexivity axiom from derives from, as the relation is not reflexive in BFO/RO and is intended to relate distinct continuants; keeping the range restriction and BFO disjointness axioms intact preserves the intended semantics.

[matentzn]

I dont think the scatlas folks care about that axiom - feel free to remove it

[anitacaron]

This might be coming from an import, scatlas ontology is only made of imports, so it would be better fix it on the source? 👀

[aleixpuigb]

This might be coming from an import, scatlas ontology is only made of imports, so it would be better fix it on the source? 👀

Yes, it is coming from the Plant Trait Ontology (TO) import. I'm trying to find the best way to deal with, it, but even removing this problem, the majority of imported classes are unsatisfiables.

[matentzn]

If you tell me what needs doing I can fix it in https://github.com/Planteome/plant-trait-ontology

[aleixpuigb]

Thank you, it might be solved in 'to' but the imports haven't been refreshed in a long time, so I'm checking if it can be solved this way. I had a look in https://github.com/Planteome/plant-trait-ontology and I could not find the reflexivity axiom.

EDIT: The axiom was removed after refreshing imports.

[aleixpuigb]

Currently there are 15471 unsatisfiable classes in the ontology. They should be solved in different ontologies, but I am not sure who would be responsible for this work. What should we do with this @jamesamcl?

[matentzn]

Can you run sh run.sh make explain_unsat and post the results here?

[aleixpuigb]

Since the file is a bit long to paste here (259 lines), I have attached the file:
explain_unsat.md

The default command only shows 10 random unsats I think:

robot --catalog catalog-v001.xml explain -i tmp/scatlas-preprocess.owl -M unsatisfiability --unsatisfiable random:10 --explanation tmp/explain_unsat.md

[matentzn]

lung cancer cell SubClassOf Nothing

• lung cancer cell SubClassOf develops from some lung
  • lung SubClassOf respiration organ
    • respiration organ SubClassOf part of some respiratory system
      • respiratory system EquivalentTo anatomical system and (capable of some GO_0007585)
        • anatomical system SubClassOf has part some organ
          • organ SubClassOf RO_0002002 some anatomical surface
            • anatomical surface SubClassOf bona-fide anatomical boundary
              • bona-fide anatomical boundary SubClassOf immaterial anatomical entity
                • immaterial anatomical entity SubClassOf anatomical entity
                  • anatomical entity SubClassOf organism part
                  • organism part SubClassOf material entity
                • immaterial anatomical entity SubClassOf immaterial entity
• material entity DisjointWith immaterial entity

lung cancer cell line SubClassOf Nothing

• lung cancer cell line SubClassOf develops from some lung cancer cell
  • lung cancer cell SubClassOf develops from some lung
    • lung SubClassOf respiration organ
      • respiration organ SubClassOf part of some respiratory system
        • respiratory system EquivalentTo anatomical system and (capable of some GO_0007585)
          • anatomical system SubClassOf has part some organ
            • organ SubClassOf RO_0002002 some anatomical surface
              • anatomical surface SubClassOf bona-fide anatomical boundary
                • bona-fide anatomical boundary SubClassOf immaterial anatomical entity
                  • immaterial anatomical entity SubClassOf anatomical entity
                  • anatomical entity SubClassOf organism part
                  • organism part SubClassOf material entity
                  • immaterial anatomical entity SubClassOf immaterial entity
• material entity DisjointWith immaterial entity

Burkitt lymphoma cell SubClassOf Nothing

• Burkitt lymphoma cell EquivalentTo cultured cell and (has characteristic some Burkitts lymphoma)
  • Burkitts lymphoma SubClassOf neoplasm of mature B-cells
    • neoplasm of mature B-cells SubClassOf B-cell neoplasm
      • B-cell neoplasm SubClassOf leukocyte disorder
        • leukocyte disorder SubClassOf immune system disease
          • immune system disease EquivalentTo disease and (has_disease_location some
            (immune system or (part of some immune system)))
            • has_disease_location SubPropertyOf: located in
              • located in Domain independent continuant and (not (spatial region))
  • has characteristic Range characteristic
• independent continuant DisjointWith characteristic

melanoma cell line SubClassOf Nothing

• melanoma cell line EquivalentTo cultured cell and (has characteristic some melanoma)
  • melanoma SubClassOf has_disease_location some zone of skin
    • has_disease_location SubPropertyOf: located in
      • located in Domain independent continuant and (not (spatial region))
  • has characteristic Range characteristic
• independent continuant DisjointWith characteristic

blood serum SubClassOf Nothing

• blood serum SubClassOf part of some blood plasma
  • blood plasma SubClassOf RO_0002221 some erythrocyte
    • erythrocyte SubClassOf blood cell
      • blood cell SubClassOf hematopoietic cell
        • hematopoietic cell EquivalentTo cell type and (located in some hematopoietic system)
          • hematopoietic system SubClassOf mesoderm-derived structure
            • mesoderm-derived structure SubClassOf develops from some mesoderm
              • mesoderm SubClassOf has part some mesodermal cell
                • mesodermal cell SubClassOf participates_in some embryo
                  • embryo SubClassOf multicellular organism
                  • multicellular organism SubClassOf multicellular anatomical structure
                  • multicellular anatomical structure SubClassOf anatomical structure
                  • anatomical structure SubClassOf material anatomical entity
                  • material anatomical entity SubClassOf material entity
                  • material entity SubClassOf independent continuant
                  • independent continuant SubClassOf continuant
                  • participates_in Range occurrent
• continuant DisjointWith occurrent

osteosarcoma cell line SubClassOf Nothing

• osteosarcoma cell line EquivalentTo cultured cell and (has characteristic some osteosarcoma)
  • osteosarcoma SubClassOf has_disease_location some bone element
    • has_disease_location SubPropertyOf: located in
      • located in Domain independent continuant and (not (spatial region))
  • has characteristic Range characteristic
• independent continuant DisjointWith characteristic

myoblast cell line SubClassOf Nothing

• myoblast cell line EquivalentTo derives from some
  (myoblast and (part of some
  (organism part and (part of some organism))))
  • myoblast SubClassOf participates_in some embryo
    • embryo SubClassOf multicellular organism
      • multicellular organism SubClassOf multicellular anatomical structure
        • multicellular anatomical structure SubClassOf anatomical structure
          • anatomical structure SubClassOf material anatomical entity
            • material anatomical entity SubClassOf material entity
              • material entity SubClassOf independent continuant
                • independent continuant SubClassOf continuant
    • participates_in Range occurrent
• continuant DisjointWith occurrent

A-549 cell SubClassOf Nothing

• A-549 cell SubClassOf lung cancer cell line
  • lung cancer cell line SubClassOf develops from some lung cancer cell
    • lung cancer cell SubClassOf develops from some lung
      • lung SubClassOf respiration organ
        • respiration organ SubClassOf part of some respiratory system
          • respiratory system EquivalentTo anatomical system and (capable of some GO_0007585)
            • anatomical system SubClassOf has part some organ
              • organ SubClassOf RO_0002002 some anatomical surface
                • anatomical surface SubClassOf bona-fide anatomical boundary
                  • bona-fide anatomical boundary SubClassOf immaterial anatomical entity
                  • immaterial anatomical entity SubClassOf anatomical entity
                  • anatomical entity SubClassOf organism part
                  • organism part SubClassOf material entity
                  • immaterial anatomical entity SubClassOf immaterial entity
• material entity DisjointWith immaterial entity

cell suspension culture SubClassOf Nothing

• cell suspension culture SubClassOf cell culture
  • cell culture SubClassOf material entity
    • material entity SubClassOf independent continuant
• cell suspension culture SubClassOf growth condition
  • growth condition SubClassOf biological role
    • biological role SubClassOf role
      • role SubClassOf characteristic
• independent continuant DisjointWith characteristic

colonic cancer cell line SubClassOf Nothing

• colonic cancer cell line EquivalentTo cultured cell and (has characteristic some colonic neoplasm)
  • colonic neoplasm SubClassOf has_disease_location some
    (colon or (part of some colon))
    • has_disease_location SubPropertyOf: located in
      • located in Domain independent continuant and (not (spatial region))
  • has characteristic Range characteristic
• independent continuant DisjointWith characteristic

Axiom Impact

Axioms used 5 times

• independent continuant DisjointWith characteristic [to_import.owl,peco_import.owl,po_import.owl,omit_import.owl]

Axioms used 4 times

• has_disease_location SubPropertyOf: located in [efo_import.owl]
• located in Domain independent continuant and (not (spatial region)) [to_import.owl,po_import.owl]
• has characteristic Range characteristic [to_import.owl,peco_import.owl,po_import.owl]

Axioms used 3 times

• respiratory system EquivalentTo anatomical system and (capable of some GO_0007585) [fbbt_import.owl,uberon_import.owl]
• material entity SubClassOf independent continuant [to_import.owl,peco_import.owl,po_import.owl,omit_import.owl]
• lung cancer cell SubClassOf develops from some lung [efo_import.owl]
• organ SubClassOf RO_0002002 some anatomical surface [fbbt_import.owl,uberon_import.owl]
• respiration organ SubClassOf part of some respiratory system [fbbt_import.owl,fbbt.owl,uberon_import.owl]
• immaterial anatomical entity SubClassOf immaterial entity [fbbt_import.owl,fbbt.owl,uberon_import.owl]
• immaterial anatomical entity SubClassOf anatomical entity [doid_import.owl,fbbt_import.owl,fbbt.owl,uberon_import.owl]
• anatomical system SubClassOf has part some organ [fbbt_import.owl,uberon_import.owl]
• anatomical entity SubClassOf organism part [efo_import.owl]
• lung SubClassOf respiration organ [doid_import.owl,fbbt_import.owl,fbbt.owl,uberon_import.owl]
• anatomical surface SubClassOf bona-fide anatomical boundary [uberon_import.owl]
• bona-fide anatomical boundary SubClassOf immaterial anatomical entity [fbbt_import.owl]
• organism part SubClassOf material entity [efo_import.owl]
• material entity DisjointWith immaterial entity [to_import.owl,po_import.owl]

Axioms used 2 times

• independent continuant SubClassOf continuant [to_import.owl,peco_import.owl,po_import.owl,omit_import.owl]
• lung cancer cell line SubClassOf develops from some lung cancer cell [bto_import.owl]
• anatomical structure SubClassOf material anatomical entity [doid_import.owl,fbbt_import.owl,fbbt.owl,uberon_import.owl]
• material anatomical entity SubClassOf material entity [fbbt_import.owl,fbbt.owl,uberon_import.owl]
• multicellular organism SubClassOf multicellular anatomical structure [fbbt_import.owl,fbbt.owl,uberon_import.owl]
• embryo SubClassOf multicellular organism [fbbt_import.owl,efo_import.owl,fbbt.owl,uberon_import.owl]
• multicellular anatomical structure SubClassOf anatomical structure [doid_import.owl,fbbt_import.owl,fbbt.owl,uberon_import.owl]
• continuant DisjointWith occurrent [to_import.owl,po_import.owl,omit_import.owl]
• participates_in Range occurrent [to_import.owl,po_import.owl]

Axioms used 1 times

• Burkitt lymphoma cell EquivalentTo cultured cell and (has characteristic some Burkitts lymphoma) [efo_import.owl]
• myoblast cell line EquivalentTo derives from some
  (myoblast and (part of some
  (organism part and (part of some organism)))) [efo_import.owl]
• osteosarcoma cell line EquivalentTo cultured cell and (has characteristic some osteosarcoma) [efo_import.owl]
• colonic cancer cell line EquivalentTo cultured cell and (has characteristic some colonic neoplasm) [efo_import.owl]
• melanoma cell line EquivalentTo cultured cell and (has characteristic some melanoma) [efo_import.owl]
• hematopoietic cell EquivalentTo cell type and (located in some hematopoietic system) [efo_import.owl]
• immune system disease EquivalentTo disease and (has_disease_location some
  (immune system or (part of some immune system))) [efo_import.owl]
• role SubClassOf characteristic [efo_import.owl]
• A-549 cell SubClassOf lung cancer cell line [bto_import.owl]
• blood serum SubClassOf part of some blood plasma [efo_import.owl]
• cell culture SubClassOf material entity [efo_import.owl]
• cell suspension culture SubClassOf cell culture [efo_import.owl,bto_import.owl]
• cell suspension culture SubClassOf growth condition [efo_import.owl]
• biological role SubClassOf role [efo_import.owl]
• myoblast SubClassOf participates_in some embryo [efo_import.owl]
• blood cell SubClassOf hematopoietic cell [fbbt_import.owl]
• mesodermal cell SubClassOf participates_in some embryo [efo_import.owl]
• erythrocyte SubClassOf blood cell [cl_import.owl,cl.owl,doid_import.owl,fbbt_import.owl,efo_import.owl,fbbt.owl]
• B-cell neoplasm SubClassOf leukocyte disorder [mondo_import.owl,efo_import.owl]
• leukocyte disorder SubClassOf immune system disease [efo_import.owl]
• mesoderm SubClassOf has part some mesodermal cell [fbbt_import.owl,uberon_import.owl]
• blood plasma SubClassOf RO_0002221 some erythrocyte [fbbt_import.owl,uberon_import.owl]
• hematopoietic system SubClassOf mesoderm-derived structure [doid_import.owl,fbbt_import.owl,fbbt.owl,uberon_import.owl]
• mesoderm-derived structure SubClassOf develops from some mesoderm [fbbt_import.owl,uberon_import.owl]
• neoplasm of mature B-cells SubClassOf B-cell neoplasm [efo_import.owl]
• Burkitts lymphoma SubClassOf neoplasm of mature B-cells [efo_import.owl]
• growth condition SubClassOf biological role [efo_import.owl]
• osteosarcoma SubClassOf has_disease_location some bone element [efo_import.owl]
• melanoma SubClassOf has_disease_location some zone of skin [efo_import.owl]
• colonic neoplasm SubClassOf has_disease_location some
  (colon or (part of some colon)) [efo_import.owl]

Ontologies used:

• to_import.owl (http://purl.obolibrary.org/obo/scatlas/imports/to_import.owl)
• cl_import.owl (http://purl.obolibrary.org/obo/scatlas/imports/cl_import.owl)
• omit_import.owl (http://purl.obolibrary.org/obo/scatlas/imports/omit_import.owl)
• uberon_import.owl (http://purl.obolibrary.org/obo/scatlas/imports/uberon_import.owl)
• fbbt_import.owl (http://purl.obolibrary.org/obo/scatlas/imports/fbbt_import.owl)
• efo_import.owl (http://purl.obolibrary.org/obo/scatlas/imports/efo_import.owl)
• doid_import.owl (http://purl.obolibrary.org/obo/scatlas/imports/doid_import.owl)
• fbbt.owl (http://purl.obolibrary.org/obo/scatlas/components/fbbt.owl)
• mondo_import.owl (http://purl.obolibrary.org/obo/scatlas/imports/mondo_import.owl)
• peco_import.owl (http://purl.obolibrary.org/obo/scatlas/imports/peco_import.owl)
• bto_import.owl (http://purl.obolibrary.org/obo/scatlas/imports/bto_import.owl)
• cl.owl (http://purl.obolibrary.org/obo/scatlas/components/cl.owl)
• po_import.owl (http://purl.obolibrary.org/obo/scatlas/imports/po_import.owl)

[matentzn]

Hmm.. Get clarity on whether this is something your team is obligated to work on; if scatlas ontology is dead, just abandon otherwise.. Cant see a super obvious fix.

[aleixpuigb]

Thanks Nico, there are some things that can be fixed in EFO (EBISPOT/efo#2612) and I need to fix anyway, but it looks like there are many more problems.