Taxon constraints should propagate over 'regulates'

[pgaudet]

Hi @balhoff

Now that we have a new relation to express regulation in another organism, we can propagate taxon constraints over the 'regulates' relation. This doesn't seem to be happening, see

has no taxon constraints

but the 'non-regulatory' parent does:

[pgaudet]

And once that is done, we should remove any asserted TCs on the regulation terms, to make sure TCs are consistent, or define cases where there should be exceptions.

[balhoff]

We have two terms with problems when we propagate 'in taxon' over 'regulates':

envenomation resulting in plasminogen activation in another organism SubClassOf Nothing

• envenomation resulting in plasminogen activation in another organism EquivalentTo envenomation resulting in modulation of process in another organism and (has_part some fibrinolysis) and (has_part some symbiont-mediated activation of host plasminogen)
  • fibrinolysis SubClassOf negative regulation of blood coagulation
    • negative regulation of blood coagulation EquivalentTo biological regulation and (negatively regulates some blood coagulation)
    • negatively regulates SubPropertyOf: regulates
    • blood coagulation EquivalentTo coagulation and (results in assembly of some blood clot)
      • results in assembly of SubPropertyOf: results in formation of
      • results in formation of SubPropertyOf: results in developmental progression of
      • blood clot SubClassOf has_part some leukocyte
      • leukocyte SubClassOf only_in_taxon some Vertebrata
        • only_in_taxon SubPropertyOf: in taxon
  • symbiont-mediated activation of host plasminogen EquivalentTo symbiont-mediated perturbation of host process and (positively regulates in another organism some plasminogen activation)
    • symbiont-mediated perturbation of host process SubClassOf in taxon some (not (Vertebrata ))
• regulates o in taxon SubPropertyOf: in taxon
• in taxon some Vertebrata DisjointWith in taxon some (not (Vertebrata ))
• results in developmental progression of o in taxon SubPropertyOf: in taxon
• has_part o in taxon SubPropertyOf: in taxon

suppression by virus of host natural killer cell activation SubClassOf Nothing

• suppression by virus of host natural killer cell activation SubClassOf negative regulation of natural killer cell activation
  • negative regulation of natural killer cell activation EquivalentTo biological regulation and (negatively regulates some natural killer cell activation)
    • negatively regulates SubPropertyOf: regulates
    • natural killer cell activation EquivalentTo cell activation and (has primary input some natural killer cell)
    • natural killer cell EquivalentTo group 1 innate lymphoid cell and (lacks_plasma_membrane_part some PR_000001002) and (lacks_plasma_membrane_part some PR_000001020) and (lacks_plasma_membrane_part some PR_000001289) and (lacks_plasma_membrane_part some PR_000001889) and (capable of some natural killer cell mediated immunity) and (capable of some regulation of immune response)
      • group 1 innate lymphoid cell SubClassOf innate lymphoid cell
      • innate lymphoid cell SubClassOf lymphocyte
        • lymphocyte EquivalentTo leukocyte and (has_part some neutrophillic cytoplasm) and (has_part some heterochromatin) and (has characteristic some mononucleate) and (has characteristic some PATO_0040072)
• suppression by virus of host natural killer cell activation EquivalentTo symbiont-mediated perturbation of host process and (negatively regulates in another organism some natural killer cell activation)
• regulates o in taxon SubPropertyOf: in taxon
• symbiont-mediated perturbation of host process DisjointWith in taxon some Vertebrata
• leukocyte activation SubClassOf only in taxon some Vertebrata
• leukocyte activation EquivalentTo cell activation and (has primary input some leukocyte)
• only in taxon SubPropertyOf: in taxon

[pgaudet]

• [x] envenomation resulting in plasminogen activation in another organism: removed logical definition: -intersection_of: GO:0035738 ! envenomation resulting in modulation of process in another organism -intersection_of: has_part GO:0042730 ! fibrinolysis -intersection_of: has_part GO:0044542 ! symbiont-mediated activation of host plasminogen

• [x] suppression by virus of host natural killer cell activation:

• removed asserted superclass GO:0032815 ! negative regulation of natural killer cell activation

Hopefully that will fix the issue.

Thanks, Pascale

[balhoff]

Thanks @pgaudet looks like those changes do clear the problems.