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EnvironmentOntology / envo

A community-driven ontology for the representation of environments
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add biome 'part of' 'climactic ecological succession' axioms for better inferred hierarchy #1459

Closed turbomam closed 1 year ago

turbomam commented 1 year ago
turbomam commented 1 year ago

I haven't yet revised the axioms for terms that

turbomam commented 1 year ago

Slightly trimmed output from

runoak --input envo.owl tree --down --predicates i biome
pbuttigieg commented 1 year ago

I haven't yet revised the axioms for terms that

  • assert themselves to be subclasses of 'biome', like 'alpine biome'
  • have an equivalence axiom that mentions 'biome' like 'ocean biome'

If there's a class like "alpine ecosystem" one could follow the pattern.

pbuttigieg commented 1 year ago

Careful, though: "subtropical grassland" is the ecosystem class rather than the biome class. Not all subtropical grasslands are in a climactic successional state

You can keep the condition axiom on the ecosystem class, so it's inherited by the biome class without affecting the pattern

turbomam commented 1 year ago

Thanks @cmungall and @pbuttigieg

I have been reading DOS-DP documentation and experimenting with it in the EnvO repository.

I recall why I added the 'has quality' constraint to some of the new axioms ... without them, there are several classes that share the same parent and therefore the same <SUPERCLASS> and ('participates in' some 'climactic ecological succession') axiom, and therefore are all asserted to be equivalent classes of one another.

That doesn't pass validation. If you agree that solving #1462 in the near future, and would result in better DOS-DP adherence, could we merge this PR now and make a release?

cmungall commented 1 year ago

Hi @turbomam

Let's try it. Try adapting the example I highlighted to conform to the pattern. If it leads to unsatisfiability or equivalence between named classes, post the explanation here. This will likely be indicative of a deeper problem (if it happens)

turbomam commented 1 year ago

Thanks. I did try it but didn't share the results. It will cause an error, but yes I should share the results.

turbomam commented 1 year ago

This is just from removing the 'has quality' axioms on the subclasses of 'coniferous forest biome' ENVO:01000196

robot --catalog catalog-v001.xml merge --input envo-edit-module-merged.owl \
        reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \
        relax \
        reduce -r ELK \
        annotate --ontology-iri http://purl.obolibrary.org/obo/envo/envo-full.owl --version-iri http://purl.obolibrary.org/obo/envo/releases/2023-09-13/envo-full.owl  -a owl:versionInfo 2023-09-13\
                --output envo-full.owl.tmp.owl && mv envo-full.owl.tmp.owl envo-full.owl

2023-09-13 17:29:58,705 ERROR org.obolibrary.robot.ReasonOperation - Only equivalent classes that have been asserted are allowed. Inferred equivalencies are forbidden. 2023-09-13 17:29:58,707 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_01000209 == http://purl.obolibrary.org/obo/ENVO_01000211 2023-09-13 17:29:58,707 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_01000196 == http://purl.obolibrary.org/obo/ENVO_01000250 2023-09-13 17:29:58,707 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_01000209 == http://purl.obolibrary.org/obo/ENVO_01000196 2023-09-13 17:29:58,707 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_01000209 == http://purl.obolibrary.org/obo/ENVO_01000250 2023-09-13 17:29:58,707 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_01000211 == http://purl.obolibrary.org/obo/ENVO_01000250 2023-09-13 17:29:58,708 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_01000196 == http://purl.obolibrary.org/obo/ENVO_01000211

pbuttigieg commented 1 year ago

If the issue is the various climate conditions as qualities, this may be fixed by having those as subclasses of a generic (climate condition free ) superclass

The examples you posted are already subclasses of coniferous forest biome, and that class is the only one that needs the pattern axiom, the subclasses will inherit it and can have the climate conditions as quality-based differentiae

cmungall commented 1 year ago

cab you post an explanation? via robot explain or protege

On Wed, Sep 13, 2023 at 10:30 AM Mark A. Miller @.***> wrote:

robot --catalog catalog-v001.xml merge --input envo-edit-module-merged.owl reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural relax reduce -r ELK annotate --ontology-iri http://purl.obolibrary.org/obo/envo/envo-full.owl --version-iri http://purl.obolibrary.org/obo/envo/releases/2023-09-13/envo-full.owl -a owl:versionInfo 2023-09-13 --output envo-full.owl.tmp.owl && mv envo-full.owl.tmp.owl envo-full.owl 2023-09-13 17:29:58,705 ERROR org.obolibrary.robot.ReasonOperation - Only equivalent classes that have been asserted are allowed. Inferred equivalencies are forbidden. 2023-09-13 17:29:58,707 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_01000209 == http://purl.obolibrary.org/obo/ENVO_01000211 2023-09-13 17:29:58,707 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_01000196 == http://purl.obolibrary.org/obo/ENVO_01000250 2023-09-13 17:29:58,707 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_01000209 == http://purl.obolibrary.org/obo/ENVO_01000196 2023-09-13 17:29:58,707 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_01000209 == http://purl.obolibrary.org/obo/ENVO_01000250 2023-09-13 17:29:58,707 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_01000211 == http://purl.obolibrary.org/obo/ENVO_01000250 2023-09-13 17:29:58,708 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_01000196 == http://purl.obolibrary.org/obo/ENVO_01000211

— Reply to this email directly, view it on GitHub https://github.com/EnvironmentOntology/envo/pull/1459#issuecomment-1718038964, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOO2KS5WFZ37AVS5ZATX2HUTZANCNFSM6AAAAAA4T4TOPI . You are receiving this because you were mentioned.Message ID: @.***>

turbomam commented 1 year ago

@cmungall @pbuttigieg: no more 'has quality' axioms in biome definitions, and no more asserted equivalencies.

I don't see how to mark the following request as addressed: https://github.com/EnvironmentOntology/envo/pull/1459#pullrequestreview-1621004997

In any case, I am requesting your re-review please

cmungall commented 1 year ago

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

broadleaf forest biome http://purl.obolibrary.org/obo/ENVO_01000197

Removed

coniferous forest biome http://purl.obolibrary.org/obo/ENVO_01000196

Added

flooded grassland biome http://purl.obolibrary.org/obo/ENVO_01000195

Added

grassland biome http://purl.obolibrary.org/obo/ENVO_01000177

Added

mediterranean forest biome http://purl.obolibrary.org/obo/ENVO_01000199

Added

mediterranean grassland biome http://purl.obolibrary.org/obo/ENVO_01000224

Added

mixed forest biome http://purl.obolibrary.org/obo/ENVO_01000198

Added

montane grassland biome http://purl.obolibrary.org/obo/ENVO_01000194

Added

subtropical dry broadleaf forest biome http://purl.obolibrary.org/obo/ENVO_01000225

Added

subtropical grassland biome http://purl.obolibrary.org/obo/ENVO_01000191

Added

subtropical moist broadleaf forest biome http://purl.obolibrary.org/obo/ENVO_01000226

Added

temperate broadleaf forest biome http://purl.obolibrary.org/obo/ENVO_01000202

Added

temperate grassland biome http://purl.obolibrary.org/obo/ENVO_01000193

Added

temperate mixed forest biome http://purl.obolibrary.org/obo/ENVO_01000212

Added

tropical broadleaf forest biome http://purl.obolibrary.org/obo/ENVO_01000200

Added

tropical coniferous forest biome http://purl.obolibrary.org/obo/ENVO_01000210

Added

tropical dry broadleaf forest biome http://purl.obolibrary.org/obo/ENVO_01000227

Added

tropical grassland biome http://purl.obolibrary.org/obo/ENVO_01000192

Added

tropical mixed forest biome http://purl.obolibrary.org/obo/ENVO_01001798

Added

tropical moist broadleaf forest biome http://purl.obolibrary.org/obo/ENVO_01000228

Added