add biome 'part of' 'climactic ecological succession' axioms for better inferred hierarchy #1459
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turbomam
commented
Sep 11, 2023
turbomam
commented
- Additional participates in some climactic ecosystem succession axioms #1458
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I haven't yet revised the axioms for terms that
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Slightly trimmed output from runoak --input envo.owl tree --down --predicates i biome
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cmungall
approved these changes
Sep 11, 2023
cmungall
requested changes
Sep 11, 2023
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Always follow the design patterns.
E.g. you have:
'subtropical grassland'
and ('participates in' some 'climactic ecological succession')
and ('has quality' some subtropical)
This doesn't follow the pattern here:
https://github.com/EnvironmentOntology/envo/blob/master/src/envo/patterns/biome.yaml
it should be:
'subtropical grassland'
and ('participates in' some 'climactic ecological succession')
It may seem the quality is superfluous but harmless - but in fact by deviating from the pattern we perpetuate confusion about how to make these terms, and more importantly, they become invisible to the tagging system
If there's a class like "alpine ecosystem" one could follow the pattern. |
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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 |
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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 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? |
This was referenced Sep 13, 2023
Open
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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) |
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Thanks. I did try it but didn't share the results. It will cause an error, but yes I should share the results. |
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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
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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 |
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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
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@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: #1459 (review) In any case, I am requesting your re-review please |
Ontology comparisonLeft
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Ontology importsOntology annotationsbroadleaf forest biome
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cmungall
requested changes
Sep 25, 2023
cmungall
approved these changes
Sep 25, 2023
turbomam
changed the title
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