Comments (9)
balhoff
commented on June 2, 2024
1
Try also passing --remove-redundant-subclass-axioms true to robot reason. I'm not completely sure but I think these will go away.
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balhoff
commented on June 2, 2024
@wdduncan you are right—currently it's outputting a very literal translation of the axioms used in the reasoning tests. An immediate thing you could do is run the output through robot reason with --axiom-generators "SubClass EquivalentClass".
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wdduncan
commented on June 2, 2024
Yes ... I was just trying a step in the output :(
Will the -- axiom-generators "SubClass EquivalentClass" option eliminate the redundant is_a statements?
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wdduncan
commented on June 2, 2024
Thanks!
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wdduncan
commented on June 2, 2024
This command:
robot reason -e all --axiom-generators "SubClass EquivalentClass" -i axioms-boomer.owl -o axioms-boomer-reasoned.owl
generates the reasoned file, but produces a number of errors:
2020-04-13 18:20:33,784 ERROR org.obolibrary.robot.ReasonOperation - Reference violations found: 6 - reasoning may be incomplete
2020-04-13 18:20:33,786 ERROR org.obolibrary.robot.ReasonOperation - Reference violation: InvalidReferenceViolation [axiom=SubClassOf(<http://boom.monarchinitiative.org/vocab/DisjointSibling#47310af97e7ead4f66b3d7f107d5880706f0cae3> <http://purl.obolibrary.org/obo/NCIT_C160214>), referencedObject=<http://purl.obolibrary.org/obo/NCIT_C160214>, category=DANGLING]
2020-04-13 18:20:33,786 ERROR org.obolibrary.robot.ReasonOperation - Reference violation: InvalidReferenceViolation [axiom=Declaration(Class(<http://purl.obolibrary.org/obo/NCIT_C160214>)), referencedObject=<http://purl.obolibrary.org/obo/NCIT_C160214>, category=DANGLING]
2020-04-13 18:20:33,786 ERROR org.obolibrary.robot.ReasonOperation - Reference violation: InvalidReferenceViolation [axiom=SubClassOf(<http://purl.obolibrary.org/obo/PECO_0000137> <http://purl.obolibrary.org/obo/NCIT_C160214>), referencedObject=<http://purl.obolibrary.org/obo/NCIT_C160214>, category=DANGLING]
2020-04-13 18:20:33,786 ERROR org.obolibrary.robot.ReasonOperation - Reference violation: InvalidReferenceViolation [axiom=SubClassOf(<http://purl.obolibrary.org/obo/NCIT_C29029> <http://purl.obolibrary.org/obo/XCO_0000543>), referencedObject=<http://purl.obolibrary.org/obo/XCO_0000543>, category=DANGLING]
2020-04-13 18:20:33,786 ERROR org.obolibrary.robot.ReasonOperation - Reference violation: InvalidReferenceViolation [axiom=Declaration(Class(<http://purl.obolibrary.org/obo/XCO_0000543>)), referencedObject=<http://purl.obolibrary.org/obo/XCO_0000543>, category=DANGLING]
2020-04-13 18:20:33,786 ERROR org.obolibrary.robot.ReasonOperation - Reference violation: InvalidReferenceViolation [axiom=SubClassOf(<http://boom.monarchinitiative.org/vocab/DisjointSibling#6212d8e82b7be24d8b37ade44a50fda4ead7c8c5> <http://purl.obolibrary.org/obo/XCO_0000543>), referencedObject=<http://purl.obolibrary.org/obo/XCO_0000543>, category=DANGLING]
Is there another flag I need to pass for the DANGLING errors?
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wdduncan
commented on June 2, 2024
Also, when I convert to obo format, there is a line called owl-axioms that lists all the axioms in functional syntax. Is this normal? I found an explanation in the documentation about them being untranslatable, but there are just a lot of them.
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balhoff
commented on June 2, 2024
but produces a number of errors:
This is normal ROBOT output, nothing to worry about here.
Also, when I convert to obo format, there is a line called owl-axioms that lists all the axioms in functional syntax. Is this normal? I found an explanation in the documentation about them being untranslatable, but there are just a lot of them.
That's right, these are axioms that can't be translated to OBO format. Do you need to use OBO format? I avoid it whenever possible.
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matentzn
commented on June 2, 2024
Plus 100 to avoid, but Bill has to live in OBO-grepistan.. no choice. I wouldn’t worry about what’s in owlaxioms for now.
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balhoff
commented on June 2, 2024
Closing this in favor of #44.
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Related Issues (20)
- Treat 1.0 probability as required axiom
- Add more documentation on how to explore output HOT 2
- Make a static site for this project
- Boomer markdown output HOT 2
- Include SiblingOf in json output HOT 2
- Bayesian calculation of unspecified probabilities from priors
- --output-internal-axioms is dropping disjointness axioms
- Provided more detailed documentation of window-count
- Consider not outputting cliques of size 2 or less HOT 1
- What is the best way to communicate changes in axioms to a user HOT 2
- allow providing prefixes declarations separate from list of prohibited within-namespace equivalents HOT 1
- Boomer: How to deal with huge cliques? HOT 3
- Output sssom mapping files rather than (just) owl HOT 1
- What do the images mean? HOT 2
- JSON filenames that are hashed have no mention in the `output.md` file HOT 1
- Supporting Mapping QC workflow
- Supporting the Mapping Integration workflow HOT 1
- Report posterior probability of each proposed axiom in a solution
- Docs: Add link to `README.md`
- Add additional diagnostics to figure out points where boomer doesn't complete HOT 1
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