Review allow_equivalents: all design decision for BERO #3
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You are doing the right thing in skipping for now
But we should simultaneously look into these do you know you to use robot
to generate explanations for these?
…On Thu, May 26, 2022 at 3:22 AM Harshad ***@***.***> wrote:
to avoid having to hack OBI, ENVO and NCIT:
ERROR Equivalence: <http://purl.obolibrary.org/obo/NCIT_C179199> == <http://purl.obolibrary.org/obo/NCIT_C1127>
ERROR Equivalence: <http://purl.obolibrary.org/obo/ENVO_01001479> == <http://purl.obolibrary.org/obo/ENVO_01001784>
ERROR Equivalence: <http://purl.obolibrary.org/obo/OBI_2100024> == <http://purl.obolibrary.org/obo/OBI_0003012>
ERROR Equivalence: <http://purl.obolibrary.org/obo/ENVO_01001483> == <http://purl.obolibrary.org/obo/ENVO_00010504>
ERROR Equivalence: <http://purl.obolibrary.org/obo/OBI_0002781> == <http://purl.obolibrary.org/obo/OBI_0002783>
This occurs during the prepare_release step :
sh run.sh make prepare_release IMP=false
We decided to skip the checks for inferred equivalences. Alternatively we
could remove the offending axioms from the ontologies 1 by 1.
Thoughts @cmungall <https://github.com/cmungall> ?
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Do you mean under |
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I have tickets in for most of these issues for a while. |
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This is an example how you get explanations: Can you also share the output of |
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Just for documentation purposes, the correct command is
Imported files: Released files: |
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Explain: check here http://robot.obolibrary.org/explain Instead of -o write --explanation |
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I have extended the pipeline to generate all related explanations: https://github.com/berkeleybop/bero/blob/main/src/ontology/bero.Makefile#L95 Something is wrong though: reason --equivalent-classes-allowed asserted-only results in the output in the first comment of this post; but NONE of the explanations work reveal anything. @balhoff do you have an idea of why, for example: https://github.com/berkeleybop/bero/blob/main/src/ontology/bero.Makefile#L87 reveals no explanation, while the reasoner reveals this exact equivalence as inferred during |
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@matentzn sometimes ELK has trouble giving explanations when it's the result of mutual subClassOf relations. Could that be the case here? |
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defin. possible! Thank you! |
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@hrshdhgd in this case, i dont know how to debug this ticket without major efforts. We will also not learn why NCI-Thesaurus/thesaurus-obo-edition#76 which is a pity, since @cmungall cannot reproduce it. |
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… On Fri, May 27, 2022 at 5:47 AM Nico Matentzoglu ***@***.***> wrote:
@hrshdhgd <https://github.com/hrshdhgd> in this case, i dont know how to
debug this ticket without major efforts. We will also not learn why
NCI-Thesaurus/thesaurus-obo-edition#76
<NCI-Thesaurus/thesaurus-obo-edition#76> which
is a pity, since @cmungall <https://github.com/cmungall> cannot reproduce
it.
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Hahah yes. Good luck @hrshdhgd :P |
to avoid having to hack OBI, ENVO and NCIT:
This occurs during the
prepare_releasestep :We decided to skip the checks for inferred equivalences. Alternatively we could remove the offending axioms from the ontologies 1 by 1.
Thoughts @cmungall ?
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