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Add EC to one-to-one-xrefs-by-value-violation.sparql #26235

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Add EC to one-to-one-xrefs-by-value-violation.sparql #26235

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@balhoff balhoff commented Oct 9, 2023 •
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These ECs are currently xrefs for multiple GO terms (and are causing this PR to fail checks):

Added to spreadsheet
https://docs.google.com/spreadsheets/d/17QvDQoIXe-Rim9ReReVlZGntr-WkIGJ0cbPhaQDB_As/edit#gid=0

2024-07-15 - updated list:

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sjm41 commented Oct 9, 2023

Thanks Jim! Does this list filter out obsolete terms (which may still have EC refs attached, as discussed?

Also, my favourite example seems missing - I see 42 terms with EC:1.13.11.- xref

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balhoff commented Oct 9, 2023

Thanks Jim! Does this list filter out obsolete terms (which may still have EC refs attached, as discussed?

Ah—this does include obsolete terms. Currently we enforce this over both current and obsolete terms for Rhea xrefs. One way we could retain this check but avoid on obsolete terms is to change the mappings scope to something besides exact (the default assumption) or narrow. It could be "related".

Also, my favourite example seems missing - I see 42 terms with EC:1.13.11.- xref

Thanks for checking that; I had a problem copying out of Github logs. I edited my comment.

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sjm41 commented Oct 9, 2023

Thanks Jim - that list more-or-less matches my simple grep over the last released go-basic.obo file.
I think we should keep the obsolete terms in this list for now - as discussed early in today's call, it's possible (likely) that the EC xref on the obsolete term should be removed by the rules we agreed.

@pgaudet pgaudet mentioned this pull request Jun 10, 2024
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pgaudet added a commit that referenced this pull request Jun 10, 2024
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fixed xrefs obsoleted term for #26235
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pgaudet added a commit that referenced this pull request Jun 10, 2024
@pgaudet
fixed xrefs obsoleted term for #26235
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pgaudet added a commit that referenced this pull request Jun 10, 2024
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removed reactions for #26235
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@sjm41 sjm41 added the QC label Jul 10, 2024
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Here's a diff of how these changes impact the classified ontology:

Ontologies are identical

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