Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Merged
merged 6 commits into from
Sep 3, 2024
Merged

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

merged 6 commits into from
Sep 3, 2024

Conversation

balhoff
Copy link
Member

@balhoff balhoff commented Oct 9, 2023 •
edited
Loading

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:

@sjm41
Copy link
Contributor

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

@balhoff
Copy link
Member Author

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.

@sjm41
Copy link
Contributor

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
Closed
pgaudet added a commit that referenced this pull request Jun 10, 2024
@pgaudet
fixed xrefs obsoleted term for #26235
eae7cd6
pgaudet added a commit that referenced this pull request Jun 10, 2024
@pgaudet
fixed xrefs obsoleted term for #26235
dbddca9
pgaudet added a commit that referenced this pull request Jun 10, 2024
@pgaudet
removed reactions for #26235
b0a7833
This was referenced Jun 14, 2024
Closed
Closed
@sjm41 sjm41 added the QC label Jul 10, 2024
@github-actions GitHub Actions
Copy link

Here's a diff of how these changes impact the classified ontology:

Ontologies are identical

@pgaudet
Copy link
Contributor

pgaudet commented Sep 2, 2024

@balhoff Can we merge this??

@balhoff balhoff merged commit 99e4663 into master Sep 3, 2024
6 checks passed
@balhoff balhoff deleted the balhoff-patch-5 branch September 3, 2024 12:32
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
QC
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@balhoff @sjm41 @pgaudet