-
Notifications
You must be signed in to change notification settings - Fork 40
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.
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
New check to detect terms with same MetaCyc/KEGG xrefs #28146
Comments
I also found a case where the same MetaCyc ID appeared twice on a single GO term, both as a narrowMatch xref and an un-typed ref. I would be good if the new check also flagged these types of case. id: GO:0016805 |
Thanks @balhoff For the first issue: I don't see BUTYRATE--COA-LIGASE-RXN on GO:0031956. |
@sjm41 sorry! This is another example of the confusing automatic move of xrefs from obsolete terms to their replacements (planning to fix that soon). It's on GO:0047760. |
OK, I've fixed 4 of the remaining cases. The other 4 will be fixed by the proposed merges in #28503 |
@balhoff I believe your associated PR should now complete. BUT BEFORE YOU DO THAT (!), I am wondering if this check for the same MetaCyc/KEGG database xref could be extended to also check for any terms that share the same MetaCyc/KEGG definition xref? Is that possible? If so, would it work best to bundle it with this current check? |
@sjm41 the current check does not compare definition xrefs. It would complicate the query to do both in one check, so I think we should make an issue to implement a one-to-one check for definition xrefs and tackle that after going ahead and merging this check. How does that sound? |
Sounds good, thanks! |
@balhoff |
@sjm41 my assumption is that the xref would be "narrow" in those cases, but waiting for Pascale sounds good to me. |
@balhoff I believe I've now fixed all these cases (making them narrowMatch), so hopefully this check will now run successfully. |
@sjm41 only 3 left!
|
Nearly there! I'll deal with those other 3 asap. |
OK, done, please try again @balhoff ! |
Hi Jim
Could you set up a check to initially flag, and subsequently prevent, GO terms having identical MetaCyc or KEGG term xrefs?
This check would be equivalent to the one you've made for duplicate EC xrefs alluded to here: #26235
Currently, there are not many KEGG xref duplicates - see #28133 for list, which are either already fixed or in the process of being fixed.
Currently, there are ~117 MetaCyc xref duplicates (https://docs.google.com/spreadsheets/d/1NihWOJ3pfG05Jon0KUrIj4xK_uj3uHs42--WaMA1RxM/edit?gid=0#gid=0).
I'll be working through these in the coming week.
@pgaudet
The text was updated successfully, but these errors were encountered: