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Broken EC links for GO:0102584 & GO:0102585 #224

Closed youngmip closed 4 years ago

youngmip commented 5 years ago

Dear the GeneOntology team,

The EC links on the following entries are broken: http://amigo.geneontology.org/amigo/term/GO:0102584 http://amigo.geneontology.org/amigo/term/GO:0102585

Many thanks in advance, Youngmi

kltm commented 5 years ago

Example problematic links are: http://www.expasy.org/enzyme/2.3.1- http://www.expasy.org/enzyme/2.4.1-

The metadata transformation originates from: https://github.com/geneontology/go-site/blob/b1694ab5de6edfc0b3d4fada97cc5f9b366f508c/metadata/db-xrefs.yaml#L634 It would appear then that the ExPASy metadata is out of date. @suzialeksander @pgaudet would you know what the best contact would be to update that? A quick look does not give an obvious new mapping.

kltm commented 5 years ago

I would note that the issue here seems to be that ExPASy cannot handle the trailing "-". Is that actually supposed to be there in the definition?

suzialeksander commented 5 years ago

@youngmip Thank you for taking the time to report this bug. You can follow any progress on this ticket if you choose, but we will mention you directly (so you will get an email) in the off chance we need you to provide any more info.

@kltm I'm thinking it is, as UniProt cannot handle a search for ec:2.3.1. but is satisfied if you leave in the dash: https://www.uniprot.org/uniprot/?query=ec:2.3.1.-

Expasy is also happy to provide a list for All UniProtKB/Swiss-Prot entries corresponding to class 2.3.1.-. if you search by EC number from their homepage, but they have a generic URL of https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec. Doesn't look like that trailing period "http://www.expasy.org/enzyme/2.3.1-." helps our link either.

If @pgaudet doesn't have a contact I'll dig around.

pgaudet commented 5 years ago

The URLs should be 'https://enzyme.expasy.org/**EC**/1.4.3.6' . I don't think we should use 'search' (I dont know how to make a branch in GH, so I dont know how to edit this file now...)

Can someone edit the yaml ?

Thanks, Pascale

kltm commented 5 years ago

Working PR at https://github.com/geneontology/go-site/pull/1131 from @pgaudet

kltm commented 5 years ago

@pgaudet Could you please make it so the example URL and the URL giving the syntax are of the same format? As it stands now, the testing URL cannot be generated from the syntax URL.

kltm commented 5 years ago

New working PR at https://github.com/geneontology/go-site/pull/1132

suzialeksander commented 5 years ago

@kltm when will we know if the PR fixed the issues? I just tried the link on http://amigo.geneontology.org/amigo/term/GO:0102584 and it's still a Not Found.

kltm commented 5 years ago

@pgaudet Looking at https://amigo-staging.geneontology.io/amigo/term/GO:0102584 , the generated https://enzyme.expasy.org/EC/2.4.1- is consistent with what is in db-xrefs.yaml, but does not generate a good link. How can determine (or who is the contact) for having the correct links?

pgaudet commented 5 years ago

The EC was missing a .dot

Updated: EC:2.4.1- -> EC:2.4.1.-

pgaudet commented 5 years ago

https://github.com/geneontology/go-ontology/pull/17615

pgaudet commented 5 years ago

Should be fixed; @kltm I leave it to you to check and close ?

kltm commented 5 years ago

@pgaudet That would seem to fix it. I've moved this item into Clearing so it can be checked after the next release (or tested snapshot).

pgaudet commented 5 years ago

https://github.com/geneontology/go-ontology/pull/17619

suzialeksander commented 5 years ago

update: still not fixed, waiting on next release to check again.

suzialeksander commented 4 years ago

Yay! working as of today. Closing as resolved.