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pombase / website

PomBase website v2
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Add links to alpha fold #1728

Closed ValWood closed 3 years ago

ValWood commented 3 years ago

example link https://alphafold.ebi.ac.uk/entry/Q9C0Y8

@mah11 can we do this with Uniprot accessions directly? I assume so? If so can you add because I'm not sure where!

kimrutherford commented 3 years ago

The cleanest way of doing this is to get that site added to the GO xrfs file

mah11 commented 3 years ago

pull request here: https://github.com/geneontology/go-site/pull/1720

ValWood commented 3 years ago

but I don' think they have a prefix in the same way, they just use the uniprot accession

we already have link which work with a uniprot accession, like https://swissmodel.expasy.org/repository/uniprot/P04551

ValWood commented 3 years ago

ok i clearly don't know what I am talking about ;)

mah11 commented 3 years ago

I think our stuff also consults GO xrefs for the URL syntax as well as IDs ...

kimrutherford commented 3 years ago

I think our stuff also consults GO xrefs for the URL syntax as well as IDs ...

Yep. That hopefully gives us a little bit of protection in the case where the URL changes. With luck the GO xrfs file will be fixed in that case and we'll pick up the change on the next load.

Once GO xrfs has an entry for AlphaFold we can make it appear in the External references section by adding something like this:


    {
      "ref_type": "Structure",
      "feature_types": ["mRNA gene"],
      "name": "AlphaFold",
      "description": "AlphaFold structure predictions",
      "field_name": "uniprot_identifier",
      "go_xrf_abbrev": "AlphaFold"
    },

to the external_gene_references setting in pombase_v2_config.json.

Some documentation is here: https://github.com/pombase/website/wiki/Config-file#external_gene_references

ValWood commented 3 years ago

well I seemed to have permission to merge the GO pull request, so I did it.....

So you can go ahead and add...

kimrutherford commented 3 years ago

So you can go ahead and add...

We'll need to wait until http://current.geneontology.org/metadata/db-xrefs.yaml is updated.

ValWood commented 3 years ago

Right doesn't the pull request do that?

kimrutherford commented 3 years ago

It probably needs to go through the GO release pipeline.

We don't get our copy of GO xrefs straight from Git. We use the version that goes with the GO releases.

ValWood commented 3 years ago

If that is the case we probably need to wait for a month ..... I hope that file isn't connected to the release.....

ValWood commented 3 years ago

Unless it is included with the snapshot. If it doesn't update I will ask.

kimrutherford commented 3 years ago

It might be the snapshot. I don't know what is on current.geneontology.org

mah11 commented 3 years ago

Every GO release and snapshot, and the "current" page, has a little "summary.txt" link that leads to a page with various tidbits including a datestamp.

The ... er, current summary for current.geneontology.org has the same datestamp as the summary for the most recent release. (Even the snapshot doesn't have the AlphaFold entry yet; it last ran before I did the pull request.)

kimrutherford commented 3 years ago

Since it seems that it's going to take a while I've temporarily added configuration for AlphaFold locally. So it will be visible in the morning.

I plan to remove the local configuration once it's available from current.geneontology.org so I'd like to leave this issue open.

kimrutherford commented 3 years ago

So it will be visible in the morning.

That worked, so there are now AlphaFold links on every protein coding gene page.

kimrutherford commented 3 years ago

I swapped the config to use the AlphaFold URL from GO db-xrefs.yaml