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Update function section evidence for HAMAP IDs #1686

Open katewarner opened 2 months ago

katewarner commented 2 months ago

In the function section of the protein pages, the HAMAP link (e.g. "MF_04099" in the image below) is not working

https://www.glygen.org/protein/P0DTC2-1#Function

image

Here's the corresponding incorrect section highlighted in the protein details page https://[api.glygen.org/protein/detail/P0DTC2](https://api.glygen.org/protein/detail/P0DTC2) image

It looks like the xref in the nt file is provided as HAMAP not UniProtKB:

[k.warner1@glygen-vm-dev 2024_06_20]$ grep P0DTC2 uniprot-proteome-sars-cov-2.nt | grep MF_04099
<http://purl.uniprot.org/uniprot/P0DTC2> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://purl.uniprot.org/hamap/MF_04099> .

I've uncommented a line in the xref_info.csv to use to correct the xref: protein_xref_hamap,HAMAP,https://hamap.expasy.org/signature/%s,MF_03070|MF_03206|MF_03070

Please update your script for creating the function.evidence section of the protein page for ids with the syntax "MF_*" (HAMAP IDs), so that "database": "UniProtKB"is changed to "database": "HAMAP", and the base url is changed from https://www.uniprot.org/uniprot/%s#function to https://hamap.expasy.org/signature/%s. So the section above when corrected should look as follows:

                {
                    "database": "HAMAP",
                    "id": "MF_04099",
                    "url": "https://hamap.expasy.org/signature/MF_04099"
                },
rykahsay commented 5 days ago

It will come up as shown below after we push to tst, please check during API test:

image