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With PFAM server going away, create domain graphics locally #42

Open ChrisMoth opened 2 years ago

ChrisMoth commented 2 years ago

From: Gustavo A. Salazar via RT interhelp@ebi.ac.uk Sent: Monday, September 12, 2022 9:20 AM To: Moth, Christopher W chris.moth@vanderbilt.edu Subject: Re: [interhelp #611641] Will PFAM graphics JSON generation be moved to interpro?

Hello there,

Thanks for your email.

Are you interested in the data itself? meaning, the coordinates matches, length of the protein, etc. If so you can get the same information, although in a different format from the InterPro API. If you want the Pfam matches for the example protein P45381 you can get them from: https://www.ebi.ac.uk/interpro/api/entry/pfam/protein/uniprot/P45381

please notice you can change that URL to get InterPro matches as well:

https://www.ebi.ac.uk/interpro/api/entry/interpro/protein/uniprot/P45381

The example you shared includes per-residue information, which you can also get from InterPro at

https://www.ebi.ac.uk/interpro/api/protein/uniprot/P45381?residues

and some proteins also have some annotations from other sources such as mobidb, phobias, etc. You can get that info from our API using a URL like:

https://www.ebi.ac.uk/interpro/api/protein/uniprot/P45381?extra_features

which in this particular example is empty.

However, as you can notice from these examples, we are not including style information (color, shape, etc) in any of those responses, and it is not part of our current plans to do so.

On the other hand, if what you are interested in, is the generation of the graphics using the JSON provided I would recommend having a look at this repo:

https://proteinswebteam.github.io/domain-gfx/

Which is the library pfam uses to do so.

Hope this helps, cheers,

Gustavo

My generating note to interpro helpdesk

Congratulations on the PFAM website move to INTERPRO.

We have used the PFAM domain graphics generator in our pipeline, and are curious as to whether this service will continue.

Example:

We also can build these json dictionaries ourselves from the interpro match_complete.xml entries. But the convenience of being able to get these graphics for canonical uniprot transcripts has been much appreciated.