[Biopython-dev] ExPASy / UniProt API for searching and fetching

[Wibowo Arindrarto]

Hi Peter, everyone,

On Mon, Nov 4, 2013 at 11:35 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Mon, Nov 4, 2013 at 12:12 AM, Wibowo Arindrarto
> <w.arindrarto at gmail.com> wrote:
>> Hello everyone,
>>
>> I'm trying a jab at this in this branch:
>> https://github.com/bow/biopython/blob/dev_uniprot-api/Bio/UniProt/API.py.
>>
>> It's still quite bare bones at the moment, but the general approach
>> shouldn't change much for the other functions. I'm still not sure
>> about the namespace, though. Should it be Bio.UniProt.API,
>> Bio.UniProt.api, or something else?
>>
>> As always, let me know what you think :).
>>
>> Cheers,
>> Bow
>
> Rather than Bio.UniProt.API, we should try to use lowercase
> PEP8 module names (I think here .api would be better).
>
> However, API seems to vague - how about www to be more
> clear this is an online resource?

Bio.UniProt.www is fine with me, too (and somewhat in line with what
we already have in Bio.Blast.NCBIWWW).

> (Unlike the NCBI Entrez Utilities, there isn't a clear branding
> for the UniProt web API is there?)

It's not as comprehensively branded as Entrez. They do have similar
functionalities, though. We can do query searches, retrieve records,
do a BLAST search, and even map identifiers across databases. The
BLAST search API doesn't seem to be very well-documented in the
website, but there is a Java API that allows you to do so:
http://www.ebi.ac.uk/uniprot/remotingAPI/. They even have their own
formats of the BLAST results (e.g.
http://www.uniprot.org/blast/uniprot/2013110441MHJHFYCR.* or
http://www.uniprot.org/blast/uniprot/2013110441MHJHFYCR.xml)

There are still some things left in Bio.ExPASy that UniProt doesn't
seem to cover, though, such as the Prosite search.

I was thinking maybe we could reorganize the existing Bio.UniProt code
base like this:

Bio.UniProt
  |
  |-- parsers
  |       |
  |       |-- GOA, etc.
  |-- www (or api, or remote)
         |-- __init__.py containing main functions


Best,
Bow