[Bioperl-l] ID mapping (or: contributing to BioPerl)

[Mark A. Jensen]

Illes-- no approval necessary (or, if you like, I approve). What you can do is 
describe what you want to do as an enhancement request at 
http://bugzilla.bioperl.org, and then attach your new code to that request. We 
can review it from there.
cheers MAJ
----- Original Message ----- 
From: "Farkas, Illes" <fij at elte.hu>
To: <bioperl-l at lists.open-bio.org>
Sent: Sunday, May 30, 2010 5:32 AM
Subject: [Bioperl-l] ID mapping (or: contributing to BioPerl)


> Hi,
>
> I've ran across a relatively simple, but specific task. I would like to put
> interaction (<protein_A>, <protein_B>, <PubMed_ID>) data from many sources
> (databases) into a single list containing the following in each record:
> <UniProt_primary_AC_of_A>, <UniProt_primary_AC_of_B>, <PubMed_ID>,
> <name_of_source_db>. (I am aware that there will be some loss during the ID
> conversion.)
>
> I have found so far the following possibilities:
>
> (1) BioMart perl API. Seems to be much smarter (and more complex) than what
> I would need. Also, I would need to parse input and output just as much as
> with newly written subroutines/modules.
>
> (2) UniProt.org -> ID mapping. I would need to convert BioGrid, HPRD and
> KEGG IDs, but I could not find them on the "From" list.
>
> (3) Synergizer. I cannot run it in remote batch mode. From what I would need
> I could not find BioGrid, ENSP and KEGG identifiers.
>
> (4) Writing it all with ID mapping files downloaded from each database and
> contributing it to BioPerl. How can I contribute? How do I find the best
> place within BioPerl to add a particular module? Whom do I need to ask for
> approval?
>
> Thanks in advance for any comments.
> Illes
>
> -- 
> http://hal.elte.hu/fij
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