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

[Chris Fields]

Another couple of options:

1) for code changes, fork the code on GitHub, add your code there, then make a push request
2) for adding code, create a repo on github with the code, 

chris

On May 30, 2010, at 8:42 AM, Mark A. Jensen wrote:

> 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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>> 
> 
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