[ensembl-dev] IPI ID to ENSP via API?

[Giuseppe Gallone]

Hi Andy

I'm not sure why but I seem to be able to retrieved Ensembl Protein IDs 
from a list of IPI ids. I'm using a translation adaptor

my @translations = 
@{$translation_adaptor->fetch_all_by_external_name($ID_IPI)};

and it does work fine. Any ideas?

Also, give array of translation, what is the best way to get the gene 
name for the corresponding gene object?

Best
G



Message: 2
Date: Wed, 23 Oct 2013 17:12:25 +0100
From: Andy Yates <ayates at ebi.ac.uk>
Subject: Re: [ensembl-dev] IPI ID to ENSP via API?
To: Ensembl developers list <dev at ensembl.org>
Message-ID: <21D4BB75-4245-4C22-B7C4-884D8654B841 at ebi.ac.uk>
Content-Type: text/plain; charset=us-ascii

Hi,

We removed IPI from our Xref sources 8 months ago as the resource was 
closed September 2011. There is no way of retrieving IPI links from the 
API. One possible alternative is to use UniParc. A large number of 
Ensembl species are imported into UniParc and would let you find those 
ENSPs whose sequence was identical to an IPI record.

Hope this helps,

Andy

------------
Andrew Yates - Ensembl Core Software Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
Tel: +44-(0)1223-492538
Fax: +44-(0)1223-494468
http://www.ensembl.org/


On 10/23/13 17:05, Giuseppe Gallone wrote:
> Hi
>
> I was wondering what's currently the best way to obtain a list of ENSP
> protein IDs given a list of IPI IDs via the API.
>
> Best
> Giuseppe