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

[Andy Yates]

Hi,

I've just done a check of the current 73 DBs and the only species to have an identifier like IPI% is cow & rat. I think you've just been lucky maybe or on an older version of the databases.

As for your other question you can descend up the object hierarchy using accessors on the various objects e.g.

my $translation = $translation_adaptor->fetch_by_stable_id('ENSP00000381386');
my $transcript = $translation->transcript();
my $gene = $transcript->get_Gene();
my $display = ($gene->display_xref()) $gene->display_xref()->primary_id() : q{};

That will be quite slow so I would probably suggest using BioMart or going in with raw SQL e.g.

select tr.stable_id, g.stable_id, `dbprimary_acc`
from translation tr
join transcript t using (`transcript_id`)
join gene g using (`gene_id`)
join xref x on (g.`display_xref_id` = x.`xref_id`)
where tr.stable_id IN ('ENSP00000381386');

Of course if you've got translation objects you can switch the stable id out for translation_id.

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 24 Oct 2013, at 16:28, Giuseppe Gallone <giuseppe.gallone at dpag.ox.ac.uk> wrote:

> 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
> 
> 
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