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

Giuseppe Gallone giuseppe.gallone at dpag.ox.ac.uk
Fri Oct 25 11:15:55 BST 2013


Thanks a lot for the useful information.

Giuseppe

On 10/24/13 21:47, Andy Yates wrote:
> 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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>
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