[ensembl-dev] Obtaining additional annotation (tissue, stage, ..) for transcripts.

[Allan Kamau]

Thank you Bert, this is exactly what I have been looking for.

Allan.

On Wed, Jun 20, 2012 at 5:22 PM, Bert Overduin <bert at ebi.ac.uk> wrote:
> Hello Allan,
>
> You can get all xrefs (cross-references) for a transcript using:
>
> my @xrefs = @{$transcript->get_all_DBEntries};
>
> or if you also want the protein xrefs:
>
> my @xrefs = @{$transcript->get_all_DBLinks};
>
> and then get their database name and id by asking for:
>
> $xref->dbname
> $xref>display_id
>
> Hope this helps.
>
> Cheers,
> Bert
>
> On Wed, Jun 20, 2012 at 3:16 PM, Allan Kamau <kamauallan at gmail.com> wrote:
>> I do have a list of ensembl transcript IDs (human) for which I would
>> like to obtain experiment specific annotation for.
>> I am interested in information such as the tissue from which the cDNA
>> was obtained.
>> Which methods of the Ensembl API can I use to obtain or at least to
>> provide ids to other databases where such data may be obtained?
>> For example I am currently able to obtain interpro data and GOids via
>> the interpro_ac method of the transcript object.
>>
>> Allan.
>>
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>
>
>
> --
> Bert Overduin, Ph.D.
> Vertebrate Genomics Team
>
> EMBL - European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge CB10 1SD
> United Kingdom
>
> http://www.ebi.ac.uk/~bert
>
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