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

Bert Overduin bert at ebi.ac.uk
Wed Jun 20 15:22:40 BST 2012

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:


Hope this helps.


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


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