[ensembl-dev] connect ensembl ID and vega ID

Andy Yates ayates at ebi.ac.uk
Wed Jul 25 10:02:47 BST 2012


Hi,

The Ensembl genes are linked to an vega entry via the DBEntry/Cross reference system. Using the API & a gene you can do the following:

####################################

use strict;
use warnings;

use Bio::EnsEMBL::Registry;
Bio::EnsEMBL::Registry->load_registry_from_db(
-HOST => 'ensembldb.ensembl.org',
-PORT => 5306,
-USER => 'anonymous',
-VERBOSE => 0,
-DB_VERSION => 67
);

my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor('human', 'core');
my $gene = $dba->get_GeneAdaptor()->fetch_by_stable_id('ENSG00000139618');
my $vegas = $gene->get_all_DBEntries('OTTG');
printf("%s -> %s\n", $gene->stable_id(), $_->primary_id()) for @{$vegas};

####################################

For release 67 this gives the following information:

ENSG00000139618 -> OTTHUMG00000017411

Mirroring what you see on the gene summary page:

http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000139618

Best regards,

Andy

Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 25 Jul 2012, at 09:28, 陈岗 wrote:

> Hi All
> 
> I try to connect ensemb ID and vega ID with the relationships:
> 
> core.gene.seq_region_start=vega.gene.seq_region_start
> core.gene.seq_region_end=vega.gene.seq_region_end
> 
> Am I right ? If you have better solution please tell me.
> 
> Thanks 
> 
> -- 
> Gang Chen
> TILSI
> Taicang Institute For Life Science Information
> Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province, P.R.China
> Phone:(+86)512-82782588
> 
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