gene names from Ensembl

[papori]

Hi,
i just download the genome of the zebrafish last version zv9 from ensembl.
Each gene there have a unique id.
i want to know each id which gene(name of the gene) it is.
For example:
if i take this id: ENSDARG00000088185
and run it in the inside search of ensembl i will get:
eif2b1 [ Ensembl: ENSDARG00000088185 ]
Description
eukaryotic translation initiation factor 2B, subunit 1 alpha [Source:ZFIN;Acc:ZDB-GENE-040625-25] [Type: protein coding Ensembl]

i just need the name.

i can take each id manually and run it into Ensembl search... but it will take forever.
where can i get the name list mapped to id in Ensembl?

Thanks,
Pap

[turnersd]

Use your ensembl IDs as a filter in the Ensembl Biomart.

[papori]

Thanks!!!!!!!!

[JQL]

My questions is a bit further. I have a list of 25,000 ensembl IDs which I want to retrieve gene names and description. But Biomart has a limit of 500 max.

Where to download biomart's database so I can parse myself?

Thanks!!!!!!!!

[GenoMax]

My questions is a bit further. I have a list of 25,000 ensembl IDs which I want to retrieve gene names and description. But Biomart has a limit of 500 max.

Where to download biomart's database so I can parse myself?

You could use the Perl API that Ensembl provides: http://www.ensembl.org/info/data/api.html.

You can download specific databases if these ID's are from a specific organism: http://www.ensembl.org/info/data/ftp/index.html

BioMart MySQL databases appear to be here: ftp://ftp.ensembl.org/pub/release-70/mysql/

[swbarnes2]

You could use the Perl API that Ensembl provides: http://www.ensembl.org/info/data/api.html.

You can download specific databases if these ID's are from a specific organism: http://www.ensembl.org/info/data/ftp/index.html

BioMart MySQL databases appear to be here: ftp://ftp.ensembl.org/pub/release-70/mysql/

You don't even need to use the Perl API. For Danio rerio, you can just download a flat text file through Biomart that can contain all kinds of info. You can make a list of all the genes, with their ensembl IDs and, say, refseq IDs (for the ones that have them) pretty easily.

Here's one output line:

ENSDARG00000077748 solute carrier family 35, member E2 [Source:HGNC Symbol;Acc:20863] SLC35E2

[JQL]

Thanks. I tried that, but it has max limit of 500 IDs. The only IDs I have are ensembl gene IDs.

Or maybe I misread you?

You don't even need to use the Perl API. For Danio rerio, you can just download a flat text file through Biomart that can contain all kinds of info. You can make a list of all the genes, with their ensembl IDs and, say, refseq IDs (for the ones that have them) pretty easily.

Here's one output line:

ENSDARG00000077748 solute carrier family 35, member E2 [Source:HGNC Symbol;Acc:20863] SLC35E2

[JQL]

Thanks GenoMax.

The BioMart MySQL databases have what I want.

It is interesting. I got the gtf file from the organism specific database. The gtf file has only gene names but not detail descriptions of the gene. The BioMart MySQL database's gene.txt file has descritpion but no gene names.

Have a nice day!

You could use the Perl API that Ensembl provides: http://www.ensembl.org/info/data/api.html.

You can download specific databases if these ID's are from a specific organism: http://www.ensembl.org/info/data/ftp/index.html

BioMart MySQL databases appear to be here: ftp://ftp.ensembl.org/pub/release-70/mysql/