[ensembl-dev] is there an easy way in the API to get a list of the English and Latin names of all the species in Ensembl?

[Javier Herrero]

Hi Michael

You can query the compara database to get access to all those names. There is 
one table called genome_db which contains one entry per species in Ensembl. 
There are another two tables with the NCBI taxonomy information 
(ncbi_taxa_node and ncbi_taxa_name). It you join the genome_db table to the 
ncbi_taxa_name, you can get all the names, aliases, misspelling and ensembl 
aliases for all the species:

mysql -u anonymous -h ensembldb.ensembl.org -P 5306 ensembl_compara_63

select genome_db.name, ncbi_taxa_name.* from genome_db join ncbi_taxa_name 
using (taxon_id);

You may want to restrict the results to the common names, genbank common 
names, etc.

I hope this helps

Javier

On Saturday 20 Aug 2011 00:33:50 Michael Yourshaw wrote:
> is there an easy way in the API to get a list of the English and Latin
> names of all the species in Ensembl?
> 
> We have been scraping this web page, which is rather inelegant.
> http://www.ensembl.org/info/about/species.html
> 
> 
> ॐ
> 
> Michael Yourshaw
> UCLA Geffen School of Medicine
> Department of Human Genetics, Nelson Lab
> 695 Charles E Young Drive S
> Gonda 5554
> Los Angeles CA 90095-8348 USA
> myourshaw at ucla.edu
> 970.691.8299
> 
> This message is intended only for the use of the addressee and may contain
> information that is PRIVILEGED and CONFIDENTIAL, and/or may contain
> ATTORNEY WORK PRODUCT. If you are not the intended recipient, you are
> hereby notified that any dissemination of this communication is strictly
> prohibited. If you have received this communication in error, please erase
> all copies of the message and its attachments and notify us immediately.
> Thank you.

-- 
Javier Herrero, PhD
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK