Hi Max
It is true that there is a mix of common names and scientific names
for the list of orthologs in Biomart. I'm not sure why it was decided
to be this way historically but all names that are used are within the
accepted species_alias list of names taken from the meta tables in
each of the core species databases. For example, in Biomart we use
dolphin. Here are the species alias names in the dolphin core database
meta table:
| 239 | 1 | species.alias | bottlenose
dolphin |
| 240 | 1 | species.alias | tursiops
truncatus |
| 234 | 1 | species.alias |
ttru |
| 233 | 1 | species.alias |
9739 |
| 238 | 1 | species.alias |
tursiopstruncatus |
| 235 | 1 | species.alias |
turtru |
| 236 | 1 | species.alias |
dolphin |
| 237 | 1 | species.alias |
ttruncatus |
| 241 | 1 | species.alias |
tursiops_truncatus |
| 242 | 1 | species.alias |
bottlenosed dolphin |
I appreciate that it is confusing and I am willing to help you set up
your scripts to access all the species that you need. Can you send me
(not the mart-dev mailing list) your scripts as they are, along with a
detailed description of the problems you are having when trying to set
up the scripts and details of the information you would like to pul
out of the orthology section from biomart. As an alternative you can
also use the Compara API to retrieve this information (http://www.ensembl.org/info/docs/api/compara/compara_tutorial.html
).
I hope that helps,
Regards
Rhoda
On 2 Nov 2009, at 11:04, Maximilian Haussler wrote:
Dear mart gurus,
I am trying to download the orthologs between human and all other
species in ensembl via biomart's REST service without hardcoding the
names into my scripts as I want the scripts to work even with the next
ensembl version. This is not easy.
The problem is that I have no idea how you name the species in the
biomart. You are not using the scientific name (which would be
probably the simplest choice). You not using the common name (at least
not the one from ensembl_website_56.species.) I have the impression
that you are sometimes using the common name (wallaby), sometimes
using the scientific name (ciona_intestinalis).
Is there any way for me to retrieve the list of species used in the
biomart and map them to the scientific names used in Ensembl?
Thanks in advance
Max
Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.
