[ensembl-dev] get COG ID, Group, KO ID and KOG by using ensembl Perl API

[Dan Staines]

On 02/13/2014 08:02 AM, 刘鹏飞 wrote:
> I have a question on how to fetch COG ID, Group, KO ID and KOG for a
> bacteria by using ensembl Perl API. I did not find where are these data
> stored, and what kind of database and database adaptor to use for
> accessing these data. I can manually download these data from IMG group
> by group, but it is too slow and time consuming.

Apologies, looks like this query was missed when first sent.

I'm afraid we don't have those cross-references in Ensembl Bacteria - 
our cross-references are restricted to ENA, UniProt, InterPro, GO and a 
selection of transitive cross-references found in the corresponding 
UniProt records (which does not currently include KO). You might be able 
to use UniProt for this purpose though - ofr instance, the ID mapping 
service at uniprot.org allows mapping to KO from various identifiers 
using UniProt cross-references (both interactively and programmatically).

Dan.

-- 
Dan Staines, PhD
Technical Coordinator, Ensembl Genomes
European Bioinformatics Institute (EMBL-EBI)
http://www.ebi.ac.uk/
http://www.ensemblgenomes.org/