[ensembl-dev] ensemblgenomes compara databases

PATERSON Trevor trevor.paterson at roslin.ed.ac.uk
Wed Feb 23 12:22:45 GMT 2011


 
Hi

Is it possible for a programmatic api to query compara information without having to be explicitly told which comparagroup database is needed (in the PERL api, you have to specify the comparagroup to get the correct adaptor - but can this be readily determined from metadata in the datasource?).

Can someone point me in the direction for information about what species are analysed in which ensemblgenomes compara databases? Is there any database in 'ensemblgenomes.org' that details the metadata about which species lie in which grouping? ( this can be scraped from the website.. http://www.ensemblgenomes.org/info/species) 

In 'ensembl.org' there is a single 'ensembl_compara' database which contains the pairwise comparison data on all the species in 'ensembl.org.

However,

in 'ensemblgenomes.otg', there are separate 'ensembl_compara' databases for the different taxonomic groupings

ensembl_compara_plants
ensembl_compara_bacteria
ensembl_compara_fungi
ensembl_compara_metazoa
ensembl_compara_protozoa

and 

ensembl_compara_pan_homology


Do the individual core databases contain information about which group the species belongs to? [it would be nice if this was listed in 'meta' table].

And is meta data stored about which species are used in pairwise comaprisons in each compara database (without having to query the compara database for which genome databases it references). 

Also what is the compara_pan database?? - the contents of all the other databases??


Ta
Trevor

Trevor Paterson PhD
email trevor.paterson at roslin.ed.ac.uk <mailto:trevor.paterson at roslin.ed.ac.uk> 

Bioinformatics 
The Roslin Institute
The Royal (Dick) School of Veterinary Studies
University of Edinburgh
Scotland EH25 9PS
phone +44 (0)131 5274197
http://bioinformatics.roslin.ed.ac.uk/ <http://bioinformatics.roslin.ed.ac.uk/> 

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