[ensembl-dev] how to get from ensembl main database schema to ensembl mart schema

[Andrea Edwards]

Hello

I was wondering if there were any documents showing how the ensembl 
marts were created from the main ensembl databases. Specifically i was 
hoping there were documents describing what tables were selected as main 
tables for the marts and how the dimension tables were mapped to the 
main tables.

As an example the ensembl_mart_61 contains a main table for human named 
translation_main (this is an abbreviation of the name but its obvious 
which one i mean) and this has a field called 
protein_feature_prints_bool which is essentially a boolean field 
indicating whether a protein translation is assocated with a row in the 
PRINTS dimension table protein_feature_prints_dm. If the translation 
does have a row in this dimension table then I am guessing it has a 
PRINTS domain in it!

The core database itself however has a table called translation which 
represents, well, a translation. Translations are linked to rows in a 
table called 'protein_feature' which in turn has a foreign key called 
analysis_id which links to an 'analysis' table with fields 'database' 
and 'program'. So in this schema, a translation is associated with a 
PRINTS annotation if it is linked to a 'protein_feature' record which is 
in turn linked to an 'analysis' record with the text 'PRINTS' somewhere 
in both/either the database/program fields.

I am interested in how the biomart software is configured with 'rules' 
to create the mart schema from the database schema. Is there a 
configuration file with these rules in that I could look at? Is there a 
worked example? As an academic exercise I'd like to recreate the ensembl 
marts. I have the biomart user manual but even with that document I do 
not know how to recreate the ensembl marts

I am NOT specifically interested in protein domains. I used the PRINTS 
example purely for illustrative purposes as I thought it was a 
straightforward example. I am interested in how you specify the 'rules' 
to get from a schema to a mart.

thanks a lot