Hi Andrea All the transformation information is stored in the XML file that MBuilder (0.7) uses to compile it's DDL for Ensembl core databases. I am sure the ensembl mart team will be happy to provide you the latest version
a On 2011-03-12, at 11:15, "Andrea Edwards" <[email protected]> wrote: > 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 > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
