Mapping From Ensembl Main Database Schema To Ensembl Mart

Question

[User 6659]

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 ensemblmart61 contains a main table for human named translationmain (this is an abbreviation of the name but its obvious which one i mean) and this has a field called proteinfeatureprintsbool which is essentially a boolean field indicating whether a protein translation is assocated with a row in the PRINTS dimension table proteinfeatureprints_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 tabled called 'proteinfeature' which in turn has a foreign key called analysisid 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 strightforward example. I am interested in how you specify the 'rules' to get from a schema to a mart.

thanks a lot

Answer 1

[Casey Bergman]

Joachim Baran posted notes on how to build a customised Ensembl biomart while he was in my group. If you look in the section "Building a Mart from Ensembl Schema" you will find examples of the information you are looking for encoded in the mart_53.zip or mart_55.zip XML files.

Answer 2

[Rhoda Kinsella]

Hi,

Please find attached a link to the xml files used to create 6 of the 7 Ensembl marts for release 61 (the sequence mart is created using a script so there is no xml for this one). The xmls are for the four visible marts on the interface (Ensembl Gene, Ensembl Variation, Ensembl Regulation and Vega mart) as well as two marts that the user does not see on the mart interface, but which are accessed via the visible marts (ontology mart, genomic features mart). We are currently using Biomart version 0.7. As Arek mentioned, the Ensembl marts are quite complex and we have a few code hacks in place as well as pre and post build patches to run in order to create the databases. Therefore it is probably best if you use the martbuilder tool to see how the mart schemas are created from the core databases and then play with a simple schema and see how you get on.
Kind regards
Rhoda

The xml files can be found here: http://www.ebi.ac.uk/~rhoda/v61_xml/

Regards
Rhoda

Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.

Answer 3

[Mary]

People here may be able to help you with the details eventually, but as no one's been by to help today I'll just offer this: you may want to try the BioMart developers list for this.

http://www.biomart.org/contact.html

The list archive looks short over there because they recently relocated it. I don't know where the older stuff is. I've put a note to myself to ask someone on Monday.

[Mary]

For the reference: I got the archived mailing lists from BioMart. Someday I'm going to look for that, so I figured I'd put it here for safe keeping.