Putting this back on the list to keep everyone else in the loop a
On 2011-03-12, at 13:56, "Arek Kasprzyk" <[email protected]> wrote: > If you are starting from scratch it would be much better to start with > 0.8 rc5. Creating new mart is as simple as choosing one or more main > tables in the source schema. You can choose different tables and > create different datasets. There is some documentation about it in > rc5. If you want to know how the transformation algorithm works I can > describe that to you too > > > a > > > > On 2011-03-12, at 12:53, "Andrea Edwards" <[email protected]> > wrote: > >> ok - thanks >> >> i don't know much about biomart as you can probably tell but i was >> told >> there are quite significant differences between 0.7 and 0.8. >> If i am interested in understanding how the schema transformations >> take >> place so that I can design my own mart and integrate it with existing >> marts, would i be better dropping back to 0.7? I'm keen to get a >> mart up >> and running very soon. >> >> On 12/03/2011 17:41, Arek Kasprzyk wrote: >>> 0.8 rc 5 has still only rudimentary support for the MBuilder >>> component. You will not be able to read 0.7 mbuilder XML with it. >>> (ccing junjun who has just taken over the coordination of the >>> BioMart >>> development to let him know that such discussions are taking place) >>> >>> a >>> >>> >>> >>> On 2011-03-12, at 12:28, "Andrea Edwards"<[email protected]> >>> wrote: >>> >>>> Brilliant - thanks for such a prompt reply. >>>> >>>> I note that you say MBuilder (0.7) whereas i have checked out the >>>> code >>>> for biomart 0.8 rc4 >>>> >>>> >>>> On 12/03/2011 16:39, Arek Kasprzyk wrote: >>>>> 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
