Hi Arek, This is because my source schema is normalized. When added as a RDBMS data source in BioMart, it is processed to build the target schema. The problem is that the target schema that is generated is denormalized and unusable. Here are 2 screenshots to illustrate the issue:
- http://ttriplet.fg.concordia.ca/sourceDB.png - http://ttriplet.fg.concordia.ca/targetDB.png I hope this clarifies my problem. Thanks Thomas -- Thomas Triplet, Ph.D. http://www.thomastriplet.net Centre for Structural and Functional Genomics Concordia University 7141 West Sherbrooke St Montreal QC H4B 1R6 On Wed, Oct 5, 2011 at 11:39 AM, Arek Kasprzyk <[email protected]>wrote: > Hi Thomas, > you lost me here. Why would you want to use the same schema for source and > target? Could you elaborate on this please? > > a > > On Wed, Oct 5, 2011 at 11:24 AM, Thomas TRIPLET > <[email protected]>wrote: > >> Syed, >> Thanks for your reply. Sorry I wasn't clear enough, I am trying to use the >> data source as it is, not materializing it as a mart. But when I add the >> data source as a Postgres RDBMS, MartConfigurator *automatically* uses >> the source schema to build the target schema. Is it possible to disable this >> feature and force MartConfigurator to use the same schema for the target >> database as for the source database? >> Thanks >> Thomas >> >> >> -- >> Thomas Triplet, Ph.D. >> http://www.thomastriplet.net >> >> Centre for Structural and Functional Genomics >> Concordia University >> 7141 West Sherbrooke St >> Montreal QC H4B 1R6 >> >> >> >> >> >> On Wed, Oct 5, 2011 at 9:07 AM, Syed Haider <[email protected]> wrote: >> >>> >>> Thomas, >>> >>> Converting your source database into a mart is not mandatory, its only >>> recommended for performance reasons. Try using the source schema & create a >>> dataset straight out of your source database (without materialising to mart) >>> and the subsequent querying and web interfaces should work just fine (at >>> least in theory). >>> >>> W.r.t your second question, Martconfigurator is not able to read GFF or >>> other text file formats. The input to Martconfigurator should either be an >>> existing biomart webserver end point or a database. >>> >>> HTH, >>> Syed >>> >>> >>> >>> On 04/10/2011 22:03, Thomas TRIPLET wrote: >>> >>>> Hello, >>>> >>>> I'm trying to build a mart (v0.8rc6) from a normalized (3NF) PostgreSQL >>>> database. So far, it looks really great, except for one issue I have. When >>>> I >>>> look at the source database schema (using MartConfigurator), it is just >>>> fine, so the database seems properly imported. However, the corresponding >>>> target database really messes things up as it tries to merge everything >>>> together. Here is a simple example to illustrate the problem: >>>> >>>> [cid:ii_132d0b1d058ca382] [cid:ii_132d0b234e4777ae] >>>> >>>> >>>> >>>> The target database is clearly problematic, and not usable as such. Is >>>> there a way to force BioMart to keep the source schema untouched, or at >>>> least, control how it is processed ? ALl relations in the source database >>>> are defined as [1:M] so I'm not sure what's wrong here. >>>> >>>> Also, it is my understanding that a database must exist in the form of a >>>> database in order to be imported (whether it is actually accessed using >>>> RDBMS/URL/registry), or can it also be defined as raw datafiles (e.g GFF >>>> files) along with a parser. Could you please confirm this? >>>> >>>> Thanks a lot for your help. >>>> >>>> Thomas >>>> >>>> -- >>>> Thomas Triplet, Ph.D. >>>> http://www.thomastriplet.net >>>> >>>> Centre for Structural and Functional Genomics >>>> Concordia University >>>> 7141 West Sherbrooke St >>>> Montreal QC H4B 1R6 >>>> >>>> >>>> >>>> >>>> >> >> _______________________________________________ >> Users mailing list >> [email protected] >> https://lists.biomart.org/mailman/listinfo/users >> >> >
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