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
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