Hi Gnani, Christina Thanks for the quick response (and for providing an example), this is exactly what I was looking for. Got it working on a test dataset already.
regards Ayton Having some issues still though. The structure is being created but the tables are empty 2009/8/28 Saravanamuttu Gnaneshan <[email protected]> > Hello Ayton > > We have now built a test mart to satisfy your requirements with some fake > data as shown in your mail. > > This mart can be browsed from this url: > http://dcc-dev.res.oicr.on.ca:9030/biomart/martview/3e46bb17a7de44e0df5e2e8deab7715c. > > > If the above link expires by the time you see this mail please use this > url: http://dcc-dev.res.oicr.on.ca:9030 > > > This mart was built as explained in Christina's email and if you need to > see the XML files created by the martbuilder and marteditor please email me > offline (not through the mart-dev list). > > If you have any queries on this please feel free to contact us. > > Best wishes > > Gnani > > > *Saravanamuttu Gnaneshan** > *Scientist, Computational Biologist > > *Ontario Institute for Cancer Research* > MaRS Centre, South Tower > 101 College Street, Suite 800 > Toronto, Ontario, Canada M5G 0A3 > > Tel: 647-260-7990 > Toll-free: 1-866-678-6427 > www.oicr.on.ca > > > > > > This message and any attachments may contain confidential and/or privileged > information for the sole use of the intended recipient. Any review or > distribution by anyone other than the person for whom it was originally > intended is strictly prohibited. If you have received this message in error, > please contact the sender and delete all copies. Opinions, conclusions or > other information contained in this message may not be that of the > organization. > > ------------------------------ > *From:* [email protected] [mailto:[email protected]] *On > Behalf Of *Christina Yung > *Sent:* August 27, 2009 9:53 AM > *To:* Ayton Meintjes > *Cc:* [email protected] > *Subject:* RE: [mart-dev] Dynamic attribute set > > Hi Ayton: > > I think a mart with partititioned tables in the following structure will > serve your needs: > > Marker [id, rsid, allele_A, alleleB] > CEU_AlleleFrequency [fk_marker_id, CEU_freq] > JPT_AlleleFrequency [fk_marker_id, JPT_freq] > YRI_AlleleFrequency [fk_marker_id, YRI_freq] > > In this mart, Marker is the main table where *_AlleleFrequency are the > dimension tables. This structure allows the addition of new populations > as dimension tables. Keep in mind that when multiple *_freq attributes are > selected, multiple tables are joined. Hence, scalability may become an > issue if the number of populations is large. > > To arrive at this mart, you may wish to use MartBuilder. First, specify > Marker as the main table. MartBuilder will merge Population and > AlleleFrequency into one dimension table [id, fk_population_id, > fk_marker_id, freq, population_name]. The next step is to partition this > dimension table by either fk_population_id or population_name. > > Hope this helps. > > Christina > > > ------------------------------ > *From:* [email protected] [mailto:[email protected]] *On > Behalf Of *Ayton Meintjes > *Sent:* Wednesday, August 26, 2009 11:37 AM > *To:* [email protected] > *Subject:* [mart-dev] Dynamic attribute set > > I have the following three tables in a custom database: > > Population [id, name] > Marker [id, rsid, allele_A, allele_B] > AlleleFrequency [id, fk_population_id, fk_marker_id, freq] > > How would I go about creating a mart that the user can query for markers > and get results in the form: > > rsid | CEU_freq | JPT_freq | YRI_freq > rs12 | 0.05 | 0.55 | 0.75 > rs34 | 0.95 | 0.65 | 0.05 > > In other words, the number of attributes available depends on how many > unique populations there are? The automate push action and partitioning seem > to suggest this sort of structure might be possible. > > Thanks in advance > >
