Joachim: Yes, you can certainly transform any chado to mart using a standard 3NF transformation algorithm as currently implemented in 0.7 MBuilder. It will work 'mechanically'. You will be able to configure it and query the data. However, it will look 'weird' to a biologist because as you say there is a lot recursive stuff going on and this will not get flattened by 3NF transformation alone. To 'really' transform chado you will need an extension to the current 3NF algorithm which first flattens all the recursive structures and only then applies 3NF transform. I implemented it once in the MBuilder prototype and it worked oK but it never made it the final MBuilder implementation.
a On Wed, Jul 27, 2011 at 3:11 PM, Joachim Baran <[email protected]> wrote: > Hi! > > Aminah, do you use a very simple Chado set-up where you do not populate > the feature (or other) tables with recursively linked data? > > From your email it sounded like you had already build an BioMart 0.7 > mart from your Chado database. If your feature table contains only "flat" > data (features are not linked via the feature_relationship table), then > you should still be able to create a mart of your database. > > Can you please check whether this is the case? I somehow doubt it > though, because one of the main aspects of Chado are the graph structures > it entails. > > Joachim > > _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
