Junjun: chado schema is publically available and i have done quite a bit of work with it in the past. The end result was that MBuilder could support 3NF transformation quite well but this was not sufficient for chado. Chado is a schema with a lot of recursive self-referencing based around 'feature' table. This, of course, can still be transformed using 3NF algorithm but the end result will not be as exiciting as one would like to. I experimented with it a bit a few years ago and came up with an alternative to 3NF algorihm which would work much better with chado. However given that current MConfigurator has not even acquired all the MBuilder features this seems to be a long way ahead. It will be better if you concentrate on implementing basic features for MConfigurator to get 3NF going properly first. This will give you the basics for chado. Once this is sorted out I"ll be glad to help with a proper algorithm for chado transformation
a On Tue, Jul 26, 2011 at 12:01 PM, Junjun Zhang <[email protected]> wrote: > Hi Aminah, > > Is that chado schema publicly available? It would be very helpful if we can > test it out here. > > Also, I am just curious how your current mart is built. If you'd like to try > 0.8 with the existing mart db, you can directly import it using > martconfigurator. > > Best regards, > > Junjun > Sent from my BBerry > > ----- Original Message ----- > From: Aminah Keliet [mailto:[email protected]] > Sent: Tuesday, July 26, 2011 10:34 AM > To: [email protected] <[email protected]> > Subject: [BioMart Users] biomart v0.8 : error creating mart from Chado schema > > Hi > > We are testing the new version of Biomart (0.8 rc 6) to replace our > current install (v 0.7). We build mart on the GMOD-Chado schema using > the feature table as main table for our marts. With the new version we > get an error when we try to do the same thing. In the Add data source > panel, we choose the feature table from the public schema, then we click > add and we get : > > [AWT-EventQueue-1] INFO martconfigurator - Done saving settings > [Thread-104] INFO martconfigurator - Initialize source schema > [Thread-104] INFO martconfigurator - Done synchronising > [Thread-104] ERROR martconfigurator - duplicated relation > feature.[feature_id_1057] -> feature__feature_genotype.[feature_id_1057] > [AWT-EventQueue-1] ERROR martconfigurator - Exception occurred in > MartBuilder > org.biomart.common.exceptions.BioMartError: > org.biomart.common.exceptions.AssociationException: A relation between > these two keys already exists. > at > org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:231) > at > org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:369) > at > org.biomart.configurator.controller.MartController.generateDatasetTable(MartController.java:484) > at > org.biomart.configurator.controller.MartController.synchronise(MartController.java:900) > at > org.biomart.configurator.controller.MartController.suggestMarts(MartController.java:1375) > at > org.biomart.configurator.controller.MartController.requestCreateMartsFromSource(MartController.java:1599) > at > org.biomart.configurator.controller.ObjectController.initMarts(ObjectController.java:98) > at > org.biomart.configurator.view.component.container.SourceGroupPanel$1.construct(SourceGroupPanel.java:85) > at org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128) > at java.lang.Thread.run(Thread.java:619) > Caused by: org.biomart.common.exceptions.AssociationException: A > relation between these two keys already exists. > at org.biomart.objects.objects.Relation.<init>(Relation.java:141) > at > org.biomart.objects.objects.RelationTarget.<init>(RelationTarget.java:17) > at > org.biomart.configurator.controller.MartController.processParentDatasetTable(MartController.java:225) > ... 9 more > > Do you have any idea ? > Thanks > > -- > Aminah Olivia KELIET > Ingenieur d'études en Bio-informatique > > Unité de recherche en Génomique-Info > INRA Centre de Versailles > Route de Saint Cyr > 78026 Versailles Cedex > > email: [email protected] > url:http://urgi.versailles.inra.fr > tel: 01.30.83.37.74 > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
