Hi Jenny, We are very busy these days, sorry for not getting you back sooner. I don't see any problem with registry file.
Could you try to run the following tests? [Test run1] perl bin/configure.pl -r conf/registry_file_with_just_your_own_mart.xml --clean Then restart apache AND [Test run2] perl bin/configure.pl -r conf/registry_file_with_your_own_mart_and_ensembl_mart.xml --clean Then restart apache Please send me the on screen message while you run the above 2 tests. Also please send me the settings.conf file. Good luck, Junjun > -----Original Message----- > From: Mead, Jennifer [mailto:[email protected]] > Sent: Thursday, June 18, 2009 4:22 AM > To: [email protected] > Cc: Junjun Zhang > Subject: FW: [mart-dev] Federating queries > > Hi > Can anyone help out with our problem with getting federated > queries working? (see emails below) We would like the > ensembl database to appear in the datasets section (with our > own mart) not in the database section of the mart. > Junjun has not been available to continue replying to our > problem. Hope you can help... > Thanks > Jenny + Luca > > -----Original Message----- > From: Mead, Jennifer > Sent: 16 June 2009 16:50 > To: Junjun Zhang > Subject: RE: [mart-dev] Federating queries > > Hi Junjun, > > > When we try to restart apache, we get this error message, > (but we did not edit the conf file it is referring to > ourselves), and the mart fails to display at all. > > Syntax error on line 71 of > /home/jenny/biomart/biomart-perl/conf/httpd.conf: > Invalid command 'PerlOptions', perhaps misspelled or defined > by a module not included in the server configuration > > However, using an old version of the httpd conf file, before > we made any changes to the mart or registry file, we get the > 2 databases, where you can either have Ensembl or 'trans' > datasets, so you cannot query all datasets together. This is > the problem we had before. > We have made the changes you described to the mart editor, > but we still do not get the desired result. Any ideas? > Thanks, J + L > > > ________________________________________ > From: Junjun Zhang [[email protected]] > Sent: 16 June 2009 15:03 > To: Mead, Jennifer > Cc: [email protected] > Subject: RE: [mart-dev] Federating queries > > Hi Jenny and Luca, > > You may want to use the current version (ie, 54) of the Ensembl mart. > > In order to federate your own mart with a fully functional > Ensembl mart, you need to have the following four entries in > your registry file together with your own one between the > <virtualSchema> tags: > > <MartDBLocation databaseType="mysql" > host="martdb.ensembl.org" database="ensembl_mart_54" > name="ensembl" displayName="ENSEMBL 54 GENES (SANGER UK)" > port="5316" schema="ensembl_mart_54" user="anonymous" > password="" visible="1" default="1" martUser="" includeDatasets="" /> > > <MartDBLocation databaseType="mysql" > host="martdb.ensembl.org" database="genomic_features_mart_54" > name="genomic_features" displayName="ENSEMBL 54 GENOMIC > FEATURES (SANGER UK)" port="5316" > schema="genomic_features_mart_54" user="anonymous" > password="" visible="0" default="0" martUser="" includeDatasets="" /> > > <MartDBLocation databaseType="mysql" > host="martdb.ensembl.org" database="ontology_mart_54" > name="ontology" displayName="ENSEMBL 54 ONTOLOGY (SANGER UK)" > port="5316" schema="ontology_mart_54" user="anonymous" > password="" visible="0" default="0" martUser="" includeDatasets="" /> > > <MartDBLocation databaseType="mysql" > host="martdb.ensembl.org" database="sequence_mart_54" > name="sequence" displayName="ENSEMBL 54 SEQUENCE (SANGER UK)" > port="5316" schema="sequence_mart_54" user="anonymous" > password="" visible="0" default="0" martUser="" includeDatasets="" /> > > As for defining Importable/Exportable pair, since Ensembl has > already an Exportable defined (see the attached screenshot), > you will just need to define an Importable in your dataset > that matches Ensembl's Exportable. The other attached > screenshot shows how to define the Importable in your dataset. > > Let us know how it goes, please feel free to get back to us > should you have any questions. > > Best regards, > Junjun > > > > > > ________________________________ > From: Mead, Jennifer [mailto:[email protected]] > Sent: Tuesday, June 16, 2009 9:02 AM > To: Junjun Zhang > Cc: [email protected] > Subject: RE: [mart-dev] Federating queries > > Hi Junjun, > > We are struggling to get federated queries working. We want > to have our mart db called 'trans' as the database, and two > federated datasets: 1) ensemble gene and 2) our own 'trans-A' > dataset. Both ensembl and trans-A have ensembl_gene_id, so > we want to link on this. In trans this field is called > 'ensg_id_1017' in ensembl this is 'ensembl_gene_id', but they > correspond to the same values. > > Where we are so far: > > 1. We have added the URL location for the ensembl > biomart to the registry file as (as Syed suggested) > > > > <MartURLLocation database="genomic_features_mart_53" default="0" > > displayName="ENSEMBL 53 GENOMIC FEATURES (SANGER UK)" > > host="www.biomart.org" includeDatasets="" martUser="" > > name="genomic_features" path="/biomart/martservice" port="80" > > serverVirtualSchema="default" visible="0" /> > > We added this between the <virtualSchema> tags, so there > are 2 blocks of text, one for trans (real) one for ensemble > (URL virtual) within the virtualschema tags. We're not sure > we put this in the right position - should both trans and > ensemble marts be inside these tags? > > 2. We added importable/exportable specifiers in mart editor. > But we don't know if we did it correctly. > The specific values are probably wrong. Should > internalname be the ensembl field name or the trans field > name in our case? And should it be the trans field name for > the exportable one, and the ensemble name for the importable > one? Also, what is the linkname in this case? The ensembl > field name or the trans one? > > When we refresh the config file, restart apache etc. in our > martview we see 2 databases, trans and ensembl. There is no > way to query both at the same time, only separately as > discrete DBs. The link is not working between the two. > > Can you help? > Thanks > Jenny and Luca > > > > > > > From: Junjun Zhang [mailto:[email protected]] > Sent: 29 April 2009 15:30 > To: Mead, Jennifer > Subject: Re: [mart-dev] Federating queries > > Hi Jennifer, > > Just thought the following email I sent to other users may be > hopeful to you as well. > > Please feel free to let us know if you have any further questions. > > Regards, > > Junjun > > > ______________________________________________ > > Let me try to give you a brief explanation on how join query > is done in BioMart. > > Join of different datasets is done through > Importable/Exportable pair predefined using MartEditor. > Importable acts as filter, it points to a filter (which you > have defined earlier under one of the FilterPages). > Similarly, Exportable acts as attribute, it points to an > attribute. See the screenshot below for an example of how > Importable/Exportable pair is defined. > > Once the pair is defined in MartEditor (Importable in one > dataset, Exportable in the other. For more detailed > instruction, please see the document Christina sent to you, > page 10?), we then prepare a registry file, which includes > both datasets. finally we run bin/configure.pl to configure > martview with the registry settings. It is at this step, all > the links (Importable/Exportable pairs) are determined and stored. > > Use the datasets in the screenshot as the example, now when > you select both datasets from MartView GUI, choose attributes > from both dataset and set filters on one or both dataset, > then fire the query. Let's say dataset MSD would return 100 > rows and dataset gene_ensembl would return 3000 rows if the > query were done independently on each dataset. But since > there is a link between these two datasets, dataset MSD will > export all 100 'pdb_id' to dataset gene_ensembl as a ID-list > to filter (searching for matching IDs) the 3000 rows returned > by gene_ensembl, after filtering, only rows with matching > pdb_ids (intersection set) will be joined and reported, > hence, join query. > > As in your example with multiple datasets to be joined, we > can do it by chaining the process described above, ie, > exporting IDs from dataset 1 to dataset 2, exporting the > intersection IDs to dataset 3, and on and on till the last > one. For non-standard IDs, as Christina pointed out you can > keep standard ID and all of it's synonyms in a dimension > table and define a filter on the ID synonym column. While > filtering on this filter, matching any of the synonyms will > lead to retrieving the desired row. > > As you may know, the current BioMart 0.7 release supports > join of two datasets. Multiple datasets join will be > supported in the next release. > > Hope this is useful. Please feel free to write to us should > you have any questions. > > Junjun > > > [cid:519133713@16062009-1528] > > > > >
