By far the easiest way to create a BioMart dataset is to use MartBuilder, point it at your relational database containing your data, and go from there. MartBuilder needs to be told which table is the main focus of your dataset - in your case, probably the gene table - and it will then suggest dimensions etc. and generate the SQL for you to run to build the mart.
Having said that, if your data is in a GMOD-style schema with one table representing multiple different data types (gene, transcript, etc.) then it does get a bit harder. Also it gets harder if you want to produce sequences, as this requires use of the (undocumented) GenomicSequence modules. If you run into this situation, drop us another email and we'll do our best to help. For now, the Ensembl datasets on martdb.ensembl.org port 5316 would be a good starting point - you can compare the tables in the databases with the configs (by pointing MartEditor at it) and see how they match up. cheers, Richard On Wed, December 19, 2007 8:45 pm, Amir Karger wrote: > Hi. > > I'd like to make a Biomart site with some fungal genomes. > > I saw lots of information of various types in the User Guide, but not > too much on how to build the tables in the first place. That is, if I > want a stripped-down Biomart (get gene locations, descs, etc., download > sequences of genes possibly with upstream/downstream sequence), then > which Biomart tables do I need to produce? > > Looking through the mailing list, I saw the gff2biomart5.pl script from > gmod. Is that a good tool to use? > > If someone can point me to an example simple Biomart site that I could > steal from, that would be great. I know enough Perl to create files in > whatever format is necessary; I just need to know what content and > format I need to get Biomart working. > > Thanks, > > - Amir Karger > Research Computing > Life Sciences Division > Harvard University > -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK
