Thanks for the near-instantaneous response. > 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.
What I may have neglected to make clear is that my stuff isn't even in a relational database yet. So I'm wondering what to put in there. I'm sure that once I get there, MartBuilder will work fine. > 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. Yes, I will want to generate sequences. Should I try and get it running without sequences and then drop you an email? Or do you want to consider this the "another email"? :) > 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. OK. It's a bit scary how many tables they have, but I'll try to find some relevant ones. Thanks, -Amir > > 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 > >
