Hi Michael, On Fri, 2007-12-07 at 09:38 +0000, Michael Wicks wrote: > Dear Biomart, > > I have been investigating the use of Biomart with our database > (http://www.eurepxress.org), following on from a recently departed > colleague (Chuang-Kee Ong, who some of you may have dealt with > recently). and I have a couple of questions: > > > 1. Once a Mart has been created, how do you refresh the contents of the > Mart if the database on which it is based changes?
You have to schedule upgrades of database into mart. This process can be done use MartBuilder's sql dump. Otherwise if you are confident about your DB -> Mart mappings, just keep a little script and schedule it to run automatically and upgrade your Mart. Richard would be able to comment on this if there is a better way. > > Our database grows daily with new data, and without some procedures or > processes, preferably non-manual, put in place, the Mart will almost > immediately become inconsistent with our base data. I can see how to do > this with the tools supplied but only manually. Also I don't really > want to start building something myself, as it occurred to me that this > must have been an issue before with other Marts, and that there might be > a pre-existing solution to refreshing Marts already. > > Have you come across this issue before, and if so, can you suggest a > solution please? > > > 2. Documentation. I can't find anywhere in the documentation any > explanation of how to go about implementing Importables and Exportable > fields. Our data has a number of potential linking fields and we would > like to implement these links when we put our Mart live. > We will additional information about this and couple of example. Usually, deployers tend to learn from marts which are already configured and publicly available. For instance, the best way to find what goes in which field is to see Ensembl Mart 'gene_ensembl' dataset XML available on host: martdb.ensembl.org port: 3316, user: anonymous, no password, database and schema: ensembl_mart_47, db driver: mysql. Using these credentials, connect using MartEditor. See how XML is configured and at the same time visit www.biomart.org/biomart/martview to see how the Ensembl Mart looks like. Would be very useful. > Do you have a document that explains this in more detail please (I have > been looking at a document called "Biomart 0.6 Documentation" so far)? > > (A minor documentation issue: when configuring a Mart, the Perl script > configure.pl has to be run. I'm still not sure of the difference > between the "Y" and "N" options that I'm presented with when this script > runs, even after looking at the documentation. So I run the script > twice! Can you explain what is going on here please?) Many user do not wish to install MartView (web interface) and on install API dependencies. So they need to say 'n'. > Many thanks for your time. > > Yours > > Mike Wicks -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
