Hi Andy, Ahhh, no we don't have any really big drop down filters like yours...
Do you really need drop downs that big*, do you know if anyone's using them? (I personally find overly large drop downs a bit cumbersome). For the ESLIM and MP names/id's, you could take an approach similar to how EnsEMBL handles Gene Ontology, (pretty much just text boxes, but these are controlled vocabularies so users can look up what they want to search by elsewhere): http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=mmusculus_gene_ensembl.default.feature_page.ensembl_gene_id|mmusculus_gene_ensembl.default.feature_page.ensembl_transcript_id&FILTERS=&VISIBLEPANEL=filterpanel And for the Gene/Line names you could offer a text box that runs a LIKE query on the database, (also you need to make sure your db is doing case-insensitve queries at this point). This would remove your need for the large drop downs and simplify your release process... Sorry I couldn't be much more help. Daz * As a side note, last time I built the IKMC mart I got a bunch of warnings for your filters: default ... Europhenome .............. 001/001 ... europhenome ............................... (WEB) www.europhenome.org:80 ........ Warning: Too many Options for filter [ line_name ] possible rendering problems for Martview Warning: Too many Options for filter [ parameter_eslim_id ] possible rendering problems for Martview Warning: Too many Options for filter [ parameter_name ] possible rendering problems for Martview Warning: Too many Options for filter [ mp_term_name ] possible rendering problems for Martview OK Do the drop downs contain all of your expected values? On 8 Sep 2010, at 14:09, Andrew Blake wrote: > > Hiya Darren > It's not really the data build that's the problem it's when we use the actual > data in the build to auto-populate a drop down in the filters section of the > biomart. When we build the next one the only way we've found of resetting > those filter dropdowns is to recreate them by hand using the gui rather than > scripted - If you don't have any drop downs populated from the data you'll > probably never run into this problem but in case we are doing something daft > any advice is welcome :-) We may have to just lose the drop downs ?? > Cheers > Andy > > On 08/09/2010 13:52, Darren Oakley wrote: >> Hi, >> >> Just out of interest - is your data changing that rapidly between releases >> that you need to reconfigure/rebuild the MartEditor XMLs each build? >> >> We automatically rebuild our biomarts nightly, all we do is just re-run the >> SQL generated by MartBuilder (incorporating your new data) and >> reconfigure/restart your webserver.* >> >> If you want some more info i'd be happy to show you some of our build code. >> >> Thanks, >> >> Daz >> >> * This is a slightly simplified version. As our mart build takes a few >> hours, (and we don't want our mart to be offline for that long), we run the >> MartBuilder SQL into a slave/redundant database and then when we >> reconfigure/restart the webserver we point it at the new database, so we get >> the minimum amount of downtime we can running off a single apache instance. >> >> On 8 Sep 2010, at 12:14, Richard Holland wrote: >> >>> Word of warning - MartEditor will (highly likely) be replaced in BioMart >>> 0.8, with entirely new source code producing an entirely new mart XML >>> format. >>> >>> cheers, >>> Richard >>> >>> On 8 Sep 2010, at 12:05, Joachim Baran wrote: >>> >>>> Hi, >>>> >>>> On 8 September 2010 11:51,<a.has...@har.mrc.ac.uk> wrote: >>>>> File => Naive >>>>> File => import >>>>> File => update all >>>>> File => export >>>>> Do you reckon that MartScript will help us? >>>> 'Naive' is not supported as such, but you could have a look at the >>>> Java code and implement it yourself. It is fairly straightforward, >>>> because I just call MartEditor code from within MartScript when >>>> mimicking MartBuilder/MartEditor functionality. The other steps would >>>> work though. >>>> >>>>> I am going to IMGC, Crete, Greece in October. Please let me know if you >>>>> will be there then we can discuss this further. Thanks. >>>> Unfortunately, I am not going there. >>>> >>>> Joachim >>>> >>>> -- >>>> B.1079 Michael Smith Building >>>> Faculty of Life Sciences >>>> The University of Manchester >>>> Oxford Road >>>> Manchester >>>> M13 9PT >>>> United Kingdom >>> -- >>> Richard Holland, BSc MBCS >>> Operations and Delivery Director, Eagle Genomics Ltd >>> T: +44 (0)1223 654481 ext 3 | E: holl...@eaglegenomics.com >>> http://www.eaglegenomics.com/ >>> >> >> > > This email may have a PROTECTIVE MARKING, for an explanation please see: > http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
