On Wed, 2007-12-12 at 12:07 -0500, Aristotelis Tsirigos wrote: > Ok, let's go with option #2 (installing MartView locally), if you can > send me a link to the relevant instructions it would be great.
For install please see the following link: http://www.biomart.org/install-overview.html where installing biomart-perl are the relevant sections if you want to talk to public marts only. If you wish to setup your own mart and then setup your own MartView, then you have to go through all sections. for details, you may consider going through complete docs: http://www.biomart.org/user-docs.pdf > Also, I > was wondering whether you are planning to make datasets available for > all genomes in Ensembl sometime soon. For example, there is no > zebrafish dataset if i not mistaken. Zebra Fish is available in Mart 'Ensembl GENE' as Danio Rerio. cheers syed > Thanks again! > Aris > > > > On Dec 12, 2007 12:05 PM, Syed Haider <[EMAIL PROTECTED]> wrote: > > Hi Aristotelis > > If you need Ensembl Mart 42 in particular which is missing from ensembl > > archives, I am happy to setup a test server so you can access the > > data. > > Let me know if thats the case, and how long do you need access to > > this ? > > If its for a long period, then I am afraid you have to install a local > > copy of MartView, again I am happy to guide you through the install > > procedure. > > > > Cheers > > Syed > > > > > > On Wed, 2007-12-12 at 11:50 -0500, Aristotelis Tsirigos wrote: > > > How can I do that using wget? > > > > > > > > > On Dec 12, 2007 11:44 AM, Syed Haider <[EMAIL PROTECTED]> wrote: > > > > Hi Aristotelis > > > > > > > > Ensembl maintains an archive for older versions which is available with > > > > in ensembl www.ensembl.org , left panel hyperlink 'View previous release > > > > of page in archive'. > > > > > > > > If you need to access through Perl API, all the marts are available as > > > > > > > > ver 48 (current) => host:martdb.ensembl.org port:5316 > > > > ver 47 and earlier => host:martdb.ensembl.org port:3316 > > > > > > > > cheers > > > > syed > > > > > > > > > > > > > > > > On Wed, 2007-12-12 at 11:26 -0500, Aristotelis Tsirigos wrote: > > > > > How can we query biomart on older ensembl datasets? Say for example I > > > > > want the GO annotations for human, release 42. > > > > > Thanks! > > > > > Aris > > > > -- > > > > ====================================== > > > > Syed Haider. > > > > EMBL-European Bioinformatics Institute > > > > Wellcome Trust Genome Campus, Hinxton, > > > > Cambridge CB10 1SD, UK. > > > > ====================================== > > > > > > > > > > -- > > > > ====================================== > > Syed Haider. > > EMBL-European Bioinformatics Institute > > Wellcome Trust Genome Campus, Hinxton, > > Cambridge CB10 1SD, UK. > > ====================================== > > > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
