Hi Steffen, this one gotten delayed. We have added a request in martservice to provide connection params for ensembl archives.
http://test.biomart.org/biomart/martservice?type=registry_archive please try it on test server and see if it provides complete information. cheers syed On Wed, 2007-12-12 at 09:47 -0800, Steffen wrote: > Hi Syed, > > That would be perfect. > > Cheers, > Steffen > > Syed Haider wrote: > > Hi Steffen, > > > > On Wed, 2007-12-12 at 09:28 -0800, Steffen wrote: > > > >> Hi Syed, > >> > >> Would it be possible for the BioMart central server to return the > >> available archives and their URL as it does for the current BioMart > >> releases? > >> > > > > Thats intended for the revised BioMart system which is under design > > these days. > > > > For now, I guess we can introduce a request similar to > > www.biomart.org/biomart/martservice?type=registry > > > > say, > > www.biomart.org/biomart/martservice?type=registry_archives > > > > which would list the ancient marts we had, that might help you get the > > host, their respective ports and other connection params. From that > > point onwards you can use these params to walk through the rest of the > > configuration (attributes/filters etc etc) requests. > > > > would that be fine ? > > > > > >> Our biomaRt users currently can't locate the archives and if we could > >> somehow tell the central server that we want to see which archives are > >> available and how to get to them that would be neat. > >> > >> Cheers, > >> Steffen > >> > >> Syed Haider wrote: > >> > >>> Hi Steffen > >>> yes they are, but they are not complete historical images of > >>> www.biomart.org. Its an image of Ensembl MartView, so it contains only > >>> ensembl,vega,snp,homologies,pairwise/multiple alignments, and genomic > >>> features Marts. Precisely the ones which were available on Ensembl > >>> Martview. > >>> > >>> Cheers > >>> syed > >>> > >>> > >>> On Wed, 2007-12-12 at 09:09 -0800, Steffen wrote: > >>> > >>> > >>>> Hi Syed, > >>>> > >>>> Are these archives also available via the web service? > >>>> > >>>> Cheers, > >>>> Steffen > >>>> > >>>> Syed Haider 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. ======================================
