Hi Syed, Yes, I noticed that there was some documentation about the semantic web services side of things for BioMart. I have to say I haven't looked at it in any detail yet - it sounds useful though, and I do plan to look into it.
As for improvements in speed etc, I won't really know, as I haven't used any other methods of programmatically accessing BioMart. If you like, if I make some general stats on access time, I can email them to the list... thanks! 2009/1/8 Syed Haider <[email protected]> > Hi Allyson, > > Glad to hear that it works for you, please do drop a line or two if you > notice any evident improvements. Also, would you be interested in ontology > part of the implementation ??? > > > Thanks > Syed > > > > Hi Richard, > > > > Thanks - a cvs update (I was indeed in the release 0.7 branch/tag) > > followed > > by re-running configure.pl, then finally stopping and starting apache > > results in a working result for the martwsdl. > > > > Thanks! :) > > > > 2009/1/8 Richard Holland <[email protected]> > > > >> Yup, if you are in release 0.7 branch already, then cvs update will fix > >> it, and you'll need to re-run bin/configure.pl afterwards to get it to > >> compile the updated service scripts correctly. > >> > >> You can check which branch you currently have checked out by running > >> 'cvs status' from inside biomart-perl/cgi-bin. It should report the > >> checked out branch in the output under the 'Existing Tags' sections. > >> > >> cheers, > >> Richard > >> > >> > >> Allyson Lister wrote: > >> > Hi Richard, > >> > > >> > Thanks for the quick reply. I do have release 0.7 (sorry I forgot to > >> > mention that in the original post), but I'm sure I checked out from > >> the > >> > head/trunk. Looking in the cgi-bin dir, it does seem that I don't have > >> > the SOAP features. Here's the contents of that directory: > >> > > >> > dsn dsn.PLS features features.PLS martresults martresults.PLS > >> > martservice martservice.PLS martview martview.PLS > >> > > >> > So does that mean that, without switching to a particular branch, I > >> can > >> > only use REST services? > >> > > >> > I'm not an expert on Biomart, so would it be relatively > >> straightforward > >> > for me to switch ? I thought I had expressly taken the 0.7 release, as > >> I > >> > just followed the user docs and they say to run the following command: > >> > > >> > cvs -d :pserver:[email protected]:/cvsroot/biomart \ > >> > co -r release-0_7 biomart-perl > >> > > >> > Hmmm - it looks like the martsoap and wsdl / xsd files were only added > >> > in December (looking here > >> > > >> > http://cvs.sanger.ac.uk/cgi-bin/viewcvs.cgi/biomart-perl/cgi-bin/Attic/martwsdl.PLS?rev=1.1.2.2&root=BioMart&only_with_tag=release-0_7&view=log > >> > < > >> > http://cvs.sanger.ac.uk/cgi-bin/viewcvs.cgi/biomart-perl/cgi-bin/Attic/martwsdl.PLS?rev=1.1.2.2&root=BioMart&only_with_tag=release-0_7&view=log > >> >) > >> > , and I think that I checked out 0.7 in November. Should I just run a > >> > cvs update command, and then re-run the whole installation process? > >> > > >> > Thanks! :) > >> > > >> > 2009/1/8 Richard Holland <[email protected] > >> > <mailto:[email protected]>> > >> > > >> > The BioMart SOAP scripts are only available on the release-0_7 > >> branch > >> of > >> > /cvsroot/biomart/biomart-perl at cvs.sanger.ac.uk > >> > <http://cvs.sanger.ac.uk>. They have not been > >> > committed to the HEAD/TRUNK. To get them, you need to make sure > >> you've > >> > checked out the release-0_7 branch. > >> > > >> > If you look in the cgi-bin folder inside biomart-perl and don't > >> see > >> > martsoap.pl etc. present there, then you probably don't have the > >> 0.7 > >> > branch checked out. > >> > > >> > cheers, > >> > Richard > >> > > >> > Allyson Lister wrote: > >> > > Hi all, > >> > > > >> > > I've made a local biomart installation, and have started with > >> just > >> the > >> > > default registry (accessing the msd and uniprot marts from the > >> ebi), > >> > > though of course the plan later is to have my own marts etc. > >> > > > >> > > I can use martview successfully on my local install, but I > >> cannot > >> seem > >> > > to see the wsdl files that should be there according to the > >> > > documentation (as I now want to programmatically query my local > >> > biomart > >> > > install using SOAP). > >> > > > >> > > My local martview: > >> > > http://mygrid.ncl.ac.uk:9002/biomart/martview (nothing special > >> > yet, but > >> > > it is running and works) > >> > > What *should* give me the wsdl: > >> > > http://mygrid.ncl.ac.uk:9002/biomart/martwsdl > >> > > > >> > > Why am I not seeing anything here? Is there some extra step in > >> the > >> > > installation that I would need to do in order to "install" the > >> web > >> > > services aspect? Any help would be most appreciated. > >> > > > >> > > Thanks :) > >> > > > >> > > -- > >> > > Thanks, > >> > > Allyson :) > >> > > > >> > > Allyson Lister > >> > > Research Associate > >> > > Centre for Integrated Systems Biology for Ageing and Nutrition > >> > > Newcastle University > >> > > http://www.cisban.ac.uk > >> > > School of Computing Science > >> > > Newcastle University > >> > > Newcastle upon Tyne, NE1 7RU > >> > > >> > -- > >> > Richard Holland, BSc MBCS > >> > Finance Director, Eagle Genomics Ltd > >> > M: +44 7500 438846 | E: [email protected] > >> > <mailto:[email protected]> > >> > http://www.eaglegenomics.com/ > >> > > >> > > >> > > >> > > >> > -- > >> > Thanks, > >> > Allyson :) > >> > > >> > Allyson Lister > >> > Research Associate > >> > Centre for Integrated Systems Biology for Ageing and Nutrition > >> > Newcastle University > >> > http://www.cisban.ac.uk > >> > School of Computing Science > >> > Newcastle University > >> > Newcastle upon Tyne, NE1 7RU > >> > >> -- > >> Richard Holland, BSc MBCS > >> Finance Director, Eagle Genomics Ltd > >> M: +44 7500 438846 | E: [email protected] > >> http://www.eaglegenomics.com/ > >> > > > > > > > > -- > > Thanks, > > Allyson :) > > > > Allyson Lister > > Research Associate > > Centre for Integrated Systems Biology for Ageing and Nutrition > > Newcastle University > > http://www.cisban.ac.uk > > School of Computing Science > > Newcastle University > > Newcastle upon Tyne, NE1 7RU > > > > > ====================================== > Syed Haider. > EMBL-European Bioinformatics Institute > Wellcome Trust Genome Campus, Hinxton, > Cambridge CB10 1SD, UK. > ====================================== > > -- Thanks, Allyson :) Allyson Lister Research Associate Centre for Integrated Systems Biology for Ageing and Nutrition Newcastle University http://www.cisban.ac.uk School of Computing Science Newcastle University Newcastle upon Tyne, NE1 7RU
