fair enough. I thought you can add it like we do for MSD and Uniprot e.g exturl|http://www.ebi.ac.uk/msd-srv/atlas?id=%s
added this on the requirements list for 0.8 release. cheers syed On Fri, 2008-03-28 at 16:18 +0000, William Spooner wrote: > Hi Syed, > > The URLs are internal (relative) to www.wormbase.org, or > dev.wormbase.org, or one of the wormbase mirrors depending on the > httpd. I set this on a per-server basis using exturl setting in > settings.conf. I cannot really hard-code the path due to mirroring > issues. > > Will > > > On 28 Mar 2008, at 16:08, Syed Haider wrote: > > > > Will, who runs Wormbase, is cc'ed would be able to comment. > > > > Will, you need to edit your XMLs and prepend servername for attributes > > with external URL links as this is expected to have www.wormbase.org > > instead of www.ensembl.org. > > > > > > > > > > On Fri, 2008-03-28 at 17:02 +0100, Isabelle Phan wrote: > >> wow that's real service! > >> > >> now the results look good: > >> > >> Anatomy Term ID Anatomy Term > >> WBbt:0003679 neuron > >> > >> however when I click on the link > >> > >> http://www.ensembl.org/db/ontology/anatomy?name=WBbt:0003679;class=Anatomy_term > >> > >> the page returns: > >> > >> 404 not found. > >> > >> ? > >> > >> > >> Isabelle > >> > >> Syed Haider wrote: > >>> Hi Isabelle, > >>> > >>> www.biomart.org has the patch now. thanks for your patience. > >>> > >>> cheers > >>> syed > >>> > >>> On Fri, 2008-03-28 at 11:32 -0400, Arek Kasprzyk wrote: > >>>> On 28-Mar-08, at 11:09 AM, Isabelle Phan wrote: > >>>> > >>>>> I have now found some queries that work great! > >>>>> However I will have a hard time explaining why some data seem to > >>>>> be > >>>>> missing from the results table.... > >>>>> > >>>>> MartView query: > >>>>> > >>>>> Dataset: MSD > >>>>> Filters: R < 2A, single crystal X-ray diffraction > >>>>> Attributes: Molecule name, Organism Name, PDB ID(s) > >>>>> > >>>>> combined with > >>>>> > >>>>> Dataset: Uniprot proteomes > >>>>> Filters: none > >>>>> Attributes: UniProt AC > >>>>> > >>>>> Filter for unique rows: selected > >>>>> View: 200 rows > >>>>> > >>>>> I am getting entries with no organism data, e.g.: > >>>>> CYCLOPHILIN 3 1e3b P52011 > >>>>> > >>>>> both the PDB and UniProt data seem to contain the correct organism > >>>>> (C.elegans) with the correct taxID. > >>>>> > >>>> Hi Isabelle, > >>>> > >>>>> Why is the query not returning the organism data? Is this a > >>>>> synchronization issue? > >>>>> > >>>> most likely, MSD as well as UNIPROT are just prototype data > >>>> sources so > >>>> not really kept up to date. > >>>> You would be probably better off using something which is regularly > >>>> updated e.g. Ensembl > >>>> > >>>> a. > >>>> > >>>> PS. We are investigating the Wormbase issue that you reported. > >>>> we'll > >>>> get back to you on this shortly > >>>> thanks for spotting it > >>>> > >>>>> thanks for any hints you may provide! > >>>> > >>>> > >>>>> I. > >>>>> -- > >>>>> Isabelle Phan, D.Phil. > >>>>> Swiss Institute of Bioinformatics Tel: (+41 22) 379 51 89 > >>>>> CMU - 1, rue Michel Servet Fax: (+41 22) 379 58 58 > >>>>> CH - 1211 Geneva 4 Switzerland email: [EMAIL PROTECTED] > >> > >> > > -- > > ====================================== > > Syed Haider. > > EMBL-European Bioinformatics Institute > > Wellcome Trust Genome Campus, Hinxton, > > Cambridge CB10 1SD, UK. > > ====================================== > > --- > William Spooner > Visiting Scientist > [EMAIL PROTECTED] > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
