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. ======================================
