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