Hi Isabelle, On Fri, 2008-04-04 at 17:46 +0200, Isabelle Phan wrote: > Hello Syed > > many thanks for helping me out. > > It seems the taverna crash problem was the memory. I increased it to 512 > and now it seems to work, hurray :-) > > There is still something weird: the Gene Name attribute is rendered in > taverna as > > hsapiens_gene_ensembl.external_gene_id
external_gene_id is the internalName just as we have in Biomart. Its displayName is what you see in the web-interface as 'Gene Name'. As of recent release (Ensembl 49), its called as 'Gene Name', prior name was 'External Gene Id'. We have kept the internalName same to keep the namespace stable, otherwise people using perl script or web services (e.g taverna or bioConductor) to access biomart had to update the name in their code. 'gene_id' should be 'ensembl_gene_id'. let me know if I misunderstood your quesiton. > > > I now managed to display the ensembl ID in the results, but still cannot > figure out how to get the other attributes to display in the workflow > output :-( > > My test workflow is simple: > > input= Ensembl Homo sapiens genes > processor= chromosome name > output= gene_id and gene_names > > so entering a value of '11' as input would list all genes on that chromosome. > > > > Syed Haider wrote: > > Isabelle, > > > > thats fine too. As long as you are not using the following filters > > - chromosome_start, > > - chromosome_end, > > - bands, > > - markers, > > in Ensembl Variation Mart, the rest should work. The said filters had a > > configuration problem which has been fixed. The central server will be > > updated soon to reflect the updates. > > > > regards > > syed > > > > On Fri, 2008-04-04 at 16:47 +0200, Isabelle Phan wrote: > >>> over all genes (no filter). > >> sorry, my filter is chromosome 11 > >> > >> > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
