probably the best way to bridge the two is to introduce your students with XML based web service and Perl API. Just an introduction would help them get the internalName with no great hassle. This is just a one click task by using the magic 'Perl' and 'XML' button on the BioMart web-interface (MartView).
cheers syed On Fri, 2008-04-04 at 18:25 +0200, Isabelle Phan wrote: > Syed Haider wrote: > > 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 understand, many thanks for the explanations. That makes using graphical > displays a bit challenging for the novice, as the data displayed is > inconsistent between tools... I may have a hard time explaining this to our > students, but I guess it's as well they get confronted with real life > bioinformatics ;-) > > best and thanks for providing BioMart, this is a great service. Sorry if I > seem to be moaning all the time (I'm French ;-) ). > > I.
