Hi Oliver, Do you know whether Ensembl Genomes have plans to bring in Toxoplasma gondii? They already carry P. falciparum and certain other protists;
http://protists.ensembl.org/biomart/martview On 22 Jan 2012, at 00:08, Arek Kasprzyk wrote: > > On Sat, Jan 21, 2012 at 10:51 AM, Olivier Lucas <[email protected]> wrote: > Dear Arek, > > I am a postdoc in Molecular Medicine at the University of South Florida. I > am an experimental biologist turning to a more computational approach (and > also looking for a job in that realm). I study gene regulation in Toxoplasma > gondii (protist). This organism, along with Plasmodium and other protists > has a great gene-centric database (toxodb.org and eupathdb.org for Plasmodium > and other protists) and a vibrant community. All the data is publicly > available and queryable through their non-user friendly webservices. > > Unfortunately it is not hosted through Biomart. I have contacted the > developers and maintainers of toxoDB and the small team is too swamped > creating a great user interface and compiling data (which they do an awesome > job at) to have time to make it compatible with biomart. Thus, data mining in > those organisms is very limited. I was wondering if there would be any > interest on your side and/or what would be the logistics (and politics) > involved. To me it does not make sens not to have such great public data not > available to a broader community. I'd love to do something about it! > > Regardless, biomart is one of the most fantastic resource out there. Keep up > the good work!! > > Sincerely, > > -- > Olivier > > > Hi Olivier, > I agree with you that toxodb and europah are fantastic resources. The BioMart > project is a software development project and all our services are provided > from the independently and remotely maintained resources. We do not host any > data ourselves. However I suspect that there are people on this list who may > have some experience in 'martifying' similar resources and perhaps would be > able to provide some advice for you or someone else who would be willing to > try to create a biomart based on these data. For instance there is an Ensembl > resource dedicated to protists available from Ensembl and described in this > paper: > > http://database.oxfordjournals.org/content/2011/bar030.full > > I am also cc'ing Paul and Rhoda who would be able to give you more pointers. > I also hope that somebody else from this list may chip in with more > information > > > a > -- > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users -- William Spooner [email protected] http://www.eaglegenomics.com _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
