On Sat, Jan 21, 2012 at 7:08 PM, Arek Kasprzyk <[email protected]>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 > > sorry, now i am really cc'ing Paul and Rhoda :) > > a > -- > > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead > > -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead
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