[BioMart Announce] BioMart Portal Initiative

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[BioMart Announce] BioMart Portal Initiative

Arek Kasprzyk

Dear All,

 

We would like to launch a new and exciting BioMart initiative. We are looking for groups with a vision and substantial domain expertise to set up BioMart Portals, much like the BioPortal and CancerPortal that can be accessed through our updated website, www.biomart.org  (if you were previously a user of biomart.org click on shift+refresh to see the new pages). The CancerPortal, which I designed for the International Cancer Genome Consortium (ICGC) is a good example of my vision for future portals. It provides a 'view' of cancer resources that span beyond the ICGC  and has a substantial TCGA component, a few additional published cancer datasets and federates a number of BioMart sources such as Reactome, Ensembl, Pancreatic Expression Database, Breast Cancer Tissue Campaign Tissue Bank and COSMIC, to name a few.

I have had preliminary discussions with Vivek Ryer
and Damian Smedley from the Mouse Informatics group at the Sanger Institute and Claude Chelala at Barts and their groups are already interested in this opportunity. There are some obvious candidates who are in a good position to build such portals (e.g Ensembl for a genomics portal and GMOD for model organism portal); however this initiative is not limited to them. If you feel that you are in a position to provide a vision for your particular area of expertise, using your own data and a number of external BioMart sources and you feel like experimenting with BioMart’s 0.8 technology, please let me know. All Portals will be hosted on their local sites but we will provide links from www.biomart.org alongside the current portals, BioPortal and CancerPortal.

To encourage you, below is proof that version 0.8 can be installed outside the BioMart group ;)  

http://biomart.i-pharm.org/
http://whis.caltech.edu:5430/

I would like to congratulate Ji-Hyun and Parul for their impressive work, which resulted in two great new additions to the BioMart community.  (Interestingly enough both of them are using the virtual mart as a data source)


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