Browser Agreement Action Plan
Contributing authors
Paul Kitts, Avi Kimchi, Mike DiCuccio, Karen Clark, Mark Cavanaugh and Deanna Church
Background
In late June, 2008 the three major genome browser and data distribution centers (Ensembl, NCBI and UCSC) agreed in principle to a common set of rules for displaying date. (see the ‘Browser_Genome_Release_Agreement.pdf’). All parties agreed that this agreement would go into effect on July 1, 2008 but no actions have taken place to move this forward. These actions include:
- contacting high volume assembly submitters in a formal way
- posting the document at all three web sites
- defining a mechanism for distribution of data from the INSDC
Proposal
Contacting high volume assembly submitters in a formal way
We should send an email to high volume assembly submitters informing them of this agreement and providing recommendations for assembly submission. This letter should go to:
- The Broad Institute (Chad Nusbaum?)
- The Wellcome Trust Sanger Institute (Richard Durbin?)
- The Genome Center at Washington University (LaDeana Hillier?)
- Baylor College of Medicine (Kim Worley)
- Steven Salzberg’s Group (Steven Salzberg)
- Joint Genome Institute (Dan Rokhsar)
- J. Craig Venter Institute (Saul Kravitz)
The letter should be signed by all centers and sent out by Sep 12, 2008.
Posting the document at all three web sites
All three centers should post a copy of the browser agreement on their web sites immediately.
Defining a mechanism for distribution of data from the INSDC
The largest implementation issue concerns the distribution of assembly data. Ideally, all members of the INSDC will produce the same set of files to be distributed to all annotating centers. We make a straw man proposal below and are actively seeking the input of other groups to ensure this structure will work for everyone. I would be useful if we could agree on this data exchange structure by Sep. 12, 2008.
Proposal:
There should be a single master directory for distribution of assemblies. For example: ftp/genbank/genome_assemblies/.
Within this directory, subdirectories will be organized in broad taxonomic groups:
