V. MAIZE GENOME DATABASE

Transition to MaizeGDB: http://www.maizegdb.org
MaizeGDB is the next generation Maize Genome Database, with interfaces and all accesses to the data under the guidance of Volker Brendel, Ames, Iowa. It will completely replace the MaizeDB site, www.agron.missouri.edu, September 30, 2003. We welcome Volker’s staff: Trent Seigfried, Darwin Campbell, Sanford Baran and Carolyn Lawrence to our community

Some history. In the fall of 2002, the first steering committee for a new Maize Genome Database, MaizeGDB, met to evaluate new interfaces to maize genome data. The Steering Committee for MaizeGDB is chaired by Tom Slezak, and currently includes: Ed Buckler, Vicki Chandler, Mike Freeling, Sarah Hake, Mary Polacco, Marty Sachs, Cari Soderlund, Lincoln Stein, and Virginia Walbot. At that time, a recommendation was made to target September 2003 as a final transition, with full migration of all data in MaizeDB to the new database, contingent on the development of a suite of curation tools. Missouri staff will continue to play a major role in curation of MaizeGDB; stocks will continure to be curated by Marty Sachs and his staff at Illinois. A major effort will be made to engage the community in curation (see below). The MaizeGDB was presented January 2003, at the Plant and Animal Genome Meetings, San Deigo, CA, and as a talk in the first general talks session of the 2003 Maize Meetings held in March at Lake Geneva, WI. It has been available for public review and inputs since Jan 2003 (see announcement on the Jan bionet bulletin board:  http://bionet.hgmp.mrc.ac.uk/hypermail/maize/maize.200301/0005.html).

Community Curation of Literature — Coming soon
In May 2003, the MaizeGDB Steering Committee proposed an Editorial Board, whose membership would participate in curation of the literature. The inaugural board, convened by Ginny Walbot, will include: Hugo Dooner, Chief; Lisa Harper, Erich Grotewold, Bill Tracy, and Nathan Springer. This first group will be intimately involved in testing the data curation forms, their utility and friendliness. Once the forms have been vetted, there will be an open invitation to all cooperators to participate. Because the editorial board will curate a limited number of papers, it is highly important that we receive your support in this effort. Your paper could be high-lighted as a ‘paper of the week’ if comprehensively curated in MaizeGDB.

Community curation of larger research projects
This past year we have successfully developed protocols whereby 2 research projects handled much of the semantic and other checking of data at their site, so that it was consistent with MaizeDB, and supplied in a routine format to MaizeDB. In both cases, the project databases had SQL access to MaizeDB, permitting access to current tables of names and synonyms for loci, probes, and stocks. While the MaizeDB curator still needs to monitor for overall data quality prior to loading, most of the work has been performed by the experts for these data sets. We gratefully acknowledge the support of Marilyn Warburton, Ed Brandon, Carlos Lopez, Juan Alarcon, and Dave Hoisington (CIMMYT); and Mike McMullen, Ed Coe, Hector Sanchez-Villeda, Steve Schroeder and Georgia Davis (Missouri). The current curator of MaizeDB plans to similarly engage other projects in the near future.

Also of note:
Consensus genetic maps with higher resolution than ‘bins’. The current version is presented in this newsletter (pages 137-179). This map, IBM2 neighbors, forms the scaffold for the physical map; note that only loci listed as Backbone have statistically defendable order, being on-frame on the IBM map. We thank the Chromatin (www.chromdb.org) and Maize Mapping (www.maizemap.org) projects for providing new map data for this map. We plan to incorporate other community IBM map data in the near future. In all cases, sources of the data are acknowledged.

Sorghum genetic maps were entered, courtesy of Andrew Paterson and John Bowers, with links to probes mapped on both the genetic and physical maps of maize. The Paterson BAC probes may be recognized as the 'SOG' markers on the Web FPC presentation at Arizona (http://genome.arizona.edu/fpc/maize).

Links from maize to Gramene rice physical maps were kindly provided by Doreen Ware and Lenny Teytelman at Gramene. These links are based on sequence similarity of maize Cornsensus and ESTs to rice, and are posted at the Gramene site. These links are also regularly forwarded to Arizona for inclusion in the Web FPC presentation of the physical map of maize.

A file of the mapped sequences of maize is one of our more requested items by larger projects and currently resides at: www.agron.missouri.edu/files_dl/SequenceMap directory. It lists sequence accessions, map coordinates on bins, IBM and IBM neighbors, and the locus name. A similar file will be maintained at the new site.
 
 

                                                                                                                                                                             Mary Polacco
                                                                                                                                                                             Curator, Maize Genome Database
                                                                                                                                                                             July 23, 2003
 
 


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