Douglas Bigwood, Database Manager
Plant Genome Data and Information Center
National Agricultural Library, USDA
The Plant Genome Data and Information Center (PGDIC) staff continues to work on the plant genome database design at USDA's National Agricultural Library (NAL) in close collaboration with the other design teams.
Technical Committee Meets
The PGDIC Technical Committee met for the first time July 10th
and 11th, 1991.
Composed of genetic and information
experts, the committee provides technical advice to PGDIC staff who are
developing the plant genome database system. As a result of the
committee members' input, the database plan of action was
improved considerably.
An important point emphasized at the meeting is that individuals involved in developing the database should not attempt to provide all data to all people in all formats. Rather, in the beginning, the project will focus on providing the most crucial data to as many people as possible. In that way, a useful service will be available quickly, then its offerings can be enhanced in the future.
Database Design Leaps Forward
As reported in the last newsletter, all species groups involved in the database project have undertaken their own database design efforts to meet their specific data processing needs. The wheat, soybean, and pine groups have banded together and contracted with the Lawrence Berkeley Laboratories (LBL) to provide them a database design. LBL has been involved in developing an information system for the Human Genome Project for a number of years. John McCarthy is leading this effort.
The maize group has contracted Stan Letovsky and Mary Berlyn of Yale University's E. coli genetic stock center to provide their group with a design. Stan and Mary were responsible for designing and developing the database that supports the center.All of the species groups will be identifying data sources and collecting data to put into their databases. This data eventually will be fed into the database being developed at NAL, where it will be made available to the public. It is critical that all involved in the project closely collaborate so that the databases are compatible.So far, collaboration has gone exceedingly well as evidenced by the joint meeting held in Tucson, Arizona, at the Third International Congress of Plant Molecular Biology. At the meeting, the species groups presented their database designs to each other. The designs appear to be similar enough so that areas of incompatibility can be reconciled.
Arabidopsis Joins the Effort
A group led by Howard Goodman of Massachusetts General Hospital (MGH) has received funds to develop a database that will include Arabidopsis genomic information. Howard and his associates have been working on generating Arabidopsis data for many years. Now they will collect and organize this information into a system that will feed the main database here at NAL.
In a separate development, the National Science Foundation (NSF) recently funded a group led by Randy Scholl of Ohio State University (OSU) to develop an Arabidopsis stock center. Another group, led by Sakti Pramanik, will develop a database system to support the center. (See Dr. Scholl's article for more information.)
OSU has joined in NAL's database design collaboration. OSU's database will be compatible not only with NAL's database but also with the database at MGH. This means that data submitted to one group will make its way to the other group and eventually to the main database at NAL.
Future Plans
The database design teams will have another joint meeting in midJanuary where, hopefully, any remaining incompatibilities in the designs can be reconciled.
In addition, PGDIC staff will begin working on prototypes of applications that will allow end users to access the database.