DOE Human Genome Program Contractor-Grantee
62. Continuation of the Genome Database
Christopher J. Porter, C. Conover Talbot Jr., Jay Snoddy, Ed Uberbacher, and A. Jamie Cuticchia
The Johns Hopkins School of Medicine, Baltimore, MD
Shortly after the last DOE Contractor and Grantee Workshop, in November
1997, DOE announced the termination of funding for the Genome Database
effective June 30th 1998. Consequently, this has been a year of transition
In the months following the announcement, work continued on version 6.4 of GDB, which was released in March. GDB 6.4 introduced a simplified query form for regional queries, enhancements to the display of integrated map information, and multiple modifications to improve the manner in which results are displayed and increase the speed with which they are returned. A new version of Mapview features a more intuitive user interface, and allows markers selectively to be hidden. Plans to overhaul the handling of polymorphisms were withdrawn, but display of allele size and frequency information were integrated.
Despite the project's announced termination, we received four requests
and set up three new international nodes in Taiwan, Belgium and Canada.
At their annual meeting, representatives from the GDB nodes offered their
support for continuation of the project. Previously, at their meeting
at HGM'98 in Turin, members of HUGO's HGMC expressed a strong desire that
the GDB project continue.
Subsequent to meetings with representatives from NCBI, OMIM and the HUGO Nomenclature Committee to explore the disposition of essential GDB activities, it became evident that the database could not be brought to a proper close in the six months allotted. Consequently we received a six month extension for the database shutdown and plans to migrate the database to Oak Ridge National Laboratory, there to be maintained as a static resource.
In late October, however, staff at the new GDB node in Toronto located
a potential source of private funds for GDB continuation. Diligent work
over the following two months has resulted in a rescue program for the
database. The primary, editable, copy of GDB will move to the Bioinformatics
Centre at the Hospital for Sick Children in Toronto, from whence it will
be replicated to all international nodes. Editing and curation of the
database will continue and we will strengthen our relationship with HUGO.
We are working with HUGO to supplement the 'classic' HUGO editors, who
oversee genes and mapping, with editors from the sequencing community
who will help to integrate physical maps and, ultimately, sequence information.
Plans are being made with the Sequence Annotation Consortium at ORNL to work on integrating GDB data into the Sequence Annotation project. Possibilities of other collaborations are also being investigated as resources allow. ORNL has received a copy of GDB, which will now be updated, to serve as primary U.S. node of the database.
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