Dear Colleagues,
The Genome Database project (GDB: http://www.gdb.org), which
provides human gene mapping data to human genetics researchers from
its base at Johns Hopkins School of Medicine, will soon be ceasing its
operations. This action is a consequence of the decision by the
project's primary funder, the U.S. Department of Energy's Office of
Energy Research, to discontinue GDB funding in order to focus its
informatics resources primarily on the results of the sequencing phase
of the human genome project. Termination of the GDB project is
expected to be completed by July 31, 1998. The database will continue
to be made available to the scientific community after that time, but
further change to its content will cease.
GDB was initially created at Johns Hopkins in 1989 by the
Howard Hughes Medical Institute to capture the data from the Human
Gene Mapping Library project at Yale. In 1991 the responsibility for
funding the project was assumed jointly by the Department of Energy,
the National Institutes of Health, and the Japan Science and
Technology Agency. A series of mirror sites in many countries helped
to insure international access to the data.
One of the first major accomplishments of the project was to
capture in electronic form much of the information about human
genetics and gene mapping accumulated by the scientific community
during the two decades prior to the Human Genome Project. These data
were reviewed and edited by a worldwide group of volunteer scientists
to assure quality, under the auspices of the Human Genome Organization
(HUGO). The data included information on human genes, probes, clones,
and allele frequencies, and represented the first significant attempt
to collect the data necessary to get the Human Genome project under
way.
During its lifetime GDB provided informatics support for a
succession of HUGO-sponsored Human Gene Mapping meetings and Single
Chromosome workshops, hosted in a variety of locations around the
world. These meetings brought together researchers from many
countries to piece together integrated chromosome maps from numerous
separate experimental results; the results were then made available to
the research community via GDB.
GDB pioneered the use of the World-Wide Web as a tool for
dissemination of bioinformatics data to the community, which has now
become routine. The project was also one of the first to deploy a Java
client application (Mapview) to graphically display database query
results. In recent years novel algorithms were developed to integrate
multiple maps into a single comprehensive chromosome model which could
be searched and displayed.
By the mid-1990's small-scale mapping was giving way to high
resolution whole-genome mapping at a small number of centers, as part
of the mapping phase of the Human Genome Project. More recently the
focus has shifted again to high-throughput sequencing. As the heyday
of traditional mapping has faded, so has the perceived need for a large
community database project focussed on maps. The decision has
therefore been made to terminate the GDB project. The database will
continue to be made available to the scientific community at the same
Web address for the forseeable future, though most curation and data
acquisition activities will cease before long. It is expected that
the international mirror sites will make their own decisions regarding
the longer term maintenance and supply of the final GDB release.
Human Gene Nomenclature will continue to be curated by Dr. Sue Povey
at the University College of London. The OMIM database, which since
1995 has had no formal connection with GDB, will not be affected and will
continue to be available through NCBI (http://www.ncbi.nlm.nih.gov/omim).
The Computational Bioscience Section (http://compbio.ornl.gov)
of the Oak Ridge National Laboratory has agreed to maintain the
servers for access to the current copy of GDB after the project ends
at Johns Hopkins University. This Section is headed by Dr. Ed
Uberbacher, the developer of the widely-used GRAIL eukaryotic
gene-finding program. Oak Ridge is the coordinating site for the
Genome Annotation Consortium (GAC, http://compbio.ornl.gov/CoLab)
project, which is developing software and data systems to assist in
assembling and annotating the results of human genome sequencing on an
ongoing basis. Having GDB available locally will facilitate the GAC's
integration of map data with sequence to produce the annotated
reference genomic sequence, which is the ultimate goal of the Human
Genome Project.
I would like to take this opportunity to applaud the GDB project
staff and management for their hard work and creative effort over the
8 year history of the project. I would also like to offer my deepest
thanks to the past and present members of both our Quarterly Review
Committee and our International Scientific Advisory Committee for
their advice and support over the years, and to thank our host
institution, the Johns Hopkins School of Medicine.
We hope that this decision does not cause any great
inconvenience to members of the scientific community. Please send
comments or concerns to comments at gdb.org, or fill out the comment form
at http://www.gdb.org/shutdown/shutdown.html, which permits comments
to be anonymous, if desired. Please be as specific as possible in
describing any use of GDB in your research for which no equivalent
resource currently exists. These comments will be forwarded to myself
and the funding agencies. Funding agency representatives can be
contacted directly at the following addresses:
Department of Energy: Daniel.Drell at oer.doe.govMarvin.Frazier at oer.doe.gov
National Institutes of Health: Lisa_Brooks at nih.gov
The GDB staff can be contacted collectively at gdbstaff at gdb.org.
Sincerely,
Stanley Letovsky, Ph.D.
Director, Genome Database
letovsky at gdb.org
