Human Genome News, November 1991; 3(4)

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Human Genome News Archive Edition

NIH-DOE Award Supports Genome Data Base at Hopkins

In a move to ensure easy worldwide access to accurate information for human genome research, NIH and DOE have awarded the Johns Hopkins University School of Medicine $5.3 million to support the Genome Data Base (GDB). Since it went online in September 1990, GDB has been the main repository for information about the location and description of genes, including disease genes, and other genetic markers on chromosomes.

The new award, said GDB Scientific Director Peter Pearson, "affirms the enormous need for a well-organized informatics component to the Human Genome Project. We see the GDB becoming the fulcrum around which all groups interested in the Human Genome Project can operate to their best advantage."

Announcement of the 3-year award came in a September 19 briefing by NIH and DOE officials and representatives of Hopkins. James D. Watson, Director of the NIH National Center for Human Genome Research, and David J. Galas, Associate Director of the DOE Office of Health and Environmental Research, announced that their agencies were making equal awards, which became effective September 1. Future funding will depend in part on support given by other countries with genome research interests.

Designed at Hopkins' Welch Medical Library Laboratory for Applied Research in Academic Information by a team of software engineers, database experts, and geneticists, GDB collects, organizes, stores, and distributes human gene mapping information. This material, generated and provided by investigators, includes data derived from Human Gene Mapping Workshops (HGMW) since their inception in 1973. An interface allows retrieval by general users, and specialized interfaces permit database editors to make and update entries at any time.

Galas said, "Some day soon scientists. . .will seek information about the functioning of living things from their computer terminals before they approach the laboratory bench. GDB is part of this revolutionary change that is catalyzed by the Human Genome Project."

Yale University supported the first gene mapping database in the mid-1970s, with some support from the NIH National Institute for General Medical Sciences. In 1985 the Gene Mapping Project of the Howard Hughes Medical Institute (HHMI) undertook the further development, management, and online support of the Human Genome Mapping Library at Yale. In 1989 HHMI, already supporting five genome-related databases, collaborated with Hopkins to create GDB. GDB is built on the Sybase relational database system and uses a powerful Sun hardware platform. (A relational database uses mathematical set theory concepts in data modeling.) The database is designed to work in a SprintNet or Internet environment with most personal computers or terminals.

GDB is expected to cost up to $15.9 million over 3 years. The new DOE-NIH award supports operational expenses, further development, and expansion. GDB staff plan to enhance and maintain interlocking database services, including:

  • Connection with other major centers to provide a more integrated set of database services to the scientific community.
  • Interaction with research laboratories to facilitate the flow of data to GDB.
  • Research and development of new and more useful database operations.
  • User services, including manuals and staff assistance for scientists.

Some 25 people work full-time on GDB at Hopkins, in addition to editors who review and standardize material to be entered in the information base. Another 12 work full- or part-time on GDB at other sites.

Arranged by cytogenetic band location, GDB entries are organized into the following categories:

  • loci (genes, fragile sites, DNA segments, and breakpoints);
  • associated symbol; disorder or syndrome name; chromosomal location; Victor McKusick's Mendelian Inheritance in Man (MIM) number; polymorphisms; alleles; allele population/frequency; and probes (cloned probes, polymerase chain reaction primers, and allele-specific oligonucleotides).
  • sources (journals, books, theses, and personal communications);
  • contacts [for probes and users of GDB and the Online Mendelian Inheritance in Man (OMIM)TM]; and
  • maps (genetic and physical).

Also online are known mouse genes that are homologous to human genes in function or DNA sequence.

Users can define searches for any category and move from one data type to another. For example, moving from the cystic fibrosis gene (CFTR) locus to polymorphisms will display all polymorphisms related to the CFTR locus.

A direct searching link through MIM numbers corresponds to entries in OMIM. Additional cross references to related databases include relevant GenBank® and American Type Culture Collection numbers.

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Human Genome Program, U.S. Department of Energy, Human Genome News (v3n4).

Human Genome Project 1990–2003

The Human Genome Project (HGP) was an international 13-year effort, 1990 to 2003. Primary goals were to discover the complete set of human genes and make them accessible for further biological study, and determine the complete sequence of DNA bases in the human genome. See Timeline for more HGP history.

Human Genome News

Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.