Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News Archive Edition
Ken Fasman (GDB) discussed the federated approach being used to guide improvements in the next release of GDB (V6.0). A new focus is an improved representation of physical and genetic maps in the Genome Data Base; the database core will tightly couple maps, map objects, and mapping reagents. The new version allows direct user submissions, updates, and third-party data annotations and will be organized on a revised editorial model that differentiates between original and consensus data. GDB V6.0 is implementing an object-oriented data model on top of a Sybase relational database using the Object Protocol Model tools developed by Victor Markowitz and his group at LBL.
V6.0 will feature increased modularity of both applications and databases, replacing the current monolithic structure with a þminifederationþ of separate databases. The key component is object-broker technology, which enables interconnections to databases such as OMIM and eventually will extend across GDB, GSDB, and other public and genome center databases.
Fasman noted the increasing importance of WWW for federated modular databases, observing that GDB has developed an extensive WWW interface. He strongly encouraged researchers to explore the Web and obtain Mosaic or other clients for accessing GDB data.
A. Jamie Cuticchia (GDB) explained GDB data acquisition and curation. GDB acquires data by paper and electronic submissions and literature scanning; scanning is being phased out as GDB moves toward more community submission and editing. Cuticchia emphasized the responsibility of researchers to submit their data promptly and of databases to facilitate submission preparation. Data is curated by Human Genome Organisation chromosome-mapping editors, who approve and produce consensus marker localizations and maps for each chromosome (GDB V6.0 will display both raw and consensus data). [GDB (http://www.gdb.org).]
Manfred Zorn (LBL) described SubmitData, a tool that allows researchers to create valid database submissions by merging their own data with a defined template. SubmitData is now available for GSDB submissions, and a GDB version will be ready soon. Future improvements will add a more-complex set of variables, a WWW server to make Mosaic a user interface, and integration with data-analysis tools such as GRAIL.
2013 post-production note: GDB (Wikipedia) is no longer operational. See http://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml
The electronic form of the newsletter may be cited in the following style:
Human Genome Program, U.S. Department of Energy, Human Genome News (v6n5).
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.
Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.