Human Genome News, November 1991; 3(4)

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Human Genome News Archive Edition

GDB Proves Itself at HGM 11

The Genome Data Base (GDB) underwent a fitness test at the Eleventh International Workshop on Human Gene Mapping (HGM 11) and came through as a solid and reliable tool for the scientific community. The database got a vigorous workout during the week of the workshop, held August 16- 23 in London. "The word I kept hearing people use in relation to the database was `robust'," said Robert Robbins, Director of the Welch Medical Library Laboratory for Applied Research in Academic Information. "There was essentially zero downtime."

The success of the database demonstration at HGM 11, in fact, can be measured by the small amount of attention given to it by the 28 committee chairpersons and their cochairs. "No one was talking much about GDB," commented Chris Brunn, the Welch Laboratory's Assistant Director for Technical Development. "The software let the committees do their work of entering and verifying data without hindrance. That's what software is supposed to do. You shouldn't have to think about it."

Figures from the meeting also show how much the system was used; the database server logged more than 58,000 connections to GDB. During the peak hours of 8 a.m. to 8 p.m., an average of 50 people were using the system simultaneously; at one point, close to 100 users were noted.

Another indication of usage is the amount of data added to the database. More than 2000 new entries were made, including 504 mapped loci, 652 probes, and 196 polymorphisms.

Because the system performed well, GDB staff had time to gather information from the committee chairs about their needs in using the database. "We learned about new things they would like to do and things they would like to do more easily," Brunn stated.

Map Manager Module

"Mapping information represents the intellectual focus of the database," said Peter Pearson, GDB Scientific Director. He added that most of the database information, such as DNA marker descriptions and probe availability, primarily supports map construction and maintenance.

The DNA committee at HGM 11 urged that each chromosome committee construct at least one map giving the order of reference markers on its chromosome. To aid this construction at HGM 11, the GDB staff provided a working version of Map Manager, a new module.

GDB consultant Ken Fasman, whose job was to get Map Manager up and running, reports that this software is at a stage of growth comparable to that of GDB a year ago. Still in a preliminary form, Map Manager will be expanded over the next few months, according to Fasman, who expects module evolution to continue for quite some time. "New mapping methods are developed continuously," he said, "and Map Manager has to keep up with new developments."

HGM11 started with only a few maps in GDB, but during the workshop over 100 maps were entered and fully approved by the chromosome committees. As with other GDB information, an approval process is required: committee members verify the map and associate it with at least one source (i.e., one reference). After this is done, the map can be viewed by general users.

Shortening the Publication Cycle

As Robbins described it, the experience of GDB at HGM 11 illustrates a new application for scientific databases. In the past, investigators built databases by extracting and reproducing the findings of other investigators from the literature. Scientific databases that can themselves be a means of publication, and no longer merely derivative products, will be possible in the future, Robbins believes.

Many of the 700 HGM 11 participants presented posters, abstracts of which were published in the proceedings. After review by Human Gene Mapping Workshops committee members, information from these posters went into the database, with the abstract cited as the source. When the updated database tapes were installed at Hopkins shortly after HGM 11, the new findings were instantly made available to GDB users worldwide. In fact, students in Heidelberg used the updated data at a European Molecular Biology Laboratory practical course held the week following HGM 11 (see related article).

Future of HGM Workshops

HGM 11 could be the last comprehensive human genome workshop, according to meeting organizers; the logistics and tremendous expense of mounting such large workshops, with the extensive support facilities they require, make their continuation doubtful, particularly when different sites are used for each meeting. The future may lie, the organizers believe, in single-chromosome workshops, which are playing an increasingly important role in the review and achievement of consensus maps. As worldwide access to GDB improves, so does the feasibility of small workshops spread throughout the international community of geneticists.


Reported by GDB Staff

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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.