Genome Informatics Meeting

National Human Genome Research Institute

National Institutes of Health
U.S. Department of Health and Human Services


Summary of Report on the DOE/NIH
Genome Informatics Meeting

Dulles Hilton Hotel
April 2-3, 1998
Meeting Purpose, Participants & Agenda

Summary

On April 2 and 3, the Department of Energy's Office of Biological and Environmental Research (DOE/OBER ) and the National Institutes of Health National Human Genome Research Institute (NIH/NHGRI) convened a workshop to identify informatics needs and goals that could be part of the next genome five-year plan and that would begin to craft a vision for genome informatics over the next five years and beyond. In attendance were 46 invited informatics and genomics experts, and six DOE, eight NHGRI, two National Institute of General Medical Sciences (NIGMS) and one National Science Foundation (NSF) staffers. The meeting was held at the Dulles Hilton in Herndon, VA.

Conclusions of the Meeting

Priorities:
  1. A reference genome map and sequence database. The sequence data should be assembled into continuous sequence, with links to the maps. The sequence should be annotated and the information should be structured so that all sorts of queries can be run on the database. The data should be updated and curated by sets of editors rather than by anybody who wishes to correct or annotate it.

  2. Integrated and linked databases

  3. Variation database - organized by individual genotype and haplotype and by population.
    The genetic variation database should include or link to information on individual phenotypic variation.

  4. Functional/expression database, including pathway/regulatory databases (e.g. WIT, KEGG, Eco Cyc).

  5. Comprehensive data capture - raw data and the summary or processed data should be captured in standard formats. The data should be well-structured using controlled vocabularies.

The breakout groups had been asked to address four sets of issues, and their conclusions on these and some other issues are summarized:

The workshop closed with some policy recommendations:

DOE/NIH Genome Informatics Meeting

Dulles Hilton Hotel
April 2-3, 1998

Purpose:

To discuss the types of queries that will be important in genome informatics, and what types of data, tools, and databases will be needed to address them. The emphasis is on setting priorities for current and future user needs. The results of this meeting will contribute to the five-year plan for the HGP that DOE and NIH are formulating. The results will also influence the agencies? plans for informatics projects and funding.

Questions to address in talks and breakout groups:

  1. Queries: What scientific questions will you want to answer? What types of data will you need to answer these questions? Which of these data types are permanent, which are temporary but important, and which will need to be regularly updated? What uses will you have for genomic sequence data in the next 5 years?

  2. Tools: What protocols and tools for data submission, viewing, analysis, annotation, curation, comparison, and manipulation will you need to make maximal use of the data? What sorts of links among datasets will be useful?

  3. Infrastructure: What critical infrastructures will be needed to support the queries you want to perform and what attributes should these infrastructures have? In what ways should they be flexible, and how should they stay current? How should they be maintained?

  4. Standards: What kind of community-agreed standards are needed, e.g. controlled vocabularies, datatypes, annotations, and structures? How should these be defined and established?

First afternoon breakout groups (the first name is the moderator):

Sequencing, mapping for sequencing, gene maps:

Raju Kucherlapati, LaDeana Hillier, Eric Green, David Lipman, Takashi Gojobori, Peter Schad, Elbert Branscomb, Ray Gesteland, David Smith, Peter Cartwright, Rainer Fuchs, Peter Weinberger

Gene finding, OMIM, variation:

Ken Buetow, David Nelson, Anne Spence, Jim Ostell, Aravinda Chakravarti, David Valle, Bob Cottingham, Bruce Weir, Deborah Nickerson, Chuck Langley, Stan Letovsky

Annotation, function:

Chris Overton, Roger Brent, Martin Ringwald, Joanna Amberger, Mark Boguski, Manfred Zorn, Ed Uberbacher, Temple Smith, Richard Mural, David Balaban, Dixon Butler, Barbara Wold, Randall Smith

Comparative genomics:

Carol Bult, Michael Cherry, Tony Kerlavage, Jean-Francois Tomb, Terry Gaasterland, Frederique Galisson, Reinhold Mann, Janan Eppig, Bill Gelbart, Katie Thompson, Paul Gilna

AGENDA

Thursday, April 2

9:00 am Aristides Patrinos, Associate Director, (unable to attend)
Office of Biological and Environmental Research, DOE
9:10 am Francis Collins, Director,
National Human Genome Research Institute, NIH
Moderator: Aravinda Chakravarti
9:20 am David Thomassen, DOE
9:30 am Aravinda Chakravarti, Chair of the NHGRI Planning Subcommittee
9:40 am LaDeana Hillier, Large-Scale Sequencing
10:00 am Takashi Gojobori, DNA Data Base of Japan
10:20 am Anne Spence, Medical Genetics
10:40 am Break
11:00 am Deborah Nickerson, Genetic Variation
11:20 am Roger Brent, Functional Genomics
11:40 am Rainer Fuchs, Industry
12:00 noon Bettie Graham, Training
12:10 pm Lunch
1:30 pm Breakout groups
5:00 pm Adjourn for day

Friday, April 3

Moderator: Aravinda Chakravarti
9:00 am Reports from the four breakout groups
11:00 am Break
11:20 am David Lipman, National Center for Biotechnology Information
11:40 am Ed Uberbacher, Annotation Consortium
12:00 noon Lunch
Moderators: Elbert Branscomb and Eric Green
1:15 pm Discussion of goals and priorities
2:30 pm Break
2:45 pm Continue discussion
4:00 pm Adjourn

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Last Reviewed: May 2006