HUNTER@HUNTERMAC.NLM.NIH.GOV (Larry Hunter) (04/11/89)
During the Bio-matrix summer program two years ago, there was a substantial amount of work done on representation, particularly on representation of enzyme function. I recall seeing a collection of terms (e.g. binds, catalyzes, etc.) objects (e.g. substrate, recombinase) and qualifiers (e.g. increases, decreases) mentioned briefly in the final report from the workshop. I would like to get in touch with whoever did that work, or with anyone else who has been working on this crucial problem. Also, I would be interested in finding anything written about the representational work done at the workshop or other work on representations for biological or biochemical function. I think this is a topic of general interest, so responses can be sent either directly to the bboard, or email to me and I will summarize. I'm trying to be complete in my coverage, so I'd appreciate even a brief response from anyone with any interest or knowledge of any work on the topic. Thank you very much. Larry Hunter Lister Hill Center National Library of Medicine 8600 Rockville Pike Bethesda, MD 20894 (301) 496-9300 hunter@mcs.nlm.nih.gov
RICKL@AI.AI.MIT.EDU (Richard H. Lathrop) (04/14/89)
Date: Tue, 11 Apr 89 08:57:02 ADT
From: Larry Hunter <HUNTER@huntermac.nlm.nih.gov>
During the Bio-matrix summer program two years ago, there was a substantial
amount of work done on representation, particularly on representation of enzyme
function. I recall seeing a collection of terms (e.g. binds, catalyzes, etc.)
objects (e.g. substrate, recombinase) and qualifiers (e.g. increases,
decreases) mentioned briefly in the final report from the workshop. I would
like to get in touch with whoever did that work, or with anyone else who has
been working on this crucial problem. Also, I would be interested in finding
anything written about the representational work done at the workshop or other
work on representations for biological or biochemical function.
I think this is a topic of general interest, so responses can be sent either
directly to the bboard, or email to me and I will summarize. I'm trying to be
complete in my coverage, so I'd appreciate even a brief response from anyone
with any interest or knowledge of any work on the topic. Thank you very much.
Larry Hunter
Lister Hill Center
National Library of Medicine
8600 Rockville Pike
Bethesda, MD 20894
(301) 496-9300
hunter@mcs.nlm.nih.gov
This is definitely a crucial topic of general interest and I urge you to
post your findings to this net.
Several groups at the Matrix of Biological Knowledge Workshop touched on
macromolecular representations in one way or another. A number of the
individuals have subsequently continued in related endeavors, and I urge
them to respond as well.
Where available, I have tried to include ``best guesses'' as to
institution and email address, but these change with time and
circumstance, and several will be unavoidably out-of-date. Contact Dan
Davison via the Matrix archive-server MATRIX-LIST for more current
information about specific people.
Reprinted from Dan Davison's MATRIX-LIST announcement:
* Reminder: if you haven't sent in a listing for the MATRIX-LIST,
please do. If you indicate, the listing will be placed on the
archive-server. The idea of the MATRIX-LIST is to have a directory of
people interested in bio-informatics, and to allow people with a
problem to contact other Matrixers (Matrixen?) that are willing to
help. If you need a form send the line
send matrix matrix-form
to the archive-server. If you would like to get the MATRIX-LIST, send
the line
send matrix matrix-list
to the archive-server.
Only groups that explicitly concentrated on some area of macromolecular
structure or function are listed below. Refer to the full Report of the
Matrix of Biological Knowledge Workshop report for more complete
coverage (available in hard-copy from Ginger Richardson, Santa Fe
Institute, 1120 Canyon Road, Santa Fe, NM 87501, USA, telephone at (505)
984-8800; or on-line from Dan Davison through the Matrix archive-server:
Dan Davison Bio-Matrix Project Communications dd@lanl.gov (internet),
dd%lanl.gov@CUNYVM (BITNET), ...cmcl2!lanl!dd (uucp old style),
dd@lanl.UUCP (new style) (*)
(*) these mail addresses will change as of 1 September 1989 to
davison@uh.edu (internet), davison@UHOU (bitnet), and the physical mail
address to Department of Biochemical and Biophysical Sciences,
University of Houston, 4800 Calhoun, Houston, Tx 77204-5500 USA.).
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The titles refer to group reports from the Report of the Matrix of
Biological Knowledge Workshop. Only groups that explicitly concentrated
on some area of macromolecular structure or function are listed.
(a) The Metabolic Map Group.
``The task of creating a computer model of the metabolic map... to
explore the feasibility of a database of metabolism and to consider the
possible uses of such a database.''
Chris Beecher, U. Illinois at Chicago (beecher@vicbal)
Bob Bolender, U. Washington at Seattle (BOLENDER@biostr.biostr.washington.edu)
Gerald Cohen
Dan Davison, Los Alamos Natl. Labs (dd@lanl.gov and see above)
(as of 1 September 1989 U. Houston,
davison@uh.edu (internet), davison@UHOU (bitnet))
Anthony Gawienowski, U. of Massachusetts
Bob Goldstein, U. British Columbia
Robert MacElroy, NASA Ames Research Center
Anthony Nichols, Florida State U.
Robert Rubin, Johns Hopkins U.
Teresa Strezelecka, Florida State U.
Ed Weinberger, U. of Pennsylvania
additionally, Chris Beecher, Dan Davison, and Ed Weinberger
reported On the Feasibility of Endowing a Metabolic Database
with Simulation Capabilities.
(b) The Metabolic Knowledge Base Group.
``Central to the Matrix concept is the task of structuring biological
knowledge.... identifying the issues involved in such a task and
studying methods for addressing those issues.''
Michael Brent, MIT Artificial Intelligence Lab (michael@wheaties.ai.mit.edu)
Peter Karp, Stanford Knowledge Systems Lab (KARP@SUMEX-AIM.Stanford.EDU)
Kimberle Koile, UNISYS/Paoli Research Center (kkoile@bigburd.prc.unisys.com)
Chris Overton, UNISYS/Paoli Research Center (overt@bigburd.prc.unisys.com)
(c) Machine Learning, Dynamic Programming, and Macromolecules.
``....We envision a data base which will also have the ability to retrieve
by similarity and determine the species a particular molecule comes from.''
Dan Davison, Los Alamos Natl.Labs (now U. Houston)
Jotun Hein, U. of Southern California
Aleksandar Milosavljevic, U. Cal. Santa Cruz
(d) The Peptide Group.
``Function extracted from peptide abstracts.''
Mira Marcus, U. Tel Aviv (t76@taunivm.bitnet)
Bruce Schatz, Bell Communications Research (schatz@bellcore.com)
Rick Lathrop, MIT Artificial Intelligence Lab (rickl@wheaties.ai.mit.edu)
James Willett, NIH (willett@vax2.nlm.nih.gov)
Derek Le Roith, NIH
(e) Macromolecular Modeling Group
``....a number of barriers preventing the incorporation of macromolecular
structure into the framework of the matrix of biological knowledge. We make
... an attempt to bridge some of these barriers.''
Donald Allison, U. of North Alabama
Ann Barber, NCI (barber@ncifcrf.gov)
David Case, Scripps Clinic
Dan Diaz, Albert Einstein College of Medicine
Richard Dickerson, U. Cal. Los Angeles
Jotun Hein, U. of Southern California
Peter Kollman, U. Cal. San Francisco
(f) Growth Factor Group
``....to test the practicality of extracting data from large sets of
abstracts, and loading them into small relational databases....''
Hans Bode, U. Cal. Irvine
Dick Campbell, U. Cal. Irvine
Randy Smith, MBCRR, Harvard School of Public Health (rsmith@mbcrr.harvard.edu)
Pat Williams, City of London Polytechnic