From: davison@menudo.uh.edu (Dan Davison)
Newsgroups: bionet.molbio.bio-matrix
Subject: The Biomatrix: Another view
Date: 3 Jan 1993 19:25:33 GMT
Organization: University of Houston
Distribution: bionet
NNTP-Posting-Host: menudo.uh.edu


[This note is from Peter Karp, pkarp@ai.sri.com, in response to my
posting on what the Biomatrix is from a biologist's point of view -
dbd] 

I thought I would stimulate discussion on this list a bit by offering
an alternative view to Dan Davison's regular postings that describe
what the Biomatrix is.  This message summarizes my own view.

The Biomatrix is several things: 

The Biomatrix exists at this moment as the set of all data bases and
knowledge bases that encode biological information, and as the
collection of existing computer programs that manipulate this
information.  Databases such as MedLine, PIR, GENBANK, and SwissProt
constitute the present-day Biomatrix.

The Biomatrix embodies a vision of how biologists of the future
will carry out their work.  To a much larger degree than today, the
biological knowledge and data of the future will reside in computer
systems, and the biologist of the future will employ computer tools to
access this information.  All forms of biological information will be
encoded electronically, including traditional forms such as laboratory
data, reference works, journal publications, and texts.  New forms of
biological information will emerge in the future Biomatrix.  The
Biomatrix will constitute a substrate for electronic communication
among scientists.  Knowledge-based systems technology will encode
biological knowledge, laws, and theories in more active forms that can
be used for tasks such as simulation, experiment planning, teaching,
and analogical reasoning.  Information repositories will be linked
together over high-speed networks so that although they will be
distributed geographically, they will be instantly available to
researchers around the globe.

The effect of the future Biomatrix will be to increase the
availability of biological information to people and machines.  The
biologist of the future will have access to information in greater
quantities and at greater speeds than today.  One result of this
organization will be to facilitate reasoning by analogy, whereby a
biologist will bring information about a distant biological system to
bear on his or her problem of interest.  A second result will be that
as these electronic repositories grow in size, they will be more and
more difficult for people to comprehend, so biologists will employ
machine learning programs of various sorts as assistants that will aid
biologists in discovering new regularities in the information stored
in these repositories.

Finally, the Biomatrix is a community of biologists and computer
scientists who share this common goal.  Many aspects of the Biomatrix
of the future are unattainable without fundamental advances in
computer science (such as networking, databases, knowledge
representation, algorithms, machine learning, and neural networks)
that will be achieved from collaborations between researchers in these
fields.


--
dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77204-5934/davison@uh.edu/DAVISON@UHOU

-----RIP Isaac Asimov 1920-1992     I'll miss him --------------------

Disclaimer: As always, I speak only for myself, and, usually, only to
myself.