Relay-Version: version B 2.10 5/3/83; site utzoo.UUCP Path: utzoo!utgpu!water!watmath!clyde!rutgers!husc6!cmcl2!beta!dd From: dd@beta.UUCP Newsgroups: sci.bio Subject: Introduction to the Matrix of Biological Knowledge Message-ID: <10874@beta.UUCP> Date: Sat, 3-Oct-87 18:28:18 EDT Article-I.D.: beta.10874 Posted: Sat Oct 3 18:28:18 1987 Date-Received: Sun, 4-Oct-87 06:52:16 EDT Organization: Los Alamos Natl Lab, Los Alamos, N.M. Lines: 119 Keywords: information retrieval, databases, artificial intelligence Introduction to the Matrix of Biological Knowledge Bulletin Board The BIO-MATRIX bulletin board is designed to continue the work begun at the Matrix of Biological Knowlede Workshop, held at St. John's College in Santa Fe, N.M July 13- August 14, 1987. The meeting has become known as "Camp Matrix". The following text is excerpted and rearranged from the Preliminary Report of the workshop. Other texts are anticipated, especially a "Primer on Matrix Biology", which will go into some detail about the Matrix concept and its realization from the biological, computer science, information retrieval, structural chemistry, and other viewpoints. We expect that chapters of the Primer will be available via e-mail or FTP but those arrangements have not yet been made. This text was written by Harold Morowitz, the guiding light of the conference. It was adapted by Dan Davison; any textual errors are strictly due to my transcription. =================================================================== Current understanding of biology is rooted in complex relationships involving enormous amounts of data. Few scientists are currently able to keep up with the enormous increase in knowledge, let alone able to search it efficently for new or unsuspected links and important analogies. Yet, this is what is required, if the continued and rapid generation of such data is to lead to major conceptual, medical, and agricultural advances anticipated over the next decades in the United States. As noted in the earlier "Models for Biomedical Research: A New Perspective" : We seem to be at a point in the history of biology where new generalizations and higher order biological laws are being approached but may be obscured by the simple mass of data. The organization of all biological experimental data coordinately within a structure incorporating our current understanding--the Matrix of Biological Knowledge--will provide the data and structure for the major advances forseen in the years ahead. In 1985 the report "Models for Biomedical Research: A New Perspective" was issued by the National Academy of Sciences Press, reporting on the work of a committee convened under the sponsorship of the National Institutes of Health. The committee conducted, over a period of two years, a series of workshops in which leading scientists from six different areas reported on the use of "models" in their areas of specialities. On the basis of these reports, the committee concluded that modeling in contemporary biology consists of: 1) decomposing a problem into its component parts, 2) searching across the vast range of biological information for linked or analogous behaviors and structures, and 3) then applying the material found to our understanding of the original problem. Where more experiments and/or theoretical analyses are required, this becomes the familiar loop. Results from the model system are fed back to the original problem. In considering the vast and highly interdisciplinary nature of biological information and the importance of accessing that information, the models committee began to focus on a concept which became known as "The Matrix of Biological Information" or "The Matrix of Biological Knowledge", and defined as: The complete database of published experiments, structured by the laws, empirical generalizations, and physical foundations of biology and connected by all the interspecific transfers of information. Subsequent to the original study, a distinction has been drawn between the Matrix of Biological Information and the Matrix of Biological Knowledge. The first is defined as the complete data base of published biological experimental data, and the latter is expanded to include the empirical generalizations, interconnections, laws, and models that are used to structure the primary data. The Matrix of Biological Knowledge thus includes the analysis of biological data as well as the data. The Matrix concept does not represent a radical departure from the conceptual approaches of many working biologists. Insightful life scientists have always scanned the horizon of biolgical information for analogies and new generalizations. What is new is the current size, complexity, and rate of expansion of this information, which makes the unaided and unstructured search virtually an impossibility. This suggested to the models committee the following: The development of the matrix and the extraction of biological generalizations from it are going to require a new kind of scientist, a person familiar enough with the subject being studied to read the literature critically, yet expert enough in information science to be innovative in develop- ing methods of classification and search. This implied the development of a new kind of theory geared explicitly to biology with it particular theory structure. It will be tied to the use of computers, will be required to eal with the vast amount and complexity of information.... Finally, the models report recommended: "the matrix of biological knowledge should be further investigated as a potential tool in biomedical research under the aegis of the NIH. The concept must be sharpened and tested as to its utility" ===================================================================== The Matrix bulletin board is available on the Arpanet/CSNET and BITNET: requests to be on the mailing list can be sent to BIO-MATRIX-REQUEST@ BIONET-20.ARPA. For those on BITNET, use the MAIL program and address your note to BIO-MATRIX-REQUEST%BIONET-20.ARPA@WISCVM.BITNET. The bulletin board is also available on USENET as bionet.bio-matrix. Contact your site manager for information about its availability. Submissions and questions about the Matrix concept can be sent to BIO-MATRIX@BIONET-20.ARPA or BIO-MATRIX%BIONET-20.ARPA@WISCVM.BITNET. Notes addressed to this address will be seen by all the Matrix participants. At present there is no way to get e-mail from USENET to BIO-MATRIX, but notes can be sent to ...cmcl2!lanl!dd (old style) or dd@lanl.uucp (new style). Dan Davison/ BIO-MATRIX editor/ bio-matrix-request@bionet-20.arpa