Searls, D.B. (1988) "Representing Genetic Information with Formal
Grammars" in Proceedings of the 1988 National Conference of the
American Association for Artificial Intelligence, AAAI/Morgan
Kaufman, 7:386-391.
Genetic information, as expressed in the four-letter code of the DNA of
living organisms, represents a complex and richly expressive natural
knowledge representation system, capturing procedural information that
describes how to create and maintain life. The study of its semantics
(i.e., the field of molecular biology) has yielded a wealth of
information, but its syntax has been elaborated primarily at the lowest
lexical levels, without benefit of formal computational approaches that
might help to organize its description and analysis. This paper
discusses such an approach, using generative grammars to express the
information in DNA sequences in a declarative, hierarchical manner. A
prototype implemented in a Prolog-based Definite Clause Grammar system
is presented, which allows such declarative descriptions to be used
directly for analysis of genetic information by parsing DNA. Examples
are given of the utility of this method in the domain, and speedups and
extensions are also proposed.
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