Talk at St anford Medical Informatics group. Special relevance: the speaker is
an SRI guy, in the AI Lab.
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Colloquium
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Title: Knowledge-Based Modeling of the E. coli Metabolic Network
Speaker: Peter Karp
Bioinformatics Research Group
SRI International
Date: November 9, 2000
Time: 12:15 PM to 1:15 PM
Location: Lee B. Lusted Library (MSOB
Conference Room x275)
Abstract:
A knowledge-based model of an organism consists of a set of static facts about
the molecular components of the organism, plus a set of rules of inference for
deriving new relationships that are implicit in those static facts. If we
consider a genome database to be a knowledge-based model, some key questions
about that genome database are: What range of static facts can the database
encode? And what new relationships can it infer?
The ontology (schema) of the Pathway Tools software can encode a wide variety
of information about the genes, gene products, metabolic pathways,
transporters, and genetic-regulatory circuitry of an organism. For example,
the EcoCyc DB describes the full genome and metabolic-pathway complement of E.
coli, as well as many of its transporters and operons.
The ontology of a genome database is of central importance because a poorly
designed ontology will distort the information that the database encodes. The
Pathway Tools software can infer a wide variety of relationships regarding the
genome and the biochemical network of the organism that are implicit in the
static facts within a Pathway Tools database. Each rule of inference is in a
sense a predefined database query that infers a biological relationship of
interest.
We present a connectivity analysis of the E. coli metabolic network that
consists of statistics on many of these inferred relationships.
The schedule for all future talks sponsored by Stanford Medical Informatics may
be found on the World Wide Web at URL <http://www-smi.stanford.edu/events/>.
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