Logical knowledge representation of regulatory relations in biomedical pathways

Authors:
Sine Zambach;Jens Ulrik Hansen
Affiliations:
Computer Science, Roskilde University, Roskilde, Denmark;Computer Science, Roskilde University, Roskilde, Denmark and Philosophy, Roskilde University, Roskilde, Denmark
Venue:
ITBAM'10 Proceedings of the First international conference on Information technology in bio- and medical informatics
Year:
2010

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Abstract

Knowledge on regulatory relations, in for example regulatory pathways in biology, is used widely in experiment design by biomedical researchers and in systems biology. The knowledge has typically either been represented through simple graphs or through very expressive differential equation simulations of smaller sections of a pathway. As an alternative, in this work we suggest a knowledge representation of the most basic relations in regulatory processes regulates, positively regulates and negatively regulates in logics based on a semantic analysis. We discuss the usage of these relations in biology and in artificial intelligence for hypothesis development in drug discovery.