Experiences using logic programming in bioinformatics

Abstract

Reverse engineering complex biological systems requires the integration of multiple different databases using detailed background knowledge. Logic programming can provide a means of both performing integrative queries and rule-based inference to account for implicit knowledge. The Biological Logic Programming toolkit (Blipkit) was developed as a means of doing this kind of data integration. Implemented in SWI-Prolog, Blipkit has models of different aspects of life sciences data, including genes and gene sequences, RNA structures, evolutionary relationships, phenotypes and biological interactions. These can be combined to answer complex questions spanning multiple datasources. Blipkit also has means of integrating with and combining life sciences databases and ontologies. © 2009 Springer Berlin Heidelberg.