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Experiences Using Logic Programming in Bioinformatics

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Logic Programming (ICLP 2009)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 5649))

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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.

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Authors
  1. Chris Mungall
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Editor information

Editors and Affiliations

  1. School of Computing, University of Leeds, LS2 9JT, Leeds, UK

    Patricia M. Hill

  2. Deptartment of Computer Science, Stony Brook University, 11794-4400, Stony Brook, NY, USA

    David S. Warren

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© 2009 Springer-Verlag Berlin Heidelberg

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Mungall, C. (2009). Experiences Using Logic Programming in Bioinformatics. In: Hill, P.M., Warren, D.S. (eds) Logic Programming. ICLP 2009. Lecture Notes in Computer Science, vol 5649. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02846-5_1

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  • DOI: https://doi.org/10.1007/978-3-642-02846-5_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-02845-8

  • Online ISBN: 978-3-642-02846-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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