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Interoperability between Bioinformatics Tools: A Logic Programming Approach

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Practical Aspects of Declarative Languages (PADL 2001)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1990))

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Abstract

The goal of this project is to develop solutions to enhance interoperability between bioinformatics applications. Most existing applications adopt different data formats, forcing biologists into tedious translation work. We propose to use of Nexus as an intermediate representation language. We develop a complete grammar for Nexus and we adopt this grammar to build a parser. The construction heavily relies on the peculiar features of Prolog, to easily derive effective parsing and translating procedures. We also develop a general parse tree format suitable for interconversion between Nexus andot her formats.

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Author information

Authors and Affiliations

  1. Dept. Computer Science, New Mexico State University, Mexico

    Juan R. Iglesias, Enrico Pontelli & Desh Ranjan

  2. Dept. of Biology, New Mexico State University, Mexico

    Brook Milligan

  3. Dept. of Computer Science, UT Dallas

    Gopal Gupta

Authors
  1. Juan R. Iglesias
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  2. Gopal Gupta
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  3. Enrico Pontelli
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  4. Desh Ranjan
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  5. Brook Milligan
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Editor information

Editors and Affiliations

  1. Department of Computer Science, State University of New York, Stony Brook, 11794, NY, USA

    I. V. Ramakrishnan

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© 2001 Springer-Verlag Berlin Heidelberg

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Iglesias, J.R., Gupta, G., Pontelli, E., Ranjan, D., Milligan, B. (2001). Interoperability between Bioinformatics Tools: A Logic Programming Approach. In: Ramakrishnan, I.V. (eds) Practical Aspects of Declarative Languages. PADL 2001. Lecture Notes in Computer Science, vol 1990. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45241-9_11

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  • DOI: https://doi.org/10.1007/3-540-45241-9_11

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-41768-2

  • Online ISBN: 978-3-540-45241-6

  • eBook Packages: Springer Book Archive

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