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Prolog Meets Biology

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Prolog: The Next 50 Years

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 13900))

Abstract

This paper provides an overview of the use of Prolog and its derivatives to sustain research and development in the fields of bioinformatics and computational biology. A number of applications in this domain have been enabled by the declarative nature of Prolog and the combinatorial nature of the underlying problems. The paper provides a summary of some relevant applications as well as potential directions that the Prolog community can continue to pursue in this important domain. The presentation is organized in two parts: “small,” which explores studies in biological components and systems, and “large,” that discusses the use of Prolog to handle biomedical knowledge and data. A concrete encoding example is presented and the effective implementation in Prolog of a widely used approximated search technique, large neighborhood search, is presented.

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Acknowledgements

We thank the anonymous reviewers that allowed us to greatly improve the focus and the presentation of the paper. This research is partially supported by INdAM-GNCS projects CUP E55F22000270001 and CUP E53C22001930001, by Interdepartmental Project on AI (Strategic Plan UniUD-22-25), and by NSF grants 2151254 and 1914635.

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Authors and Affiliations

  1. University of Parma, Parma, Italy

    Alessandro Dal Palù

  2. University of Udine, 33100, Udine, Italy

    Agostino Dovier & Andrea Formisano

  3. New Mexico State University, Las Cruces, NM, USA

    Enrico Pontelli

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  1. Alessandro Dal Palù
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  2. Agostino Dovier
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  3. Andrea Formisano
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  4. Enrico Pontelli
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Correspondence to Agostino Dovier .

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Editors and Affiliations

  1. Stony Brook University, Stony Brook, NY, USA

    David S. Warren

  2. Simon Fraser University, Burnaby, BC, Canada

    Veronica Dahl

  3. TU Wien, Vienna, Austria

    Thomas Eiter

  4. Universidad Politecnica de Madrid/IMDEA Software Institute, Madrid, Spain

    Manuel V. Hermenegildo

  5. Imperial College London, London, UK

    Robert Kowalski

  6. IBM Research, Yorktown Heights, NY, USA

    Francesca Rossi

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Dal Palù, A., Dovier, A., Formisano, A., Pontelli, E. (2023). Prolog Meets Biology. In: Warren, D.S., Dahl, V., Eiter, T., Hermenegildo, M.V., Kowalski, R., Rossi, F. (eds) Prolog: The Next 50 Years. Lecture Notes in Computer Science(), vol 13900. Springer, Cham. https://doi.org/10.1007/978-3-031-35254-6_26

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