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Annotations for Rule-Based Models

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Modeling Biomolecular Site Dynamics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1945))

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Abstract

The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated guidelines for annotating rule-based models, encoded in the commonly used Kappa and BioNetGen languages, and present prototypes that can be used to extract and query the annotations. An ontology is used to annotate models and facilitate their description.

All authors contributed equally.

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Acknowledgements

The Engineering and Physical Sciences Research Council grant EP/J02175X/1 (to V.D. and M.C.), the European Union’s Seventh Framework Programme for research, technological development and demonstration grant 320823 RULE (to W.W., R.H-Z, V.D.).

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Author notes

    Authors and Affiliations

    1. School of Computing, Mathematics and Digital Technology, Manchester Metropolitan University, Manchester, UK

      Matteo Cavaliere

    2. Centre national de la recherche scientifique, Departement d’Informatique, École normale supérieure, Paris, France

      Vincent Danos

    3. Laboratory for Foundations of Computer Science, School of Informatics, University of Edinburgh, Edinburgh, UK

      Vincent Danos & William Waites

    4. Centro Interdisciplinario de Neurociencias de ValparaÚso, Universidad de ValparaÚso, ValparaÚso, Chile

      Ricardo Honorato-Zimmer

    Authors
    1. Matteo Cavaliere
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    2. Vincent Danos
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    3. Ricardo Honorato-Zimmer
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    4. William Waites
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    Corresponding author

    Correspondence to William Waites .

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    Editors and Affiliations

    1. Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA

      William S. Hlavacek

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    Cavaliere, M., Danos, V., Honorato-Zimmer, R., Waites, W. (2019). Annotations for Rule-Based Models. In: Hlavacek, W. (eds) Modeling Biomolecular Site Dynamics. Methods in Molecular Biology, vol 1945. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9102-0_13

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    • DOI: https://doi.org/10.1007/978-1-4939-9102-0_13

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    • Publisher Name: Humana Press, New York, NY

    • Print ISBN: 978-1-4939-9100-6

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