Annotations for Rule-Based Models

Matteo Cavaliere, Vincent Danos, Ricardo Honorato-Zimmer, William Waites

Research output: Chapter in Book/Report/Conference proceedingChapter


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.
Original languageEnglish
Title of host publicationModeling Biomolecular Site Dynamics: Methods and Protocols
EditorsWilliam S. Hlavacek
Place of PublicationNew York, NY
PublisherHumana Press
Number of pages26
ISBN (Electronic)978-1-4939-9102-0
ISBN (Print)978-1-4939-9100-6
Publication statusPublished - 2019

Publication series

NameMethods in Molecular Biology
PublisherHumana Press, New York, NY
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


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