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Paper detail

Annotations for Rule-Based Models

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 of molecular interactions, 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.

preprint2018arXivOpen access
Matteo CavaliereVincent DanosRicardo Honorato-ZimmerWilliam Waites
Molecular NetworksDigital Libraries
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Matteo CavaliereVincent DanosRicardo Honorato-ZimmerWilliam Waites

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