Annotations for Rule-Based Models

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

doi:10.1007/978-1-4939-9102-0_13

Annotations for Rule-Based Models

Methods Mol Biol. 2019:1945:271-296. doi: 10.1007/978-1-4939-9102-0_13.

Authors

Matteo Cavaliere¹, Vincent Danos^{2

3}, Ricardo Honorato-Zimmer⁴, William Waites⁵

Affiliations

¹ School of Computing, Mathematics and Digital Technology, Manchester Metropolitan University, Manchester, UK.
² Centre national de la recherche scientifique, Departement d'Informatique, École normale supérieure, Paris, France.
³ Laboratory for Foundations of Computer Science, School of Informatics, University of Edinburgh, Edinburgh, UK.
⁴ Centro Interdisciplinario de Neurociencias de ValparaÚso, Universidad de ValparaÚso, ValparaÚso, Chile.
⁵ Laboratory for Foundations of Computer Science, School of Informatics, University of Edinburgh, Edinburgh, UK. wwaites@inf.ed.ac.uk.

PMID: 30945252
DOI: 10.1007/978-1-4939-9102-0_13

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.

Keywords: BNGL; BioNetGen; KaSim; Kappa; MIRIAM; RDF; Rule-Based Model Ontology (rbmo); Rule-based modelling; SPARQL; Turtle.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Data Curation / methods*
Humans
Internet
Models, Biological*
Software*