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Annotations for Rule-Based Models

  • Matteo Cavaliere
  • Vincent Danos
  • Ricardo Honorato-Zimmer
  • William WaitesEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1945)

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.

Key words

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

Notes

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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Matteo Cavaliere
    • 1
  • Vincent Danos
    • 2
    • 3
  • Ricardo Honorato-Zimmer
    • 4
  • William Waites
    • 3
    Email author
  1. 1.School of Computing, Mathematics and Digital TechnologyManchester Metropolitan UniversityManchesterUK
  2. 2.Centre national de la recherche scientifique, Departement d’InformatiqueÉcole normale supérieureParisFrance
  3. 3.Laboratory for Foundations of Computer Science, School of InformaticsUniversity of EdinburghEdinburghUK
  4. 4.Centro Interdisciplinario de Neurociencias de ValparaÚsoUniversidad de ValparaÚsoValparaÚsoChile

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