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

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

Research output: Chapter in Book/Report/Conference proceeding › Chapter

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.

Original language	English
Title of host publication	Modeling Biomolecular Site Dynamics: Methods and Protocols
Editors	William S. Hlavacek
Place of Publication	New York, NY
Publisher	Humana Press
Pages	271-296
Number of pages	26
ISBN (Electronic)	978-1-4939-9102-0
ISBN (Print)	978-1-4939-9100-6
DOIs	https://doi.org/10.1007/978-1-4939-9102-0_13
Publication status	Published - 2019

Publication series

Name	Methods in Molecular Biology
Publisher	Humana Press, New York, NY
Volume	1945
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Access to Document

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

https://link.springer.com/protocol/10.1007/978-1-4939-9102-0_13

1 Finished

RULE
Danos, V. & Plotkin, G.
EU government bodies
1/02/13 → 31/01/18
Project: Research

1 Doctoral Thesis

Modelling and Measurement in Synthetic Biology
Waites, W., 2020
Research output: Thesis › Doctoral Thesis

File

Cite this

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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.",

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AB - 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.

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Annotations for Rule-Based Models

Abstract

Publication series

Access to Document

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Projects

RULE

Research output

Modelling and Measurement in Synthetic Biology

Cite this