Annotations for Rule-Based Models.

Data Curation / methods Humans Internet Models, Biological Software
BNGL BioNetGen KaSim Kappa MIRIAM RDF Rule-Based Model Ontology (rbmo) Rule-based modelling SPARQL Turtle

Journal

Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969

Informations de publication

Date de publication:
2019
Historique:
entrez: 5 4 2019
pubmed: 5 4 2019
medline: 25 7 2019
Statut: ppublish

Résumé

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.

Identifiants

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

Types de publication

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

Langues

eng

Pagination

271-296

Auteurs

Matteo Cavaliere (M)

School of Computing, Mathematics and Digital Technology, Manchester Metropolitan University, Manchester, UK.

Vincent Danos (V)

Centre national de la recherche scientifique, Departement d'Informatique, École normale supérieure, Paris, France.
Laboratory for Foundations of Computer Science, School of Informatics, University of Edinburgh, Edinburgh, UK.

Ricardo Honorato-Zimmer (R)

Centro Interdisciplinario de Neurociencias de ValparaÚso, Universidad de ValparaÚso, ValparaÚso, Chile.

William Waites (W)

Laboratory for Foundations of Computer Science, School of Informatics, University of Edinburgh, Edinburgh, UK. wwaites@inf.ed.ac.uk.

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Curation de données › Annotations for Rule-Based Models.
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Annotations for Rule-Based Models.
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Systèmes informatiques › Réseaux de communication entre ordinateurs › Internet › Annotations for Rule-Based Models.
questionsmedicales.fr › Techniques d'investigation › Modèles théoriques › Modèles biologiques › Annotations for Rule-Based Models.
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › Annotations for Rule-Based Models.