Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualisation

Autor: Owen Gilfellon, Curtis Madsen, Goksel Misirli, Matteo Cavaliere, Paolo Zuliani, Anil Wipat, Matthew Pocock, Vincent Danos, William Waites, Ricardo Honorato-Zimmer
Přispěvatelé: School of Computing Science [Newcastle], Newcastle University [Newcastle], School of Informatics [Edimbourg], University of Edinburgh, Analyse Statique par Interprétation Abstraite (ANTIQUE), Département d'informatique - ENS Paris (DI-ENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Paris-Rocquencourt, Institut National de Recherche en Informatique et en Automatique (Inria), Département d'informatique de l'École normale supérieure (DI-ENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Inria Paris-Rocquencourt, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)
Jazyk: angličtina
Rok vydání: 2015
Předmět:
Zdroj: Bioinformatics
Bioinformatics, 2015, ⟨10.1093/bioinformatics/btv660⟩
Bioinformatics, Oxford University Press (OUP), 2015, ⟨10.1093/bioinformatics/btv660⟩
Bioinformatics, Oxford University Press (OUP), 2016, 32 (6), pp.908-917. ⟨10.1093/bioinformatics/btv660⟩
Bioinformatics, 2016, 32 (6), pp.908-917. ⟨10.1093/bioinformatics/btv660⟩
Misirli, G, Cavaliere, M, Waites, W, Pocock, M, Madsen, C, Gilfellon, O, Honorato Zimmer, R, Zuliani, P, Danos, V & Wipat, A 2016, ' Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualisation ', Bioinformatics, vol. 32, no. 6, pp. 908-917 . https://doi.org/10.1093/bioinformatics/btv660
ISSN: 1367-4803
1367-4811
DOI: 10.1093/bioinformatics/btv660⟩
Popis: International audience; Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualisation. Bioinformatics 2015, ABSTRACT Motivation: Biological systems are complex and challenging to model and therefore model reuse is highly desirable. To promote model reuse, models should include both information about the specifics of simulations and the underlying biology in the form of metadata. The availability of computationally-tractable metadata is especially important for the effective automated interpretation and processing of models. Metadata are typically represented as machine-readable annotations which enhance programmatic access to information about models. Rule-based languages have emerged as a modelling framework to represent the complexity of biological systems. Annotation approaches have been widely used for reaction-based formalisms such as SBML. However, rule-based languages still lack a rich annotation framework to add semantic information, such as machine-readable descriptions, to the components of a model. Results: We present an annotation framework and guidelines for annotating rule-based models, encoded in the commonly used Kappa and BioNetGen languages. We adapt widely adopted annotation approaches to rule-based models. We initially propose a syntax to store machine-readable annotations and describe a mapping between rule-based modelling entities, such as agents and rules, and their annotations. We then describe an ontology to both annotate these models and capture the information contained therein, and demonstrate annotating these models using examples. Finally, we present a proof of concept tool for extracting annotations from a model that can be queried and analyzed in a uniform way. The uniform representation of the annotations can be used to facilitate the creation, analysis, reuse and visualisation of rule-based models. Although examples are given, using specific implementations the proposed techniques can be applied to rule-based models in general. Availability and implementation: The annotation ontology for rule-based models can be found at http://purl.org/rbm/rbmo. The * contributed equally † developed krdf ‡ to whom correspondence should be addressed krdf tool and associated executable examples are available at http://purl.org/rbm/rbmo/krdf. Contact: anil.wipat@newcastle.ac.uk, vdanos@inf.ed.ac.uk
Databáze: OpenAIRE
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