Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop

Abstract The fast accumulation of biological data calls for their integration, analysis and exploitation through more systematic approaches. The generation of novel, relevant hypotheses from this enormous quantity of data remains challenging. Logical models have long been used to answer a variety of...

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Published in:Briefings in bioinformatics 2021-03, Vol.22 (2), p.1848-1859
Main Authors: Niarakis, Anna, Kuiper, Martin, Ostaszewski, Marek, Malik Sheriff, Rahuman S, Casals-Casas, Cristina, Thieffry, Denis, Freeman, Tom C, Thomas, Paul, Touré, Vasundra, Noël, Vincent, Stoll, Gautier, Saez-Rodriguez, Julio, Naldi, Aurélien, Oshurko, Eugenia, Xenarios, Ioannis, Soliman, Sylvain, Chaouiya, Claudine, Helikar, Tomáš, Calzone, Laurence
Format: Article
Language:English
Subjects:
Annotations
Best practice
Bioaccumulation
Bioinformatics
Biology
Community involvement
Computer applications
Computer Science
Exploitation
Mathematical models
Method Review
Reproducibility
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Summary:Abstract The fast accumulation of biological data calls for their integration, analysis and exploitation through more systematic approaches. The generation of novel, relevant hypotheses from this enormous quantity of data remains challenging. Logical models have long been used to answer a variety of questions regarding the dynamical behaviours of regulatory networks. As the number of published logical models increases, there is a pressing need for systematic model annotation, referencing and curation in community-supported and standardised formats. This article summarises the key topics and future directions of a meeting entitled ‘Annotation and curation of computational models in biology’, organised as part of the 2019 [BC]2 conference. The purpose of the meeting was to develop and drive forward a plan towards the standardised annotation of logical models, review and connect various ongoing projects of experts from different communities involved in the modelling and annotation of molecular biological entities, interactions, pathways and models. This article defines a roadmap towards the annotation and curation of logical models, including milestones for best practices and minimum standard requirements.
ISSN:1477-4054
1467-5463
1477-4054
DOI:10.1093/bib/bbaa046