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

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 model...

• Type: Journal
• Year: 2016
• Where: BIOINFORMATICS
• Authors: Goksel Misirli, Matteo Cavaliere, William Waites, Matthew R. Pocock, Curtis Madsen, Owen Gilfellon, Ricardo Honorato-Zimmer, Paolo Zuliani, Vincent Danos, Anil Wipat
• Keywords: BIOINFORMATICS 2016