Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization
作者： Goksel Misirli , Matteo Cavaliere , William Waites , Matthew Pocock , Curtis Madsen
DOI: 10.1093/BIOINFORMATICS/BTV660
关键词:
摘要: Motivation: Biological systems are complex and challenging to model therefore reuse is highly desirable. To promote reuse, models should include both information about the specifics of simulations underlying biology in form metadata. The availability computationally tractable metadata especially important for effective automated interpretation processing models. Metadata typically represented as machine-readable annotations which enhance programmatic access Rule-based languages have emerged a modelling framework represent complexity biological systems. Annotation approaches been widely used reaction-based formalisms such SBML. However, rule-based still lack rich annotation add semantic information, descriptions, components model. Results: We present an guidelines annotating models, encoded commonly Kappa BioNetGen languages. adapt adopted initially propose syntax store describe mapping between entities, agents rules, their annotations. then ontology annotate these capture contained therein, demonstrate using examples. Finally, we proof concept tool extracting from that can be queried analyzed uniform way. representation facilitate creation, analysis, visualization Although examples given, specific implementations proposed techniques applied general.
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