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2007

Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models

11 years 11 months ago
Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models
The creation of quantitative, simulatable, Systems Biology Markup Language (SBML) models that accurately simulate the system under study is a time-intensive manual process that requires careful checking. Currently, the rules and constraints of model creation, curation, and annotation are distributed over at least three separate documents: the SBML schema document (XSD), the Systems Biology Ontology (SBO), and the “Structures and Facilities for Model Definition” document. The latter document contains the richest set of constraints on models, and yet it is not amenable to computational processing. We have developed a Web Ontology Language (OWL) knowledge base that integrates these three structure documents, and that contains a representative sample of the information contained within them. This Model Format OWL (MFO) performs both structural and constraint integration and can be reasoned over and validated. SBML Models are represented as individuals of OWL classes, resulting in a si...
Allyson L. Lister, Matthew R. Pocock, Anil Wipat
Added 15 Dec 2010
Updated 15 Dec 2010
Type Journal
Year 2007
Where JIB
Authors Allyson L. Lister, Matthew R. Pocock, Anil Wipat
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