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

Lookup NU author(s): Dr Allyson Lister, Dr Matthew Pocock, Professor Anil Wipat



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 an OWL (Web Ontology Language) 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 single computationally amenable resource for model checking. Knowledge that was only accessible to humans is now explicitly and directly available for computational approaches. The integration of all structural knowledge for SBML models into a single resource creates a new style of model development and checking.

Publication metadata

Author(s): Lister A L, Pocock M, Wipat A

Publication type: Report

Publication status: Published

Series Title: School of Computing Science Technical Report Series

Year: 2007

Pages: 18

Print publication date: 01/08/2007

Source Publication Date: August 2007

Report Number: 1043

Institution: School of Computing Science, University of Newcastle upon Tyne

Place Published: Newcastle upon Tyne