Project:

Model Format OWL (MFO): Integration of constraints facilitates validation of biological models


Project Leader(s): Allyson Lister, Prof. Anil Wipat

The creation of quantitative, simulatable, 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, 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 OWL knowledge base that integrates parts of these three structure documents.

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. (From DOI:10.2390/biecoll-jib-2007-80)

Staff

Dr Allyson Lister
Research Associate

Professor Anil Wipat
Prof of Integrative Bioinformatics