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CellML2SBML: conversion of CellML into SBML.

Maria J Schilstra1, Lu Li, Joanne Matthews

  • 1Biological and Neural Computation Group, STRI, University of Hertfordshire, Hatfield AL10 9AB, UK. m.j.1.schilstra@herts.ac.uk

Bioinformatics (Oxford, England)
|February 14, 2006
PubMed
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CellML2SBML, a tool using XSLT stylesheets, converts CellML models to Systems Biology Markup Language (SBML) with high success rates. This facilitates the exchange of molecular and physiological models between different computational platforms.

Area of Science:

  • Computational biology
  • Bioinformatics
  • Systems biology

Background:

  • CellML and SBML are XML-based languages for exchanging biological models.
  • Both languages utilize similar MathML subsets for mathematical specifications.
  • Interoperability between these modeling languages is crucial for research.

Purpose of the Study:

  • To develop and evaluate a tool for converting CellML models to SBML.
  • To ensure minimal information loss during the conversion process.
  • To assess the efficiency and success rate of automated model conversion.

Main Methods:

  • Implementation of CellML2SBML as a suite of XSLT stylesheets.
  • Application of XSLT stylesheets to convert CellML version 1.1 models to SBML Level 2 Version 1.

Related Experiment Videos

  • Testing the converter on a repository of 306 CellML models.

    • Main Results:

    • CellML2SBML achieved 91% automatic conversion of CellML models to SBML.
    • Minor manual adjustments to unit definitions increased the success rate to 96%.
    • The conversion process maintained the integrity of the mathematical models.

    Conclusions:

    • CellML2SBML is an effective tool for converting CellML to SBML.
    • The tool significantly enhances interoperability between CellML and SBML modeling environments.
    • High success rates indicate the robustness of the conversion approach for physiological and molecular models.