Representing, storing and accessing molecular interaction data: a review of models and tools

Brief Bioinform. 2006 Dec;7(4):331-8. doi: 10.1093/bib/bbl039.


One important aim within systems biology is to integrate disparate pieces of information, leading to discovery of higher-level knowledge about important functionality within living organisms. This makes standards for representation of data and technology for exchange and integration of data important key points for development within the area. In this article, we focus on the recent developments within the field. We compare the recent updates to the three standard representations for exchange of data SBML, PSI MI and BioPAX. In addition, we give an overview of available tools for these three standards and a discussion on how these developments support possibilities for data exchange and integration.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Computational Biology
  • Computer Simulation*
  • Data Collection / methods
  • Data Interpretation, Statistical
  • Database Management Systems / standards*
  • Metabolic Networks and Pathways
  • Models, Biological*
  • Programming Languages
  • Proteomics / methods*
  • Software
  • Systems Biology*