Open Access Software

Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

Samuel Kerrien1*, Sandra Orchard1, Luisa Montecchi-Palazzi1, Bruno Aranda1, Antony F Quinn1, Nisha Vinod1, Gary D Bader23, Ioannis Xenarios4, Jérôme Wojcik4, David Sherman5, Mike Tyers3, John J Salama6, Susan Moore67, Arnaud Ceol8, Andrew Chatr-aryamontri8, Matthias Oesterheld9, Volker Stümpflen9, Lukasz Salwinski10, Jason Nerothin10, Ethan Cerami11, Michael E Cusick12, Marc Vidal12, Michael Gilson13, John Armstrong14, Peter Woollard14, Christopher Hogue15, David Eisenberg10, Gianni Cesareni8, Rolf Apweiler1 and Henning Hermjakob1

Author Affiliations

1 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

2 Banting & Best Department of Medical Research and Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada

3 Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada

4 Merck Serono, 9 chemin des Mines, 1211 Geneva, Switzerland

5 Laboratoire Bordelais de Recherche en Informatique, ENSI Électronique, Informatique et Radiocomm. de Bordeaux, France

6 The Blueprint Initiative of Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada

7 National University of Singapore, Office of Life Sciences (OLS), Centre for Life Sciences, Singapore

8 Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy

9 Institute for Bioinformatics, GSF – National Research Center for Environment and Health, Neuherberg, Germany

10 UCLA-DOE Institute for Genomics & Proteomics, UCLA, LA, USA

11 Computational Biology Center, Memorial Sloan-Kettering Cancer Center 1275 York Avenue, Box 460, New York, NY, USA

12 Center for Cancer Systems Biology (CCSB) and Department of Cancer, Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA, USA

13 Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MD, USA

14 Glaxo Smithkline Medicines Research Centre, Gunnels Wood Road, Stevenage, Herts, UK

15 Dept. of Biochemistry, University of Toronto, Toronto, Ontario, Canada

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BMC Biology 2007, 5:44  doi:10.1186/1741-7007-5-44

Published: 9 October 2007



Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions.


The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration.


The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel.