Perspective abstract


Nature Biotechnology 23, 1509 - 1515 (2005)
Published online: 6 December 2005 | doi:10.1038/nbt1156

Minimum information requested in the annotation of biochemical models (MIRIAM)

Nicolas Le Novère1,15, Andrew Finney2,15, Michael Hucka3, Upinder S Bhalla4, Fabien Campagne5, Julio Collado-Vides6, Edmund J Crampin7, Matt Halstead7, Edda Klipp8, Pedro Mendes9, Poul Nielsen7, Herbert Sauro10, Bruce Shapiro11, Jacky L Snoep12, Hugh D Spence13 & Barry L Wanner14


Most of the published quantitative models in biology are lost for the community because they are either not made available or they are insufficiently characterized to allow them to be reused. The lack of a standard description format, lack of stringent reviewing and authors' carelessness are the main causes for incomplete model descriptions. With today's increased interest in detailed biochemical models, it is necessary to define a minimum quality standard for the encoding of those models. We propose a set of rules for curating quantitative models of biological systems. These rules define procedures for encoding and annotating models represented in machine-readable form. We believe their application will enable users to (i) have confidence that curated models are an accurate reflection of their associated reference descriptions, (ii) search collections of curated models with precision, (iii) quickly identify the biological phenomena that a given curated model or model constituent represents and (iv) facilitate model reuse and composition into large subcellular models.

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  1. European Bioinformatics Institute, Hinxton, CB10 1SD, UK.
  2. Physiomics PLC, Magdalen Centre, Oxford Science Park, Oxford, OX4 4GA, UK.
  3. Control and Dynamical Systems, California Institute of Technology, Pasadena, California 91125, USA.
  4. National Centre for Biological Sciences, TIFR, UAS-GKVK Campus, Bangalore 560065, India.
  5. Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York 10021, USA.
  6. Center for Genomic Sciences, Universidad Nacional Autónoma de México, Av. Universidad s/n, Cuernavaca, Morelos, 62100, Mexico.
  7. Bioengineering Institute and Department of Engineering Science, The University of Auckland, Private Bag 92019, Auckland, New Zealand.
  8. Max-Planck Institute for Molecular Genetics, Berlin Center for Genome based Bioinformatics (BCB), Ihnestr. 73, 14195 Berlin, Germany.
  9. Virginia Bioinformatics Institute, Virginia Tech, Washington St., Blacksburg, Virginia 24061-0477, USA.
  10. Keck Graduate Institute, 535 Watson Drive, Claremont, California 91711, USA.
  11. Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109, USA.
  12. Triple-J Group for Molecular Cell Physiology, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa.
  13. Department of Scientific Computing & Mathematical Modeling, GlaxoSmithKline Research & Development Limited, Medicines Research Centre, Gummels Wood Road, Stevenage, Herts, SG1 2NY, UK.
  14. Purdue University, Department of Biological Sciences, Lilly Hall of Life Sciences, 915 W. State Street, West Lafayette, Indiana 47907-2054, USA.
  15. These authors have contributed equally to the work.

Correspondence to: Nicolas Le Novère1,15 e-mail: lenov@ebi.ac.uk



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