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

Nature Biotechnology volume 23, pages 1509–1515 (2005)Cite this article

Abstract

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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Author information

Author notes

  1. Nicolas Le Novère and Andrew Finney: These authors have contributed equally to the work.

Authors and Affiliations

  1. European Bioinformatics Institute, Hinxton, CB10 1SD, UK

    Nicolas Le Novère

  2. Physiomics PLC, Magdalen Centre, Oxford Science Park, Oxford, OX4 4GA, UK

    Andrew Finney

  3. Control and Dynamical Systems, California Institute of Technology, Pasadena, 91125, California, USA

    Michael Hucka

  4. National Centre for Biological Sciences, TIFR, UAS-GKVK Campus, Bangalore, 560065, India

    Upinder S Bhalla

  5. Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, 10021, New York, USA

    Fabien Campagne

  6. Center for Genomic Sciences, Universidad Nacional Autónoma de México, Av. Universidad s/n, Cuernavaca, 62100, Morelos, Mexico

    Julio Collado-Vides

  7. Bioengineering Institute and Department of Engineering Science, The University of Auckland, Private Bag 92019, Auckland, New Zealand

    Edmund J Crampin, Matt Halstead & Poul Nielsen

  8. Max-Planck Institute for Molecular Genetics, Berlin Center for Genome based Bioinformatics (BCB), Ihnestr. 73, Berlin, 14195, Germany

    Edda Klipp

  9. Virginia Bioinformatics Institute, Virginia Tech, Washington St., Blacksburg, 24061-0477, Virginia, USA

    Pedro Mendes

  10. Keck Graduate Institute, 535 Watson Drive, Claremont, 91711, California, USA

    Herbert Sauro

  11. Jet Propulsion Laboratory, California Institute of Technology, Pasadena, 91109, California, USA

    Bruce Shapiro

  12. Department of Biochemistry, Triple-J Group for Molecular Cell Physiology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa

    Jacky L Snoep

  13. Department of Scientific Computing & Mathematical Modeling, GlaxoSmithKline Research & Development Limited, Medicines Research Centre, Gummels Wood Road, Stevenage, SG1 2NY, Herts, UK

    Hugh D Spence

  14. Department of Biological Sciences, Purdue University, Lilly Hall of Life Sciences, 915 W. State Street, West Lafayette, 47907-2054, Indiana, USA

    Barry L Wanner

Authors
  1. Nicolas Le Novère
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  2. Andrew Finney
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  3. Michael Hucka
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  4. Upinder S Bhalla
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  5. Fabien Campagne
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  6. Julio Collado-Vides
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  7. Edmund J Crampin
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  8. Matt Halstead
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  9. Edda Klipp
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  10. Pedro Mendes
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  11. Poul Nielsen
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  12. Herbert Sauro
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  13. Bruce Shapiro
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  14. Jacky L Snoep
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  15. Hugh D Spence
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  16. Barry L Wanner
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Corresponding author

Correspondence to Nicolas Le Novère.

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The authors declare no competing financial interests.

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Novère, N., Finney, A., Hucka, M. et al. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 23, 1509–1515 (2005). https://doi.org/10.1038/nbt1156

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