The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)

Bioinformatics, vol. 36, pp. 5712–5718

Abstract

MOTIVATION: A large variety of molecular interactions occurs between biomolecular components in cells. When a molecular interaction results in a regulatory effect, exerted by one component onto a downstream component, a so-called 'causal interaction' takes place. Causal interactions constitute the building blocks in our understanding of larger regulatory networks in cells. These causal interactions and the biological processes they enable (e.g. gene regulation) need to be described with a careful appreciation of the underlying molecular reactions. A proper description of this information enables archiving, sharing and reuse by humans and for automated computational processing. Various representations of causal relationships between biological components are currently used in a variety of resources. RESULTS: Here, we propose a checklist that accommodates current representations, called the Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). This checklist defines both the required core information, as well as a comprehensive set of other contextual details valuable to the end user and relevant for reusing and reproducing causal molecular interaction information. The MI2CAST checklist can be used as reporting guidelines when annotating and curating causal statements, while fostering uniformity and interoperability of the data across resources. AVAILABILITY AND IMPLEMENTATION: The checklist together with examples is accessible at https://github.com/MI2CAST/MI2CAST. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Authors 26

1. Vasundra Touré corresponding

   Norwegian University of Science and Technology

   Affiliation as printed

   Department of Biology, Norwegian University of Science and Technology (NTNU) , Trondheim 7491, Norway

2. Steven Vercruysse

   Norwegian University of Science and Technology

   Affiliation as printed

   Department of Biology, Norwegian University of Science and Technology (NTNU) , Trondheim 7491, Norway

3. Márcio Luís Acencio

   Norwegian University of Science and Technology

   Affiliation as printed

   Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU) , Trondheim 7491, Norway

4. Ruth C. Lovering

   University College London

   Affiliation as printed

   Functional Gene Annotation, Preclinical and Fundamental Science, Institute of Cardiovascular Science, UCL, University College London , London WC1E 6JF, UK

5. Sandra E. Orchard

   European Bioinformatics Institute

   Affiliation as printed

   European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, UK

6. Glyn Bradley

   GlaxoSmithKline (United Kingdom)

   Affiliation as printed

   Computational Biology, Functional Genomics, GSK , Stevenage SG1 2NY, UK

7. Cristina Casals‐Casas

   SIB Swiss Institute of Bioinformatics

   Affiliation as printed

   Swiss-Prot Group, SIB Swiss Institute of Bioinformatics , 1211 Geneva 4, Switzerland

8. Claudine Chaouiya

   Centre National de la Recherche Scientifique · Aix-Marseille Université · Institut de Mathématiques de Marseille · Centrale Méditerranée

   Affiliation as printed

   Aix Marseille Univ, CNRS, Centrale Marseille , I2M Marseille 13331, France

9. Noemí del‐Toro

   European Bioinformatics Institute

   Affiliation as printed

   European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, UK

10. Åsmund Flobak

    Norwegian University of Science and Technology · St Olav's University Hospital

    Affiliation as printed

    Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU) , Trondheim 7491, Norway

    The Cancer Clinic, St. Olav’s Hospital, Trondheim University Hospital , Trondheim 7030, Norway

11. Pascale Gaudet

    SIB Swiss Institute of Bioinformatics

    Affiliation as printed

    SIB Swiss Institute of Bioinformatics , Geneva 1211, Switzerland

12. Henning Hermjakob

    European Bioinformatics Institute

    Affiliation as printed

    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, UK

13. Charles Tapley Hoyt
    Affiliation as printed

    Enveda Therapeutics , 53225 Bonn, Germany

14. Luana Licata

    University of Rome Tor Vergata

    Affiliation as printed

    Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica , 00133 Rome, Italy

15. Astrid Lægreid

    Norwegian University of Science and Technology

    Affiliation as printed

    Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU) , Trondheim 7491, Norway

16. Chris Mungall

    Lawrence Berkeley National Laboratory

    Affiliation as printed

    Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, USA

17. Anne Niknejad

    SIB Swiss Institute of Bioinformatics

    Affiliation as printed

    Vital-IT Group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, Amphipole Building , 1015 Lausanne, Switzerland

18. Simona Panni

    University of Calabria

    Affiliation as printed

    Department of Biology, Ecology and Earth Sciences, University of Calabria, Ecology and Earth Science , Via Pietro Bucci Cubo 6/C, Rende 87036, CS, Italy

19. Livia Perfetto

    European Bioinformatics Institute

    Affiliation as printed

    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, UK

20. Pablo Porras

    European Bioinformatics Institute

    Affiliation as printed

    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, UK

21. Dexter R. Pratt

    University of California San Diego

    Affiliation as printed

    Department of Medicine, University of California San Diego , La Jolla, CA 92093, USA

22. Julio Sáez-Rodríguez Aachen Joint Research Centre for Computational Biomedicine (JRC-COMBINE) Faculty of Medicine

    Heidelberg University · RWTH Aachen University

    Affiliation as printed

    Institute of Computational Biomedicine, Heidelberg University, Faculty of Medicine , 69120 Heidelberg, Germany

    Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University , Aachen 52062, Germany

23. Denis Thieffry

    Centre National de la Recherche Scientifique · Inserm · Université Paris Sciences et Lettres · École Normale Supérieure - PSL · Institut de Biologie de l'École Normale Supérieure

    Affiliation as printed

    Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL , 75005 Paris, France

24. Paul D. Thomas

    University of Southern California

    Affiliation as printed

    Division of Bioinformatics, Department of Preventive Medicine, University of Southern California , Los Angeles, CA 90007, USA

25. Dénes Türei Aachen Joint Research Centre for Computational Biomedicine (JRC-COMBINE) Faculty of Medicine

    RWTH Aachen University

    Affiliation as printed

    Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University , Aachen 52062, Germany

26. Martin T. R. Kuiper

    Norwegian University of Science and Technology

    Affiliation as printed

    Department of Biology, Norwegian University of Science and Technology (NTNU) , Trondheim 7491, Norway