Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.

Journal: Database : the journal of biological databases and curation
Published Date: Feb 4, 2015

Abstract

The evidence that two molecules interact in a living cell is often inferred from multiple different experiments. Experimental data is captured in multiple repositories, but there is no simple way to assess the evidence of an interaction occurring in a cellular environment. Merging and scoring of data are commonly required operations after querying for the details of specific molecular interactions, to remove redundancy and assess the strength of accompanying experimental evidence. We have developed both a merging algorithm and a scoring system for molecular interactions based on the proteomics standard initiative-molecular interaction standards. In this manuscript, we introduce these two algorithms and provide community access to the tool suite, describe examples of how these tools are useful to selectively present molecular interaction data and demonstrate a case where the algorithms were successfully used to identify a systematic error in an existing dataset.

Authors

  • J M Villaveces
    Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Matinsried, Germany, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive, MRL Building, Suite 1609, Los Angeles, California 90095, USA and Biomedical Hosting LLC, Arlington, Massachusetts 02474, USA.
  • R C JimĂ©nez
    Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Matinsried, Germany, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive, MRL Building, Suite 1609, Los Angeles, California 90095, USA and Biomedical Hosting LLC, Arlington, Massachusetts 02474, USA.
  • P Porras
    Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Matinsried, Germany, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive, MRL Building, Suite 1609, Los Angeles, California 90095, USA and Biomedical Hosting LLC, Arlington, Massachusetts 02474, USA.
  • N Del-Toro
    Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Matinsried, Germany, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive, MRL Building, Suite 1609, Los Angeles, California 90095, USA and Biomedical Hosting LLC, Arlington, Massachusetts 02474, USA.
  • M Duesbury
    Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Matinsried, Germany, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive, MRL Building, Suite 1609, Los Angeles, California 90095, USA and Biomedical Hosting LLC, Arlington, Massachusetts 02474, USA.
  • M Dumousseau
    Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Matinsried, Germany, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive, MRL Building, Suite 1609, Los Angeles, California 90095, USA and Biomedical Hosting LLC, Arlington, Massachusetts 02474, USA.
  • S Orchard
    Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Matinsried, Germany, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive, MRL Building, Suite 1609, Los Angeles, California 90095, USA and Biomedical Hosting LLC, Arlington, Massachusetts 02474, USA.
  • H Choi
    Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Matinsried, Germany, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive, MRL Building, Suite 1609, Los Angeles, California 90095, USA and Biomedical Hosting LLC, Arlington, Massachusetts 02474, USA.
  • P Ping
    Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Matinsried, Germany, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive, MRL Building, Suite 1609, Los Angeles, California 90095, USA and Biomedical Hosting LLC, Arlington, Massachusetts 02474, USA Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Matinsried, Germany, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive, MRL Building, Suite 1609, Los Angeles, California 90095, USA and Biomedical Hosting LLC, Arlington, Massachusetts 02474, USA.
  • N C Zong
    Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Matinsried, Germany, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive, MRL Building, Suite 1609, Los Angeles, California 90095, USA and Biomedical Hosting LLC, Arlington, Massachusetts 02474, USA Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Matinsried, Germany, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive, MRL Building, Suite 1609, Los Angeles, California 90095, USA and Biomedical Hosting LLC, Arlington, Massachusetts 02474, USA.
  • M Askenazi
    Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Matinsried, Germany, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive, MRL Building, Suite 1609, Los Angeles, California 90095, USA and Biomedical Hosting LLC, Arlington, Massachusetts 02474, USA.
  • B H Habermann
    Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Matinsried, Germany, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive, MRL Building, Suite 1609, Los Angeles, California 90095, USA and Biomedical Hosting LLC, Arlington, Massachusetts 02474, USA.
  • Henning Hermjakob
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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