title: Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.
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: 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.
authors: J M
authors: JM
authors: Villaveces
authors: 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.
authors: R C
authors: RC
authors: Jiménez
authors: 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.
authors: P
authors: P
authors: Porras
authors: 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.
authors: N
authors: N
authors: Del-Toro
authors: 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.
authors: M
authors: M
authors: Duesbury
authors: 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.
authors: M
authors: M
authors: Dumousseau
authors: 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.
authors: S
authors: S
authors: Orchard
authors: 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.
authors: H
authors: H
authors: Choi
authors: 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.
authors: P
authors: P
authors: Ping
authors: 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.
authors: N C
authors: NC
authors: Zong
authors: 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.
authors: M
authors: M
authors: Askenazi
authors: 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.
authors: B H
authors: BH
authors: Habermann
authors: 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 hhe@ebi.ac.uk.
authors: Henning
authors: H
authors: Hermjakob
mesh_terms: D000465:Algorithms; D064229:Biological Ontologies; D030562:Databases, Protein; D008954:Models, Biological; D040901:Proteomics
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