ArticleDatabase : the journal of biological databases and curation2015
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.
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Article in Database : the journal of biological databases and curation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers, 1 of them a synthesis that pooled it.
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49citing papers in PubMed, 1 pooled it
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49 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- From random to predictive: a context-specific interaction framework improves selection of drug protein-protein interactions for unknown drug pathways.Integrative biology : quantitative biosciences from nano to macro · 2022Article
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Authors and funding
13 authors.
J M VillavecesMax 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 JiménezMax 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 PorrasMax 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-ToroMax 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 DuesburyMax 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 DumousseauMax 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 OrchardMax 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 ChoiMax 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 PingMax 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 ZongMax 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 AskenaziMax 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 HabermannMax 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 HermjakobMax 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.
Funding
NHLBI NIH HHS HHSN268201000035C
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.
Indexed as
AlgorithmsBiological OntologiesDatabases, ProteinModels, BiologicalProteomics
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