Towards a unified open access dataset of molecular interactions

Pablo Porras; Elisabet Barrera; Alan Bridge; Noemi Del-Toro; Gianni Cesareni; Margaret Duesbury; Henning Hermjakob; Marta Iannuccelli; Igor Jurisica; Max Kotlyar; Luana Licata; Ruth C Lovering; David J Lynn; Birgit Meldal; Bindu Nanduri; Kalpana Paneerselvam; Simona Panni; Chiara Pastrello; Matteo Pellegrini; Livia Perfetto; Negin Rahimzadeh; Prashansa Ratan; Sylvie Ricard-Blum; Lukasz Salwinski; Gautam Shirodkar; Anjalia Shrivastava; Sandra Orchard

doi:10.1038/s41467-020-19942-z

Towards a unified open access dataset of molecular interactions

Nat Commun. 2020 Dec 1;11(1):6144. doi: 10.1038/s41467-020-19942-z.

Authors

Pablo Porras¹, Elisabet Barrera¹, Alan Bridge², Noemi Del-Toro¹, Gianni Cesareni^{3

4}, Margaret Duesbury^{1

5}, Henning Hermjakob¹, Marta Iannuccelli³, Igor Jurisica^{6

7

8}, Max Kotlyar⁶, Luana Licata³, Ruth C Lovering⁹, David J Lynn^{10

11}, Birgit Meldal¹, Bindu Nanduri¹², Kalpana Paneerselvam¹, Simona Panni¹³, Chiara Pastrello⁶, Matteo Pellegrini¹⁴, Livia Perfetto¹, Negin Rahimzadeh⁵, Prashansa Ratan⁵, Sylvie Ricard-Blum¹⁵, Lukasz Salwinski⁵, Gautam Shirodkar⁵, Anjalia Shrivastava^{1

16}, Sandra Orchard¹⁷

Affiliations

¹ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, CB10 1SD, UK.
² SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, CH-1211, Geneva, Switzerland.
³ University of Rome Tor Vergata, Rome, Italy.
⁴ IRCCS Fondazione Santa Lucia, 00143, Rome, Italy.
⁵ UCLA-DOE Institute, University of California, Los Angeles, CA, 90095, USA.
⁶ Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, and Krembil Research Institute, University Health Network, 60 Leonard Avenue, 5KD-407, Toronto, ON, M5T 0S8, Canada.
⁷ Departments of Medical Biophysics, and Computer Science, University of Toronto, Toronto, ON, Canada.
⁸ Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.
⁹ Functional Gene Annotation, Preclinical and Fundamental Science, UCL Institute of Cardiovascular Science, University College London, London, WC1E 6JF, UK.
¹⁰ Computational and Systems Biology Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia.
¹¹ College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.
¹² Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, USA.
¹³ Università della Calabria, Dipartimento di Biologia, Ecologia e Scienze della Terra, Via Pietro Bucci Cubo 6/C, Rende, CS, Italy.
¹⁴ Department of Molecular, Cell and Developmental Biology, UCLA, Box 951606, Los Angeles, CA, 90095-1606, USA.
¹⁵ ICBMS, UMR 5246 University Lyon 1 - CNRS, Univ. Lyon, 69622, Villeurbanne, France.
¹⁶ Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
¹⁷ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, CB10 1SD, UK. [email protected].

Abstract

The International Molecular Exchange (IMEx) Consortium provides scientists with a single body of experimentally verified protein interactions curated in rich contextual detail to an internationally agreed standard. In this update to the work of the IMEx Consortium, we discuss how this initiative has been working in practice, how it has ensured database sustainability, and how it is meeting emerging annotation challenges through the introduction of new interactor types and data formats. Additionally, we provide examples of how IMEx data are being used by biomedical researchers and integrated in other bioinformatic tools and resources.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Review

MeSH terms

Access to Information*
Databases, Genetic*
Humans
Information Dissemination
International Cooperation

Abstract

Publication types

MeSH terms

Grants and funding