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

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 PerfettoNegin Rahimzadeh, Prashansa Ratan, Sylvie Ricard-Blum, Lukasz Salwinski, Gautam Shirodkar, Anjalia Shrivastava, Sandra Orchard

Fondazione Santa Lucia

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	6144
Journal	Nature Communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-19942-z
Publication status	Published - Dec 2020

ASJC Scopus subject areas

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
Physics and Astronomy(all)

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10.1038/s41467-020-19942-z

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Porras, P., Barrera, E., Bridge, A., del-Toro, N., Cesareni, G., Duesbury, M., Hermjakob, H., Iannuccelli, M., Jurisica, I., Kotlyar, M., Licata, L., Lovering, R. C., Lynn, D. J., Meldal, B., Nanduri, B., Paneerselvam, K., Panni, S., Pastrello, C., Pellegrini, M., ... Orchard, S. (2020). Towards a unified open access dataset of molecular interactions. Nature Communications, 11(1), [6144]. https://doi.org/10.1038/s41467-020-19942-z

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

In: Nature Communications, Vol. 11, No. 1, 6144, 12.2020.

Research output: Contribution to journal › Article › peer-review

Porras, P, Barrera, E, Bridge, A, del-Toro, N, Cesareni, G, Duesbury, M, Hermjakob, H, Iannuccelli, M, Jurisica, I, Kotlyar, M, Licata, L, Lovering, RC, Lynn, DJ, Meldal, B, Nanduri, B, Paneerselvam, K, Panni, S, Pastrello, C, Pellegrini, M, Perfetto, L, Rahimzadeh, N, Ratan, P, Ricard-Blum, S, Salwinski, L, Shirodkar, G, Shrivastava, A & Orchard, S 2020, 'Towards a unified open access dataset of molecular interactions', Nature Communications, vol. 11, no. 1, 6144. https://doi.org/10.1038/s41467-020-19942-z

Porras, Pablo ; Barrera, Elisabet ; Bridge, Alan ; del-Toro, Noemi ; Cesareni, Gianni ; Duesbury, Margaret ; Hermjakob, Henning ; Iannuccelli, Marta ; Jurisica, Igor ; Kotlyar, Max ; Licata, Luana ; Lovering, Ruth C. ; Lynn, David J. ; Meldal, Birgit ; Nanduri, Bindu ; Paneerselvam, Kalpana ; Panni, Simona ; Pastrello, Chiara ; Pellegrini, Matteo ; Perfetto, Livia ; Rahimzadeh, Negin ; Ratan, Prashansa ; Ricard-Blum, Sylvie ; Salwinski, Lukasz ; Shirodkar, Gautam ; Shrivastava, Anjalia ; Orchard, Sandra. / Towards a unified open access dataset of molecular interactions. In: Nature Communications. 2020 ; Vol. 11, No. 1.

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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.",

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

note = "Funding Information: The IntAct team at EMBL-EBI received funding from EMBL core funding, Open Targets (grant agreements OTAR-044 and OTAR02-048) and the Wellcome Trust (Biomedical Resources grant INVAR #3367). This work by UniProt was supported by the National Eye Institute (NEI), National Human Genome Research Institute (NHGRI), National Heart, Lung, and Blood Institute (NHLBI), National Institute on Aging (NIA), National Institute of Allergy and Infectious Diseases (NIAID), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK, National Institute of General Medical Sciences (NIGMS), National Cancer Institute (NCI) and National Institute of Mental Health (NIMH) of the National Institutes of Health under Award Number [U24HG007822] (the content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health) and EMBL core funding and Open Targets (grant agreements OTAR02-048). Support for IID was supplied in part by Ontario Research Fund (#34876), Natural Sciences Research Council (NSERC #203475) and Canada Foundation for Innovation (CFI #29272, #225404 and #33536). MatrixDB was supported by the Fondation pour la Recherche M{\'e}dicale (grant DBI20141231336 to S.R.B.) and by the Institut Fran{\c c}ais de Bioinformatique (GlycoMatrixDB project-AAP IFB 2015 to S.R.B.). InnateDB was previously supported by Genome BC through the Pathogenomics of Innate Immunity (PI2) project and by the Foundation for the National Institutes of Health and the Canadian Institutes of Health Research under the Grand Challenges in Global Health Research Initiative [Grand Challenges ID: 419]. Further funding was also provided by AllerGen grants 12ASI1 and 12B&B2. D.J.L. is currently supported by an EMBL Australia Group Leader award. The Database of Interacting Proteins (DIP) was supported by National Institute of General Medical Sciences grant R01GM123126. Publisher Copyright: {\textcopyright} 2020, The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.",

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AU - Duesbury, Margaret

AU - Hermjakob, Henning

AU - Iannuccelli, Marta

AU - Jurisica, Igor

AU - Kotlyar, Max

AU - Licata, Luana

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