The IntAct database: Efficient access to fine-grained molecular interaction data

Noemi del Toro; Anjali Shrivastava; Eliot Ragueneau; Birgit Meldal; Colin Combe; Elisabet Barrera; Livia Perfetto; Karyn How; Prashansa Ratan; Gautam Shirodkar; Odilia Lu; Bálint Mészáros; Xavier Watkins; Sangya Pundir; Luana Licata; Marta Iannuccelli; Matteo Pellegrini; Maria Jesus Martin; Simona Panni; Margaret Duesbury; Sylvain D. Vallet; Juri Rappsilber; Sylvie Ricard-Blum; Gianni Cesareni; Lukasz Salwinski; Sandra Orchard; Pablo Porras; Kalpana Panneerselvam; Henning Hermjakob

doi:10.1093/nar/gkab1006

The IntAct database: Efficient access to fine-grained molecular interaction data

Noemi del Toro, Anjali Shrivastava, Eliot Ragueneau, Birgit Meldal, Colin Combe, Elisabet Barrera, Livia Perfetto, Karyn How, Prashansa Ratan, Gautam Shirodkar, Odilia Lu, Bálint Mészáros, Xavier Watkins, Sangya Pundir, Luana Licata, Marta Iannuccelli, Matteo Pellegrini, Maria Jesus Martin, Simona Panni, Margaret DuesburySylvain D. Vallet, Juri Rappsilber, Sylvie Ricard-Blum, Gianni Cesareni, Lukasz Salwinski, Sandra Orchard, Pablo Porras, Kalpana Panneerselvam, Henning Hermjakob^*

^*Corresponding author for this work

School of Biological Sciences

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

Abstract / Description of output

The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of molecular interactions, derived from the scientific literature and from direct data depositions. As of August 2021, IntAct provides more than one million binary interactions, curated by twelve global partners of the International Molecular Exchange consortium, for which the IntAct database provides a shared curation and dissemination platform. The IMEx curation policy has always emphasised a fine-grained data and curation model, aiming to capture the relevant experimental detail essential for the interpretation of the provided molecular interaction data. Here, we present recent curation focus and progress, as well as a completely redeveloped website which presents IntAct data in a much more user-friendly and detailed way.

Original language	English
Pages (from-to)	D648-D653
Number of pages	6
Journal	Nucleic Acids Research
Volume	50
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkab1006
Publication status	Published - 11 Nov 2021

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10.1093/nar/gkab1006Licence: Creative Commons: Attribution (CC-BY)

HermjakobEtalNAR2022TheIntActDatabaseFinal published version, 2.47 MBLicence: Creative Commons: Attribution (CC-BY)

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del Toro, N., Shrivastava, A., Ragueneau, E., Meldal, B., Combe, C., Barrera, E., Perfetto, L., How, K., Ratan, P., Shirodkar, G., Lu, O., Mészáros, B., Watkins, X., Pundir, S., Licata, L., Iannuccelli, M., Pellegrini, M., Martin, M. J., Panni, S., ... Hermjakob, H. (2021). The IntAct database: Efficient access to fine-grained molecular interaction data. Nucleic Acids Research, 50(D1), D648-D653. https://doi.org/10.1093/nar/gkab1006

@article{0b8f966cecd1449c96cf758f640b0922,

title = "The IntAct database: Efficient access to fine-grained molecular interaction data",

abstract = "The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of molecular interactions, derived from the scientific literature and from direct data depositions. As of August 2021, IntAct provides more than one million binary interactions, curated by twelve global partners of the International Molecular Exchange consortium, for which the IntAct database provides a shared curation and dissemination platform. The IMEx curation policy has always emphasised a fine-grained data and curation model, aiming to capture the relevant experimental detail essential for the interpretation of the provided molecular interaction data. Here, we present recent curation focus and progress, as well as a completely redeveloped website which presents IntAct data in a much more user-friendly and detailed way.",

author = "{del Toro}, Noemi and Anjali Shrivastava and Eliot Ragueneau and Birgit Meldal and Colin Combe and Elisabet Barrera and Livia Perfetto and Karyn How and Prashansa Ratan and Gautam Shirodkar and Odilia Lu and B{\'a}lint M{\'e}sz{\'a}ros and Xavier Watkins and Sangya Pundir and Luana Licata and Marta Iannuccelli and Matteo Pellegrini and Martin, {Maria Jesus} and Simona Panni and Margaret Duesbury and Vallet, {Sylvain D.} and Juri Rappsilber and Sylvie Ricard-Blum and Gianni Cesareni and Lukasz Salwinski and Sandra Orchard and Pablo Porras and Kalpana Panneerselvam and Henning Hermjakob",

note = "Funding Information: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); Open Targets [OTAR-044, OTAR02-048, OTAR02-066]; Wellcome Trust [Biomedical Resources grants INVAR #3367 and 218294, and Centre grant 203149]; the MINT database is supported by a grant from the Italian Association for Cancer Research [AIRC IG 2017 no. 20322 to G.C.]; the MatrixDB database is supported by Institut Fran?ais de Bioinformatique [ANR-11-INBS-0013, Glycomatrix project to S.R.B.]; the DIP database is supported by NIH NIGMS award [GM123126 to M.P.]. Funding for open access charge: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI). Funding Information: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); Open Targets [OTAR-044, OTAR02-048, OTAR02-066]; Wellcome Trust [Biomedical Resources grants INVAR #3367 and 218294, and Centre grant 203149]; the MINT database is supported by a grant from the Italian Association for Cancer Research [AIRC IG 2017 no. 20322 to G.C.]; the MatrixDB database is supported by Institut Franc¸ais de Bioinformatique [ANR-11-INBS-0013, Glycomatrix project to S.R.B.]; the DIP database is supported by NIH NIGMS award [GM123126 to M.P.]. Funding for open access charge: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI). Conflict of interest statement. None declared. Publisher Copyright: {\textcopyright} The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.",

year = "2021",

month = nov,

day = "11",

doi = "10.1093/nar/gkab1006",

language = "English",

volume = "50",

pages = "D648--D653",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "D1",

}

del Toro, N, Shrivastava, A, Ragueneau, E, Meldal, B, Combe, C, Barrera, E, Perfetto, L, How, K, Ratan, P, Shirodkar, G, Lu, O, Mészáros, B, Watkins, X, Pundir, S, Licata, L, Iannuccelli, M, Pellegrini, M, Martin, MJ, Panni, S, Duesbury, M, Vallet, SD, Rappsilber, J, Ricard-Blum, S, Cesareni, G, Salwinski, L, Orchard, S, Porras, P, Panneerselvam, K & Hermjakob, H 2021, 'The IntAct database: Efficient access to fine-grained molecular interaction data', Nucleic Acids Research, vol. 50, no. D1, pp. D648-D653. https://doi.org/10.1093/nar/gkab1006

TY - JOUR

T1 - The IntAct database

T2 - Efficient access to fine-grained molecular interaction data

AU - del Toro, Noemi

AU - Shrivastava, Anjali

AU - Ragueneau, Eliot

AU - Meldal, Birgit

AU - Combe, Colin

AU - Barrera, Elisabet

AU - Perfetto, Livia

AU - How, Karyn

AU - Ratan, Prashansa

AU - Shirodkar, Gautam

AU - Lu, Odilia

AU - Mészáros, Bálint

AU - Watkins, Xavier

AU - Pundir, Sangya

AU - Licata, Luana

AU - Iannuccelli, Marta

AU - Pellegrini, Matteo

AU - Martin, Maria Jesus

AU - Panni, Simona

AU - Duesbury, Margaret

AU - Vallet, Sylvain D.

AU - Rappsilber, Juri

AU - Ricard-Blum, Sylvie

AU - Cesareni, Gianni

AU - Salwinski, Lukasz

AU - Orchard, Sandra

AU - Porras, Pablo

AU - Panneerselvam, Kalpana

AU - Hermjakob, Henning

N1 - Funding Information: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); Open Targets [OTAR-044, OTAR02-048, OTAR02-066]; Wellcome Trust [Biomedical Resources grants INVAR #3367 and 218294, and Centre grant 203149]; the MINT database is supported by a grant from the Italian Association for Cancer Research [AIRC IG 2017 no. 20322 to G.C.]; the MatrixDB database is supported by Institut Fran?ais de Bioinformatique [ANR-11-INBS-0013, Glycomatrix project to S.R.B.]; the DIP database is supported by NIH NIGMS award [GM123126 to M.P.]. Funding for open access charge: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI). Funding Information: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); Open Targets [OTAR-044, OTAR02-048, OTAR02-066]; Wellcome Trust [Biomedical Resources grants INVAR #3367 and 218294, and Centre grant 203149]; the MINT database is supported by a grant from the Italian Association for Cancer Research [AIRC IG 2017 no. 20322 to G.C.]; the MatrixDB database is supported by Institut Franc¸ais de Bioinformatique [ANR-11-INBS-0013, Glycomatrix project to S.R.B.]; the DIP database is supported by NIH NIGMS award [GM123126 to M.P.]. Funding for open access charge: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI). Conflict of interest statement. None declared. Publisher Copyright: © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

PY - 2021/11/11

Y1 - 2021/11/11

N2 - The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of molecular interactions, derived from the scientific literature and from direct data depositions. As of August 2021, IntAct provides more than one million binary interactions, curated by twelve global partners of the International Molecular Exchange consortium, for which the IntAct database provides a shared curation and dissemination platform. The IMEx curation policy has always emphasised a fine-grained data and curation model, aiming to capture the relevant experimental detail essential for the interpretation of the provided molecular interaction data. Here, we present recent curation focus and progress, as well as a completely redeveloped website which presents IntAct data in a much more user-friendly and detailed way.

AB - The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of molecular interactions, derived from the scientific literature and from direct data depositions. As of August 2021, IntAct provides more than one million binary interactions, curated by twelve global partners of the International Molecular Exchange consortium, for which the IntAct database provides a shared curation and dissemination platform. The IMEx curation policy has always emphasised a fine-grained data and curation model, aiming to capture the relevant experimental detail essential for the interpretation of the provided molecular interaction data. Here, we present recent curation focus and progress, as well as a completely redeveloped website which presents IntAct data in a much more user-friendly and detailed way.

UR - https://github.com/intact-portal

U2 - 10.1093/nar/gkab1006

DO - 10.1093/nar/gkab1006

M3 - Article

C2 - 34761267

AN - SCOPUS:85123044845

SN - 0305-1048

VL - 50

SP - D648-D653

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -

The IntAct database: Efficient access to fine-grained molecular interaction data

Abstract / Description of output

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Core funding for the Wellcome Centre for Cell Biology

ProCos: Protein co-regulation scores as a new tool for systematic and large-scale protein function annotation

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The IntAct database: Efficient access to fine-grained molecular interaction data

Abstract / Description of output

Access to Document

Other files and links

Fingerprint

Projects

Core funding for the Wellcome Centre for Cell Biology

ProCos: Protein co-regulation scores as a new tool for systematic and large-scale protein function annotation

Cite this