Literature DB >> 35507258

IMEx Databases: Displaying Molecular Interactions into a Single, Standards-Compliant Dataset.

Pablo Porras1, Sandra Orchard1, Luana Licata2.   

Abstract

Molecular interaction databases aim to systematically capture and organize the experimental interaction information described in the scientific literature. These data can then be used to perform network analysis, to assign putative roles to uncharacterized proteins and to investigate their involvement in cellular pathways.This chapter gives a brief overview of publicly available molecular interaction databases and focuses on the members of the IMEx Consortium, on their curation policies and standard data formats. All of the goals achieved by IMEx databases over the last 15 years, the data types provided and the many different ways in which such data can be utilized by the research community, are described in detail. The IMEx databases curate molecular interaction data to the highest caliber, following a detailed curation model and supplying rich metadata by employing common curation rules and harmonized standards. The IMEx Consortium provides comprehensively annotated molecular interaction data integrated into a single, non-redundant, open access dataset.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Bioinformatics; Controlled vocabulary; Databases; Manual curation; Molecular interaction data standards; Molecular interactions

Mesh:

Substances:

Year:  2022        PMID: 35507258     DOI: 10.1007/978-1-0716-2095-3_2

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  31 in total

Review 1.  Network biology: understanding the cell's functional organization.

Authors:  Albert-László Barabási; Zoltán N Oltvai
Journal:  Nat Rev Genet       Date:  2004-02       Impact factor: 53.242

2.  mentha: a resource for browsing integrated protein-interaction networks.

Authors:  Alberto Calderone; Luisa Castagnoli; Gianni Cesareni
Journal:  Nat Methods       Date:  2013-08       Impact factor: 28.547

Review 3.  Network medicine: a network-based approach to human disease.

Authors:  Albert-László Barabási; Natali Gulbahce; Joseph Loscalzo
Journal:  Nat Rev Genet       Date:  2011-01       Impact factor: 53.242

Review 4.  Fundamentals of protein interaction network mapping.

Authors:  Jamie Snider; Max Kotlyar; Punit Saraon; Zhong Yao; Igor Jurisica; Igor Stagljar
Journal:  Mol Syst Biol       Date:  2015-12-17       Impact factor: 11.429

5.  ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes.

Authors:  Linh Tran; Tobias Hamp; Burkhard Rost
Journal:  PLoS One       Date:  2018-07-18       Impact factor: 3.240

6.  STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.

Authors:  Damian Szklarczyk; Annika L Gable; David Lyon; Alexander Junge; Stefan Wyder; Jaime Huerta-Cepas; Milan Simonovic; Nadezhda T Doncheva; John H Morris; Peer Bork; Lars J Jensen; Christian von Mering
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

7.  IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species.

Authors:  Max Kotlyar; Chiara Pastrello; Zara Malik; Igor Jurisica
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

Review 8.  Towards a unified open access dataset of molecular interactions.

Authors:  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
Journal:  Nat Commun       Date:  2020-12-01       Impact factor: 14.919

Review 9.  Review of biological network data and its applications.

Authors:  Donghyeon Yu; Minsoo Kim; Guanghua Xiao; Tae Hyun Hwang
Journal:  Genomics Inform       Date:  2013-12-31

10.  The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions.

Authors:  Rose Oughtred; Jennifer Rust; Christie Chang; Bobby-Joe Breitkreutz; Chris Stark; Andrew Willems; Lorrie Boucher; Genie Leung; Nadine Kolas; Frederick Zhang; Sonam Dolma; Jasmin Coulombe-Huntington; Andrew Chatr-Aryamontri; Kara Dolinski; Mike Tyers
Journal:  Protein Sci       Date:  2020-11-23       Impact factor: 6.725

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