Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

By S. Orchard, Samuel Kerrien, S. Abbani, Bruno Aranda, Jignesh Bhate, Shelby L. Bidwell, A. Bridge, Leonardo Briganti, Fiona S. L. Brinkman, G. Cesareni and 21 more. Nature Methods, 2012

509 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ecaef4ba5f6ecd0fd955a5fa8190c69655d3cda9

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets (2018, background): “Primary interaction databases (3,15–18) are jointly annotating experimental interaction evidence directly from the source publications, and they are coordinating their efforts through the IMEx consortium (19).”
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible (2016, methodology): “First, individual well-supported protein–protein interactions are curated manually from the published literature, through dedicated efforts by members of the IMEx consortium (20,21), but also as part of more general annotation workflows such as within the UniProt consortium (22).”
The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases (2013, methodology): “As of January 2012, the MPIDB database (16) ceased active curation and since that date the IMEx records for that database are present within and updated by IntAct.”
STRING v10: protein–protein interaction networks, integrated over the tree of life (2014, background): “rating (14,15) provide curated experimental data originating from a variety of biochemical, biophysical and genetic techniques.”
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes (2018, methodology): “The IMEx Consortium of interaction databases (21) now describe molecules that interact with complexes using Complex Portal entries as annotation objects.”
UniProt: a worldwide hub of protein knowledge (2018, methodology): “…in that the molecular interactions involved have also been added to the IMEx Consortium (www.imexconsortium.org) dataset by UniProt curators (23), the protein complexes involved curated into the Complex Portal (https://www.ebi.ac.uk/complexportal/) (24) and both the proteins and complexes…”
NetworkAnalyst - integrative approaches for protein–protein interaction network analysis and visual exploration (2014, methodology): “NetworkAnalyst uses a comprehensive high-quality PPI database downloaded from the InnateDB (19), which participates in the International Molecular Exchange (IMEx) consortium (20).”
The BioGRID interaction database: 2017 update (2016, background): “BioGRID content is updated on a monthly basis and is made freely accessible via the web interface, through downloadable files in standardized formats, and through dissemination by model organism database (MOD) partners (21–26) and other biological resources (27–32).”
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets (2020, background): “This includes biochemical, bio-physical and genetic experiments; all such interaction evidence is imported from the curated interaction database organized in the iMEX consortium (39), plus BioGRID (40).”
NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data (2015, methodology): “The underlying protein interaction data were obtained from InnateDB 11 (for human and mouse), a member of the International Molecular Exchange (IMEx) consortium 31 , and iRefIndex 32 (for other three species).”
Machine learning approaches and databases for prediction of drug–target interaction: a survey paper (2020, methodology): “In total, 11 molecular interaction databases (including IntAct) were incorporated into IntAct including AgBase [ 266–269], MINT [ 270–273], UniProt [274][41], I2D [275], MBINFO, MatrixDB [276], Molecular Connections, InnateDN [ 277], IMEx [278] and GOA.”
InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation (2012, background): “In 2010, InnateDB became a member of the International Molecular Exchange Consortium (IMEx) (11).”