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Navigating the Global Protein-Protein Interaction Landscape Using iRefWeb

Andrei L Turinsky¹, Sam Dupont², Alexander Botzki²

¹Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON, Canada. turinsky@sickkids.ca.

Methods in Molecular Biology (Clifton, N.J.)

|October 30, 2020

Summary

iRefWeb offers a unified interface to protein-protein interactions from multiple databases. It consolidates and validates data, providing reliable evidence for researchers studying protein networks.

Area of Science:

Bioinformatics
Molecular Biology
Computational Biology

Background:

Protein-protein interactions (PPIs) are crucial for cellular functions.
Existing PPI databases often contain redundant and inconsistently annotated data.
A unified and reliable resource for PPI data is needed.

Purpose of the Study:

To present iRefWeb, a web interface for a consolidated collection of protein-protein interactions.
To describe the iRefIndex data-consolidation process for handling redundant and disparate PPI records.
To provide tools for exploring, validating, and comparing PPI data.

Main Methods:

Aggregation of PPI data from major primary databases.
Development of the iRefIndex process to identify redundant protein sequences and integrate disparate data records.
Implementation of a unified web interface (iRefWeb) with data filters and visualization features.

Main Results:

iRefWeb provides access to a large, consolidated collection of protein-protein interactions.
The iRefIndex methodology successfully integrates data despite differences in source database identifiers.
Users can explore PPIs, assess data provenance, and compare curator annotations.

Conclusions:

iRefWeb serves as a valuable, unified resource for exploring protein-protein interactions.
The data consolidation methodology ensures data reliability and consistency.
The portal facilitates a deeper understanding of protein interaction networks.

Keywords:

Bioinformatics resources IMEx consortium Interaction networks Literature curation PSI-MI standards Protein–protein interactions Proteomics iRefIndex iRefWeb

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