OpenPIP: An Open-source Platform for Hosting, Visualizing and Analyzing Protein Interaction Data

Mohamed Helmy; Miles Mee; Aniket Ranjan; Tong Hao; Marc Vidal; Michael A Calderwood; Katja Luck; Gary D Bader

doi:10.1016/j.jmb.2022.167603

OpenPIP: An Open-source Platform for Hosting, Visualizing and Analyzing Protein Interaction Data

J Mol Biol. 2022 Jun 15;434(11):167603. doi: 10.1016/j.jmb.2022.167603. Epub 2022 Apr 26.

Authors

Mohamed Helmy¹, Miles Mee², Aniket Ranjan³, Tong Hao⁴, Marc Vidal⁵, Michael A Calderwood⁴, Katja Luck⁶, Gary D Bader⁷

Affiliations

¹ Department of Computer Science, Lakehead University, Thunder Bay, ON, Canada.
² Ontario Institute for Cancer Research, Toronto, ON, Canada.
³ Indian Institute of Technology, Kharagpur, India.
⁴ Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA.
⁵ Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA.
⁶ Institute of Molecular Biology (IMB), Mainz, Germany.
⁷ The Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; The Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada. Electronic address: gary.bader@utoronto.ca.

PMID: 35662469
DOI: 10.1016/j.jmb.2022.167603

Abstract

Knowing which proteins interact with each other is essential information for understanding how most biological processes at the cellular and organismal level operate and how their perturbation can cause disease. Continuous technical and methodological advances over the last two decades have led to many genome-wide systematically-generated protein-protein interaction (PPI) maps. To help store, visualize, analyze and disseminate these specialized experimental datasets via the web, we developed the freely-available Open-source Protein Interaction Platform (openPIP) as a customizable web portal designed to host experimental PPI maps. Such a portal is often required to accompany a paper describing the experimental data set, in addition to depositing the data in a standard repository. No coding skills are required to set up and customize the database and web portal. OpenPIP has been used to build the databases and web portals of two major protein interactome maps, the Human and Yeast Reference Protein Interactome maps (HuRI and YeRI, respectively). OpenPIP is freely available as a ready-to-use Docker container for hosting and sharing PPI data with the scientific community at http://openpip.baderlab.org/ and the source code can be downloaded from https://github.com/BaderLab/openPIP/.

Keywords: interactome; protein interaction database; protein interactions.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Databases, Factual
Genome, Human
Humans
Internet Use*
Protein Interaction Maps*
Software*