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Automated Extraction and Visualization of Protein–Protein Interaction Networks and Beyond: A Text-Mining Protocol

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Protein-Protein Interaction Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2074))

Abstract

Proteins perform their functions by interacting with other proteins. Protein–protein interaction (PPI) is critical for understanding the functions of individual proteins, the mechanisms of biological processes, and the disease mechanisms. High-throughput experiments accumulated a huge number of PPIs in PubMed articles, and their extraction is possible only through automated approaches. The standard text-mining protocol includes four major tasks, namely, recognizing protein mentions, normalizing protein names and aliases to unique identifiers such as gene symbol, extracting PPIs, and visualizing the PPI network using Cytoscape or other visualization tools. Each task is challenging and has been revised over several years to improve the performance. We present a protocol based on our hybrid approaches and show the possibility of presenting each task as an independent web-based tool, NAGGNER for protein name recognition, ProNormz for protein name normalization, PPInterFinder for PPI extraction, and HPIminer for PPI network visualization. The protocol is specific to human but can be generalized to other organisms. We include KinderMiner, our most recent text-mining tool that predicts PPIs by retrieving significant co-occurring protein pairs. The algorithm is simple, easy to implement, and generalizable to other biological challenges.

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Acknowledgments

K.R., F.K., J.S., J.T., and R.S. acknowledge funding from the Morgridge Institute for Research and a grant from Marv Conney. I.R. acknowledges the GeoDeepDive Infrastructure, funded by NSF ICER 1343760.

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Authors and Affiliations

  1. Regenerative Biology, Morgridge Institute for Research, Madison, WI, USA

    Kalpana Raja, Finn Kuusisto, John Steill, James Thomson & Ron Stewart

  2. Data Mining and Text Mining Laboratory, Department of Bioinformatics, School of Life Sciences, Bharathiar University, Coimbatore, Tamil Nadu, India

    Kalpana Raja & Jeyakumar Natarajan

  3. Computer Sciences Department, Center for High Throughput Computing, University of Wisconsin, Madison, WI, USA

    Ian Ross

  4. Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI, USA

    James Thomson

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  1. Kalpana Raja
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  2. Jeyakumar Natarajan
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  3. Finn Kuusisto
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  4. John Steill
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  5. Ian Ross
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  6. James Thomson
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  7. Ron Stewart
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Correspondence to Ron Stewart .

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Editors and Affiliations

  1. Gene Center, Ludwig-Maximilians-Universität München, München, Germany

    Stefan Canzar

  2. Gene Center, Ludwig-Maximilians-Universität München, München, Germany

    Francisca Rojas Ringeling

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Raja, K. et al. (2020). Automated Extraction and Visualization of Protein–Protein Interaction Networks and Beyond: A Text-Mining Protocol. In: Canzar, S., Ringeling, F. (eds) Protein-Protein Interaction Networks. Methods in Molecular Biology, vol 2074. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9873-9_2

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  • DOI: https://doi.org/10.1007/978-1-4939-9873-9_2

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