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A Text Mining Protocol for Mining Biological Pathways and Regulatory Networks from Biomedical Literature

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Biomedical Text Mining

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2496))

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Abstract

A biological pathway or regulatory network is a collection of molecular regulators which can activate the changes in cellular processes leading to an assembly of new molecules by series of actions among the molecules. There are three important pathways in system biology studies namely signaling pathways, metabolic pathways, and genetic pathways (or) gene regulatory networks. Recently, biological pathway construction from scientific literature is given much attention as the scientific literature contains a rich set of linguistic features to extract biological associations between genes and proteins. These associations can be united to construct biological networks. Here, we present a brief overview about various biological pathways, biomedical text resources/corpora for network construction and state-of-the-art existing methods for network construction followed by our hybrid text mining protocol for extracting pathways and regulatory networks from biomedical literature.

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Authors and Affiliations

  1. Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamilnadu, India

    Sabenabanu Abdulkadhar & Jeyakumar Natarajan

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  1. Sabenabanu Abdulkadhar
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  2. Jeyakumar Natarajan
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  1. Morgridge Institute for Research, University of Wisconsin, Madison, WI, USA

    Kalpana Raja

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Abdulkadhar, S., Natarajan, J. (2022). A Text Mining Protocol for Mining Biological Pathways and Regulatory Networks from Biomedical Literature. In: Raja, K. (eds) Biomedical Text Mining. Methods in Molecular Biology, vol 2496. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2305-3_8

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  • DOI: https://doi.org/10.1007/978-1-0716-2305-3_8

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  • Publisher Name: Humana, New York, NY

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  • Online ISBN: 978-1-0716-2305-3

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