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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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A Text Mining Protocol for Mining Biological Pathways and Regulatory Networks from Biomedical Literature.

Sabenabanu Abdulkadhar1, Jeyakumar Natarajan2

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

Methods in Molecular Biology (Clifton, N.J.)
|June 17, 2022
PubMed
Summary

This study reviews biological pathways and construction methods from scientific literature. It introduces a novel hybrid text mining protocol for extracting pathways and gene regulatory networks.

Keywords:
Automatic curationBiological pathwaysKnowledge DiscoveryRegulatory NetworksText Mining

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Area of Science:

  • System biology
  • Bioinformatics
  • Computational biology

Background:

  • Biological pathways regulate cellular processes and molecule assembly.
  • Key pathways include signaling, metabolic, and gene regulatory networks.
  • Scientific literature is a rich source for extracting biological associations.

Purpose of the Study:

  • To provide an overview of biological pathways.
  • To review biomedical text resources for network construction.
  • To present a hybrid text mining protocol for pathway and network extraction.

Main Methods:

  • Literature review of biological pathways and construction methods.
  • Analysis of biomedical text resources and corpora.
  • Development of a hybrid text mining protocol.

Main Results:

  • Overview of different biological pathway types.
  • Identification of relevant biomedical text resources.
  • Presentation of a novel hybrid text mining protocol.

Conclusions:

  • Scientific literature is crucial for biological network construction.
  • The proposed hybrid protocol offers a new approach for pathway and regulatory network extraction.