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Related Experiment Video

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Comparing Bibliometric Analysis Using PubMed, Scopus, and Web of Science Databases
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Advanced literature analysis in a Big Data world.

Chris Cheadle1,2, Hongbao Cao1, Andrey Kalinin1

  • 1Department of Genomics Research, R&D Solutions, Rockville, Maryland.

Annals of the New York Academy of Sciences
|November 19, 2016
PubMed
Summary

Pathway Studio software uses natural language processing to mine scientific literature for biological insights. This enables biomarker discovery and enhanced neuroscience research through structured data and novel brain region taxonomy.

Keywords:
Pathway Studioliterature analysisliterature data miningnatural language processing

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Neuroscience

Background:

  • Scientific literature data mining presents significant challenges due to volume and complexity.
  • Extracting specific biological information requires advanced computational techniques.

Purpose of the Study:

  • To present Elsevier's Pathway Studio software for systematic biological information extraction.
  • To demonstrate a structured information approach for biomarker discovery using a use case.
  • To introduce a novel taxonomy for enhanced neuroscience research data retrieval.

Main Methods:

  • Utilizing natural language processing (NLP) to extract biological data from scientific literature.
  • Building a large, structured literature knowledgebase with Pathway Studio.
  • Employing sophisticated visualization tools for database exploration.
  • Applying a biomarker use case across four major neuropsychiatric diseases.

Main Results:

  • A comprehensive collection of biomarkers and biomarker candidates was identified from literature.
  • Common and unique biomarker elements were demonstrated for neuropsychiatric diseases.
  • Specific enrichment patterns were observed, aiding novel biomarker discovery.
  • A new brain region identification taxonomy was introduced, enhancing information retrieval.

Conclusions:

  • Pathway Studio provides a powerful platform for structured biological data mining and knowledge discovery.
  • The structured approach facilitates biomarker identification and understanding of neuropsychiatric disease associations.
  • The novel taxonomy significantly improves data accessibility and depth for neuroscience research.