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Comparing Bibliometric Analysis Using PubMed, Scopus, and Web of Science Databases
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Published on: October 24, 2019

HERMES: an open-source mining tool for open-access literature.

Julien Charest1, Katarina Priselac1, Georg H Reischer1

  • 1Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Wien 1060, Austria.

Bioinformatics Advances
|March 4, 2026
PubMed
Summary
This summary is machine-generated.

Researchers can now efficiently find and rank open-access biomedical literature using HERMES, an open-source tool. This literature mining software offers customizable search criteria and reproducible results for specialized fields.

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Area of Science:

  • Biomedical Informatics
  • Computational Biology
  • Scientific Literature Analysis

Background:

  • The rapid expansion of open-access scientific literature creates challenges in identifying relevant publications.
  • Current search engines lack user-defined ranking, reproducibility, and domain-specific criteria integration.
  • Specialized research fields require nuanced approaches for literature prioritization.

Purpose of the Study:

  • To introduce HERMES, an open-source tool for targeted retrieval and ranking of full-text open-access publications.
  • To provide researchers with a transparent, customizable, and efficient method for literature discovery.
  • To address the limitations of existing search engines in specialized scientific domains.

Main Methods:

  • HERMES utilizes a composite scoring algorithm integrating keyword frequency, citation counts, and publication age.
  • The tool supports features like summarization, biomedical entity recognition, and PDF report generation.
  • An intuitive graphical user interface (GUI) and multithreaded processing facilitate complex and large-scale literature mining.

Main Results:

  • HERMES enables targeted retrieval and ranking of publications from PubMed Central (PMC).
  • The composite scoring algorithm effectively prioritizes relevant literature based on user-defined criteria.
  • The GUI and efficient processing empower researchers, including those without programming expertise.

Conclusions:

  • HERMES offers a reproducible and adaptable framework for scientific literature discovery.
  • The tool enhances transparency and facilitates rapid identification of relevant publications.
  • HERMES promotes community-driven extension and customization for diverse research needs.