Mining the Biomedical Literature in the Genomic Era: An Overview

Hagit Shatkay*, Ronen Feldman

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

195 Scopus citations


The past decade has seen a tremendous growth in the amount of experimental and computational biomedical data, specifically in the areas of genomics and proteomics. This growth is accompanied by an accelerated increase in the number of biomedical publications discussing the findings. In the last few years, there has been a lot of interest within the scientific community in literature-mining tools to help sort through this abundance of literature and find the nuggets of information most relevant and useful for specific analysis tasks. This paper provides a road map to the various literature-mining methods, both in general and within bioinformatics. It surveys the disciplines involved in unstructured-text analysis, categorizes current work in biomedical literature mining with respect to these disciplines, and provides examples of text analysis methods applied towards meeting some of the current challenges in bioinformatics.

Original languageAmerican English
Pages (from-to)821-855
Number of pages35
JournalJournal of Computational Biology
Issue number6
StatePublished - 2003
Externally publishedYes


  • Biomedical literature mining
  • Genomics
  • Information extraction
  • Information retrieval
  • PubMed
  • Text mining


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