Cohen and Hersh Briefings in Bioinformatics 2005

Citation

Aaron M. Cohen and William R. Hersh. 2005. A Survey of Current Work in Biomedical Text Mining. Briefings in Bioinformatics. Vol 6. No 1. 57-71.

Online version

oxfordjournals

Summary

This is a survey paper about biomedical text mining in 2005.

They describe the state of the art in 2005 for each distinct type of text-mining task below.

• Named entity recognition
  • Problems
    • No complete dictionary for most types of biological named entities
    • ambiguous words and phrases
    • multi names
  • approaches
    • lexicon based
    • rule based
      • AbGene system of Tanabe and Wilbur
      • GAPSCORE system
    • statistically based
  • performance
    • overall, the performance of gene and protein NER systems is F-scores between 75 and 85 percent.

• Text classification

• Synonym and abbreviation extraction

• Relationship extraction

• Hypothesis generation

• Integration frameworks

Related papers

The widely cited Pang et al EMNLP 2002 paper was influenced by this paper - but considers supervised learning techniques. The choice of movie reviews as the domain was suggested by the (relatively) poor performance of Turney's method on movies.

An interesting follow-up paper is Turney and Littman, TOIS 2003 which focuses on evaluation of the technique of using PMI for predicting the semantic orientation of words.