Knowledge discovery in biology and biotechnology texts: A review of techniques, evaluation strategies, and applications

J. Natarajan, D. Berrar, C. J. Hack, W. Dubitzky

Research output: Contribution to journalReview articlepeer-review

22 Citations (Scopus)

Abstract

Arguably, the richest source of knowledge (as opposed to fact and data collections) about biology and biotechnology is captured in natural-language documents such as technical reports, conference proceedings and research articles. The automatic exploitation of this rich knowledge base for decision making, hypothesis management (generation and testing) and knowledge discovery constitutes a formidable challenge. Recently, a set of technologies collectively referred to as knowledge discovery in text (KDT) has been advocated as a promising approach to tackle this challenge. KDT comprises three main tasks: information retrieval, information extraction and text mining. These tasks are the focus of much recent scientific research and many algorithms have been developed and applied to documents and text in biology and biotechnology. This article introduces the basic concepts of KDT, provides an overview of some of these efforts in the field of bioscience and biotechnology, and presents a framework of commonly used techniques for evaluating KDT methods, tools and systems.

Original languageEnglish
Pages (from-to)31-52
Number of pages22
JournalCritical Reviews in Biotechnology
Volume25
Issue number1-2
DOIs
Publication statusPublished - 2005 Jun 13

Keywords

  • Bioinformatics
  • Information extraction
  • Information retrieval
  • Knowledge discovery in text
  • Text mining

ASJC Scopus subject areas

  • Biotechnology
  • Applied Microbiology and Biotechnology

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