Concept recognition for extracting protein interaction relations from biomedical text

William A. Baumgartner, Zhiyong Lu, Helen L. Johnson, J. Gregory Caporaso, Jesse Paquette, Anna Lindemann, Elizabeth K. White, Olga Medvedeva, K. Bretonnel Cohen, Lawrence Hunter

Research output: Contribution to journalArticlepeer-review

38 Scopus citations


Background: Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasingly difficult task of assimilating the knowledge contained in the biomedical literature. We present an integrated approach to concept recognition in biomedical text. Concept recognition provides key information that has been largely missing from previous biomedical information extraction efforts, namely direct links to well defined knowledge resources that explicitly cement the concept's semantics. The BioCreative II tasks discussed in this special issue have provided a unique opportunity to demonstrate the effectiveness of concept recognition in the field of biomedical language processing. Results: Through the modular construction of a protein interaction relation extraction system, we present several use cases of concept recognition in biomedical text, and relate these use cases to potential uses by the benchside biologist. Conclusion: Current information extraction technologies are approaching performance standards at which concept recognition can begin to deliver high quality data to the benchside biologist. Our system is available as part of the BioCreative Meta-Server project and on the internet

Original languageEnglish (US)
Article numberS9
JournalGenome biology
Issue numberSUPPL. 2
StatePublished - Sep 1 2008

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology


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