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Pac Symp Biocomput. 2007:209-20.

Extracting semantic predications from Medline citations for pharmacogenomics.

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Lister Hill National Center for Biomedical Communications, National Library of Medicine Bethesda, Maryland 20894, USA.


We describe a natural language processing system (Enhanced SemRep) to identify core assertions on pharmacogenomics in Medline citations. Extracted information is represented as semantic predications covering a range of relations relevant to this domain. The specific relations addressed by the system provide greater precision than that achievable with methods that rely on entity co-occurrence. The development of Enhanced SemRep is based on the adaptation of an existing system and crucially depends on domain knowledge in the Unified Medical Language System. We provide a preliminary evaluation (55% recall and 73% precision) and discuss the potential of this system in assisting both clinical practice and scientific investigation.

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