Exploiting context for biomedical entity recognition: from syntax to the web

Authors:
Jenny Finkel;Shipra Dingare;Huy Nguyen;Malvina Nissim;Christopher Manning;Gail Sinclair
Affiliations:
Stanford University, Stanford, CA;University of Edinburgh, Edinburgh, United Kingdom;Stanford University, Stanford, CA;University of Edinburgh, Edinburgh, United Kingdom;Stanford University, Stanford, CA;University of Edinburgh, Edinburgh, United Kingdom
Venue:
JNLPBA '04 Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications
Year:
2004

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Abstract

We describe a machine learning system for the recognition of names in biomedical texts. The system makes extensive use of local and syntactic features within the text, as well as external resources including the web and gazetteers. It achieves an F-score of 70% on the Coling 2004 NLPBA/BioNLP shared task of identifying five biomedical named entities in the GENIA corpus.