Journal article

HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA

K Bretonnel Cohen, Karin Verspoor, Helen L Johnson, Chris Roeder, Philip V Ogren, William A Baumgartner, Elizabeth White, Hannah Tipney, Lawrence Hunter

Computational Intelligence | WILEY | Published : 2011

Abstract

We approached the problems of event detection, argument identification, and negation and speculation detection in the BioNLP'09 information extraction challenge through concept recognition and analysis. Our methodology involved using the OpenDMAP semantic parser with manually written rules. The original OpenDMAP system was updated for this challenge with a broad ontology defined for the events of interest, new linguistic patterns for those events, and specialized coordination handling. We achieved state-of-the-art precision for two of the three tasks, scoring the highest of 24 teams at precision of 71.81 on Task 1 and the highest of 6 teams at precision of 70.97 on Task 2. We provide a detai..

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Grants

Awarded by NIH


Awarded by NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES


Awarded by NATIONAL LIBRARY OF MEDICINE


Funding Acknowledgements

This work was supported by NIH grants R01LM009254, R01GM083649, and R01LM008111 to Lawrence Hunter and T15LM009451 to Philip Ogren.