OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein tr

Background: Information extraction (IE) efforts are widely acknowledged to be important in harnessing the rapid advance of biomedical knowledge, particularly in areas where important factual information is published in a diverse literature. Here we report on the design, implementation and several evaluations of OpenDMAP, an ontology-driven, integrated concept analysis system. It significantly advances the state of the art in information extraction by leveraging knowledge in ontological resources, integrating diverse text processing applications, and using an expanded pattern language that allows the mixing of syntactic and semantic elements and variable ordering. Results: OpenDMAP information extraction systems were produced for extracting protein transport assertions (transport), protein-protein interaction assertions (interaction) and assertions that a gene is expressed in a cell type (expression). Evaluations were performed on each system, resulting in F-scores ranging from .26

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Lawrence Hunter, Zhiyong Lu, James Firby, William A. Baumgartner Jr., Helen L. Johnson, Philip V. Ogren, K. Bretonnel Cohen
• Keywords: BMCBI 2008, Important Factual Information, Information Extraction, Protein Transport Assertions