Towards applying text mining and natural language processing for biomedical ontology acquisition

Authors:
Tasha R. Inniss;John R. Lee;Marc Light;Michael A. Grassi;George Thomas;Andrew B. Williams
Affiliations:
Spelman College, Atlanta, GA;Assistive Intelligence, Inc., Iowa City, IA;Thomson Legal and Regulatory, Eagan, MN;University of Chicago, Chicago, IL;University of Iowa, Iowa City, IA;Spelman College, Atlanta, GA
Venue:
TMBIO '06 Proceedings of the 1st international workshop on Text mining in bioinformatics
Year:
2006

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Abstract

The use of text mining and natural language processing can extend into the realm of knowledge acquisition and management for biomedical applications. In this paper, we describe how we implemented natural language processing and text mining techniques on the transcribed verbal descriptions from retinal experts of biomedical disease features. The feature-attribute pairs generated were then incorporated within a user interface for a collaborative ontology development tool. This tool, IDOCS, is being used in the biomedical domain to help retinal specialists reach a consensus on a common ontology for describing age-related macular degeneration (AMD). We compare the use of traditional text mining and natural language processing techniques with that of a retinal specialist's analysis and discuss how we might integrate these techniques for future biomedical ontology and user interface development.