Biological ontology enhancement with fuzzy relations: a text-mining framework

Abstract

Domain ontology can help in information retrieval from documents. But ontology is a pre-defined structure with crisp concept descriptions and inter-concept relations. However, due to the dynamic nature of the document repository, ontology should be upgradeable with information extracted through text mining of documents in the domain. This also necessitates that concepts, their descriptions and inter-concept relations should be associated with a degree of fuzziness that will indicate the support for the extracted knowledge according to the currently available resources. Supports may be revised with more knowledge coming in future. This approach preserves the basic structured knowledge format for storing domain knowledge, but at the same time allows for update of information. In this paper, we have proposed a mechanism which initiates text mining with a set of ontological concepts, and thereafter extracts fuzzy relations through text mining. Membership values of relations are functions of frequency of co-occurrence of concepts and relations. We have worked on the GENIA corpus and shown how fuzzy relations can be further used for guided information extraction from MEDLINE documents.