Biological relation extraction and query answering from MEDLINE abstracts using ontology-based text mining

The rapid growth of the biological text data repository makes it difficult for human beings to access required information in a convenient and effective manner. The problem arises due to the fact that most of the information is embedded within unstructured or semi-structured text that computers cannot interpret very easily. In this paper we have presented an ontology-based Biological Information Extraction and Query Answering (BIEQA) System, which initiates text mining with a set of concepts stored in a biological ontology, and thereafter mines possible biological relations among those concepts using NLP techniques and co-occurrence-based analysis. The system extracts all frequently occurring biological relations among a pair of biological concepts through text mining. A mined relation is associated to a fuzzy membership value, which is proportional to its frequency of occurrence in the corpus and is termed a fuzzy biological relation. The fuzzy biological relations extracted from a text corpus along with other relevant information components like biological entities occurring within a relation, are stored in a database. The database is integrated with a query-processing module. The query-processing module has an interface, which guides users to formulate biological queries at different levels of specificity. (c) 2006 Elsevier B.V. All rights reserved.