Topic Categorization of Biomedical Abstracts

Abstract

Nowadays, people frequently use search engines in order to find the information they need on the Web. Especially, Web search constitutes of a basic tool used by million researchers in their everyday work. A very popular indexing engine, concerning life sciences and biomedical research, is PubMed. PubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The present search engines usually return search results in a global ranking, making it difficult for the users to browse in different topics or subtopics. In this work we propose a novel system to address the issues of clustering biomedical search engine results according to their topic. A methodology that exploits semantic text clustering techniques in order to group biomedical document collections in homogeneous topics, is presented and evaluated. In order to provide more accurate clustering results, we utilize various biomedical ontologies, likeMeSH and GeneOntology. Finally, we embed the proposed methodology in an online system that post-processes the PubMed online database so as to provide users the retrieved results according to well formed topics. So as to expose our method as an online real-time service with reasonable response times, we performed a wide range of engineering optimizations along with experimentation on preprocessing time to precision of results trade off.