MyMED: A database system for biomedical research on MEDLINE data

MyMED is a database system that mirrors MEDLINETM data and that provides access to the data locally, without the restrictions involved in accessing the National Library of Medicine Web site. The implementation of MyMED is based on the IBM DB2 Universal DatabaseTM, the DB2® XML Extender and the DB2 Text Information Extender. The resulting system supports advanced queries, including wildcard searching abilities, proximity searching, scoring functions, and capabilities to build a thesaurus, and constitutes an important research tool for text mining of biomedical-citation data. The paper describes the challenges encountered in the use of DB2 ExtendersTM products, the methods used to overcome these challenges, and the implementation of MyMED. The benefits of MyMED are illustrated through some use cases, and directions for future work are outlined.