Managing MEDLINE: A Comparison of a Native XML Database System with a Relational Database System

The rapid growth of public literature databases like MEDLINE has created the need to efficiently store, retrieve and update the millions of scholarly articles and literature they contain. We believe using alternative database systems like Native XML databases (NXD) will greatly speed up the update process significantly. We used existing and selfdeveloped software packages to parse and load the 2006 release of MEDLINE into two different database systems, namely a NXD (Berkeley DB) and a relational database system (PostgreSQL). The two systems were compared using data collected on loading and parsing times, disk-space utilization and query performance. The NXD offered a significantly faster performance in terms of data parsing and loading times. It was also easier to update and maintain, compared to the relational database system. However, in comparison, the relational database system we tested offered better performance in querying large datasets and was also significantly lower on disk-space utilization.