Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases

Background: Complex biological database systems have become key computational tools used daily by scientists and researchers. Many of these systems must be capable of executing on multiple different hardware and software configurations and are also often made available to users via the Internet. We have used the Java Data Object (JDO) persistence technology to develop the database layer of such a system known as the SigPath information management system. SigPath is an example of a complex biological database that needs to store various types of information connected by many relationships. Results: Using this system as an example, we perform a critical evaluation of current JDO technology; discuss the suitability of the JDO standard to achieve portability, scalability and performance. We show that JDO supports portability of the SigPath system from a relational database backend to an object database backend and achieves acceptable scalability. To answer the performance question, we hav...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Marko Srdanovic, Ulf Schenk, Michael Schwieger, Fabien Campagne
• Keywords: Biological Databases, BMCBI 2005, Complex Biological Databases, JDO Technology