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

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 have created the SigPath JDO application benchmark that we distribute under the Gnu General Public License. This benchmark can be used as an example of using JDO technology to create a complex biological database and makes it possible for vendors and users of the technology to evaluate the performance of other JDO implementations for similar applications.The SigPath JDO benchmark and our discussion of JDO technology in the context of biological databases will be useful to bioinformaticians who design new complex biological databases and aim to create systems that can be ported easily to a variety of database backends.Biological databases are key computational tools used daily by biologists. Such a large number of biological databases have been developed for biology that the Nucleic Acids Research Journal has published an annual database issue since 1996. From the point of view of the user, these resources are most useful when they are regularly updated and when they provide user-friendly ways to browse, search and view information. These user needs are generally recognized as important requirements by the designers and developers of biological databases. To cope with these requirements, bioinformaticians who develop the biological databases have typically responded by developing increasingly customized software to manage the data and the information (e.g., [1-4]). In doing so, and to facilitate the software development effort needed to create a biological database, bioinformaticians have used a variety of information technologies. These technologies range from the ones that make it