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

Abstract

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 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.

Conclusions: 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.

Figure 1

Instance graph for representation of a reaction between three chemicals (e.g., A ↔ B + C). Some of the relationships that support navigation from reactions to chemicals are shown, as well as links between chemicals. The three chemicals are produced by the "human" organism. Quantitative kinetic parameters are also shown for the reaction (backward and forward rate of the reaction). The figure illustrates how a graph of object instances is used to represent biological information corresponding to a biochemical reaction.

Figure 2

Fragment of the UML diagram for the SigPath ontology/database schema. The Figure shows how instances of certain classes are related and how the relationships among classes can be used to represent information. The link between Reaction and Chemical expresses the information that reactions transforms chemicals, and that chemical can be substrate or products of reactions. The classes and attribute marked in orange are specific to the SigPath ontology and have no equivalent in the EcoCyc ontology.

Figure 3

Work-around for classes that contain an object field.

Figure 4

Work around for classes that have String getter and setters, when empty strings can be made persistent.

Figure 5

Example of JDO file. This file is used to define the persistent classes that are used in SigPath to represent end-users. Four persistent classes are shown: Address, Affiliation, User and UserRole. The <field> element can be used to refer to specific fields of persistent classes (such as the username field of class User on this example). The userRoles field is described to be a collection that contains elements of type UserRole. Elements called <extension> make it possible to provide vendor specific directives, such as to define indices on a persistent field.

Figure 6

Illustration of the use of interfaces to express is-a relationships among biological concepts. Circles represent interfaces while boxes represent classes. An arrow from one class to an interface indicate that the class implement the interface, and this relationship can be used to indicate that instances of the class have the properties described by one or several interfaces.