A knowledge discovery object model API for Java.
BACKGROUND
Biological data resources have become heterogeneous and derive from multiple sources. This introduces challenges in the management and utilization of this data in software development. Although efforts are underway to create a standard format for the transmission and storage of biological data, this objective has yet to be fully realized.


RESULTS
This work describes an application programming interface (API) that provides a framework for developing an effective biological knowledge ontology for Java-based software projects. The API provides a robust framework for the data acquisition and management needs of an ontology implementation. In addition, the API contains classes to assist in creating GUIs to represent this data visually.


CONCLUSIONS
The Knowledge Discovery Object Model (KDOM) API is particularly useful for medium to large applications, or for a number of smaller software projects with common characteristics or objectives. KDOM can be coupled effectively with other biologically relevant APIs and classes. Source code, libraries, documentation and examples are available at http://www.bcgsc.ca/bioinfo/software.
Zuyderduyn
Scott D
SD
Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 600 West 10th Ave, Vancouver, Canada. scottz@bcgsc.ca
Jones
Steven J M
SJ
D001185:Artificial Intelligence; D003196:Computer Graphics; D003628:Database Management Systems / Q000145:classification / Q000639:trends; D030541:Databases, Genetic / Q000145:classification / Q000639:trends; D011381:Programming Languages; D012984:Software / Q000639:trends*; D012985:Software Design; D018511:Systems Integration; D014584:User-Computer Interface