Integration of the Gene Ontology into an object-oriented architecture

Background: To standardize gene product descriptions, a formal vocabulary defined as the Gene Ontology (GO) has been developed. GO terms have been categorized into biological processes, molecular functions, and cellular components. However, there is no single representation that integrates all the terms into one cohesive model. Furthermore, GO definitions have little information explaining the underlying architecture that forms these terms, such as the dynamic and static events occurring in a process. In contrast, object-oriented models have been developed to show dynamic and static events. A portion of the TGF-beta signaling pathway, which is involved in numerous cellular events including cancer, differentiation and development, was used to demonstrate the feasibility of integrating the Gene Ontology into an object-oriented model. Results: Using object-oriented models we have captured the static and dynamic events that occur during a representative GO process, "transforming grow...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Daniel Shegogue, W. Jim Zheng
• Keywords: BMCBI 2005, Gene Ontology, Gene Products, Object-oriented