Integration of the Gene Ontology into an object-oriented architecture

Journal Article · 10 May 2005 · BMC Bioinformatics

DOI: https://doi.org/10.1186/1471-2105-6-113 · OSTI ID:1626304

Shegogue, Daniel ^[1]; Zheng, W. Jim ^[2]

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1. Medical Univ. of South Carolina, Charleston, SC (United States). Dept. of Biostatistics, Bioinformatics and Epidemiology
2. Medical Univ. of South Carolina, Charleston, SC (United States). Dept. of Biostatistics, Bioinformatics and Epidemiology; Medical Univ. of South Carolina, Charleston, SC (United States). Hollings Cancer Center. Bioinormatics Core Facility

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 growth factor-beta (TGF-beta) receptor complex assembly" (GO:0007181). Conclusion: We demonstrate that the utility of GO terms can be enhanced by object-oriented technology, and that the GO terms can be integrated into an object-oriented model by serving as a basis for the generation of object functions and attributes.

• Research Organization: Medical Univ. of South Carolina, Charleston, SC (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
• Grant/Contract Number: FG02-01ER63121
• OSTI ID: 1626304
• Journal Information: BMC Bioinformatics, Vol. 6, Issue 1; ISSN 1471-2105
• Publisher: BioMed CentralCopyright Statement
• Country of Publication: United States
• Language: English