Integration of the Gene Ontology into an object-oriented architecture
Abstract
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.
- Authors:
-
- Medical Univ. of South Carolina, Charleston, SC (United States). Dept. of Biostatistics, Bioinformatics and Epidemiology
- 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
- Publication Date:
- Research Org.:
- Medical Univ. of South Carolina, Charleston, SC (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1626304
- Grant/Contract Number:
- FG02-01ER63121
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Bioinformatics
- Additional Journal Information:
- Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 1471-2105
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Mathematical & Computational Biology
Citation Formats
Shegogue, Daniel, and Zheng, W. Jim. Integration of the Gene Ontology into an object-oriented architecture. United States: N. p., 2005.
Web. doi:10.1186/1471-2105-6-113.
Shegogue, Daniel, & Zheng, W. Jim. Integration of the Gene Ontology into an object-oriented architecture. United States. https://doi.org/10.1186/1471-2105-6-113
Shegogue, Daniel, and Zheng, W. Jim. Tue .
"Integration of the Gene Ontology into an object-oriented architecture". United States. https://doi.org/10.1186/1471-2105-6-113. https://www.osti.gov/servlets/purl/1626304.
@article{osti_1626304,
title = {Integration of the Gene Ontology into an object-oriented architecture},
author = {Shegogue, Daniel and Zheng, W. Jim},
abstractNote = {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.},
doi = {10.1186/1471-2105-6-113},
journal = {BMC Bioinformatics},
number = 1,
volume = 6,
place = {United States},
year = {Tue May 10 00:00:00 EDT 2005},
month = {Tue May 10 00:00:00 EDT 2005}
}
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Works referenced in this record:
Modeling transcriptional regulatory networks
journal, November 2002
- Bolouri, Hamid; Davidson, Eric H.
- BioEssays, Vol. 24, Issue 12
Hierarchical thinking in network biology: the unbiased modularization of biochemical networks
journal, December 2004
- Papin, J.; Reed, J.; Palsson, B.
- Trends in Biochemical Sciences, Vol. 29, Issue 12
Formation of hetero-oligomeric complexes of type I and type II receptors for transforming growth factor-beta.
journal, August 1994
- Yamashita, H.; ten Dijke, P.; Franzén, P.
- Journal of Biological Chemistry, Vol. 269, Issue 31
SARA, a FYVE Domain Protein that Recruits Smad2 to the TGFβ Receptor
journal, December 1998
- Tsukazaki, Tomoo; Chiang, Theodore A.; Davison, Anne F.
- Cell, Vol. 95, Issue 6
Ubiquitin-dependent degradation of TGF-β-activated Smad2
journal, October 1999
- Lo, Roger S.; Massagué, Joan
- Nature Cell Biology, Vol. 1, Issue 8
Systems biology markup language: Level 2 and beyond
journal, December 2003
- Finney, A.; Hucka, M.
- Biochemical Society Transactions, Vol. 31, Issue 6
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
journal, March 2003
- Hucka, M.; Finney, A.; Sauro, H. M.
- Bioinformatics, Vol. 19, Issue 4
Gene-Ontology-based clustering of gene expression data
journal, April 2004
- Adryan, Boris; Schuh, Reinhard
- Bioinformatics, Vol. 20, Issue 16
Object-oriented biological system integration: a SARS coronavirus example
journal, February 2005
- Shegogue, Daniel; Zheng, W. Jim
- Bioinformatics, Vol. 21, Issue 10
Predicting Gene Ontology Biological Process From Temporal Gene Expression Patterns
journal, April 2003
- Lægreid, Astrid; Hvidsten, Torgeir R.; Midelfart, Herman
- Genome Research, Vol. 13, Issue 5
Predicting Gene Ontology Functions from ProDom and CDD Protein Domains
journal, April 2002
- Schug, Jonathan; Diskin, Sharon; Mazzarelli, Joan
- Genome Research, Vol. 12, Issue 4
Ontologies for Biologists: A Community Model for the Annotation of Genomic Data
journal, January 2003
- Ashburner, M.; Mungall, C. J.; Lewis, S. E.
- Cold Spring Harbor Symposia on Quantitative Biology, Vol. 68, Issue 0
Requirement of Type III TGF- Receptor for Endocardial Cell Transformation in the Heart
journal, March 1999
- Brown, C. B.
- Science, Vol. 283, Issue 5410
Tumor Suppressor Smad4 Is a Transforming Growth Factor β-Inducible DNA Binding Protein
journal, December 1997
- Yingling, Jonathan M.; Datto, Michael B.; Wong, Carolyn
- Molecular and Cellular Biology, Vol. 17, Issue 12
Functional Discrimination of gene Expression Patterns in Terms of the gene Ontology
conference, December 2002
- Badea, Liviu
- Biocomputing 2003
Functional Relationship and Gene Ontology Classification of Breast Cancer Biomarkers
journal, October 2003
- Arciero, C.; Somiari, S. B.; Shriver, C. D.
- The International Journal of Biological Markers, Vol. 18, Issue 4
Design and implementation of microarray gene expression markup language (MAGE-ML)
journal, August 2002
- Spellman, Paul T.; Miller, Michael; Stewart, Jason
- Genome Biology, Vol. 3, Issue 9
An example of an activity diagram showing the main and alternative flow of events occurring during TGF-beta receptor complex assembly (GO:0007181)
image, January 2011
- Shegogue, Daniel; Zheng, W. Jim
- figshare
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- Koç, Ibrahim; Caetano-Anollés, Gustavo
- PLOS ONE, Vol. 12, Issue 5
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journal, October 2017
- Burek, Patryk; Loebe, Frank; Herre, Heinrich
- Journal of Biomedical Semantics, Vol. 8, Issue 1
GOFFA: Gene Ontology For Functional Analysis – A FDA Gene Ontology Tool for Analysis of Genomic and Proteomic Data
journal, September 2006
- Sun, Hongmei; Fang, Hong; Chen, Tao
- BMC Bioinformatics, Vol. 7, Issue S2
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journal, January 2008
- Chen, Xia; Liang, Shuang; Zheng, WenLing
- BMC Genomics, Vol. 9, Issue 1