ArticleBMC bioinformatics2005
Integration of the Gene Ontology into an object-oriented architecture.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
6 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of nasopharyngeal carcinoma microarray data explores mechanism of EBV-regulated neoplastic transformation.BMC genomics · 2008Pooled it
- The Compressed Vocabulary of Microbial Life.Frontiers in microbiology · 2021Article
- Towards refactoring the Molecular Function Ontology with a UML profile for function modeling.Journal of biomedical semantics · 2017Article
- The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data.PloS one · 2017Article
- GOFFA: gene ontology for functional analysis--a FDA gene ontology tool for analysis of genomic and proteomic data.BMC bioinformatics · 2006Article
- The eighth annual bio-ontologies meeting.PLoS computational biology · 2005Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
backgroundTo 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.
resultsUsing 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).
conclusionWe 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.
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Registered trials
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