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. 2017 Jan 4;45(D1):D331-D338.
doi: 10.1093/nar/gkw1108. Epub 2016 Nov 29.

Expansion of the Gene Ontology knowledgebase and resources

Expansion of the Gene Ontology knowledgebase and resources

The Gene Ontology Consortium. Nucleic Acids Res. .

Abstract

The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools. Among the highlights are 1) developments that facilitate access to, and application of, the GO knowledgebase, and 2) extensions to the resource as well as increasing support for descriptions of causal models of biological systems and network biology. To learn more, visit http://geneontology.org/.

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Figures

Figure 1.
Figure 1.
GO PubMed article page. All GO annotations that cite the article as evidence are shown on the page (table in lower right). Summary information on the article is obtained from NCBI web services (upper panel). Lower left panel shows general AmiGO2 filtering functionality: clicking on any of the data types (e.g. Ontology (aspect)) will allow selection of filters to apply.
Figure 2.
Figure 2.
LEGO connects annotations. (A) Conventional annotations for two genes, and (B) the same annotations connected together in a LEGO model. This example shows ‘The activity of BFA1 (in spindle pole body) inhibits the GTPase activity of TEM1, as part-of exit from mitosis.’ Additional context, e.g. cell type, etc. can be added (not shown). Curated from data in (22).

References

    1. The Gene Ontology Consortium. Gene ontology consortium: going forward. Nucleic Acids Res. 2015;43:D1049–D1056. - PMC - PubMed
    1. Dietze H., Berardini T.Z., Foulger R.E., Hill D.P., Lomax J., Osumi-Sutherland D., Roncaglia P., Mungall C.J. TermGenie—a web-application for pattern-based ontology class generation. J. Biomed. Semantics. 2014;5:48. - PMC - PubMed
    1. Mungall C.J., Dietze H., Osumi-Sutherland D. Use of OWL within the gene ontology. BioRxiv. 2014:010090.
    1. Patel S., Roncaglia P., Lovering R.C. Using gene ontology to describe the role of the neurexin-neuroligin-shank complex in human, mouse and rat and its relevance to autism. BMC Bioinformatics. 2015;16:186. - PMC - PubMed
    1. Cheung K.H., Keerthikumar S., Roncaglia P., Subramanian S.L., Roth M.E., Samuel M., Anand S., Gangoda L., Gould S., Alexander R., et al. Extending gene ontology in the context of extracellular RNA and vesicle communication. J. Biomed. Semantics. 2016;7:19. - PMC - PubMed

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