Expansion of the Gene Ontology knowledgebase and resources

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/.

[1]  Tanya Z. Berardini,et al.  TermGenie – a web-application for pattern-based ontology class generation , 2014, J. Biomed. Semant..

[2]  Sejal Patel,et al.  Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism , 2015, BMC Bioinformatics.

[3]  Lincoln D. Stein,et al.  Impact of outdated gene annotations on pathway enrichment analysis , 2016, Nature Methods.

[4]  Henning Hermjakob,et al.  The complex portal - an encyclopaedia of macromolecular complexes , 2014, Nucleic Acids Res..

[5]  P. Altevogt,et al.  Vesiclepedia: A Compendium for Extracellular Vesicles with Continuous Community Annotation , 2012, PLoS biology.

[6]  Kimberly Van Auken,et al.  A method for increasing expressivity of Gene Ontology annotations using a compositional approach , 2014, BMC Bioinformatics.

[7]  Anushya Muruganujan,et al.  PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements , 2016, Nucleic Acids Res..

[8]  Christian Duffin,et al.  The wellcome trust sanger institute. , 2015, Nursing standard (Royal College of Nursing (Great Britain) : 1987).

[9]  Rachael P. Huntley,et al.  The UniProt-GO Annotation database in 2011 , 2011, Nucleic Acids Res..

[10]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[11]  Katrin Rittinger,et al.  Control of Mitotic Exit in Budding Yeast , 2002, The Journal of Biological Chemistry.

[12]  M. Gillespie,et al.  Guidelines for the functional annotation of microRNAs using the Gene Ontology , 2016, RNA.

[13]  Huaiyu Mi,et al.  The InterPro protein families database: the classification resource after 15 years , 2014, Nucleic Acids Res..

[14]  Suzanna Lewis,et al.  Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium , 2011, Briefings Bioinform..

[15]  Shivakumar Keerthikumar,et al.  ExoCarta: A Web-Based Compendium of Exosomal Cargo. , 2016, Journal of molecular biology.

[16]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

[17]  Li Ni,et al.  The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species , 2009, PLoS Comput. Biol..

[18]  Javier Herrero,et al.  Toward community standards in the quest for orthologs , 2012, Bioinform..

[19]  Kei-Hoi Cheung,et al.  Extending gene ontology in the context of extracellular RNA and vesicle communication , 2016, Journal of Biomedical Semantics.

[20]  Maria Jesus Martin,et al.  Big data and other challenges in the quest for orthologs , 2014, Bioinform..

[21]  Chris Mungall,et al.  Use of OWL within the Gene Ontology , 2014, bioRxiv.

[22]  Evan Bolton,et al.  Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..

[23]  Judith A. Blake,et al.  Modeling biochemical pathways in the gene ontology , 2016, Database J. Biol. Databases Curation.

[24]  John Chilton,et al.  The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update , 2016, Nucleic Acids Res..

[25]  Juancarlos Chan,et al.  Gene Ontology Consortium: going forward , 2014, Nucleic Acids Res..