- Gene Ontology Consortium: going forward. [PMID: 25428369]
Nucleic acids research 2015:43(Database issue)
150 Citations (Google Scholar as of 2016-03-26)
Abstract: The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
- Gene Ontology annotations and resources. [PMID: 23161678]
null null, J A Blake, M Dolan, H Drabkin, D P Hill, Ni Li, D Sitnikov, S Bridges, S Burgess, T Buza, F McCarthy, D Peddinti, L Pillai, S Carbon, H Dietze, A Ireland, S E Lewis, C J Mungall, P Gaudet, R L Chrisholm, P Fey, W A Kibbe, S Basu, D A Siegele, B K McIntosh, D P Renfro, A E Zweifel, J C Hu, N H Brown, S Tweedie, Y Alam-Faruque, R Apweiler, A Auchinchloss, K Axelsen, B Bely, M -C Blatter, C Bonilla, L Bouguerleret, E Boutet, L Breuza, A Bridge, W M Chan, G Chavali, E Coudert, E Dimmer, A Estreicher, L Famiglietti, M Feuermann, A Gos, N Gruaz-Gumowski, R Hieta, C Hinz, C Hulo, R Huntley, J James, F Jungo, G Keller, K Laiho, D Legge, P Lemercier, D Lieberherr, M Magrane, M J Martin, P Masson, P Mutowo-Muellenet, C O'Donovan, I Pedruzzi, K Pichler, D Poggioli, P Porras Millán, S Poux, C Rivoire, B Roechert, T Sawford, M Schneider, A Stutz, S Sundaram, M Tognolli, I Xenarios, R Foulgar, J Lomax, P Roncaglia, V K Khodiyar, R C Lovering, P J Talmud, M Chibucos, M Gwinn Giglio, H -Y Chang, S Hunter, C McAnulla, A Mitchell, A Sangrador, R Stephan, M A Harris, S G Oliver, K Rutherford, V Wood, J Bahler, A Lock, P J Kersey, D M McDowall, D M Staines, M Dwinell, M Shimoyama, S Laulederkind, T Hayman, S -J Wang, V Petri, T Lowry, P D'Eustachio, L Matthews, R Balakrishnan, G Binkley, J M Cherry, M C Costanzo, S S Dwight, S R Engel, D G Fisk, B C Hitz, E L Hong, K Karra, S R Miyasato, R S Nash, J Park, M S Skrzypek, S Weng, E D Wong, T Z Berardini, E Huala, H Mi, P D Thomas, J Chan, R Kishore, P Sternberg, K Van Auken, D Howe, M Westerfield
Nucleic acids research 2013:41(Database issue)
207 Citations (Google Scholar as of 2016-03-26)
Abstract: The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.
- The Gene Ontology: enhancements for 2011. [PMID: 22102568]
Nucleic acids research 2012:40(Database issue)
156 Citations (Google Scholar as of 2016-03-26)
Abstract: The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. The number of GO annotations of gene products has increased due to curation efforts among GO Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. The GO ontologies continue to expand and improve as a result of targeted ontology development, including the introduction of computable logical definitions and development of new tools for the streamlined addition of terms to the ontology. The GOC continues to support its user community through the use of e-mail lists, social media and web-based resources.
- The Gene Ontology in 2010: extensions and refinements. [PMID: 19920128]
Nucleic acids research 2010:38(Database issue)
314 Citations (Google Scholar as of 2016-03-26)
Abstract: The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. These improve the representation of biology, facilitate querying, and allow GO developers to systematically check for and correct inconsistencies within the GO. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use.
- The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. [PMID: 19578431]
PLoS computational biology 2009:5(7)
87 Citations (Google Scholar as of 2016-03-26)
Abstract: The Gene Ontology (GO) is a collaborative effort that provides structured vocabularies for annotating the molecular function, biological role, and cellular location of gene products in a highly systematic way and in a species-neutral manner with the aim of unifying the representation of gene function across different organisms. Each contributing member of the GO Consortium independently associates GO terms to gene products from the organism(s) they are annotating. Here we introduce the Reference Genome project, which brings together those independent efforts into a unified framework based on the evolutionary relationships between genes in these different organisms. The Reference Genome project has two primary goals: to increase the depth and breadth of annotations for genes in each of the organisms in the project, and to create data sets and tools that enable other genome annotation efforts to infer GO annotations for homologous genes in their organisms. In addition, the project has several important incidental benefits, such as increasing annotation consistency across genome databases, and providing important improvements to the GO's logical structure and biological content.
- The Gene Ontology project in 2008. [PMID: 17984083]
Nucleic acids research 2008:36(Database issue)
343 Citations (Google Scholar as of 2016-03-26)
Abstract: The Gene Ontology (GO) project (http://www.geneontology.org/) provides a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see http://www.sequenceontology.org/). The ontologies have been extended and refined for several biological areas, and improvements to the structure of the ontologies have been implemented. To improve the quantity and quality of gene product annotations available from its public repository, the GO Consortium has launched a focused effort to provide comprehensive and detailed annotation of orthologous genes across a number of 'reference' genomes, including human and several key model organisms. Software developments include two releases of the ontology-editing tool OBO-Edit, and improvements to the AmiGO browser interface.
- The Gene Ontology (GO) project in 2006. [PMID: 16381878]
Nucleic acids research 2006:34(Database issue)
455 Citations (Google Scholar as of 2016-03-26)
Abstract: The Gene Ontology (GO) project (http://www.geneontology.org) develops and uses a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see http://song.sourceforge.net/). The GO Consortium continues to improve to the vocabulary content, reflecting the impact of several novel mechanisms of incorporating community input. A growing number of model organism databases and genome annotation groups contribute annotation sets using GO terms to GO's public repository. Updates to the AmiGO browser have improved access to contributed genome annotations. As the GO project continues to grow, the use of the GO vocabularies is becoming more varied as well as more widespread. The GO project provides an ontological annotation system that enables biologists to infer knowledge from large amounts of data.
- The Gene Ontology (GO) database and informatics resource. [PMID: 14681407]
M A Harris, J Clark, A Ireland, J Lomax, M Ashburner, R Foulger, K Eilbeck, S Lewis, B Marshall, C Mungall, J Richter, G M Rubin, J A Blake, C Bult, M Dolan, H Drabkin, J T Eppig, D P Hill, L Ni, M Ringwald, R Balakrishnan, J M Cherry, K R Christie, M C Costanzo, S S Dwight, S Engel, D G Fisk, J E Hirschman, E L Hong, R S Nash, A Sethuraman, C L Theesfeld, D Botstein, K Dolinski, B Feierbach, T Berardini, S Mundodi, S Y Rhee, R Apweiler, D Barrell, E Camon, E Dimmer, V Lee, R Chisholm, P Gaudet, W Kibbe, R Kishore, E M Schwarz, P Sternberg, M Gwinn, L Hannick, J Wortman, M Berriman, V Wood, N de la Cruz, P Tonellato, P Jaiswal, T Seigfried, R White, null null
Nucleic acids research 2004:32(Database issue)
2445 Citations (Google Scholar as of 2016-03-26)
Abstract: The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.
- Creating the gene ontology resource: design and implementation. [PMID: 11483584]
Genome research 2001:11(8)
960 Citations (Google Scholar as of 2016-03-26)
Abstract: The exponential growth in the volume of accessible biological information has generated a confusion of voices surrounding the annotation of molecular information about genes and their products. The Gene Ontology (GO) project seeks to provide a set of structured vocabularies for specific biological domains that can be used to describe gene products in any organism. This work includes building three extensive ontologies to describe molecular function, biological process, and cellular component, and providing a community database resource that supports the use of these ontologies. The GO Consortium was initiated by scientists associated with three model organism databases: SGD, the Saccharomyces Genome database; FlyBase, the Drosophila genome database; and MGD/GXD, the Mouse Genome Informatics databases. Additional model organism database groups are joining the project. Each of these model organism information systems is annotating genes and gene products using GO vocabulary terms and incorporating these annotations into their respective model organism databases. Each database contributes its annotation files to a shared GO data resource accessible to the public at http://www.geneontology.org/. The GO site can be used by the community both to recover the GO vocabularies and to access the annotated gene product data sets from the model organism databases. The GO Consortium supports the development of the GO database resource and provides tools enabling curators and researchers to query and manipulate the vocabularies. We believe that the shared development of this molecular annotation resource will contribute to the unification of biological information.