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AmiGO: online access to ontology and annotation data

Seth Carbon, Amelia Ireland, Christopher J. Mungall, ShengQiang Shu, Brad Marshall, Suzanna Lewis
2008 Computer applications in the biosciences : CABIOS  
AmiGO can be used online at the Gene Ontology (GO) website to access the data provided by the GO Consortium 1 ; it can also be downloaded and installed to browse local ontologies and annotations. 2 AmiGO  ...  AmiGO is a web application that allows users to query, browse and visualize ontologies and related gene product annotation (association) data.  ...  Funding: National Human Genome Research Institute (P41 grant 5P41HG002273-08 to Gene Ontology Consortium). Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btn615 pmid:19033274 pmcid:PMC2639003 fatcat:2znu7uxybrfktmoj3bkadgwxee

Get GO! Retrieving GO Data Using AmiGO, QuickGO, API, Files, and Tools [chapter]

Monica Munoz-Torres, Seth Carbon
2016 Msphere  
We here share details about the mechanics of obtaining GO annotations, both by manually browsing, querying, and downloading data from the GO website, as well as computationally accessing the resources  ...  from the command line, including the ability to restrict the data being retrieved to subsets with only certain attributes.  ...  Web Interfaces to Access the GO This section covers the online interfaces for accessing and interacting with the data using standard web browsers.  ... 
doi:10.1007/978-1-4939-3743-1_11 pmid:27812941 fatcat:tzenvai4zndmfimw5en3guu4hq

The Gene Ontology project in 2008

2007 Nucleic Acids Research  
Software developments include two releases of the ontology-editing tool OBO-Edit, and improvements to the AmiGO browser interface.  ...  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  ...  The GO and SO are available in both OBO and OWL formats and can be browsed online using AmiGO and miSO, respectively.  ... 
doi:10.1093/nar/gkm883 pmid:17984083 pmcid:PMC2238979 fatcat:dlsshwnnjrb2jo3xic3qem2cvu

The Gene Ontology: enhancements for 2011

2011 Nucleic Acids Research  
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  ...  IMPROVEMENTS FOR COMMUNITY ACCESS AmiGO is the GOC's primary web application that provides access to annotations and the ontology (http:// amigo.geneontology.org) using the GO database.  ... 
doi:10.1093/nar/gkr1028 pmid:22102568 pmcid:PMC3245151 fatcat:bigdzkzaofbylfzrnsigkfkvji

The Gene Ontology (GO) database and informatics resource

Gene Ontology Consortium
2004 Nucleic Acids Research  
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.  ...  The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats.  ...  universal access to the ontologies, annotation data sets and software tools developed for use with GO data.  ... 
doi:10.1093/nar/gkh036 pmid:14681407 pmcid:PMC308770 fatcat:ozumvynyyjgcbfrnikvg4odena

Quantification of Enterohemorrhagic Escherichia coli O157:H7 proteome using TMT-Based Analysis [article]

Wanderson Marques da Silva, Jinlong Bei, Natalia Amigo, Pia Valacco, Ariel Fernando Amadio, Qi Zhang, Xiuju Wu, ting yu, Mariano Larzábal, Zhuang Chen, Angel Cataldi
2018 bioRxiv   pre-print
On the other hand, the less abundant detected proteins are those related to DNA processes, cell respiration and prophage.  ...  Altogether, the results show a subset of important proteins that contribute to physiology and pathogenicity of EHEC O157:H7.  ...  of the identified proteins using 129 gene ontology (14).  ... 
doi:10.1101/312652 fatcat:tlqmn3apmzeubl3dv3k2oeq2dy

Gene Ontology Annotations and Resources

2012 Nucleic Acids Research  
Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations.  ...  The GOC works closely with other ontology developers to support integrated use of terminologies.  ...  ACKNOWLEDGEMENTS The GO acknowledges the annotation effort from the annotators at: Gramene, Department of Botany  ... 
doi:10.1093/nar/gks1050 pmid:23161678 pmcid:PMC3531070 fatcat:7b6qdwltrze2teonclk2sdd7ri

The Gene Ontology (GO) project in 2006

2006 Nucleic Acids Research  
Updates to the AmiGO browser have improved access to contributed genome annotations.  ...  The GO project provides an ontological annotation system that enables biologists to infer knowledge from large amounts of data.  ...  Funding to pay the Open Access publication charges for this article was provided by NIH/NHGRI.  ... 
doi:10.1093/nar/gkj021 pmid:16381878 pmcid:PMC1347384 fatcat:t4dm7drqvjcttkeiakru2iftia

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations

Shulamit Avraham, Chih-Wei Tung, Katica Ilic, Pankaj Jaiswal, Elizabeth A. Kellogg, Susan McCouch, Anuradha Pujar, Leonore Reiser, Seung Y Rhee, Martin M Sachs, Mary Schaeffer, Lincoln Stein (+4 others)
2008 Nucleic Acids Research  
The ontology allows users to ascribe attributes of plant structure (anatomy and morphology) and developmental stages to data types, such as genes and phenotypes, to provide a semantic framework to make  ...  browser (http://www.plantontology.org/amigo/go.cgi) for viewing, searching and querying.  ...  Funding to pay the Open Access publication charges for this article was provided by National Science Foundation (Grant No. 0321666).  ... 
doi:10.1093/nar/gkm908 pmid:18194960 pmcid:PMC2238838 fatcat:4pct3qkkrzabbgrud45bpbwroy

Canto: an online tool for community literature curation

Kim M. Rutherford, Midori A. Harris, Antonia Lock, Stephen G. Oliver, Valerie Wood
2014 Computer applications in the biosciences : CABIOS  
Community curation enables researchers to contribute data from their papers directly to databases, supplementing the activity of professional curators and improving coverage of a growing body of literature  ...  Canto supports curation using OBO ontologies, and can be easily configured for use with any species.  ...  ACKNOWLEDGEMENTS We thank Chris Brown, University of Otago, New Zealand and Chris Mungall, Lawrence Berkeley National Laboratory, U.S.A. for help and advice during the development of Canto.  ... 
doi:10.1093/bioinformatics/btu103 pmid:24574118 pmcid:PMC4058955 fatcat:4dsmxqf235g3hlsyageplhugtq

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

Laurel Cooper, Austin Meier, Marie-Angélique Laporte, Justin L Elser, Chris Mungall, Brandon T Sinn, Dario Cavaliere, Seth Carbon, Nathan A Dunn, Barry Smith, Botong Qu, Justin Preece (+7 others)
2017 Nucleic Acids Research  
The annotated data are freely accessible from the ontology browser (http: //browser.planteome.org/amigo) and our data repository.  ...  The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes.  ...  ACKNOWLEDGEMENTS We would like to thank all the collaborating databases and projects (listed in Tables 4 and 5 ) who contributed annotated data to the Planteome database and all the projects and genomics  ... 
doi:10.1093/nar/gkx1152 pmid:29186578 pmcid:PMC5753347 fatcat:7hbnerl4uvf47c6ikf2m3sm6se

QuickGO: a web-based tool for Gene Ontology searching

D. Binns, E. Dimmer, R. Huntley, D. Barrell, C. O'Donovan, R. Apweiler
2009 Bioinformatics  
QuickGO is a web-based tool that allows easy browsing of the Gene Ontology (GO) and all associated electronic and manual GO annotations provided by the GO Consortium annotation groups QuickGO has been  ...  a popular GO browser for many years, but after a recent redevelopment it is now able to offer a greater range of facilities including bulk downloads of GO annotation data which can be extensively filtered  ...  ACKNOWLEDGEMENTS We would like to thank Manjula Thimma for programming, and Ruth Lovering and Varsha Khodiyar for testing the tool. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btp536 pmid:19744993 pmcid:PMC2773257 fatcat:2cwzrmuz2vavrhte2ecd3ufyza

It's All GO for Plant Scientists

J. I. Clark
2005 Plant Physiology  
We annotate gene products from a broad range of model species and provide support for those groups that wish to contribute annotation of further model species.  ...  The Gene Ontology project (http://www. geneontology.org/) produces structured, controlled vocabularies and gene product annotations.  ...  ACKNOWLEDGMENTS We thank Judith Blake, Michael Ashburner, Midori Harris, Amelia Ireland, Emily Dimmer, Elisabeth Truernit, Fiona McCarthy, Daniel Barrell, Tanya Berardini, and Anuradha Pujar for constructive  ... 
doi:10.1104/pp.104.058529 pmid:16010001 pmcid:PMC1176400 fatcat:xfkfn2rdcrdqdgevxaldwy2ooa

Improvements to cardiovascular Gene Ontology

Ruth C. Lovering, Emily C. Dimmer, Philippa J. Talmud
2009 Atherosclerosis  
Gene Ontology (GO) provides a controlled vocabulary to describe the attributes of genes and gene products in any organism.  ...  In this article we review the current uses of Gene Ontology annotation to highlight why Gene Ontology should be of interest to all those involved in cardiovascular research.  ...  Where to find Gene Ontology and GO annotations A large range of applications have been developed specifically for the visualization of GO and its associated annotation data, and the computational and statistical  ... 
doi:10.1016/j.atherosclerosis.2008.10.014 pmid:19046747 pmcid:PMC2706316 fatcat:ytqlfpnwljakvep6uoasqoks4y

Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages

Pankaj Jaiswal, Shulamit Avraham, Katica Ilic, Elizabeth A. Kellogg, Susan McCouch, Anuradha Pujar, Leonore Reiser, Seung Y. Rhee, Martin M. Sachs, Mary Schaeffer, Lincoln Stein, Peter Stevens (+3 others)
2005 Comparative and Functional Genomics  
The current version of the ontology integrates diverse vocabularies used to describeArabidopsis, maize and rice (Oryzasp.) anatomy, morphology and growth stages.  ...  Using the ontology browser, over 3500 gene annotations from three species-specific databases, The Arabidopsis Information Resource (TAIR) forArabidopsis, Gramene for rice and MaizeGDB for maize, can now  ...  We are grateful to many researchers, reviewers, database groups and curators for help in reviewing, adding new terms to the ontology and using them in their annotation work.  ... 
doi:10.1002/cfg.496 pmid:18629207 pmcid:PMC2447502 fatcat:6ii7j3ibhbg2feozbvp4ar472e
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