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Resource:AmiGO

Name: Resource:AmiGO
Description: Official Web-based set tools for searching and browsing the Gene Ontology database, which consists of a controlled vocabulary of terms covering biological concepts, and a large number of genes or gene products whose attributes have been annotated using GO terms. It can be accessed online at the main installation or deployed locally.

The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases.

The GO Consortium has developed AmiGO for searching and browsing the Gene Ontology and the gene products that member databases have annotated using GO terms. Using AmiGO, you can search for one or more gene products and view its GO annotations. The results include the GO hierarchy for the term, definition and synonyms for the term, external links, and the complete set of gene product associations for the term and any of its children. AmiGO also allows you to filter your results if you wish to see only a subset of the data.

AmiGO can be used to:

  • search for a gene or gene product, or a list of gene or gene products, and view the GO term associations
  • perform a sequence identity BLAST search and view the GO term associations for the genes or proteins returned
  • search for GO terms and view the genes or gene products they are annotated to
  • browse the GO ontology and view terms
  • the slimmer tool can be used to map the granular annotations of the query set of genes to one or more high-level
  • term enrichment tool is used to discover what a set of genes may have in common by examining annotations and finding significant shared GO terms.
  • GOOSE is for advanced users who want to run custom SQL queries against the GO database.
Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Other Name(s): Gene Ontology - AmiGO, Gene Ontology Database, GO Database, The Gene Ontology Consortium: AmiGO, Gene Ontology Consortium: AmiGO, Gene Ontology: AmiGO
Parent Organization: Resource:GO
Supporting Agency: National Human Genome Research Institute
Related to: Resource:NIF Data Federation, Resource:Gene Ontology Tools, Resource:Berkeley Bioinformatics Open-Source Projects
Resource Type(s): Software application, Database, Data analysis service
Keywords: gene, gene ontology, gene product, annotation, bioinformatics, biological, blast, concept, protein, search engine, visualization, Ontology, Browser, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, slimmer-type tool, term enrichment, other analysis
Grant: P41 5P41HG002273-08
Abbreviation: AmiGO
Resource: Resource
URL: http://amigo.geneontology.org/cgi-bin/amigo/go.cgi
PMID: PMID 19033274
Availability: Open source - Free for academic use
Id: nif-0000-20935
Link to OWL / RDF: Download this content as OWL/RDF

Categories related to Resource:AmiGO

Resource:ASAP, Resource:ASPGD, Resource:Candida Genome Database, Resource:DictyBase, Resource:ECO, Resource:EcoCyc, Resource:FLYBASE, Resource:GO-Module, Resource:GeneDB Lmajor, Resource:GeneDB Pfalciparum, Resource:GeneDB Tbrucei, Resource:Gramene, Resource:JCVI CMR, Resource:MGI, Resource:MeGO, Resource:NCBI, Resource:NCBI Protein, Resource:PDB, Resource:PomBase, Resource:Pseudomonas Genome Database, Resource:RGD, Resource:RamiGO, Resource:Reactome, Resource:SGD, Resource:SGN, Resource:Songbird Brain Transcriptome Database, Resource:TAIR, Resource:UniProtKB, Resource:VMD, Resource:WormBase, Resource:ZFIN, Resource:go-db-perl

Parts of Resource:AmiGO

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Notes

This page uses this default form:Resource

Old URL: http://amigo.geneontology.org/
Alt. URL: http://amigo.geneontology.org/cgi-bin/amigo/search.cgi?session_id=5238amigo1335226792

Contributors

Aarnaud, Ccdbuser



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Facts about Resource:AmiGORDF feed
AbbrevAmiGO  +
AvailabilityOpen source - Free for academic use  +
CommentGO data updates: Daily
CurationStatuscurated  +
DefiningCitationhttp://amigo.geneontology.org/cgi-bin/amigo/go.cgi  +
DefinitionOfficial Web-based set tools for searching Official Web-based set tools for searching and browsing the Gene Ontology database, which consists of a controlled vocabulary of terms covering biological concepts, and a large number of genes or gene products whose attributes have been annotated using GO terms. It can be accessed online at the main installation or deployed locally.

The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases.

The GO Consortium has developed AmiGO for searching and browsing the Gene Ontology and the gene products that member databases have annotated using GO terms. Using AmiGO, you can search for one or more gene products and view its GO annotations. The results include the GO hierarchy for the term, definition and synonyms for the term, external links, and the complete set of gene product associations for the term and any of its children. AmiGO also allows you to filter your results if you wish to see only a subset of the data.

AmiGO can be used to:

  • search for a gene or gene product, or a list of gene or gene products, and view the GO term associations
  • perform a sequence identity BLAST search and view the GO term associations for the genes or proteins returned
  • search for GO terms and view the genes or gene products they are annotated to
  • browse the GO ontology and view terms
  • the slimmer tool can be used to map the granular annotations of the query set of genes to one or more high-level
  • term enrichment tool is used to discover what a set of genes may have in common by examining annotations and finding significant shared GO terms.
  • GOOSE is for advanced users who want to run custom SQL queries against the GO database.
Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
patible, Linux compatible, Unix compatible
ExampleImageAmiGO.PNG  +
GrantCategory:P41 5P41HG002273-08   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleSoftware application  +, Database  +, and Data analysis service  +
Idnif-0000-20935  +
Is part ofResource:GO  +
KeywordsGene  +, Gene ontology  +, Gene product  +, Annotation  +, Bioinformatics  +, Biological  +, Blast  +, Concept  +, Protein  +, Search engine  +, Visualization  +, Ontology  +, Browser  +, Ontology or annotation browser  +, Ontology or annotation search engine  +, Ontology or annotation visualization  +, Slimmer-type tool  +, Term enrichment  +, and Other analysis  +
LabelResource:AmiGO  +
ModifiedDate2 July 2013  +
PMID19033274  +
Page has default formThis property is a special property in this wiki.Resource  +
RelatedToResource:NIF Data Federation  +, Resource:Gene Ontology Tools  +, and Resource:Berkeley Bioinformatics Open-Source Projects  +
SuperCategoryResource  +
Supporting AgencyNational Human Genome Research Institute  +
SynonymGene Ontology - AmiGO  +, Gene Ontology Database  +, GO Database  +, The Gene Ontology Consortium: AmiGO  +, Gene Ontology Consortium: AmiGO  +, and Gene Ontology: AmiGO  +