Gene Ontology Tools
The GO tools collection contains tools developed by the GO Consortium and by third parties.
We are currently updating our tools listings to provide users with more information. Please fill out the GO tool submission form if you would like your tool to be displayed in the tools collection on the GO website.
We also maintain a list of useful ID mapping tools on the GO wiki.
Consortium Tools
The tools below are developed within the Gene Ontology Consortium. They continue to be improved and expanded and you can receive support in using these tools by writing to the GO helpdesk.
AmiGO
- Platform
-
- Developer
- GO Consortium.
- Contact
- GO Helpdesk
- Publications
- PMID:19033274
- License
- Free for academic use
- GO data updates
- daily
- GO data used
- terms
- definitions and comments
- synonyms
- cross-references
- relationships
- subsets or GO slims
- gene product data
- taxon
- evidence codes
- references
- qualifiers
AmiGO provides an interface to search and browse the ontology and annotation data provided by the GO consortium. Users can search for gene products and view the terms with which they are associated; alternatively, users can search or browse the ontology for GO terms of interest and see term details and gene product annotations. AmiGO also provides a BLAST search engine, which searches the sequences of genes and gene products that have been annotated to a GO term and submitted to the GO Consortium.
AmiGO accesses the GO mySQL database; more information is available from the GO database guide.
- ontology or annotation browser
- ontology or annotation search engine
- ontology or annotation visualization
- slimmer-type tool
- term enrichment
- other analysis
Tool listing last updated 10 October 2010
GO Online SQL Environment (GOOSE)
- Platform
-
- Developer
- GO Consortium.
- Contact
- GO Helpdesk
- Publications
- PMID:19033274
- License
- Free for academic use
- GO data updates
- daily
- GO data used
- terms
- definitions and comments
- synonyms
- cross-references
- relationships
- subsets or GO slims
- gene product data
- taxon
- evidence codes
- references
- qualifiers
The GO Online SQL Environment (GOOSE) provides a direct interface to the GO database, allowing users to run custom queries without having to install a copy of the GO database locally.
- database or data warehouse
Tool listing last updated 10 October 2010
go-db-perl
- Platform
-
- Developer
- GO Consortium.
- License
- Free for academic use
- GO data updates
- not applicable (e.g. because users provide data)
go-db-perl extends the functionality of go-perl (on which it depends) with GO Database access functionality.
go-db-perl comes bundled with various scripts and a shell command line interface that can be used as standalone tools.
Installation is more involved than for go-perl; you will need a MySQL database plus the requisite DBI and DBD Perl modules. Full installation instructions are included in the download.
go-db-perl is in use both to drive AmiGO and internally within Ensembl.
- database or data warehouse
- software library
Tool listing last updated 10 October 2010
go-moose
- Platform
-
- Developers
- Berkeley Bioinformatics Open-Source Projects, Lawrence Berkeley National Lab, Berkeley, California, USA.
- GO Consortium.
- Contact
- GO Helpdesk
- License
- Free for academic use
- GO data updates
- not applicable (e.g. because users provide data)
go-moose is intended as a replacement for the aging go-perl and go-db-perl Perl libraries. It is written using the object oriented Moose libraries. It can be used for performing a number of analyses on GO data, including the remapping of GO annotations to a selected subset of GO terms.
- software library
- slimmer-type tool
- other analysis
Tool listing last updated 01 January 2011
go-perl
- Platform
-
- Developer
- GO Consortium.
- License
- Free for academic use
- GO data updates
- not applicable (e.g. because users provide data)
go-perl is a set of Perl modules for parsing, manipulating and exporting ontologies and annotations. It includes parsers for the OBO and GO gene association file formats. It has a graph-based object model with methods for graph traversal. For more details, see the documentation included with the modules.
go-perl comes bundled with XSL [Extensible Stylesheet Language] transforms (which can also be used independently of Perl, provided you have files in OBO-XML format), as well as scripts that can be used as standalone tools.
Installation should be simple, provided you have some experience with Perl and CPAN; see the INSTALL file for details.
- software library
- slimmer-type tool
Tool listing last updated 10 October 2010
OBO-Edit
- Platform
-
- Developer
- GO Consortium.
- Contact
- GO Helpdesk
- Publications
- PMID:17545183
- License
- Free for academic use
- GO data updates
- not applicable (e.g. because users provide data)
- GO data used
- terms
- definitions and comments
- synonyms
- cross-references
- relationships
- subsets or GO slims
- gene product data
- taxon
- evidence codes
- references
- qualifiers
OBO-Edit is an open source, platform-independent application for viewing and editing any OBO format ontologies. OBO-Edit is a graph-based tool; its emphasis on the overall graph structure of an ontology provides a friendly interface for biologists, and makes OBO-Edit excellent for the rapid generation of large ontologies focusing on relationships between relatively simple classes.
OBO-Edit uses the OBO format flat file.
- ontology or annotation browser
- ontology or annotation search engine
- ontology or annotation visualization
- ontology or annotation editor
Tool listing last updated 10 October 2010
org.geneontology.oboedit
- Platform
-
- Developer
- GO Consortium.
- License
- Free for academic use
- GO data updates
- not applicable (e.g. because users provide data)
OBO-Edit is best known as a standalone application for editing ontologies. In fact, the UI components are cleanly separated from the data model and data adapters, so these can be reused in other applications. The oboedit foward-chaining reasoner can also be used independently (for example, for traversing ontology graphs).
org.geneontology.oboedit is used in tools such as the Ontology Lookup Service and Phenote.
See the GO wiki for instructions on downloading the source code.
- software library
Tool listing last updated 10 October 2010
Tool listings, by category
Ontology or annotation browser
Tools with an ontology or annotation browser; view page
- agriGO*
- AmiGO*
- Bioconductor*
- Gene Ontology For Functional Analysis*
- Gene Ontology Normal Usage Tracking System*
- GeneTools*
- GOSlimViewer*
- MGI GO Browser*
- OBO-Edit*
- Onto-Compare*
- Onto-Design*
- Onto-Express*
- Onto-Express To Go*
- QuickGO*
- STRAP*
- CGAP GO browser
- COBrA
- Comparative Toxicogenomics Database
- DynGO
- Gene Class Expression
- GeneInfoViz
- GenNav
- GOblet
- GOfetcher
- GoFish
- GOProfiler
- Manatee
- Ontology Evolution Explorer
- Ontology Lookup Service
- PANDORA
- TAIR Keyword Browser
- Tk-GO
- Wandora
Ontology or annotation search engine
Tools with an ontology or annotation search engine component; view page
- AmiGO*
- Bioconductor*
- Gene Ontology For Functional Analysis*
- Gene Ontology Normal Usage Tracking System*
- GeneTools*
- GOanna*
- GORetriever*
- GOTaxExplorer*
- MGI GO Browser*
- OBO-Edit*
- Onto-Compare*
- Onto-Design*
- Onto-Express*
- Onto-Express To Go*
- Onto-Miner*
- PiNGO*
- QuickGO*
- Ontology Lookup Service
Ontology or annotation visualization
Tools with an ontology or annotation visualization component; view page
- agriGO*
- AmiGO*
- Bioconductor*
- g:Profiler*
- Gene Ontology For Functional Analysis*
- Generic GO Term Finder*
- GeneTools*
- GOrilla*
- GOTaxExplorer*
- GraphWeb*
- MGI GO Browser*
- OBO-Edit*
- Onto-Compare*
- Onto-Design*
- Onto-Express*
- Onto-Express To Go*
- QuickGO*
- REViGO*
- StRAnGER*
- STRAP*
- Flash GViewer
- Gene Ontology Browsing Utility
- Web Gene Ontology Annotation Plot
Ontology or annotation editor
Tools with an ontology or annotation editor component; view page
- Gene Ontology Normal Usage Tracking System*
- GOanna*
- OBO-Edit*
- Blast2GO
- Gene Ontology for Motifs
- InterProScan
- Manatee
- PubSearch
Database or data warehouse
Tools with a database or data warehouse component; view page
- agriGO*
- Bioconductor*
- FunSimMat*
- Gene Ontology For Functional Analysis*
- GeneMANIA*
- GeneTools*
- GO Online SQL Environment*
- go-db-perl*
- GOTaxExplorer*
- Onto-Compare*
- Onto-Design*
- Onto-Express*
- Onto-Miner*
- Onto-Translate*
- QuickGO*
- ToppGene Suite*
- Db for Dummies!
- Genes2Diseases
Software library
Tools with a software library component; view page
- Bioconductor*
- GeneMANIA*
- go-db-perl*
- go-moose*
- go-perl*
- ONTO-PERL*
- org.geneontology.oboedit*
- Biomedical Logical Programming
- BioPerl
- LexGrid
- OWLAPI
Statistical analysis
Tools with a statistical analysis component; view page
- agriGO*
- BiNGO*
- Bioconductor*
- CateGOrizer*
- Functional Semantic Similarity Measure between Gene Products*
- g:Profiler*
- Gene Ontology For Functional Analysis*
- GeneMANIA*
- GeneMerge*
- GeneTools*
- GOrilla*
- GraphWeb*
- Onto-Express*
- Onto-Express To Go*
- PiNGO*
- ProteInOn*
- REViGO*
- Short Time-series Expression Miner*
- StRAnGER*
- Avadis
- Blast2GO
- ClueGO
- Cluster Assignment for Biological Inference
- Cluster Enrichment
- EASE
- ermineJ
- Exploratory Gene Association Networks
- FatiGO
- FuncAssociate
- FuncExpression
- FunCluster
- Functional Analysis of Transcriptional Networks
- Functional Information Viewer and Analyzer
- FunSpec
- GARBAN
- Gene Ontology Browsing Utility
- Gene Ontology Enrichment Analysis Software Toolkit
- Gene Ontology Explorer
- Gene Ontology for Motifs
- Gene Ontology Tree Machine
- GENECODIS
- Generalized Ontological Algorithmic Logical Invariants Extractor
- Genome Function INtegrated Discoverer
- GO Slim Mapper
- GOArray
- GOdist
- GOHyperGAll
- GOstat
- GoSurfer
- GOtcha
- GOToolBox
- InterProScan
- L2L
- MAPPFinder
- Meta Gene Profiler
- MultiExperiment Viewer
- OntoGate
- Probe Explorer
- Profiling of Complex Functionality
- SeqExpress
- SerbGO
- SOURCE
- Spotfire Gene Ontology Advantage Application
- T-Profiler
- The Ontologizer
- Tools for High-throughput Experiments Analysis
Slimmer-type tool
Tools with a slimmer-type component, remapping annotations to ancestral terms; view page
- AmiGO*
- CateGOrizer*
- g:Profiler*
- GeneMerge*
- Generic GO Term Mapper*
- go-moose*
- go-perl*
- GOSlimViewer*
- QuickGO*
- ToppGene Suite*
- Blast2GO
- Cluster Enrichment
- GO Slim Mapper
- GOHyperGAll
- GOToolBox
Term enrichment
Tools with a term enrichment component; view page
- agriGO*
- AmiGO*
- BiNGO*
- Bioconductor*
- Database for Annotation, Visualization and Integrated Discovery*
- Functional Semantic Similarity Measure between Gene Products*
- g:Profiler*
- Gene Ontology For Functional Analysis*
- GeneMANIA*
- GeneMerge*
- Generic GO Term Finder*
- Generic GO Term Mapper*
- GeneTools*
- Genomic Regions Enrichment of Annotations Tool*
- GOrilla*
- GraphWeb*
- High-Throughput GoMiner*
- Onto-Express*
- Onto-Express To Go*
- PiNGO*
- ProteInOn*
- Short Time-series Expression Miner*
- StRAnGER*
- ToppGene Suite*
Text mining
Tools with a text mining component; view page
- agriGO*
- Bioconductor*
- Database for Annotation, Visualization and Integrated Discovery*
- GeneMerge*
- GoAnnotator*
- TXTGate
Protein interactions
Tools analyzing protein-protein interactions; view page
Functional similarity
Tools performing functional similarity searches; view page
Semantic similarity
Tools performing semantic similarity searches; view page
- Functional Semantic Similarity Measure between Gene Products*
- FunSimMat*
- GOTaxExplorer*
- ProteInOn*
- G-SESAME
Other analysis
Tools performing other analyses; view page
- AmiGO*
- Bioconductor*
- Functional Semantic Similarity Measure between Gene Products*
- Functional Similarity Search Tool*
- g:Profiler*
- GeneMANIA*
- go-moose*
- GOTaxExplorer*
- Onto-Compare*
- Onto-Design*
- Onto-Express*
- Onto-Express To Go*
- Onto-Miner*
- Onto-Translate*
- ProteInOn*
- ToppGene Suite*
- Agile Protein Interaction Data Analyzer
- Expression Profiler
- GOChase
- GoPubMed
- Whatizit
All tools, alphabetical listing
Starred tools are those whose listings have been updated recently; unstarred tools may be unsupported or may no longer be active.
- Agile Protein Interaction Data Analyzer: direct link to tool • entry in GO tools listings
- agriGO*: direct link to tool • entry in GO tools listings
- AmiGO*: direct link to tool • entry in GO tools listings
- Avadis: direct link to tool • entry in GO tools listings
- BiNGO*: direct link to tool • entry in GO tools listings
- Bioconductor*: direct link to tool • entry in GO tools listings
- Biomedical Logical Programming: direct link to tool • entry in GO tools listings
- BioPerl: direct link to tool • entry in GO tools listings
- Blast2GO: direct link to tool • entry in GO tools listings
- CateGOrizer*: direct link to tool • entry in GO tools listings
- CGAP GO browser: direct link to tool • entry in GO tools listings
- ClueGO: direct link to tool • entry in GO tools listings
- Cluster Assignment for Biological Inference: direct link to tool • entry in GO tools listings
- Cluster Enrichment: direct link to tool • entry in GO tools listings
- COBrA: direct link to tool • entry in GO tools listings
- Comparative Toxicogenomics Database: direct link to tool • entry in GO tools listings
- Database for Annotation, Visualization and Integrated Discovery*: direct link to tool • entry in GO tools listings
- Db for Dummies!: direct link to tool • entry in GO tools listings
- DynGO: direct link to tool • entry in GO tools listings
- EASE: direct link to tool • entry in GO tools listings
- ermineJ: direct link to tool • entry in GO tools listings
- Exploratory Gene Association Networks: direct link to tool • entry in GO tools listings
- Expression Profiler: direct link to tool • entry in GO tools listings
- FatiGO: direct link to tool • entry in GO tools listings
- Flash GViewer: direct link to tool • entry in GO tools listings
- FuncAssociate: direct link to tool • entry in GO tools listings
- FuncExpression: direct link to tool • entry in GO tools listings
- FunCluster: direct link to tool • entry in GO tools listings
- Functional Analysis of Transcriptional Networks: direct link to tool • entry in GO tools listings
- Functional Information Viewer and Analyzer: direct link to tool • entry in GO tools listings
- Functional Semantic Similarity Measure between Gene Products*: direct link to tool • entry in GO tools listings
- Functional Similarity Search Tool*: direct link to tool • entry in GO tools listings
- FunSimMat*: direct link to tool • entry in GO tools listings
- FunSpec: direct link to tool • entry in GO tools listings
- G-SESAME: direct link to tool • entry in GO tools listings
- g:Profiler*: direct link to tool • entry in GO tools listings
- GARBAN: direct link to tool • entry in GO tools listings
- Gene Class Expression: direct link to tool • entry in GO tools listings
- Gene Ontology Browsing Utility: direct link to tool • entry in GO tools listings
- Gene Ontology Enrichment Analysis Software Toolkit: direct link to tool • entry in GO tools listings
- Gene Ontology Explorer: direct link to tool • entry in GO tools listings
- Gene Ontology For Functional Analysis*: direct link to tool • entry in GO tools listings
- Gene Ontology for Motifs: direct link to tool • entry in GO tools listings
- Gene Ontology Normal Usage Tracking System*: direct link to tool • entry in GO tools listings
- Gene Ontology Tree Machine: direct link to tool • entry in GO tools listings
- GENECODIS: direct link to tool • entry in GO tools listings
- GeneInfoViz: direct link to tool • entry in GO tools listings
- GeneMANIA*: direct link to tool • entry in GO tools listings
- GeneMerge*: direct link to tool • entry in GO tools listings
- Generalized Ontological Algorithmic Logical Invariants Extractor: direct link to tool • entry in GO tools listings
- Generic GO Term Finder*: direct link to tool • entry in GO tools listings
- Generic GO Term Mapper*: direct link to tool • entry in GO tools listings
- Genes2Diseases: direct link to tool • entry in GO tools listings
- GeneTools*: direct link to tool • entry in GO tools listings
- GenNav: direct link to tool • entry in GO tools listings
- Genome Function INtegrated Discoverer: direct link to tool • entry in GO tools listings
- Genomic Regions Enrichment of Annotations Tool*: direct link to tool • entry in GO tools listings
- GO Online SQL Environment*: direct link to tool • entry in GO tools listings
- GO Slim Mapper: direct link to tool • entry in GO tools listings
- go-db-perl*: direct link to tool • entry in GO tools listings
- go-moose*: direct link to tool • entry in GO tools listings
- go-perl*: direct link to tool • entry in GO tools listings
- GOanna*: direct link to tool • entry in GO tools listings
- GoAnnotator*: direct link to tool • entry in GO tools listings
- GOArray: direct link to tool • entry in GO tools listings
- GOblet: direct link to tool • entry in GO tools listings
- GOChase: direct link to tool • entry in GO tools listings
- GOdist: direct link to tool • entry in GO tools listings
- GOfetcher: direct link to tool • entry in GO tools listings
- GoFish: direct link to tool • entry in GO tools listings
- GOHyperGAll: direct link to tool • entry in GO tools listings
- GOProfiler: direct link to tool • entry in GO tools listings
- GoPubMed: direct link to tool • entry in GO tools listings
- GORetriever*: direct link to tool • entry in GO tools listings
- GOrilla*: direct link to tool • entry in GO tools listings
- GOSlimViewer*: direct link to tool • entry in GO tools listings
- GOstat: direct link to tool • entry in GO tools listings
- GoSurfer: direct link to tool • entry in GO tools listings
- GOTaxExplorer*: direct link to tool • entry in GO tools listings
- GOtcha: direct link to tool • entry in GO tools listings
- GOToolBox: direct link to tool • entry in GO tools listings
- GraphWeb*: direct link to tool • entry in GO tools listings
- High-Throughput GoMiner*: direct link to tool • entry in GO tools listings
- InterProScan: direct link to tool • entry in GO tools listings
- L2L: direct link to tool • entry in GO tools listings
- LexGrid: direct link to tool • entry in GO tools listings
- Manatee: direct link to tool • entry in GO tools listings
- MAPPFinder: direct link to tool • entry in GO tools listings
- Meta Gene Profiler: direct link to tool • entry in GO tools listings
- MGI GO Browser*: direct link to tool • entry in GO tools listings
- MultiExperiment Viewer: direct link to tool • entry in GO tools listings
- OBO-Edit*: direct link to tool • entry in GO tools listings
- Onto-Compare*: direct link to tool • entry in GO tools listings
- Onto-Design*: direct link to tool • entry in GO tools listings
- Onto-Express*: direct link to tool • entry in GO tools listings
- Onto-Express To Go*: direct link to tool • entry in GO tools listings
- Onto-Miner*: direct link to tool • entry in GO tools listings
- ONTO-PERL*: direct link to tool • entry in GO tools listings
- Onto-Translate*: direct link to tool • entry in GO tools listings
- OntoGate: direct link to tool • entry in GO tools listings
- Ontology Evolution Explorer: direct link to tool • entry in GO tools listings
- Ontology Lookup Service: direct link to tool • entry in GO tools listings
- org.geneontology.oboedit*: direct link to tool • entry in GO tools listings
- OWLAPI: direct link to tool • entry in GO tools listings
- PANDORA: direct link to tool • entry in GO tools listings
- PiNGO*: direct link to tool • entry in GO tools listings
- Probe Explorer: direct link to tool • entry in GO tools listings
- Profiling of Complex Functionality: direct link to tool • entry in GO tools listings
- ProteInOn*: direct link to tool • entry in GO tools listings
- PubSearch: direct link to tool • entry in GO tools listings
- QuickGO*: direct link to tool • entry in GO tools listings
- REViGO*: direct link to tool • entry in GO tools listings
- SeqExpress: direct link to tool • entry in GO tools listings
- SerbGO: direct link to tool • entry in GO tools listings
- Short Time-series Expression Miner*: direct link to tool • entry in GO tools listings
- SOURCE: direct link to tool • entry in GO tools listings
- Spotfire Gene Ontology Advantage Application: direct link to tool • entry in GO tools listings
- StRAnGER*: direct link to tool • entry in GO tools listings
- STRAP*: direct link to tool • entry in GO tools listings
- T-Profiler: direct link to tool • entry in GO tools listings
- TAIR Keyword Browser: direct link to tool • entry in GO tools listings
- The Ontologizer: direct link to tool • entry in GO tools listings
- Tk-GO: direct link to tool • entry in GO tools listings
- Tools for High-throughput Experiments Analysis: direct link to tool • entry in GO tools listings
- ToppGene Suite*: direct link to tool • entry in GO tools listings
- TXTGate: direct link to tool • entry in GO tools listings
- Wandora: direct link to tool • entry in GO tools listings
- Web Gene Ontology Annotation Plot: direct link to tool • entry in GO tools listings
- Whatizit: direct link to tool • entry in GO tools listings