Gene Ontology Tools

The information on this page is out of date. The Gene Ontology tools registry is now handled in association with NEUROLEX at this site. Please update your bookmarks.

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
Online tool Windows compatible Mac OS X compatible Linux compatible Unix compatible
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
Open Source (OSI) Logo

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
Online tool Windows compatible Mac OS X compatible Linux compatible Unix compatible
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
Open Source (OSI) Logo

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
Windows compatible Mac OS X compatible Linux compatible Unix compatible
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
Windows compatible Mac OS X compatible Linux compatible Unix compatible
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
Windows compatible Mac OS X compatible Linux compatible Unix compatible
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
Windows compatible Mac OS X compatible Linux compatible Unix compatible
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
Open Source (OSI) Logo

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
Windows compatible Mac OS X compatible Linux compatible Unix compatible
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

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Tool listings, by category

Ontology or annotation browser

Tools with an ontology or annotation browser; view page

Tools with an ontology or annotation search engine component; view page

Ontology or annotation visualization

Tools with an ontology or annotation visualization component; view page

Ontology or annotation editor

Tools with an ontology or annotation editor component; view page

Database or data warehouse

Tools with a database or data warehouse component; view page

Software library

Tools with a software library component; view page

Statistical analysis

Tools with a statistical analysis component; view page

Slimmer-type tool

Tools with a slimmer-type component, remapping annotations to ancestral terms; view page

Term enrichment

Tools with a term enrichment component; view page

Text mining

Tools with a text mining component; view page

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

Other analysis

Tools performing other analyses; view page

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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.

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