Tools for Searching and Browsing GO

AmiGO

The Gene Ontology Consortium
No publication

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.

AmiGO is developed and maintained within the GO Consortium.

CGAP GO browser

Cancer Genome Anatomy Project
No publication

With the CGAP GO browser, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term.
GO data updated every few months.

COBrA

XSPAN project, University of Edinburgh
[Publication abstract]

COBrA is a Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and verification functions. In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Semantic Web formats RDF, RDFS and OWL.

Comparative Toxicogenomics Database (CTD)

Mount Desert Island Biological Laboratory, Maine
[Publication abstracts 1, 2, 3, 4]

The Comparative Toxicogenomics Database (CTD) is a public database that enhances understanding about the effects of environmental chemicals on human health. Integrated GO data and a GO browser add functionality to CTD by allowing users to understand biological functions, processes and cellular locations that are the targets of chemical exposures.

DynGO

Georgetown University Medical Center Liu Lab
[Publication abstract]

DynGO is a client-server application that provides several advanced functionalities in addition to the standard browsing capability. DynGO allows users to conduct batch retrieval of GO annotations for a list of genes and gene products, and semantic retrieval of genes and gene products sharing similar GO annotations (which requires more disk and memory to handle the semantic retrieval). The result are shown in an association tree organized according to GO hierarchies and supported with many dynamic display options such as sorting tree nodes or changing orientation of the tree. For GO curators and frequent GO users, DynGO provides fast and convenient access to GO annotation data. DynGO is generally applicable to any data set where the records are annotated with GO terms, as illustrated by two examples.

Gene Class Expression

Molecular Genetics and Bioinformatic Laboratory, University of Sao Paolo, Brazil
[Publication abstract]

Gene Class Expression allows functional annotation of SAGE data using the Gene Ontology database. This tool performs searches in the GO database for each SAGE tag, making associations in the selected GO category for a level selected in the hierarchy. This system provides user-friendly data navigation and visualization for mapping SAGE data onto the gene ontology structure. This tool also provides graphical visualization of the percentage of SAGE tags in each GO category, along with confidence intervals and hypothesis testing.

GeneInfoViz

University of Tennessee Health Science Center
[Publication abstract]

GeneInfoViz is a web based tool for batch retrieval of gene function information, visualization of GO structure and construction of gene relation networks. It takes a input list of genes in the form of LocusLink ID, UniGeneID, gene symbol, or accession number and returns their functional genomic information. Based on the GO annotations of the given genes, GeneInfoViz allows users to visualize these genes in the DAG structure of GO, and construct a gene relation network at a selected level of the DAG.

GenNav

National Library of Medicine
No publication

GenNav searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG.

GOblet

Max Planck Institute for Molecular Genetics, Berlin
[Publication abstract]

The GOblet server performs analysis of sequences (cDNA, protein) with respect to GO terms. For similarity searches (BLAST), databases for various species are available, which were constructed using existing GO annotations. The server presents detailed descriptions of the matches and constructs a GO summary tree based on all GO terms of the respective hits.

GoFish

Roth lab at Harvard
[Publication abstract]

The GoFish program, available as a Java applet online or to download, allows the user to construct arbitrary Boolean queries using GO attributes, and orders gene products according to the extent they satisfy such queries. GoFish also estimates, for each gene product, the probability that they satisfy the Boolean query.

GONUTS (Gene Ontology Normal Usage Tracking System)

EcoliWiki
No publication

GONUTS (Gene Ontology Normal Usage Tracking System) is a wiki based browser for GO terms and gene associations for a limited set of organisms. The wiki interface allows users to record and share notes about the usage of each GO term.

MGI GO Browser

Mouse Genome Informatics
No publication

With the MGI GO Browser, you can search for a GO term and view all mouse genes annotated to the term or any subterms. You can also browse the ontologies to view relationships between terms, term definitions, as well as the number of mouse genes annotated to a given term and its subterms. The MGI GO browser directly accesses the GO data in the MGI database, which is updated nightly.

OBO-Edit

The Gene Ontology Consortium
No publication

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.

OBO-Edit is developed and maintained within the GO Consortium. OBO-Edit was previously known as DAG-Edit.

Ontology Lookup Service

European Bioinformatics Institute
[Publication abstract]

The Ontology Lookup Service (OLS) was created to integrate publicly available biomedical ontologies into a single database. All modified ontologies are updated daily. A list of currently loaded ontologies is available online. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A programmatic interface is available to query the webservice using SOAP. The service is described by a WSDL descriptor file available online. A sample Java client to connect to the webservice using SOAP is available for download from SourceForge. All OLS source code is publicly available under the open source Apache Licence. The OLS provides a user-friendly single entry point for publicly available ontologies in the Open Biomedical Ontology (OBO) format.

Ontology Evolution Explorer (OnEX)

Interdisciplinary Centre for Bioinformatics, University of Leipzig, Germany
[Publication abstract]

The Ontology Evolution Explorer (OnEX) is a web-based system for exploring ontology changes. It provides access to several versions of 16 well-known life science ontologies including the Gene Ontology. The system is based on a three-tier architecture including an ontology version repository, a middleware component and the OnEX web application. Interactive workflows allow a systematic and explorative change analysis of ontologies and their concepts as well as the semi-automatic migration of out-dated annotations to the current version of an ontology.

PANDORA

The Hebrew University of Jerusalem
No publication

With PANDORA, you can search for any non-uniform sets of proteins and detect subsets of proteins that share unique biological properties and the intersections of such sets. PANDORA supports GO annotations as well as additional keywords (from UniProt Knowledgebase, InterPro, ENZYME, SCOP etc). It is also integrated into the ProtoNet system, thus allowing testing of thousands of automatically generated protein families. Note that PANDORA replaces the ProtoGO browser developed by the same group.

QuickGO

European Bioinformatics Institute
[Publication abstracts 1, 2]

QuickGO is a web-based tool that allows easy browsing of the Gene Ontology and all associated GO annotations provided by the UniProtKB-GOA group at the EBI. It provides a comprehensive set of both electronic and manual annotations from a large number of curation groups, covering extensive taxonomic groups. QuickGO incorporates facilities including bulk downloads of GO annotation data, which can be extensively filtered by a range of different parameters, identifier mapping and the ability to create or adapt GO slims for mapping up annotations to a subset of GO terms. QuickGO additionally offers fully integrated web services using a REST-style query interface with results displayed in gene association, OBO or XML formats.

Listing updated Oct 2009

TAIR Keyword Browser

The Arabidopsis Information Resource
No publication

TAIR Keyword Browser searches and browses for Gene Ontology, TAIR Anatomy, and TAIR Developmental stage terms, and allows you to view term details and relationships among terms. It includes links to genes, publications, microarray experiments and annotations associated with the term or any children terms.

Tk-GO

Illuminae
No publication

Tk-GO is a GUI wrapping the basic functions of the GO::AppHandle library from BDGP. GO terms are presented in an explorer-like browser, and behavior can be configured by altering Perl scripts. Click 'download tarball' at the bioperl.org cvs site to download the programme. All available documentation is included in this download. Tk-GO uses the GO database (connects directly to the BDGP database by default) but is user-configurable.