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Resource:Gene Ontology Tools

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Name:	Resource:Gene Ontology Tools
Description:	Collection of tools developed by the GO Consortium and by third parties. Tools are listed by category (see tables below) or alphabetically and continue to be improved and expanded. Submit your GO Tool, http://www.geneontology.org/cgi-bin/add-tool.cgi. For adding resources to this registry through the NeuroLex, http://neurolex.org/wiki/Main_Page, please refer to https://confluence.crbs.ucsd.edu/display/NIF/Resources+and+Curation#ResourcesandCuration-IncorporatingOutsideRegistriesandAccommodatingTheirTags. You can receive support in using these tools by writing to the GO helpdesk, http://www.geneontology.org/GO.contacts.shtml Categories include: Ontology or annotation browser Ontology or annotation search engine Ontology or annotation visualization Ontology or annotation editor Database or data warehouse Software library Statistical analysis Slimmer-type tool Term enrichment Text mining Protein interactions Functional similarity Semantic similarity Other analysis The tools listings are currently being updated 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. A list of useful ID mapping tools is also maintained on the GO wiki.
Parent Organization:	Resource:GO
Related to:	Resource:NIF Data Federation
Resource Type(s):	Software repository, Registry
Keywords:	Registry, annotation browser, annotation search engine, annotation visualization, Ontology, annotation editor, Database, data warehouse, Software library, Statistical analysis, Slimmer-type tool, Term enrichment, Text mining, Protein interaction, Functional similarity, Semantic similarity, analysis, annotation, visualization, editor
Abbreviation:	GO Tools
Resource:	Resource
URL:	http://www.geneontology.org/GO.tools.shtml
Availability:	The community can contribute to this resource.
Id:	nlx_146273
Link to OWL / RDF:	Download this content as OWL/RDF

Categories related to Resource:Gene Ontology Tools

Resource:APID: Agile Protein Interaction DataAnalyzer, Resource:AmiGO, Resource:Avadis, Resource:Babelomics 4: Gene Expression and Functional Profiling Analysis Suite, Resource:BiNGO: A Biological Networks Gene Ontology tool, Resource:BioPerl, Resource:Bioconductor, Resource:Blast2GO, Resource:Blip: Biomedical Logic Programming, Resource:CGAP GO Browser, Resource:CLASSIFI - Cluster Assignment for Biological Inference, Resource:CLENCH, Resource:COBrA, Resource:Candidate Genes to Inherited Diseases, Resource:CateGOrizer, Resource:ClueGO, Resource:Comparative Toxicogenomics Database, Resource:DBD - Slim Gene Ontology, Resource:Database for Annotation Visualization and Integrated Discovery, Resource:DynGO, Resource:EASE: the Expression Analysis Systematic Explorer, Resource:EGAN: Exploratory Gene Association Networks, Resource:ErmineJ, Resource:Expression Profiler, Resource:FIVA - Functional Information Viewer and Analyzer, Resource:FSST - Functional Similarity Search Tool, Resource:FastSemSim, Resource:Flash Gviewer, Resource:FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products, Resource:FunCluster, Resource:FunNet - Transcriptional Networks Analysis, Resource:FunSimMat, Resource:FunSpec, Resource:FuncAssociate: The Gene Set Functionator, Resource:FuncExpression, Resource:G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools, Resource:G:Profiler, Resource:GARBAN, Resource:GFINDer: Genome Function INtegrated Discoverer, Resource:GO Online SQL Environment (GOOSE), Resource:GO-Module, Resource:GOALIE, Resource:GOArray, Resource:GOChase, Resource:GOEAST - Gene Ontology Enrichment Analysis Software Toolkit, Resource:GOEx - Gene Ontology Explorer, Resource:GOHyperGAll, Resource:GOMO - Gene Ontology for Motifs, Resource:GONUTS, Resource:GOProfiler … further results

Last modified date:	2013-5-15
Version number:	218077
Example image:
Curation status	curated

Curation status: Curated

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Notes

This page uses this default form:Resource

Alt. NIF URL: https://neuinfo.org/mynif/search.php?q=%2522Gene%2520Ontology%2520Tools%2522&t=indexable&nif=nlx_146273-1

Download All GO Tools

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Download Ontology or annotation browser Tools

CSV

Ontology or annotation browser: Table View

	Is part of	DefiningCitation	ExampleImage
Resource:AmiGO	Resource:GO	http://amigo.geneontology.org/cgi-bin/amigo/go.cgi
Resource:Bioconductor	Resource:Fred Hutchinson Cancer Research Center	http://www.bioconductor.org/
Resource:CGAP GO Browser	Resource:Cancer Genome Anatomy Project	http://cgap.nci.nih.gov/Genes/GOBrowser
Resource:COBrA	University of Edinburgh; Scotland; United Kingdom	http://www.xspan.org/
Resource:Comparative Toxicogenomics Database	Resource:Mount Desert Island Biological Laboratory North Carolina State University; North Carolina; USA	http://ctd.mdibl.org
Resource:DynGO	Georgetown University Medical Center; Washington D.C.; USA Resource:Softpedia	http://www.softpedia.com/get/Science-CAD/DynGO.shtml
Resource:GONUTS	Resource:EcoliHub	http://gowiki.tamu.edu/wiki/index.php/Main_Page
Resource:GOProfiler	Resource:AgBase	http://agbase.msstate.edu/cgi-bin/tools/goprofiler_select.pl
Resource:GOSlimViewer	Resource:AgBase	http://agbase.msstate.edu/cgi-bin/tools/goslimviewer_select.pl
Resource:GOblet	Max Planck Institute for Molecular Genetics; Berlin; Germany	http://goblet.molgen.mpg.de/cgi-bin/goblet2008/goblet.cgi
Resource:GOfetcher	University of Southern Mississippi; Mississippi; USA	http://mcbc.usm.edu/gofetcher/
Resource:GenNav	National Library of Medicine	http://mor.nlm.nih.gov/perl/gennav.pl
Resource:Gene Class Expression	University of Sao Paulo; Sao Paulo; Brazil	http://gdm.fmrp.usp.br/tools_bit.php
Resource:Gene Ontology Browsing Utility (GOBU)	Academia Sinica; Taipei; Taiwan	http://bc02.iis.sinica.edu.tw/gobu/manual/index.html
Resource:Gene Ontology For Functional Analysis (GOFFA)	Resource:National Center for Toxicological Research	http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/default.htm
Resource:GeneInfoViz	University of Tennessee Health Science Center; Tennessee; USA	http://genenet2.uthsc.edu/geneinfoviz/search.php
Resource:GeneTools - a collection of resources for functional annotations	Norwegian University of Science and Technology; Trondheim; Norway	http://www.genetools.microarray.ntnu.no/common/intro.php
Resource:GoFish	University of Toronto; Ontario; Canada Harvard Medical School; Massachusetts; USA	http://llama.mshri.on.ca/Software.html
Resource:MGI GO Browser	Resource:MGI	http://www.informatics.jax.org/searches/GO_form.shtml
Resource:Manatee	J. Craig Venter Institute University of Maryland School of Medicine; Maryland; USA Resource:SourceForge	http://manatee.sourceforge.net/
Resource:Network Ontology Analysis	Chinese Academy of Sciences; Beijing; China	http://app.aporc.org/NOA/
Resource:OBO-Edit	Resource:GO	http://oboedit.org/
Resource:OnEx - Ontology Evolution Explorer	University of Leipzig; Saxony; Germany	http://aprilia.izbi.uni-leipzig.de:8080/onex/
Resource:Onto-Compare	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Compare
Resource:Onto-Design	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Design
Resource:Onto-Express	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Express
Resource:OntoVisT	Jawaharlal Nehru University; New Delhi; India	http://ccbb.jnu.ac.in/OntoVisT.html
Resource:Ontology Lookup Service	Resource:European Bioinformatics Institute	http://www.ebi.ac.uk/ontology-lookup/
Resource:Pandora - Protein ANnotation Diagram ORiented Analysis	Hebrew University of Jerusalem; Jerusalem; Israel	http://www.pandora.cs.huji.ac.il/
Resource:QuickGO	Resource:European Bioinformatics Institute	http://www.ebi.ac.uk/QuickGO/
Resource:STRAP	Boston University School of Medicine; Massachusetts; USA	http://www.bumc.bu.edu/cardiovascularproteomics/cpctools/strap/
Resource:TAIR Keyword Browser	Resource:TAIR	http://www.arabidopsis.org/servlets/Search?action=new_search&type=keyword
Resource:Tk-GO	Illuminae Resource:GitHub	https://github.com/manveru/tkgo
Resource:Wandora	Grip Studios Interactive	http://www.wandora.org/wandora/wiki/index.php?title=Main_Page
Resource:agriGO	China Agricultural University; Beijing; China	http://bioinfo.cau.edu.cn/agriGO/

Download Ontology or annotation search engine Tools

CSV

Ontology or annotation search engine: Table View

	Is part of	DefiningCitation	ExampleImage
Resource:AmiGO	Resource:GO	http://amigo.geneontology.org/cgi-bin/amigo/go.cgi
Resource:Bioconductor	Resource:Fred Hutchinson Cancer Research Center	http://www.bioconductor.org/
Resource:GONUTS	Resource:EcoliHub	http://gowiki.tamu.edu/wiki/index.php/Main_Page
Resource:GORetriever	Resource:AgBase	http://agbase.msstate.edu/cgi-bin/tools/goretriever_select.pl
Resource:GOTaxExplorer	Max-Planck-Institute for Informatics; Saarbrucken; Germany	http://www.gotaxexplorer.de/
Resource:GOanna	Resource:AgBase	http://www.agbase.msstate.edu/cgi-bin/tools/GOanna.cgi
Resource:Gene Ontology For Functional Analysis (GOFFA)	Resource:National Center for Toxicological Research	http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/default.htm
Resource:GeneTools - a collection of resources for functional annotations	Norwegian University of Science and Technology; Trondheim; Norway	http://www.genetools.microarray.ntnu.no/common/intro.php
Resource:MGI GO Browser	Resource:MGI	http://www.informatics.jax.org/searches/GO_form.shtml
Resource:OBO-Edit	Resource:GO	http://oboedit.org/
Resource:Onto-Compare	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Compare
Resource:Onto-Design	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Design
Resource:Onto-Express	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Express
Resource:Onto-Miner	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Miner
Resource:OntoVisT	Jawaharlal Nehru University; New Delhi; India	http://ccbb.jnu.ac.in/OntoVisT.html
Resource:Ontology Lookup Service	Resource:European Bioinformatics Institute	http://www.ebi.ac.uk/ontology-lookup/
Resource:PiNGO	Ghent University; Ghent; Belgium	http://www.psb.ugent.be/esb/PiNGO/Home.html
Resource:QuickGO	Resource:European Bioinformatics Institute	http://www.ebi.ac.uk/QuickGO/
Resource:RamiGO	Resource:Dana-Farber Cancer Institute Resource:Bioconductor	http://bioconductor.org/packages/2.9/bioc/html/RamiGO.html

Download Ontology or annotation visualization Tools

CSV

Ontology or annotation visualization: Table View

	Is part of	DefiningCitation	ExampleImage
Resource:AmiGO	Resource:GO	http://amigo.geneontology.org/cgi-bin/amigo/go.cgi
Resource:Bioconductor	Resource:Fred Hutchinson Cancer Research Center	http://www.bioconductor.org/
Resource:Flash Gviewer	Medical College of Wisconsin; Wisconsin; USA	http://gmod.org/wiki/Flash_GViewer
Resource:G:Profiler	Resource:BIIT - Bioinformatics Algorithmics and Data Mining Group	http://biit.cs.ut.ee/gprofiler/
Resource:GO-Module	University of Illinois at Chicago; Illinois; USA	http://lussierlab.org/GO-Module/GOModule.cgi
Resource:GOTaxExplorer	Max-Planck-Institute for Informatics; Saarbrucken; Germany	http://www.gotaxexplorer.de/
Resource:GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool	Weizmann Institute of Science; Rehovot; Israel	http://cbl-gorilla.cs.technion.ac.il/
Resource:Gene Ontology Browsing Utility (GOBU)	Academia Sinica; Taipei; Taiwan	http://bc02.iis.sinica.edu.tw/gobu/manual/index.html
Resource:Gene Ontology For Functional Analysis (GOFFA)	Resource:National Center for Toxicological Research	http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/default.htm
Resource:GeneTools - a collection of resources for functional annotations	Norwegian University of Science and Technology; Trondheim; Norway	http://www.genetools.microarray.ntnu.no/common/intro.php
Resource:Generic GO Term Finder	Princeton University; New Jersey; USA Resource:Comprehensive Perl Archive Network	http://go.princeton.edu/cgi-bin/GOTermFinder
Resource:GraphWeb	Resource:BIIT - Bioinformatics Algorithmics and Data Mining Group	http://biit.cs.ut.ee/graphweb/
Resource:MGI GO Browser	Resource:MGI	http://www.informatics.jax.org/searches/GO_form.shtml
Resource:OBO-Edit	Resource:GO	http://oboedit.org/
Resource:Onto-Compare	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Compare
Resource:Onto-Design	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Design
Resource:Onto-Express	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Express
Resource:OntoVisT	Jawaharlal Nehru University; New Delhi; India	http://ccbb.jnu.ac.in/OntoVisT.html
Resource:QuickGO	Resource:European Bioinformatics Institute	http://www.ebi.ac.uk/QuickGO/
Resource:REViGO	Rudjer Boskovic Institute; Zagreb; Croatia	http://revigo.irb.hr/
Resource:RamiGO	Resource:Dana-Farber Cancer Institute Resource:Bioconductor	http://bioconductor.org/packages/2.9/bioc/html/RamiGO.html
Resource:STRAP	Boston University School of Medicine; Massachusetts; USA	http://www.bumc.bu.edu/cardiovascularproteomics/cpctools/strap/
Resource:StRAnGER	Resource:National Hellenic Research Foundation	http://www.grissom.gr/stranger/
Resource:WEGO - Web Gene Ontology Annotation Plot	Beijing Genomics Institute; Shenzhen; China	http://wego.genomics.org.cn/cgi-bin/wego/index.pl
Resource:agriGO	China Agricultural University; Beijing; China	http://bioinfo.cau.edu.cn/agriGO/

Download Ontology or annotation editor Tools

CSV

Ontology or annotation editor: Table View

	Is part of	DefiningCitation	ExampleImage
Resource:Blast2GO	Resource:Principe Felipe Research Centre; Valencia; Spain	http://www.blast2go.com/b2ghome
Resource:GOMO - Gene Ontology for Motifs	University of Queensland; Brisbane; Australia Resource:MEME Suite - Motif-based sequence analysis tools	http://meme.nbcr.net/meme/cgi-bin/gomo.cgi
Resource:GONUTS	Resource:EcoliHub	http://gowiki.tamu.edu/wiki/index.php/Main_Page
Resource:GOanna	Resource:AgBase	http://www.agbase.msstate.edu/cgi-bin/tools/GOanna.cgi
Resource:InterProScan	Resource:European Bioinformatics Institute	http://www.ebi.ac.uk/Tools/pfa/iprscan/
Resource:Manatee	J. Craig Venter Institute University of Maryland School of Medicine; Maryland; USA Resource:SourceForge	http://manatee.sourceforge.net/
Resource:OBO-Edit	Resource:GO	http://oboedit.org/
Resource:PubSearch	Resource:TAIR Stanford University; California; USA	http://pubsearch.stanford.edu/

Download Database or data warehouse Tools

CSV

Database or data warehouse: Table View

	Is part of	DefiningCitation	ExampleImage
Resource:Bioconductor	Resource:Fred Hutchinson Cancer Research Center	http://www.bioconductor.org/
Resource:DBD - Slim Gene Ontology	Resource:Db for Dummies!	http://www.dbfordummies.com/go.asp
Resource:FunSimMat	Max-Planck-Institute for Informatics; Saarbrucken; Germany	http://funsimmat.bioinf.mpi-inf.mpg.de
Resource:GO Online SQL Environment (GOOSE)	Resource:AmiGO Resource:Berkeley Bioinformatics Open-Source Projects	http://www.berkeleybop.org/goose/
Resource:GOTaxExplorer	Max-Planck-Institute for Informatics; Saarbrucken; Germany	http://www.gotaxexplorer.de/
Resource:Gene Ontology For Functional Analysis (GOFFA)	Resource:National Center for Toxicological Research	http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/default.htm
Resource:GeneMANIA	University of Toronto; Ontario; Canada	http://genemania.org/
Resource:GeneTools - a collection of resources for functional annotations	Norwegian University of Science and Technology; Trondheim; Norway	http://www.genetools.microarray.ntnu.no/common/intro.php
Resource:Onto-Compare	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Compare
Resource:Onto-Design	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Design
Resource:Onto-Express	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Express
Resource:Onto-Miner	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Miner
Resource:Onto-Translate	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Translate
Resource:QuickGO	Resource:European Bioinformatics Institute	http://www.ebi.ac.uk/QuickGO/
Resource:ToppGene Suite	Cincinnati Childrens Hospital Medical Center; Ohio; USA	http://toppgene.cchmc.org/
Resource:agriGO	China Agricultural University; Beijing; China	http://bioinfo.cau.edu.cn/agriGO/
Resource:go-db-perl	Resource:Comprehensive Perl Archive Network Resource:GO	http://search.cpan.org/~cmungall/go-db-perl/

Download Software library Tools

CSV

Software library: Table View

	Is part of	DefiningCitation	ExampleImage
Resource:BioPerl	Duke University; North Carolina; USA Resource:European Bioinformatics Institute	http://www.bioperl.org
Resource:Bioconductor	Resource:Fred Hutchinson Cancer Research Center	http://www.bioconductor.org/
Resource:Blip: Biomedical Logic Programming	Resource:Berkeley Bioinformatics Open-Source Projects	http://www.blipkit.org/
Resource:FastSemSim	University of Padua; Padua; Italy Resource:SourceForge	http://sourceforge.net/p/fastsemsim/home/Home/
Resource:Gene Ontology Browsing Utility (GOBU)	Academia Sinica; Taipei; Taiwan	http://bc02.iis.sinica.edu.tw/gobu/manual/index.html
Resource:GeneMANIA	University of Toronto; Ontario; Canada	http://genemania.org/
Resource:LexGrid	National Cancer Institute Resource:European Bioinformatics Institute	https://wiki.nci.nih.gov/display/LexEVS/LexGrid
Resource:OBO-Edit	Resource:GO	http://oboedit.org/
Resource:ONTO-PERL	Resource:Comprehensive Perl Archive Network Norwegian University of Science and Technology; Trondheim; Norway	http://search.cpan.org/dist/ONTO-PERL/
Resource:OWL API	University of Manchester; Manchester; United Kingdom Resource:SourceForge	http://owlapi.sourceforge.net/
Resource:OWLTools	Resource:GO Resource:Google Project Hosting	http://code.google.com/p/owltools/
Resource:Semantic Measures Library	Ecole des Mines d'Ales; Ales; France	http://www.semantic-measures-library.org	File:SMT.PNG
Resource:go-db-perl	Resource:Comprehensive Perl Archive Network Resource:GO	http://search.cpan.org/~cmungall/go-db-perl/
Resource:go-moose	Resource:SourceForge Resource:Berkeley Bioinformatics Open-Source Projects Lawrence Berkeley National Laboratory	http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-moose/
Resource:go-perl	Resource:Comprehensive Perl Archive Network Resource:GO	http://search.cpan.org/~cmungall/go-perl/

Download Statistical analysis Tools

CSV

Statistical analysis: Table View

	Is part of	DefiningCitation	ExampleImage
Resource:Avadis	Strand Life Sciences	http://www.strandls.com/Avadis
Resource:Babelomics 4: Gene Expression and Functional Profiling Analysis Suite	Resource:CIPF Bioinformatics and Genomics Department	http://babelomics.bioinfo.cipf.es
Resource:BiNGO: A Biological Networks Gene Ontology tool	Ghent University; Ghent; Belgium	http://www.psb.ugent.be/cbd/papers/BiNGO/Home.html
Resource:Bioconductor	Resource:Fred Hutchinson Cancer Research Center	http://www.bioconductor.org/
Resource:Blast2GO	Resource:Principe Felipe Research Centre; Valencia; Spain	http://www.blast2go.com/b2ghome
Resource:CLASSIFI - Cluster Assignment for Biological Inference	Resource:UT Southwestern Medical Center Department of Pathology	http://www.utsouthwestern.edu/education/medical-school/departments/pathology/pathdb/classifi.html
Resource:CLENCH	Resource:Stanford Center for Biomedical Informatics Research	http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=clench
Resource:CateGOrizer	Resource:NAGRP Bioinformatics Coordination Program	http://www.animalgenome.org/bioinfo/tools/catego/
Resource:ClueGO	National Institute of Health and Medical Research; Rennes; France	http://www.ici.upmc.fr/cluego/
Resource:EASE: the Expression Analysis Systematic Explorer	Resource:Database for Annotation Visualization and Integrated Discovery	http://david.abcc.ncifcrf.gov/content.jsp?file=/ease/ease1.htm&type=1
Resource:EGAN: Exploratory Gene Association Networks	Resource:UCSF Helen Diller Family Comprehensive Cancer Center Biostatistics Core	http://akt.ucsf.edu/EGAN/
Resource:ErmineJ	University of British Columbia; British Columbia; Canada Columbia University; New York; USA	http://bioinformatics.ubc.ca/ermineJ/
Resource:FIVA - Functional Information Viewer and Analyzer	Resource:MolGen	http://bioinformatics.biol.rug.nl/standalone/fiva/
Resource:FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products	University of Lisbon; Lisbon; Portugal	http://xldb.fc.ul.pt/biotools/rebil/ssm/
Resource:FunCluster	Resource:Cordelier Research Center	http://corneliu.henegar.info/FunCluster.htm
Resource:FunNet - Transcriptional Networks Analysis	Resource:Cordelier Research Center	http://www.funnet.info/
Resource:FunSpec	University of Toronto; Ontario; Canada	http://funspec.med.utoronto.ca/
Resource:FuncAssociate: The Gene Set Functionator	Resource:Roth Laboratory	http://llama.mshri.on.ca/funcassociate/
Resource:FuncExpression	Iowa State University; Iowa; USA	http://www.plexdb.org/plex.php?database=Barley/funcexpression.php
Resource:G:Profiler	Resource:BIIT - Bioinformatics Algorithmics and Data Mining Group	http://biit.cs.ut.ee/gprofiler/
Resource:GARBAN		http://www.garban.org/garban/home.php
Resource:GFINDer: Genome Function INtegrated Discoverer	Politecnico di Milano; Milan; Italy	http://www.medinfopoli.polimi.it/GFINDer/
Resource:GOALIE	Resource:NYU Bioinformatics Group	http://bioinformatics.nyu.edu/Projects/GOALIE/
Resource:GOArray	Yale School of Medicine; Connecticut; USA	http://goarray.med.yale.edu/GOArray/
Resource:GOEAST - Gene Ontology Enrichment Analysis Software Toolkit	Chinese Academy of Sciences; Beijing; China	http://omicslab.genetics.ac.cn/GOEAST/
Resource:GOEx - Gene Ontology Explorer	Resource:The Scripps Research Institute -Yates Lab	http://pcarvalho.com/patternlab/goex.shtml
Resource:GOHyperGAll	University of California at Riverside; California; USA	http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#GOHyperGAll
Resource:GOMO - Gene Ontology for Motifs	University of Queensland; Brisbane; Australia Resource:MEME Suite - Motif-based sequence analysis tools	http://meme.nbcr.net/meme/cgi-bin/gomo.cgi
Resource:GOToolBox Functional Investigation of Gene Datasets	Center for Genomic Regulation; Barcelona; Spain	http://genome.crg.es/GOToolBox/
Resource:GOdist	Hebrew University of Jerusalem; Jerusalem; Israel	http://basalganglia.huji.ac.il/links.htm
Resource:GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool	Weizmann Institute of Science; Rehovot; Israel	http://cbl-gorilla.cs.technion.ac.il/
Resource:GOstat	Walter and Eliza Hall Institute of Medical Research; Parkville; Australia	http://gostat.wehi.edu.au
Resource:GOtcha	University of Dundee; Scotland; United Kingdom	http://www.compbio.dundee.ac.uk/Software/GOtcha/gotcha.html
Resource:Gene Ontology Browsing Utility (GOBU)	Academia Sinica; Taipei; Taiwan	http://bc02.iis.sinica.edu.tw/gobu/manual/index.html
Resource:GeneCodis	Complutense University of Madrid; Madrid; Spain	http://genecodis.cnb.csic.es/
Resource:GeneMANIA	University of Toronto; Ontario; Canada	http://genemania.org/
Resource:GeneMerge	University of Maryland; Maryland; USA	http://genemerge.cbcb.umd.edu/
Resource:GeneTools - a collection of resources for functional annotations	Norwegian University of Science and Technology; Trondheim; Norway	http://www.genetools.microarray.ntnu.no/common/intro.php
Resource:GoSurfer	University of Illinois at Urbana-Champaign; Illinois; USA Harvard School of Public Health; Massachusetts; USA	http://bioinformatics.bioen.illinois.edu/gosurfer/index.htm
Resource:GraphWeb	Resource:BIIT - Bioinformatics Algorithmics and Data Mining Group	http://biit.cs.ut.ee/graphweb/
Resource:InterProScan	Resource:European Bioinformatics Institute	http://www.ebi.ac.uk/Tools/pfa/iprscan/
Resource:L2L Microarray Analysis Tool	University of Washington; Washington; USA	http://depts.washington.edu/l2l/about.html
Resource:MAPPFinder	University of California at San Francisco; California; USA Resource:Gene Map Annotator and Pathway Profiler	http://www.genmapp.org/help_v2/UsingMAPPFinder.htm
Resource:MetaGeneProfiler	Institute of Statistical Mathematics; Tokyo; Japan	http://metagp.ism.ac.jp/
Resource:Network Ontology Analysis	Chinese Academy of Sciences; Beijing; China	http://app.aporc.org/NOA/
Resource:Onto-Express	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Express
Resource:Onto-Express To Go (OE2GO)	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#OE2GO
Resource:OntoGate	Max-Planck-Institute for Informatics; Saarbrucken; Germany	http://functionalgenomics.de/ontogate/
Resource:Ontologizer	Charite - Universitatsmedizin Berlin; Berlin; Germany	http://compbio.charite.de/contao/index.php/ontologizer2.html
Resource:PiNGO	Ghent University; Ghent; Belgium	http://www.psb.ugent.be/esb/PiNGO/Home.html
Resource:ProbeExplorer	University of Salamanca; Salamanca; Spain	http://probeexplorer.cicancer.org/principal.php
Resource:ProfCom - Profiling of complex functionality	Institute of Bioinformatics and Systems Biology; Neuherberg; Germany	http://webclu.bio.wzw.tum.de/profcom/
Resource:ProteInOn	University of Lisbon; Lisbon; Portugal
Resource:REViGO	Rudjer Boskovic Institute; Zagreb; Croatia	http://revigo.irb.hr/
Resource:SGD Gene Ontology Slim Mapper	Resource:SGD	http://www.yeastgenome.org/cgi-bin/GO/goSlimMapper.pl
Resource:SOURCE	Resource:SMD	http://smd.stanford.edu/cgi-bin/source/sourceSearch
Resource:SeqExpress	Institute of Bioinformatics and Systems Biology; Neuherberg; Germany	http://www.seqexpress.com/
Resource:SerbGO	University of Barcelona; Barcelona; Spain	http://estbioinfo.stat.ub.es/apli/serbgov131/index.php
Resource:Short Time-series Expression Miner (STEM)	Carnegie Mellon University; Pennsylvania; USA	http://www.cs.cmu.edu/~jernst/stem/
Resource:Spotfire	TIBCO	http://spotfire.tibco.com/
Resource:StRAnGER	Resource:National Hellenic Research Foundation	http://www.grissom.gr/stranger/
Resource:T-profiler	Columbia University; New York; USA University of Amsterdam; Amsterdam; Netherlands	http://www.t-profiler.org
Resource:THEA - Tools for High-throughput Experiments Analysis	Resource:Virtual Biology Lab	http://thea.unice.fr/index-en.html
Resource:TM4 Microarray Software Suite: TIGR MultiExperiment Viewer	Resource:Dana-Farber Cancer Institute J. Craig Venter Institute University of Washington; Washington; USA	http://www.tm4.org/mev.html
Resource:WebGestalt: WEB-based GEne SeT AnaLysis Toolkit	Vanderbilt University; Tennessee; USA	http://bioinfo.vanderbilt.edu/webgestalt/
Resource:agriGO	China Agricultural University; Beijing; China	http://bioinfo.cau.edu.cn/agriGO/

Download Slimmer-type Tools

CSV

Slimmer-type tool: Table View

	Is part of	DefiningCitation	ExampleImage
Resource:AmiGO	Resource:GO	http://amigo.geneontology.org/cgi-bin/amigo/go.cgi
Resource:Blast2GO	Resource:Principe Felipe Research Centre; Valencia; Spain	http://www.blast2go.com/b2ghome
Resource:CLENCH	Resource:Stanford Center for Biomedical Informatics Research	http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=clench
Resource:CateGOrizer	Resource:NAGRP Bioinformatics Coordination Program	http://www.animalgenome.org/bioinfo/tools/catego/
Resource:G:Profiler	Resource:BIIT - Bioinformatics Algorithmics and Data Mining Group	http://biit.cs.ut.ee/gprofiler/
Resource:GOHyperGAll	University of California at Riverside; California; USA	http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#GOHyperGAll
Resource:GOSlimViewer	Resource:AgBase	http://agbase.msstate.edu/cgi-bin/tools/goslimviewer_select.pl
Resource:GOToolBox Functional Investigation of Gene Datasets	Center for Genomic Regulation; Barcelona; Spain	http://genome.crg.es/GOToolBox/
Resource:GeneMerge	University of Maryland; Maryland; USA	http://genemerge.cbcb.umd.edu/
Resource:Generic GO Term Mapper	Princeton University; New Jersey; USA	http://go.princeton.edu/cgi-bin/GOTermMapper
Resource:QuickGO	Resource:European Bioinformatics Institute	http://www.ebi.ac.uk/QuickGO/
Resource:SGD Gene Ontology Slim Mapper	Resource:SGD	http://www.yeastgenome.org/cgi-bin/GO/goSlimMapper.pl
Resource:ToppGene Suite	Cincinnati Childrens Hospital Medical Center; Ohio; USA	http://toppgene.cchmc.org/
Resource:go-moose	Resource:SourceForge Resource:Berkeley Bioinformatics Open-Source Projects Lawrence Berkeley National Laboratory	http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-moose/
Resource:go-perl	Resource:Comprehensive Perl Archive Network Resource:GO	http://search.cpan.org/~cmungall/go-perl/

Download Term enrichment Tools

CSV

Term enrichment: Table View

	Is part of	DefiningCitation	ExampleImage
Resource:AmiGO	Resource:GO	http://amigo.geneontology.org/cgi-bin/amigo/go.cgi
Resource:BiNGO: A Biological Networks Gene Ontology tool	Ghent University; Ghent; Belgium	http://www.psb.ugent.be/cbd/papers/BiNGO/Home.html
Resource:Bioconductor	Resource:Fred Hutchinson Cancer Research Center	http://www.bioconductor.org/
Resource:Database for Annotation Visualization and Integrated Discovery	Resource:NCI-Frederick	http://david.abcc.ncifcrf.gov/
Resource:ErmineJ	University of British Columbia; British Columbia; Canada Columbia University; New York; USA	http://bioinformatics.ubc.ca/ermineJ/
Resource:FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products	University of Lisbon; Lisbon; Portugal	http://xldb.fc.ul.pt/biotools/rebil/ssm/
Resource:G:Profiler	Resource:BIIT - Bioinformatics Algorithmics and Data Mining Group	http://biit.cs.ut.ee/gprofiler/
Resource:GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool	Weizmann Institute of Science; Rehovot; Israel	http://cbl-gorilla.cs.technion.ac.il/
Resource:GREAT: Genomic Regions Enrichment of Annotations Tool	Stanford University; California; USA	http://great.stanford.edu/public/html/splash.php
Resource:Gene Ontology Browsing Utility (GOBU)	Academia Sinica; Taipei; Taiwan	http://bc02.iis.sinica.edu.tw/gobu/manual/index.html
Resource:Gene Ontology For Functional Analysis (GOFFA)	Resource:National Center for Toxicological Research	http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/default.htm
Resource:GeneMANIA	University of Toronto; Ontario; Canada	http://genemania.org/
Resource:GeneMerge	University of Maryland; Maryland; USA	http://genemerge.cbcb.umd.edu/
Resource:GeneTools - a collection of resources for functional annotations	Norwegian University of Science and Technology; Trondheim; Norway	http://www.genetools.microarray.ntnu.no/common/intro.php
Resource:Generic GO Term Finder	Princeton University; New Jersey; USA Resource:Comprehensive Perl Archive Network	http://go.princeton.edu/cgi-bin/GOTermFinder
Resource:Generic GO Term Mapper	Princeton University; New Jersey; USA	http://go.princeton.edu/cgi-bin/GOTermMapper
Resource:GoBean: a Java application for Gene Ontology enrichment analysis	Gachon University of Medicine and Science; Incheon; South Korea	http://neon.gachon.ac.kr/GoBean/
Resource:GraphWeb	Resource:BIIT - Bioinformatics Algorithmics and Data Mining Group	http://biit.cs.ut.ee/graphweb/
Resource:High-Throughput GoMiner	National Cancer Institute	http://discover.nci.nih.gov/gominer/GoCommandWebInterface.jsp
Resource:Network Ontology Analysis	Chinese Academy of Sciences; Beijing; China	http://app.aporc.org/NOA/
Resource:Onto-Express	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Express
Resource:Onto-Express To Go (OE2GO)	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#OE2GO
Resource:PiNGO	Ghent University; Ghent; Belgium	http://www.psb.ugent.be/esb/PiNGO/Home.html
Resource:ProteInOn	University of Lisbon; Lisbon; Portugal
Resource:Short Time-series Expression Miner (STEM)	Carnegie Mellon University; Pennsylvania; USA	http://www.cs.cmu.edu/~jernst/stem/
Resource:StRAnGER	Resource:National Hellenic Research Foundation	http://www.grissom.gr/stranger/
Resource:ToppGene Suite	Cincinnati Childrens Hospital Medical Center; Ohio; USA	http://toppgene.cchmc.org/
Resource:agriGO	China Agricultural University; Beijing; China	http://bioinfo.cau.edu.cn/agriGO/

Download Text mining Tools

CSV

Text mining: Table View

	Is part of	DefiningCitation	ExampleImage
Resource:Avadis	Strand Life Sciences	http://www.strandls.com/Avadis
Resource:Babelomics 4: Gene Expression and Functional Profiling Analysis Suite	Resource:CIPF Bioinformatics and Genomics Department	http://babelomics.bioinfo.cipf.es
Resource:Bioconductor	Resource:Fred Hutchinson Cancer Research Center	http://www.bioconductor.org/
Resource:Database for Annotation Visualization and Integrated Discovery	Resource:NCI-Frederick	http://david.abcc.ncifcrf.gov/
Resource:Gene Ontology For Functional Analysis (GOFFA)	Resource:National Center for Toxicological Research	http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/default.htm
Resource:GeneMerge	University of Maryland; Maryland; USA	http://genemerge.cbcb.umd.edu/
Resource:GoAnnotator	University of Lisbon; Lisbon; Portugal	http://xldb.fc.ul.pt/biotools/rebil/goa/
Resource:TXTGate	Catholic University of Leuven; Flemish Brabant; Belgium	http://tomcat.esat.kuleuven.be/txtgate/
Resource:agriGO	China Agricultural University; Beijing; China	http://bioinfo.cau.edu.cn/agriGO/

Download Protein interaction Tools

CSV

Protein interactions: Table View

	Is part of	DefiningCitation	ExampleImage
Resource:APID: Agile Protein Interaction DataAnalyzer	University of Salamanca; Salamanca; Spain	http://bioinfow.dep.usal.es/apid
Resource:G:Profiler	Resource:BIIT - Bioinformatics Algorithmics and Data Mining Group	http://biit.cs.ut.ee/gprofiler/
Resource:GeneMANIA	University of Toronto; Ontario; Canada	http://genemania.org/
Resource:GraphWeb	Resource:BIIT - Bioinformatics Algorithmics and Data Mining Group	http://biit.cs.ut.ee/graphweb/
Resource:ProteInOn	University of Lisbon; Lisbon; Portugal
Resource:ToppGene Suite	Cincinnati Childrens Hospital Medical Center; Ohio; USA	http://toppgene.cchmc.org/

Download Functional similarity Tools

CSV

Functional similarity: Table View

	Is part of	DefiningCitation	ExampleImage
Resource:FastSemSim	University of Padua; Padua; Italy Resource:SourceForge	http://sourceforge.net/p/fastsemsim/home/Home/
Resource:FunSimMat	Max-Planck-Institute for Informatics; Saarbrucken; Germany	http://funsimmat.bioinf.mpi-inf.mpg.de
Resource:G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools	Clemson University; South Carolina; USA	http://bioinformatics.clemson.edu/G-SESAME/
Resource:G:Profiler	Resource:BIIT - Bioinformatics Algorithmics and Data Mining Group	http://biit.cs.ut.ee/gprofiler/
Resource:GO-Module	University of Illinois at Chicago; Illinois; USA	http://lussierlab.org/GO-Module/GOModule.cgi
Resource:GOTaxExplorer	Max-Planck-Institute for Informatics; Saarbrucken; Germany	http://www.gotaxexplorer.de/
Resource:IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures	University of Cape Town; Western Cape; South Africa	http://web.cbio.uct.ac.za/ITGOM/
Resource:OwlSim	Resource:Berkeley Bioinformatics Open-Source Projects Resource:OWLTools	http://code.google.com/p/owltools/wiki/OwlSim
Resource:PiNGO	Ghent University; Ghent; Belgium	http://www.psb.ugent.be/esb/PiNGO/Home.html
Resource:Semantic Measures Library	Ecole des Mines d'Ales; Ales; France	http://www.semantic-measures-library.org	File:SMT.PNG
Resource:ToppGene Suite	Cincinnati Childrens Hospital Medical Center; Ohio; USA	http://toppgene.cchmc.org/

Download Semantic similarity Tools

CSV

Semantic similarity: Table View

	Is part of	DefiningCitation	ExampleImage
Resource:FastSemSim	University of Padua; Padua; Italy Resource:SourceForge	http://sourceforge.net/p/fastsemsim/home/Home/
Resource:FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products	University of Lisbon; Lisbon; Portugal	http://xldb.fc.ul.pt/biotools/rebil/ssm/
Resource:FunSimMat	Max-Planck-Institute for Informatics; Saarbrucken; Germany	http://funsimmat.bioinf.mpi-inf.mpg.de
Resource:G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools	Clemson University; South Carolina; USA	http://bioinformatics.clemson.edu/G-SESAME/
Resource:GOTaxExplorer	Max-Planck-Institute for Informatics; Saarbrucken; Germany	http://www.gotaxexplorer.de/
Resource:IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures	University of Cape Town; Western Cape; South Africa	http://web.cbio.uct.ac.za/ITGOM/
Resource:OwlSim	Resource:Berkeley Bioinformatics Open-Source Projects Resource:OWLTools	http://code.google.com/p/owltools/wiki/OwlSim
Resource:ProteInOn	University of Lisbon; Lisbon; Portugal
Resource:Semantic Measures Library	Ecole des Mines d'Ales; Ales; France	http://www.semantic-measures-library.org	File:SMT.PNG

Download Other analysis Tools

CSV

Other analysis: Table View

	Is part of	DefiningCitation	ExampleImage
Resource:AmiGO	Resource:GO	http://amigo.geneontology.org/cgi-bin/amigo/go.cgi
Resource:Bioconductor	Resource:Fred Hutchinson Cancer Research Center	http://www.bioconductor.org/
Resource:Expression Profiler	Resource:European Bioinformatics Institute	http://www.ebi.ac.uk/expressionprofiler/
Resource:FSST - Functional Similarity Search Tool	Max-Planck-Institute for Informatics; Saarbrucken; Germany	http://www.gotaxexplorer.de/
Resource:FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products	University of Lisbon; Lisbon; Portugal	http://xldb.fc.ul.pt/biotools/rebil/ssm/
Resource:G:Profiler	Resource:BIIT - Bioinformatics Algorithmics and Data Mining Group	http://biit.cs.ut.ee/gprofiler/
Resource:GO-Module	University of Illinois at Chicago; Illinois; USA	http://lussierlab.org/GO-Module/GOModule.cgi
Resource:GOChase	Seoul National University College of Medicine; Seoul; South Korea	http://www.snubi.org/software/GOChase/
Resource:GOTaxExplorer	Max-Planck-Institute for Informatics; Saarbrucken; Germany	http://www.gotaxexplorer.de/
Resource:GeneMANIA	University of Toronto; Ontario; Canada	http://genemania.org/
Resource:GoPubMed	Resource:Biotechnology Center of the TU Dresden	http://gopubmed.org/web/gopubmed/
Resource:Onto-Compare	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Compare
Resource:Onto-Design	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Design
Resource:Onto-Express	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Express
Resource:Onto-Miner	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Miner
Resource:Onto-Translate	Wayne State University; Michigan; USA	http://vortex.cs.wayne.edu/projects.htm#Onto-Translate
Resource:ProteInOn	University of Lisbon; Lisbon; Portugal
Resource:RamiGO	Resource:Dana-Farber Cancer Institute Resource:Bioconductor	http://bioconductor.org/packages/2.9/bioc/html/RamiGO.html
Resource:ToppGene Suite	Cincinnati Childrens Hospital Medical Center; Ohio; USA	http://toppgene.cchmc.org/
Resource:Whatizit	Resource:European Bioinformatics Institute	http://www.ebi.ac.uk/webservices/whatizit/info.jsf
Resource:go-moose	Resource:SourceForge Resource:Berkeley Bioinformatics Open-Source Projects Lawrence Berkeley National Laboratory	http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-moose/

Facts about Resource:Gene Ontology ToolsRDF feed

Abbrev	GO Tools  +
Availability	The community can contribute to this resource.  +
CurationStatus	curated  +
DefiningCitation	http://www.geneontology.org/GO.tools.shtml  +
Definition	Collection of tools developed by the GO Co … Collection of tools developed by the GO Consortium and by third parties. Tools are listed by category (see tables below) or alphabetically and continue to be improved and expanded. Submit your GO Tool, http://www.geneontology.org/cgi-bin/add-tool.cgi. For adding resources to this registry through the NeuroLex, http://neurolex.org/wiki/Main_Page, please refer to https://confluence.crbs.ucsd.edu/display/NIF/Resources+and+Curation#ResourcesandCuration-IncorporatingOutsideRegistriesandAccommodatingTheirTags. You can receive support in using these tools by writing to the GO helpdesk, http://www.geneontology.org/GO.contacts.shtml Categories include: Ontology or annotation browser Ontology or annotation search engine Ontology or annotation visualization Ontology or annotation editor Database or data warehouse Software library Statistical analysis Slimmer-type tool Term enrichment Text mining Protein interactions Functional similarity Semantic similarity Other analysis The tools listings are currently being updated 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. A list of useful ID mapping tools is also maintained on the GO wiki. g tools is also maintained on the GO wiki.
ExampleImage	+
Has default formThis property is a special property in this wiki.	Resource  +
Has role	Software repository  +, and Registry  +
Id	nlx_146273  +
Is part of	Resource:GO  +
Keywords	Registry  +, Annotation browser  +, Annotation search engine  +, Annotation visualization  +, Ontology  +, Annotation editor  +, Database  +, Data warehouse  +, Software library  +, Statistical analysis  +, Slimmer-type tool  +, Term enrichment  +, Text mining  +, Protein interaction  +, Functional similarity  +, Semantic similarity  +, Analysis  +, Annotation  +, Visualization  +, and Editor  +
Label	Resource:Gene Ontology Tools  +
ModifiedDate	15 May 2013  +
Page has default formThis property is a special property in this wiki.	Resource  +
RelatedTo	Resource:NIF Data Federation  +
SuperCategory	Resource  +