[Instance]
id: TOOL:000001
type: tool
name: Blast2GO
url: http://www.blast2go.de
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000013
developer: ORG:000016
publication: PMID:16081474
license: free_academic
description: <p><a href="http://www.blast2go.de" title="Blast2GO">Blast2GO (B2G)</a> joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher's Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies.</p>


[Instance]
id: TOOL:000002
type: tool
name: g:Profiler
url: http://biit.cs.ut.ee/gprofiler/
is_online_tool: true
developer: ORG:000032
publication: PMID:17478515
license: free_academic
description: <p><a href="http://biit.cs.ut.ee/gprofiler/" title="g:Profiler">g:Profiler</a> is a public web server for characterising and manipulating gene lists resulting from mining high-throughput genomic data. g:Profiler has a simple, user-friendly web interface with powerful visualisation for capturing Gene Ontology, pathway, or transcription factor binding site enrichments down to individual gene levels. Besides standard multiple testing corrections, a new improved method for estimating the true effect of multiple testing over complex structures like GO has been introduced. Interpreting ranked gene lists is supported from the same interface with very efficient algorithms. Such ordered lists may arise when studying the most significantly affected genes from high-throughput data or genes co-expressed with the query gene. Other important aspects of practical data analysis are supported by modules tightly integrated with g:Profiler. These are:</p><ul><li>g:Convert for converting between different database identifiers;</li><li>g:Orth for finding orthologous genes from other species;</li><li>g:Sorter for searching a large body of public gene expression data for co-expression.</li></ul><p>g:Profiler supports 31 different species, and underlying data is updated regularly from sources like the Ensembl database. Bioinformatics communities wishing to integrate with g:Profiler can use alternative simple textual outputs.</p>


[Instance]
id: TOOL:000003
type: tool
name: GeneTools
url: http://www.genetools.microarray.ntnu.no/common/intro.php
is_online_tool: true
developer: ORG:000061
developer: ORG:000049
license: free_academic
description: <p><a href="http://www.genetools.microarray.ntnu.no/common/intro.php" title="GeneTools">GeneTools</a> is a collection of web-based tools that brings together information from a broad range of resources, and provides this in a manner particularly useful for genome-wide analyses. Today, the two main tools connected to this database are the NMC Annotation Database V2.0 and eGOn V2.0 (explore Gene Ontology). The NMC Annotation Database V2.0 provides information from UniGene, EntrezGene, SwissProt and Gene Ontology (GO).</p><p>Major features are:</p><ul><li>Single search/Batch search, extraction of data for single or batches of genes. </li><li>Manage reporter lists: in folders and share selected lists with other users. </li><li>Manual GO Annotation: add your own Gene Ontology (GO) annotations to genes of interest. </li><li>Export: to Excel, text or XML format. </li></ul>


[Instance]
id: TOOL:000004
type: tool
name: GOanna
url: http://agbase.msstate.edu/GOAnna.html
is_online_tool: true
developer: ORG:000044
license: free_academic
description: <p><a title="GOanna" href="http://agbase.msstate.edu/GOAnna.html">GOanna</a> is used to find annotations for proteins using a similarity search. The input can be a list of IDs or it can be a list of sequences in FASTA format. GOanna will retrieve the sequences if necessary and conduct the specified BLAST search against a user-specified database. The resulting file contains GO annotations of the top BLAST hits. The sequence alignments are also provided so the user can use these to access the quality of the match.</p>


[Instance]
id: TOOL:000005
type: tool
name: GoAnnotator
url: http://xldb.fc.ul.pt/rebil/tools/goa/
is_online_tool: true
developer: ORG:000017
publication: PMID:15719064
license: free_academic
description: <p><a href="http://xldb.fc.ul.pt/rebil/tools/goa/" title="GoAnnotator">GoAnnotator</a> is a tool for verification of electronic protein annotations using GO terms automatically extracted from literature.</p>


[Instance]
id: TOOL:000006
type: tool
name: GOCat
url: http://eagl.unige.ch/GOCat/
is_online_tool: true
developer: ORG:000068
developer: ORG:000051
publication: PMID:16287934
publication: PMID:15960836
license: free_academic
description: <p>The <a href="http://eagl.unige.ch/GOCat/" title="GOCat">Gene Ontology Categorizer (GOCat)<span class="extLink">[external website]</span></a> is an automatic text categorizer. The tool classifies any input text (a few words, an abstract, a set of PubMed Identifiers...) into Gene Ontology categories. The system, originally developed for the first BioCreative evaluation campaign, aims at facilitating functional annotation of gene and gene products using text mining methods. For every predicted category, a confidence score and a short text passage, extracted from the input text, are provided. The interface can also be used to navigate the Gene Ontology thanks to direct Quick GO links.</p>


[Instance]
id: TOOL:000007
type: tool
name: GoFigure
url: http://udgenome.ags.udel.edu/gofigure/
is_online_tool: true
developer: ORG:000028
publication: PMID:14668239
license: free_academic
description: <p><a href="http://udgenome.ags.udel.edu/gofigure/" title="GoFigure">GoFigure</a> is a web accessible tool that uses BLAST to predict Gene Ontology annotation by identifying annotated homologs of an unknown query sequence. Either DNA or protein sequences can be submitted, and multiple queries can be done by submitting a file containing FASTA formated sequences. Results are retrieved by email and may be viewed as either graphs or a tab delimited file. Results can also bedownloaded as a tar file.</p>


[Instance]
id: TOOL:000008
type: tool
name: GoPubMed
url: http://gopubmed.org/
is_online_tool: true
developer: ORG:000059
publication: PMID:15980585
license: free_academic
description: <p><a href="http://gopubmed.org/" title="GoPubMed">GoPubMed</a> is a web server which allows users to explore PubMed search results with the Gene Ontology. GoPubMed submits a user's keywords to PubMed, retrieves the abstracts, detects Gene Ontology terms in the abstracts, displays the subset of Gene Ontology relevant to the original query, and allows the user to browse through the ontology displaying associated papers and their GO annotation.</p>


[Instance]
id: TOOL:000009
type: tool
name: GOtcha
url: http://www.compbio.dundee.ac.uk/Software/GOtcha/gotcha.html
is_online_tool: true
developer: ORG:000035
publication: PMID:15550167
license: free_academic
description: <p><a href="http://www.compbio.dundee.ac.uk/Software/GOtcha/gotcha.html" title="GOtcha">GOtcha</a> provides a prediction of a set of GO terms that can be assosciated with a given query sequence. Each term is scoredindependently and the scores calibrated against reference searches to give an accurate percentage likelihood of correctness. These results can be displayed graphically.<br>The tool is currently web-based; contact <a href="http://www.compbio.dundee.ac.uk/About_Us/about_us.html#david" title="David Martin">David Martin</a> for details of the standalone version.</p>


[Instance]
id: TOOL:000010
type: tool
name: HT-GO-FAT
url: http://genome4.ars.usda.gov/farm/dload.php?action=file&amp;file_id=12
is_standalone_tool: true
compatible_os: win
developer: ORG:000079
license: free_academic
description: <p><a href="http://liru.ars.usda.gov/ht-go-fat.htm" title="High Throughput Gene Ontology Functional Annotation Toolkit">High Throughput Gene Ontology Functional Annotation Toolkit</a> allows for high throughput mapping of unknown or other genetic sequence data such as ESTs, mRNA, or protein data to Gene Ontology annotations, EC numbers and also directly to KEGG pathways. It uses sequence similarity and domain matching. The tool uses custom curated databases and has functions such as windows LAN distributed BLAST, which can distribute high throughput BLAST searches over a windows LAN. It has a high-throughput BLAST output viewer and many file type export features that allow for top hit association or manual curation of data. Data can be exported as AmiGO association files that can be loaded via the load data script. Pathways highlight those enzymes/genes that are represented in your dataset.</p>


[Instance]
id: TOOL:000011
type: tool
name: InGOt
url: http://www.biopendium.com/ingot.htm
is_online_tool: true
license: proprietary
developer: ORG:000069
description: <p><a href="http://www.biopendium.com/ingot.htm" title="InGOt">InGOt</a> is a module for Inpharmatica's new modular system for protein annotation, a proprietary system for applying Gene Ontology to all proteins. It offers an unparalleled resource to elucidate protein function: its graphical user interface enables you to investigate links from summary data through to hierarchical context and literature/evidence links. InGOt has more sequences than any public resource and assignments harvested from the broadest possible GO-linked resources. InGOt can integrate with other modules such as Domain Professor for detailed protein domain annotation and Blu-Chip for instant and accurate probe to protein assignments.</p>


[Instance]
id: TOOL:000012
type: tool
name: InterProScan
url: http://www.ebi.ac.uk/Tools/InterProScan/
is_online_tool: true
is_standalone_tool: true
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000086
publication: PMID:17202162
publication: PMID:15980438
license: free_academic
description: <p>Databases of protein domains and functional sites have become vital resources for the prediction of protein functions. During the last decade, several signature- recognition methods have evolved to address different sequence analysis problems, resulting in rather different and, for the most part, independent databases. Diagnostically, these resources have different areas of optimum application owing to the different strengths and weaknesses of their underlying analysis methods. Thus, for best results, search strategies should ideally combine all of them. <a href="http://www.ebi.ac.uk/Tools/InterProScan/" title="InterProScan">InterProScan</a> is a perl-based program which combines these different protein signature recognition methods into one resource.</p>


[Instance]
id: TOOL:000013
type: tool
name: Joint Assembly of Functional Annotations
synonym_acronym: JAFA
url: http://jafa.burnham.org
is_online_tool: true
developer: ORG:000037
license: free_academic
description: <p><a href="http://jafa.burnham.org" title="JAFA">JAFA</a> accepts a protein sequence, submits it to several function prediction programs, and provides an aggregate of the predictions in a single, easy to read display, based on GO terms. The user may click through to the individual servers, to AmiGO and QuickGO. JAFA also provides adownloadable XML file with the results, to enable incorporation in yet larger workflows.</p>


[Instance]
id: TOOL:000014
type: tool
name: Manatee
url: http://manatee.sourceforge.net/demos.shtml
is_online_tool: true
is_standalone_tool: true
compatible_os: linux
compatible_os: unix
developer: ORG:000080
license: free_academic
description: <p><a href="http://manatee.sourceforge.net" title="Manatee">Manatee</a> is a web-based gene evaluation and genome annotation tool; Manatee can store and view annotation for prokaryotic and eukaryotic genomes. The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments, such as GO classifications, using search data, paralogous families, and annotation suggestions generated from automated analysis. Manatee can bedownloaded and installed to run under the CGI area of a web server, such as Apache.</p>


[Instance]
id: TOOL:000015
type: tool
name: PubSearch
url: http://pubsearch.org
is_online_tool: true
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000062
license: free_academic
description: <p><a href="http://pubsearch.org" title="PubSearch">PubSearch</a> is a web-based literature curation tool, allowing curators to search and annotate genes to keywords from articles. It has a simple mySQL database backend and uses a set of Java Servlets and JSPs for querying, modifying, and adding gene, gene-annotation, and literature information. A <a href="http://tesuque.stanford.edu:9999/pubdemo/index.jsp" title="PubSearch demo using TAIR data">demo using data from TAIR</a> is available (runs on platforms supporting Java Servlets environment); the tool itself can bedownloaded from <a href="http://www.gmod.org/pubsearch.shtml" title="GMOD">GMOD</a>.</p>


[Instance]
id: TOOL:000016
type: tool
name: AmiGO
url: http://amigo.geneontology.org/cgi-bin/amigo/go.cgi
email: gohelp@geneontology.org
is_online_tool: true
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000009
feature: ont_view
feature: annot_view
license: free_academic
description: <p><a href="http://amigo.geneontology.org/cgi-bin/amigo/go.cgi" title="AmiGO">AmiGO</a> 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.</p><p>AmiGO accesses the GO mySQL database; more information is available from the <a href="GO.database.shtml" title="Documentation on the GO database">GO database guide</a>.</p>



[Instance]
id: TOOL:000017
type: tool
name: GO Online SQL Environment
acronym: GOOSE
url: http://www.berkeleybop.org/goose/
email: gohelp@geneontology.org
is_online_tool: true
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000009
feature: godb
feature: annot_view
license: free_academic
description: <p><a href="http://www.berkeleybop.org/goose/" title="GOOSE"><acronym title="GO Online SQL Environment">GOOSE</acronym>, the GO Online SQL Environment,</a> 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.</p>


[Instance]
id: TOOL:000018
type: tool
name: CGAP GO Browser
url: http://cgap.nci.nih.gov/Genes/GOBrowser
is_online_tool: true
developer: ORG:000053
license: free_academic
description: <p>With the <a href="http://cgap.nci.nih.gov/Genes/GOBrowser" title="CGAP GO browser">CGAP GO browser</a>, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term.<br>GO data updated every few months.</p>


[Instance]
id: TOOL:000019
type: tool
name: COBrA
url: http://www.xspan.org/cobra/
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000054
publication: PMID:15513995
license: free_academic
description: <p><a href="http://www.xspan.org/cobra/" title="COBrA">COBrA</a> 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.</p>


[Instance]
id: TOOL:000020
type: tool
name: Comparative Toxicogenomics Database
synonym_acronym: CTD
url: http://ctd.mdibl.org/
is_online_tool: true
developer: ORG:000022
publication: PMID:16902965
publication: PMID:16675512
publication: PMID:14735110
publication: PMID:12760826
license: free_academic
description: <p>The <a href="http://ctd.mdibl.org/" title="Comparative Toxicogenomics Database (CTD)">Comparative Toxicogenomics Database (CTD)</a> 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.</p>


[Instance]
id: TOOL:000021
type: tool
name: DynGO
url: http://gauss.dbb.georgetown.edu/liblab/dyngo.html
is_standalone_tool: true
compatible_os: win
compatible_os: unix
compatible_os: linux
developer: ORG:000083
publication: PMID:16091147
license: free_academic
description: <p><a class="img floatR" href="http://gauss.dbb.georgetown.edu/liblab/dyngo.html" title="download DynGO">DynGO</a> 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.</p>


[Instance]
id: TOOL:000022
type: tool
name: EP GO Browser
url: http://ep.ebi.ac.uk/EP/GO/
is_online_tool: true
developer: ORG:000086
license: free_academic
description: <p>The <a href="http://ep.ebi.ac.uk/EP/GO/" title="EP:GO browser">EP:GO browser</a> is built into EBI's <a href="http://ep.ebi.ac.uk" title="Expression Profiler">Expression Profiler</a>, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice.</p>


[Instance]
id: TOOL:000023
type: tool
name: Gene Class Expression
url: http://gdm.fmrp.usp.br/cgi-bin/gc/upload/upload.pl
is_online_tool: true
developer: ORG:000075
publication: PMID:16755502
license: free_academic
description: <p><a href="http://gdm.fmrp.usp.br/cgi-bin/gc/upload/upload.pl" title="Gene Class Expression">Gene Class Expression</a> 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.</p>


[Instance]
id: TOOL:000024
type: tool
name: GeneInfoViz
url: http://genenet2.utmem.edu/geneinfoviz
is_online_tool: true
developer: ORG:000082
publication: PMID:15724283
license: free_academic
description: <p><a href="http://genenet2.utmem.edu/geneinfoviz" title="GeneInfoViz">GeneInfoViz</a> 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.</p>


[Instance]
id: TOOL:000025
type: tool
name: GeneOntology at RZPD
url: http://www.rzpd.de/cgi-bin/asearch/GO/go4rzpd.pl.cgi
is_online_tool: true
developer: ORG:000045
license: free_academic
description: <p>With the <a href="http://www.rzpd.de/cgi-bin/asearch/GO/go4rzpd.pl.cgi" title="RZPD GeneOntology tool">RZPD GeneOntology tool</a>, you can search for GO identifiers associated with UniGene ClusterIds, Genes (Name/Symbol) and Clones provided by the RZPD. You can also search for UniGene Clusters, Genes and Clones annotated with a certain GO identifier or a combination of GO identifiers. So far, GO annotations for human and mouse genes/clones are linked.</p>
! not sure what's happening with this tool - may no longer be active.


[Instance]
id: TOOL:000026
type: tool
name: GenNav
url: http://mor.nlm.nih.gov/perl/gennav.pl
is_online_tool: true
developer: ORG:000078
license: free_academic
description: <p><a href="http://mor.nlm.nih.gov/perl/gennav.pl" title="GenNav">GenNav</a> searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG.</p>


[Instance]
id: TOOL:000027
type: tool
name: GOblet
url: http://goblet.molgen.mpg.de/
is_online_tool: true
developer: ORG:000008
publication: PMID:15215401
license: free_academic
description: <p>The <a href="http://goblet.molgen.mpg.de" title="GOblet">GOblet</a> 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.</p>


[Instance]
id: TOOL:000028
type: tool
name: GoFish
url: http://llama.med.harvard.edu/~berriz/GoFishWelcome.html
is_online_tool: true
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000014
publication: PMID:12691998
license: free_academic
description: <p>The <a href="http://llama.med.harvard.edu/Software.html" title="GoFish">GoFish</a> program, available as a Java applet online or todownload, 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.</p>


[Instance]
id: TOOL:000029
type: tool
name: GONUTS
url: http://gowiki.tamu.edu/
is_online_tool: true
developer: ORG:000088
license: free_academic
description: <p><a href="http://gowiki.tamu.edu/" title="GONUTS">GONUTS (Gene Ontology Normal Usage Tracking System)</a> 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.</p>


[Instance]
id: TOOL:000030
type: tool
name:  MGI GO Browser
url: http://www.informatics.jax.org/searches/GO_form.shtml
is_online_tool: true
developer: ORG:000006
license: free_academic
description: <p>With the <a href="http://www.informatics.jax.org/searches/GO_form.shtml" title="MGI GO Browser">MGI GO Browser</a>, 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.</p>


[Instance]
id: TOOL:000031
type: tool
name: OBO-Edit
url: https://sourceforge.net/project/showfiles.php?group_id=36855&amp;package_id=192411
email: gohelp@geneontology.org
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000009
license: free_academic
description: <p><a href="https://sourceforge.net/project/showfiles.php?group_id=36855&amp;package_id=192411" title="OBO-Edit">OBO-Edit</a> is an open source, platform-independent application for viewing and editing any <a href="GO.format.shtml#oboflat" title="The OBO file format in the File Format Guide">OBO format</a> 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.</p><p>OBO-Edit uses the <a href="GO.downloads.shtml#ont" title="Ontologies and Definitions from GOdownloads">OBO format flat file</a>.</p>


[Instance]
id: TOOL:000032
type: tool
name: Ontology Lookup Service
url: http://www.ebi.ac.uk/ontology-lookup/
is_online_tool: true
developer: ORG:000086
publication: PMID:16507094
license: free_academic
description: <p>The <a href="http://www.ebi.ac.uk/ontology-lookup/" title="Ontology Lookup Service">Ontology Lookup Service</a> (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 fordownload 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.</p>


[Instance]
id: TOOL:000033
type: tool
name: PANDORA
url: http://www.pandora.cs.huji.ac.il
is_online_tool: true
developer: ORG:000063
license: free_academic
description: <p>With <a href="http://www.pandora.cs.huji.ac.il/" title="PANDORA">PANDORA</a>, 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 <a href="http://www.protonet.cs.huji.ac.il" title="ProtoNet">ProtoNet system</a>, thus allowing testing of thousands of automatically generated protein families. Note that PANDORA replaces the ProtoGO browser developed by the same group.</p>


[Instance]
id: TOOL:000034
type: tool
name: QuickGO at EBI
url: http://www.ebi.ac.uk/ego/
is_online_tool: true
developer: ORG:000086
license: free_academic
description: <p>With <a href="http://www.ebi.ac.uk/ego/" title="QuickGO">QuickGO</a>, a GO browser integrated into <a href="http://www.ebi.ac.uk/interpro/" title="InterPro">InterPro</a> at the <a href="http://www.ebi.ac.uk" title="EBI">EBI</a>, you can search for a GO term to see its relationships and definition, as well as any available mappings to SWISS-PROT keywords, to the Enzyme Classification or Transport Classification databases, or to InterPro entries. The GO data is updated daily.</p>


[Instance]
id: TOOL:000035
type: tool
name: TAIR Keyword Browser
url: http://www.arabidopsis.org/servlets/Search?action=new_search&amp;type=keyword
is_online_tool: true
developer: ORG:000062
license: free_academic
description: <p><a href="http://www.arabidopsis.org/servlets/Search?action=new_search&amp;type=keyword" title="TAIR Keyword Browser">TAIR Keyword Browser</a> 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.</p>


[Instance]
id: TOOL:000036
type: tool
name: Tk-GO
url: http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-gui/?cvsroot=bioperl
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000070
license: free_academic
description: <p>This tool 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 <a href="http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-gui/?cvsroot=bioperl" title="bioperl.org">bioperl.org</a> cvs site todownload the programme. All available documentation is included in thisdownload. Tk-GO uses the GO database (connects directly to the BDGP database by default) but is user-configurable.</p>


[Instance]
id: TOOL:000037
type: tool
name: Agile Protein Interaction Data Analyzer
url: http://bioinfow.dep.usal.es/apid/index.htm
is_online_tool: true
developer: ORG:000046
publication: PMID:16845013
license: free_academic
description: <p><a href="http://bioinfow.dep.usal.es/apid/index.htm" title="APID">Agile Protein Interaction Data Analyzer (APID)</a> is an interactive bioinformatics web tool developed to integrate and analyze in a unified and comparative platform main currently known information about protein-protein interactions demonstrated by specific small-scale or large-scale experimental methods. At present, the application includes information coming from five main source databases enclosing an unified sever to explore more than 40000 different proteins and close to 150000 different proven interactions. The website includes search tools to query and browse upon the data, allowing selection of the interaction pairs based in calculated parameters that weight and qualify the reliability of each given protein interaction. Parameters for the proteins are connectivity, cluster coefficient, Gene Ontology (GO) functional environment, GO environment enrichment; for the interactions: number of methods, GO overlapping, iPfam domain-domain interaction. APID also includes a graphic interactive tool to visualize selected sub-networks and to navigate on them or along the whole interaction network.</p>


[Instance]
id: TOOL:000038
type: tool
name: Db for Dummies!
url: http://www.dbfordummies.com/go.asp
is_standalone_tool: true
compatible_os: win
developer: ORG:000040
license: free_academic
description: <p><a href="http://www.dbfordummies.com/go.asp" title="Db for Dummies!">Db for Dummies! (DBD)</a> is a small database that imports the Generic GO Slim. It allows data to be viewed in a tree.</p>


[Instance]
id: TOOL:000039
type: tool
name: Flash GViewer
url: http://www.gmod.org/wiki/index.php/Flashgviewer/
is_online_tool: true
developer: ORG:000026
license: free_academic
description: <p><a href="http://www.gmod.org/wiki/index.php/Flashgviewer/" title="Flash GViewer">Flash GViewer</a> is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes associated with a specific ontology term, etc., rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts.<br>This tool is not GO-specific, but was built for the purpose of viewing GO annotation data.</p>


[Instance]
id: TOOL:000040
type: tool
name: FunSpec
url: http://funspec.med.utoronto.ca/
is_online_tool: true
developer: ORG:000020
publication: PMID:12431279
license: free_academic
description: <p><a href="http://funspec.med.utoronto.ca/" title="FunSpec">FunSpec</a> is a web-based tool for statistical evaluation of groups of genes and proteins (e.g. co-regulated genes, protein complexes, genetic interactors) with respect to existing annotations, including GO terms.</p>


[Instance]
id: TOOL:000041
type: tool
name: Generic GO Term Mapper
url: http://go.princeton.edu/cgi-bin/GOTermMapper
is_online_tool: true
developer: ORG:000081
license: free_academic
description: <p>The <a href="http://go.princeton.edu/cgi-bin/GOTermMapper" title="Generic GO Term Mapper">Generic GO Term Mapper</a> is a tool for mapping the granular GO annotations for genes in a list to a set of broader, high-level GO parents terms (sometimes referred to as GO Slim terms), allowing you to bin your genes into broad categories.</p>


[Instance]
id: TOOL:000042
type: tool
name: Genes2Diseases
url: http://www.bork.embl-heidelberg.de/g2d/
is_online_tool: true
developer: ORG:000084
license: free_academic
description: <p><a href="http://www.bork.embl-heidelberg.de/g2d/" title="Genes2Diseases">Genes2Diseases</a> is a database of candidate genes for mapped inherited human diseases. The database is generated using an analysis of relations between phenotypic features and chemical objects, and from chemical objects to Gene Ontology protein function terms, based on the whole MEDLINE and RefSeq databases. Can be used to view all GO terms associated with a particular genetically inherited disease.</p>


[Instance]
id: TOOL:000043
type: tool
name: GO Slim Mapper
url: http://db.yeastgenome.org/cgi-bin/GO/goSlimMapper.pl
is_online_tool: true
developer: ORG:000025
license: free_academic
description: <p>The <a href="http://db.yeastgenome.org/cgi-bin/GO/goSlimMapper.pl" title="GO Slim Mapper">GO Slim Mapper</a> (aka GO Term Mapper) maps the specific, granular GO terms used to annotate a list of budding yeast gene products to corresponding more general parent <a href="GO.slims.shtml" title="GO slim guide">GO slim</a> terms. Uses the SGD GO Slim sets.</p>


[Instance]
id: TOOL:000044
type: tool
name: GO Terms Classifications Counter
url: http://www.animalgenome.org/bioinfo/tools/countgo/
is_online_tool: true
developer: ORG:000002
license: free_academic
description: <p><a href="http://www.animalgenome.org/bioinfo/tools/countgo/" title="GO Terms Classifications Counter">GO Terms Classifications Counter</a> takes input of GO term IDs in a list format or unformatted plain text file, allows users to choose one of the available classifications such as GO_slim, GOA, EGAD, MGI_GO_slim or GO-ROOT, performs the count, and returns the results on the web (if it takes too long, it will email the user with the results link). The results include a sorted table of counts, percentages, and a pie chart.</p>


[Instance]
id: TOOL:000045
type: tool
name: Gene Ontology Browsing Utility
synonym_acronym: GOBU
url: http://gobu.iis.sinica.edu.tw/
is_online_tool: true
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000055
license: free_academic
description: <p><a href="http://gobu.iis.sinica.edu.tw/" title="Gene Ontology Browsing Utility (GOBU)">Gene Ontology Browsing Utility (GOBU)</a> is a Java-based software program for integrating biological annotation catalogs under an extendable architecture that uses the Gene Ontology and a user-defined hierarchy as two main atalogs. GOBU has the following features: (1) user-specified hierarchical data as input data, (2) user-defined data types for describing different annotations, and (3) an extendable software architecture for handling user-defined data types.</p>


[Instance]
id: TOOL:000046
type: tool
name: GOChase
url: http://www.snubi.org/software/GOChase/
is_online_tool: true
developer: ORG:000047
publication: PMID:15513987
license: free_academic
description: <p><a href="http://www.snubi.org/software/GOChase/" title="GOChase">GOChase</a> is a set of web-based utilities to detect and correct the errors in GO-based annotations.</p><ul><li>GOChase-History resolves the whole modification history of GO IDs. </li><li>GOChase-Correct highlights merged GO IDs and redirects to the correct primary term into which the secondary ID was merged. For obsolete GO terms, the nearest non-discarded parent term is recommended by GOChase. This function may be used by GO browsers such as AmiGO and QuickGO to fix broken hyperlinks. </li><li>A whole database (such as LocusLink) as a flat file can be loaded into GOChase, reporting the annotation errors and GOChase corrections. </li><li>When one inputs a GO ID, GOChase will resolve all gene products annotated with the GO ID across all the major databases. </li></ul>


[Instance]
id: TOOL:000047
type: tool
name: GOProfiler
url: http://agbase.msstate.edu/GOProfiler.html
is_online_tool: true
developer: ORG:000044
license: free_academic
description: <p><a title="GOProfiler" href="http://agbase.msstate.edu/GOProfiler.html">GOProfiler</a> provides a summary of the GO annotations available in AgBase. The user provides a species (taxon id) and GOProfiler displays the number of GO associations and the number of annotated proteins for that species. The results are listed by evidence code and a separate list of unannotated proteins is also provided.</p>


[Instance]
id: TOOL:000048
type: tool
name: GORetriever
url: http://agbase.msstate.edu/GORetriever.html
is_online_tool: true
developer: ORG:000044
license: free_academic
description: <p><a title="GORetriever" href="http://agbase.msstate.edu/GORetriever.html">GORetriever</a> is used to find all of the GO annotations in AgBase corresponding to a list of user-supplied protein identifiers. Currently supported ID types are Uniprot ID, Uniprot Accession, and GO ID. GORetriever produces a list of proteins and their annotations and a separate list of entries with no GO annotation. The list without GO annotations can be subsequently used as in put for the <a href="http://agbase.msstate.edu/GOAnna.html" title="GOanna">GOanna</a> tool that finds similar sequences with annotations (where they are available).</p>


[Instance]
id: TOOL:000049
type: tool
name: GOSlimViewer
url: http://agbase.msstate.edu/GOSlimViewer.html
is_online_tool: true
developer: ORG:000044
license: free_academic
description: <p><a title="GOSlimViewer" href="http://agbase.msstate.edu/GOSlimViewer.html">GOSlimViewer</a> is used to provide a high level summary of the GO categories for a dataset. It is designed to use output generated by <a title="GORetriever" href="http://agbase.msstate.edu/GORetriever.html">GORetriever</a>. Note that you can add additional annotations that come from <a href="http://agbase.msstate.edu/GOAnna.html" title="GOanna">GOanna</a> (or other sources) to the GORetriever file. GOSlimViewer currently only supports the listed GOSlim sets.</p>


[Instance]
id: TOOL:000050
type: tool
name: ProteInOn
url: http://xldb.fc.ul.pt/biotools/proteinon/
is_online_tool: true
developer: ORG:000017
publication: PMID:15960834
license: free_academic
description: <p><a href="http://xldb.fc.ul.pt/biotools/proteinon/" title="ProteInOn">ProteInOn</a> can be used to find interacting proteins, find assigned GO terms and calculate the functional semantic similarity of proteins and to get the information content and calculate the functional semantic similarity of GO terms.</p><p>Additional citations:</p><ol><li>F. Couto, M. Silva and P. Coutinho. Measuring Semantic Similarity between Gene Ontology Terms. DKE - Data &amp; Knowledge Engineering, Elsevier Science, In press. </li><li>F. Couto, M. Silva and P. Coutinho. Semantic Similarity over the Gene Ontology: Family Correlation and Selecting Disjunctive Ancestors. ACM CIKM - Conference in Information and Knowledge Management, October 2005. </li></ol>


[Instance]
id: TOOL:000051
type: tool
name: TXTGate
url: http://www.esat.kuleuven.ac.be/txtgate
is_online_tool: true
developer: ORG:000067
publication: PMID:15186494
license: free_academic
description: <p><a href="http://www.esat.kuleuven.ac.be/txtgate" title="TXTGate">TXTGate</a> is a web-service that combines literature indices of selected public biological resources in a flexible text-mining system designed towards the analysis of groups of genes. By means of tailored vocabularies, selected textual fields and MedLine abstracts of LocusLink and SGD are indexed. Subclustering and links to external resources allow for an in-depth analysis of the resulting term profiles.</p>


[Instance]
id: TOOL:000052
type: tool
name: Wandora
url: http://www.wandora.org
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000071
license: free_academic
description: <p><a href="http://www.wandora.org" title="Wandora">Wandora</a> is a general purpose knowledge extraction, management, and publishing environment based on Topic Maps (ISO 13250). Wandora supports OBO flat file v1.2 format and can convert OBO files, including the Gene Ontology, to a topic map and vice versa. Wandora is well suited to OBO visualizations and knowledge mashups combining OBO, RDF(S), and Topic Map resources for example.</p><p>Wandora requires Java v6.</p>


[Instance]
id: TOOL:000053
type: tool
name: WEGO
url: http://wego.genomics.org.cn
is_online_tool: true
developer: ORG:000072
license: free_academic
description: <p><a href="http://wego.genomics.org.cn" title="WEGO (Web Gene Ontology Annotation Plot)">WEGO (Web Gene Ontology Annotation Plot)</a> is a simple but useful tool for plotting Gene Ontology (GO) annotation results. Different from other commercial software for chart creating, WEGO is designed to deal with the directed acyclic graph (DAG) structure of GO to facilitate histogram creation of GO annotation results. WEGO has been widely used in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the useful tools for downstream gene annotation analysis, especially when performing comparative genomics tasks.</p>


[Instance]
id: TOOL:000054
type: tool
name: Whatizit
url: http://www.ebi.ac.uk/Rebholz-srv/whatizit/form.jsp
is_online_tool: true
developer: ORG:000042
license: free_academic
description: <p><a href="http://www.ebi.ac.uk/Rebholz-srv/whatizit/form.jsp" title="Whatizit">Whatizit</a> is a web application which highlights all kinds of "interesting" things in a document. One of its modules marks all GO terms as well as protein and gene names from UniProt and links them to their entries in GO and UniProt respectively.</p>


[Instance]
id: TOOL:000055
type: tool
name: Avadis
url: http://avadis.strandgenomics.com
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: linux
license: proprietary
developer: ORG:000021
description: <p><a href="http://avadis.strandgenomics.com" title="Avadis">Avadis</a> is a data analysis and visualization tool for gene expression data. Avadis has a built-in Gene Ontology browser to view ontology hierarchies. There are common ontology paths for multiple genes. Genes can be clustered based on ontology terms to identify functional signatures in gene expression clusters.</p>


[Instance]
id: TOOL:000056
type: tool
name: BiNGO
url: http://www.psb.ugent.be/cbd/papers/BiNGO/
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000029
publication: PMID:15972284
license: free_academic
description: <p><a href="http://www.psb.ugent.be/cbd/papers/BiNGO/" title="BiNGO">BiNGO</a> is an open-source Java tool to determine which GO categories are statistically over-represented in a set of genes. BiNGO is implemented as a plugin for Cytoscape, which is a software platform for data integration and visualization of molecular interaction networks. BiNGO maps the predominant functional themes of a given gene set on the GO hierarchy, and outputs this mapping as a Cytoscape graph.</p>


[Instance]
id: TOOL:000057
type: tool
name: CLENCH
url: http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=clench
is_standalone_tool: true
compatible_os: win
compatible_os: linux
developer: ORG:000004
publication: PMID:14764555
license: free_academic
description: <p><a href="http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=clench" title="CLENCH">CLENCH</a> (CLuster ENriCHment) allows <i class="spp">A. thaliana</i> researchers to perform automated retrieval of GO annotations from TAIR and calculate enrichment of GO terms in gene group with respect to a reference set. Before calculating enrichment, CLENCH allows mapping of the returned annotations to arbitrary coarse levels using GO slim term lists (which can be edited by the user) and a local installation of GO.</p>


[Instance]
id: TOOL:000058
type: tool
name: DAVID
url: http://david.abcc.ncifcrf.gov/
is_online_tool: true
developer: ORG:000050
publication: PMID:12734009
license: free_academic
description: <p><a href="http://david.abcc.ncifcrf.gov" title="Database for Annotation, Visualization and Integrated Discovery (DAVID)">Database for Annotation, Visualization and Integrated Discovery (DAVID)</a> is a web-based tool that provides integrated solutions for the annotation and analysis of genome-scale datasets derived from high-throughput technologies such as microarray and proteomic platforms. Analysis results and graphical displays remain dynamically linked to primary data and external data repositories, thereby furnishing in-depth as well as broad-based data coverage. The functionality provided by DAVID accelerates the analysis of genome-scale datasets by facilitating the transition from data collection to biological meaning.</p>


[Instance]
id: TOOL:000059
type: tool
name: EASE
url: http://david.niaid.nih.gov/david/ease.htm
is_standalone_tool: true
compatible_os: win
developer: ORG:000050
publication: PMID:12734009
license: free_academic
description: <p><a href="http://david.niaid.nih.gov/david/ease.htm" title="EASE">EASE</a> is useful for summarizing the predominant biological "theme" of a given gene list. Given a list of genes resulting from a microarray or other genome-scale experiment, EASE can rapidly calculate over-representation statistics for every possible Gene Ontology term with respect to all genes represented in the data set.</p>


[Instance]
id: TOOL:000060
type: tool
name: eGOn v2.0
url: http://www.genetools.microarray.ntnu.no/common/intro.php
is_online_tool: true
developer: ORG:000061
developer: ORG:000049
license: free_academic
description: <p><a href="http://www.genetools.microarray.ntnu.no/common/intro.php" title="eGOn V2.0 (explore Gene Ontology)">eGOn V2.0 (explore Gene Ontology)</a> is a web-based tool for mapping microarray data on to the Gene Ontology structure. Several input files may be analyzed simultaneously to compare the distribution of the annotated genes for two or more experiments.</p><p>Essential features of eGOn V2.0 are:</p><ul><li>Visualization: gene annotations are visualized in the GO DAG or as a table view. The granularity of the GO DAG can be edited freely by the user. </li><li>Filtering: GO annotations can be filtered on evidence codes. </li><li>Include user defined GO annotations: previously added to the NMC Annotation database. </li><li>Statistical analysis: Several gene lists are analyzed simultaneously to compare the distribution of the annotated genes over the GO hierarchy. Statistical tests are implemented to allow the user to compute GO annotation dissimilarities within or between gene lists. </li><li>Connection to Annotation database: Links to the NMC Annotation database, gene and protein information are offered directly from the GO DAG or in exported data. </li><li>Export: GO DAG information, statistical results and gene and protein information can be exported in Excel, text or XML format. </li></ul>


[Instance]
id: TOOL:000061
type: tool
name: ermineJ
url: http://bioinformatics.ubc.ca/ermineJ/
is_online_tool: true
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000027
publication: PMID:16280084
license: free_academic
description: <p><a href="http://bioinformatics.ubc.ca/ermineJ/" title="ermineJ">ermineJ</a> is a tool for the analysis of gene sets (user defined or those defined by GO terms) in expression data. The software is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who wish to script the use of ermineJ. Several different methods for scoring gene sets are implemented, with a focus on methods that don't rely on simple "over-representation" measures.</p>


[Instance]
id: TOOL:000062
type: tool
name: FatiGO
url: http://fatigo.ochoa.fib.es
is_online_tool: true
developer: ORG:000064
publication: PMID:14990455
license: free_academic
description: <p><a href="http://www.fatigo.org" title="FatiGO">FatiGO</a> assigns representative functional information (under-represented or over-represented Gene Ontology terms) to a given set of genes. Statistical significance is obtained using multiple-testing correction. FatiGO has been designed for functional annotation in the context of DNA microarray data analysis, and is linked to the <a href="http://www.gepas.org" title="Gene Expression Pattern Analysis Suite">Gene Expression Pattern Analysis Suite</a>. FatiGO uses gene IDs from the major genomic and proteomic databases (GeneBank, UniProt, Unigene, Ensembl, etc.). FatiGO can also be used for functional annotation of any type of large-scale experiment.</p>


[Instance]
id: TOOL:000063
type: tool
name: Functional Information Viewer and Analyzer
synonym_acronym: FIVA
url: http://bioinformatics.biol.rug.nl/standalone/fiva/
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000056
publication: PMID:17237043
license: free_academic
description: <p><a href="http://bioinformatics.biol.rug.nl/standalone/fiva/" title="FIVA">FIVA</a> aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software is able to assist in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes.</p>


[Instance]
id: TOOL:000064
type: tool
name: FuncAssociate
url: http://llama.med.harvard.edu/cgi/func/funcassociate
is_online_tool: true
developer: ORG:000014
publication: PMID:14668247
license: free_academic
description: <p><a href="http://llama.med.harvard.edu/cgi/func/funcassociate" title="FuncAssociate">FuncAssociate</a> is a web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 10 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff.</p><p>A <a href="http://llama.med.harvard.edu/cgi/func1/funcassociate" title="new version of FuncAssociate">new version of FuncAssociate</a> (still at the beta stage!) is now available. This version supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented.</p>


[Instance]
id: TOOL:000065
type: tool
name: FuncExpression
url: http://www.barleybase.org/funcexpression.php
is_online_tool: true
developer: ORG:000007
license: free_academic
description: <p><a href="http://www.barleybase.org/funcexpression.php" title="FuncExpression">FuncExpression</a> is a web-based resource for functional interpretation of large scale genomics data. FuncExpression can be used for the functional comparison of plant, animal, and fungal gene name lists generated from genomics and proteomics experiments. Multiple gene lists can be classified, compared and visualized. FuncExpression supports two way-integration of plant gene functional information and the gene expression data, which allows for further cross-validation with plant microarray data from related experiments at BarleyBase.</p>


[Instance]
id: TOOL:000066
type: tool
name: Functional Profiling of Microarray Expression Data
synonym_abbr: FunCluster
url: http://corneliu.henegar.info/FunCluster.htm
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000018
publication: PMID:17007070
publication: PMID:16506959
publication: PMID:16046292
license: free_academic
description: <p><a href="http://corneliu.henegar.info/FunCluster.htm" title="FunCluster">FunCluster</a> is a genomic data analysis tool designed to perform a functional analysis of gene expression data obtained from cDNA microarray experiments. Besides automated functional annotation of gene expression data, FunCluster functional analysis allows to detect co-regulated biological processes (i.e. represented by annotating genomic themes) through a specifically designed co-clustering procedure involving biological annotations and gene expression data. FunCluster's functional analysis relies on Gene Ontology and KEGG annotations and is currently available for three organisms: <i class="spp">Homo sapiens</i>, <i class="spp">Mus musculus</i> and <i class="spp">Saccharomyces cerevisiae</i>.</p><p>FunCluster is provided as a standalone <a href="http://www.r-project.org/" title="The R project for Statistical Computing">R</a> package, which can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix).download it from the <a href="http://corneliu.henegar.info/FunCluster.htm" title="FunCluster">FunCluster website</a>, or from the <a href="http://cran.r-project.org/mirrors.html" title="CRAN mirrors">worldwide mirrors of CRAN</a>. FunCluster is provided freely under the GNU General Public License 2.0.</p>



[Instance]
id: TOOL:000067
type: tool
name: Functional Analysis of Transcriptional Networks
synonym_abbr: FunNet
url: http://www.funnet.info
is_online_tool: true
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000018
publication: PMID:18208606
license: free_academic
description: <p><a href="http://www.funnet.info" title="FunNet">FunNet</a> is designed as an integrative tool for analyzing gene co-expression networks built from microarray expression data. The analytical model implemented in this tool involves two abstraction layers: transcriptional (i.e. gene expression profiles) and functional (i.e. biological themes indicating the roles of the analyzed transcripts). A functional analysis technique, which relies on Gene Ontology and KEGG annotations, is applied to extract a list of relevant biological themes from microarray gene expression data. Afterwards multiple-instance representations are built to relate relevant biological themes to their annotated transcripts. An original non-linear dynamical model is used to quantify the contextual proximity of relevant genomic themes based on their patterns of propagation in the gene co-expression network (i.e. capturing the similarity of the expression profiles of the transcriptional instances of annotating themes). In the end an unsupervised multiple-instance spectral clustering procedure is used to explore the modular architecture of the co-expression network by grouping together biological themes demonstrating a significant relationship in the co-expression network. Functional and transcriptional representations of the co-expression network are provided, together with detailed information on the contextual centrality of related transcripts and genomic themes.</p><p>FunNet is provided both as a web-based tool and as a standalone <a href="http://www.r-project.org/" title="The R project for Statistical Computing">R</a> package. The standalone R implementation can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix) and can bedownloaded from the <a href="http://corneliu.henegar.info/FunNet.htm" title="FunNet">FunNet website</a>, or from the <a href="http://cran.r-project.org/mirrors.html" title="CRAN mirrors">worldwide mirrors of CRAN</a>. Both implementations of the FunNet tool are provided freely under the GNU General Public License 2.0.</p>


[Instance]
id: TOOL:000068
type: tool
name: G-SESAME
url: http://bioinformatics.clemson.edu/G-SESAME/
is_online_tool: true
developer: ORG:000024
publication: PMID:17344234
license: free_academic
description: <p><a href="http://bioinformatics.clemson.edu/G-SESAME/" title="G-SESAME">G-SESAME</a> contains a set of tools. They are</p><ol><li>Tools for measuring the semantic similarity of GO terms. </li><li>Tools for measuring the functional similarity of genes. </li><li>Tools for clustering genes based on their GO term annotation information. </li></ol>


[Instance]
id: TOOL:000069
type: tool
name: GARBAN
url: http://www.garban.org/garban/home.php
is_online_tool: true
developer: ORG:000033
publication: PMID:14594726
license: free_academic
description: <p><a href="http://www.garban.org/garban/home.php" title="GARBAN">GARBAN</a> is a tool for analysis and rapid functional annotation of data arising from cDNA microarrays and proteomics techniques. GARBAN has been implemented with bioinformatic tools to rapidly compare, classify, and graphically represent multiple sets of data (genes/ESTs, or proteins), with the specific aim of facilitating the identification of molecular markers in pathological and pharmacological studies. GARBAN has links to the major genomic and proteomic databases (Ensembl, GeneBank, UniProt Knowledgebase, InterPro, etc.), and follows the criteria of the Gene Ontology Consortium (GO) for ontological classifications. Source may be shared: e-mail <span class="addr"><span class="id">garban</span>@<span class="place">ceit.es</span></span>.</p>


[Instance]
id: TOOL:000070
type: tool
name: GENECODIS
url: http://genecodis.dacya.ucm.es/
is_online_tool: true
developer: ORG:000019
developer: ORG:000085
publication: PMID:17204154
license: free_academic
description: <p><a href="http://genecodis.dacya.ucm.es/" title="GENECODIS">GENECODIS</a> is a web-based tool for the functional analysis of gene lists. It integrates different sources of information to search for annotations that frequently co-occur in a set of genes and rank them by their statistical significance. It allows the analysis of annotations from different databases such as GO, KEGG or SwissProt.</p>


[Instance]
id: TOOL:000071
type: tool
name: GeneMerge
url: http://genemerge.cbcb.umd.edu/
is_online_tool: true
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000036
publication: PMID:12724301
license: free_academic
description: <p><a href="http://genemerge.cbcb.umd.edu/" title="GeneMerge">GeneMerge</a> returns functional genomic information for a given set of genes and provides statistical rank scores for over-representation of particular functions or categories in the dataset. All GO species are represented in addition to other species and functional genomic data.</p>


[Instance]
id: TOOL:000072
type: tool
name: Genome Function INtegrated Discoverer
synonym_abbr: GFINDer
url: http://www.medinfopoli.polimi.it/GFINDer/
is_online_tool: true
developer: ORG:000077
license: free_academic
description: <p><a href="http://www.medinfopoli.polimi.it/GFINDer/" title="GFINDer: Genome Function INtegrated Discoverer">GFINDer: Genome Function INtegrated Discoverer</a> is a multi-database system providing large-scale lists of user-classified sequence identifiers with genome-scale biological information and functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves updated annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list, and calculates statistical significance values for each category. Moreover, GFINDer enables to functionally classify genes according to mined functional categories and to statistically analyse the obtained classifications, aiding in better interpreting microarray experiment results.</p>


[Instance]
id: TOOL:000073
type: tool
name: Generalized Ontological Algorithmic Logical Invariants Extractor
synonym_abbr: GOALIE
url: http://bioinformatics.nyu.edu/Projects/GOALIE/
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: linux
developer: ORG:000003
license: free_academic
description: <p><a href="http://bioinformatics.nyu.edu/Projects/GOALIE/" title="GOALIE">GOALIE (Generalized Ontological Algorithmic Logical Invariants Extractor)</a> is a tool for the construction of time-course dependent enrichments. Requires an ODBC connection to an instance of the GO database.</p>


[Instance]
id: TOOL:000074
type: tool
name: GOdist
url: http://basalganglia.huji.ac.il/links.htm
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000063
publication: PMID:15550480
license: free_academic
description: <p><a href="http://basalganglia.huji.ac.il/links.htm" title="GOdist">GOdist</a> is a Matlab program that analyzes Affymetrix microarray expression data implementing Kolmogorov-Smirnov (KS) continuous statistics approach. It also implements the discrete approach using Fisher exact test employing a two-tailed hypergeometric distribution. GOdist enables detection of both kinds of changes within specific GO terms represented on the array in relation to different populations: the global array population, the direct parents of the analyzed GO term and the global parent of it (e.g. biological process, molecular function or cellular component).</p>


[Instance]
id: TOOL:000075
type: tool
name: GOHyperGAll
url: http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#go
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000015
license: free_academic
description: <p>To test a sample population of genes for overrepresentation of GO terms, the R/BioC function <a href="http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#go" title="GOHyperGAll">GOHyperGAll</a> computes for all GO nodes a hypergeometric distribution test and returns the corresponding p-values. A subsequent filter function performs a GO Slim analysis using default or custom GO Slim categories. Basic knowledge about R and BioConductor is required for using this tool.</p>


[Instance]
id: TOOL:000076
type: tool
name: High-Throughput GoMiner and MatchMiner
url: http://discover.nci.nih.gov/gominer/htgm.jsp
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000039
developer: ORG:000052
publication: PMID:14728344
license: free_academic
description: <p><a href="http://discover.nci.nih.gov/gominer/htgm.jsp" title="High-Throughput GoMiner">High-Throughput GoMiner</a> is an 'industrial-strength' integrative Gene Ontology tool for interpretation of multiple-microarray experiments. GoMiner is a Java-based program package that organizes lists of 'interesting' genes (e.g., up- and down-regulated genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. GoMiner provides quantitative and statistical output files and two useful visualizations: (i) a tree-like structure analogous to that in the AmiGO browser and (ii) a compact, dynamically interactive DAG. Genes displayed in GoMiner are linked to major public bioinformatics resources. A companion tool, <a href="http://discover.nci.nih.gov/matchminer/" title=" MatchMiner">MatchMiner</a>, can be used as a preprocessor to obtain gene names for input to GoMiner or other GO tools. For users running under a Unix-based operating system, there is an <a href="http://discover.nci.nih.gov/gominer/enhance.jsp" title="automated installation script">automated script</a> for easy installation of the local database.</p>


[Instance]
id: TOOL:000077
type: tool
name: GOstat
url: http://gostat.wehi.edu.au
is_online_tool: true
developer: ORG:000011
publication: PMID:14962934
license: free_academic
description: <p><a href="http://gostat.wehi.edu.au" title="GOstat">GOstat</a>, is an easy to use web tool to determine statistically significant over- or under-represented GO categories within lists of genes. Data files are updating monthly.</p>


[Instance]
id: TOOL:000078
type: tool
name: GoSurfer
url: http://biosun1.harvard.edu/complab/gosurfer/
is_standalone_tool: true
compatible_os: win
developer: ORG:000038
license: free_academic
description: <p><a href="http://biosun1.harvard.edu/complab/gosurfer/" title="GoSurfer">GoSurfer</a> uses Gene Ontology information in the analysis of gene sets obtained from genome-wide computations, microarray analysis or any other highly parallel method. It includes rigorous statistical testing, interactive graphics and automated updating of the annotation available for common gene identifiers (UniGene, LocusLink) or Affymetrix probe sets.</p><p>See also the <a href="http://biosun1.harvard.edu/complab/Zhong_S_GoSurfer2.pdf" title="GO Surfer paper (PDF format)">GO Surfer paper (PDF format)</a>.</p>


[Instance]
id: TOOL:000079
type: tool
name: GO Term Finder
url: http://db.yeastgenome.org/cgi-bin/GO/goTermFinder.pl
is_online_tool: true
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000025
publication: PMID:15297299
license: free_academic
description: <p>The GO Term Finder searches for significant shared GO terms, or parents of the GO terms, used to annotate gene products in a given list. A web-based <a href="http://db.yeastgenome.org/cgi-bin/GO/goTermFinder.pl" title="GO Term Finder">GO Term Finder</a> at <a href="http://www.yeastgenome.org/" title="SGD"><span class="spp">Saccharomyces</span> Genome Database</a> searches annotations of budding yeast gene products. A generic <a href="http://search.cpan.org/dist/GO-TermFinder/" title="GO Term Finder">GO Term Finder</a> has been created by <a href="http://genome-www5.stanford.edu/MicroArray/SMD/" title="Stanford Microarray Database">Stanford Microarray Database</a> and can bedownloaded from <a href="http://www.cpan.org" title="CPAN">CPAN</a>. This code has been used to implement a web-based generic <a href="http://go.princeton.edu/cgi-bin/GOTermFinder" title="GO Term Finder">GO Term Finder</a> by the Princeton genomics group; this implementation provides analysis, via a web tool, of genes from any species (including human) for which there are GO annotations publicly available through the GO web site.</p>


[Instance]
id: TOOL:000080
type: tool
name: Gene Ontology Tree Machine
synonym_acronym: GOTM
url: http://bioinfo.vanderbilt.edu/gotm/
is_online_tool: true
developer: ORG:000074
developer: ORG:000057
publication: PMID:14975175
license: free_academic
description: <p><a href="http://bioinfo.vanderbilt.edu/gotm/" title="GOTM">GOTM</a> is a web-based tool for the analysis and visualization of sets of interesting genes based on Gene Ontology hierarchies. This tool provides user friendly data navigation and visualization. It generates expandable tree for browsing the GO hierarchy, fixed tree as HTML output for archive and Bar charts at different annotation levels for publication. GOTM provides statistical analysis to indicate GO categories with relatively enriched gene numbers and suggest biological areas that warrant further study. Enriched GO categories can be visualized in Sub-trees or DAGs. Subset of genes can be retrieved by GO term or keyword searching. Detailed information for each gene can be retrieved directly from our a local database GeneKeyDB.</p>


[Instance]
id: TOOL:000081
type: tool
name: GOToolBox
url: http://gin.univ-mrs.fr/GOToolBox/
is_online_tool: true
developer: ORG:000048
publication: PMID:15575967
license: free_academic
description: <p><a href="http://gin.univ-mrs.fr/GOToolBox/" title="GOToolBox">GOToolBox</a> is a series of web-based programs allowing the identification of statistically over- or under-represented terms in a gene dataset relative to a reference gene set; the clustering of functionally related genes within a set; and the retrieval of genes sharing annotations with a query gene. GO annotations can also be constrained to a slim hierarchy or a given level of the ontology and terms can be filtered on evidence codes. Updated monthly with GO and gene association files.</p>


[Instance]
id: TOOL:000082
type: tool
name: L2L
url: http://depts.washington.edu/l2l/
is_online_tool: true
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000073
publication: PMID:16168088
license: free_academic
description: <p><a href="http://depts.washington.edu/l2l/" title="L2L">L2L</a> is a simple but powerful tool for discovering the hidden biological significance in microarray data. Through an easy-to-use web interface, L2L will mine a list of up- or down-regulated genes for Gene Ontology terms that are significantly enriched. L2L can also compare the list of genes to a database of hundreds of published microarray experiments, in order to identify common patterns of gene regulation. Adownloadable command-line version can run customized and batch analyses.</p>


[Instance]
id: TOOL:000083
type: tool
name: MAPPFinder
url: http://www.genmapp.org/
is_standalone_tool: true
compatible_os: win
developer: ORG:000034
publication: PMID:12540299
license: free_academic
description: <p><a href="http://www.genmapp.org/" title="MAPPFinder">MAPPFinder</a> is an accessory program for <a href="http://www.genmapp.org/" title="GenMAPP">GenMAPP</a>. This program allows users to query any existing GenMAPP Expression Dataset Criterion against GO gene associations and GenMAPP MAPPs (microarray pathway profiles). The resulting analysis provides the user with results that can be viewed directly upon the Gene Ontology hierarchy and within GenMAPP, by selecting terms or MAPPs of interest.</p>


[Instance]
id: TOOL:000084
type: tool
name: Onto-Compare
url: http://vortex.cs.wayne.edu/projects.htm#Onto-Compare
is_online_tool: true
developer: ORG:000031
publication: PMID:12664686
publication: PMID:15215428
license: free_academic
description: <p><a href="http://vortex.cs.wayne.edu/projects.htm#Onto-Compare" title="Onto-Compare">Onto-Compare</a> is a web based tool that permits comparison of commercial microarrays based on GO. Onto-Compare allows the user to assess the functional bias associated with each array and helps determine the best microarray for a given biological phenomenon described using GO terms.</p>


[Instance]
id: TOOL:000085
type: tool
name: Onto-Design
url: http://vortex.cs.wayne.edu/projects.htm#Onto-Design
is_online_tool: true
developer: ORG:000031
publication: PMID:15215428
license: free_academic
description: <p><a href="http://vortex.cs.wayne.edu/projects.htm#Onto-Design" title="Onto-Design ">Onto-Design</a> allows the user to design custom microarrays by selecting a set of UniGene cluster IDs that represent a given subset of biological processes described using GO terms.</p>


[Instance]
id: TOOL:000086
type: tool
name: Onto-Express
url: http://vortex.cs.wayne.edu/projects.htm#Onto-Express
is_online_tool: true
developer: ORG:000031
publication: PMID:11829497
publication: PMID:12620386
publication: PMID:15215428
license: free_academic
description: <p><a href="http://vortex.cs.wayne.edu/projects.htm#Onto-Express" title="Onto-Express">Onto-Express</a> searches the public databases and returns tables that correlate expression profiles with the cytogenetic gene locations, the biochemical and molecular functions, the biological processes, cellular components and cellular roles of the translated proteins.</p>


[Instance]
id: TOOL:000087
type: tool
name: Onto-Miner
url: http://vortex.cs.wayne.edu/projects.htm#Onto-Miner
is_online_tool: true
developer: ORG:000031
publication: PMID:15215428
license: free_academic
description: <p><a href="http://vortex.cs.wayne.edu/projects.htm#Onto-Miner" title="Onto-Miner">Onto-Miner</a> allows searching of various public bioinformatics databases via clone ID, UniGene gene symbol, LocusLink ID, accession number etc. and can carry out batch mode queries using entire lists of genes. The site can be used as a resource by third party developers who would like to provide detailed gene information for arbitrary lists of genes.</p>


[Instance]
id: TOOL:000088
type: tool
name: Onto-Translate
url: http://vortex.cs.wayne.edu/projects.htm#Onto-Translate
is_online_tool: true
developer: ORG:000031
publication: PMID:15215428
license: free_academic
description: <p><a href="http://vortex.cs.wayne.edu/projects.htm#Onto-Translate" title="Onto-Translate">Onto-Translate</a> is a web based tool that allows the user to quickly translate lists of accession IDs, UniGene cluster IDs and Affymetrix probe IDs from one to another. Onto-Translate helps identifying the same information across various databases and reduce the redundancy in arbitrary lists of genes.</p>


[Instance]
id: TOOL:000089
type: tool
name: OntoGate
url: http://functionalgenomics.de/ontogate/
is_online_tool: true
developer: ORG:000008
publication: PMID:12824422
license: free_academic
description: <p><a href="http://functionalgenomics.de/ontogate/" title="OntoGate">OntoGate</a> provides access to <a href="http://www.genome-matrix.org" title="GenomeMatrix">GenomeMatrix</a> (GM) entries from Ontology terms and external datasets which have been associated with ontology terms, to find genes from different species in the GM, which have been mapped to the ontology terms. OntoGate includes a BLAST search of amino acid sequences corresponding to annotated genes.</p>


[Instance]
id: TOOL:000090
type: tool
name: Ontologizer
url: http://www.charite.de/ch/medgen/ontologizer/
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000023
publication: PMID:14764576
license: free_academic
description: <p><a href="http://www.charite.de/ch/medgen/ontologizer/" title="Ontologizer">Ontologizer</a> can be used to generate listings of GO annotations for one or many groups of genes/gene products. GO annotations, ranked according to frequency for each cluster, are displayed in HTML or XML format. If a population dataset is provided, statistical analysis for overrepresentation of individual GO terms is performed. "Dot" (GraphViz) files can be generated to provide a graphical overview of overrepresented GO terms in the GO graph structure. Detailed listings for each gene are also provided.</p>


[Instance]
id: TOOL:000091
type: tool
name: Ontology Traverser
url: http://franklin.imgen.bcm.tmc.edu/rho/services/index.jsp?page=OntologyTraverser
is_online_tool: true
developer: ORG:000066
publication: PMID:15333457
license: free_academic
description: <p><a href="http://franklin.imgen.bcm.tmc.edu/rho/services/index.jsp?page=OntologyTraverser" title="OntologyTraverser">OntologyTraverser</a> is a microarray gene list enrichment tool. Our tool provides an easy upload format accepting AffyIDs or NIAIDs for some cDNA chips and comparison of the lists against the entire probe/clone collection for the array type used. We support several report formats: flat html, flat tsv, xml and a dynamic/clickable HTML which displays the GO structure. A variety of statistics/results are reported for each GO node: the list fq, array fq, fold change, a Fisher's exact test p-value and the identities of the genes mapped at or below each node.</p>


[Instance]
id: TOOL:000092
type: tool
name: Probe Explorer
url: http://probeexplorer.cicancer.org/
is_online_tool: true
developer: ORG:000001
country-name: Spain
license: free_academic
description: <p><a href="http://probeexplorer.cicancer.org/" title="Probe Explorer">Probe Explorer</a> is an open access web-based bioinformatics application designed to show the association between microarray oligonucleotide probes and transcripts in the genomic context, but flexible enough to serve as a simplified genome and transcriptome browser. Coordinates and sequences of the genomic entities (loci, exons, transcripts), including vector graphics outputs, are provided for fifteen metazoa organisms and two yeasts. Alignment tools are used to built the associations between Affymetrix microarrays probe sequences and the transcriptomes (for human, mouse, rat and yeasts). Search by keywords is available and user searches and alignments on the genomes can also be done using any DNA or protein sequence query.</p>


[Instance]
id: TOOL:000093
type: tool
name: Profiling of Complex Functionality
synonym_abbr: ProfCom
url: http://webclu.bio.wzw.tum.de/profcom/
is_online_tool: true
developer: ORG:000065
publication: PMID:16959266
license: free_academic
description: <p><a href="http://webclu.bio.wzw.tum.de/profcom/" title="ProfCom">ProfCom</a> is a web-based tool for the functional interpretation of a gene list that was identified to be related by experiments. A trait which makes ProfCom a unique tool is an ability to profile enrichments of not only available Gene Ontology (GO) terms but also of <i>complex function</i>. A <i>complex function</i> is constructed as Boolean combination of available GO terms. The complex functions inferred by ProfCom are more specific in comparison to single terms and describe more accurately the functional role of genes.</p>


[Instance]
id: TOOL:000094
type: tool
name: SeqExpress
url: http://www.seqexpress.com/
is_standalone_tool: true
compatible_os: win
developer: ORG:000010
publication: PMID:14988116
license: free_academic
description: <p><a href="http://www.seqexpress.com" title="SeqExpress">SeqExpress</a> is a comprehensive analysis and visualisation package for gene expression experiments. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualisation, file export/import, searching, integration (with R), and clustering options.</p>


[Instance]
id: TOOL:000095
type: tool
name: SerbGO
url: http://estbioinfo.stat.ub.es/apli/serbgo/
is_online_tool: true
developer: ORG:000043
license: free_academic
description: <p><a href="http://estbioinfo.stat.ub.es/apli/serbgo/" title="SerbGO">SerbGO</a> is a web-based tool intended to assist researchers determine which microarray tools for gene expression analysis which make use of the GO ontologies are best suited to their projects. SerbGO is a bidirectional application. The user can ask for some features by checking on the Query Form to get the appropriate tools for their interests. The user can also compare tools to check which features are implemented in each one.</p>


[Instance]
id: TOOL:000096
type: tool
name: SOURCE
url: http://source.stanford.edu/
is_online_tool: true
developer: ORG:000060
publication: PMID:12519986
license: free_academic
description: <p><a href="http://source.stanford.edu/" title="SOURCE">SOURCE</a> compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE.</p>


[Instance]
id: TOOL:000097
type: tool
name: Spotfire Gene Ontology Advantage Application
url: http://www.spotfire.com/services/advantage.asp
is_standalone_tool: true
compatible_os: win
developer: ORG:000012
license: proprietary
description: <p>The <a href="http://www.spotfire.com/services/advantage.asp" title="Spotfire Gene Ontology Advantage Application">Spotfire Gene Ontology Advantage Application</a> integrates GO annotations with gene expression analysis in Spotfire DecisionSite for Functional Genomics. Researchers can select a subset of genes in DecisionSite visualizations and display their distribution in the Gene Ontology hierarchy. Similarly, selection of any process, function or cellular location in the Gene Ontology hierarchy automatically marks the corresponding genes in DecisionSite visualizations.</p>


[Instance]
id: TOOL:000098
type: tool
name: Short Time-series Expression Miner
synonym_acronym: STEM
url: http://www.cs.cmu.edu/~jernst/stem/
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000030
publication: PMID:15961453
publication: PMID:16597342
license: free_academic
description: <p>The <a href="http://www.cs.cmu.edu/~jernst/stem/" title="Short Time-series Expression Miner (STEM)">Short Time-series Expression Miner (STEM)</a> is a Java program for clustering, comparing, and visualizing short time series gene expression data (8 time points or less). STEM allows researchers to identify significant temporal expression profiles and the genes associated with these profiles and to compare the behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology (GO) database and supports GO category gene enrichment analyses for sets of genes having the same temporal expression pattern. STEM also supports the ability to easily determine and visualize the behavior of genes belonging to a given GO category, identifying which temporal expression profiles were enriched for these genes.</p>


[Instance]
id: TOOL:000099
type: tool
name: T-Profiler
url: http://www.t-profiler.org/
is_online_tool: true
developer: ORG:000076
developer: ORG:000087
publication: PMID:15980543
license: free_academic
description: <p><a href="http://www.t-profiler.org/" title="T-Profiler">T-Profiler</a> uses the t-test to score changes in the average activity of pre-defined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif, and location on the same chromosome, respectively. A jack-knife procedure is used to make calculations more robust against outliers. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters.</p>


[Instance]
id: TOOL:000100
type: tool
name: THEA
url: http://bioinfo.unice.fr
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000059
publication: PMID:15130932
license: free_academic
description: <p><a href="http://thea.unice.fr/index-en.html" title="THEA">THEA</a> (Tools for High-throughput Experiments Analysis) is an integrated information processing system dedicated to the analysis of post-genomic data. It allows automatic annotation of data issued from classification systems with selected biological information (including the Gene Ontology). Users can either manually search and browse through these annotations, or automatically generate meaningful generalizations according to statistical criteria (data mining).</p>


[Instance]
id: TOOL:000101
type: tool
name: FuSSiMeG
url: http://xldb.fc.ul.pt/biotools/rebil/ssm/
is_online_tool: true
developer: ORG:000005
license: free_academic
description: <p>With <a href="http://xldb.fc.ul.pt/biotools/rebil/ssm/" title="FuSSiMeG (Functional Semantic Similarity Measure between Gene Products)">FuSSiMeG (Functional Semantic Similarity Measure between Gene Products)</a>, you can measure the functional similarity between gene products, by comparing the semantic similarity between the GO terms in their annotations. You can also measure the semantic similarity between any GO terms.</p>



[Instance]
name: GOArray
url: http://ycmi.med.yale.edu/gomine/
is_standalone_tool: true
compatible_os: win
compatible_os: mac
compatible_os: unix
compatible_os: linux
developer: ORG:000041
license: free_academic
description: <p><a href="http://ycmi.med.yale.edu/gomine" title="GOArray">GOArray</a> is a Perl program which inputs a lists of genes annotated as "of interest" (GOI) or not, and determines if any associated GO terms have an overrepresentation of GOI. A permutation test is optionally used to assess confidence in the results. Output includes multiple visualizations and supplementary information and, for future reference, a summary of the statistical methods used.</p>
! lost!


[Instance]
id: ORG:000001
type: developer
name: Centro de Investigacion del Cancer
organization-name: University of Salamanca
url: http://www.cicancer.org
locality: Salamanca
country-name: Spain

[Instance]
id: ORG:000002
type: developer
name: U.S. National Animal Genome Research Program (NAGRP)
url: http://www.animalgenome.org

[Instance]
id: ORG:000003
type: developer
name: NYU Bioinformatics Group
url: http://bioinformatics.nyu.edu

[Instance]
id: ORG:000004
type: developer
name: Huck Institutes of the Life Sciences
organization-name: Penn State
url: http://www.hils.psu.edu
region: Pennsylvania
country-name: USA

[Instance]
id: ORG:000005
type: developer
name: University of Lisbon
url: http://www.ul.pt
country-name: Portugal

[Instance]
id: ORG:000006
type: developer
name: Mouse Genome Informatics
url: http://www.informatics.jax.org

[Instance]
id: ORG:000007
type: developer
name: Iowa State University
url: http://www.iastate.edu

[Instance]
id: ORG:000008
type: developer
name: Max Planck Institute for Molecular Genetics
url: http://www.molgen.mpg.de
locality: Berlin
country-name: Germany

[Instance]
id: ORG:000009
type: developer
name: The Gene Ontology Consortium
url: http://www.geneontology.org

[Instance]
id: ORG:000010
type: developer
name: SeqExpress
url: http://www.seqexpress.com

[Instance]
id: ORG:000011
type: developer
name: Walter and Eliza Hall Institute of Medical Research
url: http://www.wehi.edu.au
locality: Melbourne
country-name: Australia

[Instance]
id: ORG:000012
type: developer
name: Spotfire, Inc.
url: http://www.spotfire.com

[Instance]
id: ORG:000013
type: developer
name: Bioengineering, Electronics and Telemedicine Group
organization-name: ITACA, Universidad Polit&eacute;cnica de Valencia
url: http://www.bet.upv.es
locality: Valencia
country-name: Spain

[Instance]
id: ORG:000014
type: developer
name: Roth lab
organization-name: Harvard Medical School
url: http://llama.med.harvard.edu

[Instance]
id: ORG:000015
type: developer
name: University of California, Riverside
url: http://www.ucr.edu

[Instance]
id: ORG:000016
type: developer
name: Centro de Genmica
organization-name: Instituto Valenciano de Investigaciones Agrarias
url: http://www.ivia.es/centrogenomica/inicioconmarco.htm
locality: Valencia
country-name: Spain

[Instance]
id: ORG:000017
type: developer
name: XLDB Group
organization-name: Faculty of Sciences at the University of Lisbon
url: http://xldb.fc.ul.pt
locality: Lisbon
country-name: Portugal

[Instance]
id: ORG:000018
type: developer
name: Institut National de la Sant&eacute; et de la Recherche Medicale
synonym_acronym: INSERM
organization-name: Centre de Recherche des Cordeliers
url: http://www.inserm.fr/en/
locality: Paris
country-name: France

[Instance]
id: ORG:000019
type: developer
name: National Center of Biotechnology (CNB-CSIC)
url: http://www.cnb.csic.es
locality: Madrid
country-name: Spain

[Instance]
id: ORG:000020
type: developer
name: University of Toronto
url: http://www.utoronto.ca/bandb
country-name: Canada

[Instance]
id: ORG:000021
type: developer
name: Strand Genomics
url: http://www.strandgenomics.com

[Instance]
id: ORG:000022
type: developer
name: Mount Desert Island Biological Laboratory
url: http://www.mdibl.org
region: Maine
country-name: USA

[Instance]
id: ORG:000023
type: developer
name: Charit&eacute; University Hospital
url: http://www.charite.de/ch/medgen/
country-name: Germany

[Instance]
id: ORG:000024
type: developer
name: Clemson Bioinformatics Center
url: http://bioinformatics.clemson.edu
region: South Carolina
country-name: USA

[Instance]
id: ORG:000025
type: developer
name: Saccharomyces Genome Database
url: http://www.yeastgenome.org

[Instance]
id: ORG:000026
type: developer
name: Twigger Lab
organization-name: Medical College of Wisconsin
url: http://www.phys.mcw.edu/fac_twigger.htm

[Instance]
id: ORG:000027
type: developer
name: Center for Computational Biology and Bioinformatics
organization-name: Columbia University
url: http://www.c2b2.columbia.edu

[Instance]
id: ORG:000028
type: developer
name: University of Delaware
url: http://www.udel.edu

[Instance]
id: ORG:000029
type: developer
name: Department of Plant Systems Biology
organization-name: VIB / Ghent University
url: http://www.psb.ugent.be

[Instance]
id: ORG:000030
type: developer
name: Carnegie Mellon University
url: http://www.cmu.edu

[Instance]
id: ORG:000031
type: developer
name: Intelligent Systems and Bioinformatics Laboratory
organization-name: Wayne State University 
url: http://vortex.cs.wayne.edu

[Instance]
id: ORG:000032
type: developer
name: University of Tartu
url: http://www.ut.ee
country-name: Estonia

[Instance]
id: ORG:000033
type: developer
name: University of Navarra
url: http://www.unav.es
country-name: Spain

[Instance]
id: ORG:000034
type: developer
name: Gladstone Institutes
organization-name: University of California
url: http://www.gladstone.ucsf.edu

[Instance]
id: ORG:000035
type: developer
name: Barton group
organization-name: University of Dundee
url: http://www.compbio.dundee.ac.uk

[Instance]
id: ORG:000036
type: developer
name: Harvard University
url: http://www.oeb.harvard.edu

[Instance]
id: ORG:000037
type: developer
name: Burnham Institute for Medical Research
url: http://www.burnham.org
country-name: USA

[Instance]
id: ORG:000038
type: developer
name: Harvard School of Public Health
url: http://www.hsph.harvard.edu

[Instance]
id: ORG:000039
type: developer
name: Genomics and Bioinformatics Group of LMP, NCI, NIH
url: http://discover.nci.nih.gov

[Instance]
id: ORG:000040
type: developer
name: Custom Microsystems
url: http://www.dbfordummies.com/ContactInfo.asp

[Instance]
id: ORG:000041
type: developer
name: Yale Center for Medical Informatics
url: http://ycmi.med.yale.edu

[Instance]
id: ORG:000042
type: developer
name: Rebholz group
organization-name: European Bioinformatics Institute
url: http://www.ebi.ac.uk/Rebholz/

[Instance]
id: ORG:000043
type: developer
name: Statistics and Bioinformatics Research Group
organization-name: University of Barcelona
url: http://estbioinfo.stat.ub.es/estbioinfo/index.htm

[Instance]
id: ORG:000044
type: developer
name: AgBase
url: http://www.agbase.msstate.edu

[Instance]
id: ORG:000045
type: developer
name: RZPD Deutsches Ressourcenzentrum f&uuml;r Genomforschung
url: http://www.rzpd.de

[Instance]
id: ORG:000046
type: developer
name: Bioinformatics and Functional Genomics Research Group
synonym_acronym: CiC, CSIC-USAL
organization-name: Cancer Research Center
url: http://bioinfow.dep.usal.es
locality: Salamanca
country-name: Spain

[Instance]
id: ORG:000047
type: developer
name: Seoul National University Biomedical Informatics
url: http://www.snubi.org

[Instance]
id: ORG:000048
type: developer
name: Developmental Biology Institute of Marseille
url: http://www.ibdm.univ-mrs.fr
country-name: France

[Instance]
id: ORG:000049
type: developer
name: Norwegian Microarray Consortium
url: http://www.microarray.no

[Instance]
id: ORG:000050
type: developer
name: National Institute of Allergy and Infectious Diseases
url: http://www.niaid.nih.gov

[Instance]
id: ORG:000051
type: developer
name: Swiss-Prot group
organization-name: Swiss Institute of Bioinformatics
url: http://www.isb-sib.ch/groups/Swiss-Prot.htm

[Instance]
id: ORG:000052
type: developer
name: Medical Informatics and Bioimaging group
organization-name: BME, Georgia Tech/Emory University
url: http://www.miblab.gatech.edu

[Instance]
id: ORG:000053
type: developer
name: Cancer Genome Anatomy Project
url: http://cgap.nci.nih.gov

[Instance]
id: ORG:000054
type: developer
name: XSPAN project
organization-name: University of Edinburgh
url: http://www.xspan.org
country-name: UK

[Instance]
id: ORG:000055
type: developer
name: Institute of Information Science
organization-name: Academia Sinica
url: http://www.iis.sinica.edu.tw/index.htm
country-name: Taiwan

[Instance]
id: ORG:000056
type: developer
name: Groningen Biomolecular Sciences and Biotechnology Institute
url: http://molgen.biol.rug.nl/molgen/index.php
locality: Haren
country-name: the Netherlands

[Instance]
id: ORG:000057
type: developer
name: Oak Ridge National Laboratory (ORNL) 
url: http://gst.ornl.gov

[Instance]
id: ORG:000058
type: developer
name: Virtual Biology Lab
organization-name: Institute of Signaling, Developmental Biology and Cancer Research
url: http://bioinfo.unice.fr
country-name: France

[Instance]
id: ORG:000059
type: developer
name: Biotechnological Centre
organization-name: Technological University, Dresden
url: http://www.biotec.tu-dresden.de
locality: Dresden
country-name: Germany

[Instance]
id: ORG:000060
type: developer
name: Stanford Microarray Database
url: http://genome-www5.stanford.edu

[Instance]
id: ORG:000061
type: developer
name: Norwegian University of Science and Technology
url: http://www.ntnu.no
locality: Trondheim
country-name: Norway

[Instance]
id: ORG:000062
type: developer
name: The Arabidopsis Information Resource
url: http://www.arabidopsis.org

[Instance]
id: ORG:000063
type: developer
name: The Hebrew University of Jerusalem
url: http://www.huji.ac.il/huji/eng/index_e.htm
country-name: Israel

[Instance]
id: ORG:000064
type: developer
name: Bioinformatics Department
organization-name: Centro de Investigacion Principe Felipe
url: http://bioinfo.ochoa.fib.es
locality: Valencia
country-name: Spain

[Instance]
id: ORG:000065
type: developer
name: The Institute of Bioinformatics and Systems Biology
organization-name: Helmholtz Zentrum M&uuml;nchen
url: http://mips.gsf.de
locality: Munich
country-name: Germany

[Instance]
id: ORG:000066
type: developer
name: Baylor College of Medicine
url: http://franklin.imgen.bcm.tmc.edu

[Instance]
id: ORG:000067
type: developer
name: Bioinformatics group
organization-name: ESAT / K. U. Leuven
url: http://www.kuleuven.be/bioinformatics/
country-name: Belgium

[Instance]
id: ORG:000068
type: developer
name: Text Mining group
organization-name: University of Geneva
url: http://www.natlang.hcuge.ch
country-name: Switzerland

[Instance]
id: ORG:000069
type: developer
name: Inpharmatica
url: http://www.inpharmatica.co.uk

[Instance]
id: ORG:000070
type: developer
name: Illuminae
url: http://www.illuminae.com

[Instance]
id: ORG:000071
type: developer
name: Grip Studios Interactive, Inc.
url: http://www.gripstudios.com

[Instance]
id: ORG:000072
type: developer
name: Beijing Genomics Institute
url: http://www.genomics.org.cn
country-name: China

[Instance]
id: ORG:000073
type: developer
name: Department of Biochemistry
organization-name: University of Washington
url: http://depts.washington.edu/biowww/

[Instance]
id: ORG:000074
type: developer
name: University of Tennessee Genome Science and Technology
url: http://gst.tennessee.edu

[Instance]
id: ORG:000075
type: developer
name: Molecular Genetics and Bioinformatic Laboratory
organization-name: University of Sao Paolo
url: http://gdm.fmrp.usp.br
country-name: Brazil

[Instance]
id: ORG:000076
type: developer
name: Columbia University
url: http://www.columbia.edu

[Instance]
id: ORG:000077
type: developer
name: Bio-Medical Informatics Laboratory
organization-name: Politecnico di Milano
url: http://www.medinfopoli.polimi.it
locality: Milan
country-name: Italy

[Instance]
id: ORG:000078
type: developer
name: National Library of Medicine
url: http://www.nlm.nih.gov

[Instance]
id: ORG:000079
type: developer
name: Livestock Issues Research Unit
organization-name: USDA Agricultural Research Service
url: http://liru.ars.usda.gov

[Instance]
id: ORG:000080
type: developer
name: The Institute for Genomic Research
url: http://www.tigr.org

[Instance]
id: ORG:000081
type: developer
name: Lewis-Sigler Institute for Integrative Genomics
organization-name: Princeton University
url: http://genomics.princeton.edu

[Instance]
id: ORG:000082
type: developer
name: University of Tennessee Health Science Center
url: http://www.utmem.edu

[Instance]
id: ORG:000083
type: developer
name: Georgetown University Medical Center Liu Lab
url: http://gauss.dbb.georgetown.edu/liblab

[Instance]
id: ORG:000084
type: developer
name: Bork group
organization-name: European Molecular Biology Laboratory
url: http://www.bork.embl-heidelberg.de

[Instance]
id: ORG:000085
type: developer
name: Universidad Complutense de Madrid
url: http://www.ucm.es
country-name: Spain

[Instance]
id: ORG:000086
type: developer
name: European Bioinformatics Institute
url: http://www.ebi.ac.uk
country-name: UK

[Instance]
id: ORG:000087
type: developer
name: University of Amsterdam
url: http://www.english.uva.nl
country-name: Holland

[Instance]
id: ORG:000088
type: developer
name: EcoliWiki
url: http://ecoliwiki.org
