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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Ontologizer Resource Report Resource Website 100+ mentions |
Ontologizer (RRID:SCR_005801) | Ontologizer | analysis service resource, data analysis service, data processing software, production service resource, service resource, software application, software resource, source code | The Ontologizer is a Java webstart application for GO term enrichment analysis that provides browsing and graph visualization capabilities. The Ontologizer allows users to analyze data with the standard Fisher exact test and also the parent-child method and topology methods. The tool can be started directly from the web using Java webstart. For graph visualizations, users need to install the GraphViz library. The tool is freely available to all, and source code is available at SourceForge. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | high-throughput, biological data, gene ontology, statistical analysis, fisher exact test, visualization, graph, java, annotation, parent-child, topology |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
DFG SFB 760 | PMID:18511468 PMID:17848398 |
Free for academic use | nlx_149289 | SCR_005801 | SciCrunch Registry | The Ontologizer | 2026-10-24 12:45:33 | 124 | |||||
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GREAT: Genomic Regions Enrichment of Annotations Tool Resource Report Resource Website 50+ mentions |
GREAT: Genomic Regions Enrichment of Annotations Tool (RRID:SCR_005807) | GREAT | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | Data analysis service that predicts functions of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. The utility of GREAT extends to data generated for transcription-associated factors, open chromatin, localized epigenomic markers and similar functional data sets, and comparative genomics sets. Platform: Online tool | term enrichment, cis-regulatory region, function, gene, genomic, annotation, ontology, chromatin immunoprecipitation, sequencing, chip-seq, comparative genomics, transcription factor binding |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: PRISM (Stanford database) is related to: Gene Ontology has parent organization: Stanford University School of Medicine; California; USA |
Bio-X ; Howard Hughes Medical Institute ; Stanford University; California; USA ; Packard ; Searle Scholar ; Microsoft Research ; Alfred P. Sloan Foundation ; Edward Mallinckrodt Jr. Foundation ; NIH ; Human Frontier Science Program fellowship LT000896/2009-l; NICHD 1R01HD059862; NHGRI R01HG005058; NSF CCF-0939370; DFG Hi 1423/2-1 |
PMID:20436461 PMID:23814184 |
Free for academic use, Acknowledgement requested | nlx_149295, OMICS_00635 | SCR_005807 | SciCrunch Registry | Genomic Regions Enrichment of Annotations Tool (GREAT), Genomic Regions Enrichment of Annotations Tool | 2026-10-24 12:45:32 | 89 | |||||
|
FSST - Functional Similarity Search Tool Resource Report Resource Website |
FSST - Functional Similarity Search Tool (RRID:SCR_005819) | FSST | software application, software resource | The Functional Similarity Search Tool (FSST) has been implemented for comparing user defined sets of annotated entities. FSST supports the computation of functional similarity scores based on an individual ontology and of combined scores. Its multi-threaded Java implementation takes advantage of symmetric multi-processing computers, decreasing runtime considerably. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | other analysis, functional similarity search, annotation, ontology, java, training tools |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: GOTaxExplorer has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
BMBF 016R0453; DFG KFO 129/1-1; European Union F6 contract LSHG-CT-2003-503265 |
PMID:17346342 | Free for academic use | nlx_149320 | SCR_005819 | SciCrunch Registry | Functional Similarity Search Tool (FSST), Functional Similarity Search Tool | 2026-10-24 12:51:26 | 0 | |||||
|
OnEx - Ontology Evolution Explorer Resource Report Resource Website 1+ mentions |
OnEx - Ontology Evolution Explorer (RRID:SCR_000602) | OnEx | software resource, web application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web-based application that integrates versions of 16 life science ontologies including the Gene Ontology, NCI Thesaurus and selected OBO ontologies with data leading back to 2002 in a common repository to explore ontology changes. It allows to study and apply the evolution of these integrated ontologies on three different levels. It provides global ontology evolution statistics and ontology-specific evolution trends for concepts and relationships and it allows the migration of annotations in case a new ontology version was released | ontology, gene, protein, function, process, component, ontology or annotation browser, evolution, trend, annotation, version |
is listed by: OMICtools is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: NCI Thesaurus is related to: OBO has parent organization: University of Leipzig; Saxony; Germany |
BMBF 01AK803E; DFG |
PMID:19678926 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02273, nlx_149129 | http://www.izbi.de/onex, http://aprilia.izbi.uni-leipzig.de:8080/onex/ | SCR_000602 | SciCrunch Registry | Ontology Evolution Explorer (OnEx), Ontology Evolution Explorer | 2026-10-24 12:44:20 | 1 | ||||
|
ProfCom - Profiling of complex functionality Resource Report Resource Website 1+ mentions |
ProfCom - Profiling of complex functionality (RRID:SCR_005797) | ProfCom | analysis service resource, data analysis service, production service resource, service resource | Profiling of Complex Functionality (ProfCom) 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 complex function. A complex function 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. Platform: Online tool | gene, function, profile, gene ontology, complex function, statistical analysis, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Institute of Bioinformatics and Systems Biology; Neuherberg; Germany |
DFG | PMID:16959266 | Free for academic use | biotools:profcom, nlx_149276 | https://bio.tools/profcom | SCR_005797 | SciCrunch Registry | Profiling of Complex Functionality, Profiling of Complex Functionality (ProfCom) | 2026-10-24 12:50:36 | 4 | ||||
|
GOstat Resource Report Resource Website 100+ mentions |
GOstat (RRID:SCR_008535) | GOstat | analysis service resource, data analysis service, production service resource, service resource | GOstat is a tool that allows you to find statistically overrepresented Gene Ontologies within a group of genes. The Gene-Ontology database (GO: http://www.geneontology.org) provides a useful tool to annotate and analyze the function of large numbers of genes. Modern experimental techniques, as e.g. DNA microarrays, often result in long lists of genes. To learn about the biology in this kind of data it is desirable to find functional annotation or Gene-Ontology groups which are highly represented in the data. This program (GOstat) should help in the analysis of such lists and will provide statistics about the GO terms contained in the data and sort the GO annotations giving the most representative GO terms first. Run GOstat: * Go to search form - Computes GO statistics of a list of genes selected from a microarray. * GOstat Display - You can store results from a previously run and view them here, either by uploading them as a file or putting them on a selected URL. * Upload Custom GO Annotations - This allows you to upload your own GO annotation database and use it with GOstat. Variants of GOstat: * Rank GOstat - Takes input from all genes on microarray instead of using a fixed cutoff and uses ranks using a Wilcoxon test or either ranks or pvalues to score GOs using Kolmogorov-Smirnov statistics. * Gene Abundance GOstats - Takes input from all genes on microarray and sums up the gene abundances for each GO to compute statistics. * Two list GOstat - Compares GO statistics in two independent lists of genes, not necessarily one of them being the complete list the other list is sampled from. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, gene ontology, annotation, statistical analysis, FASEB list |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Walter and Eliza Hall Institute of Medical Research; Victoria; Australia |
DFG | PMID:14962934 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30625 | SCR_008535 | SciCrunch Registry | 2026-10-24 12:50:56 | 159 | ||||||
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GOTaxExplorer Resource Report Resource Website |
GOTaxExplorer (RRID:SCR_005720) | GOTaxExplorer | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource | GOTaxExplorer presents a new approach to comparative genomics that integrates functional information and families with the taxonomic classification. It integrates UniProt, Gene Ontology, NCBI Taxonomy, Pfam and SMART in one database. GOTaxExplorer provides four different query types: selection of entity sets, comparison of sets of Pfam families, semantic comparison of sets of GO terms, functional comparison of sets of gene products. This permits to select custom sets of GO terms, families or taxonomic groups. For example, it is possible to compare arbitrarily selected organisms or groups of organisms from the taxonomic tree on the basis of the functionality of their genes. Furthermore, it enables to determine the distribution of specific molecular functions or protein families in the taxonomy. The comparison of sets of GO terms allows to assess the semantic similarity of two different GO terms. The functional comparison of gene products makes it possible to identify functionally equivalent and functionally related gene products from two organisms on the basis of GO annotations and a semantic similarity measure for GO. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, molecular function, protein family, taxonomy, visualization, functional similarity, semantic similarity, analysis, comparative genomics analysis, comparative genomics, search engine, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, function, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: UniProt is related to: NCBI Taxonomy is related to: Pfam is related to: SMART is related to: FSST - Functional Similarity Search Tool has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
German National Genome Research Network ; BMBF 016R0453; DFG KFO 129/1-1; European Union contract LSHG-CT-2003-503265 |
PMID:17346342 | Free for academic use | nlx_149179 | SCR_005720 | SciCrunch Registry | 2026-10-24 12:45:31 | 0 | ||||||
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SuperTarget Resource Report Resource Website 10+ mentions |
SuperTarget (RRID:SCR_002696) | SuperTarget | data or information resource, database | Database for analyzing drug-target interactions, it integrates drug-related information associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins. At present (May 2013), the updated database contains >6000 target proteins, which are annotated with >330 000 relations to 196 000 compounds (including approved drugs); the vast majority of interactions include binding affinities and pointers to the respective literature sources. The user interface provides tools for drug screening and target similarity inclusion. A query interface enables the user to pose complex queries, for example, to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target proteins within a certain affinity range. | drug metabolism, drug, cytochrome p450, ontology, pathway, target, compound, cytochrome, drug target, protein, side effect, protein-protein interaction |
is listed by: OMICtools has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
BMBF MedSys 0315450A; DFG RTG Computational Systems Biology GRK1772; DFG IRTG Systems Biology of Molecular Networks GRK1360; European Union SynSys ; NIGMS GM070064 |
PMID:22067455 PMID:17942422 |
Free, Freely available | r3d100012195, nif-0000-00416, OMICS_01591 | http://bioinf-tomcat.charite.de/supertarget/, http://bioinformatics.charite.de/supertarget, https://doi.org/10.17616/R3TM0F | SCR_002696 | SciCrunch Registry | 2026-10-24 12:50:24 | 29 |
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