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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Flash Gviewer Resource Report Resource Website 1+ mentions |
Flash Gviewer (RRID:SCR_012870) | Flash GViewer | software resource | Flash GViewer 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 and QTLs associated with a specific phenotype, 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. In addition the bands on the chromosomes can link to defineable URL and new region selection sliders can be used to select a specific chromosome region and then link out to a genome browser for higher resolution information. 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. This tool is not GO-specific, but was built for the purpose of viewing GO annotation data. Platform: Online tool | visualization, chromosome, video, gene, qtl, genome, navitgation, phenotype, ontology or annotation visualization |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Medical College of Wisconsin; Wisconsin; USA |
Free for academic use | nlx_149333 | http://gmod.org/flashgviewer | SCR_012870 | 2026-07-25 12:07:38 | 2 | |||||||
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LexGrid Resource Report Resource Website 1+ mentions |
LexGrid (RRID:SCR_006627) | LexGrid | software resource | LexGrid (Lexical Grid) provides support for a distributed network of lexical resources such as terminologies and ontologies via standards-based tools, storage formats, and access/update mechanisms. The Lexical Grid Vision is for a distributed network of terminological resources. It is the foundation of the National Center for Biomedical Ontology BioPortal interface and web-services, and can parse OBO format, as well as other formats such as OWL. Currently, there are many terminologies and ontologies in existence. Just about every terminology has its own format, its own set of tools, and its own update mechanisms. The only thing that most of these pieces have in common with each other is their incompatibility. This makes it very hard to use these resources to their full potential. We have designed the Lexical Grid as a way to bridge terminologies and ontologies with a common set of tools, formats and update mechanisms. The Lexical Grid is: * accessible through a set of common APIs * joined through shared indices * online accessible * downloadable * loosely coupled * locally extendable * globally revised * available in web-space on web-time * cross-linked The realization of this vision requires three interlocking components, which are: * Standards - access methods and formats need to be published and openly available * Tools - standards based tools must be readily available * Content - commonly used terminologies have to be available for access and download Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, parse, ontology |
is listed by: BioPortal is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: OBO has parent organization: European Bioinformatics Institute has parent organization: National Cancer Institute |
NIH ; Cancer Biomedical Informatics Grid ; NLM LM07319 |
PMID:19261933 | Free for academic use | nlx_149194 | http://www.lexgrid.org/ | SCR_006627 | Lexical Grid | 2026-07-25 12:06:27 | 1 | ||||
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RamiGO Resource Report Resource Website 10+ mentions |
RamiGO (RRID:SCR_006922) | RamiGO | software resource | Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape. | visualization, analysis, ontology or annotation search engine, ontology or annotation visualization, other analysis, classification, go, graph, network, third party client, windows, mac os x, linux, unix, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: Cytoscape is related to: AmiGO has parent organization: Dana-Farber Cancer Institute has parent organization: Bioconductor |
PMID:23297033 | Artistic License, v2 | biotools:ramigo, OMICS_02267, nlx_149331 | http://bioconductor.org/packages/release/bioc/html/RamiGO.html, https://bio.tools/ramigo | SCR_006922 | ramigo, RamiGO - AmiGO visualize R interface | 2026-07-25 12:06:30 | 11 | |||||
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PiNGO Resource Report Resource Website |
PiNGO (RRID:SCR_000692) | PiNGO | software resource | A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, annotation, network, candidate gene, biological network, ontology or annotation search engine, statistical analysis, term enrichment, functional similarity, functional prediction, search engine, windows, mac os x, linux, unix |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Cytoscape has parent organization: Ghent University; Ghent; Belgium |
PMID:21278188 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149330, OMICS_02281 | SCR_000692 | 2026-07-25 12:04:49 | 0 | |||||||
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GOlr Resource Report Resource Website 1+ mentions |
GOlr (RRID:SCR_003939) | GOlr | software resource | A public Solr index for the Gene Ontology. This index will replace some of the query functionality for GOOSE as well as become the new backend for AmiGO 2 and other services. | solr |
is used by: AmiGO has parent organization: Gene Ontology |
Public | nlx_158322 | http://golr.berkeleybop.org/ | SCR_003939 | Gene Ontology Solr index | 2026-07-25 12:05:44 | 4 | ||||||
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COBrA Resource Report Resource Website 1000+ mentions |
COBrA (RRID:SCR_005677) | COBrA | software resource | COBrA is a Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and verification functions. In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Semantic Web formats RDF, RDFS and OWL. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | ontology, anatomy, browser, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: OBO has parent organization: University of Edinburgh; Scotland; United Kingdom |
BBSRC 15/BEP 17046 | PMID:15513995 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149117 | SCR_005677 | COBrA - An Ontology Browser for Anatomy, COBrA: a bio-ontology editor | 2026-07-25 12:06:07 | 1396 | |||||
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GOProfiler Resource Report Resource Website 1+ mentions |
GOProfiler (RRID:SCR_005683) | GOProfiler | service resource | Service that provides a summary of GO annotations available for each species. The user provides a 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. | ontology or annotation browser, annotation, protein, gene ontology |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: AgBase |
PMID:16961921 | Free for academic use | OMICS_02269, nlx_149127 | SCR_005683 | 2026-07-25 12:06:08 | 2 | |||||||
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GOEx - Gene Ontology Explorer Resource Report Resource Website 10+ mentions |
GOEx - Gene Ontology Explorer (RRID:SCR_005779) | GOEx | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. Gene Ontology Explorer (GOEx) combines data from protein fold changes with GO over-representation statistics to help draw conclusions in proteomic experiments. It is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. A recent hack included in GOEx is to load the sparse matrix index file directly into GOEx, instead of going through the report generation using the AC/T-fold methods. This makes it easy for GOEx to analyze any list of proteins as long as the list follows the index file format (described in manuscript) . Please note that if using this alternative strategy, there will be no protein fold information. Platform: Windows compatible | proteomics, visualization, statistical analysis, gene ontology, parse, pattern recognition, spectral counting, analysis, protein fold |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Scripps Research Institute |
CNPq ; CAPES ; FAPERJ BBP grant ; PAPES ; PDTIS ; Ary Frauzino Foundation ; NIAID ; NIH ; genesis molecular biology laboratory ; Fiocruz-INCA collaboration ; NIAID UCSD/MCB0237059; NCRR P41RR011823; NIMH 5R01 MH067880 |
PMID:19239707 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149249 | http://pcarvalho.com/patternlab/goex.shtml | SCR_005779 | Gene Ontology Explorer, GO Explorer | 2026-07-25 12:06:12 | 26 | ||||
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OWLTools Resource Report Resource Website 10+ mentions |
OWLTools (RRID:SCR_005732) | OWLTools | software resource | OWLTools (aka OWL2LS - OWL2 Life Sciences) is a java API for accessing ontologies in either OBO or OWL. OWLTools provides a bio-ontologies friendly wrapper on top of the Manchester OWL API. It provides many features, including: * convenience methods for OBO-like properties such as synonyms, textual definitions, obsoletion, replaced_by * simple graph-like operations over ontologies * visualization using the QuickGO graphs libraries Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, ontology |
is listed by: Gene Ontology Tools is related to: OBO has parent organization: Gene Ontology has parent organization: Google Project Hosting is parent organization of: OwlSim |
Open unspecified license - Free for academic use | nlx_149192 | SCR_005732 | OWL2LS - OWL2 Life Sciences, OWL Tools | 2026-07-25 12:06:11 | 18 | |||||||
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Blip: Biomedical Logic Programming Resource Report Resource Website 1+ mentions |
Blip: Biomedical Logic Programming (RRID:SCR_005733) | Blip, blipkit | software resource | Biomedical Logical Programming (Blip) is a research-oriented deductive database and prolog application library for handling biological and biomedical data. It includes packages for advanced querying of ontologies and annotations. Blip underpins the Obol tool. Here are some distinguishing characteristics of Blip * Lightweight. Bloat-free: Blip only has as many modules as it needs to do its job. * Fast. * Declarative. Say what you want to do, not how you want to do it * Blip can be Query-oriented: specify your data sources and ask your query * Blip can be Application-oriented: it is designed to be used as an application library used by other bioinformatics tools * Mature and fully functional ontology module for handling both OBO-style ontologies and OWL ontologies. * Modules for handling biological sequences and sequence features. (currently limited functionality, added as needed) * A systems biology module for querying pathway and interaction data. (currently limited functionality, added as needed) * Relational database integration. SQL can be viewed as a highly restricted dialect of Prolog. Although the SWI-Prolog in-memory database is fast and scalable, sometimes it is nice to be able to fetch data from an external database. Blip contains a generic SQL utility module and predicate mappings for the GO database, Ensembl and Chado * Integration with a variety of bioinformatics file formats. SWI-Prolog has a variety of fast libraries for dealing with XML, RDF and tabular data files. Blip provides bridges from bio file formats encoded using these syntaxes into its native models. For other syntaxes, Blip seamlessly integrates other packages such as BioPerl and go-perl. Although these dependencies require extra installation, there is no point reinventing the wheel * Rapid development of web applications. Blip extends SWI-Prolog''''s excellent http support with a simple and powerful logical-functional-programming style application server, serval. This has been used to prototype a fully-featured next-generation replacement for the GO project amigo browser. * Scalable. Blip is not intended to be a toy system on toy data (although it is happy to be used as a toy if you like!). It is intended to be used as an application component and a tool operating on real-world biological and biomedical data Blip is written in SWI-Prolog, a fast, robust and scalable implementation of ISO Prolog. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | biology, biomedical, ontology, annotation, software library, bioinformatics, module |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Berkeley Bioinformatics Open-Source Projects |
GNU Lesser General Public License | nlx_149193 | SCR_005733 | Blip - Biomedical Logic Programming, Biomedical Logical Programming (Blip), Biomedical Logic Programming | 2026-07-25 12:06:08 | 2 | |||||||
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ClueGO Resource Report Resource Website 1000+ mentions |
ClueGO (RRID:SCR_005748) | ClueGO | software resource | A Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network. It can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easily extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be combined to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | statistical analysis, function, gene ontology, pathway, annotation, network, plugin, gene |
is listed by: Gene Ontology Tools is listed by: SoftCite is related to: Gene Ontology is related to: Cytoscape is related to: KEGG is related to: BioCarta Pathways has parent organization: National Institute of Health and Medical Research; Rennes; France |
National Institute of Health and Medical Research; Rennes; France ; Ville de Paris ; INCa ; Austrian Ministry for Science and Research ; BINII ; European Union 7FP 202230 |
PMID:19237447 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149209 | SCR_005748 | 2026-07-25 12:06:11 | 2943 | ||||||
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Honey Bee Brain EST Project Resource Report Resource Website 1+ mentions |
Honey Bee Brain EST Project (RRID:SCR_002389) | Bee-ESTdb | biomaterial supply resource, material resource | A database integrating data from the bee brain EST sequencing project with data from sequencing and gene research projects from other organisms, primarily the fruit fly Drosophila melanogaster. The goal of Bee-ESTdb is to provide updated information on the genes of the honey bee, currently using annotation primarily from flies to suggest cellular roles, biological functions, and evolutionary relationships. The site allows searches by sequence ID, EST annotations, Gene Ontology terms, Contig ID and using BLAST. Very nice resource for those interested in comparative genomics of brain. A normalized unidirectional cDNA library was made in the laboratory of Prof. Bento Soares, University of Iowa. The library was subsequently subtracted. Over 20,000 cDNA clones were partially sequenced from the normalized and subtracted libraries at the Keck Center, resulting in 15,311 vector-trimmed, high-quality, sequences with an average read length of 494 bp. and average base-quality of 41. These sequences were assembled into 8966 putatively unique sequences, which were tested for similarity to sequences in the public databases with a variety of BLAST searches. The Clemson University Genomics Institute is the distributor of these public domain cDNA clones. For information on how to purchase an individual clone or the entire collection, please contact www.genome.clemson.edu/orders/ or generobi (at) life.uiuc.edu. | expressed sequence tag, brain, behavior, cdna, blast, gene, annotation, microarray, gene expression, comparative genomics, cdna clone, resource:genbank |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: Gene Ontology has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NSF ; University of Illinois Critical Research Initiatives Program ; Burroughs Wellcome Fund |
PMID:11932240 | Free | nif-0000-00118 | SCR_002389 | Honeybee EST Project | 2026-07-25 12:12:24 | 5 | |||||
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Blast2GO Resource Report Resource Website 5000+ mentions |
Blast2GO (RRID:SCR_005828) | B2G | software application, software resource | An ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Blast2GO (B2G) 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. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | annotation, visualization, analysis, functional genomics, editor, statistical analysis, slimmer-type tool, ontology or annotation editor, functional analysis, direct acyclic graph, analysis, high throughput, functional genomics |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Principe Felipe Research Centre; Valencia; Spain |
MCyT GEN 2001 - 4885-C05-03; eTumour Project FP6-2002-LIFESCIHEALTH 503094 |
PMID:16081474 | Free for academic use | OMICS_01475, nlx_149335 | SCR_005828 | Blast2GO (B2G) | 2026-07-26 09:04:01 | 8422 | |||||
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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 | Functional Similarity Search Tool (FSST), Functional Similarity Search Tool | 2026-07-26 09:04:03 | 0 | |||||
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GoMiner Resource Report Resource Website 100+ mentions |
GoMiner (RRID:SCR_002360) | GoMiner | software application, software resource, data processing software | GoMiner is a tool for biological interpretation of "omic" data including data from gene expression microarrays. Omic experiments often generate lists of dozens or hundreds of genes that differ in expression between samples, raising the question, What does it all mean biologically? To answer this question, GoMiner leverages the Gene Ontology (GO) to identify the biological processes, functions and components represented in these lists. Instead of analyzing microarray results with a gene-by-gene approach, GoMiner classifies the genes into biologically coherent categories and assesses these categories. The insights gained through GoMiner can generate hypotheses to guide additional research. GoMiner displays the genes within the framework of the Gene Ontology hierarchy in two ways: * In the form of a tree, similar to that in AmiGO * In the form of a "Directed Acyclic Graph" (DAG) The program also provides: * Quantitative and statistical analysis * Seamless integration with important public databases GoMiner uses the databases provided by the GO Consortium. These databases combine information from a number of different consortium participants, include information from many different organisms and data sources, and are referenced using a variety of different gene product identification approaches. | experiment, expression, function, gene, genomics, biological, genomic, microarray, omic, process, gene expression, gene ontology, biological process, biological function, biological component, proteomic, database, FASEB list |
is related to: Gene Ontology is related to: High-Throughput GoMiner has parent organization: Georgia Institute of Technology; Georgia; USA has parent organization: Emory University; Georgia; USA has parent organization: National Cancer Institute |
NCI ; Georgia Institute of Technology; Georgia; USA ; Emory University; Georgia; USA |
PMID:12702209 | nif-0000-21181 | SCR_002360 | 2026-07-26 09:03:10 | 115 | |||||||
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FIVA - Functional Information Viewer and Analyzer Resource Report Resource Website 1+ mentions |
FIVA - Functional Information Viewer and Analyzer (RRID:SCR_005776) | FIVA | software application, software resource, data processing software | Functional Information Viewer and Analyzer (FIVA) 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. Currently, seven different modules containing functional information have been implemented: (i) gene regulatory interactions, (ii) cluster of orthologous groups (COG) of proteins, (iii) gene ontologies (GO), (iv) metabolic pathways (v) Swiss Prot keywords, (vi) InterPro domains - and (vii) generic functional categories. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, gene expression, gene expression pattern, functional profile, statistical analysis, metabolic pathway, gene ontology, function, ortholog, gene regulatory interaction, biological process, transcriptome, visualization, analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: MolGen |
Netherlands Organization for Scientific Research ; industrial partners in the NWO-BMI project number 050.50.206 on Computational Genomics of Prokaryotes ; Center IOP Genomics ; European Union QLK3-CT-2001-01473 |
PMID:17237043 | Free for academic use | nlx_149245 | SCR_005776 | FIVA - Functional Information Viewer Analyzer, Functional Information Viewer and Analyzer (FIVA), Functional Information Viewer and Analyzer | 2026-07-26 09:04:04 | 1 | |||||
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GoBean - a Java application for Gene Ontology enrichment analysis Resource Report Resource Website 10+ mentions |
GoBean - a Java application for Gene Ontology enrichment analysis (RRID:SCR_005808) | GoBean | software application, software resource, data processing software | GoBean is a Java application for gene ontology enrichment analysis. It utilizes the NetBeans platform framework. Features * Graphical comparison of multiple enrichment analysis results * Versatile filter facility for focused analysis of enrichment results * Effective exploitation of the graphical/hierarchical structure of GO * Evidence code based association filtering * Supports local data files such as the ontology obo file and gene association files * Supports late enrichment methods and multiple testing corrections * Built-in ID conversion for common species using Ensembl biomart service Platform: Windows compatible, Mac OS X compatible, Linux compatible | java, gene ontology, ontology, gene association, analysis, enrichment, term enrichment |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Gachon University of Medicine and Science; Incheon; South Korea |
PMID:22360891 | Free for academic use | nlx_149296 | http://neon.gachon.ac.kr/GoBean/ | SCR_005808 | 2026-07-26 09:04:03 | 22 | ||||||
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SeqExpress Resource Report Resource Website |
SeqExpress (RRID:SCR_007075) | software application, software resource, data processing software | A comprehensive analysis and visualization software package for gene expression experiments that provides: a number of clustering and analysis techniques; integrated gene expression and analysis result visualizations, integration with the Gene Expression Omnibus; and an optional data sharing architecture. 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, visualization, file export/import, searching, integration (with R), and clustering options. | gene, gene expression, function, analysis, visualization, statistical analysis, windows, c#, gene function, chromosome location, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Gene Expression Omnibus |
PMID:14988116 | Free | nlx_149285, biotools:seqexpress | https://bio.tools/seqexpress | SCR_007075 | 2026-07-26 09:04:28 | 0 | |||||||
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OwlSim Resource Report Resource Website 1+ mentions |
OwlSim (RRID:SCR_006819) | OwlSim | software application, software resource, data processing software | Software package that provides the ability to do a number of standard semantic similarity methods and includes novel methods for combining these with dynamic selection of anonymous grouping classes. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | functional similarity, semantic similarity, ontology, phenotype, annotation, windows, mac os x, linux, unix |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Berkeley Bioinformatics Open-Source Projects has parent organization: OWLTools |
Biomedical Information Science and Technology Initiative ; National Center for Biomedical Ontology ; NHGRI U54 HG004028; NHGRI HG002659 |
PMID:19956802 | Open unspecified license - Free for academic use | nlx_149312 | SCR_006819 | 2026-07-26 09:04:22 | 5 | ||||||
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High-Throughput GoMiner Resource Report Resource Website 1+ mentions |
High-Throughput GoMiner (RRID:SCR_000173) | web application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A web program that organizes lists of genes of interest (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology and automates the analysis of multiple microarrays then integrates the results across all of them in exportable output files and visualizations. High-Throughput GoMiner is an enhancement of GoMiner and is implemented with both a command line interface and a web interface. The program can also: efficiently perform automated batch processing of an arbitrary number of microarrays; produce a human- or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories; integrate the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories; provide a fast form of false discovery rate multiple comparisons calculation; and provide annotations and visualizations for relating transcription factor binding sites to genes and GO categories. | term enrichment, gene ontology, gene, microarray, common variable immune deficiency, high-throughput, visualization, database |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: GoMiner has parent organization: National Cancer Institute has parent organization: National Cancer Institute |
NCI 1Z01BC010842-01 | PMID:15998470 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149300 | SCR_000173 | 2026-07-27 09:30:53 | 2 |
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