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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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TXTGate Resource Report Resource Website |
TXTGate (RRID:SCR_005812) | TXTGate | production service resource, service resource, data analysis service, analysis service resource | TXTGate is a literature index database and is part of an experimental platform to evaluate (combinations of) information extraction and indexing from a variety of biological annotation databases. It is designed towards the summarization and analysis of groups of genes based on text. 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. You need to be registered in order to use the TXTGate application. Platform: Online tool | gene, annotation, database, text mining |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: SGD has parent organization: Catholic University of Leuven; Flemish Brabant; Belgium |
European Union ; Instituut voor de aanmoediging van Innovatie door Wetenschap en Technologie Vlaanderen ; Research Council K.U. Leuven GOA-Mefisto-666; Fonds voor Wetenschappelijk Onderzoek - Vlaanderen G.0115.01; Fonds voor Wetenschappelijk Onderzoek - Vlaanderen G.0240.99; Fonds voor Wetenschappelijk Onderzoek - Vlaanderen G.0407.02; Fonds voor Wetenschappelijk Onderzoek - Vlaanderen G.0413.03; Fonds voor Wetenschappelijk Onderzoek - Vlaanderen G.0388.03; Fonds voor Wetenschappelijk Onderzoek - Vlaanderen G.0229.03; Fonds voor Wetenschappelijk Onderzoek - Vlaanderen G.0241.04; Belgian Federal Science Policy Office IUAP V-22 |
PMID:15186494 | Free for academic use | nlx_149305 | SCR_005812 | 2026-02-16 09:46:41 | 0 | ||||||
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IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures Resource Report Resource Website 1+ mentions |
IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures (RRID:SCR_005815) | IT-GOM | production service resource, service resource, data analysis service, analysis service resource | The Integrated Tool for IC-based GO Semantic Similarity Measures (IT-GOM) integrates the currently known GO semantic similarity measures into a single tool. It provides the information content (IC) of GO terms, semantic similarity between GO terms and GO-based protein functional similarity scores. The specificity of GO terms and the similarity of biological content between GO terms or proteins are transformed into numeric values for protein analyses at the functional level. The integration of the different measures enables users to choose the measure best suited to their application and to compare results between different semantic similarity measures. Platform: Online tool | semantic similarity, gene ontology, protein, functional similarity, function, annotation, topology |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: UniProt is related to: GOA has parent organization: University of Cape Town; Western Cape; South Africa |
National Bioinformatics Network in South Africa ; University of Cape Town; Western Cape; South Africa ; Computational Biology research group at the Institute of Infectious Disease and Molecular Medicine |
Open unspecified license - Free for academic use | nlx_149310 | SCR_005815 | Integrated Tool for IC-based GO Semantic Similarity Measures (IT-GOM), Integrated Tool for IC-based GO Semantic Similarity Measures | 2026-02-16 09:46:33 | 1 | ||||||
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GORetriever Resource Report Resource Website 10+ mentions |
GORetriever (RRID:SCR_005633) | GORetriever | production service resource, service resource, data analysis service, analysis service resource | GORetriever is used to find all of the GO annotations corresponding to a list of user-supplied protein identifiers. GORetriever produces a list of proteins and their annotations and a separate list of entries with no GO annotation. Platform: Online tool | gene, annotation, protein, ontology or annotation search engine |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: AgBase |
USDA ; Mississippi State University; Mississippi; USA ; MSU Office of Research ; MSU Bagley College of Engineering ; MSU College of College of Veterinary Medicine ; MSU Life Science and Biotechnology Institute |
PMID:17135208 PMID:16961921 |
Free for academic use | nlx_149140 | SCR_005633 | AgBase GORetriever | 2026-02-16 09:46:30 | 13 | |||||
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CLASSIFI - Cluster Assignment for Biological Inference Resource Report Resource Website |
CLASSIFI - Cluster Assignment for Biological Inference (RRID:SCR_005752) | CLASSIFI | production service resource, service resource, data analysis service, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 10, 2012. Cluster Assignment for Biological Inference (CLASSIFI) is a data-mining tool that can be used to identify significant co-clustering of genes with similar functional properties (e.g. cellular response to DNA damage). Briefly, CLASSIFI uses the Gene Ontology gene annotation scheme to define the functional properties of all genes/probes in a microarray data set, and then applies a cumulative hypergeometric distribution analysis to determine if any statistically significant gene ontology co-clustering has occurred. Platform: Online tool | statistical analysis, gene, gene expression, data mining, biological process, function, gene ontology, annotation, microarray |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: UT Southwestern Medical Center Department of Pathology |
PMID:16670020 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149214 | SCR_005752 | Cluster Assignment for Biological Inference, Cluster Assignment for Biological Inference (CLASSIFI) | 2026-02-16 09:46:32 | 0 | ||||||
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GraphWeb Resource Report Resource Website 10+ mentions |
GraphWeb (RRID:SCR_005746) | GraphWeb | production service resource, service resource, data analysis service, analysis service resource | GraphWeb allows the detection of modules from biological, heterogeneous and multi-species networks, and the interpretation of detected modules using Gene Ontology, cis-regulatory motifs and biological pathways. GraphWeb is a public web server for graph-based analysis of biological networks that: * analyses directed and undirected, weighted and unweighted heterogeneous networks of genes, proteins and microarray probesets for many eukaryotic genomes; * integrates multiple diverse datasets into global networks; * incorporates multispecies data using gene orthology mapping; * filters nodes and edges based on dataset support, edge weight and node annotation; * detects gene modules from networks using a collection of algorithms; * interprets discovered modules using Gene Ontology, pathways, and cis-regulatory motifs. Platform: Online tool | analysis, biological network, ontology or annotation visualization, protein interaction, gene id conversion, orthology mapping, network visualization, graph clustering, gene ontology, cis-regulatory motif, module, network, pathway, biological pathway, motif, visualization, protein interaction, orthology mapping, network visualization, graph clustering, analysis, statistical analysis, term enrichment |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: BIIT - Bioinformatics Algorithmics and Data Mining Group |
European Union FP6 ENFIN LSHG-CT-2005-518254; European Union FP6 COBRED LSHB-CT-2007-037730; Estonian Science Foundation ETF7437 |
PMID:18460544 | Open unspecified license - Free for academic use | nlx_149205 | SCR_005746 | 2026-02-16 09:46:32 | 12 | ||||||
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ProteInOn Resource Report Resource Website 1+ mentions |
ProteInOn (RRID:SCR_005740) | production service resource, service resource, data analysis service, analysis service resource | ProteInOn calculates semantic similarity between GO terms or proteins annotated with GO terms. It also calculates term enrichment of protein sets, by applying a term representativity score, and gives additional information on protein interactions. The query compute protein semantic similarity returns the semantic similarity scores between all proteins entered, in matrix format. The option Measure allows users to choose one of several semantic similarity measures: Resnik, Lin, or Jiang & Conrath's measures with or without the DCA approach, plus the graph-based simUI and simGIC measures. These measures are listed by order of performance as evaluated with protein sequence similarity. The option GO type allows users to choose one of the aspects of GO: molecular function, biological process and cellular component. The option Ignore IEA limits the query to non-electronic annotations, excluding evidence types: IEA, NAS, ND, NR. | protein, ontology, gene ontology, annotation, statistical analysis, term enrichment, protein interaction, semantic similarity, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products has parent organization: University of Lisbon; Lisbon; Portugal |
Free for academic use | nlx_149206 | SCR_005740 | Protein Interactions Ontology, ProteInOn - Protein Interactions and Ontology, Protein Interactions and Ontology | 2026-02-16 09:46:41 | 2 | ||||||||
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CateGOrizer Resource Report Resource Website 50+ mentions |
CateGOrizer (RRID:SCR_005737) | CateGOrizer | production service resource, service resource, data analysis service, analysis service resource | CateGOrizer takes batch 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, GO-ROOT, or a self-defined classification list, find its parental branch and performs an accumulative classification count, and returns the results in a sorted table of counts, percentages, and a pie chart (if it takes longer than standard time out period, it will email the user with a URL link to the results). This tool is comprised with a set of perl CGI programs coupled with a MySQL DBMS that stores the GO terms DAG data. Platform: Online tool | gene ontology, statistical analysis, slimmer-type tool, go term classification, classification, analysis, go slim |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: NAGRP Bioinformatics Coordination Program |
Free for academic use | nlx_149197 | SCR_005737 | GO Terms Classifications Counter | 2026-02-16 09:46:32 | 81 | |||||||
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ProbeExplorer Resource Report Resource Website |
ProbeExplorer (RRID:SCR_007116) | ProbeExplorer | production service resource, service resource, data analysis service, analysis service resource | Probe Explorer 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. Platform: Online tool | bioinformatics, microarray, oligonucleotide probe, transcript, genomic, genome, transcriptome, alignment, affymetrix, probe sequence, dna, protein, sequence, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Salamanca; Salamanca; Spain |
Open unspecified license - Free for academic use | nlx_149275 | SCR_007116 | Probe Explorer | 2026-02-16 09:46:53 | 0 | |||||||
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CRCView Resource Report Resource Website |
CRCView (RRID:SCR_007092) | CRCView | production service resource, service resource, data analysis service, analysis service resource | Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in. | microarray, gene expression, cluster, gene, expression profile, data repository, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
University of Michigan; Michigan; USA ; Institutional Fund ; NIH U013422; NIAID 1R21AI057875-01 |
PMID:17485426 | Registration required | biotools:crcview, nlx_99864 | https://bio.tools/crcview | http://helab.bioinformatics.med.umich.edu/crcview/ | SCR_007092 | Chinese Restaurant ClusterView | 2026-02-16 09:46:53 | 0 | |||
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FunSpec Resource Report Resource Website 50+ mentions |
FunSpec (RRID:SCR_006952) | FunSpec | production service resource, service resource, data analysis service, analysis service resource | FunSpec 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. FunSpec (an acronym for Functional Specification) inputs a list of yeast gene names, and outputs a summary of functional classes, cellular localizations, protein complexes, etc. that are enriched in the list. The classes and categories evaluated were downloaded from the MIPS Database and the GO Database . In addition, many published datasets have been compiled to evaluate enrichment against. Hypertext links to the publications are given. The p-values, calculated using the hypergeometric distribution, represent the probability that the intersection of given list with any given functional category occurs by chance. The Bonferroni-correction divides the p-value threshold, that would be deemed significant for an individual test, by the number of tests conducted and thus accounts for spurious significance due to multiple testing over the categories of a database. After the Bonferroni correction, only those categories are displayed for which the chance probability of enrichment is lower than: p-value/#CD where #CD is the number of categories in the selected database. Without the Bonferroni Correction, all categories are displayed for which the same probability of enrichment is lower than: p-value threshold in an individual test Note that many genes are contained in many categories, especially in the MIPS database (which are hierarchical) and that this can create biases for which FunSpec currently makes no compensation. Also the databases are treated as independent from one another, which is really not the case, and each is searched seperately, which may not be optimal for statistical calculations. Nonetheless, we find it useful for sifting through the results of clustering analysis, TAP pulldowns, etc. Platform: Online tool | gene, protein, annotation, gene ontology, gene expression, clustering, prediction, statistical analysis, functional class, cellular localization, protein complex, yeast, FASEB list |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: CYGD - Comprehensive Yeast Genome Database has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; CIHR ; University of Toronto Connaught Foundation |
PMID:12431279 | nlx_149246 | SCR_006952 | Functional Specification | 2026-02-16 09:46:50 | 87 | ||||||
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GFINDer: Genome Function INtegrated Discoverer Resource Report Resource Website 1+ mentions |
GFINDer: Genome Function INtegrated Discoverer (RRID:SCR_008868) | GFINDer | production service resource, service resource, data analysis service, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 16, 2019. 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 analyze the obtained classifications, aiding in better interpreting microarray experiment results. | annotation, statistical analysis, mining, genome, function, sequence, functional profile, gene, microarray, 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: Polytechnic University of Milan; Milan; Italy |
PMID:15980570 PMID:15215397 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149256, biotools:gfinder | https://www.hsls.pitt.edu/obrc/index.php?page=URL1098209538 https://bio.tools/gfinder |
SCR_008868 | Genome Function INtegrated Discoverer, Genome Function INtegrated Discoverer (GFINDer) | 2026-02-16 09:47:17 | 1 | |||||
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Avadis Resource Report Resource Website 1+ mentions Rating or validation data |
Avadis (RRID:SCR_000644) | Avadis | software resource, software toolkit, software library | Software integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports workflows for RNA-Seq, DNA-Seq, ChIP-Seq and small RNA-Seq experiments. Avadis has a built-in Gene Ontology browser to view ontology hierarchies. There are common ontology paths for multiple genes. Platform has collection of data / text mining algorithms, data visualization libraries, workflow/application automation layers, and enterprise data organization functions. These functions are available as libraries that allow developers to rapidly build software prototypes, applications and off-the-shelf products. The collection of algorithms and visualizations in AVADIS grows as new applications using the platform are developed. Currently, the algorithms that AVADIS platform contains range from general purpose statistical mining and modelling algorithms, to text mining algorithms, to very application-specific algorithms for microarray / NGS data analysis, QSAR modelling and biological networks analysis. AVADIS has a collection of powerful mining algorithms like PCA, ANOVA, T-test, clustering, classification and regression methods. The range of visualizations includes most statistical and data modelling related graphing views, and very application-specific visualizations. Some of the statistical views include 2D/3D scatter plots, profile plots, heat maps, histograms and matrix plot; data modelling relevant views include dendrograms, cluster profiles, similarity images and SOM U-matrices. Application-specific views in AVADIS include pathway network views, genome browsers, chemical structure views and pipe-line views. Platform: Windows compatible, Mac OS X compatible, Linux compatible, | pathway network views, genome browsers, chemical structure views, pipe-line views, next-generation sequencing data, integrated platform, view ontology hierarchies, statistical mining and modelling, collection of data, text mining algorithms collection, data visualization libraries, |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01120, nlx_149208 | http://www.strandls.com/Avadis | SCR_000644 | Access Visualize Analyze Discover, Avadis NGS | 2026-02-16 09:45:18 | 2 | ||||||
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Short Time-series Expression Miner (STEM) Resource Report Resource Website 50+ mentions |
Short Time-series Expression Miner (STEM) (RRID:SCR_005016) | STEM | data processing software, software application, software resource | The Short Time-series Expression Miner (STEM) is a Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments (~8 time points or fewer). 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 supporting 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 or user defined gene set, identifying which temporal expression profiles were enriched for these genes. (Note: While STEM is designed primarily to analyze data from short time course experiments it can be used to analyze data from any small set of experiments which can naturally be ordered sequentially including dose response experiments.) Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | statistical analysis, term enrichment, visualization, cluster, compare, short time series, gene expression, microarray, expression profile, gene, gene ontology, gene enrichment analyses, FASEB list |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Carnegie Mellon University; Pennsylvania; USA |
NIAID NO1 AI-5001; NSF 0448453 |
PMID:16597342 PMID:15961453 |
Open unspecified license - Free for academic use | nlx_97053 | SCR_005016 | Short Time-series Expression Miner | 2026-02-16 09:46:25 | 81 | |||||
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STRAP Resource Report Resource Website 100+ mentions |
STRAP (RRID:SCR_005675) | STRAP | data processing software, software application, software resource | Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible | protein, gene, annotation, mass spectrometry, proteomics, visualization, browser, differential analysis, analysis, ontology or annotation browser, ontology or annotation visualization, differential analysis of proteomics data sets, windows, protein annotation, data visualization, c#, pathway, FASEB list |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: QuickGO has parent organization: Boston University School of Medicine; Massachusetts; USA |
NHLBI contract N01 HV28178; NCRR P41 RR10888 |
PMID:19839595 | Open unspecified license, Acknowledgement requested | OMICS_02277, nlx_149115 | SCR_005675 | Software Tool for Rapid Annotation of Proteins, STRAP for GO Annotation, STRAP - Software Tool for Rapid Annotation of Proteins | 2026-02-16 09:46:31 | 120 | |||||
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Proteome Analyst PA-GOSUB Resource Report Resource Website 1+ mentions |
Proteome Analyst PA-GOSUB (RRID:SCR_008234) | PA-GOSUB | data set, data or information resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 30, 2015. Refer to Proteome Analyst 3.0. Subcellular Localization and GO General Molecular Function predictions for many model organism proteomes using Protein Analyst, with a very high coverage rate. When users blast their proteins against the database of results, they will not only be shown blast homologs from the model organisms, but also the Subcellular Localization and GO General Molecular Function predictions as well. | subcellular localization, homolog, localization, molecular, organism, prediction, protein, proteome, subcellular, organelle, gene ontology cellular component, nucleus, golgi apparatus, mitochondrion |
is listed by: 3DVC is related to: Proteome Analyst is related to: Gene Ontology is related to: Proteome Analyst has parent organization: University of Alberta; Alberta; Canada |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21342 | SCR_008234 | Proteome Analyst | 2026-02-16 09:47:08 | 2 |
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