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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Graph2GO Resource Report Resource Website 1+ mentions |
Graph2GO (RRID:SCR_018726) | data analysis software, data processing software, software application, software resource | Software tool as graph based representation learning method for protein function prediction. Multi modal graph based representation learning model that can integrate heterogeneous information including multiple types of interaction networks including sequence similarity network and protein-protein interaction network, and protein features including amino acid sequence, sub cellular location and protein domains, to predict protein functions on Gene Ontology. | Protein function prediction, graph neural network, attributed network embedding, representation learning, multi-modal model, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ohio State University College of Medicine; Ohio; USA |
Free, Available for download, Freely available | SCR_018727, biotools:graph2go | https://integrativeomics.shinyapps.io/graph2go/, https://bio.tools/graph2go | SCR_018726 | SciCrunch Registry | 2026-10-24 12:48:02 | 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 | SciCrunch Registry | 2026-10-24 12:45:32 | 2951 | ||||||
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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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ONTO-PERL Resource Report Resource Website |
ONTO-PERL (RRID:SCR_005731) | ONTO-PERL | software resource, source code | ONTO-PERL is a collection of Perl modules to handle OBO-formatted ontologies (like the Gene Ontology). This code distribution gathers object-oriented modules (for dealing with ontology elements such as Term, Relationship and so forth), scripts (for typical tasks such as format conversions: obo2owl, owl2obo; besides, there are also many examples that can be easily adapted for specific applications), and a set of test files to ensure the suite''''s implementation quality. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | application programming interface, software library, ontology, analysis, development, biomedical |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: OBO has parent organization: Comprehensive Perl Archive Network has parent organization: Norwegian University of Science and Technology; Trondheim; Norway |
European Union FP6 LSHG-CT-2004-512143; European Union FP6 MEST-CT-2004-414632 |
PMID:18245124 | Free for academic use | nlx_149191 | SCR_005731 | SciCrunch Registry | 2026-10-24 12:52:08 | 0 | ||||||
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OwlSim Resource Report Resource Website 1+ mentions |
OwlSim (RRID:SCR_006819) | OwlSim | data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-10-24 12:49:53 | 5 | ||||||
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FunSpec Resource Report Resource Website 50+ mentions |
FunSpec (RRID:SCR_006952) | FunSpec | analysis service resource, data analysis service, production service resource, 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 | SciCrunch Registry | Functional Specification | 2026-10-24 12:50:41 | 91 | ||||||
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GOanna Resource Report Resource Website 10+ mentions |
GOanna (RRID:SCR_005684) | GOanna | analysis service resource, data analysis service, production service resource, service resource | GOanna 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 of GO annotated proteins. 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. Platform: Online tool | agriculture, annotation, protein, ontology or annotation search engine, ontology or annotation editor |
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_149139 | SCR_005684 | SciCrunch Registry | AgBase GOanna | 2026-10-24 12:50:35 | 17 | |||||
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SeqExpress Resource Report Resource Website |
SeqExpress (RRID:SCR_007075) | data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-10-24 12:49:53 | 0 | |||||||
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GoFish Resource Report Resource Website 1+ mentions |
GoFish (RRID:SCR_005682) | GoFish | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | Software program, available as a Java applet online or to download, allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, ontology or annotation browser, java, 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 has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard Medical School; Massachusetts; USA |
Aventis Pharmaceuticals ; Howard Hughes Medical Institute ; NHGRI |
PMID:12691998 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:gofish, nlx_149126, OMICS_02272 | http://llama.mshri.on.ca/Software.html, https://bio.tools/gofish | SCR_005682 | SciCrunch Registry | 2026-10-24 12:45:30 | 1 | |||||
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Whatizit Resource Report Resource Website 1+ mentions |
Whatizit (RRID:SCR_005824) | Whatizit | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | A text processing system that allows you to do textmining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases. Whatizit is also a Medline abstracts retrieval/search engine. Instead of providing the text by Copy&Paste, you can launch a Medline search. The abstracts that match your search criteria are retrieved and processed by a pipeline of your choice. Whatizit is also available as 1) a webservice and as 2) a streamed servlet. The webservice allows you to enrich content within your website in a similar way as in the wikipedia. The streamed servlet allows you to process large amounts of text. | textual analysis, protein, gene, gene ontology, text-mining, annotation, literature analysis |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: MEDLINE is related to: NCBI Taxonomy has parent organization: European Bioinformatics Institute |
Free for academic use | OMICS_01200, nlx_149329 | http://www.ebi.ac.uk/webservices/whatizit | SCR_005824 | SciCrunch Registry | 2026-10-24 12:45:32 | 8 | |||||||
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Lists2Networks Resource Report Resource Website 1+ mentions |
Lists2Networks (RRID:SCR_006323) | L2N | analysis service resource, data analysis service, production service resource, service resource | A web-based software system that allows users to upload lists of mammalian genes/proteins onto a server-based program for integrated analysis. The system includes web-based tools to manipulate lists with different set operations, to expand lists using existing mammalian networks of protein-protein interactions, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, gene ontology terms, kinase-substrate, microRNA-mRAN, and protein-protein interactions, metabolites, and protein domains. Such analyses can be applied to several lists at once against many prior knowledge libraries of gene-lists associated with specific annotations. The system also contains features that allow users to export networks and share lists with other users of the system. | high-throughput sequencing, analysis, gene, protein |
is listed by: OMICtools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:20152038 | Free, Public, Account required | OMICS_02231 | http://www.lists2networks.org | SCR_006323 | SciCrunch Registry | Lists2Networks: Integrated analysis of gene/protein lists | 2026-10-24 12:50:38 | 3 | |||||
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Biofactoid Resource Report Resource Website 1+ mentions |
Biofactoid (RRID:SCR_021011) | data access protocol, data or information resource, knowledge environment resource, portal, project portal, software resource, web service | Web tool for creating digital profile of scientific discoveries in article and connecting them to related research. Authors describe molecular interactions supported by their results, letting researchers explore first hand account of article findings and connect to related articles and knowledge. Web based system for scientists to compose structured representation of networks of interactions between genes, their products, and chemical compounds, represented using power of formal ontology. | Knowledge management, molecular interactions, pathway, compose network structured representation, digital profile, connect related articles, formal ontology |
is related to: Biological Pathways Exchange is related to: Biological Pathways Exchange has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard University; Cambridge; United States has parent organization: University of Oregon; Oregon; USA |
DARPA Big Mechanism ; NHGRI U41HG006623 |
Free, Freely available | SCR_021011 | SciCrunch Registry | 2026-10-24 12:48:48 | 1 | |||||||||
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Yeast Search for Transcriptional Regulators And Consensus Tracking Resource Report Resource Website 100+ mentions |
Yeast Search for Transcriptional Regulators And Consensus Tracking (RRID:SCR_006076) | YEASTRACT | data or information resource, database | A curated repository of more than 206000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1300 bibliographic references. It also includes the description of 326 specific DNA binding sites shared among 113 characterized TFs. Further information about each Yeast gene has been extracted from the Saccharomyces Genome Database (SGD). For each gene the associated Gene Ontology (GO) terms and their hierarchy in GO was obtained from the GO consortium. Currently, YEASTRACT maintains a total of 7130 terms from GO. The nucleotide sequences of the promoter and coding regions for Yeast genes were obtained from Regulatory Sequence Analysis Tools (RSAT). All the information in YEASTRACT is updated regularly to match the latest data from SGD, GO consortium, RSA Tools and recent literature on yeast regulatory networks. YEASTRACT includes DISCOVERER, a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes. DISCOVERER is based on the MUSA algorithm. These algorithms take as input a list of genes and identify over-represented motifs, which can then be compared with transcription factor binding sites described in the YEASTRACT database. | yeast, gene, regulatory association, transcription factor, target gene, genomic, transcription regulation, transcription, web service, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SGD is related to: Gene Ontology is related to: Regulatory Sequence Analysis Tools |
Fundacao para a Ciencia e a Tecnologia contract Pest-OE/EQB/LA0023/2011_research line: Systems and Synthetic Biology; Fundacao para a Ciencia e a Tecnologia ERA-IB/0002/2010; Fundacao para a Ciencia e a Tecnologia PTDC/EIA-EIA/111239/2009; Fundacao para a Ciencia e a Tecnologia PTDC/EIA-CCO/118522/2010 |
PMID:24170807 PMID:20972212 PMID:18032429 PMID:16381908 |
Free | nif-0000-03652, OMICS_00547, biotools:yeastract | https://bio.tools/yeastract | SCR_006076 | SciCrunch Registry | 2026-10-24 12:50:37 | 130 | |||||
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HOCTAR Resource Report Resource Website 10+ mentions |
HOCTAR (RRID:SCR_010842) | HOCTAR | data or information resource, database | Database serving as a tool for microRNA target prediction. The HOCTAR procedure is based on the integration of expression profiling and sequence-based miRNA target recognition softwares. HOCTAR database (db) is the first and unique database to use transcriptomic data to score putative miRNA targets looking at the expression behaviour of their host genes, and it includes and re-analyzes all miRNA target predictions generated by softwares such as miRanda, TargetScan and PicTar. The HOCTARdb contains the prediction target lists for 290 human intragenic miRNAs and also provides tentative assignments of miRNA function based on Gene Ontology analyses of their predicted targets. There are two ways to interrogate HOCTARdb: (i) by selecting a miRNA using either an alphabetically sorted pull-down menu in the microRNA query, or (ii) by typing a target gene symbol (HUGO Gene Name-approved) in the Target Gene Name query. | microrna, target prediction. | is listed by: OMICtools | PMID:21435384 PMID:19088304 |
Public | OMICS_00398 | SCR_010842 | SciCrunch Registry | Host gene Opposite Correlated TARgets, HOCTARdb, HOCTAR database | 2026-10-24 12:51:01 | 11 | ||||||
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DFLAT Resource Report Resource Website 1+ mentions |
DFLAT (RRID:SCR_010738) | DFLAT | data or information resource, data set, narrative resource, standard specification | We are an interdisciplinary team dedicated to annotating gene function related to human fetal development. We are contributing new functional annotation to the Gene Ontology, curating and mining gene sets suitable for the interpretation of developmental genomic data, and creating the computational tools needed to apply genomics for better understanding the molecular mechanisms of human development. Our GO annotation is in the process of being incorporated into the GOA public release. The GONE (Gene Ontology Non-Eligible) database is where we store annotations relevant to our research but that don''t quite meet GOA''s standards. Usually an annotation falls into this category because either the gene/protein described is a family of genes/proteins rather than a specific one, there is no UniProt ID to identify the gene/protein in the system, a GO term does not yet exist to describe the particular function, process, or location of the gene/protein, the species is not clearly identifiable in the paper, or the evidence is not as reliable (GO evidence codes TAS and NAS). As individual annotations these are more suspect than current GO annotation. However, for functional analysis of expression data, these gene sets can be valuable even with a certain amount of noise. We also include here a link to the supplementary data from our forthcoming PSB 2011 paper on gene set mining. | human, fetal, development | has parent organization: Tufts University; Massachusetts; USA | NICHD R01 HD058880 | PMID:21121032 | nlx_95610 | SCR_010738 | SciCrunch Registry | Developmental FunctionaL Annotation at Tufts | 2026-10-24 12:46:22 | 2 | ||||||
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LegumeIP Resource Report Resource Website 10+ mentions |
LegumeIP (RRID:SCR_008906) | LegumeIP | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular based breeding tools to improve quality of crop legumes. LegumeIP currently hosts large-scale genomics and transcriptomics data, including: * Genomic sequences of three model legumes, i.e. Medicago truncatula, Glycine max (soybean) and Lotus japonicus, including two reference plant species, Arabidopsis thaliana and Poplar trichocarpa, with the annotation based on UniProt TrEMBL, InterProScan, Gene Ontology and KEGG databases. LegumeIP covers a total 222,217 protein-coding gene sequences. * Large-scale gene expression data compiled from 104 array hybridizations from L. japonicas, 156 array hybridizations from M. truncatula gene atlas database, and 14 RNA-Seq-based gene expression profiles from G. max on different tissues including four common tissues: Nodule, Flower, Root and Leaf. * Systematic synteny analysis among M. truncatula, G. max, L. japonicus and A. thaliana. * Reconstruction of gene family and gene family-wide phylogenetic analysis across the five hosted species. LegumeIP features comprehensive search and visualization tools to enable the flexible query on gene annotation, gene family, synteny, relative abundance of gene expression. | gene function, genome evolution, legume, gene, genome, plant, genomics, transcriptomic, gene annotation, gene family, synteny, gene expression, blast, genomic sequence, microarray, rna-seq, comparative genomics, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: UniProt is related to: InterProScan is related to: Gene Ontology is related to: KEGG has parent organization: Samuel Roberts Noble Foundation |
Samuel Roberts Noble Foundation ; NSF ABI-0960897 |
PMID:22110036 | biotools:legumeip, nlx_151455 | https://bio.tools/legumeip | SCR_008906 | SciCrunch Registry | LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes, LegumeIP - An Integrative Platform to Study Gene Function and Genome Evolution in Legumes | 2026-10-24 12:46:15 | 23 | |||||
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Spark Resource Report Resource Website 100+ mentions |
Spark (RRID:SCR_006207) | Spark | data analysis software, data processing software, data visualization software, software application, software resource | A clustering and visualization tool that enables the interactive exploration of genome-wide data, with a specialization in epigenomics data. Spark is also available as a service within the Epigenome toolset of the Genboree Workbench. The approach utilizes data clusters as a high-level visual guide and supports interactive inspection of individual regions within each cluster. The cluster view links to gene ontology analysis tools and the detailed region view connects to existing genome browser displays taking advantage of their wealth of annotation and functionality. | epigenomics, genome browser, clustering, visualization, genome, computation, pattern discovery, cluster |
is related to: Genboree Discovery System is related to: Roadmap Epigenomics Project has parent organization: BC Cancer Agency |
Canadian Institutes of Health Research ; Michael Smith Foundation for Health Research ; Natural Sciences and Engineering Research Council of Canada ; NIDA U01 DA025956; NIEHS 5U01ES017154-02; NHGRI HG004558 |
PMID:22960372 | Available for download without charge. Please cite. | nlx_151753 | SCR_006207 | SciCrunch Registry | Sparkinsight | 2026-10-24 12:45:38 | 417 | |||||
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GeneMerge Resource Report Resource Website 10+ mentions |
GeneMerge (RRID:SCR_005744) | GeneMerge | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, genomics, functional genomic data, analysis, post-genomic analysis, data mining, hypothesis testing, statistical analysis, slimmer-type tool, term enrichment, text mining, false discovery rate, bonferroni correction, false discovery rate and bonferroni correction, perl, microarray |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Harvard University; Cambridge; United States |
PMID:12724301 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149203 | http://genemerge.cbcb.umd.edu/ | SCR_005744 | SciCrunch Registry | 2026-10-24 12:49:07 | 26 | ||||||
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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 | SciCrunch Registry | Short Time-series Expression Miner | 2026-10-24 12:49:53 | 90 | |||||
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Wandora Resource Report Resource Website |
Wandora (RRID:SCR_005689) | Wandora | software application, software resource | Wandora is a general purpose information extraction, management and publishing application based on Topic Maps and Java. Wandora has graphical user interface, layered and merging information model, multiple visualization models, huge collection of information extraction, import and export options, embedded HTTP server with several output modules and open plug-in architecture. Wandora is a FOSS application with GNU GPL license. Wandora is well suited for constructing ontologies and information mashups. Wandora is capable of extracting and converting a wide range of open data feeds to topic map formats. Beyond topic map conversion, this feature allows Wandora user to aggregate multidimensional information mashups where information from Flickr interleaves with information from GeoNames and YouTube, for example. Wandora is a software application to build, edit, publish and visualize information graphs, especially topic maps. Wandora is written in Java and suits for * Collecting, combining, aggregating, managing, refining and publishing information and knowledge graphs * Designing information, information modeling and prototyping * Information mashups * Ontology creation and management * Mind and concept mapping * Language technology applications * Graph visualizations * Knowledge format conversions * Digital preservation * Data journalism * Open data projects * Linked data projects Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | visualization, ontology, ontology or annotation browser, knowledge management system |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: OBO |
Open unspecified license (GNU GPL v3) - Free for academic use | nlx_149134 | SCR_005689 | SciCrunch Registry | 2026-10-24 12:51:26 | 0 |
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