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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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CRCView Resource Report Resource Website |
CRCView (RRID:SCR_007092) | CRCView | data analysis service, production service resource, service resource, 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 | 2026-02-14 02:05:58 | 0 | |||
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FunSpec Resource Report Resource Website 50+ mentions |
FunSpec (RRID:SCR_006952) | FunSpec | data analysis service, production service resource, service resource, 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 | 2026-02-14 02:06:27 | 87 | ||||||
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ECgene: Gene Modeling with Alternative Splicing Resource Report Resource Website 10+ mentions |
ECgene: Gene Modeling with Alternative Splicing (RRID:SCR_007634) | ECgene | data or information resource, database | Database of functional annotation for alternatively spliced genes. It uses a gene-modeling algorithm that combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. It contains genome, mRNA, and EST sequence data, as well as a genome browser application. Organisms included in the database are human, dog, chicken, fruit fly, mouse, rhesus, rat, worm, and zebrafish. Annotation is provided for the whole transcriptome, not just the alternatively spliced genes. Several viewers and applications are provided that are useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. Two unique ways of analyzing gene expression is also provided. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publicly. The cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns. | est cluster, genome, alternative splicing, splice, gene, mrna, est, annotation, gene modeling, structure, function, gene expression, transcript, genome browser, differential expression, snp |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Ewha Womans University; Seoul; South Korea |
PMID:17132829 PMID:15805497 PMID:15608289 |
nif-0000-02780, OMICS_01884 | http://genome.ewha.ac.kr/ECgene/ | SCR_007634 | ECgene - Genome Annotation for Alternative Splicing | 2026-02-14 02:06:00 | 12 | ||||||
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UniProtKB Resource Report Resource Website 5000+ mentions |
UniProtKB (RRID:SCR_004426) | data repository, storage service resource, data or information resource, service resource, database | Central repository for collection of functional information on proteins, with accurate and consistent annotation. In addition to capturing core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and experimental and computational data. The UniProt Knowledgebase consists of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. UniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database which brings together experimental results, computed features, and scientific conclusions. UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization that await full manual annotation. Users may browse by taxonomy, keyword, gene ontology, enzyme class or pathway. | protein, annotation, amino acid sequence, taxonomy, proteome |
uses: UniportKB is used by: NIF Data Federation is used by: PINT is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is related to: ESTHER is related to: PIRSF is related to: AmiGO is related to: UniSave is related to: ProRepeat is related to: UniProt Chordata protein annotation program is related to: neXtProt is related to: TopFIND is related to: UniPathway is related to: NCBI Protein Database is related to: Biomine is related to: Gene Ontology is related to: UniProt DAS is related to: FunTree is related to: ConceptWiki is related to: InterProScan is related to: UniProtKB/Swiss-Prot is related to: FuzDrop has parent organization: UniProt is parent organization of: UniProtKB Keywords is parent organization of: UniProtKB Subcellular Locations works with: PremierBiosoft Proteo IQ Software works with: Cello2Go works with: UniprotR works with: Kinase Associated Neural Phospho Signaling |
PMID:15888679 PMID:18287689 |
Available to the research community, The community can contribute to this resource | r3d100011521, nlx_53981 | https://doi.org/10.17616/R3NK9Z | SCR_004426 | UniProtKB, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, UniProt Knowledgebase | 2026-02-14 02:04:28 | 6654 | ||||||
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EMAGE Gene Expression Database Resource Report Resource Website 10+ mentions |
EMAGE Gene Expression Database (RRID:SCR_005391) | EMAGE | data repository, storage service resource, data or information resource, atlas, service resource, database | A database of in situ gene expression data in the developing mouse embryo and an accompanying suite of tools to search and analyze the data. mRNA in situ hybridization, protein immunohistochemistry and transgenic reporter data is included. The data held is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. The conceptual framework which houses the descriptions of the gene expression patterns in EMAGE is the EMAP Mouse Embryo Anatomy Atlas. This consists of a set of 3D virtual embryos at different stages of development, as well as an accompanying ontology of anatomical terms found at each stage. The raw data images can be conventional 2D photographs (of sections or wholemount specimens) or 3D images of wholemount specimens derived from Optical Projection Tomography (OPT) or confocal microscopy. Users may submit data using a Data submission tool or without. | genetics, 3d model, anatomy, development, mouse morphology, molecular neuroanatomy resource, gene expression, in situ hybridization, immunohistochemistry, embryo, in situ reporter, embryonic mouse, optical projection tomography, confocal microscopy, annotation, pathway, gene association, protein, theiler stage, gene expression, embryology, dna, protein, protein-protein interaction, protein binding, gene, embryology, anatomy, genetics, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: HUDSEN Electronic Atlas of the Developing Human Brain is related to: eMouseAtlas is related to: eMouseAtlas is related to: HUDSEN Human Gene Expression Spatial Database is related to: aGEM is related to: Eurexpress is related to: Gene Expression Database is related to: Gene Ontology is related to: NIDDK Information Network (dkNET) is related to: GUDMAP Ontology |
MRC | PMID:19767607 | Except where noted, Creative Commons Attribution License, The community can contribute to this resource | biotools:emage, nif-0000-00080, r3d100010564 | https://bio.tools/emage https://doi.org/10.17616/R3860B |
SCR_005391 | Emage (e-Mouse Atlas of Gene Expression), e-Mouse Atlas of Gene Expression | 2026-02-14 02:04:31 | 23 | ||||
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GeneMerge Resource Report Resource Website 10+ mentions |
GeneMerge (RRID:SCR_005744) | GeneMerge | data analysis service, analysis service resource, 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 | 2026-02-14 02:04:52 | 26 | ||||||
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Candidate Genes to Inherited Diseases Resource Report Resource Website 1+ mentions |
Candidate Genes to Inherited Diseases (RRID:SCR_008190) | G2D | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases. | function, gene, genetic, chromosome, disease, disorder, genome, homology, human, phenotype, protein, region, candidate gene, database, data warehouse, data set, bio.tools |
is listed by: 3DVC is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: European Molecular Biology Laboratory has parent organization: EMBL - Bork Group |
PMID:16115313 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21162, biotools:g2d | http://www.bork.embl-heidelberg.de/g2d/ http://www.ogic.ca/projects/g2d_2/ https://bio.tools/g2d |
SCR_008190 | G2D - Candidate Genes to Inherited Diseases, Genes2Diseases | 2026-02-14 02:04:33 | 2 | |||||
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GeneCodis Resource Report Resource Website 100+ mentions |
GeneCodis (RRID:SCR_006943) | GeneCodis | web service, data analysis service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional analysis, gene, annotation, statistical analysis, functional genomics, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: KEGG has parent organization: Spanish National Research Council; Madrid; Spain |
Juan de la Cierva research program ; Spanish Minister of Science and Innovation BIO2010-17527; Government of Madrid P2010/BMD-2305 |
PMID:22573175 PMID:19465387 PMID:17204154 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02221, biotools:genecodis3, nlx_149254 | https://bio.tools/genecodis3 | SCR_006943 | Gene annotations co-ocurrence discovery, GeneCodis - Gene annotations co-ocurrence discovery | 2026-02-14 02:04:48 | 348 | ||||
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Avadis Resource Report Resource Website 1+ mentions Rating or validation data |
Avadis (RRID:SCR_000644) | Avadis | software resource, software library, software toolkit | 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 | 2026-02-14 02:05:00 | 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 | software resource, data processing software, software application | 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 | 2026-02-14 02:05:25 | 81 | |||||
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STRAP Resource Report Resource Website 100+ mentions |
STRAP (RRID:SCR_005675) | STRAP | software resource, data processing software, software application | 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 | 2026-02-14 02:05:21 | 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 or information resource, software resource, data set | 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 | 2026-02-14 02:05:32 | 2 | |||||||
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EASE: the Expression Analysis Systematic Explorer Resource Report Resource Website 50+ mentions |
EASE: the Expression Analysis Systematic Explorer (RRID:SCR_013361) | EASE | software resource, data processing software, software application | Windows(c) desktop software application, customizable and standalone, that facilitates the biological interpretation of gene lists derived from the results of microarray, proteomic, and SAGE experiments. Provides statistical methods for discovering enriched biological themes within gene lists, generates gene annotation tables, and enables automated linking to online analysis tools. Offers statistical models to deal with multi-test comparison problem. Platform: Windows compatible | gene, microarray, genome, gene ontology, statistical analysis, enrichment analysis, FASEB list |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Database for Annotation Visualization and Integrated Discovery |
NIAID | PMID:12734009 PMID:19131956 PMID:19033363 |
Free for academic use | nlx_149218 | SCR_013361 | Expression Analysis Systematic Explorer | 2026-02-14 02:05:32 | 94 | |||||
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DIANA-mirPath Resource Report Resource Website 100+ mentions |
DIANA-mirPath (RRID:SCR_017354) | web service, data analysis service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Pathway, analysis, statistics, assessment, miRNA, identify, regulatory, role, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Thessaly; Thessaly; Greece is provided by: DIANA Tools works with: KEGG works with: Gene Ontology |
European Social Fund ; John S. Latsis Public Benefit Foundation ; Development Grants For Research Institutions – KRIPIS ; General Secretariat for Research and Technology ; Ministry of Education ; Greece ; European Regional Development Fund |
PMID:25977294 PMID:19435746 PMID:22649059 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017495, biotools:diana-mirpath | http://diana.imis.athena-innovation.gr/DianaTools/ http://www.microrna.gr/miRPathv3 https://bio.tools/diana-mirpath |
http://www.microrna.gr/miRPathv2 | SCR_017354 | miRPath, miRPathv3, miRPathv2, DIANA-miRPath v2.0, DIANA-miRPath v3.0 | 2026-02-14 02:03:24 | 366 | ||||
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Functional Annotation Resource Report Resource Website 1+ mentions |
Functional Annotation (RRID:SCR_017519) | service resource | MGI GO project provides functional annotations for mouse gene products using Gene Ontology. Functional annotation using Gene Ontology (GO). | MGI, GO, functional, annotation, mouse, gene, product, Gene Ontology |
uses: Gene Ontology has parent organization: Mouse Genome Informatics (MGI) |
Free, Freely available | SCR_017519 | 2026-02-14 02:03:13 | 4 | ||||||||||
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Integrated Manually Extracted Annotation Resource Report Resource Website |
Integrated Manually Extracted Annotation (RRID:SCR_008876) | Integrated MEA, Integrated LinkOut, Manually Extracted Annotation, | data or information resource, database | A virtual database of annotations made by 50 database providers (April 2014) - and growing (see below), that map data to publication information. All NIF Data Federation sources can be part of this virtual database as long as they indicate the publications that correspond to data records. The format that NIF accepts is the PubMed Identifier, category or type of data that is being linked to, and a data record identifier. A subset of this data is passed to NCBI, as LinkOuts (links at the bottom of PubMed abstracts), however due to NCBI policies the full data records are not currently associated with PubMed records. Database providers can use this mechanism to link to other NCBI databases including gene and protein, however these are not included in the current data set at this time. (To view databases available for linking see, http://www.ncbi.nlm.nih.gov/books/NBK3807/#files.Databases_Available_for_Linking ) The categories that NIF uses have been standardized to the following types: * Resource: Registry * Resource: Software * Reagent: Plasmid * Reagent: Antibodies * Data: Clinical Trials * Data: Gene Expression * Data: Drugs * Data: Taxonomy * Data: Images * Data: Animal Model * Data: Microarray * Data: Brain connectivity * Data: Volumetric observation * Data: Value observation * Data: Activation Foci * Data: Neuronal properties * Data: Neuronal reconstruction * Data: Chemosensory receptor * Data: Electrophysiology * Data: Computational model * Data: Brain anatomy * Data: Gene annotation * Data: Disease annotation * Data: Cell Model * Data: Chemical * Data: Pathways For more information refer to Create a LinkOut file, http://neuinfo.org/nif_components/disco/interoperation.shtm Participating resources ( http://disco.neuinfo.org/webportal/discoLinkoutServiceSummary.do?id=4 ): * Addgene http://www.addgene.org/pgvec1 * Animal Imaging Database http://aidb.crbs.ucsd.edu * Antibody Registry http://www.neuinfo.org/products/antibodyregistry/ * Avian Brain Circuitry Database http://www.behav.org/abcd/abcd.php * BAMS Connectivity http://brancusi.usc.edu/ * Beta Cell Biology Consortium http://www.betacell.org/ * bioDBcore http://biodbcore.org/ * BioGRID http://thebiogrid.org/ * BioNumbers http://bionumbers.hms.harvard.edu/ * Brain Architecture Management System http://brancusi.usc.edu/bkms/ * Brede Database http://hendrix.imm.dtu.dk/services/jerne/brede/ * Cell Centered Database http://ccdb.ucsd.edu * CellML Model Repository http://www.cellml.org/models * CHEBI http://www.ebi.ac.uk/chebi/ * Clinical Trials Network (CTN) Data Share http://www.ctndatashare.org/ * Comparative Toxicogenomics Database http://ctdbase.org/ * Coriell Cell Repositories http://ccr.coriell.org/ * CRCNS - Collaborative Research in Computational Neuroscience - Data sharing http://crcns.org * Drug Related Gene Database https://confluence.crbs.ucsd.edu/display/NIF/DRG * DrugBank http://www.drugbank.ca/ * FLYBASE http://flybase.org/ * Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/ * Gene Ontology Tools http://www.geneontology.org/GO.tools.shtml * Gene Weaver http://www.GeneWeaver.org * GeneDB http://www.genedb.org/Homepage * Glomerular Activity Response Archive http://gara.bio.uci.edu * GO http://www.geneontology.org/ * Internet Brain Volume Database http://www.cma.mgh.harvard.edu/ibvd/ * ModelDB http://senselab.med.yale.edu/modeldb/ * Mouse Genome Informatics Transgenes ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenotypicAllele.rpt * NCBI Taxonomy Browser http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html * NeuroMorpho.Org http://neuromorpho.org/neuroMorpho * NeuronDB http://senselab.med.yale.edu/neurondb * SciCrunch Registry http://neuinfo.org/nif/nifgwt.html?tab=registry * NIF Registry Automated Crawl Data http://lucene1.neuinfo.org/nif_resource/current/ * NITRC http://www.nitrc.org/ * Nuclear Receptor Signaling Atlas http://www.nursa.org * Olfactory Receptor DataBase http://senselab.med.yale.edu/ordb/ * OMIM http://omim.org * OpenfMRI http://openfmri.org * PeptideAtlas http://www.peptideatlas.org * RGD http://rgd.mcw.edu * SFARI Gene: AutDB https://gene.sfari.org/autdb/Welcome.do * SumsDB http://sumsdb.wustl.edu/sums/ * Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat http://www.temporal-lobe.com/ * The Cell: An Image Library http://www.cellimagelibrary.org/ * Visiome Platform http://platform.visiome.neuroinf.jp/ * WormBase http://www.wormbase.org * YPED http://medicine.yale.edu/keck/nida/yped.aspx * ZFIN http://zfin.org | biomedical, bibliographic, linkout, literature |
is used by: NIF Data Federation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Gene Ontology Tools is related to: BAMS Connectivity is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: BioNumbers is related to: PubMed is related to: Brain Architecture Management System is related to: CellML Model Repository is related to: CHEBI is related to: Comparative Toxicogenomics Database (CTD) is related to: Coriell Cell Repositories is related to: Drug Related Gene Database is related to: DrugBank is related to: Gene Weaver is related to: Internet Brain Volume Database is related to: Cell Centered Database is related to: Brede Database is related to: ModelDB is related to: NeuronDB is related to: NeuroMorpho.Org is related to: Nuclear Receptor Signaling Atlas is related to: Cell Image Library (CIL) is related to: Animal Imaging Database is related to: Olfactory Receptor DataBase is related to: Glomerular Activity Response Archive is related to: CRCNS is related to: OMIM is related to: Rat Genome Database (RGD) is related to: Visiome Platform is related to: NIDA Data Share is related to: bioDBcore is related to: Addgene is related to: Antibody Registry is related to: Beta Cell Biology Consortium is related to: FlyBase is related to: SumsDB is related to: SciCrunch Registry is related to: Mouse Genome Informatics Transgenes is related to: NCBI Taxonomy is related to: OpenNeuro is related to: PeptideAtlas is related to: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat is related to: NIF Registry Automated Crawl Data is related to: AutDB is related to: Gene Expression Omnibus is related to: Gene Ontology is related to: Avian Brain Circuitry Database is related to: Zebrafish Information Network (ZFIN) is related to: GeneDB is related to: WormBase is related to: YPED has parent organization: Integrated |
PMID:20387131 PMID:18975149 |
Data are licensed by their respective owners. Use and distribution is subject to the Terms of Use by the original resource as well as the, Creative Commons Attribution License | nlx_149407 | http://neuinfo.org/nif/nifgwt.html?query=nlx_149407, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_149407-1 | SCR_008876 | Integrated Manually Extracted Annotation View, NIF Integrated LinkOut, NIF Integrated Manually Extracted Annotation, NIF LinkOut | 2026-02-14 02:06:10 | 0 | |||||
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GFINDer: Genome Function INtegrated Discoverer Resource Report Resource Website 1+ mentions |
GFINDer: Genome Function INtegrated Discoverer (RRID:SCR_008868) | GFINDer | data analysis service, production service resource, service resource, 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) | 2026-02-14 02:06:43 | 1 | |||||
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SynaptomeDB Resource Report Resource Website |
SynaptomeDB (RRID:SCR_000157) | SynaptomeDB | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Ontology-based knowledgebase for synaptic genes. These genes encode components of the synapse including neurotransmitters and their receptors, adhesion / cytoskeletal proteins, scaffold proteins, transporters, and others. It integrates various and complex data sources for synaptic genes and proteins., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, protein, pathway, synaptome, protein-protein interaction, synaptic gene, synapse, motif, presynaptic, postsynaptic, vesicle |
is related to: Gene Ontology has parent organization: Johns Hopkins University; Maryland; USA |
PMID:22285564 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157656 | SCR_000157 | 2026-02-14 02:05:31 | 0 | |||||||
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biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | data analysis software, software resource, data processing software, software application | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | biomaRt v 2.42.1 | 2026-02-14 02:03:30 | 2638 | ||||||
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AgingDB Resource Report Resource Website |
AgingDB (RRID:SCR_010226) | AgingDB | data repository, storage service resource, data or information resource, service resource, database | A database that stores information on the biomolecules which are modulated during aging and by caloric restriction (CR). To enhance its usefulness, data collected from studies of CR''''s anti-oxidative action on gene expression, oxidative stress, and many chronic age-related diseases are included. AgingDB is organized into two sections A) apoptosis and the various mitochondrial biomolecules that play a role in aging; B) nuclear transcription factors known to be_sensitive to oxidative environment. AgingDB features an imagemap of biomolecular signal pathways and visualized information that includes protein-protein interactions of biomolecules. Authorized users can submit a new biomolecule or edit an existing biomolecule to reflect latest developments. | oxidative stress, calorie restriction, pathway, biomolecule, signal pathway, interaction, gene, protein, protein-protein interaction, apoptosis, mitochondrial, nuclear transcription factor |
is related to: Gene Ontology has parent organization: Pusan National University; Busan; South Korea |
Aging | PMID:23604914 | The community can contribute to this resource | nlx_156773 | http://aging.pharm.pusan.ac.kr/AgingDB/ | SCR_010226 | Aging Database, Aging DB | 2026-02-14 02:01:43 | 0 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
