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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SOURCE Resource Report Resource Website 50+ mentions |
SOURCE (RRID:SCR_005799) | SOURCE | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool | genomic, functional annotation, ontology, gene expression, gene, genome, statistical analysis, bio.tools, FASEB list |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: SMD |
NIGMS ; NCI CA85129-04; NIGMS GM07365 |
PMID:12519986 | Restricted | biotools:source, nlx_149287 | https://login.stanford.edu/idp/profile/SAML2/Redirect/SSO?execution=e1s1 https://bio.tools/source |
SCR_005799 | 2026-02-16 09:46:41 | 69 | |||||
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Gene Class Expression Resource Report Resource Website 1+ mentions |
Gene Class Expression (RRID:SCR_005679) | Gene Class | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 29, 2012. Gene Class Expression allows functional annotation of SAGE data using the Gene Ontology database. This tool performs searches in the GO database for each SAGE tag, making associations in the selected GO category for a level selected in the hierarchy. This system provides user-friendly data navigation and visualization for mapping SAGE data onto the gene ontology structure. This tool also provides graphical visualization of the percentage of SAGE tags in each GO category, along with confidence intervals and hypothesis testing. Platform: Online tool | serial analysis of gene expression, functional annotation, annotation, gene expression, tag classification, gene ontology, gene, ontology, browser, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Sao Paulo; Sao Paulo; Brazil |
Center for Cell-Based Therapy/FAPESP ; CNPq |
PMID:16755502 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149119 | http://gdm.fmrp.usp.br/cgi-bin/gc/upload/upload.pl | SCR_005679 | GC Browser, Gene Classification Browser Tool, Gene Class expression: analysis tool of Gene Ontology terms with gene expression data | 2026-02-16 09:46:31 | 1 | ||||
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Onto-Compare Resource Report Resource Website 1+ mentions |
Onto-Compare (RRID:SCR_005669) | Onto-Compare | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | Microarrays are at the center of a revolution in biotechnology, allowing researchers to screen tens of thousands of genes simultaneously. Typically, they have been used in exploratory research to help formulate hypotheses. In most cases, this phase is followed by a more focused, hypothesis driven stage in which certain specific biological processes and pathways are thought to be involved. Since a single biological process can still involve hundreds of genes, microarrays are still the preferred approach as proven by the availability of focused arrays from several manufacturers. Since focused arrays from different manufacturers use different sets of genes, each array will represent any given regulatory pathway to a different extent. We argue that a functional analysis of the arrays available should be the most important criterion used in the array selection. We developed Onto-Compare as a database that can provide this functionality, based on the GO nomenclature. Compare commercially available microarrays based on GO. User account required. Platform: Online tool | microarray, gene, ontology, gene expression, data-mining, browser, visualization, analysis, compare, search engine, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, other analysis, compare commercially available microarrays based on go |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
PMID:12664686 PMID:15215428 |
Free for academic use | nlx_149108 | SCR_005669 | 2026-02-16 09:46:31 | 1 | |||||||
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Pathbase Resource Report Resource Website 10+ mentions |
Pathbase (RRID:SCR_006141) | Pathbase | web service, controlled vocabulary, image repository, data access protocol, image collection, data repository, database, storage service resource, software resource, ontology, service resource, data or information resource | Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development) | histopathology, photomicrograph, macroscopic, mutant, genetically manipulated, pathology, transgenic, rodent, mpath ontology, mouse pathology ontology, skinbase, genotype, skin, gene, tissue, hair, mutant mouse strain, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: University of Cambridge; Cambridge; United Kingdom is parent organization of: Mouse Pathology Ontology |
Lesion, Mutant mouse strain, Inbred mouse strain | North American Hair Research Society ; Ellison Medical Foundation ; European Union QLRI-1999-00320; European Union LSHG-CT-2006-037188; NCI CA089713; NCRR RR17436; NIH AR49288 |
PMID:20587689 PMID:15623888 PMID:14681470 |
Except where otherwise noted, Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported, Images on the database remain the property of the persons generously allowing their images to be used and are acknowledged within each record. Images should not be modified, Reproduced or disseminated without the express permission of the submitter. | biotools:pathbase, nlx_151637 | https://bio.tools/pathbase | SCR_006141 | Pathbase - European mutant mouse pathology database | 2026-02-16 09:46:38 | 11 | |||
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TreeBASE Resource Report Resource Website 500+ mentions |
TreeBASE (RRID:SCR_005688) | TreeBASE | data repository, database, storage service resource, service resource, data or information resource | Repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all kinds of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but will not be available to the public until they have passed peer review. | taxonomy, matrix, tree, topology, phylogeography, cladistic analysis, amino acid sequence, animal behavior, morphology, nucleotide sequence, genetics, dna, phylogeny, evolution, gene, population, web service, FASEB list |
is listed by: re3data.org is listed by: SoftCite has parent organization: NESCent - National Evolutionary Synthesis Center |
NSF DEB 9318325; NSF EF 0331654 |
Public, The community can contribute to this resource | r3d100010170, nif-0000-03587 | https://doi.org/10.17616/R3DK58 | SCR_005688 | TreeBASE - A Database of Phylogenetic Knowledge | 2026-02-16 09:46:31 | 806 | |||||
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Allen Institute for Brain Science Resource Report Resource Website 500+ mentions |
Allen Institute for Brain Science (RRID:SCR_006491) | portal, data or information resource, topical portal, atlas | Seattle based independent, nonprofit medical research organization dedicated to accelerating the understanding of how human brain works. Provides free data and tools to researchers and educators and variety of unique online public resources for exploring the nervous system. Integrates gene expression data and neuroanatomy, along with data search and viewing tools, these resources are openly accessible via the Allen Brain Atlas data portal. Provides Allen Mouse Brain, Allen Spinal Cord Atlas, Allen Developing Mouse Brain Atlas, Allen Human Brain Atlas,Allen Mouse Brain Connectivity Atlas, Allen Cell Type Database, The Ivy Glioblastoma Atlas Project (Ivy GAP), The BrainSpan Atlas of the Developing Human Brain. | Institute, embryonic, gene, expression, data, neuroscience, medical, research, neuroanatomy |
is listed by: Brain Architecture Project is related to: VisiGene Image Browser is related to: Recombinase (cre) Activity is related to: Cytosplore Viewer is related to: Mozak is related to: Microns Explorer is related to: CellLocator is related to: Seattle Alzheimer Disease Brain Cell Atlas is related to: Atlasplot is related to: Atlas Ontology Model is related to: Allen Brain Atlas-Driven Visualizations is related to: Brain heatmap is related to: Brainmapr is related to: ABAEnrichment is related to: Hippo-ATESC is related to: AllenDigger is related to: Cocoframer is related to: Process Genes List is related to: AIDAhisto is related to: MeshGen is related to: PET-CT mouse brain toolbox is related to: Multimodal Environment for Neuroimaging and Genomic Analysis is related to: goi2roimapping is related to: Spatiotemporal pattern Exploration of Brain is related to: Allen Mouse Brain ImageLoader is related to: ARA Tools is related to: allenCCF is related to: CutNII is related to: Genomic-and-High-Dimensional-Data is related to: Mouse_abi_tool is related to: Abagen is related to: VoxHunt is related to: ABI-expression-data-generator is related to: GCEA_FalsePositives is related to: Atlas Splitter is related to: ABAnnotate is related to: JuGEx is related to: Alleninf is related to: Atlas Alignment Meter is related to: Pinpoint is related to: Atlas Densities is related to: Atlas Direction Vectors is related to: SageBionetworks Portals is related to: brain-mapping is related to: BrainModules is related to: BrainRegionMarkers is related to: AP-histology is related to: Brainreg-segment is related to: Segmenting Brain Regions is related to: DeepSlice is related to: Cell Type Analysis Toolbox is related to: BrainGlobe Atlas API is related to: QUINT is related to: BRain area Input Output is related to: Brainreg is related to: MorphAPI is related to: Aligning Big Brains and Atlases is related to: Allen Brain Atlas Tools is related to: Brain Gene Expression Analysis toolbox is related to: Blue Brain Cell Atlas is related to: 3DBar is related to: Brainrender is related to: QuickNII is related to: Brain Architecture Project is related to: NeuroInfo is related to: Azimuth is related to: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas is related to: Integrated Brain Gene Expression is related to: MIRACL is related to: Linked Neuron Data is related to: BrainStars is related to: MouseLight Project is related to: Distributed Archives for Neurophysiology Data Integration is related to: Open Source Brain is related to: VisuAlign is related to: NS-Forest is related to: SHARCQ is related to: ModelDB is related to: Gene Expression Omnibus (GEO) is related to: NCBI database of Genotypes and Phenotypes (dbGap) is related to: CellFinder is related to: Nutil - Neuroimaging utilities is related to: NeuroMorpho.Org is related to: Semi-Manual Alignment to Reference Templates is related to: MeshView is related to: Single Cell Portal is related to: Brain Image Library is related to: UCSC Cell Browser is related to: National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) is related to: cellxgene is related to: Atlas Ontology Model has parent organization: Allen Institute is parent organization of: Allen Mouse Brain Reference Atlas is parent organization of: Allen Institute for Brain Science Sleep Study is parent organization of: Allen Developing Mouse Brain Atlas is parent organization of: Allen Institute for Brain Science Transgenic Mouse Study is parent organization of: Allen Institute Neurowiki is parent organization of: Ivy Glioblastoma Atlas Project is parent organization of: Allen Brain Atlas API is parent organization of: Allen Human Brain Atlas is parent organization of: Allen Mouse Spinal Cord Atlas is parent organization of: Allen Institute Mouse Diversity Study is parent organization of: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) is parent organization of: Allen Mouse Brain Connectivity Atlas is parent organization of: ABA Adult Mouse Brain Ontology is parent organization of: NIH Blueprint NHP Atlas is parent organization of: Aging Dementia and Traumatic Brain Injury Study is parent organization of: ACQ4 is parent organization of: CellTax vignette is parent organization of: Allen Brain Atlas is parent organization of: BRAIN Cell Data Center is parent organization of: BICCN Cell Registry is parent organization of: ABA Mouse Brain: Atlas is parent organization of: Allen Institute Mouse Whole Cortex and Hippocampus SMART-seq is parent organization of: Allen Mouse Brain Common Coordinate Framework is parent organization of: Allen Mouse Reference Atlas Ontology is parent organization of: BICCN is parent organization of: BRAIN Initiative Cell Atlas Network is parent organization of: Brain Knowledge Platform |
nif-0000-00146 | SCR_006491 | The Allen Institute for Brain Science, Allen Mouse Brain | 2026-02-16 09:46:43 | 759 | |||||||||
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HDBase Resource Report Resource Website |
HDBase (RRID:SCR_007132) | HDBase | data set, topical portal, portal, data or information resource, disease-related portal | A community website for Huntington''s Disease (HD) research that currently contains Y2H and Mass spectrometry protein-protein interaction data centered around the HD protein (huntingtin) and information on therapeutic studies in mouse. Also available are raw Human and Mouse Affymetrix Microarray data. The protein interaction data is from several sources, including interactions curated from the literature by ISB staff, experimentally determined interactions produced by Bob Hughes and colleagues at Prolexys (currently password protected), and interactions reported in a recent publication by Goehler et al from Eric Wanker''s lab. Content areas that may be covered by the site include the following: * Therapeutic studies in mouse, primarily drug screens. * HD mouse models with a focus on timelines of disease progression. * Antibodies used in HD research. * Microarray gene expression studies. * Genes and proteins relevant to HD research. This includes HD itself, the growing list of proteins thought to interact directly or indirectly with huntingtin (Htt), and other genes and proteins implicated in the disease process. * Molecular pathways thought to be involved in the disease process. * Timelines of disease for Mouse models | drug, gene expression, huntingtin, mass spectrometry, microarray, protein interaction, protein-protein interaction, y2h, mouse model, treatment, disease, phenotype, brain, striatum, adipose, muscle, gene, protein, antibody, pathway |
uses: Cytoscape has parent organization: Institute for Systems Biology; Washington; USA |
Huntington''s disease, Control | Hereditary Disease Foundation | nif-0000-00153 | SCR_007132 | HDBase - A Community Website for Huntingtons Disease Research, HDBase - A Community Website for Huntington''s Disease Research | 2026-02-16 09:46:53 | 0 | ||||||
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Genetic and Rare Diseases Information Center Resource Report Resource Website 10+ mentions |
Genetic and Rare Diseases Information Center (RRID:SCR_008695) | GARD | data or information resource, topical portal, disease-related portal, portal | Genetic and Rare Diseases Information Center (GARD) is a collaborative effort of two agencies of the National Institutes of Health, The Office of Rare Diseases Research (ORDR) and the National Human Genome Research Institute (NHGRI) to help people find useful information about genetic conditions and rare diseases. GARD provides timely access to experienced information specialists who can furnish current and accurate information about genetic and rare diseases. So far, GARD has responded to 27,635 inquiries on about 7,147 rare and genetic diseases. Requests come not only from patients and their families, but also from physicians, nurses and other health-care professionals. GARD also has proved useful to genetic counselors, occupational and physical therapists, social workers, and teachers who work with people with a genetic or rare disease. Even scientists who are studying a genetic or rare disease and who need information for their research have contacted GARD, as have people who are taking part in a clinical study. Community leaders looking to help people find resources for those with genetic or rare diseases and advocacy groups who want up-to-date disease information for their members have contacted GARD. And members of the media who are writing stories about genetic or rare diseases have found the information GARD has on hand useful, accurate and complete. GARD has information on: :- What is known about a genetic or rare disease. :- What research studies are being conducted. :- What genetic testing and genetic services are available. :- Which advocacy groups to contact for a specific genetic or rare disease. :- What has been written recently about a genetic or rare disease in medical journals. GARD information specialists get their information from: :- NIH resources. :- Medical textbooks. :- Journal articles. :- Web sites. :- Advocacy groups, and their literature and services. :- Medical databases. | genetic, disease, information, genome, human, rare disease, health, physician, counselor, gene, journal, medical | has parent organization: National Institutes of Health | Office of Rare Diseases Research ; NHGRI |
nif-0000-37627 | SCR_008695 | Genetic Rare Diseases Information Center | 2026-02-16 09:47:15 | 14 | |||||||
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Pig Genome Mapping Resource Report Resource Website |
Pig Genome Mapping (RRID:SCR_012884) | PiGMaP | image collection, data or information resource, database, atlas | Map of identifyied genes controlling traits of economic and welfare significance in the pig. The project objectives were to produce a genetic map with markers spaced at approximately 20 centiMorgan intervals over at least 90% of the pig genome; to produce a physical map with at least one distal and one proximal landmark locus mapped on each porcine chromosome arm and also genetically mapped; to develop a flow karyotype for the pig based on FACS sorted chromosomes; to develop PCR based techniques to enable rapid genotyping for polymorphic markers; to evaluate synteny conservation between pigs, man, mice and cattle; to develop and evaluate the statistical techniques required to analyze data from QTL mapping experiments and to plan and initiate the mapping of QTLs in the pig; to map loci affecting traits of economic and biological significance in the pig; and to develop the molecular tools to allow the future identification and cloning of mapped loci. Animal breeders currently assume that economically important traits such as growth, carcass composition and reproductive performance are controlled by an infinite number of genes each of infinitessimal effect. Although this model is known to be unrealistic, it has successfully underpinned the genetic improvement of livestock, including pigs, over recent decades. A map of the pig genome would allow the development of more realistic models of the genetic control of economic traits and the ultimately the identification of the major trait genes. This would allow the development of more efficient marker assisted selection which may be of particular value for traits such as disease resistance and meat quality. | gene, genetic, artificial chromosome, bacteriophage, biological, carcass, cattle, cdna, comparative, disease, genome, genotype, growth, human, karyotpe, linkage, livestock, locus, map, mapping, marker, mice, molecular, p1, pig, quality, quantitative, sus scrofa, trait, yeast | has parent organization: Roslin Institute | PMID:7749223 | nif-0000-20987 | http://www.projects.roslin.ac.uk/pigmap/pigmap.html | SCR_012884 | PGM | 2026-02-16 09:48:31 | 0 | ||||||
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Ascidian Network for InSitu Expression and Embryological Data Resource Report Resource Website 50+ mentions |
Ascidian Network for InSitu Expression and Embryological Data (RRID:SCR_013030) | ANISEED | data repository, database, storage service resource, software resource, service resource, data or information resource |
Database of ascidian embryonic development at the level of the genome (cis-regulatory sequences, gene expression, protein annotation), of the cell (morphology, fate, induction, lineage) or of the whole embryo (anatomy, morphogenesis). Currently, four organism models are described in Aniseed: Ciona intestinalis, Ciona savignyi, Halocynthia roretzi and Phallusia mammillata. This version supports four sets of Ciona intestinalis transcript models: JGI v1.0, KyotoGrail 2005, KH and ENSEMBL, all functionally annotated, and grouped into Aniseedv3.0 gene models. Users can explore their expression profiles during normal or manipulated development, access validated cis-regulatory regions, get the molecular tools used to assay gene function, or all articles related to the function, or regulation of a given gene. Known transcriptional regulators and targets are listed for each gene, as are the gene regulatory networks acting in individual anatomical territories. ANISEED is a community tool, and the direct involvement of external contributors is important to optimize the quality of the submitted data. Virtual embryo: The 3D Virtual embryo is available to download in the download section of the website. |
embryology, embryo, gene, genome, anatomy, cis-regulatory, development, morphogenesis, morphology, protein, molecular neuroanatomy resource, cis-regulatory sequence, gene expression, protein annotation, cell, expression profile, function, regulation, blast, visualization, data analysis service, clone, FASEB list | CNRS ; French Ministry of Research ; Marseille-Nice Genopole ; ARC ; European Network QLK3-CT-2001-01890 |
PMID:20647237 | nif-0000-10155 | http://crfb.univ-mrs.fr/aniseed/index.php | SCR_013030 | Aniseed database | 2026-02-16 09:48:15 | 60 | ||||||
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CLC Genomics Workbench Resource Report Resource Website 100+ mentions |
CLC Genomics Workbench (RRID:SCR_011853) | software application, data processing software, data visualization software, data analysis software, software resource | Commercially available software for visualization and analysis of next generation sequencing data. Used for viewing, exploring, and sharing of NGS analysis results. Complete toolkit for genomics, transcriptomics, epigenomics, and metagenomics in one program. | ngs, next, generation, sequencing, gene, rna, visualisation, analysis |
is listed by: OMICtools is listed by: SoftCite works with: CLC Genomics Server |
Restricted | SCR_016245, OMICS_01124 | SCR_011853 | 2026-02-16 09:48:03 | 181 | |||||||||
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SNPFILE Resource Report Resource Website 1+ mentions |
SNPFILE (RRID:SCR_009402) | software resource, software application, software toolkit, software library | Software library and API for manipulating large SNP datasets with associated meta-data, such as marker names, marker locations, individuals'' phenotypes, etc. in an I/O efficient binary file format. In its core, SNPFile assumes very little about the metadata associated with markers and individuals, but leaves this up to application program protocols. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, linux, unix | is listed by: Genetic Analysis Software | nlx_154641 | SCR_009402 | 2026-02-16 09:47:23 | 1 | ||||||||||
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FunDO Resource Report Resource Website 10+ mentions |
FunDO (RRID:SCR_001725) | FunDO | production service resource, service resource, data analysis service, analysis service resource | Tool that takes a list of genes and finds relevant diseases based on statistical analysis of the Disease Ontology annotation database. It accepts Entrez gene ids or gene symbols, separated by tabs, newlines, or commas. This list of genes can be obtained by microarray, proteomics, sequencing or other high-throughput screening methods. | gene, disease, ontology, function |
is related to: KOBAS is related to: Human Disease Ontology has parent organization: Northwestern University; Illinois; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10225 | SCR_001725 | FunDO - Exploring Genes Using Functional Disease Ontology Annotations | 2026-02-16 09:45:34 | 11 | |||||||
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HOMOZYGOSITYMAPPER Resource Report Resource Website 100+ mentions |
HOMOZYGOSITYMAPPER (RRID:SCR_001714) | HomozygosityMapper | production service resource, service resource, data analysis service, analysis service resource | A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, genotype, homozygosity score, homozygosity, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
PMID:19465395 | Free, Freely Available | nlx_154069, biotools:homozygositymapper, OMICS_00123 | https://bio.tools/homozygositymapper | SCR_001714 | 2026-02-16 09:45:33 | 121 | ||||||
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Human Gene Mutation Database Resource Report Resource Website 1000+ mentions |
Human Gene Mutation Database (RRID:SCR_001621) | HGMD | data or information resource, database | Curated database of known (published) gene lesions responsible for human inherited disease. | gene, disease, gene lesion, mutation, deletion, insertion, duplication, rearrangement, nuclear gene, functional polymorphism, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: BIOBASE Corporation has parent organization: Cardiff University; Wales; United Kingdom |
Inherited disease | PMID:22948725 PMID:20368137 PMID:20038494 PMID:19348700 PMID:18428754 PMID:18245393 PMID:12754702 PMID:10612821 PMID:9399854 PMID:9066272 PMID:8882888 |
Free, Freely available | nlx_153887, SCR_001888, biotools:hgmd, nif-0000-10459, OMICS_00281 | http://www.hgmd.cf.ac.uk/ac/index.php https://bio.tools/hgmd |
SCR_001621 | The Human Gene Mutation Database, The Human Gene Mutation Database at the Institute of Medical Genetics in Cardiff | 2026-02-16 09:45:33 | 2462 | ||||
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Phevor Resource Report Resource Website 1+ mentions |
Phevor (RRID:SCR_002273) | Phevor | production service resource, service resource, data analysis service, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Tool that integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles. It works by combining knowledge resident in multiple biomedical ontologies with the outputs of variant prioritization tools. It does so using an algorithm that propagates information across and between ontologies. This process enables Phevor to accurately reprioritize potentially damaging alleles identified by variant prioritization tools in light of gene function, disease, and phenotype knowledge. Phevor is especially useful for single exome and family trio-based diagnostic analyses, the most commonly occurring clinical scenarios, and ones for which existing personal-genomes diagnostic tools are most inaccurate and underpowered. Phevor not only improves diagnostic accuracy for individuals presenting with established disease phenotypes, but also for those with previously undescribed and atypical disease presentations. Importantly, Phevor is not limited to known diseases, or known disease-causing alleles. | genome interpretation, variant prioritization, disease gene prioritization, phenotype, gene function, disease, genomic, disease-causing allele, gene, function, allele | has parent organization: University of Utah School of Medicine; Utah; USA | PMID:24702956 | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000139 | SCR_002273 | Phenotype Driven Variant Ontological Re-Ranking Tool | 2026-02-16 09:45:43 | 9 | ||||||
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MADELINE Resource Report Resource Website 1+ mentions |
MADELINE (RRID:SCR_001979) | MADELINE | service resource, software application, software resource | Software tool designed for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. It converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review. | gene, genetic, genomic, c, unix, solaris, freebsd, openbsd, macos, ms-windows, cygwin, linux, pedigree, draw, linkage association, family association |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:17488757 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154446, OMICS_00210 | http://eyegene.ophthy.med.umich.edu/#madeline | SCR_001979 | Madeline | 2026-02-16 09:45:38 | 5 | |||||
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ECARUCA Project Resource Report Resource Website 1+ mentions |
ECARUCA Project (RRID:SCR_000797) | data or information resource, database, group | A database of cytogenetic and clinical information on rare chromosomal disorders, including microdeletions and microduplications. The database is meant to be easily accessible for all participants, to improve patient care and collaboration between genetic centers, and collect the results of research and clinical features. The acronym ECARUCA stands for "European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations". | cytogenetic, clinical, chromosome, gene, microdeletion, microduplication, europe, aberrations, genetics | European Union FP5 | PMID:16829349 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31901 | SCR_000797 | ECARUCA | 2026-02-16 09:45:20 | 3 | |||||||
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ERGO Resource Report Resource Website 50+ mentions |
ERGO (RRID:SCR_001243) | ERGO | production service resource, service resource, data analysis service, analysis service resource | A web-based genome analysis platform that integrates proprietary functional genomic data, metabolic reconstructions, expression profiling, and biochemical and microbiological data with publicly available information. Focused on microbial genomics, it provides better and faster identification of gene function across all organisms. Building upon a comprehensive genomic database integrated with a collection of microbial metabolic and non-metabolic pathways and using proprietary algorithms, it assigns functions to genes, integrates genes into pathways, and identifies previously unknown or mischaracterized genes, cryptic pathways and gene products. . * Automated and manual annotation of genes and genomes * Analysis of metabolic and non-metabolic pathways to understand organism physiology * Comparison of multiple genomes to identify shared and unique features and SNPs * Functional analysis of gene expression microarray data * Data-mining for target gene discovery * In silico metabolic engineering and strain improvement | genome analysis, genome, annotation, database, software, comparative genomics, function, gene, pathway, gene expression, microarray, FASEB list | is listed by: OMICtools | Restricted | OMICS_02097 | SCR_001243 | ERGO Genome Analysis and Discovery System, ERGO Genome Analysis & Discovery System | 2026-02-16 09:45:26 | 66 | |||||||
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INMEX Resource Report Resource Website 10+ mentions |
INMEX (RRID:SCR_004173) | INMEX | production service resource, service resource, data analysis service, analysis service resource | A web-based tool to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module supports flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows researchers to combine multiple data sets based on P-values, effect sizes, rank orders and other features. The significant genes can be examined in functional analysis module for enriched Gene Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support for common gene/metabolite identifiers (IDs), as well as 45 popular microarray platforms for human, mouse and rat. Complex operations are performed through a user-friendly web interface in a step-by-step manner. | gene expression, meta-analysis, metabolomics, pathway, gene, metabolite, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: KEGG is related to: Human Metabolome Database has parent organization: University of British Columbia; British Columbia; Canada |
Killam Trust ; Canadian Institutes of Health Research |
PMID:23766290 | Acknowledgement requested | biotools:inmex, OMICS_01546 | https://bio.tools/inmex | SCR_004173 | INtegrative Meta-analysis of EXpression data, INMEX - INtegrative Meta-analysis of EXpression data | 2026-02-16 09:46:17 | 19 |
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Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
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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.
