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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Jackson Laboratory Cytogenetic Models Resource Resource Report Resource Website 1+ mentions |
Jackson Laboratory Cytogenetic Models Resource (RRID:SCR_003270) | biomaterial supply resource, material resource, organism supplier | Maintains and distributes chromosome aberration stocks that provide primarily mouse models for Down syndrome. The Resource currently provides models for Down syndrome research, including: Rb(6.16)24Lub x Rb(16.17)7Bnr F1 hybrids that are used to produce Chr 16 trisomy (Ts16) embryos, which have many of the fetal developmental features of DS, and; Ts(1716)65Dn, segmental trisomy mice that survive to adulthood and have many of the features of DS. The Resource also includes stocks with selected reciprocal translocations involving Chr 16 and some Chr 16 transgenic stocks. In addition, a large number of Robertsonian chromosome stocks are held as frozen embryos in the Cryopreservation Resource. Each mouse chromosome is present in at least two different Robertsonian chromosomes in these strains so that specific trisomies for each of the 19 mouse autosomes can be produced. Breeding pairs and individual mice are provided. | chromosome mutation, mouse model, down syndrome model, transgenic mouse | has parent organization: Jackson Laboratory | Down syndrome | NICHD contract N01-HD-73265 | Free, Available for download, Freely available | nif-0000-01258 | https://www.jax.org/research-and-faculty/resources/cytogenetic-and-down-syndrome-models-resource | SCR_003270 | Jackson Lab: Cytogenetic Models Resource, Cytogenetic Models Resource | 2026-10-17 01:25:50 | 1 | |||||
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BrainInfo Resource Report Resource Website 10+ mentions |
BrainInfo (RRID:SCR_003142) | atlas, data or information resource, database, narrative resource, portal, standard specification, topical portal | Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures. | brain, neuroanatomy |
is used by: NIF Data Federation is listed by: Biositemaps is related to: INIA19 Primate Brain Atlas has parent organization: University of Washington; Seattle; USA has parent organization: University of California at San Diego; California; USA |
The Human Brain Project ; NIBIB ; NLM LM/OD-06243; NIH Office of the Director LM/OD-06243; NIMH MHO69259; NCRR RR-00166 |
PMID:21789500 PMID:21163300 PMID:18368361 PMID:15055392 |
Free, Freely available | nif-0000-00019 | SCR_003142 | Brain Info | 2026-10-17 01:25:46 | 16 | ||||||
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Mouse Phenome Database (MPD) Resource Report Resource Website 100+ mentions |
Mouse Phenome Database (MPD) (RRID:SCR_003212) | MPD | data or information resource, data repository, database, experimental protocol, narrative resource, service resource, storage service resource | Database enables integration of genomic and phenomic data by providing access to primary experimental data, data collection protocols and analysis tools. Data represent behavioral, morphological and physiological disease-related characteristics in naive mice and those exposed to drugs, environmental agents or other treatments. Collaborative standardized collection of measured data on laboratory mouse strains to characterize them in order to facilitate translational discoveries and to assist in selection of strains for experimental studies. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect., protocols, projects and publications, and SNP, variation and gene expression studies. Provides tools for online analysis. Data sets are voluntarily contributed by researchers from variety of institutions and settings, or retrieved by MPD staff from open public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys. MPD collects data on classical inbred strains as well as any fixed-genotype strains and derivatives that are openly acquirable by the research community. New panels include Collaborative Cross (CC) lines and Diversity Outbred (DO) populations. Phenotype data include measurements of behavior, hematology, bone mineral density, cholesterol levels, endocrine function, aging processes, addiction, neurosensory functions, and other biomedically relevant areas. Genotype data are primarily in the form of single-nucleotide polymorphisms (SNPs). MPD curates data into a common framework by standardizing mouse strain nomenclature, standardizing units (SI where feasible), evaluating data (completeness, statistical power, quality), categorizing phenotype data and linking to ontologies, conforming to internal style guides for titles, tags, and descriptions, and creating comprehensive protocol documentation including environmental parameters of the test animals. These elements are critical for experimental reproducibility. | female, genomic location, genotype, inbred strain, male, mouse strain, phenome, phenotype, qtl, reference data, single-nucleotide polymorphism, strain allele, strain characteristic, strain, trait, gene expression, variation, hypothesis testing, data set, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: Integrated Datasets is used by: NIH Heal Project is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Special Mouse Strains Resource is related to: Vertebrate Trait Ontology is related to: GenomeMUSter has parent organization: Jackson Laboratory |
NHGRI HG003057; NHLBI HL66611; NIA AG025707; NIA AG038070; NIDA ; NIDA DA028420; NIMH MH071984 |
PMID:24243846 PMID:22102583 PMID:18987003 PMID:17151079 |
Free, Freely available | biotools:mpd, nif-0000-03160, r3d100010101 | https://bio.tools/mpd, https://doi.org/10.17616/R3PC7F | http://www.jax.org/phenome | SCR_003212 | Mouse Phenome Database | 2026-10-17 01:25:26 | 230 | |||
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Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) Resource Report Resource Website 10000+ mentions |
Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) | RCSB PDB | data or information resource, data repository, database, service resource, storage service resource | Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results. | 3-dimensional, annotation, molecule, nucleic acid, protein, visualization, sequence, function, macromolecule, ligand, model, dna, x-ray crystallography, ribosome, structure, oncogene, nucleic acids, molecular structure, cryomicroscopy, gold standard, FASEB list |
is used by: Structural Genomics Consortium is used by: Ligand Expo is used by: DARC - Database for Aligned Ribosomal Complexes is used by: FireDB is used by: Protein Data Bank Bind Database is used by: Protein Data Bank Site is used by: NIF Data Federation is used by: ChannelPedia is used by: MobiDB is used by: BALBES is used by: Structural Antibody Database is used by: BioLiP is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is affiliated with: EMDataResource.org is affiliated with: ConSurf Database is related to: pdb-data is related to: PDB2MultiGif is related to: GlyProt is related to: pdb-care is related to: pdb2linucs is related to: GlyVicinity is related to: GlyTorsion is related to: GlySeq is related to: AffinDB is related to: StatAlign is related to: Community Structure-Activity Resource is related to: Binding MOAD is related to: ConSurf Database is related to: glycosciences.de is related to: DOMINE: Database of Protein Interactions is related to: Jenalib: Jena Library of Biological Macromolecules is related to: SynSysNet is related to: EMDataResource.org is related to: PDBe - Protein Data Bank in Europe is related to: TFinDIT is related to: HOLLOW is related to: ccPDB - Compilation and Creation of datasets from PDB is related to: DOMMINO - Database Of MacroMolecular INteractiOns is related to: InterEvol database is related to: Polbase is related to: PoSSuM is related to: ProtChemSI is related to: RNA CoSSMos is related to: PDBsum is related to: Worldwide Protein Data Bank (wwPDB) is related to: canSAR is related to: CAPS Database is related to: Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING is related to: Combinatorial Extension (CE) is related to: Metalloprotein Site Database is related to: PDBj - Protein Data Bank Japan is related to: Statistical Torsional Angles Potentials of NMR Refinement Database is related to: Metalloprotein Ligand Interaction Database is related to: CARP is related to: PDBTM is related to: RNA FRABASE - RNA FRAgments search engine and dataBASE is related to: AmiGO is related to: ConsensusPathDB is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: DNA DataBank of Japan (DDBJ) is related to: FlyMine is related to: NCBI Protein Database is related to: NCBI Nucleotide is related to: FunTree is related to: IndelFR - Indel Flanking Region Database is related to: NMR Restraints Grid is related to: Enzyme Structures Database is related to: Electron Microscopy Data Bank at PDBe (MSD-EBI) is related to: Worldwide Protein Data Bank (wwPDB) is related to: DNA DataBank of Japan (DDBJ) is related to: PDBe - Protein Data Bank in Europe is related to: MINAS - Metal Ions in Nucleic AcidS is related to: PDBj - Protein Data Bank Japan has parent organization: University of California at San Diego; California; USA has parent organization: Rutgers University; New Jersey; USA is parent organization of: RCSB PDB Software Tools is parent organization of: Protein Data Bank Markup Language is parent organization of: Ligand Expo works with: CellPhoneDB |
DOE ; NIH ; NSF DBI-1338415 |
PMID:12037327 | Public, Acknowledgement requested | nif-0000-00135, SCR_017379, r3d100010327 | http://www.rcsb.org, http://www.pdb.org, | http://www.rcsb.org/pdb/ | SCR_012820 | RCSB, Research Collaboratory for Structural Bioinformatics Protein Data Bank, The Protein Data Bank, PDB, Protein Databank, RCSB Protein Data Bank, Protein Data Bank | 2026-10-17 01:28:06 | 12459 | |||
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Flash Gviewer Resource Report Resource Website 1+ mentions |
Flash Gviewer (RRID:SCR_012870) | Flash GViewer | software resource | Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes and QTLs associated with a specific phenotype, etc. rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. In addition the bands on the chromosomes can link to defineable URL and new region selection sliders can be used to select a specific chromosome region and then link out to a genome browser for higher resolution information. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts. This tool is not GO-specific, but was built for the purpose of viewing GO annotation data. Platform: Online tool | visualization, chromosome, video, gene, qtl, genome, navitgation, phenotype, ontology or annotation visualization |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Medical College of Wisconsin; Wisconsin; USA |
Free for academic use | nlx_149333 | http://gmod.org/flashgviewer | SCR_012870 | 2026-10-17 01:28:32 | 2 | |||||||
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MitoBreak Resource Report Resource Website 10+ mentions |
MitoBreak (RRID:SCR_012949) | MitoBreak | data or information resource, data repository, database, service resource, storage service resource | Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements. | mitochondrial dna rearrangement, mitochondrial dna, deletion, duplication, linear, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24170808 | Free, The community can contribute to this resource | biotools:mitobreak, OMICS_01640 | https://bio.tools/mitobreak | SCR_012949 | 2026-10-17 01:28:10 | 11 | ||||||
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Annmap Resource Report Resource Website 1+ mentions |
Annmap (RRID:SCR_011783) | Annmap | data or information resource, database, software resource | A genome browser that includes mappings between genomic features and Affymetrix microarrays. Associated with annmap is: * a Bioconductor package, annmap that provides programmatic access to the underlying MySQL database tables (which are freely available for download on this site) * xmapbridge, a Bioconductor package that outputs numeric data in a form suitable for presentation in the browser. This is supported by XMapBridge, a Java client that sits on the local desktop and performs the graph rendering for the browser. | is listed by: OMICtools | Cancer Research UK ; Cancer Research UK Manchester Institute |
OMICS_00900 | SCR_011783 | 2026-10-17 01:28:18 | 6 | |||||||||
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IITC Life Sciences: Plantar Test Apparatus Resource Report Resource Website 1+ mentions |
IITC Life Sciences: Plantar Test Apparatus (RRID:SCR_012152) | Plantar Test Apparatus | instrument resource | The IITC Plantar Analgesia Meter for thermal paw can be used on 12 mice, 6 rats and other animals (cats, rabbits) unrestrained when testing for narcotic drugs. Experiments are easy to perform, simply slide the test head under test subject, align the heat source via our exclusive guide light (idle state) by the attached, adjustable, angled mirror on test head to test subject and perform tests. | testing apparatus, hargreaves, paw radiant heat assay, toe toaster, hargreaves method, hardware, instrument, equipment | https://drive.google.com/file/d/1b8M9g_eTkJqkJzUFYijHFNj6yW9HLIWa/view?usp=drivesdk | rid_000075 | https://www.iitcinc.com/pdf/Plantar%20Test%20Hargreaves.pdf | SCR_012152 | Plantar Test Apparatus for Mice and Rats, Plantar Test Apparatus (Hargreaves Method) for Mice and Rats | 2026-10-17 01:28:39 | 2 | |||||||
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InParanoid: Eukaryotic Ortholog Groups Resource Report Resource Website 100+ mentions |
InParanoid: Eukaryotic Ortholog Groups (RRID:SCR_006801) | InParanoid | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Collection of pairwise comparisons between 100 whole genomes generated by a fully automatic method for finding orthologs and in-paralogs between TWO species. Ortholog clusters in the InParanoid are seeded with a two-way best pairwise match, after which an algorithm for adding in-paralogs is applied. The method bypasses multiple alignments and phylogenetic trees, which can be slow and error-prone steps in classical ortholog detection. Still, it robustly detects complex orthologous relationships and assigns confidence values for in-paralogs. The original data sets can be downloaded. | protein, ortholog, genome, drosophila pseudoobscura, duplication, entamoeba histolytica, escherichia colik12, eukaryotic, gasterosteus aculeatus, gene, aedes aegypti, apis mellifera, bos taurus, caenorhabditis remanei, candida glabrata, canis familiaris, ciona intestinalis, cryptococcus neoformans, debaromyces hansenii, dictyostelium discoideum, genomic, homolog, inparalog, kluyveromyces lactis, macaca mulatta, monodelphis domestica, orthology, oryza sativa, outparalog, proteome, tetraodon nigroviridis, xenopus tropicalis, blast, proteome, ortholog cluster, cluster, in-paralog, paralog, automatic clustering, genome comparison, FASEB list | has parent organization: Stockholm University; Stockholm; Sweden | Swedish Research Council ; Karolinska Institutet; Stockholm; Sweden ; Pfizer Corporation |
PMID:19892828 PMID:18055500 PMID:15608241 PMID:11743721 |
Acknowledgement requested | nif-0000-03024 | http://www.cgb.ki.se/inparanoid/ | SCR_006801 | Inparanoid eukaryotic ortholog database | 2026-10-17 01:26:42 | 189 | ||||
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PeptideAtlas Resource Report Resource Website 500+ mentions |
PeptideAtlas (RRID:SCR_006783) | PeptideAtlas | data or information resource, data repository, database, service resource, storage service resource | Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. The raw data, search results, and full builds can be downloaded for other uses. All results of sequence searching are processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner ensuring a high quality database. All peptides are mapped to Ensembl and can be viewed as custom tracks on the Ensembl genome browser. The long term goal of the project is full annotation of eukaryotic genomes through a thorough validation of expressed proteins. The PeptideAtlas provides a method and a framework to accommodate proteome information coming from high-throughput proteomics technologies. The online database administers experimental data in the public domain. You are encouraged to contribute to the database. | proteomics, peptide, mass spectrometry, annotation, eukaryotic, genome, peptide sequence, high-throughput mass spectrometry, ensembl, peptideprophet, protein sequence, blood plasma, protein, eukaryotic cell, dna, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: ProteomeXchange is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Biositemaps is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: ProteomeXchange is related to: NIH Data Sharing Repositories is related to: Integrated Manually Extracted Annotation has parent organization: Institute for Systems Biology; Washington; USA |
NCI ; NHGRI ; NIGMS |
PMID:20013378 PMID:23215161 PMID:16381952 PMID:15642101 |
Public, The community can contribute to this resource, Acknowledgement requested | nif-0000-03266, r3d100010889, biotools:peptideatlas | https://bio.tools/peptideatlas, https://doi.org/10.17616/R3BK61 | SCR_006783 | Peptide Atlas, PeptideAtlas | 2026-10-17 01:26:47 | 511 | ||||
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Chemical Effects in Biological Systems (CEBS) Resource Report Resource Website 10+ mentions |
Chemical Effects in Biological Systems (CEBS) (RRID:SCR_006778) | CEBS | data or information resource, data repository, database, service resource, storage service resource | Repository for toxicogenomics data, including study design and timeline, clinical chemistry and histopathology findings and microarray and proteomics data. Data derived from studies of chemicals and of genetic alterations, and is compatible with clinical and environmental studies. Data relating to environmental health, pharmacology, and toxicology. It is not necessary to have microarray data, but study design and phenotypic anchoring data are required.CEBS contains raw microarray data collected in accordance with MIAME guidelines and provides tools for data selection, pre-processing and analysis resulting in annotated lists of genes of interest. Biomedical Investigation Database is another component of CEBS system. used to load and curate study data prior to export to CEBS, in addition to capturing and displaying novel data types such as PCR data, or additional fields of interest, including those defined by the HESI Toxicogenomics Committee. BID has been shared with Health Canada and the US Environmental Protection Agency. | caenorhabditis elegans, chemical study, microarray, genetic alteration, toxicogenomics, environmental health, study design, timeline, clinical chemistry, histopathology, proteomics, chemical, clinical, microarray hybridization, gel image, phenotype, pharmacology, toxicology |
is recommended by: National Library of Medicine has parent organization: National Institute of Environmental Health Sciences |
NIEHS ; NIGMS |
PMID:17962311 | Free, Freely available | nif-0000-02649, r3d100010314 | https://doi.org/10.17616/R3W02M | SCR_006778 | CEBS, Chemical Effects in Biological Systems (CEBS), Chemical Effects in Biological Systems | 2026-10-17 01:26:47 | 19 | ||||
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HAMSTeRS - The Haemophilia A Mutation Structure Test and Resource Site Resource Report Resource Website 1+ mentions |
HAMSTeRS - The Haemophilia A Mutation Structure Test and Resource Site (RRID:SCR_006883) | HAMSTeRS, HADB, HADB/HAMSTeRS, HADB / HAMSTeRS | data or information resource, data repository, database, service resource, storage service resource |
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 27, 2019. Database for those interested in the consequences of Factor VIII genetic variation at the DNA and protein level, it provides access to data on the molecular pathology of haemophilia A. The database presents a review of the structure and function of factor VIII and the molecular genetics of haemophilia A, a real time update of the biostatistics of each parameter in the database, a molecular model of the A1, A2 and A3 domains of the factor VIII protein (based on the crystal structure of caeruloplasmin) and a bulletin board for discussion of issues in the molecular biology of factor VIII. The database is completely updated with easy submission of point mutations, deletions and insertions via e-mail of custom-designed forms. A methods section devoted to mutation detection is available, highlighting issues such as choice of technique and PCR primer sequences. The FVIII structure section now includes a download of a FVIII A domain homology model in Protein Data Bank format and a multiple alignment of the FVIII amino-acid sequences from four species (human, murine, porcine and canine) in addition to the virtual reality simulations, secondary structural data and FVIII animation already available. Finally, to aid navigation across this site, a clickable roadmap of the main features provides easy access to the page desired. Their intention is that continued development and updating of the site shall provide workers in the fields of molecular and structural biology with a one-stop resource site to facilitate FVIII research and education. To submit your mutants to the Haemophilia A Mutation Database email the details. (Refer to Submission Guidelines) |
function, gene, genetic, analysis, bioinformatic, biological, biostatistic, caeruloplasmiin, crystal, haemophilia a, human, murine, porcine, canine, level, molecular, molecule, mutation, nucleic acid, or disease- specific databases, pathology, structural, structure, system-, vitromutagenesis, fviii genetic variation, dna, protein, factor viii, blood-clotting protein, point mutation, deletion, insertion | has parent organization: Imperial College London; London; United Kingdom | Pfizer UK ; MRC |
PMID:9399839 PMID:9016520 PMID:8594555 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21184 | http://europium.csc.mrc.ac.uk/WebPages/Main/main.htm, http://hadb.org.uk/ | SCR_006883 | HAMSTeRS - The Haemophilia A Mutation Structure Test Resource Site, Haemophilia A Mutation Database, Haemophilia A Mutation Structure Test and Resource Site, Haemophilia A Mutation Structure Test Resource Site | 2026-10-17 01:26:48 | 9 | ||||
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Europhenome Mouse Phenotyping Resource Resource Report Resource Website 10+ mentions |
Europhenome Mouse Phenotyping Resource (RRID:SCR_006935) | EuroPhenome | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Open source software system for capturing, storing and analyzing raw phenotyping data from SOPs contained in EMPReSS, it provides access to raw and annotated mouse phenotyping data generated from primary pipelines such as EMPReSSlim and secondary procedures from specialist centers. Mutants of interest can be identified by searching the gene or the predicted phenotype. You can also access phenotype data from the EMPReSSlim Pipeline for inbred mouse strains. Initially EuroPhenome was developed within the EUMORPHIA programme to capture and store pilot phenotyping data obtained on four background strains (C57BL/6J, C3H/HeBFeJ, BALB/cByJ and 129/SvPas). EUMORPHIA (European Union Mouse Research for Public Health and Industrial Applications) was a large project comprising of 18 research centers in 8 European countries, with the main focus of the project being the development of novel approaches in phenotyping, mutagenesis and informatics to improve the characterization of mouse models for understanding human molecular physiology and pathology. The current version of EuroPhenome is capturing data from the EUMODIC project as well as the WTSI MGP, HMGU GMC pipeline and the CMHD. EUMODIC is undertaking a primary phenotype assessment of up to 500 mouse mutant lines derived from ES cells developed in the EUCOMM project as well as other lines. Lines showing an interesting phenotype will be subject to a more in depth assessment. EUMODIC is building upon the comprehensive database of standardized phenotyping protocols, called EMPReSS, developed by the EUMORPHIA project. EUMODIC has developed a selection of these screens, called EMPReSSslim, to enable comprehensive, high throughput, primary phenotyping of large numbers of mice. Phenovariants are annotated using a automated pipeline, which assigns a MP term if the mutant data is statistically different to the baseline data. This data is shown in the Phenomap and the mine for a mutant tool. Please note that a statistically significant result and the subsequent MP annotation does not necessarily mean a true phenovariant. There are other factors that could cause this result that have not been accounted for in the analysis. It is the responsibility of the user to download the data and use their expert knowledge or further analysis to decide whether they agree or not. EuroPhenome is primarily based in the bioinformatics group at MRC Harwell. The development of EuroPhenome is in collaboration with the Helmholtz Zentrum Munchen, Germany, the Wellcome Trust Sanger Institute, UK and the Institut Clinique de la Souris, France. | phenotype, gene, mutant mouse strain, inbred mouse strain, annotation, ortholog, high-throughput, phenovariant, disorder, c57bl/6j, c3h/hebfej, balb/cbyj, 129/svpas |
is related to: European Mouse Phenotyping Resource of Standardised Screens is related to: OMIM is related to: Understanding Human Disease Through Mouse Genetics is related to: European Conditional Mouse Mutagenesis Program is related to: European Mouse Phenotyping Resource of Standardised Screens has parent organization: MRC Mammalian Genetics Unit |
European Union FP6 contract LSHG-CT-2006-037188; MRC ; National Genome Research Network |
PMID:19933761 PMID:17905814 |
Open unspecified license, Acknowledgement requested | nif-0000-30535 | SCR_006935 | 2026-10-17 01:26:48 | 19 | ||||||
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Scalable Brain Atlas Resource Report Resource Website 10+ mentions |
Scalable Brain Atlas (RRID:SCR_006934) | SBA | atlas, data or information resource, reference atlas, service resource, software application, software resource | A web-based, interactive brain atlas viewer, containing a growing number of atlas templates for various species, including mouse, macaque and human. Standard features include fast brain region lookup, point and click to select a region and view its full 3D extent, mark a stereotaxic coordinate and view all regions in a hierarchy. Built-in extensions are the CoCoMac plugin, which provides a spatial display of Macaque connectivity, and a service to transform stereotaxic coordinates to and from the INCF Waxholm space for the mouse. Three dimensional renderings of brain regions are available through a Matlab interface (local installation of Matlab required). The SBA is designed to be customizable. External users can create plugins, hosted on their own servers, to interactively attach images or data to spatial atlas locations. This fully web-based display engine for brain atlases and topologies allows client websites to show brain region related data in a 3D interactive context. Currently available atlases are: * Macaque: The Paxinos Rhesus Monkey atlas (2000) * Macaque: Various templates available through Caret, registered to F99 space: Felleman and Van Essen (1991), Lewis and Van Essen (2000), Regional Map from K��tter and Wanke (2005), Paxinos Rhesus Monkey (2000) * Macaque: The NeuroMaps Macaque atlas (2008) * Mouse: The INCF Waxholm Space for the mouse (2011). Previous versions available. * Mouse: The Allen Mouse Brain volumetric atlas (ABA07) * Human: The LPBA40 parcellation, registered to SRI24 space A variety of services are being developed around the templates contained in the Scalable Brain Atlas. For example, you can include thumbnails of brain regions in your own webpage. Other applications include: * Analyze atlas templates in Matlab * List all regions belonging to the given template * List of supported atlas templates * Find region by coordinate * Color-coded PNG (bitmap) or SVG (vector) image of a brain atlas slice * Region thumbnail in 2D (slice) or 3D (stack of slices) The Scalable Brain Atlas is created by Rembrandt Bakker and Gleb Bezgin, under supervision of Rolf K��tter in the NeuroPhysiology and -Informatics group of the Donders Institute, Radboud UMC Nijmegen. | atlas application, atlas data, image display, javascript, magnetic resonance, os independent, php, three dimensional display, tractography, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CoCoMac is related to: 3DBar has parent organization: International Neuroinformatics Coordinating Facility |
International Neuroinformatics Coordinating Facility | GNU General Public License | nlx_98156 | http://www.nitrc.org/projects/sba | SCR_006934 | INCF Scalable Brain Atlas | 2026-10-17 01:26:45 | 22 | |||||
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The WWW Virtual Library: Model Organisms Resource Report Resource Website |
The WWW Virtual Library: Model Organisms (RRID:SCR_007007) | data or information resource, portal, topical portal | Catalog of internet resources relating to biological model organisms, and is part of the Biosciences area of the Virtual Library project. The main Model Organisms Library discussed in this website are: * E. coli (bacterium) * Yeasts (Saccharomyces cerevisiae, and other species) * Dictyostelium discoideum (slime mold) * Drosophila melanogaster (fruit fly) * Xenopus laevis (African clawed frog) Many aspects of biology are similar in most or all organisms, but it is frequently much easier to study particular aspects in particular organisms - for instance, genetics is easier in small organisms that breed quickly, and very difficult in humans! The most popular model organisms have strong advantages for experimental research, and become even more useful when other scientists have already worked on them, discovering techniques, genes and other useful information. | bacterium, cerevisiae, model organism, saccharomyces, s. cerevisiae, slime mold, xenopus, catalog, link aggregator | is listed by: 3DVC | nif-0000-20953 | SCR_007007 | VL | 2026-10-17 01:26:45 | 0 | |||||||||
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Mouse Genome Databases Resource Report Resource Website 1+ mentions |
Mouse Genome Databases (RRID:SCR_007147) | MGD | data or information resource, data set, database, organism-related portal, portal, topical portal | A mouse-related portal of genomic databases and tables of mouse brain data. Most files are intended for you to download and use on your own personal computer. Most files are available in generic text format or as FileMaker Pro databases. The server provides data extracted and compiled from: The 2000-2001 Mouse Chromosome Committee Reports, Release 15 of the MIT microsatellite map (Oct 1997), The recombinant inbred strain database of R.W. Elliott (1997) and R. W. Williams (2001), and the Map Manager and text format chromosome maps (Apr 2001). * LXS genotype (Excel file): Updated, revised positions for 330 markers genotyped using a panel of 77 LXS strain. * MIT SNP DATABASE ONLINE: Search and sort the MIT Single Nucleotide Polymorphism (SNP) database ONLINE. These data from the MIT-Whitehead SNP release of December 1999. * INTEGRATED MIT-ROCHE SNP DATABASE in EXCEL and TEXT FORMATS (1-3 MB): Original MIT SNPs merged with the new Roche SNPs. The Excel file has been formatted to illustrate SNP haplotypes and genetic contrasts. Both files are intended for statistical analyses of SNPs and can be used to test a method outlined in a paper by Andrew Grupe, Gary Peltz, and colleagues (Science 291: 1915-1918, 2001). The Excel file includes many useful equations and formatting that will help in navigating through this large database and in testing the in silico mapping method. * Use of inbred strains for the study of individual differences in pain related phenotypes in the mouse: Elissa J. Chesler''s 2002 dissertation, discussing issues relevant to the integration of genomic and phenomic data from standard inbred strains including genetic interactions with laboratory environmental conditions and the use of various in silico inbred strain haplotype based mapping algorithms for QTL analysis. * SNP QTL MAPPER in EXCEL format (572 KB, updated January 2002 by Elissa Chesler): This Excel workbook implements the Grupe et al. mapping method and outputs correlation plots. The main spreadsheet allows you to enter your own strain data and compares them to haplotypes. Be very cautious and skeptical when using this spreadsheet and the technique. Read all of the caveates. This excel version of the method was developed by Elissa Chesler. This updated version (Jan 2002) handles missing data. * MIT SNP Database (tab-delimited text format): This file is suitable for manipulation in statistics and spreadsheet programs (752 KB, Updated June 27, 2001). Data have been formatted in a way that allows rapid acquisition of the new data from the Roche Bioscience SNP database. * MIT SNP Database (FileMaker 5 Version): This is a reformatted version of the MIT Single Nucleotide Polymorphism (SNP) database in FileMaker 5 format. You will need a copy of this application to open the file (Mac and Windows; 992 KB. Updated July 13, 2001 by RW). * Gene Mapping and Map Manager Data Sets: Genetic maps of mouse chromosomes. Now includes a 10th generation advanced intercross consisting of 500 animals genetoyped at 340 markers. Lots of older files on recombinant inbred strains. * The Portable Dictionary of the Mouse Genome, 21,039 loci, 17,912,832 bytes. Includes all 1997-98 Chromosome Committee Reports and MIT Release 15. * FullDict.FMP.sit: The Portable Dictionary of the Mouse Genome. This large FileMaker Pro 3.0/4.0 database has been compressed with StuffIt. The Dictionary of the Mouse Genome contains data from the 1997-98 chromosome committee reports and MIT Whitehead SSLP databases (Release 15). The Dictionary contains information for 21,039 loci. File size = 4846 KB. Updated March 19, 1998. * MIT Microsatellite Database ONLINE: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB. MITDB is a subset of the Portable Dictionary of the Mouse Genome. ONLINE. Updated July 12, 2001. * MIT Microsatellite Database: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB. MITDB is a subset of the Portable Dictionary of the Mouse Genome. File size = 3.0 MB. Updated March 19, 1998. * OurPrimersDB: A small database of primers. Download this database if you are using numerous MIT primers to map genes in mice. This database should be used in combination with the MITDB as one part of a relational database. File size = 149 KB. Updated March 19, 1998. * Empty copy (clone) of the Portable Dictionary in FileMaker Pro 3.0 format. Download this file and import individual chromosome text files from the table into the database. File size = 231 KB. Updated March 19, 1998. * Chromosome Text Files from the Dictionary: The table lists data on gene loci for individual chromosomes. | gene, genetic, chromosome, genotype, inbred mouse strain, pain, phenotype, polygenic, recombinant, trait, genome, genomic, single nucleotide polymorphism, primer, brain, recombinant inbred mouse strain |
has parent organization: University of Tennessee Health Science Center; Tennessee; USA is organization facet of: Alliance of Genome Resources |
nif-0000-20982 | SCR_007147 | 2026-10-17 01:26:52 | 2 | |||||||||
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RTPrimerDB- The Real-Time PCR and Probe Database Resource Report Resource Website 10+ mentions |
RTPrimerDB- The Real-Time PCR and Probe Database (RRID:SCR_007106) | RTPrimerDB | data or information resource, data repository, database, service resource, storage service resource | Database for primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridization Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimization, and to introduce a certain level of uniformity and standardization among different laboratories. Researchers are encouraged to submit their validated primer and probe sequence, so that other users can benefit from their expertise. The database can be queried using the official gene name or symbol, Entrez or Ensembl Gene identifier, SNP identifier, or oligonucleotide sequence. Different options make it possible to restrict a query to a particular application (Gene Expression Quantification/Detection, DNA Copy Number Quantification/Detection, SNP Detection, Mutation Analysis, Fusion Gene Quantification/Detection, Chromatin immunoprecipitation (ChIP)), organism (Human, Mouse, Rat, and others) or detection chemistry. | primer, probe, sequence, real-time pcr, gene, assay, real-time pcr assay, FASEB list |
is listed by: OMICtools has parent organization: Ghent University; Ghent; Belgium |
PMID:18948285 PMID:16381959 PMID:12519963 |
Public, The community can contribute to this resource | nif-0000-03431, OMICS_02322 | SCR_007106 | 2026-10-17 01:26:48 | 49 | |||||||
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NIA Aged Rodent Colonies Resource Report Resource Website 10+ mentions |
NIA Aged Rodent Colonies (RRID:SCR_007317) | Aged Rodent Colonies | biomaterial supply resource, material resource, organism supplier | Colonies of barrier-raised, Specific Pathogen-Free (SPF) rodents under contractual arrangement with commercial vendors, specifically for use in aging research. They are not available for use as a general source of adult animals for unrelated areas of research. Animals from the NIA aged rodent colonies are available to investigators at academic and non-profit research institutions under the terms described on the Eligibility Criteria page. Orders must be submitted through the online rodent ordering system (ROS) (http://arc.niapublications.org/acb/stores/1/). Available strains: * Inbred Rats: Fischer 344 (F344), Brown Norway (BN) * Hybrid Rats: F344xBN F1 (F344BN); * Inbred Mice: BALB/cBy, CBA, C57BL/6, DBA/2 * Hybrid Mice: CB6F1 (BALB/cBy x C57BL/6), B6D2F1 (C57BL/6 x DBA/2) * Caloric Restricted Rats: F344 (males only), F344BN F1 (males only) * Caloric Restricted Mice: C57BL/6; B6D2F1 (males only) | rodent, inbred mouse strain, inbred rat strain, hybrid rat strain, hybrid mouse strain, caloric restricted, male, mouse strain, adult mouse, rat strain |
is listed by: One Mind Biospecimen Bank Listing is related to: NIA Aged Rodent Tissue Bank has parent organization: NIA Scientific Resources |
Aging, Inbred mouse strain, Inbred rat strain, Hybrid rat strain, Hybrid mouse strain, Caloric Restricted | NIA ; NIH Blueprint for Neuroscience Research |
Public: For use in aging research only. Available to investigators at academic and non-profit research institutions - see Eligibility Criteria page. | nif-0000-00184 | http://www.nia.nih.gov/ResearchInformation/ScientificResources/default.htm | SCR_007317 | NIA Aged Rodent Colonies Handbook, Aged Rodent Colonies Handbook, Aging-Related Rodent Colonies, Aging-Related Rat Colonies | 2026-10-17 01:26:52 | 26 | ||||
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Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource Resource Report Resource Website |
Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource (RRID:SCR_007312) | Deltagen and Lexicon Knockout Mice | biomaterial supply resource, material resource, organism supplier | Repository of knockout mice that have been extensively characterized. For each mouse line, the contractors will provide not only the mouse line itself, but also detailed, objective data on the impact of the specific gene deletion on the mouse''s phenotype, which includes appearance, health, fitness, behavior, ability to reproduce, and radiological and microscopic data. Such comprehensive information on such a large group of mice has never been available to public sector researchers, and is expected to greatly accelerate efforts to explore gene functions in health and disease. This resource will give researchers unprecedented access to two private collections of knockout mice, providing valuable models for the study of human disease and laying the groundwork for a public, genome-wide library of knockout mice. The contracts also provide for the opportunity for NIH to obtain up to 1500 additional mouse lines and phenotypic data over the next three years, pending available funds. The new contracts provide NIH with irrevocable, perpetual, worldwide, royalty-free licenses to use and distribute to academic and non-profit researchers these lines of knockout mice. The mouse lines, which will be stored in the form of frozen embryos, frozen sperm and frozen embryonic stem (ES) cells, will be delivered to NIH-funded mouse repositories that supply mice to universities, medical schools and research labs all over the world. When researchers express interest in obtaining a certain knockout mouse line, the repositories will send them live mice, frozen embryos, sperm, and/or ES cells, so they can study the mice in their own labs. All data on the mice will be made available to researchers worldwide without restriction in publicly available databases on the Web. This resource will be available for a nominal fee which will be used to cover the cost of handling, shipping and replenishing the stock. Under the license agreements with Deltagen and Lexicon, researchers who receive the knockout mice lines through NIH are free to publish any results from research involving the line and also to seek patent or other intellectual property protection for any of the inventions or discoveries resulting from such research. List of Available Knockout Mice: http://www.informatics.jax.org/external/ko/ | knockout mouse, phenotype, mouse model, mutant, appearance, health, fitness, behavior, reproduction, human disease |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Mouse Genome Informatics (MGI) has parent organization: Mutant Mouse Resource and Research Center has parent organization: National Institutes of Health |
NIH Blueprint for Neuroscience Research | Public: For academic and non-profit researchers worldwide | nif-0000-00177 | SCR_007312 | NIH Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource | 2026-10-17 01:26:56 | 0 | ||||||
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fMRI Data Center Resource Report Resource Website 10+ mentions |
fMRI Data Center (RRID:SCR_007278) | fMRIDC | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2013 Public curated repository of peer reviewed fMRI studies and their underlying data. This Web-accessible database has data mining capabilities and the means to deliver requested data to the user (via Web, CD, or digital tape). Datasets available: 107 NOTE: The fMRIDC is down temporarily while it moves to a new home at UCLA. Check back again in late Jan 2013! The goal of the Center is to help speed the progress and the understanding of cognitive processes and the neural substrates that underlie them by: * Providing a publicly accessible repository of peer-reviewed fMRI studies. * Providing all data necessary to interpret, analyze, and replicate these fMRI studies. * Provide training for both the academic and professional communities. The Center will accept data from those researchers who are publishing fMRI imaging articles in peer-reviewed journals. The goal is to serve the entire fMRI community. | fmri, cognitive, cortex, mri, talairach, neuroimaging, cognitive neuroscience, brain, structure, function, magnetic resonance, intellect, image collection, data set |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: re3data.org has parent organization: University of California at Santa Barbara; California; USA |
NSF ; W. M. Keck Foundation ; NIMH ; Sun Microsystems Center of Excellence |
PMID:11545705 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00025 | http://www.fmridc.org/ | SCR_007278 | The fMRI Data Center | 2026-10-17 01:26:52 | 16 |
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