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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Ancora Resource Report Resource Website 10+ mentions |
Ancora (RRID:SCR_001623) | Ancora | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Web resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements (HCNEs) for multiple genomes. It includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains. They identify HCNEs as non-exonic regions of high similarity between genome sequences from distantly related organisms, such as human and fish, and provide tools for studying the distribution of HCNEs along chromosomes. Major peaks of HCNE density along chromosomes most often coincide with developmental regulatory genes. Their aim with this site is to aid discovery of developmental regulatory genes, their regulatory domains and their fundamental regulatory elements. | genome, highly conserved noncoding element, noncoding element, regulatory gene, regulatory domain, regulatory element, developmental regulatory gene, evolution, enhancer |
is related to: MONARCH Initiative has parent organization: University of Bergen; Bergen; Norway |
Research Council of Norway ; Bergen Research Foundation ; Sars Centre |
PMID:18279518 | Free, Freely available | nlx_153891 | SCR_001623 | Atlas of Noncoding Conserved Regions in Animals | 2026-02-13 10:54:53 | 19 | |||||
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PhenoGen Informatics Resource Report Resource Website 10+ mentions |
PhenoGen Informatics (RRID:SCR_001613) | PhenoGen | data repository, storage service resource, data analysis service, analysis service resource, data set, data or information resource, production service resource, source code, service resource, data access protocol, software resource, application programming interface | Website for analyzing microarray data. Software toolbox for storing, analyzing and integrating microarray data and related genotype and phenotype data. The site is particularly suited for combining QTL and microarray data to search for candidate genes contributing to complex traits. In addition, the site allows, if desired by the investigators, sharing of the data. Investigators can conduct in-silico microarray experiments using their own and/or shared data. There are five major sections of the site: Genome/Transcriptome Data Browser, Microarray Analysis Tools, Gene List Analysis Tools, QTL Tools, and Downloads. The genome/transcriptome data browser combines a genome browser with all the microarray, RNA-Seq, and Genomic Sequencing data. This provides an effective platform to view all of this data side by side. Source code is available on GitHub. | genome, transcription, microarray, gene, quantitative trait loci, analysis, complex trait, genotype, phenotype, high-throughput, rna-seq, snp, genomic marker, region, data sharing, normalize, statistics, gene list, pathway, expression value, expression, correlation, exon, annotation, promoter, homolog, brain, heart, liver, adipose, candidate gene, genetics, transcriptome, eqtl, genome browser, inbred panel |
is related to: MONARCH Initiative has parent organization: University of Colorado Denver; Colorado; USA |
NIAAA R24 AA013162; NIAAA R01 AA13162; NIAAA U01 AA013524 |
PMID:17760997 | Free, Freely available | rid_000093, nlx_153879, r3d100011596 | https://github.com/TabakoffLab/PhenogenCloud https://doi.org/10.17616/R3WS7F |
http://phenogen.ucdenver.edu, http://phenogen.uchsc.edu | SCR_001613 | PhenoGen Informatics - The site for quantitative genetics of the transcriptome. | 2026-02-13 10:54:53 | 22 | |||
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North American Conditional Mouse Mutagenesis Project Resource Report Resource Website 1+ mentions |
North American Conditional Mouse Mutagenesis Project (RRID:SCR_001614) | NorCOMM | biomaterial manufacture, material service resource, service resource, production service resource | Large-scale research initiative focused on developing and distributing a library of mouse embryonic stem (ES) cell lines carrying single gene trapped or targeted mutations across the mouse genome. NorCOMM's large and growing archive of ES cells is publicly available on a cost-recovery basis from the Canadian Mouse Mutant Repository. As an international public resource, access to clones is unrestricted and nonexclusive. Through NorCOMM's affiliation with the Canadian Mouse Consortium (CMC), NorCOMM also provides clients with a single point of access to regional mouse derivation, phenotyping, genetic and archiving services across Canada. These value-added services can help your company harness NorCOMM's resources for drug discovery, target discovery and preclinical validation. | gene, target, embryonic stem cell line, gene trap, targeted mutation, mouse genome, mutation, genome, derivation, phenotype, genetic, archive, phenotyping, archiving, gene target, clone |
is related to: CMMR - Canadian Mouse Mutant Repository is related to: CMMR - Canadian Mouse Mutant Repository has parent organization: International Knockout Mouse Consortium |
Genome Canada | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153880 | SCR_001614 | 2026-02-13 10:54:53 | 4 | |||||||
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Texas A and M Institute for Genomic Medicine Resource Report Resource Website 10+ mentions |
Texas A and M Institute for Genomic Medicine (RRID:SCR_001615) | TIGM | biomaterial supply resource, organism supplier, cell repository, material resource | Resource for any researcher looking to obtain knockout mice and embryonic stem (ES) cells quickly and with favorable intellectual property (IP) terms. Our resources include the world’s largest gene trap library of ES cells in the C57BL/6N mouse strain and a constantly expanding repository of cryopreserved germplasm of knockout lines. TIGM provides both ES cell clones and mice as well as other transgenic core services including CRISPR/Cas9-based genome modifications within the Texas A&M system and to the public and private international research community. | RIN, Resource Information Network, embryonic stem cell, knockout mouse, transgenic, phenotyping, phenotype, c57bl/6, 129/svevbrd, gene trap, clone, knockout mouse line, 129, database, gene, mutation, RRID Community Authority |
is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network is related to: International Knockout Mouse Consortium has parent organization: Texas A and M University; Texas; USA works with: International Mouse Strain Resource |
Free, Freely available | nlx_153881 | SCR_001615 | Texas A&M Institute for Genomic Medicine | 2026-02-13 10:54:53 | 19 | |||||||
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International Mouse Strain Resource Resource Report Resource Website 10+ mentions |
International Mouse Strain Resource (RRID:SCR_001526) | IMSR | biomaterial supply resource, organism supplier, material resource | Database of mouse strains and stocks available worldwide, that will assist international research community in finding mouse resources they need, including inbred, mutant, and genetically engineered mice. IMSR is multi institutional international collaboration supporting use of mouse as model system for studying human biology and disease. IMSR began with initial collaboration between Mouse Genome Informatics (MGI) group at Jackson Laboratory and Medical Research Council Mammalian Genetics Unit at Harwell. Additional institutions and collaborators are now contributing mouse resource information to IMSR. Data content found in IMSR is as it was supplied by data provider sites. You are encouraged to participate in making this database as complete as possible for all worldwide mouse strain resources. If you or your institution hold mice, cryopreserved gametes or embryos, or ES cell lines that you distribute to other researchers, contributing information about them to IMSR catalog will make them more widely known. | RIN, Resource Information Network, mouse, strain, stock, inbred, mutant, genetically engineered, embryo, embryonic stem cell line, database, knockout mouse, mutant mouse strain, transgenic mouse, embryonic mouse, live mouse, gamete, ovary, sperm, germplasm, model organism, RRID Community Authority |
uses: Vanderbilt Cryopreserved Mouse Repository uses: Janvier Labs uses: Korea Mouse Phenotyping Center uses: CLEA Japan, Inc. uses: genOway uses: Inotiv uses: Cyagen Biosciences uses: Cam-Su Genomic Resource Center is used by: BioSample Database at EBI is used by: Integrated Animals lists: Oak Ridge Collection at JAX lists: National Resource Center for Mutant Mice lists: JAX Mice and Services lists: National Applied Research Laboratories lists: Oriental BioService Inc. is listed by: Resource Information Network is related to: NIF Data Federation is related to: Recombinase (cre) Activity is related to: One Mind Biospecimen Bank Listing is related to: Integrated Cell Lines is related to: Mouse Genome Informatics (MGI) has parent organization: MRC Mammalian Genetics Unit works with: Shanghai Model Organisms Center works with: European Mouse Mutant Archive works with: Texas A and M Institute for Genomic Medicine works with: JAX Mice and Services works with: CMMR - Canadian Mouse Mutant Repository works with: RIKEN BioResource Center works with: Center for Animal Resources and Development works with: National Institute of Genetics; Shizuoka; Japan works with: NHMRC Australian PhenomeBank works with: Taconic Biosciences works with: Charles River Laboratories works with: Medical Research Council Harwell: An International Centre for Mouse Genetics |
NLM LM009693 | PMID:10098412 PMID:26373861 |
Restricted | nif-0000-09876 | http://www.findmice.org/ | SCR_001526 | IMSR, International Mouse Strain Resource | 2026-02-13 10:54:52 | 13 | ||||
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Brain Gene Expression Map Resource Report Resource Website 10+ mentions |
Brain Gene Expression Map (RRID:SCR_001517) | BGEM | expression atlas, data or information resource, atlas, database | This database contains gene expression patterns assembled from mouse nervous tissues at 4 time points throughout brain development including embryonic (e) day 11.5, e15.5, postnatal (p) day 7 and adult p42. Using a high throughput in situ hybridization approach we are assembling expression patterns from selected genes and presenting them in a searchable database. The database includes darkfield images obtained using radioactive probes, reference cresyl violet stained sections, the complete nucleotide sequence of the probes used to generate the data and all the information required to allow users to repeat and extend the analyses. The database is directly linked to Pubmed, LocusLink, Unigene and Gene Ontology Consortium housed at the National Center for Biotechnology Information (NCBI) in the National Library of Medicine. These data are provided freely to promote communication and cooperation among research groups throughout the world. | embryonic, expression pattern, gene expression, gene, adult, brain, brain development, in situ hybridization, mouse, nervous tissue, postnatal, molecular neuroanatomy resource, image | NINDS 5R37NS036558; NINDS N01-NS-0-2331 |
PMID:16602821 | nif-0000-09579 | SCR_001517 | BGEM - Brain Gene Expression Map, Mousebrain Gene Expression Map | 2026-02-13 10:54:52 | 10 | |||||||
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GenitoUrinary Development Molecular Anatomy Project Resource Report Resource Website 100+ mentions |
GenitoUrinary Development Molecular Anatomy Project (RRID:SCR_001554) | GUDMAP | biomaterial supply resource, organism supplier, material resource | Project aggregates and provides experimental gene expression data from genito-urinary system. International consortium providing molecular atlas of gene expression for developing organs of GenitoUrinary (GU) tract. Mouse strains to facilitate developmental and functional studies within GU system. Experimental protocols and standard specifications. Tutorials describing GU organogenesis and primary data via database. Data are from large-scale in situ hybridization screens (wholemount and section) and microarray gene expression data of microdissected, laser-captured and FACS-sorted components of developing mouse genitourinary (GU) system. | gene expression, genitourinary tract, molecular anatomy, genitourinary system, organogenesis, genitourinary, in situ hybridization, immunohistochemistry, microarray, mutant mouse strain, development, rna, protein, theiler stage, gene, anatomy, male, female, embryonic mouse, kidney, urogenital tract, urinary, reproductive, disease, molecule, cell, gene, phenotype, functional annotation, protein interaction, transgenic transgene, image, rna extraction, sample preparation, fluorescent immunohistochemistry, rna isolation, rna amplification, labeling, fluorescent in situ-hybridization, riboprobe synthesis, cellular localization, tissue isolation, embedding, cryostat sectioning, laser capture microdissection, paraffin, whole mount, optimal cutting temperature, riboprobe synthesis, target amplification, sectioning, FASEB list |
is used by: NIDDK Information Network (dkNET) is listed by: One Mind Biospecimen Bank Listing is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology is related to: ToppCluster is related to: One Mind Biospecimen Bank Listing is parent organization of: GUDMAP Ontology is parent organization of: GATACA GUDMAP Gene Explorer |
NIDDK DK070136; NIDDK DK070200; NIDDK DK070181 |
PMID:21652655 PMID:18287559 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152871, nif-0000-33426 | SCR_001554 | Murine Atlas for Genitourinary Development | 2026-02-13 10:54:52 | 287 | |||||
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Atlas3D Resource Report Resource Website 10+ mentions |
Atlas3D (RRID:SCR_001808) | data visualization software, data processing software, data or information resource, atlas, software application, software resource | A multi-platform visualization tool which allows import and visualization of 3-D atlas structures in combination with tomographic and histological image data. The tool allows visualization and analysis of the reconstructed atlas framework, surface modeling and rotation of selected structures, user-defined slicing at any chosen angle, and import of data produced by the user for merging with the atlas framework. Tomographic image data in NIfTI (Neuroimaging Informatics Technology Initiative) file format, VRML and PNG files can be imported and visualized within the atlas framework. XYZ coordinate lists are also supported. Atlases that are available with the tool include mouse brain structures (3-D reconstructed from The Mouse Brain in Stereotaxic Coordinates by Paxinos and Franklin (2001)) and rat brain structures (3-D reconstructed from The Rat Brain in Stereotaxic Coordinates by Paxinos and Watson (2005)). Experimental data can be imported in Atlas3D and warped to atlas space, using manual linear registration, with the possibility to scale, rotate, and position the imported data. This facilitates assignment of location and comparative analysis of signal location in tomographic images. | analysis, brain, histological, mouse, rat, slicing, structure, 3d, tomographic, visualization, neuroimaging, image, magnetic resonance, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Oslo; Oslo; Norway |
Research Council of Norway ; NIH ; NIBIB R01-EB00790; NCRR U24-RR021382 |
Free, Freely available | nif-0000-10373 | http://www.nitrc.org/projects/incf_atlas3d | SCR_001808 | Neural Systems and Graphics Computing Laboratory: Atlas3D Software, NeSys Atlas3D | 2026-02-13 10:54:55 | 17 | ||||||
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NCI Mouse Repository Resource Report Resource Website 10+ mentions |
NCI Mouse Repository (RRID:SCR_002264) | NCIMR | biomaterial supply resource, organism supplier, material resource | The NCI Mouse Repository cryoarchives and distributes strains of genetically engineered mice that are of immediate interest to the cancer research community. These are either gene-targeted or transgenic mice that display a cancer-related phenotype, or tool strains (e.g., cre transgenics) that can be used to develop new cancer models. You do not have to be a member of the NCI Mouse Repository or a recipient of NCI funding to have your mouse model distributed through the NCI Mouse Repository. NCI Mouse Repository strains are maintained as live colonies or cryoarchived as frozen embryos, depending on demand. Up to three breeder pairs may be ordered from live colonies. Cryoarchived strains are supplied as frozen embryos or recovery of live mice by the NCI Mouse Repository may be requested. | embryo, engineered, frozen, gene, genetically, breed, breeder, cancer, colony, cryoarchive, human, live, model, mouse model, phenotype, strain, transgenic, mutant, female, male |
is listed by: One Mind Biospecimen Bank Listing has parent organization: NCI-Frederick |
NCI | Free, Freely available | nif-0000-20985 | http://mouse.ncifcrf.gov/ | SCR_002264 | MMHCC, MMHCC Repository, Mouse Models of Human Cancers Consortium (MMHCC) Repository, Mouse Models of Human Cancers Consortium Repository | 2026-02-13 10:55:00 | 19 | |||||
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Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. | pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: DisGeNET is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: WikiPathways is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: AmiGO is related to: PSICQUIC Registry is related to: Integrated Molecular Interaction Database is related to: NCBI BioSystems Database is related to: MOPED - Model Organism Protein Expression Database is related to: KOBAS is related to: PSICQUIC Registry is related to: Pathway Interaction Database is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: Algal Functional Annotation Tool has parent organization: Ontario Institute for Cancer Research has parent organization: Cold Spring Harbor Laboratory has parent organization: European Bioinformatics Institute has parent organization: New York University School of Medicine; New York; USA works with: PathwayMatcher |
Ontario Research Fund ; European Molecular Biology Laboratory ; NHGRI P41 HG003751; European Union FP6 ENFIN LSHG-CT-2005-518254; NIGMS GM080223; NIGMS R01 GM100039 |
PMID:21082427 PMID:21067998 |
Open source, Public, Freely available | r3d100010285, nif-0000-03390, biotools:reactome | https://bio.tools/reactome https://doi.org/10.17616/R3V59P |
SCR_003485 | Reactome Functional Interaction Network | 2026-02-13 10:55:15 | 4282 | |||||
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Open Connectome Project Resource Report Resource Website 1+ mentions |
Open Connectome Project (RRID:SCR_004232) | Open Connectome Project | data repository, storage service resource, web service, data analysis service, image repository, analysis service resource, data set, data or information resource, production service resource, source code, service resource, data access protocol, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or which neurons synapse onto this one. Create your own annotations or browse others. *Sample Downloads - In addition to being able to select arbitrary downloads from the datasets, they have also collected a few choice volumes of interest. * Volume Viewer - A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. The code and program can be downloaded. * Machine Vision Pipeline - They are building a machine vision pipeline that pulls volumes from the 3ddb and outputs neural circuits. - a work in progress. As soon as we have a stable version, it will be released. * Mr. Cap - The Magnetic Resonance Connectome Automated Pipeline (Mr. Cap) is built on JIST/MIPAV for high-throughput estimation of connectomes from diffusion and structural imaging data. * Graph Invariant Computation - Upload your graphs or streamlines, and download some invariants. * iPad App - WholeSlide is an iPad app that accesses utilizes our open data and API to serve images on the go. | human, primary visual cortex, data sharing, male, electron microscopy, mri, connectome, annotation, image collection, array tomography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CATMAID is related to: neurodata is parent organization of: Rambo3D |
Johns Hopkins University; Maryland; USA ; JHU Applied Research Laboratory IRAD ; JHU Whiting School of Engineering ; Dean's Award ; NIBIB 1RO1EB016411-01 (CRCNS); DARPA N66001-14-1-4028 (GRAPHS); NSF ACI-1261715; NSF OCI-1040114; NIDA 1R01DA036400-01; |
PMID:23707591 | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000189, nlx_143645 | http://openconnecto.me http://www.nitrc.org/projects/ocp/ |
SCR_004232 | openconnectomeproject, Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time., Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time | 2026-02-13 10:55:25 | 7 | ||||
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Stem Cell Commons Resource Report Resource Website 1+ mentions |
Stem Cell Commons (RRID:SCR_004415) | Stem Cell Commons | data repository, storage service resource, analysis service resource, data set, data or information resource, production service resource, source code, service resource, software resource, database | Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development. | therapeutic target, blood, stem cell, self-renewal, embryonic stem cell, hematopoietic stem cell, leukemia stem cell, gene, protein, phenotype, therapeutic, annotate, share, analyze, data sharing, statistics, visualize, analyze, microarray, next-generation sequencing, statistics, transcription profiling, genome, genome browser, disease model |
is related to: Galaxy is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Harvard Stem Cell Institute |
Normal, Acute Myelogenous Leukemia, Glioblastoma, Primitive Neuroectodermal Tumor, Etc. | PMID:24303302 | Open unspecified license | nlx_42085 | http://bloodprogram.hsci.harvard.edu/ | SCR_004415 | HSCI Blood Genomics, Harvard Stem Cell Institute Blood Genomics, Harvard Stem Cell Institute Blood Program, HSCI Blood Program | 2026-02-13 10:55:26 | 2 | ||||
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GeneNetwork Resource Report Resource Website 100+ mentions |
GeneNetwork (RRID:SCR_002388) | GeneNetwork, WebQTL | data repository, storage service resource, data or information resource, service resource, database | Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data. | Variation, trait, vertebrate trait ontology, phenotype, systems genetics, quantitative trait, gene mapping, experimental precision medicinenetwork analysis, causal modeling, genomic location, genotype, inbred strain, sex, heterogeneous stock, phenome, phenotype, QTL, expression QTL, genetic reference population, single nucleotide polymorphism, RNA expression, protein expression, metabolite expression, metagenomics, epigenomics, gene-by-environmental interaction, epistasis, FAIR data standards, open source software, FASEB list |
is used by: NIF Data Federation is used by: Hypothesis Center is related to: NIH Data Sharing Repositories has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
NIGMS R01 GM123489; NIAAA U01 AA016662; NIAAA U01 AA13499; NIAAA U24 AA13513; NIAAA U01 AA014425; NIA R01 AG043930; NIDA P20 DA21131; NCI U01 CA105417; NCRR U24 RR021760 |
PMID:8043953 PMID:11737945 PMID:15043217 PMID:15114364 PMID:15043220 PMID:15043219 PMID:15711545 PMID:18368372 PMID:27933521 |
Restricted | nif-0000-00380 | SCR_002388 | GeneNetwork and WebQTL, GeneNetwork / WebQTL, www.genenetwork.org, GeneNetwork WebQTL, The GeneNetwork / WebQTL | 2026-02-13 10:55:02 | 473 | |||||
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ESTHER Resource Report Resource Website 100+ mentions |
ESTHER (RRID:SCR_002621) | ESTHER | data or information resource, database | Database and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | alpha hydrolase, beta hydrolase, cholinesterase, protein, protein superfamily, blast, gene, protein binding, protein-protein interaction, nucleotide, nucleotide sequence, enzyme, genetics, genome, genomics, mutation, disease, gene expression, peptide, chromosome |
is listed by: re3data.org is related to: UniProtKB is related to: AceDB has parent organization: INRA - French National Institute for Agricultural Research; Paris; France |
PMID:23193256 | Free, Available for download, Freely available | nif-0000-30526, SCR_008479, nif-0000-02817, r3d100010542 | https://doi.org/10.17616/R33K77 | SCR_002621 | ESTerases and alpha/beta-Hydrolase Enzymes and Relatives, ESTHER Database, ESTerases and alpha / beta-hydrolase Enzymes and Relatives | 2026-02-13 10:55:05 | 134 | |||||
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GUDMAP Ontology Resource Report Resource Website 1+ mentions |
GUDMAP Ontology (RRID:SCR_002637) | GUDMAP Ontology | data or information resource, ontology, controlled vocabulary, resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A high-resolution ontology has been developed by members of the GUDMAP consortium to describe the subcompartments of the developing murine genitourinary tract. This ontology incorporates what can be defined histologically and begins to encompass other structures and cell types already identified at the molecular level. The GUDMAP ontology encompasses Theiler stage (TS) 17-27 of development as well as the sexually mature adult. It has been written as a partonomic, text-based, hierarchical ontology that, for the embryological stages, has been developed as a high-resolution expansion of the existing Edinburgh Mouse Atlas Project (EMAP) ontology. It also includes group terms for well-characterized structural and/or functional units comprising several sub-structures, such as the nephron and juxtaglomerular complex. Each term has been assigned a unique identification number. Synonyms have been used to improve the success of query searching and maintain wherever possible existing EMAP terms relating to this organ system. | murine, genitourinary tract, development, in situ hybridization, theiler stage, adult mouse, newborn mouse, adolescent mouse, embryonic mouse |
is used by: GATACA GUDMAP Gene Explorer is used by: Kidney Development Database lists: GOA lists: EuReGene lists: Embryo Images Normal and Abnormal Mammalian Development lists: Stem Cell Genome Anatomy Projects lists: Eurexpress lists: Gene Expression Database lists: ToppGene Suite is related to: eMouseAtlas is related to: GenePaint Interactive Anatomy Atlas is related to: EMAGE Gene Expression Database is related to: Gene Expression Omnibus has parent organization: GenitoUrinary Development Molecular Anatomy Project |
NIDDK DK070136-02; NIDDK DK070181; NIDDK DK07020001; European Union FP6 005085 |
PMID:17452023 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156063 | SCR_002637 | 2026-02-13 10:55:05 | 2 | ||||||
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GeneSpeed- A Database of Unigene Domain Organization Resource Report Resource Website |
GeneSpeed- A Database of Unigene Domain Organization (RRID:SCR_002779) | data analysis service, analysis service resource, resource, data or information resource, production service resource, service resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Database and customized tools to study the PFAM protein domain content of the transcriptome for all expressed genes of Homo sapiens, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans tethered to both a genomics array repository database and a range of external information resources. GeneSpeed has merged information from several existing data sets including the Gene Ontology Consortium, InterPro, Pfam, Unigene, as well as micro-array datasets. GeneSpeed is a database of PFAM domain homology contained within Unigene. Because Unigene is a non-redundant dbEST database, this provides a wide encompassing overview of the domain content of the expressed transcriptome. We have structured the GeneSpeed Database to include a rich toolset allowing the investigator to study all domain homology, no matter how remote. As a result, homology cutoff score decisions are determined by the scientist, not by a computer algorithm. This quality is one of the novel defining features of the GeneSpeed database giving the user complete control of database content. In addition to a domain content toolset, GeneSpeed provides an assortment of links to external databases, a unique and manually curated Transcription Factor Classification list, as well as links to our newly evolving GeneSpeed BetaCell Database. GeneSpeed BetaCell is a micro-array depository combined with custom array analysis tools created with an emphasis around the meta analysis of developmental time series micro-array datasets and their significance in pancreatic beta cells. | molecular neuroanatomy resource, drosophila melanogaster, genome, caenorhabditis elegans, c. elegans, genomics, homo sapiens, mus musculus, protein domain, transcriptome |
is related to: Gene Ontology is related to: InterPro is related to: Pfam is related to: UniGene has parent organization: University of Colorado Denver; Colorado; USA |
NIDDK P30DK57516; NIDDK DK61248 |
PMID:17132830 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02887 | http://genespeed.uchsc.edu/, http://genespeed.ccf.org | SCR_002779 | GeneSpeed Database | 2026-02-13 10:55:07 | 0 | |||||
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CRE Driver Network Resource Report Resource Website 1+ mentions |
CRE Driver Network (RRID:SCR_002720) | CRE Driver Network | biomaterial supply resource, organism supplier, material resource | Project to provide Neuroscience Community with mouse strains that are suitable for tissue and cell-type-specific perturbation of gene function in nervous system. NIH Neuroscience Blueprint has established three centers in the USA for generation of genetically modified mice expressing CRE recombinases in nervous system on the C57BJ/6 genetic background. Mouse lines are generated at Cold Spring Harbor Lab, at Scripps Research Institute, and at Baylor College of Medicine. | cre-recombinase, expression, neuroscience, mutant mouse strain, knock out mouse, phenotype, expression profile, image collection, microarray, electrophysiology, atlas, morphology, cell, annotation |
is related to: JAX Cre Repository is related to: Recombinase (cre) Activity has parent organization: NIH Blueprint for Neuroscience Research is parent organization of: Mouse Neuronal Expression Database |
NIH Blueprint for Neuroscience Research ; NIH |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-23753 | SCR_002720 | Mouse Models for Neuroscience Research, CRE-driver Network, CRE-Driver Network, NIH Neuroscience Blueprint CRE Driver Network | 2026-02-13 10:55:06 | 9 | ||||||
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Aging Genes and Interventions Database Resource Report Resource Website 1+ mentions |
Aging Genes and Interventions Database (RRID:SCR_002701) | AGEID | data repository, storage service resource, data or information resource, service resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17,2023. A database of genes and interventions connected with aging phenotypes including those with respect to their effects on life-span or age-related neurological diseases. Information includes: organism, aging phenotype, allele type, strain, gene function, phenotypes, mutant, and homologs. If you know of published data (or your own unpublished data that you'd like to share) not currently in the database, please use the Submit a Gene/Intervention link. | allele, strain, gene function, phenotype, mutant, homolog, mutation, degeneration, gene, intervention, life-span |
is used by: Aging Portal is used by: NIF Data Federation has parent organization: University of Washington; Seattle; USA |
Aging, Age-related neurological disease, Neurological disease | Ellison Medical Foundation | PMID:12044961 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-23326 | http://sageke.sciencemag.org/highlights/gidb/ | SCR_002701 | Aging Genes DB, Aging Genes Database, Genes/Interventions Database | 2026-02-13 10:55:06 | 2 | |||
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Rodent Brain WorkBench Resource Report Resource Website 10+ mentions |
Rodent Brain WorkBench (RRID:SCR_002727) | rbwb | data visualization software, data processing software, data or information resource, atlas, software application, software resource, database | The Rodent Brain WorkBench is the portal to atlases, databases and tools developed by the Neural Systems and Graphics Computing Laboratory (NeSys) at the Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway. The Rodent Brain WorkBench presents a collection of brain mapping and atlasing oriented database applications and tools. The main category of available data is high resolution mosaic images covering complete histological sections through the rat and mouse brain. A highly structured relational database system for archiving, retrieving, viewing, and analysing microscopy and imaging data, aiming at presentation in standardized brain atlas space, is used to present a series of web applications for individual research projects. * Brain Connectivity * Atlases of Mouse Brain Promoter Gene Expression * General Brain Atlas and Navigation Systems * Downloadable tools for 3-DVisualization Open Access: * Atlas 3D * Cerebro-Cerebellar I * Cerebro-Cerebellar II * Neurotransporter Atlas * Rat Hippocampus * Tet-Off Atlas I (PrP) * Tet-Off Atlas II (PrP/CamKII) * Whole Brain Connectivity Atlas The data presented have been produced in collaboration with a large number of laboratories in Europe and the United States. | electron microscopy, image, brain, cerebellar cortex, hippocampus, connectivity, coronal section, high resolution, light microscopy, histology, microscopy, mouse brain, mouse brain atlas, mpeg, mri, nerve cell, nifti, neuroimaging, rat, rat brain, rodent brain, stereotaxic coordinate, xyz coordinate, gene expression | has parent organization: University of Oslo; Oslo; Norway | Free, Freely available | nif-0000-00424 | SCR_002727 | Rodent Brain Work Bench | 2026-02-13 10:55:06 | 21 | |||||||
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Special Mouse Strains Resource Resource Report Resource Website |
Special Mouse Strains Resource (RRID:SCR_002885) | SMSR | biomaterial supply resource, organism supplier, material resource | Resource of special strains of mice that are valuable tools for genetic analysis of complex diseases. They include panels of recombinant inbred (RI) and chromosome substitution (CS) strains. | strain panel, frozen, cryopreserved, recombinant inbred mouse, chromosome substitution mouse, consomic strain, gene, disease, strain |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: Mouse Phenome Database (MPD) has parent organization: Jackson Laboratory |
Recombinant inbred mouse, Chromosome substitution mouse, Consomic strain | NCRR P40 RR016049; NIH Office of the Director P40 OD011102 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25593 | SCR_002885 | Special Mouse Strains Resource (SMSR) | 2026-02-13 10:55:08 | 0 |
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