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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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eMouseAtlas Resource Report Resource Website 50+ mentions |
eMouseAtlas (RRID:SCR_002981) | EMAP, EMA, EMAGE, MAP, EMAP, MAP2.0, | atlas, data or information resource, database | Detailed multidimensional digital multimodal atlas of C57BL/6J mouse nervous system with data and informatics pipeline that can automatically register, annotate, and visualize large scale neuroanatomical and connectivity data produced in histology, neuronal tract tracing, MR imaging, and genetic labeling. MAP2.0 interoperates with commonly used publicly available databases to bring together brain architecture, gene expression, and imaging information into single, simple interface.Resource to visualise mouse development, identify anatomical structures, determine developmental stage, and investigate gene expression in mouse embryo. eMouseAtlas portal page allows access to EMA Anatomy Atlas of Mouse Development and EMAGE database of gene expression.EMAGE is freely available, curated database of gene expression patterns generated by in situ techniques in developing mouse embryo. EMA, e-Mouse Atlas, is 3-D anatomical atlas of mouse embryo development including histology and includes EMAP ontology of anatomical structure, provides information about shape, gross anatomy and detailed histological structure of mouse, and framework into which information about gene function can be mapped. | Mouse Atlas Project, molecular neuroanatomy resource, adult mouse, mouse, brain, c57bl/6j, magnetic resonance microscopy, diffusion-weighted image, blockface imaging, immunohistochemistry, in situ hybridization, neuroanatomy, mri, dti, brain architecture, gene expression, neuroimaging, ontology, connectivity, histology, neuronal tract tracing, genetic labeling, newborn mouse, experimental protocol, bio.tools, ontology, histology, mouse embryo, gene expression, gxd query interface, digital anatomical atlas, spatial region, domain, 2d, 3d, virtual embryo model, development atlas, standard anatomical nomenclature, developmental staging criteria, spatially mapped, anatomy nomenclature, molecular neuroanatomy resource, embryonic mouse, FASEB list |
is related to: GUDMAP Ontology is related to: EMAGE Gene Expression Database is related to: EMAGE Gene Expression Database is related to: HUDSEN is related to: Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project has parent organization: University of Edinburgh; Scotland; United Kingdom has parent organization: Jackson Laboratory is parent organization of: Minimal Anatomical Terminology |
Medical Research Council ; NIA ; NIBIB ; NIDA ; NIDCD ; NINDS |
PMID:15043218 PMID:18077470 PMID:16381949 |
Free, Freely available | nif-0000-00038, nif-0000-00505, biotools:emap, SCR_007281, biotools:ma | http://www.emouseatlas.org/emap/home.html, https://bio.tools/emap, https://bio.tools/ma | http://genex.hgu.mrc.ac.uk/, http://www.loni.ucla.edu/MAP/ | SCR_002981 | SciCrunch Registry | emouseatlas, e-mouse Atlas, EMAGE Gene Expression Database, EMA, Edinburgh Mouse Atlas of Gene Expression, e-Mouse Atlas, EMA Anatomy Atlas of Mouse Development | 2026-10-24 12:50:25 | 71 | |||
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HUDSEN Resource Report Resource Website 1+ mentions |
HUDSEN (RRID:SCR_006324) | HUDSEN | community building portal, data or information resource, portal | Forum for researchers in human developmental biology and related fields to meet and establish links. | development, genetics, embryology, embryonic, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: eMouseAtlas is related to: aGEM has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom is parent organization of: HUDSEN Electronic Atlas of the Developing Human Brain is parent organization of: HUDSEN Human Gene Expression Spatial Database |
nlx_152025, biotools:hudsen | https://bio.tools/hudsen | SCR_006324 | SciCrunch Registry | Human Developmental Studies Network | 2026-10-24 12:45:42 | 5 | |||||||
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EMAGE Gene Expression Database Resource Report Resource Website 10+ mentions |
EMAGE Gene Expression Database (RRID:SCR_005391) | EMAGE | atlas, data or information resource, data repository, database, service resource, storage service resource | A database of in situ gene expression data in the developing mouse embryo and an accompanying suite of tools to search and analyze the data. mRNA in situ hybridization, protein immunohistochemistry and transgenic reporter data is included. The data held is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. The conceptual framework which houses the descriptions of the gene expression patterns in EMAGE is the EMAP Mouse Embryo Anatomy Atlas. This consists of a set of 3D virtual embryos at different stages of development, as well as an accompanying ontology of anatomical terms found at each stage. The raw data images can be conventional 2D photographs (of sections or wholemount specimens) or 3D images of wholemount specimens derived from Optical Projection Tomography (OPT) or confocal microscopy. Users may submit data using a Data submission tool or without. | genetics, 3d model, anatomy, development, mouse morphology, molecular neuroanatomy resource, gene expression, in situ hybridization, immunohistochemistry, embryo, in situ reporter, embryonic mouse, optical projection tomography, confocal microscopy, annotation, pathway, gene association, protein, theiler stage, gene expression, embryology, dna, protein, protein-protein interaction, protein binding, gene, embryology, anatomy, genetics, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: HUDSEN Electronic Atlas of the Developing Human Brain is related to: eMouseAtlas is related to: eMouseAtlas is related to: HUDSEN Human Gene Expression Spatial Database is related to: aGEM is related to: Eurexpress is related to: Gene Expression Database is related to: Gene Ontology is related to: NIDDK Information Network (dkNET) is related to: GUDMAP Ontology |
MRC | PMID:19767607 | Except where noted, Creative Commons Attribution License, The community can contribute to this resource | biotools:emage, nif-0000-00080, r3d100010564 | https://bio.tools/emage, https://doi.org/10.17616/R3860B | SCR_005391 | SciCrunch Registry | Emage (e-Mouse Atlas of Gene Expression), e-Mouse Atlas of Gene Expression | 2026-10-24 12:49:06 | 25 | ||||
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Minimal Anatomical Terminology Resource Report Resource Website |
Minimal Anatomical Terminology (RRID:SCR_003385) | MAT | controlled vocabulary, data or information resource, ontology | An ontology of minimal set of terms for anatomy. | obo, anatomy, organismal, ontology |
is listed by: BioPortal is listed by: OBO has parent organization: eMouseAtlas |
Free, Available for download, Freely available | nlx_157480 | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/multispecies/minimal_anatomical_terminology.obo | SCR_003385 | SciCrunch Registry | 2026-10-24 12:44:56 | 0 | |||||||
|
Jackson Laboratory Resource Report Resource Website 10000+ mentions |
Jackson Laboratory (RRID:SCR_004633) | JAX | institution | An independent, nonprofit organization focused on mammalian genetics research to advance human health. Their mission is to discover the genetic basis for preventing, treating, and curing human disease, and to enable research for the global biomedical community. Jackson Laboratory breeds and manages colonies of mice as resources for other research institutions and laboratories, along with providing software and techniques. Jackson Lab also conducts genetic research and provides educational material for various educational levels. | genomic, disease, mouse model, human disease, biomaterial manufacture |
is listed by: One Mind Biospecimen Bank Listing is affiliated with: Integrative Human Microbiome Project is related to: ScienceExchange is related to: Federation of International Mouse Resources is related to: MGI strains is related to: One Mind Biospecimen Bank Listing is related to: Beta Cell Biology Consortium is related to: Mouse Mutagenesis Center for Developmental Defects is related to: GenomeMUSter is parent organization of: Mouse Models For Alzheimer's Disease Research is parent organization of: Type 1 Diabetes Resource is parent organization of: MouseCyc is parent organization of: Special Mouse Strains Resource is parent organization of: Gene Weaver is parent organization of: Mouse Phenome Database (MPD) is parent organization of: Jackson Laboratory Cytogenetic Models Resource is parent organization of: Parkinson's Disease Mouse Model Resource is parent organization of: Eye mutant resource - The Jackson Laboratory is parent organization of: Brainbow mouse resource at Jackson Labs is parent organization of: Short Course on the Genetics of Addiction is parent organization of: JAX Cre Repository is parent organization of: Donate a strain to The Jackson Laboratory Repository is parent organization of: Jackson Laboratory Neurobiology is parent organization of: QTL Archive is parent organization of: Mouse Genome Informatics: The Gene Ontology Project is parent organization of: Mouse Genome Informatics (MGI) is parent organization of: Mouse Tumor Biology Database is parent organization of: Gene Expression Database is parent organization of: The Jackson Laboratory Hearing Research Program is parent organization of: JAX Mice: Neural Tube Defects is parent organization of: JAX Neuroscience Mutagenesis Facility is parent organization of: Induced Mutant Resource is parent organization of: Mouse Mutant Resource is parent organization of: Mouse Genome Database is parent organization of: Mutant Mouse Resource and Research Center is parent organization of: eMouseAtlas is parent organization of: GBRS is parent organization of: Jackson Laboratory Scientific Instrument Services Core Facility provides: Knockout Mouse Project Repository |
Types 1 diabetes, Type 2 diabetes, Diabetes, Cardiovascular diseases, Metabolic disease, Cancer, Rare disease, Alzheimer's disease, Demantia | Available to the research community, Available to the educational community | ISNI: 0000 0004 0374 0039, nlx_63162, grid.249880.f, Crossref funder ID: 100005946 | https://ror.org/021sy4w91 | SCR_004633 | SciCrunch Registry | JAX Lab, Jackson Lab | 2026-10-24 12:45:14 | 15196 | |||||
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GUDMAP Ontology Resource Report Resource Website 1+ mentions |
GUDMAP Ontology (RRID:SCR_002637) | GUDMAP Ontology | controlled vocabulary, data or information resource, ontology, 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 | SciCrunch Registry | 2026-10-24 12:44:45 | 2 | ||||||
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Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project Resource Report Resource Website |
Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project (RRID:SCR_006630) | MGEIR | analysis service resource, atlas, data analysis service, data or information resource, database, expression atlas, production service resource, service resource | A unified resource that combines text-based and 3D graphical methods to store, display, and analyze mouse developmental gene expression information. The Mouse Gene Expression Information Resource resource will integrate the following components: * Gene Expression Database (GXD) - Integrates different types of expression data and provides links to many other resources to place the data into the larger biological and analytical context. * Anatomy Database - Provides the standard nomenclature for developmental anatomy. * 3D Atlas / Graphical Gene Expression Database - Provides a high-resolution digital representation of mouse anatomy reconstructed from serial sections of single embryos at each representative developmental stage enabling 3D graphical display and analysis of in situ expression data. | embryo, gene expression, gene, 3d, anatomy, atlas, biological, developmental, high-resolution, in situ, mouse, nomenclature, development, developmental stage, embryonic mouse, image |
is related to: Gene Expression Database is related to: eMouseAtlas has parent organization: Mouse Genome Informatics (MGI) |
MRC ; BBSRC ; European Science Foundation ; NICHD HD062499 |
nif-0000-10305 | SCR_006630 | SciCrunch Registry | Gene Expression Information Resource, Mouse Gene Expression Information Resource Project | 2026-10-24 12:45:46 | 0 | |||||||
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University of Edinburgh; Scotland; United Kingdom Resource Report Resource Website 10+ mentions |
University of Edinburgh; Scotland; United Kingdom (RRID:SCR_011637) | university | Research university in Edinburgh, Scotland, founded in 1582. Has five main campuses. Known for arts, humanities and computer science. |
is related to: International AMD Genetics Consortium is parent organization of: Schizophrenia and Bipolar Disorder Genetics Blog is parent organization of: Neural Open Simulation is parent organization of: eMouseAtlas is parent organization of: flytrap is parent organization of: nematodes.org is parent organization of: BrainTrap: Fly Brain Protein Trap Database is parent organization of: Roslin Wellcome Trust Tick Cell Biobank is parent organization of: Virtual Fly Brain is parent organization of: COBrA is parent organization of: BioLayout Express 3D is parent organization of: Protein-Protein Interaction Database is parent organization of: GPX-Macrophage is parent organization of: LumbriBASE is parent organization of: BoLA Nomenclature: International Society for Animal Genetics is parent organization of: CaDBase: Genetic diversity in cattle is parent organization of: CVonline: The Evolving, Distributed, Non-Proprietary Online Compendium of Computer Vision is parent organization of: FigTree is parent organization of: CAMARADES Protocols for Systematic Reviews of Animal Studies is parent organization of: BEAST is parent organization of: Edinburgh Brain and Tissue Banks is parent organization of: University of Edinburgh GenePool Next Generation Sequencing and Bioinformatics is parent organization of: University of Edinburgh Labs and Facilities is parent organization of: Roslin Institute Labs and Facilities is parent organization of: University of Edinburgh Immunodetection and Imaging is parent organization of: Queens Medical Research Institute Labs and Facilities is parent organization of: GeneProf is parent organization of: NCJDSU is parent organization of: Kidney Development Database is parent organization of: Genes to Cognition - Biological Resources is parent organization of: 959 Nematode Genomes is parent organization of: Biological General Repository for Interaction Datasets (BioGRID) is parent organization of: Parallel Stochastic Ion Channel Simulator is parent organization of: Seq-Gen is parent organization of: eHistology is parent organization of: Simple Neurite Tracer is parent organization of: University of Edinburgh Wellcome Trust Centre for Cell Biology Bioinformatics Core Facility is parent organization of: University of Edinburgh College of Medicine and Veterinary Medicine MRC Institute of Genetics and Molecular Medicine Bioinformatics Analysis Core Facility is parent organization of: GeneATLAS is parent organization of: Systematic Review Facility is parent organization of: University of Edinburgh Clinical Research Mass Spectrometry Core Facility is parent organization of: University of Edinburgh EdinOmics Core Facility is parent organization of: University of Edinburgh Genomics Core Facility is parent organization of: Automated Systematic Search Deduplicator is parent organization of: University of Edinburgh UK Zebrafish Imaging and Screening Core Facility is parent organization of: University of Edinburgh Institute of Genetics and Cancer IGC Mass Spectrometry Core Facility hosts: BRAINS Imagebank |
ISNI 0000 0004 1936 7988, , Crossref Funder ID 501100000848, GRID grid.4305.2, Wikidata Q160302, nlx_37972 | https://ror.org/01nrxwf90 | SCR_011637 | SciCrunch Registry | 2026-10-24 12:52:30 | 10 |
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