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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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HomoloGene Resource Report Resource Website 100+ mentions |
HomoloGene (RRID:SCR_002924) | HomoloGene | data or information resource, database, service resource | Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase. | homolog, paralog, ortholog, genome, gene, protein, protein alignment, phenotype, conserved domain, homology, amino acid sequence, cell, dna, gold standard |
is used by: NIF Data Federation is used by: Nowomics is used by: MitoMiner is listed by: OMICtools is listed by: re3data.org is related to: OMIM is related to: Mouse Genome Informatics (MGI) is related to: Zebrafish Information Network (ZFIN) is related to: SGD is related to: FlyBase is related to: ProbeMatchDB 2.0 is related to: Biomine is related to: Consensus CDS has parent organization: NCBI |
PMID:23193264 | Free, Freely availalbe | nif-0000-02975, r3d100010781, OMICS_01544 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene, https://doi.org/10.17616/R3889F | SCR_002924 | SciCrunch Registry | NCBI HomoloGene | 2026-11-07 12:02:03 | 459 | |||||
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Zebrafish Information Network (ZFIN) Resource Report Resource Website 500+ mentions |
Zebrafish Information Network (ZFIN) (RRID:SCR_002560) | ZFIN | data or information resource, database | Model organism database that serves as central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations.Serves as primary community database resource for laboratory use of zebrafish. Developed and supports integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases. | expression, gene, anatomy, development, disease, genomic, model, molecular, mutant, neuronal, organism, phenotype, physiological, synteny, zebrafish, gene expression, genome sequence, molecular neuroanatomy resource, genotype, anatomical structure, publication, genome, image collection, gold standard, bio.tools, FASEB list, RRID Community Authority |
uses: InterMOD is used by: NIF Data Federation is used by: Resource Identification Portal is used by: Morpholino Database is used by: Integrated Animals is used by: NIH Heal Project is recommended by: Resource Identification Portal 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: OMICtools is listed by: InterMOD is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: Phenoscape Knowledgebase is related to: MONARCH Initiative is related to: Bgee: dataBase for Gene Expression Evolution is related to: NIH Data Sharing Repositories is related to: HomoloGene is related to: Zebrafish International Resource Center is related to: Integrated Manually Extracted Annotation is related to: Zebrafish Genome Project has parent organization: University of Oregon; Oregon; USA is parent organization of: ZFIN Antibody Database is parent organization of: Zebrafish Anatomical Ontology is parent organization of: ZFIN Protocol Wiki is parent organization of: ZFIN Antibody Wiki is organization facet of: Alliance of Genome Resources |
NHGRI P41 HG002659; NHGRI R01 HG004834 |
PMID:23074187 PMID:21036866 PMID:16381936 |
Free, Available for download, Freely available | OMICS_01666, nif-0000-21427, biotools:zfin, r3d100010421, SCR_017504 | http://zfin.org/ZFIN/misc_html/tips.html#newrecord, https://wiki.zfin.org/display/general/ZFIN+Data+Submissions, https://bio.tools/zfin, https://doi.org/10.17616/R3CK5Z | SCR_002560 | SciCrunch Registry | Zebrafish Database, The Zebrafish Model Organism Database, Zebra Model Organism Database, ZebraFish Information Network, ZFIN | 2026-11-07 12:01:59 | 978 | ||||
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EcoGene Resource Report Resource Website 50+ mentions |
EcoGene (RRID:SCR_002437) | ECK, ECOGENE, ECOGENE G | data or information resource, database | Database that contains updated information about the Escherichia coli K-12 genome and proteome sequences, including extensive gene bibliographies. Users are able to download customized tables, perform Boolean query comparisons, generate sets of paired DNA sequences, and download any E. coli K-12 genomic DNA sub-sequence. BLAST functions, microarray data, an alphabetical index of genes, and gene overlap queries are also available. The Database Table Downloads Page provides a full list of EG numbers cross-referenced to the new cross-database ECK numbers and other common accession numbers, as well as gene names and synonyms. Monthly release archival downloads are available, but the live, daily updated version of EcoGene is the default mysql database for download queries. | life sciences, genomics, proteomics, gene, gene expression, genetics, protein, protein binding, protein-protein interaction, membrane, rna, dna, structure, function, functional annotation, annotation, blast, FASEB list |
is listed by: re3data.org is related to: RefSeq is related to: Colibri has parent organization: University of Miami Miller School of Medicine; Florida; USA |
NIH ; Lucille P. Markey Foundation ; NIGMS 5-R01-GM58560-05 |
PMID:23197660 PMID:10592181 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02784, r3d100010546 | https://doi.org/10.17616/R3KP5V | http://bmb.med.miami.edu/ http://bmb.med.miami.edu/EcoGene/EcoWeb/ http://www.ecogene.org/old/ | SCR_002437 | SciCrunch Registry | EcoGene Database of Escherichia coli Sequence and Function | 2026-11-07 12:02:27 | 58 | |||
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DrugBank Resource Report Resource Website 5000+ mentions |
DrugBank (RRID:SCR_002700) | DrugBank | data or information resource, database | Bioinformatics and cheminformatics database that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. | drug, target, pathway, structure, pharmacology, drug class, chemical, pharmaceutical, drug target, sequence, reaction, interaction, protein, proteome, blast, data analysis service, small molecule-protein, small molecule, clinical medicine, pharmacy, medicine, pharmaceutical biotechnology, cheminformatics, FASEB list |
is used by: NIF Data Federation is used by: Open PHACTS is used by: In vivo - In silico Metabolite Database is used by: GEROprotectors is listed by: OMICtools is listed by: re3data.org is related to: ConsensusPathDB is related to: PharmGKB Ontology is related to: Allen Institute Neurowiki is related to: Coremine Medical is related to: MalaCards is related to: PSICQUIC Registry is related to: DrugPort is related to: Integrated Manually Extracted Annotation has parent organization: University of Alberta; Alberta; Canada |
Genome Alberta ; Genome Canada ; GenomeQuest Inc. ; Canadian Institutes of Health Research |
PMID:16381955 PMID:21059682 PMID:18048412 |
Free, Freely available | nif-0000-00417, OMICS_01580, r3d100010544 | https://doi.org/10.17616/R3V60M | SCR_002700 | SciCrunch Registry | 2026-11-07 12:02:28 | 5839 | |||||
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Entrez Gene Resource Report Resource Website 1000+ mentions |
Entrez Gene (RRID:SCR_002473) | NCBI_Gene, NCBI Genen NCBI Entrez | data or information resource, database | Database for genomes that have been completely sequenced, have active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. Includes nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases. All entries follow NCBI's format for data collections. Content of Entrez Gene represents result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. Content is updated as new information becomes available. | gene, gene expression, gene location, gene map, gene prediction, genome, genome sequence analysis, phenotype, nomenclature, gene mapping, protein, genetic code, function, annotation, gold standard, bio.tools |
is used by: Animal QTLdb is used by: NIF Data Federation is used by: LIPID MAPS Proteome Database is used by: DisGeNET is used by: Nowomics is used by: Cytokine Registry is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: Vesiclepedia is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Rat Gene Symbol Tracker is related to: Gene Reference into Function is related to: Integrated Molecular Interaction Database is related to: Biomine is related to: SEGS is related to: STOP is related to: Coremine Medical is related to: Consensus CDS is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: Array Information Library Universal Navigator is related to: biomaRt has parent organization: NCBI works with: Open Regulatory Annotation Database |
PMID:17148475 PMID:21115458 |
Free, Freely available | nif-0000-02801, biotools:entrez_gene, OMICS_01651, r3d100010650 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene, https://bio.tools/entrez_gene, https://doi.org/10.17616/R3603S | SCR_002473 | SciCrunch Registry | NCBI Gene, Gene - Gene mapped phenotypes, Gene - Gene and mapped phenotypes, Gene Database, GeneID | 2026-11-07 12:02:02 | 2912 | |||||
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Protein Clusters Resource Report Resource Website 1+ mentions |
Protein Clusters (RRID:SCR_003459) | ProtClustDB | data or information resource, database | Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP | bacteriophage, mitochondrial organelle, chloroplast organelle, plasmid, phylogeny, nucleotide sequence, chloroplast, dna, virus, genome, organelle, gold standard |
is listed by: re3data.org has parent organization: NCBI |
NIH ; Intramural Research Program ; NLM |
PMID:18940865 | Free, Available for download, Freely available | nif-0000-03354, r3d100010861 | https://doi.org/10.17616/R3TS52 | SCR_003459 | SciCrunch Registry | Protein Clusters Database, NCBI Protein Clusters, Entrez Protein Clusters | 2026-11-07 12:02:19 | 4 | ||||
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NCBI Protein Database Resource Report Resource Website 1000+ mentions |
NCBI Protein Database (RRID:SCR_003257) | NCBI_GP, NCBI Protein, NCBI GP | data or information resource, database | Databases of protein sequences and 3D structures of proteins. Collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. | amino acid sequence, nucleotide, dna sequence, protein, sequence, sequence data, structure, function, dna, nucleotide sequence, genomics, protein binding, gold standard |
is used by: NIF Data Federation is listed by: re3data.org is related to: AmiGO is related to: GenBank is related to: RefSeq is related to: TPA is related to: UniProtKB is related to: Protein Information Resource is related to: Protein Research Foundation is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: BioExtract is related to: DIG IT - Database of Immunoglobulins and Integrated Tools has parent organization: NCBI |
Free, Freely available | SCR_017486, r3d100011331, nif-0000-03178 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=protein, https://doi.org/10.17616/R3JH0X | SCR_003257 | SciCrunch Registry | Entrez Protein, Protein Database, NCBI Protein Database, Protein sequence database, Entrez Protein Database | 2026-11-07 12:02:18 | 1025 | ||||||
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Influenza Virus Resource Resource Report Resource Website 50+ mentions |
Influenza Virus Resource (RRID:SCR_002984) | Influenza Virus Resource | data or information resource, database | Database of data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis and annotation. In addition, it provides links to other resources that contain flu sequences, publications and general information about flu viruses. Users can search the Flu database, build queries, retrieve sequences, and apply analysis tools. This includes selecting influenza sequences by virus, subtype, host, and other criteria, finding complete genome sets, aligning sequence and others in the database (up to 1000 sequences), viewing clustering and phylogenetic trees, BLAST searching a flu sequence against the database, and more. | genomics, genome, flu, variation, annotation, blast, cluster, phylogenetic tree, align, data analysis service |
is listed by: re3data.org is related to: GenBank is related to: Virus Variation has parent organization: NCBI |
Influenza virus | PMID:17942553 | Free, Available for download, Freely available | nif-0000-03023, r3d100011004 | https://doi.org/10.17616/R3S61C | SCR_002984 | SciCrunch Registry | NCBI Influenza Virus Resource | 2026-11-07 12:02:00 | 83 | ||||
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The NINDS Human Cell and Data Repository (NHCDR) Resource Report Resource Website 10+ mentions |
The NINDS Human Cell and Data Repository (NHCDR) (RRID:SCR_016319) | NHCDR | biomaterial supply resource, material resource, tissue bank | Cell sources currently include fibroblasts and/or induced pluripotent stem cells for Alzheimer's Disease, Amyotrophic Lateral Sclerosis (ALS), Ataxia-telangiectasia, Frontotemporal Lobar Degeneration (FTD), Huntington's Disease, Parkinson's Disease, and healthy controls. Cell sources, including isogenic cell lines for current and new diseases covered by the NINDS will be added over the next several years. | Stem, cell, fibroblast, plutipotent, isogenic |
is used by: NIH Heal Project is recommended by: National Library of Medicine is listed by: re3data.org works with: Cellosaurus |
Alzheimer's Disease, Amyotrophic Lateral Sclerosis (ALS), Ataxia-telangiectasia, Frontotemporal Lobar Degeneration (FTD), Huntington's Disease, Parkinson's Disease | NINDS ; NLM |
Restricted | https://nindsgenetics.org/ | SCR_016319 | SciCrunch Registry | NINDS Human Cell and Data Repository (NHCDR) | 2026-11-07 12:03:20 | 21 | |||||
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Microphysiology Systems Database Resource Report Resource Website 1+ mentions |
Microphysiology Systems Database (RRID:SCR_021126) | MPS-Db | data or information resource, database | Open source database used for analyzing and modeling compound interactions with human and animal organ models.Platform for experimental design, data management, and analysis, and to combine experimental data with reference data, to enable computational modeling. Resource for relating in vitro organ model data to multiple biochemical, preclinical, and clinical data sources on in vivo drug effects. | Compound interactions, human organ models, animal organ models, analyzing interactions, modeling interactions, |
is used by: NIH Heal Project is listed by: re3data.org |
NCATS UH3 TR00503; OD S10 OD01226; U.S. Environmental Protection Agency |
PMID:28781990 | Free, Freely available | SCR_021126 | SciCrunch Registry | MPS database | 2026-11-07 12:03:22 | 4 | ||||||
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INPTDAT Resource Report Resource Website |
INPTDAT (RRID:SCR_022167) | data or information resource, data repository, service resource, storage service resource | Interdisciplinary data platform provides access to research data and information from all fields of applied plasma physics and plasma medicine. Aims at distributing, publishing and archiving of data and information, supporting findability, accessibility, interoperability and re-use of data, for low temperature plasma physics community.Most of data are freely available and can be used under terms of license listed on dataset description page. Each dataset can be identified, cited and shared by using Digital Object Identifier. | Leibniz Institute for Plasma Science and Technology, FAIR data, applied plasma physics, plasma medicine, low temperature plasma physics community |
is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing |
Federal Ministry of Education and Research BMBF | Free, Freely available | r3d100013120, DOI:10.34711, DOI:10.17616/R31NJMM8, DOI:10.25504/FAIRsharing.2VADoR | https://doi.org/10.17616/R31NJMM8, https://doi.org/10.17616/r31njmm8, , https://doi.org/10.34711/, https://dx.doi.org/10.34711/, https://fairsharing.org/10.25504/FAIRsharing.2VADoR, https://doi.org/10.17616/R31NJMM8 | SCR_022167 | SciCrunch Registry | 2026-11-07 12:00:27 | 0 | |||||||
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BOLD Resource Report Resource Website 100+ mentions |
BOLD (RRID:SCR_004278) | BOLD | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | DNA barcode data with an online workbench that supports data validation, annotation, and publication for specimen, distributional, and molecular data. The data platform consists of three main modules, a data portal, a database of barcode clusters, and data collection workbench. The Public Data Portal provides access to all public barcode data which consists of data generated using the Workbench module as well as data mined from other sources. The Barcode Index Number (BIN) system assigns a unique identifier to each sequence cluster of COI, providing an interim taxonomic system for species in the animal kingdom. The workbench module integrates secure databases with analytical tools to provide a private collaborative environment for researchers to collect, analyze, and publish barcode data and ancillary DNA sequences. This platform also provides an annotation framework that supports tagging and commenting on records and their components (i.e. taxonomy, images, and sequences), allowing for community-based validation of barcode data. By providing specialized services, it aids in the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. Public data records include record identifiers, taxonomy, specimen details, collection information and sequence data. Data that has been publicly released through BOLD can be retrieved manually through the BOLD public interface or automatically through BOLD web services. BOLD analytical tools are available for any data set that exists in BOLD (including publicly available data). Analytical tools can be accessed through the BOLD Project Console under the headings Sequences Analysis or Specimen Aggregates. Some examples include Taxon ID Tree, Alignment Viewer, Distribution Maps, and Image Library. | protists, taxonomy, dna, barcode, dna barcode, gene sequence, primer, publication, barcode index number, unique identifier, annotation, platform, data management, data sharing, dna sequence, bioinformatics, molecular biology, biology, geography, species, sequence cluster, map, web service, image collection, FASEB list |
is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing has parent organization: University of Guelph; Ontario; Canada |
Canada Foundation for Innovation ; Genome Canada ; Ontario Innovation Trust ; NSERC ; Gordon and Betty Moore Foundation |
PMID:18784790 | Free, Public | DOI:10.17616/R3PP7J, nlx_29236, DOI:10.25504/FAIRsharing.en9npn, DOI:10.5883, r3d100010129 | http://www.boldsystems.org/, https://doi.org/10.17616/R3PP7J, https://doi.org/10.17616/r3pp7j, https://doi.org/10.5883/, https://dx.doi.org/10.5883/, https://fairsharing.org/10.25504/FAIRsharing.en9npn, https://doi.org/10.17616/R3KG65 | SCR_004278 | SciCrunch Registry | BOLD Systems, Barcode of Life Database Systems, Barcode of Life Database, Barcode of Life Data Systems, BOLD : The Barcode of Life Data System | 2026-11-07 12:00:32 | 499 | ||||
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BeetleBase Resource Report Resource Website 50+ mentions |
BeetleBase (RRID:SCR_001955) | BEETLEBASE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A centralized sequence database and community resource for Tribolium genetics, genomics and developmental biology containing genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The current version of Beetlebase is built on the Tribolium castaneum 3.0 Assembly (Tcas 3.0) released by the Human Genome Sequencing Center at the Baylor College of Medicine. The database is constructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relational database using the Chado schema and visualized as tracks in GBrowse. The genetic map is visualized using the comparative genetic map viewer CMAP. To enhance search capabilities, the BLAST search tool has been integrated with the GMOD tools. Tribolium castaneum is a very sophisticated genetic model organism among higher eukaryotes. As the member of a primitive order of holometabolous insects, Coleoptera, Tribolium is in a key phylogenetic position to understand the genetic innovations that accompanied the evolution of higher forms with more complex development. Coleoptera is also the largest and most species diverse of all eukaryotic orders and Tribolium offers the only genetic model for the profusion of medically and economically important species therein. The genome sequences may be downloaded. | red flour beetle, tribolium castaneum, sequence data, gene, mutant, genetic marker, expressed sequence tag, genome, blast, model organism, insect, developmental biology, genomics, genetics, entomology, development, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: RefSeq has parent organization: Kansas State University; Kansas; USA |
NCRR P20 RR16475 | PMID:18362917 PMID:17090595 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02599, biotools:beetlebase, r3d100010921 | https://bio.tools/beetlebase, https://doi.org/10.17616/R3G61K | http://bioinformatics.k-state.edu/BeetleBase/, http://www.bioinformatics.ksu.edu/BeetleBase/ | SCR_001955 | SciCrunch Registry | 2026-11-07 12:00:28 | 82 | ||||
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DataONE Resource Report Resource Website 10+ mentions |
DataONE (RRID:SCR_003999) | DataONE | catalog, data or information resource, data repository, database, portal, service resource, software resource, storage service resource | A distributed framework and cyberinfrastructure for open, persistent, and secure access to Earth observational data. It ensures the preservation, access, use and reuse of multi-scale, multi-discipline, and multi-national science data via three primary cyberinfrastucture elements and a broad education and outreach program. The DataONE Investigator Toolkit is a collection of software tools for finding, using, and contributing data in DataONE. DataONE currently hosts three Coordinating Nodes that provide network-wide services to enhance interoperability of the Member Nodes and support indexing and replication services. Coordinating Nodes provide a replicated catalog of Member Node holdings and make it easy for scientists to discover data wherever they reside, also enabling data repositories to make their data and services more broadly available to the international community. DataONE Coordinating Nodes are located at the University of New Mexico, the University of California Santa Barbara and at the University of Tennessee (in collaboration with Oak Ridge National Laboratory). DataONE comprises a distributed network of data centers, science networks or organizations. These organizations can expose their data within the DataONE network through the implementation of the DataONE Member Node service interface. In addition to scientific data, Member Nodes can provide computing resources, or services such as data replication, to the DataONE community. | earth, environment, data sharing, cyberinfrastructure, earth observational data, data management, data set, FASEB list |
uses: DataUp is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing has parent organization: University of New Mexico; New Mexico; USA |
NSF 0830944; NSF 1430508 |
Acknowledgement requested | DOI:10.25504/FAIRsharing.yyf78h, nlx_158410, DOI:10.17616/R3101G, r3d100010478, DOI:10.2586 | https://doi.org/10.17616/R3101G, https://doi.org/10.17616/r3101g, https://doi.org/10.2586/, https://dx.doi.org/10.2586/, https://fairsharing.org/10.25504/FAIRsharing.yyf78h, https://doi.org/10.17616/R3TG83 | SCR_003999 | SciCrunch Registry | Data Observation Network for Earth | 2026-11-07 12:00:12 | 45 | |||||
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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 | 2026-11-07 12:00:13 | 25 | ||||
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Synapse Resource Report Resource Website 1000+ mentions |
Synapse (RRID:SCR_006307) | Synapse | data or information resource, data repository, database, service resource, storage service resource | A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data. | data sharing, collaboration, data management, analysis, genome, phenotype, crowd sourcing, open data, provenance, resource management, annotation, authoring, markup, r, python, java, command-line, cloud, FASEB list |
is used by: NF Data Portal is listed by: FORCE11 is listed by: DataCite is listed by: re3data.org is related to: clearScience is related to: Exemplar Microscopy Images of Tissues has parent organization: Sage Bionetworks |
Cancer, Normal, Cardiovascular disease, Floppy hat syndrome | Life Sciences Discovery Fund ; NCI ; NHLBI ; Alfred P. Sloan Foundation |
The community can contribute to this resource | nlx_151983, DOI:10.17616/R3B934, r3d100011894, DOI:10.7303 | https://doi.org/10.17616/R3B934, https://doi.org/10.48550/arxiv.1506.00272, https://doi.org/10.7303/, https://dx.doi.org/10.7303, https://doi.org/10.17616/R3B934 | SCR_006307 | SciCrunch Registry | 2026-11-07 12:00:33 | 1104 | |||||
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B2SHARE Eudat Resource Report Resource Website 1+ mentions |
B2SHARE Eudat (RRID:SCR_023135) | data repository, service resource, storage service resource | Used to store, publish and share research data in FAIR way. Facilitates research data storage, guarantees long-term persistence of data and allows data, results or ideas to be shared worldwide.Supports community domains with metadata extensions, access rules and publishing workflows. |
is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing |
Free, Freely available | r3d100011394, DOI:10.25504/FAIRsharing.da9307, DOI:10.17616/R3VK72, DOI:10.3473 | https://doi.org/10.3473, https://dx.doi.org/10.3473, http://doi.org/10.17616/R3VK72, https://fairsharing.org/10.25504/FAIRsharing.da9307, https://doi.org/10.17616/R3VK72 | SCR_023135 | SciCrunch Registry | B2SHARE | 2026-11-07 12:00:57 | 3 | ||||||||
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Polar Data Catalogue Resource Report Resource Website 1+ mentions |
Polar Data Catalogue (RRID:SCR_023131) | data repository, service resource, storage service resource | Repository of metadata and data that describes and provides access to diverse data sets generated by Arctic and Antarctic researchers. The metadata records follow ISO 19115 and Federal Geographic Data Committee (FGDC) standard formats to provide exchange with other data centres. The records cover a wide range of disciplines from natural sciences and policy, to health and social sciences. The PDC Geospatial Search tool is available to the public and researchers alike and allows searching data using a mapping interface and other parameters. | Arctic and Antarctic researcher data, Federal Geographic Data Committee standard format, |
is listed by: DataCite is listed by: re3data.org |
Free, Freely available | DOI:10.17616/R3QK86, r3d100010953, DOI:10.5884 | https://doi.org/10.5884, https://dx.doi.org/10.5884, http://doi.org/10.17616/R3QK86, https://doi.org/10.17616/R3QK86 | SCR_023131 | SciCrunch Registry | ArcticNet | 2026-11-07 12:00:56 | 1 | |||||||
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Aperta Turkey Open Archive Resource Report Resource Website 1+ mentions |
Aperta Turkey Open Archive (RRID:SCR_023128) | data repository, service resource, storage service resource | Aperta is the name of the Turkish Open Archive.You can upload your scientific studies within the scope of Aperta to this portal or you can easily access the uploaded studies. |
is listed by: DataCite is listed by: re3data.org |
Free, Freely available | DOI:10.48623, DOI:10.17616/r31njmv8, r3d100013444 | https://doi.org/10.48623, https://dx.doi.org/10.48623, https://doi.org/10.17616/r31njmv8, https://doi.org/10.17616/R31NJMV8 | SCR_023128 | SciCrunch Registry | Aperta Turkey Open Archive | 2026-11-07 12:01:03 | 4 | ||||||||
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BioHeritage National Science Challenge Data Repository Resource Report Resource Website |
BioHeritage National Science Challenge Data Repository (RRID:SCR_023141) | data repository, service resource, storage service resource | Data catalogue and repository for New Zealand's Biological Heritage National Science Challenge. |
is listed by: DataCite is listed by: re3data.org |
Free, Freely available | DOI:10.17616/R31NJN01, DOI:10.34721, r3d100013617 | https://doi.org/10.34721, https://dx.doi.org/10.34721, http://doi.org/10.17616/R31NJN01, https://doi.org/10.17616/R31NJN01 | SCR_023141 | SciCrunch Registry | BioHeritage National Science Challenge Data Repository | 2026-11-07 12:01:09 | 0 |
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