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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Metabolomics Workbench Resource Report Resource Website 500+ mentions |
Metabolomics Workbench (RRID:SCR_013794) | MetWB | service resource, data or information resource, data repository, storage service resource | Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops. | repository, metabolomics, database, funding, training, protocol, bio.tools, FASEB list, DRKB |
is used by: NIH Heal Project is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases lists: NIH Metabolomics program lists: MetaCore lists: JMP lists: STATISTICA lists: Spotfire lists: Coordination of Standards in Metabolomics lists: MetaboLights lists: MetabolomeXchange lists: Metabolomics Society lists: Birmingham Metabolite Library lists: Glycan Mass Spectral Database (GMDB) lists: Mass Spectral Library lists: mzCloud lists: MetabolomeExpress lists: Spectral Database System (SDBS) lists: CTSgetR lists: Hierarchical Clustering lists: imDEV lists: Linear Discriminant Analysis lists: Principal Components Analysis lists: mwtabR lists: 3Omics lists: ACD/ NMR Processor lists: NIST Mass Spectrometry Data Center lists: Chemical Translation Service lists: Chenomx NMR Suite lists: DeviumWeb lists: MBRole lists: MetaMapR lists: MetaP lists: Metscape lists: SIMCA lists: TeachingDemos is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is listed by: re3data.org is listed by: DataCite has parent organization: University of California; California; USA is parent organization of: Metabolomics Workbench Metabolite Database |
NIH ; NIDDK DK141185 |
Free, Freely available | biotools:Metabolomics_Workbench, r3d100012314 | https://bio.tools/Metabolomics_Workbench, https://api.datacite.org/dois?prefix=10.21228 | SCR_013794 | Metabolomics Workbench, MetWB, UCSD Metabolomics Workbench, Metabolomics Workbench (MetWB) | 2026-08-03 09:35:32 | 534 | |||||
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Cancer Imaging Archive (TCIA) Resource Report Resource Website 100+ mentions |
Cancer Imaging Archive (TCIA) (RRID:SCR_008927) | TCIA | data repository, data or information resource, database, image repository, catalog, storage service resource, service resource, data set | Archive of medical images of cancer accessible for public download. All images are stored in DICOM file format and organized as Collections, typically patients related by common disease (e.g. lung cancer), image modality (MRI, CT, etc) or research focus. Neuroimaging data sets include clinical outcomes, pathology, and genomics in addition to DICOM images. Submitting Data Proposals are welcomed. | dicom, imaging, ct, pet, pt, x-ray, mri, magnetic resonance, medical, clinical, research, clinical neuroinformatics, computed tomography, dicom, imaging genomics, magnetic resonance, pet, spect, test data, web service, image collection, image, FASEB list |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing is affiliated with: BraTumIA (Brain Tumor Image Analysis) is related to: NIH Data Sharing Repositories is related to: NCI Imaging Data Commons has parent organization: Frederick National Laboratory for Cancer Research has parent organization: NCI-Frederick |
Cancer | NCI | Restricted | DOI:10.25504/FAIRsharing.jrfd8y, DOI:10.17616/R3NH0V, DOI:10.7937, nlx_151749, r3d100011559 | http://www.nitrc.org/projects/tcia, http://www.cancerimagingarchive.net/, http://www.cancerimagingarchive.net/primary-data/, https://wiki.cancerimagingarchive.net/display/Public/Collections, https://doi.org/10.17616/R3NH0V, https://doi.org/10.17616/r3NH0V, https://doi.org/10.7937/, https://dx.doi.org/10.7937/, https://fairsharing.org/10.25504/FAIRsharing.jrfd8y, https://doi.org/10.17616/R3NH0V, https://doi.org/10.17616/R3NH0V | SCR_008927 | TCIA, Cancer Imaging Archive, The Cancer Imaging Archive (TCIA), Cancer Imaging Archive (TCIA), The Cancer Imaging Archive | 2026-08-03 09:34:16 | 287 | ||||
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Biodiversity Heritage Library Resource Report Resource Website 1+ mentions |
Biodiversity Heritage Library (RRID:SCR_008969) | BHL | data or information resource, database, bibliography | Collection of legacy literature in biodiversity assembled by an international consortium of natural history and botanical libraries. It also serves as the foundational literature component of the Encyclopedia of Life. Browse by author, title, subject, collection, map, year, language, and contributor. Taxonomic search using UBio. Also supports data export and a variety of machine interfaces. | literature, taxonomy, scientific illustration, botany, biology, natural history, biodiversity, extinct animal, herbaria, ecology, botanical library, extinct |
is listed by: re3data.org is related to: EOL - Encyclopedia of Life |
MacArthur Foundation via the Encyclopedia of Life ; Gordon and Betty Moore Foundation ; Richard Lounsbery Foundation ; Institute of Museum and Library Services ; Smithsonian Institution ; Atherton Seidell Endowment Fund |
If files in, Public domain, Acknowledgement requested, If files are from a copyrighted work for which we have obtained permission, Then all of the files on http://www.biodiversitylibrary.org are, Creative Commons Attribution-NonCommercial-ShareAlike License, v3, If a work in the BHL is published in 1923 or after, The work may be in copyright. More at, Http://biodivlib.wikispaces.com/Licensing+and+Copyright | nlx_152035 | SCR_008969 | Biodiversity Library | 2026-08-03 09:34:01 | 5 | ||||||
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ACADIS Gateway Resource Report Resource Website |
ACADIS Gateway (RRID:SCR_010473) | ACADIS Gateway | data repository, data or information resource, database, storage service resource, service resource | A repository and data management services for Arctic research data. Data include long-term observational timeseries, local, regional, and system-scale research from many diverse domains. | arctic region, permafrost, oceanography, cryosphere, sea ice, arctic people, atmosphere, remote sensing, biogeochemistry, glacier, physical sciences, arctic, agriculture, atmosphere, biological classification, biosphere, climate indicator, cryosphere, human dimension, land surface, ocean, paleoclimate, solid earth, terrestrial hydrosphere |
is listed by: re3data.org has parent organization: National Snow and Ice Data Center |
NSF | nlx_157746, r3d100010964 | SCR_010473 | ACADIS Gateway - An Arctic Data Repository, Advanced Cooperative Arctic Data and Information Service (ACADIS) Gateway, Advanced Cooperative Arctic Data and Information Service Gateway | 2026-08-03 09:34:50 | 0 | |||||||
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Data and Specimen Hub (NICHD DASH) Resource Report Resource Website 50+ mentions |
Data and Specimen Hub (NICHD DASH) (RRID:SCR_016314) | NICHD DASH, DASH | data repository, biospecimen repository, material storage repository, storage service resource, service resource | Repository to store and access de-identified data from NICHD funded research studies for purposes of secondary research use. It serves as mechanism for NICHD-funded extramural and intramural investigators to share research data from studies in accordance with NIH Data Sharing Policy and NIH Genomic Data Sharing Policy. |
is used by: NIH Heal Project is recommended by: National Library of Medicine is listed by: re3data.org |
NICHD | Restricted | r3d100012915 | https://doi.org/10.17616/R31NJMGJ | SCR_016314 | NICHD Data and Specimen Hub, Data and Specimen Hub | 2026-08-03 09:36:42 | 73 | ||||||
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NeuroMorpho.Org Resource Report Resource Website 50+ mentions |
NeuroMorpho.Org (RRID:SCR_002145) | data repository, data or information resource, database, storage service resource, service resource | Centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact. | neuron, morphological reconstruction, morphometry, axonal arborization, digital neuronal reconstruction, neuronal reconstruction, neuronal morphology, data sharing, annotation, brain region, neocortex, digital reconstruction, neurogenetics, neurochemistry, neuroscience, neurology, FASEB list |
is used by: NIF Data Federation is used by: BICCN is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: DONE: Detection of Outlier NEurons is related to: NIF Literature is related to: Computational Neurobiology and Imaging Center is related to: Integrated Manually Extracted Annotation is related to: xyz2swc is related to: Allen Institute for Brain Science has parent organization: George Mason University; Virginia; USA is parent organization of: NeuroMorpho.Org species ontology is parent organization of: NeuroMorpho.Org species ontology old |
NINDS R01 NS39600; MURI ONR N000141010198 |
PMID:17728438 PMID:16552417 PMID:18949582 |
Free, Available for download, Freely available | nif-0000-00006, r3d100010107 | http://www.nitrc.org/projects/neuromorpho_org, http://neuromorpho.org/, https://doi.org/10.17616/R3WW2K | SCR_002145 | Neuro Morpho, NeuroMorpho.org, NeuroMorpho | 2026-08-03 09:31:46 | 96 | |||||
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Marine Geoscience Data System Resource Report Resource Website 10+ mentions |
Marine Geoscience Data System (RRID:SCR_002164) | MGDS | service resource, data repository, storage service resource | Repository providing free access to marine geophysical data (e.g. bathymetry, seismic data, magnetics, gravity, images) and related land-based data from NSF-funded research conducted throughout the global oceans. Data Portals include GeoPRISMS, MARGINS, Ridge 2000, Antarctic and Southern Ocean Data Synthesis, the Global Multi-Resolution Topography Synthesis, and Seismic Reflection Field Data Portal. Primary data types served are multibeam bathymetric data from the ocean floor, seismic reflection data imaging below the seafloor, and multi-disciplinary ship based data from the Southern Ocean. Other holdings include deep-sea photographic transects, and ultra-high resolution bathymetry, temperature probe data, biological species compilations, MAPR and CTD data. Derived data products and sets include microseismicity catalogs, images, visualization scenes, magnetic and gravity compilations, grids of seismic layer thickness, velocity models, GIS project files, and 3D visualizations. Tools to discover, explore, and visualize data are available. They deliver catalogs, maps, and data through standard programmatic interfaces. GeoMapApp, a standalone data visualization and analysis tool, permits dynamic data exploration from a map interface and the capability to generate and download custom grids and maps and other data. Through GeoMapApp, users can access data hosted at the MGDS, at other data repositories, and import their own data sets. Global Multi-Resolution Topography (GMRT) is a continuously-updated compilation of seafloor bathymetry integrated with global land topography. It can be used to create maps and grids and it can be accessed through several standard programmatic interfaces including GeoMapApp and Google Earth. The GMRT compilation can also be explored in 3D using Virtual Ocean. The MGDS MediaBank contains high quality images, illustrations, animations and video clips that are organized into galleries. Media can be sorted by category, and keyword and map-based search options are provided. Each item in the MediaBank is accompanied by metadata that provides access to a cruise catalog and data repository. | observation, solid earth, ocean, earth, polar sciences, marine, geophysical, bathymetry, seismic, magnetics, gravity, image, geology, bathymetric map, topographic map, mid-ocean ridge, submarine topography, continental margin, continental shelf, continental slope, expedition, catalog, web service, dynamic map |
uses: DataCite is listed by: re3data.org is listed by: CINERGI is related to: PetDB is related to: GeoMapApp has parent organization: Integrated Earth Data Applications is parent organization of: Antarctic and Southern Ocean Data Portal is parent organization of: Academic Seismic Portal at LDEO is parent organization of: U.S. Antarctic Program Data Coordination Center |
NSF | Free, Freely available | r3d100010273, nlx_154713, DOI:10.26022/ | https://doi.org/10.26022/, https://dx.doi.org/10.26022/, https://doi.org/10.17616/R38C83 | SCR_002164 | 2026-08-03 09:31:41 | 16 | ||||||
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Cell Centered Database Resource Report Resource Website 10+ mentions |
Cell Centered Database (RRID:SCR_002168) | CCDB | data repository, data or information resource, database, image repository, storage service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented June 5, 2017. It has been merged with Cell Image Library. Database for sharing and mining cellular and subcellular high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging that makes unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. Techniques range from wide field mosaics taken with multiphoton microscopy to 3D reconstructions of cellular ultrastructure using electron tomography. Contributions from the community are welcome. The CCDB was designed around the process of reconstruction from 2D micrographs, capturing key steps in the process from experiment to analysis. The CCDB refers to the set of images taken from microscope the as the Microscopy Product. The microscopy product refers to a set of related 2D images taken by light (epifluorescence, transmitted light, confocal or multiphoton) or electron microscopy (conventional or high voltage transmission electron microscopy). These image sets may comprise a tilt series, optical section series, through focus series, serial sections, mosaics, time series or a set of survey sections taken in a single microscopy session that are not related in any systematic way. A given set of data may be more than one product, for example, it is possible for a set of images to be both a mosaic and a tilt series. The Microscopy Product ID serves as the accession number for the CCDB. All microscopy products must belong to a project and be stored along with key specimen preparation details. Each project receives a unique Project ID that groups together related microscopy products. Many of the datasets come from published literature, but publication is not a prerequisite for inclusion in the CCDB. Any datasets that are of high quality and interest to the scientific community can be included in the CCDB. | electron microscope, light microscopy, electron tomography, electron microscopy, image, cell, microscopy, tomography |
is used by: NIF Data Federation is used by: Integrated Datasets is listed by: re3data.org is related to: Cell Image Library (CIL) is related to: Cell Image Library (CIL) is related to: Whole Brain Catalog is related to: Integrated Manually Extracted Annotation has parent organization: University of California at San Diego; California; USA has parent organization: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR is parent organization of: Subcellular Anatomy Ontology is parent organization of: CCDB Image Converter is parent organization of: Jinx is parent organization of: WebImageBrowser is parent organization of: Image Workflow is parent organization of: Animal Imaging Database |
PMID:18054501 PMID:12160711 |
Free, Freely available | nif-0000-00007, r3d100000018 | SCR_002168 | CCDB, Cell-Centered Database | 2026-08-03 09:31:35 | 31 | ||||||
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National Snow and Ice Data Center Resource Report Resource Website 10+ mentions |
National Snow and Ice Data Center (RRID:SCR_002220) | NSIDC | image collection, data repository, data or information resource, database, storage service resource, service resource | National data center / repository for snow and ice data including snow, ice, glaciers, frozen ground, and climate interactions that make up Earth's cryosphere. The center manages and distributes scientific data, creates tools for data access, supports data users, performs scientific research, and educates the public about the cryosphere. Users may explore the Earth's frozen places in the collection of photographs and images. Photographs from field research trips, images captured by satellites of the changing cryosphere, and photos and images are available. Data sets are organized into the following groups: sea ice, frozen ground, snow cover, snow hydrology, glaciers and ice sheets, arctic people. | polar, snow, ice, climate, photo, visualization, sea ice, arctic, meteorology, frozen, antarctica, arctic region, sea ice, satellite, ice sheet, global warming, glacier, frozen ground, cryosphere, climatology, arctic people, snow cover, snow hydrology, catalog, data set, interaction, FASEB list |
is listed by: CINERGI is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing has parent organization: University of Colorado Boulder; Colorado; USA is parent organization of: Antarctic Glaciological Data Center is parent organization of: ACADIS Gateway |
NASA ; NSF ; NOAA |
PMID:32116128 | Public, Unless specifically stated that the information has limitations for its use, Acknowledgement requested, Free, Photos come from a variety of sources, And may have different copyright restrictions and credits. | DOI:10.7265, nlx_154742, DOI:10.25504/FAIRsharing.k9vqye, DOI:10.17616/R3HP4V, DOI:10.5067/ | https://doi.org/10.17616/R31NJMJB, https://doi.org/10.17616/r3HP4V, https://doi.org/10.7265/, https://dx.doi.org/10.7265/, https://fairsharing.org/10.25504/FAIRsharing.k9vqye, https://doi.org/10.5067/, https://dx.doi.org/10.5067/ | SCR_002220 | National Snow & Ice Data Center | 2026-08-03 09:31:36 | 48 | ||||
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Ensembl Resource Report Resource Website 10000+ mentions |
Ensembl (RRID:SCR_002344) | data or information resource, database | Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species. | collection, genome, dataset, database, vertebrate, eukaryotic, DNA, protein, sequence, search, automaticly, annotate, data, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: Animal QTLdb is used by: ChannelPedia is used by: Blueprint Epigenome is used by: HmtPhenome lists: Ensembl Covid-19 is listed by: OMICtools is listed by: Biositemaps is listed by: re3data.org is listed by: LabWorm is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Ensembl Genomes is related to: GermOnline is related to: CandiSNPer is related to: Human Splicing Finder is related to: NGS-SNP is related to: Sanger Mouse Resources Portal is related to: DECIPHER is related to: Ensembl Genomes is related to: PeptideAtlas is related to: AnimalTFDB is related to: Bgee: dataBase for Gene Expression Evolution is related to: FlyMine is related to: Rat Gene Symbol Tracker is related to: UniParc at the EBI is related to: go-db-perl is related to: UniParc is related to: g:Profiler is related to: RIKEN integrated database of mammals is related to: VBASE2 is related to: p300db is related to: ShinyGO has parent organization: European Bioinformatics Institute has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: Ensembl Metazoa is parent organization of: Ensembl Variation is parent organization of: Pre Ensembl is parent organization of: Variant Effect Predictor is parent organization of: Ensembl Bacteria is parent organization of: Ensembl Plants is parent organization of: Ensembl Fungi is parent organization of: Ensembl Protists is parent organization of: Ensembl Genome Browser works with: Genotate works with: CellPhoneDB works with: Open Regulatory Annotation Database works with: Database of genes related to Repeat Expansion Diseases works with: TarBase |
Wellcome Trust ; EMBL ; European Union ; FP7 ; FP6 ; MRC ; NHGRI ; BBSRC |
PMID:24316576 PMID:23203987 |
nif-0000-21145, OMICS_01647, biotools:ensembl, r3d100010228 | https://bio.tools/ensembl, https://sources.debian.org/src/ensembl/, https://doi.org/10.17616/R39K5B | SCR_002344 | ENSEMBL | 2026-08-03 09:31:53 | 11652 | ||||||
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dbSNP Resource Report Resource Website 5000+ mentions |
dbSNP (RRID:SCR_002338) | dbSNP | data repository, data or information resource, database, storage service resource, service resource | Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource. | insertion, polymorphism, short, deletion, single, nucleotide, genetic, variation, genomics, genotype, disease, allele, microsatellite, marker, multinucleotide, heterozygous, sequence, gold standard, bio.tools |
is used by: ExAc is used by: GEMINI is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl Variation is related to: GWAS Central is related to: TopoSNP is related to: GWAS Central has parent organization: NCBI has parent organization: National Human Genome Research Institute works with: Open Regulatory Annotation Database |
NLM | PMID:21154707 | Free, Freely available | nif-0000-02734, biotools:dbsnp, OMICS_00264, r3d100010652 | http://www.ncbi.nlm.nih.gov/projects/SNP/, https://bio.tools/dbsnp, https://doi.org/10.17616/R3XG81 | SCR_002338 | dbSNP: Database for Short Genetic Variations, Entrez SNP - Single Nucleotide Polymorphism, SNV Database, NCBI SNV Database, NCBI Short Genetic Variations Database, NCBI Short Genetic Variations, NCBI Single Nucleotide Polymorphism, Entrez SNP, dbSNP, NCBI Short Genetic Variations (SNV) database | 2026-08-03 09:31:39 | 8619 | ||||
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OpenTopography Resource Report Resource Website 10+ mentions |
OpenTopography (RRID:SCR_002204) | OpenTopo | service resource, data or information resource, data repository, storage service resource | Accepts and provides access to high-resolution (meter to sub-meter scale) Earth science-oriented topography data (e.g. LiDAR) and bathymetric data, and related tools and resources. The OpenTopography Tool Registry provides a community populated clearinghouse of software, utilities, and tools oriented towards high-resolution topography data (e.g. collected with LiDAR technology) handling, processing, and analysis. Tools registered range from source code to full-featured software applications. Contributions to the registry via the Contribute a Tool page are welcome. OpenTopography also hosts a dataset catalog to which users can register datasets hosted elsewhere; these entries are discoverable by users alongside OpenTopography hosted datasets. Lidar point cloud data are available in LAS, LAZ and ASCII formats. Raster datasets and derived products can be downloaded in Arc ASCII, IMG, and GeoTIFF formats. Derived products and visualizations are available in Google Earth KML format. The OpenTopography user community and advisory committee provides feedback to define the scope of collaborations on data hosting and cyberinfrastructure development | topography, topographical surveying, cloud, earth sciences, aerial photography, topographic map, geography, bathymetric map, geological mapping, geographic information system, bathymetry |
is listed by: CINERGI is listed by: re3data.org is listed by: DataCite has parent organization: San Diego Supercomputer Center has parent organization: University of California; California; USA |
NSF 1948997; NSF 1948994; NSF 1948857 |
Free, Available for download, Freely available | nlx_154717, r3d100010655 | https://api.datacite.org/dois?prefix=10.5069, https://doi.org/10.17616/R3J616 | SCR_002204 | , OpenTopography Facility, Open Topography, NSF OpenTopography Facility | 2026-08-03 09:31:42 | 14 | |||||
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Simtk.org Resource Report Resource Website 10+ mentions |
Simtk.org (RRID:SCR_002680) | SimTK | software repository, software resource, software application, simulation software | A National NIH Center for Biomedical Computing that focuses on physics-based simulation of biological structures and provides open access to high quality simulation tools, accurate models and the people behind them. It serves as a repository for models that are published (as well as the associated code) to create a living archive of simulation scholarship. Simtk.org is organized into projects. A project represents a research endeavor, a software package or a collection of documents and publications. Includes sharing of image files, media, references to publications and manuscripts, as well as executables and applications for download and source code. Simulation tools are free to download and space is available for developers to manage, share and disseminate code. | model, modeling, rna folding, protein folding, myosin dynamics, neuromuscular biomechanics, cardiovascular dynamics, biomolecular simulation, biomedical computing, repository, cardiovascular, neuromuscular, myosin, rna, simulation, biocomputation |
is used by: NIF Data Federation lists: Adaptively Sampled Particle Fluids lists: OpenMM lists: CPODES numerical integrator is listed by: Biositemaps is listed by: Integrated Models is listed by: DataCite is listed by: re3data.org is related to: OpenSim is related to: Simbody(tm): SimTK Multibody Dynamics Toolset is related to: SimVascular is related to: SAFA Footprinting Software is related to: Ion Simulator Interface is related to: LAPACK linear algebra library is related to: Neuromuscular Models Library has parent organization: Simbios is parent organization of: FEATURE is parent organization of: Cardiovascular Model Repository is parent organization of: ConTrack is parent organization of: Allopathfinder is parent organization of: Molecular Simulation Trajectories Archive of a Villin Variant is parent organization of: LAPACK linear algebra library is parent organization of: SimTKCore |
NIH ; NIGMS U54 GM072970 |
Free, Available for download, Freely available | nif-0000-23302, DOI:10.17616/R3QJ4B, DOI:10.18735 | https://doi.org/10.17616/R3QJ4B, https://doi.org/10.17616/r3qj4b, https://doi.org/10.18735/, https://dx.doi.org/10.18735/ | SCR_002680 | Simulation Toolkit, SimTK - the Simulation Toolkit | 2026-08-03 09:31:47 | 18 | |||||
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Neuroscience Information Framework Resource Report Resource Website 100+ mentions |
Neuroscience Information Framework (RRID:SCR_002894) | NIF | systems interoperability software, software development tool, data repository, portal, data or information resource, database, software application, storage service resource, service resource, software resource | Framework for identifying, locating, relating, accessing, integrating, and analyzing information from neuroscience research. Users can search for and add neuroscience-related resources at NIF portal and receive and RRID to track and cite resources within scientific manuscripts. | neuroscience, bioinformatics, data sharing, metadata standard, ontology, resource, registry, literature, grant, service, software, neuinfo, cerebral circulation, neuron, antibody diversity, neuroanatomy, atlas, bio.tools, bio.tools |
uses: UBERON recommends: Resource Identification Portal is recommended by: National Library of Medicine is listed by: FORCE11 is listed by: OMICtools is listed by: re3data.org is listed by: National Institute of Mental Health is listed by: Debian is listed by: bio.tools is related to: NIDDK Information Network (dkNET) is related to: SciCrunch is related to: SenseLab is related to: Linked Neuron Data is related to: Whole Brain Catalog is related to: FAIR Data Informatics Laboratory is related to: Atlas Ontology Model has parent organization: University of California at San Diego; California; USA is parent organization of: ModelRun is parent organization of: NIF Web Services is parent organization of: NIF Blog is parent organization of: Integrated is parent organization of: Drug Related Gene Database is parent organization of: DISCO is parent organization of: NIF Data Federation is parent organization of: BioMarkers for SMA Data Portal is parent organization of: SciCrunch Registry is parent organization of: NIF Literature is parent organization of: NeuroLex is parent organization of: NIFSTD is parent organization of: Antibody Registry is parent organization of: ConceptMapper is parent organization of: NIF Dysfunction Ontlogy is parent organization of: NIF Subcellular Ontology is parent organization of: OntoQuest is parent organization of: One Mind Biospecimen Bank Listing is parent organization of: ResearchCrossroads is parent organization of: Neuroscience Gateway is parent organization of: NIF Registry Automated Crawl Data |
NIH Blueprint for Neuroscience Research ; NIDA HHSN27120080035C |
PMID:18946742 PMID:22434839 |
Free, Freely available | nif-0000-25673, OMICS_01190, biotools:neuroscinfframework, r3d100010106 | https://www.force11.org/node/4695, https://bio.tools/neuroscinfframework, https://bio.tools/neuroscinfframework, https://doi.org/10.17616/R31P4H | SCR_002894 | neuinfo, NIF, neuinfo.org | 2026-08-03 09:32:10 | 128 | ||||
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Gramene Resource Report Resource Website 500+ mentions |
Gramene (RRID:SCR_002829) | GR | data or information resource, database | Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site. | crop, plant genome, genetic, blast, gene, genome, genetic diversity, pathway, protein, marker, quantitative trait locus, comparative map, phenotype, genomics, physiology, comparative, grain, expressed sequence tag, trait, mutation, environment, taxonomy, web service, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: Gene Ontology is related to: Plant Ontology is related to: Trait Ontology is related to: EnvO is related to: BioCyc has parent organization: Cold Spring Harbor Laboratory has parent organization: Cornell University; New York; USA is parent organization of: Trait Ontology is parent organization of: Plant Environmental Conditions is parent organization of: Plant Trait Ontology is parent organization of: Cereal Plant Development Ontology is parent organization of: Cereal Plant Gross Anatomy Ontology |
USDA IFAFS 00-52100-9622; USDA 58-1907-0-041; USDA 1907-21000-030; NSF 0321685; NSF 0703908; NSF 0851652 |
PMID:21076153 PMID:17984077 PMID:16381966 |
Free, Freely available | r3d100010856, nif-0000-02926, nlx_65829, biotools:gramene | https://bio.tools/gramene, https://doi.org/10.17616/R3GG7M | SCR_002829 | GR PROTEIN, RiceGenes, GR REF, GR GENE, Gramene: A Resource for Comparative Grass Genomics, GR QTL | 2026-08-03 09:31:51 | 778 | ||||
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HGNC Resource Report Resource Website 500+ mentions |
HGNC (RRID:SCR_002827) | controlled vocabulary, data or information resource, database | Only worldwide authority that provides standardized nomenclature, i.e. gene names and symbols (short form abbreviations), for all known human genes, and stores all approved symbols in the HGNC database. Approved human gene nomenclature. Database of gene symbols and names. Manually curated genes into groups based on shared characteristics such as homology, function or phenotype. Data for protein-coding genes, pseudogenes and non-coding RNAs. | gene, owl, gene symbol, phenotype, nomenclature, gene family, gene groups, genomic, proteomic, ortholog, web service, locus, protein coding, genetics, gold standard, bio.tools, FASEB list, GCBR, ELIXIR Core Data Resource, DRKB |
is used by: Nowomics is used by: Cytokine Registry is listed by: BioPortal is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Rat Gene Symbol Tracker is related to: INFEVERS is related to: VGNC has parent organization: University of Cambridge School of Clinical Medicine; Cambridge; United Kingdom |
NHGRI U24HG003345 | PMID:36243972 PMID:32747822 PMID:34615987 PMID:33152070 |
Free, Freely available | biotools:genenames.org, nif-0000-02955, r3d100010901 | http://bioportal.bioontology.org/ontologies/HUGO, https://bio.tools/genenames.org, https://doi.org/10.17616/R3XC80 | SCR_002827 | HUGO symbols, HGNC Database, HGNC - HUGO Gene Nomenclature Committee, HUGO Gene Nomenclature Committee, Human Genome Organization Gene Symbols | 2026-08-03 09:32:09 | 974 | |||||
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Gene Expression Nervous System Atlas Resource Report Resource Website 100+ mentions |
Gene Expression Nervous System Atlas (RRID:SCR_002721) | GENSAT | biomaterial supply resource, material resource, organism supplier | Gene expression data and maps of mouse central nervous system. Gene expression atlas of developing adult central nervous system in mouse, using in situ hybridization and transgenic mouse techniques. Collection of pictorial gene expression maps of brain and spinal cord of mouse. Provides tools to catalog, map, and electrophysiologically record individual cells. Application of Cre recombinase technologies allows for cell-specific gene manipulation. Transgenic mice created by this project are available to scientific community. | molecular neuroanatomy resource, gene expression, cre mice, rodent, adult mouse, development, developing mouse, histology, annotation, central nervous system, in situ hybridization, mutant mouse strain, brain, spinal cord, transgenic bac-egfp reporter, bac-cre recombinase driver mouse line, transgenic mouse, young mouse, genetics, neurology, bac, transgenic, histology, annotation, bioinformatics, FASEB list |
is used by: NIF Data Federation is listed by: One Mind Biospecimen Bank Listing is listed by: re3data.org is related to: Integrated Brain Gene Expression is related to: VisiGene Image Browser is related to: aGEM has parent organization: Rockefeller University; New York; USA is parent organization of: Gensat Cre-Mice |
NIH ; NIH Blueprint for Neuroscience Research ; NINDS N01 NS02331 |
Free, Freely available | nif-0000-00130 | http://www.gensat.org/index.html | SCR_002721 | Gene Expression Nervous System Atlas, GENSAT | 2026-08-03 09:31:59 | 380 | |||||
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Mendeley Resource Report Resource Website 1000+ mentions |
Mendeley (RRID:SCR_002750) | Mendeley | web service, database, data access protocol, data or information resource, software resource | Web application as free reference manager and academic social network to organize your research, collaborate with others online, and discover the latest research. Automatically generate bibliographies, Collaborate easily with other researchers online, Easily import papers from other research software, Find relevant papers based on what you're reading, Access your papers from anywhere online, Read papers on the go with the iPhone app. The software, Mendeley Desktop, offers: * Automatic extraction of document details * Efficient management of your papers * Sharing and synchronization of your library (or parts of it) * Additional features: A plug-in for citing your articles in Microsoft Word, OCR (image-to-text conversion, so you can full-text search all your scanned PDFs), etc The website, Mendeley Web, complements Mendeley Desktop by offering these features: * An online back up of your library * Statistics of all things interesting * A research network that allows you to keep track of your colleagues' publications, conference participations, awards etc * A recommendation engine for papers that might interest you. | journal, collaborate, organize, bibliography, mac, windows, linux |
uses: Citation Style Language is used by: Nowomics is used by: NIH Heal Project is listed by: FORCE11 is listed by: re3data.org is related to: Paper Critic is related to: ImpactStory is related to: Overleaf is parent organization of: CitationStyles is parent organization of: Mendeley Data |
Free | nif-0000-24120 | SCR_002750 | , Mendeley Data, Mendeley Research Network, Mendeley | 2026-08-03 09:32:08 | 2421 | |||||||
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WormBase Resource Report Resource Website 1000+ mentions |
WormBase (RRID:SCR_003098) | WB, WB REF, WP | data repository, data or information resource, database, storage service resource, service resource | Central data repository for nematode biology including complete genomic sequence, gene predictions and orthology assignments from range of related nematodes.Data concerning genetics, genomics and biology of C. elegans and related nematodes. Derived from initial ACeDB database of C. elegans genetic and sequence information, WormBase includes genomic, anatomical and functional information of C. elegans, other Caenorhabditis species and other nematodes. Maintains public FTP site where researchers can find many commonly requested files and datasets, WormBase software and prepackaged databases. | RIN, Resource Information Network, catalog, database, blast, genomic sequence, gene prediction, orthology assignment, gene function, ortholog, roundworm, geneotype, phenotype, gene mapping, genomics, gene expression, transposon family, c elegans, wormmart, FASEB list, RRID Community Authority |
uses: InterMOD is used by: NIF Data Federation is used by: Resource Identification Portal is used by: PhenoGO is used by: Integrated Animals is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: InterMOD is listed by: Resource Information Network is affiliated with: InterMOD is related to: AmiGO is related to: GBrowse is related to: Textpresso is related to: Expression Patterns for C. elegans promoter GFP fusions is related to: C. elegans Gene Knockout Consortium is related to: NIH Data Sharing Repositories is related to: UniParc at the EBI is related to: UniParc is related to: Integrated Manually Extracted Annotation is related to: PhenoGO has parent organization: Cold Spring Harbor Laboratory has parent organization: Washington University in St. Louis; Missouri; USA has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: C. elegans Development Vocabulary is parent organization of: C. elegans Gross Anatomy Vocabulary is parent organization of: C. elegans Phenotype Vocabulary is parent organization of: OpenWorm works with: A plasmid Editor is organization facet of: Alliance of Genome Resources |
NHGRI ; NIH Blueprint for Neuroscience Research ; MRC ; BBSRC ; NHGRI U41 HG002223; NIHGRI P41 HG02223 |
PMID:24194605 PMID:19910365 PMID:17991679 PMID:15608221 |
nif-0000-00053, OMICS_01664, r3d100010424 | http://www.wormbase.org/#01-23-6, https://doi.org/10.17616/R3089Z | SCR_003098 | , WB, Worm Base, WB REF, WP | 2026-08-03 09:32:10 | 1825 | |||||
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miRBase Resource Report Resource Website 5000+ mentions |
miRBase (RRID:SCR_003152) | miRBase | data repository, data or information resource, database, storage service resource, service resource, naming service | Central online repository for microRNA nomenclature, sequence data, annotation and target prediction.Collection of published miRNA sequences and annotation. | gene, annotation, hairpin, microrna, nomenclature, rna, sequence, target, transcript, unique name, mirna registry, genetics, bio.tools, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: bio.tools is listed by: Debian has parent organization: University of Manchester; Manchester; United Kingdom |
BBSRC ; Wellcome Trust Sanger Institute |
PMID:24275495 PMID:21037258 PMID:20205188 PMID:17991681 PMID:16957372 PMID:16381832 PMID:14681370 |
Free, Available for download, Freely available | SCR_017497, r3d100010670, nif-0000-03134, biotools:mirbase | http://microrna.sanger.ac.uk/, https://bio.tools/mirbase, https://doi.org/10.17616/R3VG8D | SCR_003152 | microRNA database | 2026-08-03 09:32:12 | 9669 |
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