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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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BioMAJ Resource Report Resource Website |
BioMAJ (RRID:SCR_023983) | data processing software, software application, software resource, workflow software | Software workflow engine dedicated to data synchronization and processing. Software automates the update cycle and the supervision of the locally mirrored databank repository. | workflow engine, data synchronization and processing, | is listed by: Debian | Free, Available for download, Freely available | OMICS_21717 | https://sources.debian.org/src/biomaj3/, http://genouest.github.io/biomaj/ | SCR_023983 | SciCrunch Registry | BioMAJ3, BIOlogie Mise A Jour, biomaj3 | 2026-11-07 12:01:15 | 0 | |||||||
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OpenICPSR Resource Report Resource Website 10+ mentions |
OpenICPSR (RRID:SCR_019106) | data access protocol, data or information resource, data repository, portal, service resource, software resource, storage service resource, web service | Web service of Inter-university Consortium for Political and Social Research. Self-publishing repository for social, behavioral, and health sciences research data. Used for deposit of replication data sets for researchers who need to publish their raw data associated with journal article so that other researchers can replicate their findings. | Political and social research data, data repository, replication data sets, replicate data, raw data, journal article data |
is related to: COVID-19 Data Repository has parent organization: University of Michigan; Ann Arbor; USA |
Free, Freely available | r3d100012693 | https://doi.org/10.17616/R3D81N | SCR_019106 | SciCrunch Registry | Inter-university Consortium for Political and Social Research | 2026-11-07 12:00:51 | 12 | |||||||
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spatial_tri-omics Resource Report Resource Website 1+ mentions |
spatial_tri-omics (RRID:SCR_026194) | software resource, source code | Software repository to share the raw data processing and visualization codes used in the spatial tri-omics project. | raw data processing and visualization codes, spatial tri-omics project, | Free, Available for download, Freely available | SCR_026194 | SciCrunch Registry | 2026-11-07 12:06:36 | 2 | |||||||||||
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chronopolis Resource Report Resource Website |
chronopolis (RRID:SCR_003116) | Chronopolis | data repository, service resource, software repository, software resource, storage service resource | Services for the long-term preservation and curation of America's digital data - data of any type or size, with minimal requirements on the data provider. It has the capacity to preserve hundreds of terabytes of digital data and comprises several partner organizations that provide a wide range of services. The project leverages high-speed networks, mass-scale storage capabilities, and the expertise of the partners in order to provide a geographically distributed, heterogeneous, and highly redundant archive system. Features of the project include: * Three geographically distributed copies of the data * Curatorial audit reporting * Development of best practices for data packaging and sharing Chronopolis is available to anyone who wants to have their data preserved. Storage is based on a yearly, per-terabyte charge. The smallest unit available is one terabyte; collections smaller than this will be charged the one terabyte rate. | digital preservation |
is related to: Digital Asset Management System has parent organization: San Diego Supercomputer Center |
Library of Congress | Free, Freely available | nlx_156729 | https://library.ucsd.edu/chronopolis/ | SCR_003116 | SciCrunch Registry | 2026-11-07 11:55:03 | 0 | ||||||
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JCB DataViewer Resource Report Resource Website 10+ mentions |
JCB DataViewer (RRID:SCR_002633) | JCB DataViewer | data or information resource, data repository, database, image repository, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A web-based, multi-dimensional image data-viewing application for original microscopy image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal published by The Rockefeller University Press. The JCB DataViewer can host multidimensional fluorescence microscopy images, 3D tomogram data, very large (gigapixel) images, and high content imaging screens. Images are presented in an interactive viewer, and the scores from high content screens are presented in interactive graphs with data points linked to the relevant images. The JCB DataViewer uses the Bio-Formats library to read over 120 different imaging file formats and convert them to the OME-TIFF image data standard. Image data are archived by the Journal and may be freely accessed by readers using the JCB DataViewer. Download of author-provided image data and associated metadata in OME-TIFF format is also possible with author permission, allowing for independent analysis of image data irrespective of acquisition or viewing software. Although the JCB DataViewer is designed to host and facilitate sharing and analysis of original microscopy image data, authors may also upload other types of original image data as supplements to their manuscripts, including histology and electron micrographs and digital scans of gels or blots. | microscopy, standardization, data sharing, archiving, data management, metadata standard, visualization, analysis, image collection, histology, electron micrograph, digital scan, gel, blot |
is listed by: FORCE11 is listed by: SoftCite is related to: OME-TIFF Format has parent organization: Rockefeller University; New York; USA |
Glencoe Software ; OME - Open Microscopy Environment |
PMID:22869591 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156057, r3d100010895 | https://doi.org/10.17616/R3PW4G | SCR_002633 | SciCrunch Registry | 2026-11-07 11:54:43 | 14 | |||||
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LANDMark BioBanks Resource Report Resource Website 1+ mentions |
LANDMark BioBanks (RRID:SCR_014534) | biobank, biospecimen repository, data or information resource, data set, material storage repository, service resource, storage service resource | A repository of human tissue samples collected during the LANDMark study (Longitudinal Assessment of Neuropathy in Diabetes using novel ophthalmic markers). The LANDMark Biobank longitudinal dataset contains blood and tissue (skin) samples and matching detailed phenotypic data of three microvascluar complications of type 1 diabetes: neuropathy, nephropathy and retinopathy. | biospecimen repository, data set, type 1 diabetes, biobank, human tissue, landmark study, longitudinal data set, blood, skin, neuropathy, nephropathy, retinopathy | is listed by: NIDDK Information Network (dkNET) | Type 1 diabetes, Diabetes | Available to the research community, Apply to the Tissue Access Committee to access tissue samples | SCR_014534 | SciCrunch Registry | 2026-11-07 11:58:12 | 2 | |||||||||
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fiddle Resource Report Resource Website 1+ mentions |
fiddle (RRID:SCR_017327) | FIDDLE | service resource, software application, software resource | Software interactive tool to help researchers to identify most appropriate publication format for their dataset that may be hard to publish in traditional journals. Formats include data repositories, micropublications, preprints, data journals, publishing platforms and journals that are open to null results. Users can search for publication format that meets their needs, compare and contrast formats, and find links to publishers. Open source tool to combat publication bias by getting research out of file drawer and into scientific community. | identify, publication, format, dataset, , result, file, drawer, data, liberation, effort | DOI:10.31219/osf.io/6mcu3 | Free, Freely available | https://github.com/quest-bih/FIDDLE | SCR_017327 | SciCrunch Registry | file drawer data liberation effort, fiddle | 2026-11-07 12:02:52 | 2 | |||||||
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The Immunology Database and Analysis Portal (ImmPort) Resource Report Resource Website 1000+ mentions |
The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) | ImmPort | controlled vocabulary, data or information resource, data repository, database, disease-related portal, ontology, portal, service resource, storage service resource, topical portal | Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology. | immunology, basic, clinical, data, share, store, analyze, exchange, dataset, immune, mediated, disease, analysis, tool, 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: NIDDK Research Resources is affiliated with: Cytokine Registry is related to: MetaCyto is related to: The 10000 Immunomes is related to: NIAID |
Immune mediated disease | DAIT ; NIAID ; NIAID HHSN266200400076C; NIAID HHSN272201200028C; NIH |
PMID:24791905 | nlx_152691, r3d100012529 | http://www.immport.org/immport-open/public/home/home, http://www.immport.org/ | http://www.immport.org | SCR_012804 | SciCrunch Registry | Immunology Data and Analysis Portal, ImmPort system, ImmPort, Immunology Database and Analysis Portal | 2026-11-07 11:57:39 | 1383 | |||
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Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis Resource Report Resource Website 50+ mentions |
Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (RRID:SCR_002676) | CAMERA | analysis service resource, data analysis service, data or information resource, data repository, organization portal, portal, production service resource, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data. | ecology, energy, environment, gene, analysis, bioinformatics, biological, biology, community, cyberinfrastructure, data, dna, genome, genomics, health care, map, marine, metadata, metagenomic, microbial, microbiology, molecular biology, organism, research, scientific, sequence, sequencing, software, tool, training, viral |
is listed by: OMICtools is related to: VIROME has parent organization: University of California at San Diego; California; USA |
Gordon and Betty Moore Foundation | PMID:21045053 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_011924, OMICS_01476, nif-0000-23292 | SCR_002676 | SciCrunch Registry | 2026-11-07 11:54:56 | 83 | ||||||
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PubChem Resource Report Resource Website 10000+ mentions |
PubChem (RRID:SCR_004284) | data or information resource, data repository, database, service resource, storage service resource | Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI). | collection, information, data, chemical, structure, biological, property, small, molecule, siRNA reagent, bio.tools |
uses: ChEMBL is used by: NIF Data Federation is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: GEROprotectors is listed by: OMICtools is listed by: re3data.org is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: NCBI Structure is related to: Molecular Libraries Program is related to: NIH Data Sharing Repositories is related to: PubChem BioAssay has parent organization: NCBI is parent organization of: PubChem Substance works with: MiMeDB |
NLM | PMID:21418625 PMID:21272340 PMID:20970519 PMID:20298522 PMID:19825798 |
Free, Freely Available | biotools:pubchem, nlx_42691, nlx_29861, r3d100010538, OMICS_01587 | https://bio.tools/pubchem, https://doi.org/10.17616/R3GW37 | SCR_004284 | SciCrunch Registry | 2026-11-07 11:55:19 | 15598 | ||||||
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Eukaryotic Pathogen Database Resources Resource Report Resource Website 10+ mentions |
Eukaryotic Pathogen Database Resources (RRID:SCR_004512) | EuPathDB, ApiDB | data access protocol, data or information resource, data repository, database, portal, service resource, software resource, storage service resource, topical portal, web service | EuPathDB integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises veterinary and medically important parasitic protozoa including human pathogenic species of genera Cryptosporidium, Plasmodium and Toxoplasma. ApiDB serves not only as database but unifies access to three major existing individual organism databases, PlasmoDB.org, ToxoDB.org and CryptoDB.org, and integrates these databases with data available from additional sources. Through ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases. EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with eukaryotic pathogens. | Data, Apicomplexa, parasitic, protozoa, Cryptosporidium, Plasmodium, Toxoplasma, database, pathogen, dataset, FASEB list |
is listed by: NIH Data Sharing Repositories is related to: ApiDots is related to: NIH Data Sharing Repositories is related to: AmoebaDB is related to: MicrobiomeDB has parent organization: University of Georgia; Georgia; USA is parent organization of: FungiDB is parent organization of: TriTrypDB is parent organization of: PlasmoDB is parent organization of: ApiDB ToxoDB is parent organization of: ApiDB CryptoDB |
malaria, kala-azar, african sleeping sickness, chagas disease, aids-related, aids | Bill and Melinda Gates Foundation ; Wellcome Trust ; NIAID |
PMID:19914931 PMID:17098930 |
nlx_49652, r3d100011557 | http://ApiDB.org, https://doi.org/10.17616/R3X06F | SCR_004512 | SciCrunch Registry | EuPath, Apicomplexan Database Resources, Eukaryotic Pathogen Genome Database, EuPathDB, Eukaryotic Pathogen Database Resources, ApiDB, Apicomplexan Database | 2026-11-07 11:55:47 | 39 | ||||
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Physiobank Resource Report Resource Website 10+ mentions |
Physiobank (RRID:SCR_006949) | PhysioBank | catalog, data or information resource, data repository, database, service resource, storage service resource | Archive of well-characterized digital recordings of physiologic signals and related data for use by the biomedical research community. PhysioBank currently includes databases of multi-parameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and patients with a variety of conditions with major public health implications, including sudden cardiac death, congestive heart failure, epilepsy, gait disorders, sleep apnea, and aging. The PhysioBank Archives now contain over 700 gigabytes of data that may be freely downloaded. PhysioNet is seeking contributions of data sets that can be made freely available in PhysioBank. Contributions of digitized and anonymized (deidentified) physiologic signals and time series of all types are welcome. If you have a data set that may be suitable, please review PhysioNet''s guidelines for contributors and contact them. | physiologic, signal, data, biomedical, research, community, cardiopulmonary, neural, biomedical, health, cardiac, death, congestive heart failure, epilepsy, gait, disorder, sleep apnea, bibliographic, normal, physiologic signal, time series, FASEB list |
is used by: NIF Data Federation is used by: Integrated Datasets is related to: PhysioToolkit is parent organization of: Gait in Aging and Disease Database is parent organization of: Gait in Parkinson's Disease is parent organization of: Gait Dynamics in Neuro-Degenerative Disease Data Base is parent organization of: Noise Enhancement of Sensorimotor Function |
Healthy, Sudden cardiac death, Congestive heart failure, Epilepsy, Gait disorder, Sleep apnea, Aging | NIGMS ; NIBIB U01-EB-008577 |
PMID:10851218 | Free, The community can contribute to this resource, Acknowledgement requested | nlx_48903, r3d100011236 | https://doi.org/10.17616/R3J048 | SCR_006949 | SciCrunch Registry | 2026-11-07 11:56:19 | 40 | ||||
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hfoGUI Resource Report Resource Website 1+ mentions |
hfoGUI (RRID:SCR_016726) | hfoGUI | data analysis software, data processing software, data visualization software, signal processing software, software application, software repository, software resource | Graphical user interface to visualize EEG data. The applications can vary from scoring High Frequency Oscillations, to observing Theta and Gamma Synchrony. | graphical, user, interface, python, processing, data, EEG, LFP, frequency, oscillation | Alzheimer’s Association 2015-NIRG-341570; NIA R01 AG050425 |
Free, Available for download, Freely available | SCR_016726 | SciCrunch Registry | hfoGraphical User Interface | 2026-11-07 11:58:33 | 1 | ||||||||
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Leginon Resource Report Resource Website 10+ mentions |
Leginon (RRID:SCR_016731) | data acquisition software, data or information resource, data processing software, data repository, image acquisition software, portal, service resource, software application, software resource, storage service resource | System designed for automated collection of images from a transmission electron microscope. | automated, collection, acquisition, data, image, electron, microscope |
uses: Python Programming Language has parent organization: Scripps Research Institute |
NCRR RR17573; NIGMS GM61939; NSF DBI0352386; NSF DBI9730056; NSF DBI9904547 |
PMID:15890530 | Free, Available for download, Freely available, Registration suggested | SCR_016731 | SciCrunch Registry | 2026-11-07 11:58:33 | 45 | ||||||||
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Inorganic Crystal Structure Database (ICSD) Resource Report Resource Website 10+ mentions |
Inorganic Crystal Structure Database (ICSD) (RRID:SCR_017429) | ICSD | data or information resource, data repository, database, service resource, storage service resource | Database for completely identified inorganic crystal structures. Collection of known inorganic crystal structures published since 1913, including their atomic coordinates. Includes only data which have passed thorough quality checks. Tool for materials research. | Inorganic, crystal, structure, data, atomic, coordinate, quality, FIZ Karlsruhe — Leibniz Institute for Information Infrastructure |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Restricted | r3d100010085 | http://www2.fiz-karlsruhe.de/icsd_home.html, https://doi.org/10.17616/R3GW2V | SCR_017429 | SciCrunch Registry | Inorganic Crystal Structure Database, Inorganic Crystal Structure Database (ICSD), ICSD | 2026-11-07 11:58:50 | 11 | ||||||
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NIH Figshare Archive Resource Report Resource Website 1+ mentions |
NIH Figshare Archive (RRID:SCR_017580) | NIH Figshare | data or information resource, data repository, database, service resource, storage service resource | Repository to make datasets resulting from NIH funded research more accessible, citable, shareable, and discoverable. Data submitted will be reviewed to ensure there is no personally identifiable information in data and metadata prior to being published and in line with FAIR -Findable, Accessible, Interoperable, and Reusable principles. Data published on Figshare is assigned persistent, citable DOI (Digital Object Identifier) and is discoverable in Google, Google Scholar, Google Dataset Search, and more.Complited on July,2020. Researches can continue to share NIH funded data and other research product on figshare.com. | Respository, data, NIH funded, data set, FAIR |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: FigShare is related to: FigsharePlus |
NIH | Restricted | SCR_017580 | SciCrunch Registry | NIH, Figshare, Fig Share, NIH Figshare, NIH Fig share, National Institute of Health | 2026-11-07 11:58:51 | 9 | |||||||
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Swedish Twin Registry Resource Report Resource Website 10+ mentions |
Swedish Twin Registry (RRID:SCR_017478) | data or information resource, data repository, database, service resource, storage service resource | Registry contains information about twin pairs for which zygosity is known, both mono- and dizygotic pairs. Registry covers older, middle, and younger cohorts. There are approximately 30 projects ongoing based on data from this registry. | Twin, registry, zygosity, monozygotic, dizygotic, pair, data | has parent organization: Karolinska Institute; Stockholm; Sweden | Free, Freely available | SCR_017478 | SciCrunch Registry | 2026-11-07 11:58:50 | 11 | ||||||||||
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Clowder Resource Report Resource Website |
Clowder (RRID:SCR_017599) | data management software, data repository, service resource, software application, software resource, storage service resource | Web based data management system that allows users to share, annotate, organize and analyze large collections of datasets. Software tool for creating some metadata about software tools automatically. Open source data management for long tail data. Provides support for extensible metadata annotation and distributed analytics for automatic curation of uploaded data. Open source software that can be customized and deployed on your own cloud. | Share, annotate, organize, analyze, metadata, long, tail, data, management, custom | has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA | Restricted | https://github.com/clowder-framework | SCR_017599 | SciCrunch Registry | 2026-11-07 11:58:49 | 0 | |||||||||
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Mousebytes Resource Report Resource Website 1+ mentions |
Mousebytes (RRID:SCR_017904) | data or information resource, data repository, database, service resource, storage service resource | Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available. | Data, mouse, cognition, imaging, genomics, integration, bio.tools, OpenBehavior |
is listed by: Debian is listed by: bio.tools is listed by: OpenBehavior has parent organization: Western University; Ontario; Canada |
Alzheimer’s Society of Canada ; Brain Canada ; Canadian First Research Excellence Fund (BrainsCAN) ; Canadian Institute of Health Research ; NSERC ; Weston Brain Institute (Canada) |
PMID:31825307 | Free, Freely available | SCR_021549, SCR_021598, r3d100013886, biotools:Mousebytes | https://bio.tools/MouseBytes, https://edspace.american.edu/openbehavior/project/touchscreen-cognition-mousebytes/, https://doi.org/10.17616/R31NJN7I | SCR_017904 | SciCrunch Registry | MouseBytes | 2026-11-07 11:58:53 | 4 | |||||
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SARS-CoV-2-Sequences Resource Report Resource Website 10+ mentions |
SARS-CoV-2-Sequences (RRID:SCR_018319) | data or information resource, data repository, data set, service resource, storage service resource | Collection of SARS-CoV-2 sequences currently available in GenBank genetic sequence database and Sequence Read Archive. Updated as additional sequences are released. | SARS-CoV-2, SARS coronavirus, SARS-CoV infection, Coronavirus, data, SARS-CoV-2 sequence collection, nucleotide, genome, Betacoronavirus, protein |
works with: GenBank works with: NCBI Sequence Read Archive (SRA) |
COVID-19 | The Federal Government | Free, Available for download, Freely available | SCR_018319 | SciCrunch Registry | Severe Acute Respiratory Syndrome CoronaVirus 2 Sequences | 2026-11-07 11:58:59 | 37 |
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