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https://www.go-fair.org/implementation-networks/overview/vodan/
Network as federated AI-ready repository of COVID-19 data adherent to FAIR principles. SARS CoV-2 virus data FAIR, meaning that they are Findable, Accessible, Interoperable and thus Reusable by both humans and machines, during this epidemic of COVID-19.
Proper citation: Virus Outbreak Data Network (RRID:SCR_018285) Copy
Institution which compiles and distributes small molecule crystallography data from the Cambridge Structural Database (CSD), a repository of experimentally determined organic and metal-organic crystal structures. CCDC also produces associated knowledge-based application software for structural chemists. Structures deposited with CCDC are made publically available for download at the point of publication or at consent from the depositor.
Proper citation: Cambridge Crystallographic Data Centre (CCDC) (RRID:SCR_014707) Copy
http://www.ebi.ac.uk/pdbe/emdb/
Repository for electron microscopy density maps of macromolecular complexes and subcellular structures at Protein Data Bank in Europe. Covers techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.
Proper citation: Electron Microscopy Data Bank at PDBe (MSD-EBI) (RRID:SCR_006506) Copy
The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules.
Proper citation: PDBe - Protein Data Bank in Europe (RRID:SCR_004312) Copy
Platform for health data sharing and analytics that emphasizes patient privacy and security, provides transparent and speedy access, and simplifies data discovery and analysis. Houses datasets for applied AI learning and research. Repository of freely-available medical research data, managed by the University of Toronto Temerty Centre for AI Research and Education in Medicine.
Proper citation: Health Data Nexus (RRID:SCR_026576) Copy
National genetics data repository facilitating access to genotypic and phenotypic data for Alzheimer's disease (AD). Data include GWAS, whole genome (WGS) and whole exome (WES), expression, RNA Seq, and CHIP Seq analyses. Data for the Alzheimer’s Disease Sequencing Project (ADSP) are available through a partnership with dbGaP (ADSP at dbGaP). Repository for many types of data generated from NIA supported grants and/or NIA funded biological samples. Data are deposited at NIAGADS or NIA-approved sites. Genetic Data and associated Phenotypic Data are available to qualified investigators in scientific community for secondary analysis.
Proper citation: National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) (RRID:SCR_007314) Copy
Central data repository containing clinical, research, and administrative data sourced from UNC Health Care System. Both Epic and legacy hospital systems are represented, with ability to query most data elements as far back as mid-2004. Used to mine UNC Health Care data to aid with trial recruitment, retrospective analyses, inter-institutional data sharing and much more.
Proper citation: Carolina Data Warehouse for Health (RRID:SCR_023295) Copy
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.
Proper citation: Marine Geoscience Data System (RRID:SCR_002164) Copy
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.
Proper citation: National Snow and Ice Data Center (RRID:SCR_002220) Copy
http://www.icpsr.umich.edu/icpsrweb/NACDA/
Archive of data relevant to gerontological and aging research. Used to advance research on aging. Subjects include demographic, social, economic, and psychological characteristics of older adults, physical health and functioning of older adults, and health care needs of older adults. NACDA staff represents team of professional researchers, archivists and technicians who work together to obtain, process, distribute, and promote data relevant to aging research.
Proper citation: National Archive of Computerized Data on Aging (NACDA) (RRID:SCR_005876) Copy
Comprehensive lists of plant and animal species, with a rarity rank and legal status for each. It has has over 635,000 geo-located records of species occurrences and over 40,000 records of extremely rare to uncommon species in the Atlantic region, including New Brunswick, Nova Scotia, Prince Edward Island, Newfoundland, and Labrador. The Atlantic CDC also maintains biological and other types of data in a variety of linked databases. The CDC welcomes inquiries from those who would like to contribute data about plant or animal species at risk or rare communities in Atlantic Canada. Its mission is to assemble and provide objective and understandable data and expertise about species and ecological communities of conservation concern, including those at risk, and undertake field biological inventories to support decision-making, research, and education in Atlantic Canada. The Atlantic CDC develops species location data, known as element occurrence records. Occurrence precision (accuracy) ranges from quite precise (within meters) to less precise (within counties) but most commonly it is within 1 5 km. Element occurrence (EO) refers to one or more locations considered important to the continued existence of a species or ecological community. For species, over 30 types of data: taxonomy, biology, etc. are typically examined when identifying EOs. An EO is generally the habitat occupied by a local population. However, occurrence varies among species and some species have more than one type of occurrence (e.g., breeding and winter occurrences). Breeding colonies, breeding ponds, denning sites, and hibernacula are general examples of different types of animal EOs. For an ecological community, an EO may be the area containing a patch of that community type.
Proper citation: Atlantic Canada Conservation Data Centre (RRID:SCR_006061) Copy
Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves.
Proper citation: Data Archive BRAIN Initiative (RRID:SCR_017114) Copy
Free, cloud-based platform for publishing, sharing, and processing standardized neurophysiology data, primarily using the Neurodata Without Borders (NWB) format. Supported by the BRAIN Initiative, it enables researchers to collaborate, reuse datasets, and adhere to FAIR data principles.
Proper citation: Distributed Archives for Neurophysiology Data Integration (RRID:SCR_017571) Copy
A data warehouse that integrates information on patients from multiple sources and consists of patient information from all the visits to Cincinnati Children''''s between 2003 and 2007. This information includes demographics (age, gender, race), diagnoses (ICD-9), procedures, medications and lab results. They have included extracts from Epic, DocSite, and the new Cerner laboratory system and will eventually load public data sources, data from the different divisions or research cores (such as images or genetic data), as well as the research databases from individual groups or investigators. This information is aggregated, cleaned and de-identified. Once this process is complete, it is presented to the user, who will then be able to query the data. The warehouse is best suited for tasks like cohort identification, hypothesis generation and retrospective data analysis. Automated software tools will facilitate some of these functions, while others will require more of a manual process. The initial software tools will be focused around cohort identification. They have developed a set of web-based tools that allow the user to query the warehouse after logging in. The only people able to see your data are those to whom you grant authorization. If the information can be provided to the general research community, they will add it to the warehouse. If it cannot, they will mark it so that only you (or others in your group with proper approval) can access it.
Proper citation: i2b2 Research Data Warehouse (RRID:SCR_013276) Copy
http://www.icpsr.umich.edu/icpsrweb/content/DSDR/index.html
DSDR disseminates, archives, and preserves data for population-based studies. By providing access to data on topics including mortality and health, fertility, family and household structure, and children and youth, DSDR aims to facilitate demographic research.
Proper citation: Data Sharing for Demographics Research (DSDR) (RRID:SCR_016310) Copy
https://github.com/HicServices/RDMP/wiki
Software toolkit which automates the loading, storage, linkage and provision of data sets. It also cleans, transforms and documents provenance meta-data and domain knowledge to make data sets “research ready”.
Proper citation: Research Data Management Platform (RRID:SCR_016268) Copy
Portal to make cancer related proteomic datasets easily accessible to public. Facilitates multiomic integration in support of precision medicine through interoperability with other resources. Developed to advance our understanding of how proteins help to shape risk, diagnosis, development, progression, and treatment of cancer. One of several repositories within NCI Cancer Research Data Commons which enables researchers to link proteomic data with other data sets (e.g., genomic and imaging data) and to submit, collect, analyze, store, and share data throughout cancer data ecosystem. PDC provides access to highly curated and standardized biospecimen, clinical, and proteomic data, intuitive interface to filter, query, search, visualize and download data and metadata. Provides common data harmonization pipeline to uniformly analyze all PDC data and provides advanced visualization of quantitative information. Cloud based (Amazon Web Services) infrastructure facilitates interoperability with AWS based data analysis tools and platforms natively. Application programming interface (API) provides cloud-agnostic data access and allows third parties to extend functionality beyond PDC. Structured workspace that serves as private user data store and also data submission portal. Distributes controlled access data, such as patient-specific protein fasta sequence databases, with dbGaP authorization and eRA Commons authentication.
Proper citation: Proteomic Data Commons (RRID:SCR_018273) Copy
https://edal.ipk-gatersleben.de
Software tool as Java based framework to store, share and publish research data. Free software infrastructure to FAIRly maintain and publish in-house stored research data. Used for version tracking, metadata management, information retrieval, journal and founding agency proven registration of persistent identifiers (DOI), embedded HTTP(S) server for public data access, access as network file system, and scalable storage backend.
Proper citation: electronic Data Archive Library (RRID:SCR_019017) Copy
https://portal.imaging.datacommons.cancer.gov
Portal for finding and analyzing cancer imaging data. Part of Cancer Research Data Commons to support cancer imaging research. Provides cloud based access to medical imaging data and library of analytical tools and workflows to share, analyze, and visualize multi modal imaging data from both clinical and basic cancer research studies.
Proper citation: NCI Imaging Data Commons (RRID:SCR_019127) Copy
https://datacommons.cancer.gov
Cloud based data science infrastructure that provides secure access to cancer research data from NCI programs and key external cancer programs. Serves as coordinated resource for public data sharing of NCI funded programs. Users can explore and use analytical and visualization tools for data analysis. Enables to search and aggregate data across repositories including Cancer Data Service, Clinical Trial Data Commons, Genomic Data Commons, Imaging Data Commons, Integrated Canine Data Commons, Proteomic Data Commons.
Proper citation: Cancer Research Data Commons (RRID:SCR_019128) Copy
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