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http://www.marine-geo.org/

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   

•   Source: SciCrunch Registry

http://ccdb.ucsd.edu

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.

Proper citation: Cell Centered Database (RRID:SCR_002168) Copy   

•   Source: SciCrunch Registry

http://nsidc.org/

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   

•   Source: SciCrunch Registry

http://www.opentopography.org/

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

Proper citation: OpenTopography (RRID:SCR_002204) Copy   

•   Source: SciCrunch Registry

http://146.20.110.164/about/

Tools for researchers to connect their data, code and computational methods to their published or soon to be published research in a convenient and easily citeable form. ResearchCompendia provides the tools to publish digital scholarly objects by hosting data, code, and methods in a form that is accessible, trackable, and persistent. They provide hosting and computational cloud resources for all researchers. Data and code should be citable and linked to the original publication.

Proper citation: ResearchCompendia (RRID:SCR_003223) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/dbvar/

Structural variation database designed to store data on variant DNA > / = 1 bp in size from all organisms. Associations of defined variants with phenotype information is also provided. Users can browse data containing number of variant cells from each study, and filter studies by organism, study type, method and genomic variant. Organisms include human, mouse, cattle and several additional animals.

Proper citation: dbVar (RRID:SCR_003219) Copy   

•   Source: SciCrunch Registry

http://talkbank.org/

Databases of transcript and media data collected from conversations with adults and older children to foster fundamental research in the study of human and animal communication. Conversations with children are available from CHILDES. All of the data is transcribed in CHAT and CA/CHAT formats. Databases of the following types are included in the collection: Aphasia patient speech, Child speech, Study of Phonological Development, Conversation Analysis, and Bilingualism and Second Language Acquisition. TalkBank will use these databases to advance the development of standards and tools for creating, sharing, searching, and commenting upon primary materials via networked computers.

Proper citation: TalkBank (RRID:SCR_003242) Copy   

•   Source: SciCrunch Registry

http://www.mirbase.org/

Central online repository for microRNA nomenclature, sequence data, annotation and target prediction.Collection of published miRNA sequences and annotation.

Proper citation: miRBase (RRID:SCR_003152) Copy   

•   Source: SciCrunch Registry

http://www.eyemoviepedia.com/

Archive and access films from the field of Ophthalmology for free on highly secure servers for permanent access and citeability. A citeable identification number (specific addressing using DOI), allows for citation of individual films in journal publications. Films may be commented by the author either in speech, or in text. Key wording provided by the authors at the time of submission, make each film recognizable to internet search machines.

Proper citation: eyeMoviePedia (RRID:SCR_003541) Copy   

•   Source: SciCrunch Registry

http://www.ahrq.gov/data/

Agency that produces evidence to make health care safer, higher quality, more accessible, equitable, and affordable. Funding opportunities, grants, and a large collection of longitudinal hospital care data in the United States including the Systematic Review Data Repository and data sources on healthcare cost, quality, and accessibility, emergency room visits, hospitalization, and medical insurance are available. It works within the U.S. Department of Health and Human Services and with other partners to make sure that the evidence is understood and used.

Proper citation: Agency for Healthcare Research and Quality (RRID:SCR_003604) Copy   

•   Source: SciCrunch Registry

http://dgv.tcag.ca/dgv/app/home

Public repository that accepts direct submissions and provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species. Variants are accessioned at the study and sample level, granting stable identifiers that can be used in publications. DGVa data is integrated with other EBI resources, including comprehensive EBI search and Ensembl genome browser. Exchanges data with companion database, dbVar, at National Center for Biotechnology Information.NOTE: since 2019 DGVa doesn't accept submissions. Please send the data for submission to European Variation Archive (EVA).

Proper citation: Database of Genomic Variants Archive (DGVa) (RRID:SCR_004896) Copy   

•   Source: SciCrunch Registry

http://smd.princeton.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 17, 2021. Database to store, annotate, view, analyze and share microarray data. It provides registered users access to their own data, provides users access to public data, and tools with which to analyze those data, to any public user anywhere in the world. The GenePattern software package has been incorporated directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability. SMD search options allow the user to Search By Experiments, Search By Datasets, or Search By Gene Names. Web services are provided using common standards, such as Simple Object Access Protocol (SOAP). This enables both local and remote researchers to connect to an installation of the database and retrieve data using pre-defined methods, without needing to resort to use of a web browser.

Proper citation: SMD (RRID:SCR_004987) Copy   

•   Source: SciCrunch Registry

http://force11.org/

A collaboration which works to transform scholarly communications through advanced use of computers and the Web. FORCE11 advocates the digital publishing of papers in order to enable more effective scholarly communication. The virtual community also advocates the publication of software tools and research communication by means of social media channels. As such, FORCE11 provides access to information and tools for the wider scientific community.

Proper citation: FORCE11 (RRID:SCR_005334) Copy   

•   Source: SciCrunch Registry

http://pubchem.ncbi.nlm.nih.gov/

Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI).

Proper citation: PubChem (RRID:SCR_004284) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/pdbe/

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   

•   Source: SciCrunch Registry

http://figshare.com/

Repository for all data, figures, theses, publications, posters, presentations, filesets, videos, datasets, negative data in a citable, shareable and discoverable manner with Digital Object Identifiers. Allows to upload any file format to be made visualisable in the browser so that figures, datasets, media, papers, posters, presentations and filesets can be disseminated in a way that the current scholarly publishing model does not allow. Features integration with ORCID, Symplectic Elements, can import items from Github and is a source tracked by Altmetric.com. Figshare gives users unlimited public space and 1GB of private storage space for free. Data are digitally preserved by CLOCKSS. Supported by Digital Science, a division of Macmillan Publishers Limited, as a community-based, open science project that retains its autonomy.

Proper citation: FigShare (RRID:SCR_004328) Copy   

•   Source: SciCrunch Registry

https://nda.nih.gov/

The National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains. Research data repository for data sharing and collaboration among investigators. Used to accelerate scientific discovery through data sharing across all of mental health and other research communities, data harmonization and reporting of research results. Infrastructure created by National Database for Autism Research (NDAR), Research Domain Criteria Database (RDoCdb), National Database for Clinical Trials related to Mental Illness (NDCT), and NIH Pediatric MRI Repository (PedsMRI).

Proper citation: NIMH Data Archive (RRID:SCR_004434) Copy   

•   Source: SciCrunch Registry

http://www.data.gov/

Catalog of data sets that are generated and held by the Federal Government, including data, tools and resources to conduct research, develop web and mobile applications, design data visualizations, etc. Data.gov provides descriptions of the Federal datasets (metadata), information about how to access the datasets, and tools that leverage government datasets. The data catalogs will continue to grow as datasets are added. Federal, Executive Branch data are included in the first version of Data.gov.

Proper citation: Data.gov (RRID:SCR_004712) Copy   

•   Source: SciCrunch Registry

http://www.rhea-db.org/

Manually annotated reaction database where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both elemental and charge balance of the reactions. The database has been populated with the reactions found in the Enzyme Commission (EC) list (and in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalyzed reactions, other biochemical reactions are also included. Rhea is a manually annotated resource and it provides: stable reaction identifiers for each of its reactions; directionality information if the physiological direction of the reaction is known; the possibility to link several reactions together to form overall reactions; extensive cross-references to other resources including enzyme-catalyzed and other metabolic reactions, such as the EC list (in IntEnz), KEGG, MetaCyc and UniPathway; and chemical substructure and similarity searches on compounds in Rhea.

Proper citation: RHEA (RRID:SCR_004713) Copy   

•   Source: SciCrunch Registry

http://www.arabidopsis.org

Database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from data pages to other Arabidopsis resources. The data can be searched, viewed and analyzed. Datasets can also be downloaded. Pages on news, job postings, conference announcements, Arabidopsis lab protocols, and useful links are provided.

Proper citation: TAIR (RRID:SCR_004618) Copy   

•   Source: SciCrunch Registry