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http://www.cancerimagingarchive.net/
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.
Proper citation: Cancer Imaging Archive (TCIA) (RRID:SCR_008927) Copy
Repository to host data and tools associated with articles published by GigaScience & GigaByte journals. GigaDB defines a dataset as a group of files (e.g., sequencing data, analyses, imaging files, software programs) that are related to and support an article or study. Through their association with DataCite, each dataset will be assigned a DOI that can be used as a standard citation for future use of these data in other articles by the authors and other researchers. Datasets in GigaDB all require a title that is specific to the dataset, an author list, and an abstract that provides information specific to the data included within the dataset. Detailed information about the dataset is curated by dedicated biocurators in collaboration with the article authors at the time of publication of the associated manuscript to ensure full transparency and reproducibility of all journal articles published in GigaScience and GigaByte journals.
Proper citation: GigaDB (RRID:SCR_004002) Copy
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
Online repository of information about Australian plants, animals, and fungi. Development started in 2006. The Commonwealth Scientific and Industrial Research Organisation is organisation significantly involved in development of ALA.
Proper citation: Atlas of Living Australia (RRID:SCR_006467) Copy
Online repository of open access images including MR Sessions, MRI, Freesurfer APARC, Freesurfer ASEGs, Clinical Assessments, Atlas Scaling Factors, and Fast Segmentations data. CENTRAL currently contains 374 Projects, 3808 Subjects, and 5174 Imaging Sessions (June 2014). Central is powered by XNAT (The Extensible Neuroimaging Archive Toolkit), an open source software platform designed to facilitate management and exploration of neuroimaging and related data. XNAT includes a secure database backend and a rich web-based user interface.
Proper citation: XNAT Central (RRID:SCR_006235) Copy
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
Open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. Direct user submissions of molecular interaction data are encouraged, which may be deposited prior to publication in a peer-reviewed journal. The IntAct Database contains (Jun. 2014): * 447368 Interactions * 33021 experiments * 12698 publications * 82745 Interactors IntAct provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows "zooming in" on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available.
Proper citation: IntAct (RRID:SCR_006944) Copy
Repository for all research outputs from across all fields of science in any file format as well as both positive and negative results. They assign all publicly available uploads a Digital Object Identifier (DOI) to make the upload easily and uniquely citeable. They further support harvesting of all content via the OAI-PMH protocol. They promote peer-reviewed openly accessible research, and curate uploads. ZENODO allows users to create their own collection and accept or reject all uploads to it. They allow for uploading under a multitude of different licenses and access levels.
Proper citation: ZENODO (RRID:SCR_004129) Copy
http://www.fishbase.org/home.htm
A global species database and encyclopedia of over 32,800 species and subspecies of fishes that is searchable by common name, genus, species, geography, family, ecosystem, references literature, tools, etc. It links to other, related databases such as the Catalog of Fishes, GenBack, and LarvalBase. It is associated with a partner journal, Acta Ichthyologica et Piscatoria. It is available in English, Greek, Spanish, Portuguese, French, Dutch, Italian, and German. Photo and video submissions are welcome. FishBase 2004 is also available on DVD or CD-ROMs with full information on 28,500 species. It comes together with the FishBase 2000 book and can be ordered for 95 US$ including air-mail.
Proper citation: FishBase (RRID:SCR_004376) Copy
http://www.med.harvard.edu/AANLIB/
An atlas of normal and abnormal brain images intended as an introduction to basic neuroanatomy, with emphasis on the pathoanatomy of several leading central nervous system diseases that integrates clinical information with magnetic resonance (MR), x-ray computed tomography (CT), and nuclear medicine images. A range of brain abnormalities are presented including examples of certain brain disease presented with various combinations of image type and imaging frequency. Submissions of concise, exemplary, clinically driven examples of neuroimaging are welcome.
Proper citation: Whole Brain Atlas (RRID:SCR_005390) Copy
An NSF supported image repository of over 374,000 high-resolution photographs of approximately 4,000 species for research and education, used largely but not exclusively in the area of biodiversity research. Images can be annotated by users and browsed by specimen, view, taxonomy, location, collection, or annotation.
Proper citation: MorphBank (RRID:SCR_003147) Copy
http://researchdata.4tu.nl/en/home/
Multidisciplinary data repository for a consortium of universities in the Netherlands housing over datasets with a focus on scientific and technical data. Most data were produced by Dutch researchers including datasets from doctoral research. Users can deposit up to 1G by completing an upload form. Collection development foci include applied sciences, biomedical technology, earth sciences, and technology and construction. 4TU.Datacentrum is a collaboration of the libraries of the three leading technical universities - Delft University of Technology, Eindhoven University of Technology and the University of Twente.
Proper citation: 4TU.Datacentrum (RRID:SCR_006295) Copy
http://arch.library.northwestern.edu/
Arch is an open access repository for the research and scholarly output of Northwestern University. Log in with your NetID to deposit, describe, and organize your research for public access and long-term preservation. We'll use our expertise to help you curate, share, and preserve your work.
Proper citation: Arch (RRID:SCR_023130) Copy
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.
Proper citation: Simtk.org (RRID:SCR_002680) Copy
Platform to support research and enable collaboration. Used to discover projects, data, materials, and collaborators helpful to your own research.
Proper citation: Open Science Framework (RRID:SCR_003238) Copy
Professionally curated repository for genetics, genomics and related data resources for soybean that contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase includes annotated Williams 82 genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. The repository maintains controlled vocabularies for soybean growth, development, and traits that are linked to more general plant ontologies. Contributions to SoyBase or the Breeder''s Toolbox are welcome.
Proper citation: SoyBase (RRID:SCR_005096) Copy
Used to store, publish and share research data in FAIR way. Facilitates research data storage, guarantees long-term persistence of data and allows data, results or ideas to be shared worldwide.Supports community domains with metadata extensions, access rules and publishing workflows.
Proper citation: B2SHARE Eudat (RRID:SCR_023135) Copy
A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.
Proper citation: Synapse (RRID:SCR_006307) Copy
Collection of data related to crop plant and model organism Zea mays. Used to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models and to provide support services to the community of maize researchers. Data stored at MaizeGDB was inherited from the MaizeDB and ZmDB projects. Sequence data are from GenBank. Data are searchable by phenotype, traits, Pests, Gel Pattern, and Mutant Images.
Proper citation: MaizeGDB (RRID:SCR_006600) Copy
https://phenome.jax.org/centers/QTLA
Raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data. These data are provided as a courtesy to the genetic mapping community and may be used for purposes of developing or testing new analysis methods or software and for meta-analysis of quantitative traits. The authors of the datasets retain individual ownership of the data. As a courtesy to the authors, please alert them in advance of any publications that result from reanalysis of these data or obtain permission prior to redistribution of data or results. In all data sets and files, the marker locations have been translated to Cox build 37 coordinates unless otherwise stated. Please consider contributing your data to the QTL Archive.
Proper citation: QTL Archive (RRID:SCR_006213) Copy
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