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http://central.xnat.org

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   

•   Source: SciCrunch Registry

http://www.chemspider.com/

Collection of chemical structures. Provides access to structures, properties and associated information from hundreds of data sources to find compounds of interest and provides services to improve this data by curation and annotation and to integrate it with users applications.

Proper citation: ChemSpider (RRID:SCR_006360) Copy   

•   Source: SciCrunch Registry

http://aws.amazon.com/datasets

A multidisciplinary repository of public data sets such as the Human Genome and US Census data that can be seamlessly integrated into AWS cloud-based applications. AWS is hosting the public data sets at no charge for the community. Anyone can access these data sets from their Amazon Elastic Compute Cloud (Amazon EC2) instances and start computing on the data within minutes. Users can also leverage the entire AWS ecosystem and easily collaborate with other AWS users. If you have a public domain or non-proprietary data set that you think is useful and interesting to the AWS community, please submit a request and the AWS team will review your submission and get back to you. Typically the data sets in the repository are between 1 GB to 1 TB in size (based on the Amazon EBS volume limit), but they can work with you to host larger data sets as well. You must have the right to make the data freely available.

Proper citation: Amazon Web Services Public Data Sets (RRID:SCR_006318) Copy   

•   Source: SciCrunch Registry

http://www.researchgate.net/

A professional, social network and publication database geared to researchers where the latest field specific publications can be read, publications with other specialists can be discussed, and collaboration with colleagues is facilitated. They provide researchers with access to around 40 million abstracts and tens of thousands of Full texts, uploaded by the authors themselves. Researchers can search through 7 of the largest databases simultaneously, such as PubMed, IEEE & CiteSeer.

Proper citation: ResearchGate (RRID:SCR_006505) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.phytozome.net/

A comparative platform for green plant genomics. Families of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology / paralogy relationships as well as clade specific genes and gene expansions. As of release v9.1, Phytozome provides access to forty-one sequenced and annotated green plant genomes which have been clustered into gene families at 20 evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are hyper-linked and searchable., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Phytozome (RRID:SCR_006507) Copy   

•   Source: SciCrunch Registry

https://repository.niddk.nih.gov/home/

NIDDK Central Repositories are two separate contract funded components that work together to store data and samples from significant, NIDDK funded studies. First component is Biorepository that gathers, stores, and distributes biological samples from studies. Biorepository works with investigators in new and ongoing studies as realtime storage facility for archival samples.Second component is Data Repository that gathers, stores and distributes incremental or finished datasets from NIDDK funded studies Data Repository helps active data coordinating centers prepare databases and incremental datasets for archiving and for carrying out restricted queries of stored databases. Data Repository serves as Data Coordinating Center and website manager for NIDDK Central Repositories website.

Proper citation: NIDDK Central Repository (RRID:SCR_006542) Copy   

•   Source: SciCrunch Registry

http://www.rcsb.org/#Category-welcome

Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.

Proper citation: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) Copy   

•   Source: SciCrunch Registry

http://www.viprbrc.org/brc/home.do?decorator=vipr

Provides searchable public repository of genomic, proteomic and other research data for different strains of pathogenic viruses along with suite of tools for analyzing data. Data can be shared, aggregated, analyzed using ViPR tools, and downloaded for local analysis. ViPR is an NIAID-funded resource that support the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It provides a dedicated gateway to SARS-CoV-2 data that integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank), direct submissions, analysis pipelines and expert curation, and provides a suite of bioinformatics analysis and visualization tools for virology research.

Proper citation: Virus Pathogen Resource (ViPR) (RRID:SCR_012983) Copy   

•   Source: SciCrunch Registry

http://gigadb.org/

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   

•   Source: SciCrunch Registry

https://zenodo.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them.

Proper citation: NCBI BioSystems Database (RRID:SCR_004690) Copy   

•   Source: SciCrunch Registry

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

Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL.

Proper citation: European Bioinformatics Institute (RRID:SCR_004727) Copy   

•   Source: SciCrunch Registry

http://www.icpsr.umich.edu/

Data archive of more than 500,000 files of research in the social sciences, hosting 16 specialized collections of data in education, aging, criminal justice, substance abuse, terrorism, and other fields. ICPSR comprises a consortium of about 700 academic institutions and research organizations providing training in data access, curation, and methods of analysis for the social science research community. ICPSR welcomes and encourages deposits of digital data. ICPSR's educational activities include the Summer Program in Quantitative Methods of Social Research external link, a comprehensive curriculum of intensive courses in research design, statistics, data analysis, and social methodology. ICPSR also leads several initiatives that encourage use of data in teaching, particularly for undergraduate instruction. ICPSR-sponsored research focuses on the emerging challenges of digital curation and data science. ICPSR researchers also examine substantive issues related to our collections, with an emphasis on historical demography and the environment.

Proper citation: Inter-university Consortium for Political and Social Research (ICPSR) (RRID:SCR_003194) Copy   

•   Source: SciCrunch Registry

http://isps.yale.edu/research/data

Data archive to assist in the sharing of research grade information pertaining to the social and economic sciences. The majority of digital content currently consists of social science research data from experiments, program files with the code for analyzing the data, requisite documentation to use and understand the data, and associated files. Access to the ISPS Data Archive is provided at no cost and is granted for scholarship and research purposes only. When possible, Data is linked to Projects and Publications, via the ISPS KnowledgeBase. ISPS operates in accordance with the prevailing standards and practices of the digital preservation community including the Open Archival Information System (OAIS) Reference Model (ISO 14721:2003) and the Data Documentation Initiative (DDI) standard. Accordingly, ISPS supports digital life-cycle management, interoperability, and preferred methods of preservation. The ISPS Data Archive is intended for use by social science researchers, policy-makers, and practitioners who are conducting or analyzing field (and other) experiments in various social science disciplines. Currently, Replication Files originate with ISPS-affiliated scholars.

Proper citation: ISPS Data Archive (RRID:SCR_003127) Copy   

•   Source: SciCrunch Registry

https://osf.io/

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   

•   Source: SciCrunch Registry

http://www.morphobank.org

Web application providing online database and workspace for evolutionary research, specifically systematics (the science of determining the evolutionary relationships among species). It enables researchers to upload images and affiliate data with those images (labels, species names, etc.) and allows researchers to upload morphological data and affiliate it with phylogenetic matrices. MorphoBank is project-based, meaning a team of researchers can create a project and share the images and associated data exclusively with each other. When a paper associated with the project is published, the research team can make their data permanently available for view on MorphoBank where it is now archived.

Proper citation: MorphoBank (RRID:SCR_003213) Copy   

•   Source: SciCrunch Registry

http://phenome.jax.org/

Database enables integration of genomic and phenomic data by providing access to primary experimental data, data collection protocols and analysis tools. Data represent behavioral, morphological and physiological disease-related characteristics in naive mice and those exposed to drugs, environmental agents or other treatments. Collaborative standardized collection of measured data on laboratory mouse strains to characterize them in order to facilitate translational discoveries and to assist in selection of strains for experimental studies. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect., protocols, projects and publications, and SNP, variation and gene expression studies. Provides tools for online analysis. Data sets are voluntarily contributed by researchers from variety of institutions and settings, or retrieved by MPD staff from open public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys. MPD collects data on classical inbred strains as well as any fixed-genotype strains and derivatives that are openly acquirable by the research community. New panels include Collaborative Cross (CC) lines and Diversity Outbred (DO) populations. Phenotype data include measurements of behavior, hematology, bone mineral density, cholesterol levels, endocrine function, aging processes, addiction, neurosensory functions, and other biomedically relevant areas. Genotype data are primarily in the form of single-nucleotide polymorphisms (SNPs). MPD curates data into a common framework by standardizing mouse strain nomenclature, standardizing units (SI where feasible), evaluating data (completeness, statistical power, quality), categorizing phenotype data and linking to ontologies, conforming to internal style guides for titles, tags, and descriptions, and creating comprehensive protocol documentation including environmental parameters of the test animals. These elements are critical for experimental reproducibility.

Proper citation: Mouse Phenome Database (MPD) (RRID:SCR_003212) Copy   

•   Source: SciCrunch Registry

http://www.emdataresource.org/

Portal for deposition and retrieval of cryo electron microscopy (3DEM) density maps, atomic models, and associated metadata. Global resource for 3 Dimensional Electron Microscopy structure data archiving and retrieval, news, events, software tools, data standards, validation methods.

Proper citation: EMDataResource.org (RRID:SCR_003207) Copy   

•   Source: SciCrunch Registry