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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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.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
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
http://www.ncbi.nlm.nih.gov/probe
Public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications including genotyping, gene expression studies, SNP discovery, genome mapping, and gene silencing. Probe records contain information on reagent distributors, probe effectiveness, and computed sequence similarities. The database is constantly updated, with over 11,000,000 probes available. Users may deposit their data into NCBI Probe Database.
Proper citation: NCBI Probe (RRID:SCR_004816) Copy
A large multidisciplinary world leader in genomic research with locations in Rockville, Maryland and San Diego, California. It was formed through the merger of several affiliated and legacy organizations - The Institute for Genomic Research (TIGR) and The Center for the Advancement of Genomics (TCAG), The J. Craig Venter Science Foundation, The Joint Technology Center, and the Institute for Biological Energy Alternatives (IBEA).
Proper citation: J. Craig Venter Institute (RRID:SCR_011269) Copy
Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. The raw data, search results, and full builds can be downloaded for other uses. All results of sequence searching are processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner ensuring a high quality database. All peptides are mapped to Ensembl and can be viewed as custom tracks on the Ensembl genome browser. The long term goal of the project is full annotation of eukaryotic genomes through a thorough validation of expressed proteins. The PeptideAtlas provides a method and a framework to accommodate proteome information coming from high-throughput proteomics technologies. The online database administers experimental data in the public domain. You are encouraged to contribute to the database.
Proper citation: PeptideAtlas (RRID:SCR_006783) Copy
SEER collects cancer incidence data from population-based cancer registries covering approximately 47.9 percent of the U.S. population. The SEER registries collect data on patient demographics, primary tumor site, tumor morphology, stage at diagnosis, and first course of treatment, and they follow up with patients for vital status.There are two data products available: SEER Research and SEER Research Plus. This was motivated because of concerns about the increasing risk of re-identifiability of individuals. The Research Plus databases require more rigorous process for access that includes user authentication through Institutional Account or multiple-step request process for Non-Institutional users.
Proper citation: Surveillance Epidemiology and End Results (RRID:SCR_006902) Copy
https://www.nitrc.org/projects/fmridatacenter/
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2013 Public curated repository of peer reviewed fMRI studies and their underlying data. This Web-accessible database has data mining capabilities and the means to deliver requested data to the user (via Web, CD, or digital tape). Datasets available: 107 NOTE: The fMRIDC is down temporarily while it moves to a new home at UCLA. Check back again in late Jan 2013! The goal of the Center is to help speed the progress and the understanding of cognitive processes and the neural substrates that underlie them by: * Providing a publicly accessible repository of peer-reviewed fMRI studies. * Providing all data necessary to interpret, analyze, and replicate these fMRI studies. * Provide training for both the academic and professional communities. The Center will accept data from those researchers who are publishing fMRI imaging articles in peer-reviewed journals. The goal is to serve the entire fMRI community.
Proper citation: fMRI Data Center (RRID:SCR_007278) Copy
http://www.ccdc.cam.ac.uk/Solutions/CSDSystem
It records bibliographic, chemical and crystallographic information for organic molecules and metal-organic compounds whose 3D structures have been determined using X-ray diffraction and neutron diffraction.
The CSD records results of single crystal studies and powder diffraction studies which yield 3D atomic coordinate data for at least all non-H atoms. In some cases the CCDC is unable to obtain coordinates, and incomplete entries are archived to the CSD.
The CSD includes crystal structure data arising from:
* publications in the open literature
* Private Communications to the CSD (via direct data deposition)
The Cambridge Structural Database System (CSDS) is a single product that comprises the following components: The Cambridge Structural Database (CSD); CSDS Software: search and information retrieval (ConQuest), structure visualization (Mercury), statistical analysis of retrieved data (VISTA), and software for database creation (PreQuest); Knowledge bases derived from the CSD: Mogul (intramolecular geometry) and IsoStar (intermolecular interactions, including data from the PDB).
Cambridge Structural Database (CSD) is the world repository of small-molecule crystal structures. For example, the crystal structures supported by the National Institute on Drug Abuse are deposited here.
Proper citation: Cambridge Structural Data Base (RRID:SCR_007310) Copy
Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts.
Proper citation: Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) Copy
http://hymenopteragenome.org/beebase/
Gene sequences and genomes of Bombus terrestris, Bombus impatiens, Apis mellifera and three of its pathogens, that are discoverable and analyzed via genome browsers, blast search, and apollo annotation tool. The genomes of two additional species, Apis dorsata and A. florea are currently under analysis and will soon be incorporated.BeeBase is an archive and will not be updated. The most up-to-date bee genome data is now available through the navigation bar on the HGD Home page.
Proper citation: BeeBase (RRID:SCR_008966) Copy
Project aims to promote data sharing, archiving, and reuse among researchers who study human development. Focuses on creating tools for scientists to store, manage, preserve, analyze and share video and related data.
Proper citation: Databrary (RRID:SCR_010471) Copy
http://www.icpsr.umich.edu/icpsrweb/NAHDAP/
Archive that acquires, preserves and disseminates data relevant to drug addiction and HIV research. Collection of data on drug addiction and HIV infection in United States. Most of datasets are raw data from surveys, interviews, and administrative records. They were originally gathered in research projects and for administrative purposes. Some datasets have been used in published studies. Bibliographies of these studies are available . Provides access to research data and technical assistance for data depositors. Provides e-workshops on data preparation and data systems.
Proper citation: National Addiction and HIV Data Archive Program (NAHDAP) (RRID:SCR_000636) Copy
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
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
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
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
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
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
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