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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   

•   Source: SciCrunch Registry

http://seer.cancer.gov/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://fmf.igh.cnrs.fr/ISSAID/infevers

Registry for Familial Mediterranean Fever (FMF) and hereditary inflammatory disorders mutations. As of 2014, it includes twenty genes including: MEFV, MVK, TNFRSF1A, NLRP3, NOD2, PSTPIP1, LPIN2 and NLRP7, and contains over 1338 sequence variants. Confidential data, simple and complex alleles are accepted. For each gene, a menu offers: 1) a tabular list of the variants that can be sorted by several parameters; 2) a gene graph providing a schematic representation of the variants along the gene; 3) statistical analysis of the data according to the phenotype, alteration type, and location of the mutation in the gene; 4) the cDNA and gDNA sequences of each gene, showing the nucleotide changes along the sequence, with a color-based code highlighting the gene domains, the first ATG, and the termination codon; and 5) a download menu making all tables and figures available for the users, which, except for the gene graphs, are all automatically generated and updated upon submission of the variants. The entire database was curated to comply with the HUGO Gene Nomenclature Committee (HGNC) and HGVS nomenclature guidelines, and wherever necessary, an informative note was provided.

Proper citation: INFEVERS (RRID:SCR_007738) Copy   

•   Source: SciCrunch Registry

http://bioweb.ensam.inra.fr/esther

Database and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ESTHER (RRID:SCR_002621) Copy   

•   Source: SciCrunch Registry

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

Database that organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations in six major organism groups: Archaea, Bacteria, Eukaryotes, Viruses, Viroids, and Plasmids. Genomes of over 1,200 organisms can be found in this database, representing both completely sequenced organisms and those for which sequencing is in progress. Users can browse by organism, and view genome maps and protein clusters. Links to other prokaryotic and archaeal genome projects, as well as BLAST tools and access to the rest of the NCBI online resources are available.

Proper citation: NCBI Genome (RRID:SCR_002474) Copy   

•   Source: SciCrunch Registry

http://www.genomesonline.org/

Database of information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. It also provides information related to organism properties such as phenotype, ecotype and disease. Both complete and ongoing projects, along with their associated metadata, can be accessed. Users can also register, annotate and publish genome and metagenome data.

Proper citation: Genomes Online Database (RRID:SCR_002817) Copy   

•   Source: SciCrunch Registry

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

Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits.

Proper citation: NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) Copy   

•   Source: SciCrunch Registry

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

NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP.

Proper citation: GenBank (RRID:SCR_002760) Copy   

•   Source: SciCrunch Registry

http://sumsdb.wustl.edu/sums/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures

Proper citation: SumsDB (RRID:SCR_002759) 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

http://www.humanproteinpedia.org/

A community portal for sharing and integration of human protein data that allows research laboratories to contribute and maintain protein annotations. The Human Protein Reference Database (HPRD) integrates data that is deposited along with the existing literature curated information in the context of an individual protein. Data pertaining to post-translational modifications, protein-protein interactions, tissue expression, expression in cell lines, subcellular localization and enzyme substrate relationships can be submitted.

Proper citation: Human Proteinpedia (RRID:SCR_002948) Copy   

•   Source: SciCrunch Registry

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

International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus.

Proper citation: ArrayExpress (RRID:SCR_002964) Copy   

•   Source: SciCrunch Registry

http://dip.doe-mbi.ucla.edu/

Database to catalog experimentally determined interactions between proteins combining information from a variety of sources to create a single, consistent set of protein-protein interactions that can be downloaded in a variety of formats. The data were curated, both, manually and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks. Tools are available to analyze, visualize and integrate user's own experimental data with the information about protein-protein interactions available in the DIP database. The DIP database lists protein pairs that are known to interact with each other. By interact they mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organization and complexity of the protein interaction network at the cellular level. Registration is required to gain access to most of the DIP features. Registration is free to the members of the academic community. Trial accounts for the commercial users are also available.

Proper citation: Database of Interacting Proteins (DIP) (RRID:SCR_003167) 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://www.ebi.ac.uk/pride/

Centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester.

Proper citation: Proteomics Identifications (PRIDE) (RRID:SCR_003411) 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://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