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https://www.niddk.nih.gov/research-funding/research-programs/urologic-disease-centers

Program that aims to enhance the effectiveness of research related to noncancerous urologic dysfunction by encouraging collaboration amongst investigators.

Proper citation: O'Brien Urology Centers (RRID:SCR_015473) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/metagenomics/

Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020.

Proper citation: MGnify (RRID:SCR_016429) Copy   

•   Source: SciCrunch Registry

http://zfin.org

Model organism database that serves as central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations.Serves as primary community database resource for laboratory use of zebrafish. Developed and supports integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases.

Proper citation: Zebrafish Information Network (ZFIN) (RRID:SCR_002560) Copy   

•   Source: SciCrunch Registry

http://www.ndexbio.org/

Repository where scientists and organizations can share, store, manipulate, and publish biological network data. Users can also run their own copies of NDEx Server software in cases where stored networks must be kept in highly secure environment (such as for HIPAA compliance) or where high application load is incompatible with shared public resource. Open source software system that is part of Cytoscape family. Project of Cytoscape Consortium in conjunction with Ideker lab at UCSD School of Medicine. Public forum where biologists can exchange and publish computable network models in many types and formats. NDEx is based on REST web API which can be accessed by any application, including NDEx website and NDEx Cytoscape App. NDEx networks are assigned stable, globally unique URIs and so can be referenced by publications, by other networks, and by analytic applications.

Proper citation: Network Data Exchange (NDEx) (RRID:SCR_003943) Copy   

•   Source: SciCrunch Registry

https://www.immport.org/home

Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology.

Proper citation: The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) Copy   

•   Source: SciCrunch Registry

http://www.peptideatlas.org

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   

•   Source: SciCrunch Registry

http://www.thebiogrid.org/

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   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/pcsubstance?db=pcsubstance

As one of three primary databases of PubChem (Pcsubstance, Pccompound, and PCBioAssay), PubChem Substance Database contains descriptions of chemical samples, from a variety of sources, and links to PubMed citations, protein 3D structures, and biological screening results that are available in PubChem BioAssay. If the contents of a chemical sample are known, the description includes links to PubChem Compound. A PubChem FTP is available and new data is accepted into the repository. Pcsubstance contains more than 81 million records (2011).

Proper citation: PubChem Substance (RRID:SCR_004742) Copy   

•   Source: SciCrunch Registry

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

Web service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The repository allows you to explore datasets from numerous genotype experiments, supplied by a range of data providers. The EGA''s role is to provide secure access to the data that otherwise could not be distributed to the research community. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. As an example, only members of the EGA team are allowed to process data in a secure computing facility. Once processed, all data are encrypted for dissemination and the encryption keys are delivered offline. The EGA also supports data access only for the consortium members prior to publication.

Proper citation: European Genome phenome Archive (RRID:SCR_004944) Copy   

•   Source: SciCrunch Registry

http://openneuro.org

Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data.

Proper citation: OpenNeuro (RRID:SCR_005031) Copy   

•   Source: SciCrunch Registry

http://www.thegpm.org/

The Global Proteome Machine Organization was set up so that scientists involved in proteomics using tandem mass spectrometry could use that data to analyze proteomes. The projects supported by the GPMO have been selected to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results. The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. This database has been integrated into GPM server pages, allowing users to quickly compare their experimental results with the best results that have been previously observed by other scientists.

Proper citation: Global Proteome Machine Database (GPM DB) (RRID:SCR_006617) 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

https://dataverse.org/

Project portal for publishing, citing, sharing and discovering research data. Software, protocols, and community connections for creating research data repositories that automate professional archival practices, guarantee long term preservation, and enable researchers to share, retain control of, and receive web visibility and formal academic citations for their data contributions. Researchers, data authors, publishers, data distributors, and affiliated institutions all receive appropriate credit. Hosts multiple dataverses. Each dataverse contains studies or collections of studies, and each study contains cataloging information that describes the data plus the actual data files and complementary files. Data related to social sciences, health, medicine, humanities or other sciences with an emphasis in human behavior are uploaded to the IQSS Dataverse Network (Harvard). You can create your own dataverse for free and start adding studies for your data files and complementary material (documents, software, etc). You may install your own Dataverse Network for your University or organization.

Proper citation: Dataverse Network Project (RRID:SCR_001997) Copy   

•   Source: SciCrunch Registry

https://bmrb.io

Public depository that collects, annotates, archives, and disseminates important spectral and quantitative data derived from nuclear magnetic resonance spectroscopic investigations of biological macromolecules and metabolites. Provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR.

Proper citation: Biological Magnetic Resonance Data Bank (BMRB) (RRID:SCR_002296) Copy   

•   Source: SciCrunch Registry

http://www.ddbj.nig.ac.jp

Maintains and provides archival, retrieval and analytical resources for biological information. Central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: DDBJ Omics Archive and BioProject. DOR is archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides organizational framework to access metadata about research projects and data from projects that are deposited into different databases.

Proper citation: DNA DataBank of Japan (DDBJ) (RRID:SCR_002359) 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.mmrrc.org/

National public repository system for mutant mice. Archives and distributes scientifically valuable spontaneous and induced mutant mouse strains and ES cell lines for use by biomedical research community. Includes breeding/distribution facilities and information coordinating center. Mice strains are cryopreserved, unless live colony must be established. Live mice are supplied from production colony, from colony recovered from cryopreservation, or via micro-injection of cell line into host blastocysts. MMRRC member facilities also develop technologies to improve handling of mutant mice, including advances in assisted reproductive techniques, cryobiology, genetic analysis, phenotyping and infectious disease diagnostics.

Proper citation: Mutant Mouse Resource and Research Center (RRID:SCR_002953) 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://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://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   

•   Source: SciCrunch Registry