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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
Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.
Proper citation: Reactome (RRID:SCR_003485) Copy
Portal of geological information, including geology maps, reports, and GIS datasets, to help with the exploration, development and conservation of Alberta's resources.
Proper citation: Alberta Geological Survey (RRID:SCR_003402) Copy
Satellite facility that downlinks, processes, archives, and distributes remote-sensing data to scientific users around the world. Three major components: * Satellite Tracking Ground Station: Part of NASA?s Near Earth Network system of ground stations around the world. * Synthetic Aperture Radar Distributed Active Archive Center (SAR DAAC): ASF maintains the NASA archive of SAR data from a variety of satellites and aircraft, and provides these data and associated specialty support services to U.S. Government-approved researchers in support of NASA?s Earth Science Data and Information System project. * ASF Enterprise Center (ASFE): In support of UAF?s mission to be a student-centered research university, the ASF-E focuses on applications of remote-sensing data, specifically for UAF research. The ASF-E includes the GeoData Center (GDC), which provides data management and archive services for UAF principal investigators and maintains a variety of geophysical data collections in support of scientific research.
Proper citation: Alaska Satellite Facility (RRID:SCR_003610) Copy
https://www.projectdatasphere.org/
Initiative to advance oncology research by enabling collaborative sharing of historical oncology clinical trial data through a universal platform (database). The initiative aims to network all stakeholders in the cancer community researchers, industry, academia, advocacy, and other organizations to share insights and collaborate on issues that could not be solved individually. To do this, they have made efforts to address issues of data privacy, security, intellectual property, resources, and incentives as part of its effort to maximize participation. Data contributions include control arms of clinical trials, and the platform uses data-security precautions and analytics to pool multiple studies associated with the same diagnosis in a manner that seeks to protect the privacy of patients and the security of the data contributed.
Proper citation: Project Data Sphere (RRID:SCR_003726) 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
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
https://array.nci.nih.gov/caarray/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on Sep 18, 2018. Open-source, web and programmatically accessible microarray data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG). caArray furthers translational cancer research through acquisition, dissemination and aggregation of semantically interoperable array data to support subsequent analysis by tools and services on and off the Grid. As array technology advances and matures, caArray will extend its logical library of assay management.
Proper citation: caArray (RRID:SCR_006053) 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
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A public resource for sharing general proteomics information including data (Tranche repository), tools, and news. Joining or creating a group/project provides tools and standards for collaboration, project management, data annotation, permissions, permanent storage, and publication.
Proper citation: Proteome Commons (RRID:SCR_006234) 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
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
https://www.fludb.org/brc/home.spg?decorator=influenza
The Influenza Research Database (IRD) serves as a public repository and analysis platform for flu sequence, experiment, surveillance and related data.
Proper citation: Influenza Research Database (IRD) (RRID:SCR_006641) 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
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
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
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
Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response. Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases. InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions. InnateDB Capabilities: * View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly. * Search for genes and proteins of interest. * Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc. * Search genes/interactions belonging to 3,900 pathways. * Visualize interactions using an intuitive subcellular localization-based layout in Cerebral. * Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. * Access curated interaction data via a dedicated PSICQUIC webservice.
Proper citation: InnateDB (RRID:SCR_006714) 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
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