Table 1.
Repositories harvested to generate the corpus of dataset metadata
| Arrayexpress (60 881) | ArrayExpress Archive of Functional Genomics Data stores data from high-throughput functional genomics experiments, and provides these data for reuse to the research community. |
| Bioproject (155 850) | A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. |
| The cancer imaging archive (63) | The Cancer Imaging Archive (TCIA) is a large archive of medical images of cancer accessible for public download. All images are stored in DICOM file format. The images are organized as ‘Collections’, typically patients related by a common disease (e.g. lung cancer), image modality (MRI, CT, etc) or research focus. |
| Clinicaltrials (192 500) | ClinicalTrials.gov is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world. |
| Clinical trials network (46) | A repository of data from completed CTN clinical trials to be distributed to investigators in order to promote new research, encourage further analyses, and disseminate information to the community. Secondary analyses produced from data sharing multiply the scientific contribution of the original research. |
| Cardiovascular research Grid (29) | The CardioVascular Research Grid (CVRG) project is creating an infrastructure for sharing cardiovascular data and data analysis tools. CVRG tools are developed using the Software as a Service model, allowing users to access tools through their browser, thus eliminating the need to install and maintain complex software. |
| Dataverse (60 303) | A Dataverse repository is the software installation, which then hosts multiple dataverses. Each dataverse contains datasets, and each dataset contains descriptive metadata and data files (including documentation and code that accompany the data). As an organizing method, dataverses may also contain other dataverses. |
| Dryad (67 455) | DataDryad.org is a curated general-purpose repository that makes the data underlying scientific publications discoverable, freely reusable, and citable. |
| Gemma (2285) | Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. |
| Gene expression omnibus (105 033) | Gene Expression Omnibus is a public functional genomics data repository supporting MIAME-compliant submissions of array- and sequence-based data. Tools are provided to help users query and download experiments and curated gene expression profiles. |
| Mouse phenome database (235) | The Mouse Phenome Database (MPD) has characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies. |
| Neuromorpho (34 082) | NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications. It contains contributions from over 80 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. |
| Nuclear receptor signaling atlas (NURSA) (389) | The Nuclear Receptor Signaling Atlas (NURSA) was created to foster the development of a comprehensive understanding of the structure, function, and role in disease of nuclear receptors (NRs) and coregulators. NURSA seeks to elucidate the roles played by NRs and coregulators in metabolism and the development of metabolic disorders (including type 2 diabetes, obesity, osteoporosis, and lipid dysregulation), as well as in cardiovascular disease, oncology, regenerative medicine and the effects of environmental agents on their actions. |
| Openfmri (36) | OpenfMRI.org is a project dedicated to the free and open sharing of functional magnetic resonance imaging (fMRI) datasets, including raw data. The focus of the database is on task fMRI data. |
| Peptideatlas (76) | PeptideAtlas is a 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. |
| Phenodisco (dbGaP) (429) | Phendisco is derived from the database of Genotypes and Phenotypes (dbGap), with additional metadata (9). |
| Physiobank (70) | PhysioBank is a large and growing archive of well-characterized digital recordings of physiologic signals and related data for use by the biomedical research community. PhysioBank currently includes databases of multi-parameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and patients with a variety of conditions with major public health implications, including sudden cardiac death, congestive heart failure, epilepsy, gait disorders, sleep apnea, and aging. |
| Protein data bank (113 493) | The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids found in all organisms including bacteria, yeast, plants, flies, other animals, and humans. |
| ProteomeXchange (1716) | The ProteomeXchange consortium has been set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. |
| Yale protein expression database (21) | The Yale Protein Expression Database (YPED) is an open source system for storage, retrieval, and integrated analysis of large amounts of data from high throughput proteomic technologies. YPED currently handles LCMS, MudPIT, ICAT, iTRAQ, SILAC, 2D Gel and DIGE, Label Free Quantitation (Progenesis), Label Free Quantitation (Skyline), MRM analysis and SWATH This repository contains data sets which have been released for public viewing and downloading by the responsible Primary Investigators. |
| Total (794 992) |
The numbers in parentheses indicate the number of datasets in each repository when the corpus was constructed.