Data Sources

AccessClinicalData@NIAID is a NIAID cloud-based, secure data platform that enables sharing of and access to reports and data sets from NIAID COVID-19 and other sponsored clinical trials for the basic and clinical research community.

The BD2K-LINCS DCIC is comprised of four major components: Integrated Knowledge Environment (IKE), Data Science Research (DSR), Community Training and Outreach (CTO) and Consortium Coordination and Administration (CCA). The Center is constructing a high-capacity scalable integrated knowledge environment enabling federated access, intuitive querying and integrative analysis and visualization across all LINCS resources and many additional external data types from other relevant resources. The Center’s data science research projects are aimed at addressing various data integration and intracellular molecular regulatory network challenges. The Center aims to develop: 1) methods to connect cellular and organismal phenotypes with molecular cellular signatures, and 2) novel data visualization methods for dynamically interacting with large-genomics and proteomics datasets.

The use of bioinformatics is ubiquitous within the life sciences. In bio.tools, we are striving to provide a comprehensive registry of software and databases, facilitating researchers from across the spectrum of biological and biomedical science to find, understand, utilise and cite the resources they need in their day-to-day work. Everything from simple command-line tools and online services, through to databases and complex, multi-functional analysis workflows is included. Resources are described in a rigorous semantics and syntax, providing end-users with the convenience of concise, consistent and therefore comparable information. Each bio.tools entry is assigned a human-readable, unique identifier based on the resource name, e.g. biotools:signalp. These identifiers provide a persistent reference to our Tool Cards of essential information, as well as a means to trace resources and integrate bio.tools data with other resources. bio.tools was supported by ELIXIR through the ELIXIR-EXCELERATE grant, which was funded by the European Union Horizon 2020 program under grant agreement 676559.

Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology. It holds a repository of R packages that facilitates rigorous and reproducible analysis of data from current and emerging biological assays. BioConductor delivers releases where a set of packages is published at once and intended for compatibility only with a certain version of R. This is in contrast to CRAN where packages are added continuously with no reference to particular versions of R. Additionally, BioConductor also comes with its own installation tool, BiocManager::install().

BioContainers is a community-driven project that provides the infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics fields such as proteomics, genomics, transcriptomics and metabolomics. The currently available BioContainers containers facilitate the usage, and reproducibility of software and algorithms. They can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, Cloud environments or HPC clusters). BioContainers is based on the popular frameworks Conda, Docker and Singularity.

The mission of BioStudies is to provide access to all the data outputs of a life sciences study from a single place, by organising links to data in other databases at EMBL-EBI or elsewhere, as well as hosting data and metadata that do not fit anywhere else. The database accepts submissions via an online tool, or in a simple tab-delimited format. BioStudies provides rich mechanisms for defining and using metadata guidelines specific for a particular data source such as a project or a community, and organises datasets in collections.

ClinEpiDB, launched in February 2018, is an open-access exploratory data analysis platform. We integrate data from high quality epidemiological studies, and offer tools and visualizations to explore the data within the browser in a point and click interface. We enable investigators to maximize the utility and reach of their data and to make optimal use of data released by others. ClinEpiDB is led by a team of scientists and developers based at the University of Pennsylvania, the University of Georgia, Imperial College London, and several other academic institutions. Currently, we are funded by the Bill and Melinda Gates Foundation for resource development and data integration, and by NIAID for integration of data from the International Centers of Excellence in Malaria Research (ICEMR).

The NIH Rapid Acceleration of Diagnostics Data Hub (RADx Data Hub) is a centralized data repository that provides access to analytic tools and de-identified COVID-19 data from the RADx Initiative. The RADx Data Hub supports scientific efforts to better understand COVID-19 and factors associated with disparities in morbidity and mortality in underserved and vulnerable populations, by allowing researchers to discover, access, and perform analyses of COVID-19 datasets in a cloud-enabled platform.

The Data Discovery Engine is a streamlined process to create, distribute and harves findable metadata via interoperable Schema.org schemas. The biomedical and informatics communities have largely endorsed the spirit and basic components of the FAIR Data Principles. Biomedical data producers, including CTSA hubs, need actionable best-practice guidance on how to make their data discoverable and reusable, and bring the practical benefits of data sharing to researcher's own research projects, as well as the research community as a whole.

The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in Humans. Such studies include genome-wide association studies, medical sequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits. The individual level data hosted at the dbGaP is distributed through a controlled access system. The types of data distributed through the dbGaP include phenotype data, association (GWAS) data, summary level analysis data, SRA (Short Read Archive) data, reference alignment (BAM) data, VCF (Variant Call Format) data, expression data, imputed genotype data, image data, etc.

Dockstore provides a place where users can share tools encapsulated in Docker and described with the Common Workflow Language(CWL) or Workflow Description Language(WDL), workflow languages used by members of and APIs created by the GA4GH Cloud Work Stream. This enables scientists, for example, to share analytical tools in a way that makes them machine readable and runnable in a variety of environments. While the Dockstore is focused on serving researchers in the biosciences, the combination of Docker + CWL/WDL can be used by anyone to describe the tools and services in their Docker images in a standardized, machine-readable way. Dockstore also attempts to work with new and alternative languages/standards such as Nextflow as popular challengers to CWL and WDL. While contributing work on the GA4GH Tool Registry standard as a way of sharing data with workflow platforms and partners.

Dryad is an open source, community driven project that takes a unique approach to data publication and digital preservation. Dryad focuses on search, presentation, and discovery and delegates the responsibility for the data preservation function to the underlying repository with which it is integrated. Dryad aims to allow researchers to validate published findings, explore new analysis methodologies, re-purpose data for research questions unanticipated by the original authors, and perform synthetic studies such as formal meta-analyses.

FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field.

The Harvard Dataverse Repository is a free data repository open to all researchers from any discipline, both inside and outside of the Harvard community, where you can share, archive, cite, access, and explore research data. Each individual Dataverse collection is a customizable collection of datasets (or a virtual repository) for organizing, managing, and showcasing datasets.

HuBMAP is part of a rich ecosystem of established and emerging atlasing programs supported by NIH and globally by other funding organizations, many of which are focused on specific organs or diseases. HuBMAP has connected with these programs to ensure data interoperability, avoid duplication of work, and leverage and synergize gained knowledge. The consortium has organized a number of events to bring together these communities to discuss topics of shared interest and is committed to improving coordination and collaboration among different programs. In addition, many of the HuBMAP PIs had been or are still actively participating in these efforts, helping with cross-pollination and advancing our global understanding. HuBMAP, as its name implies, was specifically initiated to resolve the challenge of building integrated, comprehensive, high-resolution spatial maps of human tissues and organs, which has resulted in HuBMAP providing leadership in the ecosystem around techniques for integrating disparate, multi-dimensional and multi-scale datasets, the development of a Common Coordinate Framework (CCF) for integrating data across many individuals, and the development and validation of these assays. To further increase interoperability, HuBMAP has adopted a number of standards and processes developed by other domain expert consortia, working and is actively involved in the knowledge exchange. The consortium sees itself as an integral part of the ecosystem, sharing its strengths and actively contributing to the community.

Thanks to new single cell genomics and spatial imaging technologies developed since the late 2000s and early 2010s, it is now possible to measure gene expression profiles in individual cells. These large scale data can be used with machine learning algorithms to decipher how the cells differ from and interact with their neighbors, and how they form and function in the tissue. This now allows scientists to identify and understand cell types in unprecedented detail, resolution and breadth. The Human Cell Atlas (HCA) is an international group of researchers using a combination of these new technologies to create cellular reference maps with the position, function and characteristics of every cell type in the human body.

The ImmPort project provides advanced information technology support in the archiving and exchange of scientific data for the diverse community of life science researchers supported by NIAID/DAIT and serves as a long-term, sustainable archive of research and clinical data. The core component of ImmPort is an extensive data warehouse containing experimental data and metadata describing the purpose of the study and the methods of data generation. The functionality of ImmPort will be expanded continuously over the life of the BISC project to accommodate the needs of expanding research communities. The shared research and clinical data, as well as the analytical tools in ImmPort are available to any researcher after registration.

MalariaGEN is an international network of researchers focused on understanding the genetic variations in humans, Plasmodium parasites, and Anopheles mosquitoes to better control malaria transmission. By leveraging advanced genomic tools and techniques, MalariaGEN aims to uncover how genetic differences influence susceptibility to malaria, track insecticide resistance in mosquitoes, and detect drug resistance in parasites. The network's efforts are crucial for developing new interventions and maintaining the effectiveness of existing ones. Coordinated from the Wellcome Sanger Institute in the UK, MalariaGEN collaborates with over 200 partners across more than 40 countries, primarily in malaria-endemic regions.

Mendeley Data, a product of Elsevier, is one of the newest entrants in the research data repository landscape; the platform was released in April 2016. Mendeley Data is a general-purpose repository, allowing researchers in any field to upload and publish research data. Mendeley Data also allows researchers to share unpublished data privately with research collaborators.

MicrobiomeDB was developed as a discovery tool that empowers researchers to fully leverage their experimental metadata to construct queries that interrogate microbiome datasets.

GEO is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles.

PubMed Central® (PMC) is a free full-text archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM). In keeping with NLM's legislative mandate to collect and preserve the biomedical literature, PMC is part of the NLM collection, which also includes NLM's extensive print and licensed electronic journal holdings and supports contemporary biomedical and health care research and practice as well as future scholarship. Available to the public online since 2000, PMC was developed and is maintained by the National Center for Biotechnology Information(NCBI) at NLM.

Sequence Read Archive(SRA) data, available through multiple cloud providers and NCBI servers, is the largest publicly available repository of high throughput sequencing data. The archive accepts data from all branches of life as well as metagenomic and environmental surveys. SRA stores raw sequencing data and alignment information to enhance reproducibility and facilitate new discoveries through data analysis.

The NICHD Data and Specimen Hub(DASH) is a centralized resource that allows researchers to share and access de-identified data from studies funded by NICHD. DASH also serves as a portal for requesting biospecimens from selected DASH studies. DASH serves as a mechanism for NICHD-funded extramural and intramural investigators to share research data from studies in accordance with NIH Data Sharing Policies. Many of the NICHD-funded research studies also collected biospecimens that are stored in the NICHD Contracted Biorepository. To provide access to these biospecimens, DASH will store and make available to other investigators the biospecimen catalog for studies that have associated research data in DASH. By supporting data and biospecimen access through DASH, NICHD aims to accelerate scientific findings and improve human health.

The Omics Discovery Index (OmicsDI) provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics).

The Project Tycho Repository for Global Health Data aims to advance the availabilty and use of data for improving global health. Project Tycho unlocks global health data to a rapidly growing user community of over 3,000 researchers, students, journalists, officials, and others in over 90 countries. A Project Tycho dataset includes case counts for a disease condition in a country. Data for Project Tycho datasets can come from various sources and have been pre-processed into the standard Project Tycho data format.

Qiita(canonically pronounced cheetah) is an entirely open-source microbial study management platform. It allows users to keep track of multiple studies with multiple 'omics data. Additionally, Qiita is capable of supporting multiple analytical pipelines through a 3rd-party plugin system, allowing the user to have a single entry point for all of their analyses. Qiita provides database and compute resources to the global community, alleviating the technical burdens that are typically limiting for researchers studying microbial ecology(e.g. familiarity with the command line or access to compute power).Qiita's platform allows for quick reanalysis of the datasets that have been deposited using the latest analytical technologies. This means that Qiita's internal datasets are living data that is periodically re-annotated according to current best practices.

The ReFRAME collection of 12,000 compounds is a best-in-class drug repurposing library containing nearly all small molecules that have reached clinical development or undergone significant preclinical profiling. The purpose of such a screening collection is to enable rapid testing of compounds with demonstrated safety profiles in new indications, such as neglected or rare diseases, where there is less commercial motivation for expensive research and development.

The Seven Bridges Public Apps Gallery offers a repository of publicly available apps suitable for many different types of data analysis. Apps include both tools (individual bioinformatics utilities) and workflows (chains or pipelines of connected tools). The publicly available apps are maintained by the Seven Bridges Platform bioinformatics team to represent the latest tool versions.

VDJServer is a free, scalable resource for performing immune repertoire analysis and sharing data. VDJServer Community Data Portal is part of the AIRR Data Commons. Funded by a National Institute of Allergy and Infectious Diseases research grant (#1R01A1097403), the VDJServer project is led by The University of Texas Southwestern (UTSW) Medical Center in collaboration with the J. Craig Venter Institute and Yale University. The Texas Advanced Computing Center (TACC) at The University of Texas at Austin leads the cyberinfrastructure implementation, including the high performance computing (HPC) systems, storage, and software solutions.

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB) is one of two Bioinformatics Resource Centers (BRCs) funded by the US National Institute of Allergy and Infectious Diseases (NIAID), with additional support from the Wellcome Trust (UK). VEuPathDB provides access to diverse genomic and other large scale datasets related to eukaryotic pathogens and invertebrate vectors of disease. Organisms supported by this resource include (but are not limited to) the NIAID list of emerging and re-emerging infectious diseases.

Vivli is an independent non-profit organization launched in 2016. Vivli evolved from a project of The Multi-Regional Clinical Trials Center of Brigham and Women’s Hospital and Harvard(MRCT Center) to enhance access to clinical trials data by promoting data sharing and transparency. In 2013, the MRCT Center and a diverse group of global stakeholders embarked on a mission to define, design, and launch an innovative platform solution for global clinical trial data sharing. The Vivli platform provides access to anonymized individual participant-level data(IPD) or the raw data that is collected during a clinical trial. The clinical trials represented in Vivli are global and contributed by a diverse group of data contributors. By serving as a global trusted platform, Vivli increases the discoverability of available data in the wider research ecosystem, and increases the overall capacity worldwide for effective data sharing, aggregation, re-use, and novel analysis of valuable clinical research data to advance science and improve public health. The Vivli platform is a cloud-based platform that consists of a dynamic search engine, a data repository, and a secure research environment.

WorkflowHub is a registry for describing, sharing and publishing scientific computational workflows. The registry supports any workflow in its native repository. WorkflowHub aims to facilitate discovery and re-use of workflows in an accessible and interoperable way. This is achieved through extensive use of open standards and tools, including Common Workflow Language (CWL), RO-Crate, BioSchemas and TRS, in accordance with the FAIR principles.

The OpenAIRE project, in the vanguard of the open access and open data movements in Europe was commissioned by the EC to support their nascent Open Data policy by providing a catch-all repository for EC funded research. CERN, an OpenAIRE partner and pioneer in open source, open access and open data, provided this capability and Zenodo was launched in May 2013.