Reporting Guidelines

No guidelines defined

The European Genome-phenome Archive
The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).

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Human Protein Atlas
The Human Protein Atlas (HPA) portal is a publicly available database with millions of high-resolution images showing the spatial distribution of proteins in a number of different wild-type tissues, cancer types and human cell lines. The goal of the HPA is to map all the human proteins in cells, tissues and organs using an integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. The HPA is composed of six parts: the Tissue Atlas, the Single Cell Type Atlas, the Pathology Atlas, the Blood Atlas, the Brain Atlas, and the Cell Atlas.

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Database of Single Nucleotide Polymorphism
dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations.

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Dryad
Dryad is an open-source, community-led data curation, publishing, and preservation platform for CC0 publicly available research data. Dryad has a long-term data preservation strategy, and is a Core Trust Seal Certified Merritt repository with storage in US and EU at the San Diego Supercomputing Center, DANS, and Zenodo. While data is undergoing peer review, it is embargoed if the related journal requires / allows this. Dryad is an independent non-profit that works directly with: researchers to publish datasets utilising best practices for discovery and reuse; publishers to support the integration of data availability statements and data citations into their workflows; and institutions to enable scalable campus support for research data management best practices at low cost. Costs are covered by institutional, publisher, and funder members, otherwise a one-time fee of $120 for authors to cover cost of curation and preservation. Dryad also receives direct funder support through grants.

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GWAS Central
GWAS Central stores genome-wide association study data. The database content comprises direct submissions received from GWAS authors and consortia in addition to actively gathered data sets from various public sources. GWAS data are discoverable from the perspective of genetic markers, genes, genome regions or phenotypes, via graphical visualizations and detailed downloadable data reports.

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OpenNeuro
The OpenNeuro project (formerly known as the OpenfMRI project) was established in 2010 to provide a resource for researchers interested in making their neuroimaging data openly available to the research community. It is managed by Russ Poldrack and Chris Gorgolewski of the Center for Reproducible Neuroscience at Stanford University. The project has been developed with funding from the National Science Foundation, National Institute of Drug Abuse, and the Laura and John Arnold Foundation.

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MobiDB
MobiDB is a database of intrinsically disordered regions (IDRs) and related features from various sources and prediction tools. Different levels of reliability and different features are reported as different and independent annotations. The database features three levels of annotation: manually curated, indirect and predicted. MobiDB annotates the binding modes of disordered proteins, whether they undergo disorder-to-order transitions or remain disordered in the bound state. In addition, disordered regions undergoing liquid-liquid phase separation or post-translational modifications are defined.

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Open Science Framework
The Open Science Framework (OSF) is a free and open source project management tool that supports the entire research lifecycle: planning, execution, reporting, archiving, and discovery. Features include automated versioning, logging of all actions, collaboration support, free and unlimited file storage, registrations, and connections to other tools/services (ie. Dropbox, figshare, Amazon S3, Dataverse, GitHub). It is 100% free to researchers, open source, and intended for use in all domain areas. OSF has an open, public API to support broad indexing, as well as a partnership with Internet Archive for long-term preservation with a $250k preservation fund and an IMLS grant for transfer to Internet Archive (currently in progress). The OSF supports embargoing during peer review via a view-only link with the ability to anonymize contributor list. It also provides managed access by allowing access requests and private sharing settings. OSF is a non-profit with direct funder support through grants, government contracts, and community memberships.

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Structural Biology Data Grid
The Structural Biology Data Grid (SBGrid-DG) community-driven repository to preserve primary experimental datasets that support scientific publications. The SBGrid Data Bank is an open source research data management system enabling Structural Biologists to preserve x-ray diffraction data and to make it accessible to the broad research community.

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Advanced Ecological Knowledge and Observation System
The Advanced Ecological Knowledge and Observation System from the Terrestrial Ecosystem Research Network (TERN AEKOS) focuses on ecological plot data that are generated by land-based ecosystem projects that use survey, monitoring and experimental studies to collect raw data on plants, animals (including traits) and their immediate environments at the same location. Plot data are observations sampled by using scientific techniques such as quadrants, grids, transects, animal trap arrays and other structured sampling techniques.

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Zenodo
Zenodo is a generalist research data repository built and developed by OpenAIRE and CERN. It was developed to aid Open Science and is built on open source code. Zenodo helps researchers receive credit by making the research results citable and through OpenAIRE integrates them into existing reporting lines to funding agencies like the European Commission. Citation information is also passed to DataCite and onto the scholarly aggregators. Content is available publicly under any one of 400 open licences (from opendefinition.org and spdx.org). Restricted and Closed content is also supported. Free for researchers below 50 GB/dataset. Content is both online on disk and offline on tape as part of a long-term preservation policy. Zenodo supports managed access (with an access request workflow) as well as embargoing generally and during peer review. The base infrastructure of Zenodo is provided by CERN, a non-profit IGO. Projects are funded through grants.

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Open Targets
Open Targets is a data integration platform for access to and visualisation of potential drug targets associated with disease. Each drug target is linked to a disease using integrated genome-wide data from a broad range of data sources.

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MorphoBank
MorphoBank provides a digital archive of biodiversity and evolutionary research data, specifically systematics (the science of determining the evolutionary relationships among species). MorphoBank aids development of the Tree of Life - the genealogy of all living and extinct species. Heritable features - both genotypes (e.g., DNA sequences) and phenotypes (e.g., anatomy, behavior, physiology) are stored as part of the Tree of Life project. While the genomic part of this work is archived at the National Center for Biotechnology Information (NCBI), MorphoBank is part of the infrastructure for storing and sharing phenotype data, including information on anatomy, physiology, behavior and other features of species. One can think of MorphoBank as two databases in one: one that permits researchers to upload images and affiliate data with those images (labels, species names, etc.) and a second database that allows researchers to upload morphological data and affiliate it with phylogenetic matrices. In both cases, MorphoBank is project-based, meaning a team of researchers can create a project and share the images and associated data exclusively with each other. When a paper associated with the project is published, the research team can make their data permanently available for view on MorphoBank where it is now archived. The phylogenetic matrix aspect of MorphoBank is designed to aid systematists working alone or in teams to build large phylogenetic trees using morphology (anatomy, histology, neurology, or any aspect of phenotypes) or a combination of morphology and molecular data.

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Harvard Dataverse
Harvard Dataverse is a research data repository running on the open source web application Dataverse. Harvard Dataverse is fully open to the public, and allows upload and browsing of data from all fields of research, and is free for all researchers worldwide (up to 1 TB). Links to related grants, authors, software and research products are provided. Harvard Dataverse supports managed access (with an access request workflow) as well as embargoing generally and during peer review. Dataverse allows users to share, preserve, cite, explore, and analyse research data. It facilitates making data available to others, and allows you to replicate others' work more easily. Researchers, data authors, publishers, data distributors, and affiliated institutions all receive academic credit and web visibility. The Harvard Database receives support from Harvard University, public and private grants, and an emergent consortium model.

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Mendeley Data
Mendeley Data is a multidisciplinary, free-to-use open repository specialized for research data. Data files of up to 10GB can be uploaded and shared. Search more than 20+ million datasets indexed from 1000s of data repositories and collect and share datasets with the research community following the FAIR data principles. Links are available to related authors, software, grants and research. Each version of a dataset is given a unique DOI, and dark archived with DANS (Data Archiving and Networking Services), ensuring that every dataset and citation will be valid in perpetuity. Metadata is licensed CC0, and datasets are and will continue to be free access. Mendeley Data will shortly support managed access, and currently supports embargoing of data both generally and while undergoing peer review. It is funded by a subscription model for Academic & Government entities.

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High Energy Physics Data Repository
The Durham High Energy Physics Database (HEPData) has been built up over the past four decades as a unique open-access repository for scattering data from experimental particle physics. It currently comprises the data points from plots and tables related to several thousand publications including those from the Large Hadron Collider (LHC). HEPData is funded by a grant from the UK STFC and is based at the IPPP at Durham University.

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FAIRsharing
FAIRsharing is a FAIR-supporting resource that provides an informative and educational registry on data standards, databases, repositories and policy, alongside search and visualization tools and services that interoperate with other FAIR-enabling resources. FAIRsharing guides consumers to discover, select and use standards, databases, repositories and policy with confidence, and producers to make their resources more discoverable, more widely adopted and cited. Each record in FAIRsharing is curated in collaboration with the maintainers of the resource themselves, ensuring that the metadata in the FAIRsharing registry is accurate and timely. Every record is manually reviewed at least once a year. Records can be collated into collections, based on a project, society or organisation, or Recommendations, where they are collated around a policy, such as a journal or funder data policy.

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Alliance of Genome Resources
The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease.

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smartAPI repository
The smartAPI repository is a human and machine accessible database of web-based application programming interfaces that are described using the smartAPI specification (based on the OpenAPI initiative).

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PLAZA
PLAZA is a platform for comparative, evolutionary, and functional genomics. The platform consists of multiple instances, where each instance contains additional genomes, improved genome annotations, new software tools, etc.

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4DNucleome Data Portal
The 4D Nucleome Data Portal (4DN) hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization. It is a platform to search, visualize, and download nucleomics data.

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Center for Expanded Data Annotation and Retrieval Workbench
The Center for Expanded Data Annotation and Retrieval (CEDAR) Workbench is a database of metadata templates that define the data elements needed to describe particular types of biomedical experiments. The templates include controlled terms and synonyms for specific data elements. CEDAR is an end-to-end process that enables community-based organizations to collaborate to create metadata templates, investigators or curators to use the templates to define the metadata for individual experiments, and scientists to search the metadata to access and analyze the corresponding online datasets.

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GlyGen: Computational and Informatics Resources for Glycoscience
GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data. This web portal allows exploring this data and performing unique searches that cannot be executed in any of the integrated databases alone.

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Information Commons for Rice
Information Commons for Rice (IC4R) is a rice knowledgebase that incorporates rice data through multiple modules such as genome-wide expression profiles derived entirely from RNA-Seq data, resequencing-based genomic variations obtained from re-sequencing data of thousands of rice varieties, plant homologous genes covering multiple diverse plant species, post-translational modifications, rice-related literatures and gene annotations contributed by the rice research community.

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Global Research Identifier Database
Global Research Identifier Database (GRID) stores information on research-related organisations worldwide. GRID record contains a unique GRID ID, relevant metadata, and relationships between associated institutions.

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RESIF Seismic data portal
The RESIF Seismic data portal offers access to seismological and other associated geophysical data from permanent and temporary seismic networks operated all over the world by French research institutions and international partners, to support research on source processes and imaging of the Earth's interior at all scales. RESIF (French seismologic and geodetic network) is a French national equipment for the observation and understanding of the solid Earth.

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UNdata
UNdata is an international statistical database providing search and download options for a variety of statistical resources compiled by the United Nations (UN) statistical system and other international agencies. The numerous databases or tables, collectively known as "datamarts", contain over 60 million data points and cover a wide range of statistical themes including agriculture, crime, communication, development assistance, education, energy, environment, finance, gender, health, labour market, manufacturing, national accounts, population and migration, science and technology, tourism, transport and trade.

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Integrated Carbon Observation System Data Portal
ICOS Data Portal provides observational data and elaborated products on greenhouse gases. Data sets can be visualised and downloaded fully and/or partially. ICOS data meets the global standards for atmospheric, ecosystem flux and marine observations of greenhouse gases. All information on observations and the metadata is stored in persistent long-term repositories.

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Sciflection
Sciflection is a chemical database which allows researchers to publish and share their experiments as well as analytical data. Sciflection accepts structured data directly uploaded from Electronic Laboratory Notebooks (open enventory, Sciformation ELN, open for others) in JSON format. The repository is searchable by chemical structure, text parts, numeric parameters, etc.

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Bolin Centre Database
The Bolin Centre Database is a storage and management facility for data collected and collated at the Bolin Centre for Climate Research. Most of the data are available with open access and can be used under the terms given in the data description. The purpose of the center is to host all datasets produced within the Bolin Centre, to visualise the data and make the data publicly available.

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Bicocca Open Archive Research Data
BOARD (Bicocca Open Archive Research Data) is the institutional data repository of the University of Milano-Bicocca. BOARD is an open, free-to-use research data repository, which enables members of University of Milano-Bicocca to make their research data publicly available. By depositing their research data in BOARD researchers can make their research data citable, share their data privately or publicly, ensure long-term storage for their data, keep access to all versions and link their article to their data.

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Paired Omics Data Platform
Paired Omics Data Platform (PoDP) was created to streamline access to paired omics data so humans and computers can access and read paired datasets as well as record and exploit validated links between BGCs and metabolites. The aim of the PoDP is to connect public metabolomics datasets to their genomic origins. The PoDP does not store any metabolomics or genomics datasets, but captures metadata defining pairs of omics datasets in existing public databases and platforms already validated and utilized by the genomics and metabolomics communities.

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Software Heritage
The Software Heritage database stores source code with the goal of preserving software. Various metadata, including software origin and development history are retained. Software Heritage aims to ensure the availability, traceability and uniformity of the software it collects.

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BioImage Informatics Index
BioImage Informatics Index (BIII) is a bioimaging resource that describes software tools, training materials and imaging datasets with the aim of helping researchers find, identify and propagate image analysis tools or workflows. BIII aims to help biologists find any tool or workflow available for a particular image analysis problem; software and algorithm developers find missing tools (or components); and bioimaging analysts identify and edit workflows. It also helps raise awareness of bioimaging analysis solutions, even when they are not associated with a publication.

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data.sciencespo
data.sciencespo is a repository that offers visibility, sharing and preservation of Humanities and Social Science data collected, curated and processed at Sciences Po.

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Balearic Islands Coastal Observing and Forecasting System Data Repository
The Balearic Islands Coastal Observing and Forecasting System Data Repository (SOCIB) Data Repository contains data collected for both coastal and open ocean regions. The collection includes data from, high frequency radar, gliders, drifters, research vessel instruments, profilers, and moorings, amongst others, and advanced numerical model simulations from the Forecasting System.

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DatumKB: A Database of Biological Experimental Results
DatumKB is a freely accessible database of experimental results involving the function and regulation of human proteins in cultured cells. The results are manually curated from biological research literature using a shorthand language and stored as datums.

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