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Platforms and Repositories

This index covers all data platforms, repositories, and data capture systems in the graph.

Research data repositories and publications

General-purpose open repositories, publication archives, and preprint servers used across research domains.

  • data.gouv.fr is the French government open data portal operated by Etalab/DINUM, the umbrella infrastructure within which Recherche Data Gouv and Health Data Hub operate.
  • HAL is the French national open-access publication archive operated by CCSD/CNRS. Deposit is mandatory under ANR Open Science Policy, CNRS Open Science, and Inserm Open Science mandates.
  • OpenAIRE is the EU open science infrastructure that operates Zenodo, harvests 900+ repositories, and monitors Horizon Europe open-access compliance.
  • OSF (Open Science Framework) is the Center for Open Science platform for pre-registration, data and code sharing, and preprints.
  • arXiv is the original open-access preprint repository, founded in 1991, covering physics, mathematics, computer science, quantitative biology (including the Neurons and Cognition subcategory relevant to computational neuroscience), statistics, and economics, with nearly 3 million articles as of 2025. It is transitioning to an independent nonprofit in July 2026.
  • bioRxiv is the Cold Spring Harbor Laboratory open preprint server for all biological sciences, providing immediate open access with DOI assignment and ORCID integration. It is a cOAlition S compliant deposit route under the Rights Retention Strategy.
  • medRxiv is the sister preprint server for clinical medicine, epidemiology, and public health, operated jointly by Cold Spring Harbor Laboratory, Yale University, and BMJ.
  • Recherche Data Gouv is the French national multidisciplinary research data repository recommended by ANR Open Science Policy, CNRS Open Science, and Inserm Open Science.
  • Software Heritage is the universal software source code archive providing SWHIDs and integrated with HAL for code deposit under French open science mandates.
  • Zenodo is the CERN and OpenAIRE general-purpose repository assigning DOIs to any research output, recommended for EU-funded projects.
  • Figshare is a Digital Science general-purpose repository accepting all file types with DOI assignment and ORCID integration, operated alongside institutional and publisher deployments and widely used for supplementary data sharing.

Research infrastructure, tools, and identifiers

Cross-domain tools for data management planning, persistent identification, and FAIR guidance.

  • DataCite is the international DOI registration agency for research data and software, underpinning Zenodo, OpenNeuro, DANDI Archive, and Recherche Data Gouv.
  • FAIRsharing is a curated registry of data standards, repositories, and data policies.
  • ORCID provides persistent digital identifiers for researchers, embedded across all repositories, funders, and publishers in the graph.
  • OPIDoR is the French national RDM tools suite operated by INIST-CNRS, comprising DMP OPIDoR, Cat OPIDoR, DORANum, and JurisDoR.
  • Protocols.io is an open-access platform for creating, versioning, and sharing step-by-step research protocols with DOI assignment and version control, acquired by Springer Nature in 2024.
  • RDMkit is the ELIXIR research data management toolkit providing life sciences FAIR guidance, with French resources maintained by IFB.

Neuroimaging repositories

Open repositories for brain imaging data across MRI, PET, EEG, MEG, and related modalities.

  • C-BIG is the Montreal Neurological Institute’s institutional open science repository for clinical, neuroimaging, genomic, and biospecimen data, built on LORIS and part of TOSI.
  • Public-nEUro is a GDPR-compliant European open-access repository for human brain imaging data in BIDS format, funded by the Novo Nordisk Foundation and hosted at the University of Copenhagen.
  • EBRAINS is the EU brain research infrastructure supporting BIDS, NWB, and openMINDS, with brain atlas services and simulation environments.
  • NEMAR is an open-access EEG, MEG, and iEEG data portal and compute gateway that automatically mirrors relevant datasets from OpenNeuro and adds quality checks and HPC processing via the Neuroscience Gateway.
  • Neurosynth is a platform for large-scale automated fMRI meta-analysis, mapping activation coordinates from thousands of publications to Cognitive Atlas terms.
  • NeuroVault hosts unthresholded statistical maps, parcellations, and atlases and enables meta-analysis workflows.
  • NITRC is the NIH-funded neuroimaging tools registry and image repository, hosting 800+ tools and a searchable collection of MRI datasets.
  • OpenNeuro is an open repository for BIDS-formatted datasets (MRI, EEG, MEG, iEEG, PET) released under CC0/PDDL licences.

Bioimaging

Archives, management platforms, and format tools for biological microscopy data.

  • Bio-Formats is the OME Java library for reading over 160 proprietary microscopy file formats and converting them to the OME data model. It is embedded in OMERO, Fiji, and most open-source bioimaging software.
  • BioImage Archive is the EMBL-EBI broad-intake repository for all biological image data accompanying publications.
  • EMPIAR (Electron Microscopy Public Image Archive) is the EMBL-EBI repository for raw cryo-electron microscopy image data, three-dimensional reconstructions, and X-ray tomography datasets.
  • IDR (Image Data Resource) is the EMBL-EBI reference image repository built on OMERO, hosting published microscopy datasets.
  • NeuroMorpho.Org is the primary open archive for digitally reconstructed neuron and glia morphologies, standardising all reconstructions in SWC format.
  • OMERO is the OME institutional image management platform, deployed at Euro-BioImaging and France BioImaging nodes worldwide.

Neurophysiology repositories

  • DANDI Archive is the open archive for neurophysiology data funded by the NIH BRAIN Initiative. All submissions must be in NWB format.
  • G-Node (German Neuroinformatics Node) is the German national neuroinformatics repository for electrophysiology, neurophysiology, and neuroimaging data, with ten-year preservation and GDPR compliance.

Neuroscience data management tools

Tools and platforms for managing, harmonising, and federating neuroscience datasets across sites.

  • BrainLife.io is a cloud platform for BIDS and NWB analysis with automatic provenance tracking.
  • DataLad is a distributed data management system providing version control and provenance tracking for large research datasets.
  • LORIS is an open-source platform for multisite neuroimaging data management, developed at MNI and used by ADNI, CONP, TOSI, and Ontario Brain Institute.
  • LONI IDA (Image and Data Archive) is the USC Stevens Neuroimaging and Informatics Institute controlled-access repository hosting ADNI, PPMI, ABIDE, and other landmark neuroimaging cohorts.
  • Neurobagel enables federated participant-level cohort search across BIDS datasets without centralising data.
  • NIMH Data Archive (NDA) is the NIH NIMH controlled-access repository for human subjects neuroscience data, including the ABCD Study.
  • NIF (Neuroscience Information Framework) provides RRID identifiers for research resources and maintains a registry of recommended neuroscience repositories.
  • Neurostars is the INCF-operated community Q&A forum serving as the primary support channel for open neuroscience tools and standards.
  • XNAT is a DICOM management and pipeline platform used at EBRAINS member sites.

Genomics, single-cell, and multiomics

Sequence archives, controlled-access genomics repositories, expression databases, and single-cell portals.

  • Brain-CODE is the Ontario Brain Institute neuroinformatics platform serving 240+ researchers, federating data across LORIS, XNAT, and CONP.
  • CELLxGENE is the Chan Zuckerberg Initiative portal for curated single-cell transcriptomics data, requiring Cell Ontology and AnnData format, hosting 169+ million cells.
  • dbGaP is the NIH controlled-access repository for GWAS and human genotype-phenotype data.
  • dbSNP is the NCBI reference database for small-scale human genomic variants, assigning stable RefSNP (rs) identifiers to over 1.1 billion unique variants as of 2024. It is the US open-access counterpart to EVA.
  • DDBJ is the Japanese national sequence database and INSDC partner that mirrors ENA and SRA data.
  • EGA is the EMBL-EBI and CRG controlled-access repository for sensitive human genomics and phenotypic data.
  • ENA is the EMBL-EBI open-access raw sequence archive and INSDC partner that mirrors SRA and DDBJ.
  • EVA is the EMBL-EBI open-access variant archive covering short variants and structural variants.
  • NCBI GEO is the primary open-access repository for gene expression and functional genomics data.
  • NeMO Archive is the primary NIH BRAIN Initiative and BICAN multi-omics repository, focusing on single-cell brain atlas data.
  • SRA (Sequence Read Archive) is a public repository for high-throughput sequencing data, operated by NCBI/NIH and an INSDC partner with ENA and DDBJ.
  • Synapse AMP-AD is the Sage Bionetworks platform hosting the AMP-AD Knowledge Portal, CommonMind, and PsychENCODE open Alzheimer’s and psychiatric brain multiomics datasets.

Rare disease

  • Orphanet is the European rare disease reference portal managed by INSERM, providing ORPHAcodes, the ORDO ontology, and structured disease information across 6,000+ rare disease entities.

Clinical research

Platforms for clinical trial registration, data capture, health data warehousing, and trial data sharing.

  • BNDMR (Base Nationale de Données Maladies Rares) is the French national patient registry for rare diseases, operated by AP-HP using Orphanet ORPHAcodes across over 200 reference centres.
  • CleanWEB is the Telemedicine Technologies eClinical suite and the AP-HP institutional eCRF platform for regulatory-grade clinical trials.
  • ClinicalTrials.gov is the US national clinical trial registry and results database, operated by NLM/NIH.
  • CTIS is the EU Clinical Trials Information System, the mandatory registration and results portal for all EU/EEA clinical trials under EU Regulation 536/2014.
  • EDS AP-HP is the AP-HP clinical data warehouse covering 19 million patients, using OMOP CDM and HL7 FHIR, with the Cohort360 query tool.
  • Health Data Hub is the French national health data platform providing access to the SNDS (67 million people) via a secure Datalab, using OMOP CDM.
  • i2b2 is a clinical data warehousing platform deployed at AP-HP alongside OMOP CDM.
  • REDCap is a secure web-based eCRF and clinical data capture platform with 7,000+ institutional partners in 159 countries.
  • SNDS (Système National des Données de Santé) is the French national health data system and the core resource for epidemiological and health economics research.
  • VIVLI is a global platform for clinical trial individual patient data sharing via a controlled-access enclave.