# 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. - [[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. ## 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. - [[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.