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The Neurobagel ecosystem comprises four primary tools:

  • The annotation tool (
    • to create harmonized annotations of phenotypic variables
    • intended for use by researchers and domain experts
    • static site, deployed on GitHub Pages
  • The command-line interface
    • to extract subject-specific metadata from annotated phenotypic and BIDS data
    • intended for data managers to create graph-ready harmonized data
  • The knowledge graph store and Neurobagel API (e.g.,
    • to store and query extracted metadata using RDF and the SPARQL query language
    • intended for research/data platform owners and for isolated deployments
  • The query tool (
    • to search across datasets and obtain metadata for subjects based on harmonized subject-level attributes
    • intended to help researchers and scientific data users find cohorts
    • static site, deployed on GitHub Pages

You can also find official Docker images for our containerized tools on the Neurobagel Docker Hub profile.

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