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DimensionJoplin MCP ServerManage Joplin notes through MCP.BioMCPOne binary. One grammar. Evidence from the biomedical sources you already trust.
FMRS55 / 100 · C75 / 100 · B
Reliability9 / 2010 / 20
Security and permissions11 / 2016 / 20
Maintenance8 / 2018 / 20
Documentation14 / 2017 / 20
Setup experience13 / 2014 / 20
Best for
  • Users who want to manage a personal Joplin knowledge base through AI.
  • MCP client users who need note, notebook, and tag search and organization.
  • Users who need to restrict AI access by notebook path.
  • Biomedical researchers
  • Clinicians
  • AI agents that need efficient access to biomedical literature and data analysis
Not for
  • Users who do not use Joplin or cannot enable Web Clipper.
  • Users who cannot provide a Joplin API authorization token.
  • Read-only scenarios where write, update, or import permissions are not desired.
  • Users needing to write to upstream databases (read-only)
  • Users requiring direct access to closed datasets (e.g., COSMIC is not directly integrated)
  • Users expecting all advanced features without API keys
Required permissions
  • Requires a running Joplin Web Clipper authorization token supplied through JOPLIN_TOKEN.
  • Read permissions cover searching, viewing notebooks and tags, and connectivity checks.
  • Write, update, delete, and import operations can be controlled individually through configuration or environment variables.
  • Delete operations, retrieving all notes, and file imports are disabled by default.
  • notebook_allowlist can restrict read and write access by notebook path.
  • Requires internet access to query public biomedical APIs
  • Optional API keys (NCBI, Semantic Scholar, OpenFDA, etc.) to improve rate limits or unlock features
  • Local read/write access for skills, cache, and local study data (e.g., `~/.local/share/biomcp`)
Risks and side effects
  • After enabling delete, update, or import tools, an AI assistant can modify or delete Joplin content; delete operations are disabled by default.
  • Without a notebook allowlist, all notebooks are accessible by default.
  • Search results and individual notes can expose content; content_exposure settings control previews and full bodies.
  • When exposing HTTP or SSE publicly, operators must configure a reverse proxy and TLS; the documentation recommends a reverse proxy for public exposure.
  • The token is a secret credential and should not be exposed or placed in untrusted configuration.
  • Upstream API rate limits may affect performance
  • Some data sources (e.g., KEGG) have licensing terms that restrict non-academic use
  • Features requiring API keys (e.g., OncoKB) may be incomplete without them
  • Local binary installations need regular updates for compatibility
Supported clientsClaude Desktop, Jan AI, OllMCPClaude Desktop, Claude Code, Codex, Other MCP stdio clients
Tools2611