mosaic for drug target intelligence

mosaic-mcp

Pre-clinical drug-target intelligence as an MCP server: target profiles, compounds, literature, structure, clinical pipeline, validation precedent and whitespace analysis — 11 tools, 5 free and 6 Pro. Every count carries a coverage state, so "we did not look" never renders as zero.

Which one do you want?

This package is bring-your-own-database. It is the MCP tool layer only — it ships the queries, not the data. You point it at a PostgreSQL instance you control, with the Mosaic schema, and it serves the tools over it. There is no public read-only credential for Mosaic's knowledge graph.

If you want Mosaic's curated knowledge graph — 60 oncology targets, ~128K compounds linked to them, 57,896 papers and 9,062 clinical trials (counted 2026-10-07), refreshed monthly — use the hosted server. It needs no database and no local install:

• Claude.ai connector (OAuth, Streamable HTTP): https://mcp.getmosaic.dev/mcp
• Remote MCP with an API key (SSE): https://mcp.getmosaic.dev/sse
• Sign in, API keys and on-demand dossiers for any human gene: https://getmosaic.dev

Quick start (self-hosted)

pip install mosaic-mcp

With Claude Desktop

Add to your claude_desktop_config.json:

{
  "mcpServers": {
    "mosaic": {
      "command": "mosaic-mcp",
      "env": {
        "DATABASE_URL": "postgresql://USER:PASSWORD@YOUR-HOST:5432/mosaic_db?sslmode=require"
      }
    }
  }
}

With Claude Code

claude mcp add mosaic -- mosaic-mcp

Standalone

export DATABASE_URL="postgresql://..."   # your own Postgres
mosaic-mcp                               # stdio transport

uvx mosaic-mcp and python -m mosaic_mcp.server work too. This package is stdio-only: --transport sse exits with NotImplementedError, because remote transport is the hosted server above.

Tools

Free (5)

Tool	What it returns
mosaic_get_target_profile	The target dossier: biology, approved and clinical drugs, disease associations ranked by Open Targets, validation evidence, organisations, scores — each axis with its coverage state
mosaic_get_target_compounds	Compounds with measured activity on the target; sort by potency (default) or by max clinical phase
mosaic_get_target_papers	Papers about the target, matched by NCBI Gene ID (PubTator3) where your database has the annotations, up to the declared corpus cutoff
mosaic_get_target_structure	AlphaFold structural snapshot and pockets, with a caution when a pocket is lined by low-confidence residues
mosaic_get_coverage_grid	A coverage grid for any human gene symbol: identity (HGNC) and structure (AlphaFold DB) resolve live; the other axes are marked queued

Free calls return up to 10 compounds or papers; Pro up to 50.

Pro (6)

Tool	What it returns
mosaic_clinical_pipeline	Clinical trials for compounds acting on the target (a ChEMBL mechanism link or pChEMBL ≥ 6)
mosaic_target_validation	Assay precedent: what has been tried, in what model system
mosaic_pathway_context	The pathways the target sits in
mosaic_target_network	The target's 1-hop neighbourhood: compounds, diseases, pathways, organisations, interacting proteins
mosaic_synthetic_lethal_whitespace	Partners functionally coupled to the target with little drug activity — assessed candidates and unassessed partners kept apart
mosaic_resistance_bypass_map	Candidate resistance-bypass and escape targets

mosaic_request_dossier and mosaic_get_dossier (on-demand dossiers) run only on the hosted server; they need its fetch and synthesis pipeline.

Configuration

Variable	Required	Description
DATABASE_URL	Yes	PostgreSQL connection string for your own instance; the path must name the database that holds the Mosaic schema.
MOSAIC_TIER	No	pro (or enterprise) enables the Pro tools in a self-hosted install.
MOSAIC_API_KEY	No	In stdio mode any value is treated as Pro; it is not checked locally. Keys are validated by the hosted server.

Changelog

Full history in CHANGELOG.md. Latest: 2.1.1 — the mosaic-mcp command starts again (it had failed with ImportError since 1.7.0). 2.1.0 capped mcp below 2, without which a fresh install died on import, and carried the fixes from a live audit of the hosted server.

License

Apache 2.0 for the MCP server tools. The hosted knowledge graph data requires a subscription for Pro-tier access.