Mosaic Pre-Clinical Intelligence

io.github.sourabhnkPublished by GitHub account sourabhnkv2.2.1Updated Oct 25, 2026

Pre-clinical drug-target intelligence: 60 curated targets, 1,969 counted partner genes, 11 tools

The publisher's own server: [PREPROD] Clinical.ly Research Suite

VerifiedSTDIODesktop onlyDatabasesAI & ML

Overview

AI-generated overview

A local MCP server that answers pre-clinical drug-target questions from your own PostgreSQL Mosaic database, with 5 free and 6 Pro tools.

What you can do
Look up target dossiers, compounds with measured activity, papers and AlphaFold structures, each with a coverage state so missing data is not shown as zero. Check a coverage grid for any human gene symbol, resolving identity and structure live. With Pro enabled, review clinical trials, assay validation precedent, pathway context and the target's 1-hop network. Assess synthetic-lethal whitespace and candidate resistance-bypass targets. Free calls return up to 10 compounds or papers; Pro up to 50.
When to use it
Use it when you already hold a PostgreSQL instance with the Mosaic schema and want an assistant to query drug-target intelligence locally over stdio. It is not a source of Mosaic's curated data; for that, the README points to a separate hosted server.
Requirements
A local Python runtime (pip, uvx or python -m) and a PostgreSQL or Neon connection string in DATABASE_URL ending in /mosaic_db, holding the Mosaic schema. Optional MOSAIC_TIER and MOSAIC_API_KEY. Stdio only; remote transport is not implemented in this package.
Before you install
DATABASE_URL is a secret connection string with credentials and is required. MOSAIC_API_KEY is not validated locally: in stdio mode any value is treated as Pro, so tier gating is not enforced. The package ships queries only, not data, and no shared read-only instance is provided. Dossier tools exist only on the hosted server.

Installation

In SourceWeft

  1. Open Mosaic Pre-Clinical Intelligence in the dashboard and add it to a workspace.
  2. Enable the server for the chats that should use its tools.

Desktop only via STDIO. STDIO servers start a local process, so they need the SourceWeft desktop host.

Other MCP clients

Follow the launch instructions in the repository.

README

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)

bash
pip install mosaic-mcp

With Claude Desktop

Add to your claude_desktop_config.json:

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

With Claude Code

bash
claude mcp add mosaic -- mosaic-mcp

Standalone

bash
export DATABASE_URL="postgresql://..."   # your own Postgresmosaic-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)

ToolWhat it returns
mosaic_get_target_profileThe 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_compoundsCompounds with measured activity on the target; sort by potency (default) or by max clinical phase
mosaic_get_target_papersPapers about the target, matched by NCBI Gene ID (PubTator3) where your database has the annotations, up to the declared corpus cutoff
mosaic_get_target_structureAlphaFold structural snapshot and pockets, with a caution when a pocket is lined by low-confidence residues
mosaic_get_coverage_gridA 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)

ToolWhat it returns
mosaic_clinical_pipelineClinical trials for compounds acting on the target (a ChEMBL mechanism link or pChEMBL ≥ 6)
mosaic_target_validationAssay precedent: what has been tried, in what model system
mosaic_pathway_contextThe pathways the target sits in
mosaic_target_networkThe target's 1-hop neighbourhood: compounds, diseases, pathways, organisations, interacting proteins
mosaic_synthetic_lethal_whitespacePartners functionally coupled to the target with little drug activity — assessed candidates and unassessed partners kept apart
mosaic_resistance_bypass_mapCandidate 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

VariableRequiredDescription
DATABASE_URLYesPostgreSQL connection string for your own instance; the path must name the database that holds the Mosaic schema.
MOSAIC_TIERNopro (or enterprise) enables the Pro tools in a self-hosted install.
MOSAIC_API_KEYNoIn 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.

Source: README.md at commit 49b7ac1

Tools

0
SourceWeft has not started this package in its sandbox yet, so its tools are not known.

Version history

6
  1. v2.2.1LatestOct 17, 2026
  2. v2.2.0Oct 16, 2026
  3. v2.1.3Oct 14, 2026
  4. v2.1.1Oct 7, 2026
  5. v2.0.0Sep 22, 2026
  6. v1.7.2Sep 16, 2026

Score

50% of the applicable checks met

How complete this listing is, computed from the registry entry, the endpoint and public sources. Not a rating of the server and not a statement that it is safe or working today: reachability is a dated check, and no installs or reviews go into the score.

  • Reached in the last 30 days25 pts

    Keep the endpoint answering the MCP handshake; SourceWeft probes it every 30 days.

  • Auth declared10 pts

    Declare the credential headers in the registry entry, or keep the endpoint answering the probe so its auth can be classified.

  • Tools listed15 pts

    Answer tools/list without a credential, or ship a package that starts in a sandbox without one.

  • DescriptionRequired15 pts
  • Logo10 pts
  • Documentation15 pts
  • License10 pts

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