ToolUniverse

MCP server developed by the Zitnik Lab at Harvard Medical School with MIT Lincoln Laboratory, exposing 600+ vetted scientific tools spanning literature search, cheminformatics, omics, and clinical trial discovery. Designed as the tool backbone for AI-scientist workflows.

   
Type MCP server (also distributed as MCPB bundle and Claude.ai extension)
Supplier Zitnik Lab, Harvard Medical School; listed in anthropics/life-sciences marketplace
Availability GA — PyPI tooluniverse 1.0.x, surfaced as an Anthropic Life Sciences connector at J.P. Morgan 2026
Pricing Free / OSS; some wrapped APIs require user-supplied keys (e.g., Azure OpenAI for AI-tool-search features)
Capabilities Read/Write — most tools are read-only over public APIs; a few orchestrate analysis steps

How to install

  • Claude Code — direct stdio via uvx (simplest; no environment to manage): 
    claude mcp add --transport stdio tooluniverse -- uvx tooluniverse
  • Claude Code — anthropics/life-sciences marketplace (if you already use the marketplace): 
    /plugin marketplace add anthropics/life-sciences
/plugin install tooluniverse@life-sciences
  • Claude Desktop — MCPB bundle: download the .mcpb bundle from the ToolUniverse releases page and double-click to install via the Claude Desktop extensions UI.
  • Manual uv environment (useful if you want a filtered tool subset or to pin a version): 
    # 1) install uv (https://docs.astral.sh/uv/)
# 2) create and populate a dedicated env (replace /abs/path/to/claude_toolu_env with a directory you choose — e.g., $HOME/.tooluniverse-env)
mkdir -p /abs/path/to/claude_toolu_env
uv --directory /abs/path/to/claude_toolu_env pip install tooluniverse
# 3) register with Claude Code
claude mcp add tooluniverse --scope local -- uv --directory /abs/path/to/claude_toolu_env run tooluniverse-smcp-stdio

    Filter to a research-focused subset with --include-tools EuropePMC_search_articles,ChEMBL_search_similar_molecules,openalex_literature_search,search_clinical_trials appended to the tooluniverse-smcp-stdio invocation.

What it does

A single MCP surface that exposes 600+ tools covering:

  • Literature — EuropePMC, OpenAlex, PubMed search and full-text retrieval
  • Chemistry / pharmacology — ChEMBL, PubChem, drug-target lookups, similarity search
  • Omics & targets — Open Targets, Ensembl, UniProt, gene/protein cross-references
  • Clinical trials & regulatory — ClinicalTrials.gov search, FDA datasets
  • Knowledge graphs and ontologies — disease, phenotype, pathway lookups

Includes an AI-powered tool-search facility that lets Claude pick the right tool from the catalogue at runtime rather than overwhelming the context window with 600 definitions at once.

Primary use cases: AI-scientist agents that need broad coverage; hypothesis generation and iterative refinement across literature → omics → chemistry → trials; comparing competing hypotheses by pulling evidence from multiple databases in one session.

Notes

stdio transport when registered locally. Many wrapped APIs are public, but the AI-tool-search feature can be configured to use an LLM via environment variables (e.g., AZURE_OPENAI_API_KEY, AZURE_OPENAI_ENDPOINT). The MCPB bundle entry point is tooluniverse-smcp-stdio; the uvx tooluniverse shortcut is preferred for Claude Code because it doesn’t require maintaining a separate env.

Sources

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