MCP Server MCP

io.github.mims-harvard/tooluniverse

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2,500+ scientific tools for AI scientists: life science, research, literature, and more.

Homepage Verified source GitHub

Install

uvx tooluniverse

Configuration Example

{
  "remotes": [],
  "packages": [
    {
      "registryType": "pypi",
      "registryBaseUrl": "https://pypi.org",
      "identifier": "tooluniverse",
      "version": "1.4.1",
      "runtimeHint": "uvx",
      "transport": {
        "type": "stdio"
      },
      "packageArguments": [
        {
          "value": "tooluniverse-smcp-stdio",
          "type": "positional"
        },
        {
          "description": "Compact mode enabled by default: only exposes 4 core tools (tool finder, tool executor, etc.) to prevent context window overflow. All 2,500+ tools remain accessible via the execute_tool function.",
          "value": "--compact-mode",
          "type": "positional"
        },
        {
          "description": "Specific tool categories to load (e.g., uniprot ChEMBL opentarget pubmed). Omit to load all tools. See full list: https://zitniklab.hms.harvard.edu/ToolUniverse/tools/tools_config_index.html",
          "type": "named",
          "name": "--categories",
          "valueHint": "CATEGORY",
          "isRepeated": true
        }
      ],
      "environmentVariables": [
        {
          "description": "OpenAI API key for LLM-based tool finding and embedding features",
          "isSecret": true,
          "name": "OPENAI_API_KEY"
        },
        {
          "description": "Anthropic API key for Claude-based features",
          "isSecret": true,
          "name": "ANTHROPIC_API_KEY"
        },
        {
          "description": "Google Gemini API key for Gemini-based features",
          "isSecret": true,
          "name": "GEMINI_API_KEY"
        },
        {
          "description": "OpenRouter API key for accessing 100+ LLM models",
          "isSecret": true,
          "name": "OPENROUTER_API_KEY"
        },
        {
          "description": "Azure OpenAI API key (alternative to OpenAI)",
          "isSecret": true,
          "name": "AZURE_OPENAI_API_KEY"
        },
        {
          "description": "HuggingFace token for accessing models and datasets",
          "isSecret": true,
          "name": "HF_TOKEN"
        },
        {
          "description": "NCBI/PubMed API key for higher rate limits (10 req/sec vs 3 req/sec). Register at https://www.ncbi.nlm.nih.gov/account/",
          "isSecret": true,
          "name": "NCBI_API_KEY"
        },
        {
          "description": "Semantic Scholar API key for higher rate limits (100 req/sec vs 1 req/sec). Register at https://www.semanticscholar.org/product/api",
          "isSecret": true,
          "name": "SEMANTIC_SCHOLAR_API_KEY"
        },
        {
          "description": "BioGRID API key for protein-protein interaction queries. Register free at https://webservice.thebiogrid.org/",
          "isSecret": true,
          "name": "BIOGRID_API_KEY"
        },
        {
          "description": "DisGeNET API key for gene-disease association data. Register free at https://www.disgenet.org/",
          "isSecret": true,
          "name": "DISGENET_API_KEY"
        },
        {
          "description": "OMIM API key for Mendelian disease data. Register at https://omim.org/api",
          "isSecret": true,
          "name": "OMIM_API_KEY"
        },
        {
          "description": "OncoKB API token for precision oncology annotations. Register at https://www.oncokb.org/apiAccess",
          "isSecret": true,
          "name": "ONCOKB_API_TOKEN"
        },
        {
          "description": "NVIDIA NIM API key for AlphaFold2 structure prediction, molecular docking, and genomics tools. Get key at https://build.nvidia.com",
          "isSecret": true,
          "name": "NVIDIA_API_KEY"
        },
        {
          "description": "USPTO API key for patent data access. Register at https://developer.uspto.gov/",
          "isSecret": true,
          "name": "USPTO_API_KEY"
        },
        {
          "description": "UMLS API key for medical terminology and concept mapping. Register at https://uts.nlm.nih.gov/uts/",
          "isSecret": true,
          "name": "UMLS_API_KEY"
        },
        {
          "description": "BRENDA enzyme database login email. Register at https://www.brenda-enzymes.org/",
          "name": "BRENDA_EMAIL"
        },
        {
          "description": "BRENDA enzyme database login password",
          "isSecret": true,
          "name": "BRENDA_PASSWORD"
        }
      ]
    }
  ]
}

mcp model-context-protocol pypi