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    "featureList": [
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      "Data exploration"
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    "description": "OmniPath integrates data from 150+ resources to provide a comprehensive view of molecular interactions, pathways, and biological annotations. This MCP server enables LLMs to execute SQL queries against the Omnipath database. The tool description includes context about the database schema and some template queries to facilitate accurate query generation.\n",
    "codeRepository": "https://github.com/saezlab/omnipath-next",
    "url": "https://explore.omnipathdb.org/api/mcp",
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    "license": "https://spdx.org/licenses/GPL-3.0-only.html",
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    "keywords": [
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      "biological annoations",
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      "basic research"
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    "datePublished": "2025-08-19",
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    "programmingLanguage": [
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    "@type": "SoftwareApplication",
    "@id": "https://github.com/scmcphub/scmcp",
    "identifier": "scmcphub/scmcp",
    "name": "SCMCP",
    "description": "An MCP server for scRNA-Seq analysis with natural language!\n",
    "codeRepository": "https://github.com/scmcphub/scmcp",
    "softwareHelp": {
      "@type": "CreativeWork",
      "url": "https://docs.scmcphub.org",
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        "identifier": "scmcphub",
        "url": "https://github.com/scmcphub/"
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    ],
    "license": "https://spdx.org/licenses/BSD-3-Clause.html",
    "applicationCategory": "HealthApplication",
    "keywords": [
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      "single-cell",
      "RNA sequencing",
      "scverse"
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    "featureList": [
      "decoupler",
      "cellrank",
      "liana",
      "scanpy",
      "infercnv"
    ],
    "datePublished": "2025-06-11",
    "operatingSystem": [
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    "programmingLanguage": [
      "Python"
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    "@context": "https://schema.org",
    "@type": "SoftwareApplication",
    "@id": "https://github.com/sib-swiss/sparql-llm",
    "additionalType": [
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    "identifier": "sib-swiss/sparql-llm",
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    "description": "Provide tools that helps users to access biological data resources from the SIB Swiss Institute of Bioinformatics, such as UniProt, Bgee, Rhea, SwissLipids, through the SPARQL query language.\n",
    "codeRepository": "https://github.com/sib-swiss/sparql-llm",
    "softwareHelp": {
      "@type": "CreativeWork",
      "url": "https://github.com/sib-swiss/sparql-llm",
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        "name": "SIB Swiss Institute of Bioinformatics",
        "identifier": "sib-swiss",
        "url": "https://github.com/sib-swiss"
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      {
        "@type": "Person",
        "name": "Vincent Emonet",
        "identifier": "vemonet",
        "url": "https://github.com/vemonet"
      }
    ],
    "license": "https://spdx.org/licenses/MIT.html",
    "applicationCategory": "HealthApplication",
    "keywords": [
      "knowledge bases",
      "SPARQL",
      "Protein",
      "Gene",
      "Orthologs",
      "Lipids"
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    "datePublished": "2026-06-02",
    "operatingSystem": [
      "Cross-platform"
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    "programmingLanguage": [
      "Python"
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    "featureList": [
      "UniProt",
      "Bgee",
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      "Cellosaurus",
      "OMA",
      "OrthoDB",
      "MetaNetX",
      "SwissLipids"
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  },
  {
    "@context": "https://schema.org",
    "@type": "SoftwareApplication",
    "@id": "https://github.com/sviatkh/flybase-mcp-server",
    "identifier": "sviatkh/flybase-mcp-server",
    "name": "FlyBase MCP",
    "description": "This MCP server allows accessing and retrieving information from FlyBase, a comprehensive database for the genetics and molecular biology of Drosophila melanogaster.\n",
    "codeRepository": "https://github.com/sviatkh/flybase-mcp-server",
    "softwareHelp": {
      "@type": "CreativeWork",
      "url": "https://github.com/sviatkh/flybase-mcp-server/blob/main/README.md",
      "name": "FlyBase MCP"
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    "maintainer": [
      {
        "@type": "Person",
        "name": "Sviatoslav Kharuk",
        "identifier": "sviatkh",
        "url": "https://github.com/sviatkh"
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    "license": "https://spdx.org/licenses/Apache-2.0.html",
    "applicationCategory": "HealthApplication",
    "keywords": [
      "FlyBase",
      "Drosophila melanogaster",
      "Fruit fly"
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    "datePublished": "2025-09-12",
    "operatingSystem": [
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    "programmingLanguage": [
      "Python"
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    "@context": "https://schema.org",
    "@type": "SoftwareApplication",
    "@id": "https://github.com/tamerh/biobtree",
    "additionalType": [
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    ],
    "identifier": "tamerh/biobtree",
    "name": "BioBTree v2 MCP server",
    "description": "A unified biomedical graph database that integrates 50+ primary data sources — genes, proteins, compounds, diseases, pathways, and clinical data — into a single queryable graph with billions of cross-reference edges. Its native MCP server gives LLMs direct access to structured, authoritative biomedical data, complementing their reasoning with reliable identifiers and up-to-date database content.\n",
    "codeRepository": "https://github.com/tamerh/biobtree",
    "url": "https://sugi.bio/biobtree/mcp",
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      "url": "https://github.com/tamerh/biobtree#readme",
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        "@type": "Person",
        "name": "Tamer Gür",
        "identifier": "tamerh",
        "url": "https://github.com/tamerh"
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    ],
    "license": "https://spdx.org/licenses/GPL-3.0-or-later.html",
    "applicationCategory": "HealthApplication",
    "keywords": [
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      "biomedical graph database",
      "cross-reference mapping",
      "drug discovery",
      "genomics",
      "proteomics"
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      "Tissue and cell-type expression analysis (Bgee, CELLxGENE, Expression Atlas, FANTOM5)",
      "Drug target and bioactivity lookup (ChEMBL, PubChem, BindingDB, HMDB)",
      "Disease-gene associations and clinical variants (ClinVar, MONDO, GenCC, GWAS Catalog, PharmGKB)",
      "Protein structure and function (UniProt, AlphaFold, AlphaMissense, PDB, InterPro)",
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    "datePublished": "2026-03-11",
    "operatingSystem": [
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    "programmingLanguage": [
      "Python",
      "Go"
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  },
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    "@type": "SoftwareApplication",
    "@id": "https://github.com/tianqitang1/enrichr-mcp-server",
    "identifier": "tianqitang1/enrichr-mcp-server",
    "name": "Enrichr MCP Server",
    "description": "A Model Context Protocol (MCP) server that provides gene set enrichment analysis using the Enrichr API. This server supports all available gene set libraries from Enrichr and returns only statistically significant results (corrected-$p$ < 0.05) for LLM tools to interpret.\n",
    "codeRepository": "https://github.com/tianqitang1/enrichr-mcp-server",
    "softwareHelp": {
      "@type": "CreativeWork",
      "url": "https://github.com/tianqitang1/enrichr-mcp-server/blob/main/README.md",
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    "maintainer": [
      {
        "@type": "Person",
        "name": "Tianqi Tang",
        "identifier": "tianqitang1",
        "url": "https://github.com/tianqitang1"
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    "license": "https://spdx.org/licenses/MIT.html",
    "applicationCategory": "HealthApplication",
    "keywords": [
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    "featureList": [
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    "datePublished": "2025-08-01",
    "operatingSystem": [
      "Cross-platform"
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    "programmingLanguage": [
      "TypeScript"
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  },
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    "@type": "SoftwareApplication",
    "@id": "https://github.com/vrtejus/pymol-mcp",
    "identifier": "vrtejus/pymol-mcp",
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    "description": "PyMOL-MCP connects PyMOL to Claude AI through the Model Context Protocol (MCP), enabling Claude to directly interact with and control PyMOL. This powerful integration allows for conversational structural biology, molecular visualization, and analysis through natural language.\n",
    "codeRepository": "https://github.com/vrtejus/pymol-mcp",
    "softwareHelp": {
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      "url": "https://github.com/vrtejus/pymol-mcp/blob/main/README.md",
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        "@type": "Person",
        "name": "Vishnu Rajan Tejus",
        "identifier": "vrtejus",
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    "license": "https://spdx.org/licenses/MIT.html",
    "applicationCategory": "HealthApplication",
    "keywords": [
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    "featureList": [
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    "datePublished": "2025-06-12",
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    "programmingLanguage": [
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  },
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    "@context": "https://schema.org",
    "@type": "SoftwareApplication",
    "@id": "https://github.com/winninghealth/medcalcmcp",
    "additionalType": [
      "https://schema.org/SoftwareSourceCode"
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    "identifier": "winninghealth/medcalcmcp",
    "name": "Medical Calculator MCP Service",
    "description": "Medical Calculator MCP Service Implementation.\n",
    "codeRepository": "https://github.com/winninghealth/medcalcmcp",
    "softwareHelp": {
      "@type": "CreativeWork",
      "url": "https://github.com/winninghealth/medcalcmcp#readme",
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        "name": "Winning Health AI Research",
        "identifier": "winninghealth",
        "url": "https://github.com/winninghealth"
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    "license": "https://spdx.org/licenses/Apache-2.0.html",
    "applicationCategory": "HealthApplication",
    "keywords": [
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    "datePublished": "2025-10-17",
    "operatingSystem": [
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    "programmingLanguage": [
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    "featureList": [
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]