"Can I take Ozempic?"       → Checks GLP1R variants against your genotype
"How about Vyvanse?"        → Cross-references CYP2D6 + COMT studies
"What's my Alzheimer risk?" → 19 disease conditions analyzed with odds ratios

{
  "gene": "ALDH2",
  "category": "drug_metabolism",
  "gene_description": "Alcohol metabolism, nitroglycerin bioactivation",
  "drugs": ["nitroglycerin", "ethanol"],
  "source": {
    "pmid": "16395407",
    "doi": "10.1172/JCI26564",
    "source_type": "pubmed",
    "title": "ALDH2 Glu504Lys polymorphism and nitroglycerin efficacy",
    "journal": "Journal of Clinical Investigation",
    "year": 2006,
    "cohort_size": 986,
    "url": "https://pubmed.ncbi.nlm.nih.gov/16395407/",
    "finding": "ALDH2*2 carriers show reduced nitroglycerin bioactivation."
  },
  "snps": [
    {
      "rsid": "rs671",
      "risk_allele": "A",
      "reference_allele": "G",
      "interpretations": {
        "AA": { "phenotype": "ALDH2 Deficient", "effect": "Nitroglycerin ineffective", "severity": "severe" },
        "AG": { "phenotype": "Reduced Activity", "effect": "33-40% less efficacy", "severity": "moderate" },
        "GG": { "phenotype": "Normal", "effect": "Standard response", "severity": "info" }
      }
    }
  ],
  "evidence_level": "established"
}

{
  "mcpServers": {
    "openpgx": {
      "command": "npx",
      "args": ["-y", "openpgx"]
    }
  }
}

claude mcp add openpgx -- npx -y openpgx

{
  "mcpServers": {
    "openpgx": {
      "command": "npx",
      "args": ["-y", "openpgx"]
    }
  }
}

npx openpgx

{
  "mcpServers": {
    "openpgx": {
      "type": "streamable-http",
      "url": "https://mcp.openpgx.ai/mcp"
    }
  }
}

"Upload my genome"                    → parse your raw DNA file
"Can I take Ozempic?"                 → check semaglutide + GLP1R
"What about Venvanse?"                → brand names work (60+ brands mapped)
"Is modafinil right for me?"          → checks COMT + CYP2C19 interactions
"Compare sertraline vs escitalopram"  → head-to-head comparison
"Weight loss medications"             → search by category
"antidepressivo"                      → Portuguese works too
"ozmpic"                              → typos are auto-corrected

"What's my cancer risk?"              → check specific conditions
"Full risk report"                    → all 19 conditions analyzed
"Do I have the Alzheimer gene?"       → APOE status
"Am I at risk for blood clots?"       → Factor V Leiden check

"Trait report"                        → all 25+ traits
"Am I lactose intolerant?"            → lactose persistence check
"Am I a morning person?"              → chronotype analysis

"Supplement protocol"                 → MTHFR, COMT, VDR, BCMO1, FUT2, CBS
"Should I take methylfolate?"         → based on your MTHFR status

{
  "gene": "GENE_SYMBOL",
  "category": "drug_metabolism",
  "gene_description": "What this gene does",
  "drugs": ["generic_drug_name"],
  "source": {
    "pmid": "12345678",
    "doi": "10.xxxx/xxxxx",
    "source_type": "pubmed",
    "title": "Study title",
    "journal": "Journal name",
    "year": 2024,
    "cohort_size": 1000,
    "url": "https://pubmed.ncbi.nlm.nih.gov/12345678/",
    "finding": "One-line summary of the key finding"
  },
  "snps": [
    {
      "rsid": "rs12345",
      "risk_allele": "A",
      "reference_allele": "G",
      "interpretations": {
        "AA": { "phenotype": "Poor Metabolizer", "effect": "...", "recommendation": "...", "severity": "severe" },
        "AG": { "phenotype": "Intermediate", "effect": "...", "recommendation": "...", "severity": "moderate" },
        "GG": { "phenotype": "Normal", "effect": "...", "recommendation": "...", "severity": "info" }
      }
    }
  ],
  "evidence_level": "established"
}

{
  "openpgx_version": "0.4.0"
}

{
  "openpgx_version": "0.4.0",
  "metadata": {
    "generated_at": "2026-04-12T12:00:00Z",
    "generator": "openpgx-mcp/1.x",
    "sources": ["CPIC", "PharmGKB"]
  },
  "patient": {
    "raw_data_source": "23andMe",
    "ancestry": "european"
  },
  "observations": [
    {
      "gene": "CYP2C19",
      "rsid": "rs4244285",
      "genotype": "AG"
    }
  ],
  "medications": [
    {
      "drug": { "name": "clopidogrel", "class": "antiplatelet" },
      "pgx_associations": [
        {
          "gene": "CYP2C19",
          "rsid": "rs4244285",
          "effect": "Reduced active metabolite formation",
          "evidence": { "level": "established", "sources": [] },
          "clinical_recommendation": "Consider alternative antiplatelet per guideline"
        }
      ],
      "parsed_at": "2026-04-12T12:00:00Z",
      "parse_source": "cpic_guideline",
      "confidence": { "score": 0.9, "evidence_level": "established" }
    }
  ],
  "fhir_mapping": {
    "resource_mappings": {
      "observations": "Observation (code: LOINC 81247-9 'Master HL7 genetic variant reporting panel')",
      "medications": "DiagnosticReport (code: LOINC 51969-4 'Genetic analysis report') + MolecularSequence",
      "risks": "RiskAssessment (method: LOINC 75321-0 'Clinical genomics report')",
      "traits": "Observation (category: genomics)"
    }
  }
}

Raw DNA file (23andMe .txt / Genera .csv)
        |
        v
+------------------+
|  Parser           | --> Extracts relevant SNPs from 600K+ raw data
|  (local, private) |
+------------------+
        |
        v
+------------------+
|  Study Catalog    | --> 118 studies x 109 genes x 219 drugs
|  (data/pgx/       |     Auto-creates gene definitions
|   studies/*.json)  |     Builds drug-gene index at runtime
+------------------+
        |
        v
+------------------+
|  MCP Tools        | --> 9 tools for AI interaction
|  (server-core.ts) |     Falls back to AI web search when needed
+------------------+
        |
        v
    AI Assistant (Claude, Cursor, ChatGPT, etc.)

git clone https://github.com/open-pgx/open-pgx.git
cd open-pgx/mcp-server
npm install
npm run build
npm start

mcp-server/
├── src/
│   ├── index.ts            # Entry point (stdio transport)
│   ├── server-core.ts      # MCP tools (11 tools)
│   ├── pgx-catalog.ts      # Study loader, gene index, phenotype inference
│   ├── parsers.ts           # 23andMe & Genera raw data parsers
│   ├── pharmacogenes.ts     # Barrel re-exports
│   ├── drug-resolver.ts     # 6-layer smart drug resolution
│   ├── risk-catalog.ts      # Disease risk definitions
│   ├── trait-catalog.ts     # Trait definitions
│   └── types.ts             # Shared TypeScript interfaces
├── data/
│   ├── pgx/studies/         # 118 study files (the knowledge base)
│   ├── risks/               # Disease risk condition definitions
│   ├── traits/              # Trait definitions
│   ├── drugs_embeddings.json # TF-IDF vectors for semantic search
│   └── tfidf_vocab.json     # TF-IDF vocabulary
├── genomes/                  # Safe gitignored dir for your DNA files
└── package.json