{
  "name": "biosingularity",
  "summary": "Deterministic, receipt-bearing verifier of biomedical claims. Call it BEFORE you assert a biomedical claim; it returns one verdict (pass / review / reject) with a receipt behind every finding.",
  "positioning": "The trust layer beneath biomedical AI — the fact-checker an agent calls before it asserts.",
  "deterministic": true,
  "cardinal_rule": "A false 'pass' is the only unforgivable failure. Anything unverifiable degrades to review, never waved through.",
  "verdicts": [
    "pass",
    "review",
    "reject"
  ],
  "discovery_verdicts": [
    "publish",
    "review",
    "reject"
  ],
  "claim_types": [
    {
      "type": "reference",
      "sources": [
        "PubMed",
        "Crossref/Retraction-Watch 74k-DOI local index"
      ],
      "demo": true
    },
    {
      "type": "gene_disease",
      "sources": [
        "Open Targets",
        "DisGeNET",
        "GWAS Catalog",
        "STRING"
      ],
      "demo": true
    },
    {
      "type": "drug",
      "sources": [
        "ChEMBL",
        "FDA Orange Book",
        "OpenFDA/FAERS",
        "PharmGKB",
        "DGIdb"
      ],
      "demo": "basic"
    },
    {
      "type": "drug_interaction",
      "sources": [
        "DDInter"
      ],
      "demo": false
    },
    {
      "type": "variant",
      "sources": [
        "ClinVar",
        "gnomAD",
        "dbNSFP",
        "eQTL/GTEx"
      ],
      "demo": false
    },
    {
      "type": "gene_essentiality",
      "sources": [
        "DepMap"
      ],
      "demo": false
    },
    {
      "type": "phenotype",
      "sources": [
        "HPO"
      ],
      "demo": false
    },
    {
      "type": "trial",
      "sources": [
        "ClinicalTrials.gov"
      ],
      "demo": true
    }
  ],
  "endpoints": [
    {
      "method": "GET",
      "path": "/api/verify",
      "params": [
        "q"
      ],
      "returns": "verdict",
      "demo": true,
      "hosted": true,
      "auth": "x-api-key (hosted)"
    },
    {
      "method": "GET",
      "path": "/api/discovery",
      "params": [
        "q"
      ],
      "returns": "discovery_verdict",
      "demo": false,
      "hosted": true,
      "auth": "x-api-key"
    },
    {
      "method": "GET",
      "path": "/api/audit",
      "params": [
        "q"
      ],
      "returns": "reference_audit",
      "demo": true,
      "hosted": true,
      "auth": "x-api-key (hosted)"
    },
    {
      "method": "GET",
      "path": "/api/target",
      "params": [
        "gene",
        "disease"
      ],
      "returns": "gene_disease",
      "demo": true,
      "hosted": true,
      "auth": "x-api-key (hosted)"
    },
    {
      "method": "GET",
      "path": "/api/entities",
      "params": [
        "drug",
        "nct"
      ],
      "returns": "drug_or_trial",
      "demo": true,
      "hosted": true,
      "auth": "x-api-key (hosted)"
    },
    {
      "method": "GET",
      "path": "/api/decompose",
      "params": [
        "q"
      ],
      "returns": "entities",
      "demo": true,
      "hosted": true,
      "auth": "x-api-key (hosted)"
    },
    {
      "method": "GET",
      "path": "/api/provenance",
      "params": [
        "ref"
      ],
      "returns": "receipt",
      "demo": false,
      "hosted": true,
      "auth": "x-api-key"
    },
    {
      "method": "GET",
      "path": "/api/health",
      "params": [],
      "returns": "datalake_health",
      "demo": false,
      "hosted": true,
      "auth": "none"
    },
    {
      "method": "GET",
      "path": "/api/capabilities",
      "params": [],
      "returns": "this_manifest",
      "demo": true,
      "hosted": false,
      "auth": "none"
    }
  ],
  "auth": {
    "header": "x-api-key",
    "idempotency_header": "Idempotency-Key",
    "quota": "per-key monthly; the key is reserved before work, so an exhausted key returns 429 without running the verifier"
  },
  "mcp": {
    "package": "biosingularity[mcp,store]",
    "install": "pip install 'biosingularity[mcp,store]'",
    "command": "biosingularity-mcp",
    "transport": "stdio",
    "add": "claude mcp add biosingularity -- biosingularity-mcp",
    "config": {
      "mcpServers": {
        "biosingularity": {
          "command": "biosingularity-mcp"
        }
      }
    },
    "start_here": [
      "verify_answer",
      "verify_discovery",
      "attest_answer"
    ],
    "tools": [
      "verify_answer",
      "verify_discovery",
      "attest_answer",
      "audit_references",
      "verify_variant",
      "check_drug_interaction",
      "gene_essentiality",
      "corroborate_gene_disease",
      "verify_variant_trait",
      "verify_phenotype",
      "check_drug",
      "check_trial",
      "provenance",
      "scan_folder",
      "data_freshness"
    ]
  },
  "response_schema": {
    "recommend": "pass|review|reject",
    "overall_severity": "red|amber|info|green",
    "confidence": "number|null (share of checkable claims that resolved to a real source)",
    "summary": "string",
    "counts": {
      "red": "int",
      "amber": "int",
      "info": "int",
      "green": "int"
    },
    "coverage": {
      "level": "low|partial|high",
      "ratio": "number|null",
      "claims_checked": "int",
      "statements": "int"
    },
    "claims": [
      {
        "kind": "string",
        "ref": "string",
        "severity": "red|amber|info|green",
        "detail": "string",
        "receipt": "url|null",
        "grounded": "bool"
      }
    ],
    "graph": {
      "nodes": "[]",
      "edges": "[]",
      "relations": "{supports,contradicts,cautions,retracts,replicates,unverified}"
    }
  },
  "accuracy": {
    "benchmark_variants": 142119,
    "acmg_ba1_precision_pct": 100,
    "acmg_ba1_flagged": 5179,
    "false_contradiction_rate_pct": 0,
    "insilico_f1_pct": 83.69,
    "insilico_recall_pct": 96.86,
    "note": "ACMG BA1 (>=5% population frequency) reject rule scored on ClinVar-derived, gnomAD-frequencied variants; in-silico dbNSFP consensus is used as supporting evidence only, never a standalone verdict."
  },
  "docs": {
    "integrate": "/integrate.html",
    "methodology": "/methodology.html",
    "llms_txt": "/llms.txt"
  }
}