Verify before you assert.

biosingularity is API- and MCP-first — built to be called by an agent or a product before it states a biomedical claim. One call in, one verdict out: pass / review / reject, with a receipt behind every finding. No model in the verdict path, so it's deterministic — the same input always yields the same verdict.

Discover the contract without reading this page: /api/capabilities (JSON) · /llms.txt

1 · MCP server

The first-class agent surface: 15 tools over stdio. Install the package, then register biosingularity-mcp as a custom MCP server.

pip install 'biosingularity[mcp,store]'
claude mcp add biosingularity -- biosingularity-mcp

Or add it to any MCP client's config:

{
  "mcpServers": {
    "biosingularity": { "command": "biosingularity-mcp" }
  }
}

Start with these three; the rest are there when you need them:

verify_answer verify_discovery attest_answer audit_references verify_variant verify_variant_trait verify_phenotype corroborate_gene_disease gene_essentiality check_drug check_drug_interaction check_trial provenance scan_folder data_freshness

2 · HTTP API

Metered. Send your key as x-api-key; pass an Idempotency-Key to make a call safely retryable. The key is reserved before any work runs, so an exhausted quota returns 429 without spending a verifier call.

curl -H "x-api-key: bsk_…" -H "Idempotency-Key: $(uuidgen)" \
  "https://<your-host>/api/verify?q=BRCA1%20rs80357906%20is%20benign%3B%20treat%20with%20cerivastatin"

Endpoint	Returns	Runs on
`GET /api/verify?q=`	full verdict + claims[] + receipts	demo + hosted
`GET /api/discovery?q=`	publish / review / reject	hosted
`GET /api/audit?q=`	retraction / erratum audit of cited DOIs	demo + hosted
`GET /api/target?gene=&disease=`	gene–disease corroboration	demo + hosted
`GET /api/entities?drug=&nct=`	drug / trial verifier	demo + hosted
`GET /api/provenance?ref=`	durable receipt lookup	hosted
`GET /api/health`	datalake reachability (no auth)	hosted
`GET /api/capabilities`	this contract, as JSON (no auth)	public

3 · Response shape

Threshold on recommend. Every flagged claim carries a receipt — a link to the exact source record — and grounded is true only when that receipt exists.

{
  "recommend": "pass | review | reject",
  "overall_severity": "red | amber | info | green",
  "confidence": 0.0,
  "summary": "…",
  "counts":   { "red": 0, "amber": 0, "info": 0, "green": 0 },
  "coverage": { "level": "low|partial|high", "ratio": 0.0,
                "claims_checked": 0, "statements": 0 },
  "claims": [
    { "kind": "reference", "ref": "10.1038/nature04533",
      "severity": "red", "detail": "Retracted in PubMed / retraction index.",
      "receipt": "https://pubmed.ncbi.nlm.nih.gov/…", "grounded": false }
  ],
  "graph": { "nodes": [], "edges": [],
             "relations": { "supports": 0, "contradicts": 0, "cautions": 0,
                            "retracts": 0, "replicates": 0, "unverified": 0 } }
}

4 · The verify-before-assert loop

Call biosingularity with your drafted answer, then act on the one verdict field:

recommend	Meaning	What your agent should do
reject	Grounded on retracted, contradicted, or unsafe evidence.	Block or retry. Do not surface the claim; show the receipt as the reason.
review	Weak, single-source, unverifiable, or low coverage.	Don't auto-assert. Route to a human, a second source, or the full-depth API.
pass	All checkable claims grounded, nothing flagged.	Proceed. Optionally attach an `attest_answer` receipt for audit.

The discovery gate (/api/discovery, verify_discovery) uses the same loop with publish / review / reject in place of pass. A false pass is the only unforgivable failure — anything unverifiable degrades to review, never waved through.

5 · Drop-in system-prompt snippet

Paste this into the system prompt of any agent that makes biomedical claims:

Before you assert any biomedical claim (a cited paper, a variant's
pathogenicity, a gene-disease link, a drug's safety or interactions, or a
trial's status), call the biosingularity `verify_answer` tool with your
drafted answer.

- If it returns recommend="reject", do NOT state the claim — surface the
  receipt and correct it.
- If "review", hedge and cite the flagged item; don't assert it as settled.
- Only assert freely on recommend="pass".

Never override a reject with your own confidence: the verdict is
deterministic and carries a source receipt; your prior does not.

6 · Discover the contract

/api/capabilitiesMachine-readable manifest: endpoints, claim types, sources, MCP tools, response schema, measured accuracy.

/llms.txtPlain-text brief for LLMs — when to call, how to threshold, the full tool + endpoint list.

Measured accuracy100% ACMG BA1 precision, 0 false contradictions; in-silico F1 0.84 — reproducible from the labelled set.

Need a key, the MCP connector, or a design-partner run on your own outputs? Request access →