Hormonaly Clinical Intelligence

Hormonaly — Public API & Integration Reference

The AI-native infrastructure for peptide, hormone, and longevity medicine.

This repository is the public-facing integration reference for enterprise partners and API integrators. The MCP server source is published in this repository at Hormonaly-ai/hormonaly-public. For clinical access, visit hormonaly.ai.

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Table of Contents

1. Platform Overview
2. Architecture Overview
3. Partner API Reference
4. MCP Server — Tool Schema
5. Authentication
6. Rate Limits & Quotas
7. Errors & Status Codes
8. Subscription Tiers
9. Scribe API
10. Security & Compliance
11. Getting Access
12. Three-Lens Scoring
13. Webhook Events
14. API Versioning & Stability
15. Hormonaly-1 LLM
16. About Hormonaly

Platform Overview

Hormonaly combines three pillars into one platform:

• Evidence Synthesis — Multi-agent RAG over PubMed + 594 curated protocols with GRADE-style grading (A–D). 6 biomedical databases queried per response: PubMed, ClinicalTrials.gov, Cochrane, Europe PMC, OpenAlex, Semantic Scholar.
• Clinical Decision Support — Real-time answers, SOAP/DAP/Narrative notes, interaction checks, dosing, and monitoring plans grounded in verified citations.
• Workflow Tools — The operating layer for clinics, compounding pharmacies, and research teams in the peptide/hormone/longevity space.

By the numbers:

Core products available via API:

Architecture Overview

Hormonaly is built on a 42-agent orchestration architecture organized into six categories: Evidence, Research, Clinical, Content, Copilot, and Extraction — plus six continuously-running background agents.

Query Pipeline

Every Helix API call flows through the same deterministic pipeline:

Client query

│ ▼ NeMo Guardrails (PII redaction · off-topic filter · nvidia/llama-3.1-nemotron-nano-8b-v1) │ ▼ Agent Router (intent classification → tier selection) │ ├── TIER_1_BEST: Claude Sonnet 4.6 → GPT-4o fallback (complex/clinical queries) ├── TIER_2_BALANCED: Claude Sonnet 4.6 → GPT-4o → Claude Haiku 4.5 fallback (Scribe, CDS, Rx) └── TIER_3_FAST: Claude Haiku 4.5 → GPT-4o Mini → Gemini 2.5 Flash → Claude Sonnet 4.6 fallback (free tier, Three-Lens scoring) │ ▼ Multi-Database RAG Retrieval (6 databases · 80K token cap) │ ▼ Cross-Encoder Reranker (threshold ≥ 0.35, fallback 0.15) │ ▼ NeMo Parse — Full-text PMC enrichment (top 5 citations) │ ▼ Supervisor/Worker agents (complex multi-compound queries) │ ▼ Quality Gate (13 checks · 70% composite threshold · async) │ ▼ Citation Grounding (PMID verification · 4s timeout per citation) │ ▼ NeMo Output Guardrail (dosing safety scan · inline flags) │ ▼ Streaming SSE response → client

Agent Categories

Model Routing

Model routing note: All tiers use a primary + fallback chain. TIER_1: Claude Sonnet 4.6 → GPT-4o. TIER_2: Claude Sonnet 4.6 → GPT-4o → Claude Haiku 4.5. TIER_3: Claude Haiku 4.5 → GPT-4o Mini → Gemini 2.5 Flash → Claude Sonnet 4.6. NVIDIA NIM (nvidia/llama-3.3-nemotron-super-49b-v1, self-hosted on 8×H100 SXM) is used for citation grounding and the Ask Hormonaly copilot agent. Hormonaly-1 is Hormonaly's proprietary fine-tuned model — deployed on the same H100 infrastructure and progressively integrated to reduce third-party API dependence. See Hormonaly-1 LLM.

Evidence Quality Pipeline

• Reranker — Cross-encoder scores every RAG chunk ≥ 0.35 (fallback 0.15 for niche compounds)
• Token cap — 80,000 tokens max RAG context passed to LLM
• Quality gate — 13 checks across citation validity, answer completeness, clinical coherence, safety flags — composite score ≥ 70% threshold (async, post-hoc)
• Citation grounding — Every PMID verified against PubMed with 4s timeout; unverified citations are dropped
• NeMo Parse — Full PMC article text fetched for top 5 citations, structured into intro/methods/results, passed as enriched context

Partner API Reference

Base URL: https://hormonaly.ai/api/v1

Auth: Authorization: Bearer YOUR_API_KEY on every request.

Machine-readable OpenAPI spec: GET /api/v1/helix/openapi.json

All endpoint paths below are relative to the base URL.

Helix Endpoints

POST /helix/query

Submit a clinical question and receive a full Helix response with evidence grade, citations, and clinical verdict.

Request:

{

"query": "What is the evidence for BPC-157 in tendon repair?", "mode": "evidence", "stream": true }

Response (streaming SSE):

data: {"type":"agent_step","step":"classifying intent"}

data: {"type":"agent_step","step":"searching evidence","sources":26} data: {"type":"agent_step","step":"verifying citations"} data: {"type":"content","text":"BPC-157 has demonstrated..."} data: {"type":"metadata","evidence_grade":"C","confidence":62,"verdict":"CONSIDER","citations":5,"sources_consulted":26} data: {"type":"done"}

Response metadata fields:

GET /helix/protocols/:compound

Look up evidence-quality-rated protocols for a specific compound.

Example: GET /helix/protocols/bpc-157

Response:

{

"compound": "bpc-157", "evidence_grade": "C", "protocols": [ { "indication": "Tendon repair", "dose_range": "200–500 mcg/day", "route": ["subcutaneous", "intramuscular"], "cycle_duration": "4–12 weeks", "monitoring": ["liver enzymes at baseline", "symptom review at 4 weeks"] } ], "interactions": [], "citations": 5 }

POST /helix/dossier

Generate a comprehensive evidence dossier for a compound (async job). Advanced or Enterprise tier required.

Request:

{ "compound": "semaglutide", "sections": ["mechanism", "efficacy", "safety", "dosing"] }

Response: { "job_id": "dossier_abc123", "status": "queued" }

Poll with GET /helix/dossier/:job_id until status: "complete".

POST /helix/compare

Compare 2–3 protocols head-to-head across evidence grade, safety, dosing, and clinical readiness. Advanced or Enterprise tier required.

Request:

{ "compounds": ["testosterone-cypionate", "testosterone-enanthate"] }

GET /helix/health

Service health check. No authentication required.

{ "status": "ok", "latency_p50_ms": 4200, "citation_coverage": "99%" }

MCP Server — Tool Schema

Package: @hormonaly/mcp-server

The Hormonaly MCP server exposes 24 tools that allow Claude Desktop, Cursor, or any MCP-compatible agent to query the full Helix clinical intelligence stack directly — with no HTTP client code required on your side.

Installation (Claude Desktop)

The MCP server source is available in our GitHub repository. Clone and build locally:

git clone https://github.com/Hormonaly-ai/hormonaly-public.git

cd hormonaly-public/mcp/hormonaly-mcp-server npm install && npm run build

Then configure Claude Desktop as follows:

// ~/Library/Application Support/Claude/claude_desktop_config.json

{ "mcpServers": { "hormonaly": { "command": "node", "args": ["/path/to/hormonaly-mcp-server/dist/index.js"], "env": { "HORMONALY_API_URL": "https://hormonaly.ai", "HORMONALY_API_KEY": "YOUR_API_KEY" } } } }

Restart Claude Desktop — tools appear immediately.

HTTP/SSE mode (for server-side agents):

HTTP_PORT=3100 node dist/index.js

SSE: GET http://localhost:3100/sse?sessionId=YOUR_ID

POST: POST http://localhost:3100/messages?sessionId=YOUR_ID

Health: GET http://localhost:3100/health

See the mcp/README.md for full setup instructions.

Remote MCP — Claude.ai One-Click Connect

Live · Published May 2026 · Registry: registry.modelcontextprotocol.io

The Hormonaly MCP server is deployed as a remote HTTP/SSE server and listed on the official MCP Registry as io.github.Hormonaly-ai/hormonaly. Enterprise customers using Claude.ai get a one-click Connect experience — no local installation, no Docker, no `claude_deskto