docs/index.md

DeepBoner Documentation

Sexual Health Research Agent

AI-powered deep research system for sexual wellness, reproductive health, and hormone therapy research.

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Quick Links

Architecture

• Overview - Project overview, use case, architecture
• Design Patterns - Technical patterns, data models
• Workflow Diagrams - Visual architecture (Magentic v2.0)

Implementation (Phases 1-14 ✅ COMPLETE)

• Roadmap - Phased execution plan with TDD
• Phase 1: Foundation ✅ - Tooling, config, first tests
• Phase 2: Search ✅ - PubMed search
• Phase 3: Judge ✅ - LLM evidence assessment
• Phase 4: UI ✅ - Orchestrator + Gradio
• Phase 5: Magentic ✅ - Multi-agent orchestration
• Phase 6: Embeddings ✅ - Semantic search + dedup
• Phase 7: Hypothesis ✅ - Mechanistic reasoning
• Phase 8: Report ✅ - Structured scientific reports
• Phase 9: Source Cleanup ✅ - Remove DuckDuckGo
• Phase 10: ClinicalTrials ✅ - Clinical trials API
• Phase 11: Europe PMC ✅ - Preprint search
• Phase 12: MCP Server ✅ - Claude Desktop integration
• Phase 13: Modal Integration ✅ - Secure code execution
• Phase 14: Demo Submission ✅ - Hackathon submission

Future Roadmap

• Overview - Planned phases 15-17
• Phase 15: OpenAlex - Citation network integration
• Phase 16: PubMed Full-text - BioC API
• Phase 17: Rate Limiting - Production hardening
• Deep Research Mode - GPT-Researcher style enhancements

Bugs & Issues

• Active Bugs - Current issues and workarounds

Decisions

• PR #55 Evaluation - Architecture decision record
• Magentic + PydanticAI - Framework architecture decisions

Guides

• Deployment Guide - Gradio, MCP, and Modal launch steps

Development

• Testing Strategy - Unit, Integration, and E2E testing patterns

Brainstorming (Source Improvements)

• Roadmap Summary - Data source enhancement ideas
• PubMed Improvements
• ClinicalTrials Improvements
• Europe PMC Improvements

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What We're Building

One-liner: AI agent that searches medical literature to find evidence for sexual health research questions.

Example Queries:

"What drugs improve female libido post-menopause?" "Evidence for testosterone therapy in women with HSDD?" "Clinical trials for erectile dysfunction alternatives to PDE5 inhibitors?"

Output: Research report with drug candidates, mechanisms, evidence quality, and citations.

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Architecture Summary

User Question → Research Agent (Orchestrator)
                      ↓
              Search Loop:
                → Tools (PubMed, ClinicalTrials, Europe PMC)
                → Judge (Quality + Budget)
                → Repeat or Synthesize
                      ↓
              Research Report with Citations

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Features

Feature	Status	Description
Gradio UI	✅ Complete	Streaming chat interface
MCP Server	✅ Complete	Tools accessible from Claude Desktop
Modal Sandbox	✅ Complete	Secure statistical analysis
Multi-Source Search	✅ Complete	PubMed, ClinicalTrials, Europe PMC

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Status

Phase	Status
Phases 1-14	✅ COMPLETE

Tests: 142+ passing, 0 warnings Known Issues: See Active Bugs