feat: add rare disease MDT copilot team with ontology-first workflow

[hazelian0619]

Summary

Introduce a production rare disease multi-agent team for evidence-backed differential reasoning. The "Rare Disease MDT Copilot" coordinates six specialized agents through a structured clinical decision-support workflow.

What's included

Agent definitions (6 agents)

• leader — workflow coordinator, case structuring, delegation, candidate synthesis
• phenotype_structurer — free-text → structured HPO-aligned phenotype package
• evidence_researcher — ontology-first evidence retrieval (rd_ontology → BioMCP → web)
• genotype_analyst — variant/gene interpretation when genomic data is available
• auditor — contradiction and evidence-quality review before final delivery
• reporter — clinician-facing structured report writer

Team template

• rare_disease_team — assembles the 6 agents with a hard workflow contract

Ontology layer

• rd_ontology ToolSet — agent-native SQLite queries against Orphanet/OMIM/HPO (6 tools: resolve_term, search_disease, get_disease, get_hpo_term, find_by_hpo, stats)
• rd_ontology_first skill — enforces ontology-before-online retrieval pattern
• ETL pipeline (build_rd_ontology.py) — Orphanet XML + HPO .obo/.hpoa + OMIM → rd_ontology.sqlite
• CLI query helper (query_rd_ontology.py) — resolve disease aliases, fetch detailed records

Architecture

Dual-layer design: offline ontology layer (Orphanet/OMIM/HPO → local SQLite) for deterministic normalization, then online evidence layer (BioMCP/Web/DB API) for literature and current evidence.

Design notes

• The team is designed for clinician support, not automatic diagnosis
• All agents follow a strict ontology-first workflow: standardize before search
• The skill is a single consolidated file loaded by 3 agents (leader, phenotype_structurer, evidence_researcher)
• Non-goals explicitly documented in each agent: no definitive diagnosis claims, no treatment decisions, uncertainty must be preserved

🤖 Generated with Claude Code

[hazelian0619]

Superseded by v2.