alg-precision-therapeutics

name	alg-precision-therapeutics
description	Investigate rare disease mechanism of harm and therapeutic strategies from a known MONDO diagnosis

Algorithm for Precision Therapeutics (APT)

Use this skill when the diagnosis is KNOWN and the goal is to understand the mechanism of harm and identify therapeutic strategies. Follows Matt Might's APM Phase 2 (Therapeutic Phase) applied systematically to a MONDO disease ID.

Central innovation: apt-mechanism is a first-class entity linking gene -> pathway -> phenotype -> drug, not just a relation attribute.

Triggers: "mechanism of harm", "investigate disease X", "MONDO disease", "therapeutic landscape", "rare disease mechanism", "what can treat X", "APM analysis", "how does X cause disease", "disease knowledge graph", "build disease KG", "what genes cause X", "rational therapy design", "precision therapeutics", "Algorithm for Precision Medicine"

NOT for: differential diagnosis, variant pathogenicity, or finding a diagnosis from symptoms - use clinical tools for those.

Prerequisites

• TypeDB running (install alhazen-core first and run /alhazen-core:init)
• uv installed

Path note: Replace <skill-path> with your installation directory (e.g. ~/.claude/plugins/cache/alg-precision-therapeutics/ when installed as a plugin).

Quick Start

SCRIPT="<skill-path>/alg_precision_therapeutics.py"

# 1. Search for MONDO ID
uv run --project <skill-path> python $SCRIPT search-disease --query "NGLY1 deficiency"

# 2. Initialize investigation
uv run --project <skill-path> python $SCRIPT init-investigation MONDO:0800044

# 3. Ingest all external data
uv run --project <skill-path> python $SCRIPT ingest-disease --mondo-id MONDO:0800044

# 4. View mechanism map (after Claude adds mechanisms)
uv run --project <skill-path> python $SCRIPT show-mechanisms --mondo-id MONDO:0800044

# 5. View therapeutic map
uv run --project <skill-path> python $SCRIPT show-therapeutic-map --mondo-id MONDO:0800044

Read USAGE.md before executing commands.