Skills: ALG Precision Therapeutics

ALG Precision Therapeutics Skill

Investigate rare disease mechanism of harm and identify therapeutic strategies from a known MONDO diagnosis.

Purpose

The alg-precision-therapeutics skill implements Phase 2 of the Algorithm for Precision Medicine (APM): given a confirmed MONDO diagnosis, build a comprehensive disease knowledge graph covering pathophysiology mechanisms, gene associations, clinical phenotypes, and therapeutic targets. The central concept is the apt-mechanism entity, which links gene → pathway → phenotype → drug into a structured causal chain.

Important limitation: This skill is for investigating a known diagnosis. It is not a differential diagnosis tool and cannot suggest diagnoses from symptoms.

Prerequisites

• TypeDB running (make db-start)
• uv installed
• Internet access (queries Monarch Initiative API v3)

Commands

uv run python .claude/skills/alg-precision-therapeutics/alg_precision_therapeutics.py <command> [args]

Command	What it does
search-disease	Search for a disease by name and return MONDO IDs
init-investigation	Create an investigation record for a MONDO disease
ingest-disease	Ingest disease data from Monarch Initiative (phenotypes, genes, mechanisms)
show-mechanisms	Display the causal mechanism chains for an ingested disease
show-therapeutic-map	Display therapeutic targets and candidate treatments

Typical Workflow

You: I want to investigate Fibrodysplasia Ossificans Progressiva
You: Search for this disease and find its MONDO ID
You: Initialize an investigation for MONDO:0009143
You: Ingest the disease data from Monarch Initiative
You: Show me the mechanisms of harm
You: What therapeutic targets exist for this disease?

Schema

The skill adds an apt-* namespace to TypeDB:

• apt-mechanism — causal chain entity linking gene → pathway → phenotype → drug
• apt-disease — disease node (domain-thing subtype, linked to MONDO ID)
• apt-gene — gene associated with the disease (HGNC ID)
• apt-phenotype — clinical phenotype (HPO term)
• apt-therapeutic-target — drug or candidate treatment

Dashboard

The skill contributes a Disease Mechanism Dashboard at /apt (port 3001 in deployed mode). It shows:

• Investigation list with disease summary cards
• Mechanism chain visualization
• Therapeutic landscape map

Data Sources

• Monarch Initiative API v3 — phenotype associations, causal gene associations, disease metadata
• DisMech (via the dismech skill) — curated disease mechanism entries with PubMed evidence