dismech

name	dismech
description	Browse and query the DisMech disease mechanism knowledge graph (750+ curated disorders in TypeDB 3.x)
triggers	["show me disease mechanisms for","what genes are associated with","list diseases with phenotype","pathophysiology of","dismech","disease mechanism","rare disease"]
prerequisites	["Docker running (TypeDB auto-starts on session start)","uv installed"]

Disease Mechanism Knowledge Graph (DisMech)

750+ curated disease entries with pathophysiology mechanisms, HPO phenotypes, gene associations, and therapeutic targets — all stored in TypeDB 3.x.

When to use: Research disease mechanisms, find gene-disease associations, explore pathophysiology, or query curated disorder data.

Quick Start

The TypeDB database auto-initializes on session start via the SessionStart hook. To manually ingest data, first obtain the disorders directory:

# If no local copy of the disorder YAML files exists, clone the source:
git clone https://github.com/monarch-initiative/dismech /tmp/dismech-kb

Then ingest:

uv run --project <skill-path> python <skill-path>/dismech.py ingest \
  --source /tmp/dismech-kb/kb/disorders

Query a disease:

uv run --project <skill-path> python <skill-path>/dismech.py show-disease \
  --name "Achondroplasia"

For the full command reference, read USAGE.md.