| 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:
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.
