dismech

Files (13)

• plugin.json · .claude-plugin/
• .standalone-db
• SKILL.md
• USAGE.md
• .gitkeep · dashboard/
• dismech.py
• hooks.json · hooks/
• pyproject.toml
• refresh.sh
• schema.tql
• skill.yaml
• SKILL.md · skills/dismech/
• uv.lock

SKILL.md (first lines)

# 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:

```bash
# 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:

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

Query a disease:
```bash
uv run --project <skill-path> python <skill-path>/dismech.py show-disease \
  --name "Achondroplasia"
```

**For the full command reference, read USAGE.md.**

From sciknow-io/alhazen-skill-deep-research, MIT.

More from sciknow-io/alhazen-skill-deep-research