dismech-notebook

Files (41)

• plugin.json · .claude-plugin/
• .standalone-db
• SKILL.md
• USAGE.md
• lib.ts · dashboard/
• page.tsx · dashboard/pages/dismech/disease/[name]/
• page.tsx · dashboard/pages/dismech/
• layout.tsx · dashboard/pages/
• route.ts · dashboard/routes/disease/[name]/
• route.ts · dashboard/routes/diseases/
• route.ts · dashboard/routes/search/
• route.ts · dashboard/routes/stats/
• dismech_notebook.py
• hooks.json · hooks/
• README.md · mapping/
• .gitkeep · mapping/rules/
• 01_disease.yaml · mapping/rules/
• 02_gene_descriptor.yaml · mapping/rules/
• 03_phenotype_descriptor.yaml · mapping/rules/
• 04_disease_descriptor.yaml · mapping/rules/
• 05_anatomical_descriptor.yaml · mapping/rules/
• 06_celltype_descriptor.yaml · mapping/rules/
• 07_process_descriptor.yaml · mapping/rules/
• 08_papers.yaml · mapping/rules/
• 10_mechanism.yaml · mapping/rules/
• 11_phenotype.yaml · mapping/rules/
• 12_genetic.yaml · mapping/rules/
• 13_treatment.yaml · mapping/rules/
• 15_disease_term.yaml · mapping/rules/
• 20_causal_edge.yaml · mapping/rules/
• 21_mechanism_gene.yaml · mapping/rules/
• 22_mechanism_location.yaml · mapping/rules/
• 23_mechanism_celltype.yaml · mapping/rules/
• 24_mechanism_process.yaml · mapping/rules/
• 25_phenotype_term.yaml · mapping/rules/
• 30_evidence_notes.yaml · mapping/rules/
• 31_findings.yaml · mapping/rules/
• schema.deps
• schema.tql
• skill.yaml
• SKILL.md · skills/dismech-notebook/

SKILL.md (first lines)

# DisMech Notebook

Maps the Monarch Initiative **DisMech** rare-disease corpus into the Alhazen
notebook's ICE (information-content-entity) model in TypeDB, using the
cross-database schema mapper, so disease-mechanism knowledge is browsable and
searchable alongside the rest of the notebook.

**Triggers:** disease mechanism curation, DisMech, rare disease knowledge graph

## Prerequisites

- Docker + `uv`.
- `alhazen-core` installed and initialized:
  `/plugin install alhazen-core@skillful-alhazen` then `/alhazen-core:init`.
  (The SessionStart hook auto-runs init and loads this skill's `schema.tql`.)

## Quick start

```bash
CLI="${CLAUDE_PLUGIN_ROOT}/dismech_notebook.py"
uv run --project "${CLAUDE_PLUGIN_ROOT}" python "$CLI" stats
uv run --project "${CLAUDE_PLUGIN_ROOT}" python "$CLI" search --query lysosomal
```

## Commands

| Command | Description |
|---|---|
| `stats` | Entity counts (diseases, mechanisms, terms) |
| `list-diseases [--category C] [--limit N] [--offset N]` | List diseases |
| `show-disease --name NAME` | Full detail for one disease |
| `search --query TEXT [--limit N]` | Search diseases and mechanisms |

**Read `USAGE.md` for the full reference.**

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

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