DisMech Notebook
The DisMech Notebook skill maps the Monarch Initiative’s DisMech rare disease corpus into the Alhazen notebook’s information content entity (ICE) model. It acts as a GLAV (Global-as-View/Local-as-View) bridge between the standalone DisMech knowledge base and the Alhazen notebook memory system.
What It Does
The DisMech knowledge base is a separately curated TypeDB database containing 750+ rare disease mechanisms. This skill provides a read-through interface that queries the DisMech KB and maps results into the Alhazen notebook’s entity model, enabling cross-referencing with other skills (scientific literature, agentic memory).
Architecture
DisMech KB (separate TypeDB database)
↓ GLAV mapping
DisMech Notebook (Alhazen notebook namespace)
↓ Standard aboutness/tagging
Other Alhazen skills (scientific-literature, agentic-memory)
The skill depends on dismech (the standalone KB skill) being available and loaded in a separate TypeDB database.
Data Model
| DisMech Source | Alhazen Target | Purpose |
|---|---|---|
| Disease | dm-disease (domain-thing) |
Rare disease entry |
| Mechanism | dm-mechanism (domain-thing) |
Disease mechanism |
| Gene | dm-gene (domain-thing) |
Causal/correlated gene |
| Phenotype | dm-phenotype (domain-thing) |
Clinical phenotype (HPO) |
| Process | dm-process (domain-thing) |
Biological process |
| Cell Type | dm-celltype (domain-thing) |
Affected cell type |
| Evidence | dm-evidence-note (note) |
Literature evidence for mechanism edges |
Key Commands
# Statistics
uv run python dismech_notebook.py stats
# Browse diseases
uv run python dismech_notebook.py list-diseases --limit 50
uv run python dismech_notebook.py list-diseases --category "neurodegenerative"
# Disease detail
uv run python dismech_notebook.py show-disease --name "Huntington disease"
# Search
uv run python dismech_notebook.py search --query "mitochondrial dysfunction" --limit 20
When to Use
- Browsing rare disease mechanisms curated from the literature
- Cross-referencing disease genes/phenotypes with scientific literature searches
- Finding evidence-backed mechanism pathways for a known diagnosis
- Exploring which diseases share common mechanisms or affected pathways
Relationship to DisMech Skill
The standalone dismech skill operates on its own TypeDB database with the full DisMech schema. This dismech-notebook skill provides the bridge layer that makes DisMech data accessible through the standard Alhazen notebook interfaces (aboutness, tagging, collection membership).