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DisMech Notebook

Application: Deep Research · Database: alh_deep_research · bridges from the standalone dismech knowledge base

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).