DisMech Skill

Browse and query the DisMech disease mechanism knowledge graph — 750+ curated disorders with pathophysiology mechanisms, gene associations, clinical phenotypes, and therapeutic targets.

Purpose

The dismech skill provides access to the DisMech knowledge base, a curated collection of disease mechanism entries. Each entry is authored by Claude using a structured YAML format with PubMed evidence citations and HPO/HGNC/MAXO ontology bindings, then validated by human curators via a PR-based workflow.

This skill lets the agent query DisMech for disease-specific information: what genes are involved, what phenotypes are associated, what pathophysiology mechanisms are described, and what therapeutic targets exist.

Prerequisites

Docker running (TypeDB starts automatically via make build-db)
The DisMech database populated (run dismech.py ingest after cloning the YAML data)

Commands

uv run python .claude/skills/dismech/dismech.py <command> [args]

Command	What it does
`ingest`	Load DisMech YAML entries into the TypeDB `dismech` database
`list-diseases`	List all diseases in the database
`show-disease`	Display full disease entry including mechanisms, phenotypes, genes
`search`	Full-text search across disease entries
`query-phenotypes`	Find diseases associated with given HPO terms
`query-genes`	Find diseases associated with given genes (HGNC)
`stats`	Show database statistics (disease count, mechanism count, etc.)
`add-evidence`	Add a PubMed evidence citation to an existing disease entry

Database Isolation

DisMech runs in its own TypeDB database (dismech), separate from alhazen_notebook. This means:

Disease entities in DisMech cannot be directly linked to entities in alhazen_notebook (no shared schema root)
PubMed evidence in DisMech cannot be cross-referenced to scilit-paper entities ingested via scientific-literature
The aboutness relation (for attaching notes to entities) is not defined in the DisMech schema

These are tracked as open schema gaps. See sciknow-io/alhazen-skill-dismech issues for current status.

Typical Workflow

You: Show me the DisMech entry for Marfan syndrome
You: What genes are associated with connective tissue disorders in DisMech?
You: Search for diseases involving the RAS/MAPK pathway
You: Show me all diseases with the HPO phenotype "aortic root dilation"

DisMech Curation Pipeline

DisMech entries are authored using a YAML format with LinkML-validated structure. Each entry requires:

PubMed PMIDs with exact verbatim quotes from abstracts as evidence
HPO terms for phenotypes
HGNC gene symbols
MAXO treatment terms

Submissions go through a GitHub PR workflow with automated CI review (claude-code-review.yml) that checks PMID authenticity, quote accuracy, and ontology binding correctness before human approval.

To contribute a new disease entry, see the DisMech repository for the YAML schema and submission instructions.

Source Repository

The dismech skill lives in its own repository: github.com/sciknow-io/alhazen-skill-dismech. Gap issues for this skill are filed there, not in the main alhazen-skill-examples repository.