Disorder Mechanisms Knowledge Base (dismech)

A curated knowledge base of disease pathophysiology, with structured evidence from the literature.

Browse the Knowledge Base

View all disorders online | QC Dashboard

Each disorder page includes:

• Disease mechanisms and pathophysiology
• Clinical phenotypes with HPO term links
• Genetic factors and variants
• Treatment options with MAXO term links
• All claims backed by PubMed evidence

How It Works

Source of Truth: YAML Files

The knowledge base is stored as structured YAML files in kb/disorders/. Each disorder has its own file (e.g., Asthma.yaml) containing:

name: Asthma
pathophysiology:
  - name: Airway Inflammation
    description: Chronic inflammation of the airways
    biological_processes:
      - preferred_term: inflammatory response
        term:
          id: GO:0006954
          label: inflammatory response
    evidence:
      - reference: PMID:12345678
        supports: SUPPORT
        snippet: "Exact quote from the paper"
        explanation: "Why this supports the claim"
phenotypes:
  - name: Wheezing
    frequency: FREQUENT
    phenotype_term:
      preferred_term: Wheezing
      term:
        id: HP:0030828
        label: Wheezing
treatments:
  - name: Bronchodilators
    description: Relax airway smooth muscle
    treatment_term:
      preferred_term: respiratory tract agent therapy
      term:
        id: MAXO:0000312
        label: respiratory tract agent therapy

Ontology Bindings

Entities are linked to authoritative ontologies:

• Phenotypes: Human Phenotype Ontology (HP)
• Cell types: Cell Ontology (CL)
• Biological processes: Gene Ontology (GO)
• Diseases: Mondo Disease Ontology (MONDO)
• Treatments: Medical Action Ontology (MAXO)
• Anatomy: Uberon (UBERON)

Evidence Requirements

All claims must cite PubMed references with exact quotes. This prevents misinformation and enables verification.

Validation Pipeline

Multiple layers of automated validation ensure data quality and prevent AI hallucinations:

1. Schema validation: Ensures correct YAML structure against the LinkML schema
2. Ontology term validation: Verifies term IDs exist and labels match authoritative sources (HPO, MONDO, GO, etc.)
3. Reference validation: Confirms that quoted snippets actually appear in cited PubMed abstracts
4. Compliance analysis: Measures coverage of recommended fields (descriptions, evidence, ontology terms)

# Run schema + term validation
just qc

# Validate a single file
just validate kb/disorders/Asthma.yaml

# Validate references against PubMed abstracts
just validate-references kb/disorders/Asthma.yaml

# Analyze compliance with recommended field coverage
just compliance-all

# Compliance with weighted scoring and threshold checks
just compliance-weighted

Why Reference Validation Matters

All evidence snippets must be exact quotes from paper abstracts, not paraphrases. The reference validator fetches abstracts from PubMed and checks that the quoted text appears verbatim. This catches:

• AI-generated paraphrases that don't match the actual paper
• Wrong PMIDs (e.g., a PMID that points to an unrelated paper)
• Fabricated citations

When validation fails, either fix the snippet to match the actual abstract or remove the evidence item.

QC Dashboard

Generate a visual dashboard showing compliance metrics across all disorder files:

just gen-dashboard

This creates dashboard/index.html with:

• Summary metrics (files analyzed, average compliance, violations)
• Slot compliance comparison chart
• Detailed views of the 10 lowest-compliance files (priority curation targets)
• Full table of all files sorted by compliance

View online: QC Dashboard or locally: open dashboard/index.html

HTML Generation

YAML files are rendered to browsable HTML pages with clickable ontology term links.

uv run python -m dismech.render --all

For Curators

See CONTRIBUTING.md for curation guidelines.

Schema Documentation

• LinkML Schema Docs
• Schema source: src/dismech/schema/dismech.yaml