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Clinical Crosswalks

For healthcare ontologies, three tools bridge clinical coding systems:

  • onto_crosswalk — Look up mappings between ICD-10 (diagnoses), SNOMED CT (clinical terms), and MeSH (medical literature) from a Parquet-backed crosswalk file
  • onto_enrich — Insert skos:exactMatch triples linking ontology classes to clinical codes
  • onto_validate_clinical — Check that class labels align with standard clinical terminology

Setup

Build the crosswalk data file:

python3 scripts/build_crosswalks.py

This creates data/crosswalks.parquet from public terminology sources.

Usage

# Look up a code
open-ontologies crosswalk I10 --system ICD10

# Enrich a class with a mapping
open-ontologies enrich http://example.org/Hypertension I10 --system ICD10

# Validate all labels against clinical terms
open-ontologies validate-clinical