create-definitions-from-ohdsi

name: create-definitions-from-ohdsi description: Generate dismech definitions from OHDSI/ATLAS cohort definitions or other computable phenotype logic. Use when converting OMOP cohort JSON, drafting PheKB-style phenotype algorithms, or mapping FHIR/CQL/OMOP rules into dismech definitions blocks.

Create Definitions From OHDSI

Use this skill to convert OHDSI/ATLAS cohort definitions into dismech definitions blocks and to map FHIR/CQL logic into the same structure.

Quick start

1. Export an ATLAS/WebAPI cohort definition JSON.
2. Generate a YAML fragment:

uv run python .claude/skills/create-definitions-from-ohdsi/scripts/ohdsi_cohort_to_definition.py /path/to/cohort.json --wrap

3. Paste the fragment into the target disorder file under definitions.
4. Normalize to dismech norms (add evidence snippets, scope, criteria set names, and any available term objects).
5. Validate:

just validate kb/disorders/<Disease>.yaml

Workflow guardrails

• Keep logic concise: express cohort entry, inclusion rules, and exit criteria in criteria_sets.
• Use minimum_required for numeric logic; put temporal logic in description.
• Add evidence snippets from abstracts when the algorithm is derived from a publication.
• Only add term objects when the CURIE is in a configured prefix (ICD10CM, NCIT, HP, etc.).

References

• Mapping guide: references/model-mapping.md (FHIR/OHDSI/CQL to dismech)

Scripts

• scripts/ohdsi_cohort_to_definition.py: Convert ATLAS/WebAPI cohort JSON to a dismech definition fragment.
  • Use --wrap to emit a top-level definitions key.