omop-phenotype-query

name: omop-phenotype-query description: Query the OMOP CDM to identify patient phenotypes and clinical concepts

Use this skill when the user wants to define or query patient phenotypes using the OMOP Common Data Model at UCSF.

When to activate

• User asks about OMOP, phenotypes, standard concepts, or the OHDSI framework
• User wants to count patients with specific conditions using standard vocabularies

Approach

1. Use list_ucsf_omop_tables to show the available OMOP domain tables
2. Write a phenotyping query using standard OMOP concepts (condition_occurrence, drug_exposure, measurement, observation, procedure_occurrence)
3. Run with query_ucsf_omop and present results with concept names
4. Suggest refinements using concept ancestors for broader/narrower definitions

Notes

• OMOP uses standard concept IDs — avoid local source codes
• All queries are read-only on de-identified data
• concept_id = 0 means unmapped — filter these out for clean phenotypes