| 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
- Use
list_ucsf_omop_tables to show the available OMOP domain tables
- Write a phenotyping query using standard OMOP concepts (condition_occurrence,
drug_exposure, measurement, observation, procedure_occurrence)
- Run with
query_ucsf_omop and present results with concept names
- 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