Defining Cohort Phenotypes
Authors computable phenotype and cohort definitions in the OHDSI ATLAS / CIRCE style...
Install
npx skills add maziyarpanahi/openmed --skill defining-cohort-phenotypes -g -a claude-code -y- Repository
- maziyarpanahi/openmed5.8k
- Category
- Writing
- Updated
- 4d ago
- License
- Apache-2.0
- Context cost
- Mediumabout 1,688 tokens
- Runs scripts
- No, instructions only
What it does
Authors computable phenotype and cohort definitions in the OHDSI ATLAS / CIRCE style over the OMOP CDM, combining standard concept sets with NLP-derived features that OpenMed extracts. Use when the user wants to define a patient cohort, write a computable phenotype, reuse PheKB or OHDSI Phenotype Library logic, build concept sets, or augment code-based criteria with text features. Trigger keywords: phenotype, cohort definition, OHDSI, ATLAS, CIRCE, OMOP CDM, concept set, PheKB, Phenotype Library, eMERGE, computable phenotype. Pairs adjacent to OpenMed: NLP features from openmed.analyze_text augment code-based phenotypes for entities that are poorly captured by structured codes. OMOP CDM and OHDSI tools are open source; restricted vocabularies (SNOMED, CPT) are user-supplied.
Defining cohort phenotypes (OHDSI / OMOP CDM)
A computable phenotype is a portable, executable definition of "which patients have condition X", concept sets plus inclusion logic that runs against any OMOP CDM-compliant database. In the OHDSI stack, ATLAS authors these visually, CIRCE serializes them to a standardized JSON representation, and that JSON compiles to database-specific SQL. This skill helps you author such definitions and augment them with NLP features that OpenMed extracts from clinical text, exactly the signals that structured codes miss.
OMOP CDM, ATLAS, CIRCE, and the OHDSI Phenotype Library are open source. The vocabulary content you reference (SNOMED CT, CPT4, ICD) is user-supplied, do not bundle restricted terminologies; load them into your own OMOP vocabulary tables with your own licenses.
When to use
- You need a reproducible cohort definition for analytics or research.
- You want to reuse an existing PheKB or OHDSI Phenotype Library definition and adapt it.
- A phenotype depends on facts that live only in free text (e.g. smoking status, symptom severity, social context) and code-based logic alone is weak.
For terminology grounding of individual entities, see coding-icd10,
normalizing-rxnorm, mapping-loinc; this skill is about composing them into a
cohort.
Anatomy of a CIRCE cohort definition
A CIRCE cohort definition JSON has two parts: ConceptSets (the code lists) and an expression (entry event + inclusion rules). Shape (abridged):
