defining-cohort-phenotypes
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 au
Profile →npx skills add maziyarpanahi/openmed --skill defining-cohort-phenotypes --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 termi
- When to use
- Anatomy of a CIRCE cohort definition
- Augmenting with OpenMed NLP features
- Workflow
- Hand-off to / from OpenMed
- Edge cases & gotchas
- Standards & references
What does the defining-cohort-phenotypes skill do?
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 au
How do I install it?
Run `npx skills add maziyarpanahi/openmed --skill defining-cohort-phenotypes --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From maziyarpanahi/openmed, a repository with 4,851 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.