defining-cohort-phenotypes SKILL.md skillA
defining-cohort-phenotypes from maziyarpanahi/openmed is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add maziyarpanahi/openmed/defining-cohort-phenotypes@v1.0Pins v1.0 in mdr.lock. Pin the fingerprint instead.
- Audit grade
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- Kind
- SKILL.md skill
- Repository
- maziyarpanahi/openmed
- Path
skills/defining-cohort-phenotypes/SKILL.md- Versions recorded
- 1
- Latest version
- v1.0, committed Jul 20, 2026
- Size
- 7,743 bytes
- Repository stars
- 5,784
- License
- Apache-2.0
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…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# 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. …
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How to install
mdr add maziyarpanahi/openmed/defining-cohort-phenotypes@sha256:b989d987706532d8The line at the top of this page pins the label v1.0, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
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Versions
The registry has recorded 1 version of this file, committed on Jul 20, 2026.
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Source
maziyarpanahi/openmed · 5,784 stars · license Apache-2.0 · pushed 2026-11-07 · branch master
API
GET https://markdownregistry.com/api/v1/artifacts/art_6zyqxfobtwx2usof GET https://markdownregistry.com/api/v1/resolve?ref=maziyarpanahi/openmed/defining-cohort-phenotypes GET https://markdownregistry.com/api/v1/blob/b989d987706532d83f708ecba9d8791a257d69992504a2e4a03bdb84bf0bfbce
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