maziyarpanahi/openmed · skills/defining-cohort-phenotypes/SKILL.md

defining-cohort-phenotypes skillA

defining-cohort-phenotypes is agent-read markdown (skill) from maziyarpanahi/openmed: 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.

Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.

How to install

Latest version
mdr add maziyarpanahi/openmed/defining-cohort-phenotypes@v1.0
Exact content
mdr add maziyarpanahi/openmed/defining-cohort-phenotypes@sha256:b989d987706532d8

Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.

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Versions

versioncommittedcommitsizeaudit
v1.0 latest2026-07-20 74f7d6b 7,743 BA view

Audit of the latest version

A  17 of 17 checks passed. Deterministic, no model, same answer every run.
  • pass: Frontmatter block present
  • pass: Frontmatter declares a name
  • pass: Frontmatter declares a description
  • pass: Size between 200 bytes and 200 KB (7743 bytes)
  • pass: No zero-width or bidi control characters
  • pass: No instruction hidden inside an HTML comment
  • pass: No link to an exfiltration or paste host
  • pass: No credential-shaped string
  • pass: No instruction to send local credentials anywhere
  • pass: No text hidden with inline styles
  • pass: No prompt-injection phrasing
  • pass: No curl or wget piped into a shell
  • pass: No recursive delete of root, home or parent
  • pass: No instruction to read or print local credentials
  • pass: No base64 blob over 200 characters
  • pass: No link to a raw IP address
  • pass: No script tag

Source

GitHub

maziyarpanahi/openmed · 5,376 stars · license Apache-2.0 · pushed 2026-09-24 · 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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