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create-definitions-from-ohdsi

Convert OHDSI/ATLAS cohort JSON into dismech definitions fragments.

50|9|Updated Dec 4, 2025
Search Tags:#definition#mapping#atlas#cohort#phenotype#dismech#ohdsi
One-click install
npx skills add https://github.com/monarch-initiative/dismech --skill create-definitions-from-ohdsi
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: create-definitions-from-ohdsi
Source: https://github.com/monarch-initiative/dismech/tree/main/.claude/skills/create-definitions-from-ohdsi
Command: npx skills add https://github.com/monarch-initiative/dismech --skill create-definitions-from-ohdsi

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pyyaml, and includes scripts (resource) and references (resource) components.

What problem does it solve?

Transforms OHDSI/ATLAS cohort definitions into dismech definitions blocks to enable consistent representation of computable phenotypes in the knowledge base.

Core Features & Use Cases

  • Convert ATLAS/WebAPI cohort JSON into a dismech definitions fragment.
  • Wrap the fragment under a top-level definitions key and map FHIR/CQL logic into the same structure.
  • Align with dismech norms by adding evidence snippets, scope, and term objects; example use: converting a published OHDSI cohort for a case-control study.

Quick Start

Export an ATLAS cohort JSON and run the included ohdsi_cohort_to_definition.py script to generate a dismech definition fragment.

Frequently Asked Questions about create-definitions-from-ohdsi

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I convert an OHDSI ATLAS cohort definition to a dismech definition?▼

Use this Skill to parse ATLAS cohort JSON, extract concept_sets and inclusion_rules, and generate a dismech definitions block for computable phenotype representation.

Can I map OMOP computable phenotype logic into dismech definitions blocks?▼

Yes, the Skill translates OMOP-based research computable phenotype logic by parsing ATLAS cohort JSON and building concept_sets and inclusion_rules into a structured dismech definitions fragment.

Does this Skill support mapping FHIR and CQL rules alongside OMOP cohorts?▼

Yes, it wraps FHIR and CQL logic under a top-level definitions key, mapping them into the same dismech structure used for OMOP cohort definitions.

What format do I need to export from ATLAS to generate dismech definitions?▼

You must export the standard ATLAS/WebAPI cohort JSON file, which the script parses to build concept_sets and inclusion_rules into the dismech definition fragment.

Are there validation hooks to check the generated dismech definitions?▼

Yes, the Skill provides validation hooks using the validate module to verify that generated dismech definitions fragments align with required structural norms.

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