mapping-to-snomed

Map clinical concept spans to validated SNOMED CT concepts via FHIR terminology servers.

5.0k|615|Updated Oct 4, 2025
One-click install
npx skills add https://github.com/maziyarpanahi/openmed --skill mapping-to-snomed
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: mapping-to-snomed
Source: https://github.com/maziyarpanahi/openmed/tree/main/skills/mapping-to-snomed
Command: npx skills add https://github.com/maziyarpanahi/openmed --skill mapping-to-snomed

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill converts clinical concept spans extracted by OpenMed into precise, hierarchy-aware SNOMED CT concepts without bundling or redistributing restricted terminology content.

Core Features & Use Cases

  • Clinical Concept Mapping: Map diseases, findings, procedures, body structures, and substances to SNOMED CT concepts through a user-supplied terminology server.
  • FHIR Terminology Operations: Search with ECL, resolve concepts with lookup and validation, and translate local or ICD-10 codes through ConceptMap services.
  • Auditable Workflows: Preserve OpenMed entity offsets, apply semantic hierarchy constraints, handle negation and uncertainty, and avoid unsupported over-specification.
  • Use Case: Send de-identified disease spans from an OpenMed analysis to a licensed Snowstorm or Ontoserver instance and return validated SNOMED CT identifiers with displays and source offsets.

Quick Start

Use the mapping-to-snomed skill with your licensed FHIR terminology server to map OpenMed-extracted clinical entities to validated SNOMED CT concepts while preserving their source offsets.

Frequently Asked Questions about mapping-to-snomed

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

FAQPage Schema
How do I map clinical text to SNOMED CT codes using a FHIR terminology server?

You can map clinical concept spans to SNOMED CT codes by sending de-identified text extracts to a user-supplied FHIR terminology server. The process validates diseases, findings, and procedures against the hierarchy and returns identifiers with source offsets.

Can I translate ICD-10 codes to SNOMED CT through ConceptMap services?

Yes, you can translate local or ICD-10 codes to SNOMED CT concepts through FHIR ConceptMap services. This requires connecting to a licensed compliant terminology server to perform the validation and code translation.

What is the best way to search SNOMED CT concepts using ECL constraints?

The best way to search SNOMED CT concepts using ECL constraints is through a FHIR terminology server. This approach applies semantic hierarchy constraints to queries and resolves concepts via lookup and validation without redistributing restricted terminology content.

Do I need a licensed terminology server to use SNOMED CT concept mapping?

Yes, you need access to a licensed compliant FHIR terminology server like Snowstorm or Ontoserver. The mapping process queries your external server to validate clinical spans and return SNOMED CT identifiers without bundling restricted content.

How does clinical concept mapping handle negation and uncertainty in medical NLP?

Clinical concept mapping handles negation and uncertainty by preserving entity offsets and applying semantic hierarchy constraints during the mapping process. This avoids unsupported over-specification when resolving SNOMED CT concepts from extracted clinical text.

Why does clinical coding preserve source offsets during SNOMED CT mapping?

Preserving source offsets during SNOMED CT mapping maintains auditable workflows by linking validated concepts back to their exact original text locations. This ensures traceability when mapping de-identified disease spans from medical NLP analyses.