Mapping To Snomed
Maps clinical concept spans extracted by OpenMed to SNOMED CT concepts through a...
Install
npx skills add maziyarpanahi/openmed --skill mapping-to-snomed -g -a claude-code -y- Repository
- maziyarpanahi/openmed5.8k
- Category
- Writing
- Updated
- 4d ago
- License
- Apache-2.0
- Context cost
- Mediumabout 1,900 tokens
- Runs scripts
- No, instructions only
What it does
Maps clinical concept spans extracted by OpenMed to SNOMED CT concepts through a USER-SUPPLIED terminology server (the user's own Ontoserver, Snowstorm, or UMLS/UTS), never a bundled vocabulary. Use when the user wants to code findings, disorders, procedures, body structures, or substances to SNOMED CT, run an ECL query, translate via a ConceptMap, or resolve a span to a concept id with FHIR $lookup/$translate/$validate-code. Trigger keywords: SNOMED CT, SNOMED concept id, ECL, ConceptMap, $translate, $lookup, Ontoserver, Snowstorm, SCTID, post-coordination, terminology server. Pairs after OpenMed NER: consume Disease/Anatomy/Pharmaceutical entities from openmed.analyze_text and map each span out-of-process. SNOMED CT is license-restricted, it is NEVER bundled; the user calls their own affiliate-licensed server.
Mapping OpenMed spans to SNOMED CT
Ground clinical concept spans that OpenMed extracts, disorders, findings, procedures, body structures, substances, to SNOMED CT, the comprehensive clinical reference terminology. The atom is the SCTID (a SNOMED CT concept identifier), organized into a description-logic hierarchy you can query with ECL (Expression Constraint Language).
Hard licensing boundary, read first. SNOMED CT is license-restricted. OpenMed and this skill never bundle, ship, cache, or redistribute any SNOMED CT content. All mapping happens out-of-process against a terminology server the user supplies and is licensed for, their own Ontoserver, Snowstorm, the NLM's UTS/UMLS FHIR endpoint, or a national release server. SNOMED International requires an Affiliate License (free in member territories like the US via the NLM; check your country). Your code receives a base URL + credentials from the user; it must work with any compliant FHIR terminology server and store nothing but the returned codes.
When to use
- You need rich, hierarchy-aware clinical codes (more granular than ICD-10) for problems, procedures, or body sites.
- You want to translate an existing code (ICD-10-CM, local code) to SNOMED CT
via a
ConceptMap/$translate. - You need subsumption/ECL queries ("is this a descendant of Diabetes mellitus?") for cohorting or decision support.
For billing codes use coding-icd10; for drugs normalizing-rxnorm; for labs
mapping-loinc. SNOMED CT is the clinical-meaning layer.
Quick start (user-supplied FHIR terminology server)
Configuration is injected, never hardcoded. The operations are standard FHIR R4.
import os, requests
