minimal Common Oncology Data Elements (mCODE) Implementation Guide
2.0.0 - STU 2

This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v2.0.0: STU 2) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

Terminology

This implementation guide draws on a number of formal terminologies (code systems). Several guiding principles were applied in selecting terminologies for mCODE:

  1. Fit for purpose
  2. Conformance with US Core and FHIR
  3. Commonly used in real world practice

The following table presents the external code systems (and naming conventions) adopted in mCODE, and their primary purpose:

Code System Application FHIR IG Publishing support? HL7 Canonical [1] Proposed HTA, if different [2]
AJCC Cancer staging codes No Missing https://cancerstaging.org/
CPT Procedure codes No http://www.ama-assn.org/go/cpt  
HGNC Gene identification No http://www.genenames.org  
HGVS Sequence variant nomenclature Yes http://varnomen.hgvs.org OID: 2.16.840.1.113883.6.282
HTA Various HL7 V2 and FHIR-specific codes Yes http://terminology.hl7.org  
ICD-O-3 Cancer morphology and topology codes No http://terminology.hl7.org/CodeSystem/icd-o-3  
ICD-10-CM Diagnosis codes Yes http://hl7.org/fhir/sid/icd-10-cm  
ICD-10-PCS Procedure codes No http://www.cms.gov/Medicare/Coding/ICD10  
LOINC Observation and laboratory codes, answer codes Yes http://loinc.org  
NCBI GTR Genomic test codes No Missing https://www.ncbi.nlm.nih.gov/gtr/
NCBI ClinVar Genomic variations No Missing Missing
NCIT Cancer terminology No http://ncithesaurus-stage.nci.nih.gov http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
RxNorm Medication codes Yes http://www.nlm.nih.gov/research/umls/rxnorm  
Sequence Ontology DNA change types No Missing http://www.sequenceontology.org/
SNOMED CT Disorders, body structures, findings, qualifiers Yes http://snomed.info/sct  
UCUM Units of measure Yes http://unitsofmeasure.org  

[1] Official HL7 Terminology (v2.1.0: Release)

[2] HL7 Terminology Authority Recommendation (as of 1 Nov 2021)

Key:

  • AJCC - American Joint Committee on Cancer
  • CPT - Current Procedural Terminology (American Medical Association)
  • HGNC - Human Genome Organisation (HUGO) Gene Nomenclature Committee
  • HGVS - Human Genome Variation Society
  • HTA - HL7 Terminology Authority
  • ICD - International Classification of Diseases (World Health Organization)
    • ICD-O-3 - Oncology, 3rd revision
    • ICD-10-CM - Clinical Modification, 10th revision
    • ICD-10-PCS - Procedure Coding System, 10th revision
  • LOINC - Logical Observation Identifiers Names and Codes
  • NCBI - National Center for Biotechnology Information (National Institutes of Health) (US)
    • NCBI GTR - Genomic Testing Registry
    • NCBI ClinVar - Not an acronym
  • NCIT - National Cancer Institute Thesaurus
  • RxNorm - From National Library of Medicine (US)
  • SNOMED CT - Systematized Nomenclature of Medicine Clinical Terms
  • UCUM - Unified Code for Units of Measure
  • UMLS - Unified Medical Language System Metathesaurus

Local Code Systems

Local code systems SnomedRequestedCS and LoincRequestedCS are provided for terms submitted but not yet published and/or approved by LOINC and SNOMED. It is expected that the local codes will be replaced with approved LOINC and SNOMED terms in a future technical correction to the STU2 IG. Where codes have already been assigned by SNOMED, but not yet published, those codes are used as local codes to reduce future changes. In other cases, the submission numbers are used as the local codes.

For the purposes of mCODE, comorbidities are classified using the Elixhauser system. This is a somewhat arbitrary choice, and other systems such as Charlson could have been selected, and profiles and value sets would have to change accordingly.

One set of LOINC submissions deals with the 30+ Elixhauser comorbidity categories. Currently, there are no LOINC codes for Elixhauser categories such as “Liver disease, mild”, “Renal failure, moderate”, or “Thyroid disorders other than hypothyroidism”. In some cases, not all, there are SNOMED CT disorder codes that superficially correspond to Elixhauser categories, such as congestive heart failure (SCTID: 42343007). However, the SNOMED codes subsumed under that code do not necessarily correspond to the disorders included in the Elixhauser category. Therefore, new codes are needed. More discussion is found here.

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