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MedDRA Overhaul Discussion

After extensive deliberations, including discussion during the Common Data Model WG - VOCABULARY Subgroup meeting on October 3, 2023, we’re presenting the following plan to the community for the MedDRA overhaul in 2024 and MedDRA future in OMOP:

  1. We will focus on the Preferred Term (PT). It means that we cover with “Maps to” links to SNOMED mostly PT level of MedDRA concepts because:
  • PT concepts are used in RWD much more often than LLT terms
  • PT concepts are more convenient for analytics needs
  • in most cases, LLTs only represent the synonyms of PT (with some sort of granularity)
  1. We utilise available mapping candidates from various existing sources (OHDSI internally built mappings, UMLS thesaurus, MedDRA-SNOMED / SNOMED-MedDRA mappings from MSSO, ICD10-MedDRA mappings), including newly created mappings, to establish “Maps to” links between MedDRA and SNOMED.

  2. MedDRA remains a classification vocabulary (important: please see the details below in 6) and will be used in two directions:

  • to map source data with MedDRA codes to OMOP standard codes during ETL (using ‘Maps to’ / ‘Maps to value’ links)
  • to use MedDRA codes as classification concepts for concept set construction
  1. In case of complete semantic correspondence between the MedDRA and SNOMED concepts, the MedDRA concept is positioned above the SNOMED concept when constructing the hierarchy.

In case of incomplete correspondence, various scenarios are possible, where the MedDRA concept in the hierarchy can be either higher (downhill mapping to SNOMED) or lower (uphill mapping to SNOMED) than the corresponding SNOMED concept. See the schema attached.

  1. It is essential to understand that when using MedDRA concepts to construct concept sets based on the MedDRA-SNOMED hierarchy, there might be cases where not all underlying child concepts from SNOMED are fully included. In such instances, it is recommended to conduct additional checks for the potential inclusion of additional SNOMED concepts when constructing the final concept set.

  2. Using MedDRA concepts as classification will be available for PT and LLT concepts with valid “Maps to” links (and ‘is a / subsumes’ links accordingly constructed on their basis). Other PT and LLT MedDRA concepts without corresponding “maps to” links will be considered non-standard (previously they were classification concepts).

  3. At higher levels of MedDRA (SOC, HLT, and HLGT), “maps to” links between MedDRA and SNOMED are not planned due to the complex differences in the hierarchy of these two vocabularies on higher levels. These levels will stay classificational.

For example, MedDRA PT concept “HIV infection” (concept id 36009928) and related SNOMED concept “Human immunodeficiency virus infection” (concept id 439727) belong to different axes of hierarchy:

MedDRA: Immune system disorders(SOC)-Infections and infestations(SOC)-Immunodeficiency syndromes(HLGT)-Viral infectious disorders(HLGT)-Retroviral infections(HLT)-Acquired immunodeficiency syndromes(HLT)

SNOMED: Clinical finding - Disease - Disorder due to infection - Viral disease - Disease due to Retroviridae - Disease due to Lentivirus

So, SOC, HLT, and HLGT MedDRA levels are planned to be used only to identify relevant PT/LLT concepts.

In conclusion, MedDRA will continue to serve as a classification vocabulary and support two primary use cases: source data mapping and concept set construction (using OMOP standard concepts only).

The changes will be included in the planned February 2024 release.

point 7. about SOC, HLT, LHGT - makes perfect sense to me.
Classification concepts are a bit described in (I think now outdated) old documentation here: documentation:vocabulary:standard_classification_and_source_concepts [Observational Health Data Sciences and Informatics]

And very briefly in the latest documentation:

standard_concept This flag determines where a Concept is a Standard Concept, i.e. is used in the data, a Classification Concept, or a non-standard Source Concept. The allowable values are ‘S’ (Standard Concept) and ‘C’ (Classification Concept), otherwise the content is NULL.

It seems some Athena included vocabularies have only source concepts while other may have source+classification.