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Using MedDRA for analysis and source code mapping coverage

CDM Builders
#21

I’m exploring using the OHDSI vocabularies and concept relationships to map MedDRA PTs to corresponding ICD9CM codes.

When I map from MedDRA to ICD9CM using the “MedDRA – ICD9CM” concept_relationship, I am able to map 3966 of the approximately 12000 active MedDRA PTs to one or more ICD9 codes.

In an earlier post to this topic, @Christian_Reich mentioned that the “MedDRA – ICD9CM” relationships are not the preferred approach, so I’ve also tried mapping from MedDRA -> SNOMED -> ICD9CM (see below for the SQL query I’m using). That approach produces mappings for 3643 PTs.

As a check to make sure there isn’t a mapping directionality issue, I also tried a query going from ICD9CM -> SNOMED -> MedDRA. That query also yielded mappings for 3643 PTs.

Am I thinking about this the right way? Are there other ways to use the concepts and concept_relationships that might allow more MedDRA PT terms to be mapped?

SELECT c1.concept_code AS pt_code,
       c3.concept_code AS icd9_code,
       c3.concept_name AS icd9_desc,
       c3.concept_class_id AS icd9_class
  FROM
  -- Restrict concept1 (c1) to MedDRA vocabulary
       (SELECT *
          FROM concept c1
         WHERE c1.vocabulary_id = 'MedDRA' AND c1.concept_class_id = 'PT'
           AND c1.valid_end_date > current_date) c1
  -- Use the 'MedDRA - SNOMED eq' relationship to map from concept1 (MedDRA vocab)
  -- to concept2 (SNOMED)
  LEFT JOIN concept_relationship cr12
    ON c1.concept_id = cr12.concept_id_1
       AND cr12.relationship_id IN ('MedDRA - SNOMED eq')
       AND cr12.valid_end_date > current_date
  -- Left join with concept (c2) to decode the attributes for concept2
  LEFT JOIN concept c2
    ON cr12.concept_id_2 = c2.concept_id AND c2.valid_end_date > current_date
  -- Left join using the 'Mapped from' relationship to map from concept2 (SNOMED vocab)
  -- to concept3 (ICD9CM vocab)
  LEFT JOIN concept_relationship cr23
    ON c2.concept_id = cr23.concept_id_1
       AND cr23.relationship_id IN ('Mapped from')
       AND cr23.valid_end_date > current_date
  -- Left join with concept (c3) to decode the attributes for concept3
  LEFT JOIN concept c3
    ON cr23.concept_id_2 = c3.concept_id AND c3.vocabulary_id = 'ICD9CM'
       AND c3.valid_end_date > current_date
#22

@rschaaf:

Looks like you got them all. MedDRA mappings haven’t been defined on an exhaustive basis. Particularly non-Conditions are not well covered, since the use case was outcomes, not just anything. We probably should put some effort into that, but that would require some resources. Any good ideas?

t