OMOP phenotype dx code handling

National-Clinical-Cohort-Collaborative / Phenotype_Data_Acquisition

The repository for code and documentation produced by the N3C Phenotype and Data Acquisition workstream

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OMOP phenotype dx code handling #73

Closed empfff closed 4 years ago

empfff commented 4 years ago

Noticed by @LoraLingrey-TriNetX : There is no special handling for B97.21 and B97.29 included in the OMOP phenotype code; those are our dxs that are treated differently (weak/strong) based on date. There is no reference to 4/1/2020 in the OMOP code.

kmkostka commented 4 years ago

These codes map to:

B97.21 (SARS-associated coronavirus as the cause of diseases classified elsewhere) maps to SNOMED 398447004 (Severe acute respiratory syndrome)
B97.29 (Other coronavirus as the cause of diseases classified elsewhere) maps to SNOMED 27619001 (Disease due to Coronaviridae)

The logic will be reviewed and updated. New scripts will be regenerated.

Do we want to add these SNOMEDs to the list with the same date-time distinction?

kmkostka commented 4 years ago

Phenotype script and JSONs are updated.

@rtmill can you double check my work on the mssqlserver script? If kosher, we can run through JAR.

kmkostka commented 4 years ago

Validated. We can close.