UNMCCC / CRIIS_Source_Extracts_for_OMOP

Cancer Clinical Data integration - Set of SQL extractions from disparate health system sources targeting the OMOP data model
MIT License
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CNExT observation - do you want '0's hardcoded in output? #104

Open isangil opened 2 years ago

isangil commented 2 years ago

Original code sets two fields hard coded to zero. Is this correct? ,0 AS OBSERVATION_SOURCE_CONCEPT_ID ,0 AS UNIT_SOURCE_VALUE

OMOP best practices asks for zeroes under circunstances, but these are pre-omop, (LDS).

mbernauer commented 2 years ago

I'll let @KJDonovan-RS21 respond but my rec would be to use null whenever possible and reserve 0 only for cases where 0 represents an actual code. Looking at the OMOP vocabulary there are only 6 or so entries where 0 is a valid source code so it's really unlikely that we'd see it in the extracts

| a    | b           | c                  | d                                                                            |
| ---- | ----------- | ------------------ | ---------------------------------------------------------------------------- |
| 0    | Procedure   | ICD10PCS           | Medical and Surgical (Procedure)                                             |
| 00   | Procedure   | ICD10PCS           | Medical and Surgical @ Central Nervous System and Cranial Nerves (Procedure) |
| 00   | Procedure   | ICD9Proc           | Procedures and interventions, Not Elsewhere Classified                       |
| 00.0 | Procedure   | ICD9Proc           | Therapeutic ultrasound                                                       |
| 0    | Observation | MDC                | Ungroupable                                                                  |
| 0    | Visit       | UB04 Pt dis status | Unknown Value (but present in data)                                          |
| 0    | Observation | UB04 Typ bill      | Non-Payment/Zero                                                             |
KJDonovan-RS21 commented 2 years ago

If no analogous source value exists, just cast as NULL as SOME_COLUMN_NAME.

isangil commented 2 years ago

kk- will put '' (nulls). The zeros are probably inspired on the OMOP strategy on putting zeros when there is no mapping. -- but important is that we have a way forward here - make'em nulls