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FHIR Patient Race and Ethnicity should be seperated in i2b2 ETL #119

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comorbidity opened this issue Dec 27, 2022 · 2 comments
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FHIR Patient Race and Ethnicity should be seperated in i2b2 ETL #119

comorbidity opened this issue Dec 27, 2022 · 2 comments
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@comorbidity
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The outmost Extension.url should be
http://hl7.org/fhir/us/core/StructureDefinition/us-core-race
http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity

Example:
http://hl7.org/fhir/us/core/STU5.0.1/Patient-example.json.html

cumulus-etl
current:
def extension_race(code: str, display: str) -> dict:
is hardcoded us-core-race even for ethnicity.

Since i2b2 doesn't have an ethnicity column, we should instead do a "check" to see if the RACE_CD is actually ethnicity
There are only two ETHNICITY codes usually supported by i2b2

RACE = {
...
'Hispanic or Latino': '2135-2', # ethnicity
'Not Hispanic or Latino': '2186-5' # ethnicity
}

@comorbidity
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comorbidity commented Dec 27, 2022

FYI in library SQL
create or replace view fhir_ethnicity as select * from
(VALUES
('Ethnicity', '2135-2', 'Hispanic or Latino')
,('Ethnicity', '2186-5', 'Not Hispanic or Latino')
)
as t(category, code, display);

AND

create or replace view fhir_race as select * from
(VALUES
('Race', '1002-5', 'American Indian or Alaska Native')
,('Race', '2028-9', 'Asian')
,('Race', '2054-5', 'Black or African American')
,('Race', '2076-8', 'Native Hawaiian or Other Pacific Islander')
,('Race', '2106-3', 'White')
) AS t (category, code, display);

`

@mikix
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mikix commented Dec 28, 2022

Fixed by #108

@mikix mikix closed this as completed Dec 28, 2022
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