How can I find the number of participants that consented to EHR data collection

  • Updated

You can find what participants have given consent to their EHR by querying the observation table for participants who have observation_source_concept_id = 1586099 (EHRConsentPII_ConsentPermission) with value_as_concept_id = 1586100 (Yes). 

 

You can use the following code in python to get this information:

SELECT DISTINCT person_id

FROM `{CDR_DATASET}.observation`

WHERE observation_source_concept_id = 1586099

and value_source_concept_id = 1586100 #ConsentPermission_Yes

 

You can use the following code in R to get this information:

library(bigrquery)

library(tidyverse)

 

CDR_DATASET= Sys.getenv('WORKSPACE_CDR')

# helper function

download_data <- function(query) {

               tb <- bq_project_query(Sys.getenv('GOOGLE_PROJECT'), query)

               bq_table_download(tb)

}

 

query = str_glue("

               SELECT DISTINCT person_id

               FROM `{CDR_DATASET}.observation`

               WHERE observation_concept_id = 1586099

               AND value_source_concept_id = 1586100 #ConsentPermission_Yes"

               )

ehr_consented_pids_df = download_data(query)

head(ehr_consented_pids_df)

 

 

 

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