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

You can find what participants have given consent to their EHR by querying the observation table for participants who have observation_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 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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