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Receiving HERON Data

After a data request has been approved by the Data Request Oversight Committee (DROC) a HERON team member will provide you with the data. You will receive a REDCap project and the raw data. The raw data will be attached in the file repository of the REDCap project or sent via KUMC's securefiles. 

Understanding the REDCap Project: 

  1. There is one record per patient in the query. 
  2. Each concept (i.e., lab value, diagnosis, etc.) has the first recorded date and the last recorded date. For concept with numeric values (such as lab results), the REDCap project will also contain the first and last value.
    1. To look at specific values, such as BMI 1 month before or 1 month after a surgery date, you will need to access the raw data found in the file repository.
  3. The "Stats and Charts" feature of REDCap can be very helpful to look at things such as demographics. 
    1. Be cautious when looking at lab values in "stats and charts," because it only takes into account the values uploaded into REDCap, not all of the values.

Understanding the raw data: 

  1. Four CSV files are contained within the zip file: patient table, variable table, data table, and a code info table.
    1. The patient table contains one row per patient and includes basic demographic data.
    2. The variable table has one record for each of the i2b2 concepts you requested.
    3. The data table is in a long-skinny format containing multiple rows per patient. For example, if Vitamin D was requested in your search, patient 123 could have 30 rows just of Vitamin D levels (1 row per lab result). 
    4. The code info table has information about the codes requested in the HERON query.
  2. More information regarding what is contained in each CSV file is found here.
  3. Raw data can be transformed using SQLite in preparation for analysis in a statistical software. 
    1. Instructions to upload de-identified data into SQLite using sql-schema.sql
    2. Instructions to upload identified data into SQLite using dataset_import_identified.db

Upload HERON Data into SQLite

Learning SQL Training Videos:

**Please note all data are fabricated in the following examples. The code written in the videos is found starting on page 24 of the HERON training manual.

Last modified: Aug 11, 2021