How to Export Data
To export your data, go to the “Data Export” section.
Brim provides 3 options for data export:
- Patient Export CSV
- Detailed Export CSV
- Export to REDCap.
Option 1: Patient Export
This export is great for when you want the high level values, but don't need all of the note-level detail or abstraction methodology.
The Patient Export includes all values for One Per Patient Variables and Dependent Variables in a simple format: one line for each patient, and one column for each patient-level variable:
| Patient ID | Variable A | Variable B | ... every patient-level variable |
| 1 | Value 1-A | Value 1-B |
|
| 2 | Value 2-A | Variable 2-B |
|
Once you initiate the export, you'll see a task appear in "Export History". You can download your Patient Export CSV file when it's ready by clicking "Download Result".
Option 2: Detailed Export
This export includes all of the detail for all of the variables. Exported results include all LLM generated labels, the raw text associated with those labels, and details about any corrections or additions from the human reviewer.
The export CSV has one row for each generated variable value. Below is a description of the columns in this CSV.
| Column Name | Column description | Notes |
| Name | The name of the variable |
|
| Scope | The variable scope: One Per Patient, One Per Note, Many Per Note, or Dependent Variable. |
|
| Patient_id | The alphanumeric patient ID associated with this value. |
|
| Note_id | The Note ID associated with this value (N/A for patient-level variables). |
|
| Note_date | The date of the note or document |
|
| Note_Title | The title of the note/document |
|
| Generated Value | The value generated by the LLM for this variable. |
|
| Value | The most correct value for this variable. |
If this value was Edited by a human reviewer, "Value" is the human-provided value. If this value was Removed by a human reviewer, "Value" is blank. Otherwise, it is the same as the Generated Value. |
| Raw Text | The raw text used by Brim to create this value. |
|
| Value Start Offset | The position of the first character of the extracted value within the source document text for a Many Per Note variable. | Offsets only show for Many Per Note Variables |
| Value End Offset | The position after the last character of the extracted value within the source document text for a Many Per Note variable. | Offsets only show for Many Per Note Variables |
| Reasoning | Brim's reasoning for aggregated variables and dependent variables. | Patient-Level and Dependent Variable only |
| Review Status |
The accept/edit/remove status of a reviewed variable instance. Blank if this value has not yet been reviewed. |
|
| Reviewed | TRUE if a human reviewer selected Accept/Edit/Remove. Otherwise, FALSE. |
|
| Reviewing User | The username of the abstractor. Blank unless Reviewed is TRUE. |
|
| Reviewed At | The timestamp when the value was reviewed. Blank if not reviewed. |
|
| Validation Value |
The matching value in the comparison dataset. Blank if no matching value or no comparison dataset. |
|
| Validation Agreement |
TRUE if the Brim Value agrees with the matching value in the comparison dataset. FALSE if there is a matching value but it does not agree. Blank if no matching value or no comparison dataset. |
|
| Match Rule | The rule used to validation matching. | Example: If value is a date, you can set a range for it to match on for validation. |
| Confidence | The confidence score Brim assigned the generated value. |
|
| Flag last edited by | The user who last edited the flag for that variable results. |
|
| Flag last edited | The date and time the flag was last edited. |
|
| Comment | Displays the comment that a user has written on this variable result. |
|
| Comment last edited by | The user who last edited the comment for that variable results. |
|
| Comment last edited | The date and time the comment was last edited. |
|
| Results Link | Provides a link to the value and reasoning in Brim for One per Patient or One per Note labels |
|
| Patient Link | Provides a link to the Patient Label view. |
|
Detailed Reports also have advanced settings. This allows a user filter the detailed export to specific patients(s), note id, or variables. You can also choose to include structured data fields, default/blank values, and only "reviewed values".
Once you initiate the export, you'll see a task appear in "Export History". You can download your Detail Export CSV file when it's ready by clicking "Download Result".
Option 3: Export to REDCap
Select "Export to REDCap".
- Choose whether you want to Include Empty Values.
- Choose whether to Overwrite existing values in your REDCap project.
- Enter the URL for your REDCap instance.
- This should be "{{Base URL of your REDCap Instance}}/api/"
- If you go to your API playground at [Your Project] > Applications > API and reference the code, you can use the URL used in the playground API calls.
- Enter the token for the project you want to export to.
- You can find this in [Your Project] > Applications > API. You may need to generate a token if you have not generated a token for this project before.
Troubleshooting REDCap Export
- First read any error messages you get in Brim - many are directly from REDCap.
- Check that you have correct permissions - you need API permission and import/export permission for the REDCap project.
- Loosen restrictions on data types in your REDCap project (as appropriate).
Option 4: Export to PDF
This is a per patient PDF export of labels. To export to PDF visit the Label Review page, Click "By Patient", Choose the patient you would like to export the labels to PDF and click the PDF button.
