9 Extract Data

Extract Data

Datasets allow the user to select specific Events, Forms, and/or items (or all data) to be included in a set.

You can create a dataset with any data that has been entered into OpenClinica. You can also combine data from different Events and Forms as needed when creating a dataset. 

Once you define the data that you want to extract, you can choose from a number of different formats in which to view and work with that data. Once the extract is run, datasets include data from all sites and all participants within those sites.

Note: Participant Casebooks only include data from a single participant.

Create a Dataset

To create a dataset:

1. Click Tasks in the header bar, and select Create Dataset.

2. In the left panel, expand the Event that contains the Form data that you want to extract. If the Form is in multiple Events, select one Event now, and add more Events and Forms later.

3. Select the Form that contains the data you want to extract.

4. Select individual items, or to select all items in that Form, check the Select All Items checkbox above the item list.

5. (Optional) To select additional items, either from the same Form in other Events, or from a different Form, click Save and Add More Items. Then repeat steps 2 through 4 until you have selected all of the items you want to include in the dataset.

Note: In addition to selecting data from Forms, you can also select data from Events, Participants, and CRFs from the Event/Participant/CRF Attributes screens . You can also click Select All Items in the Study to include all items in the study.

6. Once you have selected all of the items you want to include in the dataset, click Save and Define Scope. The Name and Description screen appears.

7. Enter a name and description for the dataset.

 

Note: Names must be alphanumeric characters, but underscores are permitted.

 

8. In the Item Status field, select the completion status of the data you want to include in the extract. You can choose to include data from: CRFs marked Complete, CRFs not marked Complete, and all CRFs.

9. Ignore the message and fields on the lower portion of the screen, and click Confirm and Save.

 

10. On the Select Format screen, select the output format for the extracted dataset, and click Run Now to extract the data.

Note: The first option is the most complete extract format, and it is the only option that includes the audit log data as well as all of the clinical data and metadata. If using Participate forms with data entered by the participant, it is included in study data. It can also be included in extracts if those forms are added.

OpenClinica displays a screen that indicates your extract is running. Click Back to Dataset to view the status of extracted data. The Select Format screen appears again, and your dataset  is listed at the bottom of the screen. For large datasets it might take a while to extract data. If not complete, you will see that the dataset is still IN PROGRESS.

12. To download the dataset, in the Action column, click the Download button. To delete the dataset (this only deletes the data extract; it does NOT delete data from the database), click the Delete button.

Notes: The data in the dataset reflects the OpenClinica database at the time the dataset file was generated, not at the time when you downloaded the file. The dataset file name includes the date and time that the file was generated.

You can run the same extract in a number of different formats. OpenClinica retains one dataset file for each format for the dataset definition. If you generate a dataset and the dataset format already exists, the file you create overwrites the existing file. 

 

For example, if the same extract was run and you selected Excel, that extract would overwrite the original Excel file. However, if you selected HTML for the second extract of this dataset, both the Excel file and the HTML file would be available.

 

If there is a permission tag on the Form that prevents you from accessing the Form data, you also cannot extract the data. 

 

If you do not have access to any of the selected Forms, an error message appears to inform you that you do not have permission to access that data. If you do not have access to one or more Forms in the extracted dataset file, you cannot access, download, or delete the dataset.

Downloading Participant Casebooks

You can access a Participant Casebook from the Participant Details screen.

 

A Participant Casebook includes Participant data, excluding data that you do not have permission to view.

 

1. Click the Participant Matrix header button in Runtime.

2. Click the View button next to the participant you want to download data for.

 

Note: You can also skip steps 1 and 2 and go directly to the Participant Details screen by entering the Participant ID in the Search box in the upper-righthand corner of any screen within the Runtime.

 

3. Scroll to the bottom of the Participant Details screen, and select Casebook.

4. Under Format, click the radio button next to JSON or CDISC ODM XML or PDF to choose the format in which you want the data downloaded.

5. Uncheck the checkboxes if you do not want to include certain options in the data. You can choose to include or exclude: Notes & Discrepancies (Queries, Annotations, and Reason for Change), Audit Trail, Metadata, and/or Archived Form data.

 

Note: Casebooks always include Clinical Data.

 

6. Choose how to view the data (if applicable):

 

For XML or JSON files:

  • To get a link, select the Get Link button. Highlight and copy the link into the URL bar in your browser to view the data.
  • To open the webpage directly, select the Open button.

For PDFs, click Get PDF.

 

Note: PDF version of Participant Casebooks are available for download from the Bulk Action Log screen. 

 

 

 

 

 


Approved for publication by ktamm. Signed on 2020-03-05 11:30AM

Not valid unless obtained from the OpenClinica document management system on the day of use.