Data Exports

Instructions for Exporting or Downloading Study Data by Form, Subject, and Site/Study (Metadata)

There are two kinds of data to export, Subject data and Metadata.  These are described below. 

Extract Study by Form or Subject

Extract Study By Form or Subject Using Data Packs

Exporting or Downloading all Subject and Site/Study data (Metadata)

 

 

Extract Study by Form or Subject

This document will explain how to export or download all Subject and Site/Study-related form data collected within TrialKit.


Access and Properties

Prerequisite: User has access to Extract All Study Data

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Field blinding is enforced in the data outputs, based on the user role executing the export.

If the user accessing the exports is a site-level user, the date exported will only be for the site(s) they belong to, or a single site can be selected to export. This saves needing to filter out that site’s data across every data set. 

The following screen of options is seen when exporting all data.  

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Option Descriptions

Include Archived Records

Archived records are past versions of records over time as data changes were made and records were resaved by users.

Include Deleted Records

Records that have been deleted from the study can still be accessed in the exports

Include Draft Records

Draft records are non-final versions of a record. This depends on the study function of draft saving having been enabled.

Include Administrative Site  Records

Check this to INCLUDE admin site data in export.  This is good for testing and validation.

Split Date fields into 3 parts

This option will take any date field and create three separate columns of data with "FIELDNAME_day", "FIELDNAME_month",  and "FIELDNAME_year"

Use Labels as Headers

This will use the reporting label for each field - defined in the form builder - in place of the default field name.

Version

It is necessary to select which version of the study to export. If multiple sites/subjects are on different versions, they will need to be exported separately. The reason exports are separated by version, is due to the extensive study design changes that can be made from one version to the next. Combining versions into a single export would lead to an inaccurate reflection of data.

Export Formats

Background versus Direct Download

These options will produce the same results. The only difference is how they get processed.

Direct Download will require the user to wait for the file to process while the status bar indicates progress. Once complete it will automatically download. Navigating away from the screen will stop the export.

The background option is helpful for larger data volumes to avoid waiting on the screen for the download to finish. You can return later on to the background exports screen to retrieve the file.

CDISC ODM

The CDISC ODM (Operational Data Model) XML is a Snapshot format that supports version 1.3 of the specification as published at http://www.cdisc.org. There are 3 options for the ODM export in TrialKit: Metadata Only export, the Data Only export, and Metadata and Data in one file export.

Metadata Only Export

The Metadata Only export defines events, forms, and questions that make up a study.  The metadata can be downloaded by clicking on the Click here to Export Metadata to ODM link as shown in the figure below.

Data Only Export

The Data Only export provides a data transport and storage mechanism for the actual clinical data as entered in the CRFs. The data can be downloaded by clicking on the Click Here to Export Data To ODM link as shown in the figure below.

Metadata and Data Export

The Metadata and Data export option combines both the Metadata and Data in one ODM export file. The data can be the system's unique file ID which is also seen in the file repository, to help with identifying files.

 

 

Extract Study by Form or Subject - Data Packs

There is the ability to extract data by form or exportable data packs.  This allows administrators to create data packages from case report forms and export them to a variety of formats and with additional information.  These data packs hold the specific form of data that has been joined with Subject and Event data.

Prerequisite:  Users with a role of Administrator (role hierarchy of 200) are the only Users that can configure new exports.

Any study role with a hierarchy of less than 200 will only be able to view exports that have been targeted to their role (determined in the export configuration) - assuming the role has access to data extraction.

Field blinding is enforced in the data outputs, based on the user role executing the export.

NOTE: If the user accessing the exports is a site-level user, they will only see data for their own site(s).

 

These exports enforce field blinding. If the role viewing or exporting a data pack is blinded to a field on that form, the column data will display “*****”.

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NOTE: If a user role should not see that a blinded variable exists, they should not be granted access to the exports.

 

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See the annotated numbers in the image below with descriptions below the image to learn how to configure new exports and export data packs that have been made available.

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  1. Select which form to create a data pack for. 

  2. Export data types:

    • Decode choice fields - Replaces the coded value of choice type fields (radio fields and dropdowns/picklists) with the choice text.

    • Use label as a header - Uses the reporting label as the column header rather than the field name for each field

    • Archived records - Includes all archived records as well as the final ones. An archived record is a past version of the same record which was then saved again and replaced by a subsequent one - such as when data is changed and a form is re-saved. An "Archived" column will indicate which records are archived versions versus which ones are final.

    • Deleted records - Includes any deleted records in the export. A "Deleted" column will indicate which ones are deleted status.

    • Draft records - Includes records saved in draft mode, if the study was set up to allow draft saving.

    • Include Admin site records - Includes Admin/testing data in the exports. This data comes from any Administrative type sites, as defined in the Site Manager. 

  3. Related columns - Subject Fields and Visit/Event Fields:

    • Primary key (sub_id) - This is the database's primary key that is assigned to the given subject. It is used as a PK->FK relationship between the Subject Fields and the Event Fields.

    • Profile ID - The subject's ID which is seen throughout the system. This can potentially be changed by users, but the sub_id cannot.

    • Treatment start date - The visit/event date from the subject registration form

    • Version - The version of the study where the record currently exists

    • Site - The study site where the record exists

    • Study - The name of the study defined in the Study Manager

    • Primary key (trans_id) - A unique key to each subject event and is used to establish a link between the event and the actual form and sub-form data.

    • Event Date - The date key field that must be entered into each subject form.

    • Form status - The current state of each record. For example, saved 

    • Form Frozen - Indicates True if the record has been frozen

    • Interval - The name of the visit

    • Unscheduled ID - The name of the visit if it's an unscheduled one

    • Randomization Allocation - This will only show as an option if the study is randomized. It can be used to display the allocation (Unblinding) for each record.

  4. Targeted Roles - Dictates which user roles will have access to the data pack export when they open the same page. Only Administrator roles (hierarchy level of 200) are able to set up exports as described here and access all data. Other lower roles can only export what has been set up for them.

  5. Export description - Brief description of what the export is intended for.

  6. Save data pack - Saves the export into the table at the top of the page

  7. Export data pack - Click this link to open the data pack and run the export (described in more detail below).

  8. Edit data pack - Use this option to adjust any of the pre-defined parameters described in items 1-5.

  9. Delete data pack (rights dependent)

Once you have completed the Add New Data Pack form and saved the form, it will be added to the Current Data Packages data table. In that data table is an export link. When clicked, the data will be exported to the selected data format and downloaded to the client's computer as shown in the figure.

Clicking the Export link will load “Grid Views” of your Form data. You will see 1 or more “Grid View” depending on how the form is created.

The figure below shows the Subject Profile Form with two grid views.

  1. The first “Grid View” displays the Main Form of Data
  2. The second “Grid View” displays the “SubForm Table” data, which comes from having a normalized table on the form.  

Depending on how a form is created, it may have no sub-form table or more than one sub-form table.

2022-11-01_14-35-23Pick the format of the Data on the Grid Views to be exported and click Export.

2022-11-01_14-15-37There are currently three types of export formats; Excel, SAS XML, and SPSS SAV. Choose the format you would like the form data to be displayed when you do the actual export. For Excel and SAS XML Format, you will need to pick the format for each Grid View that you want to export. For SPSS SAV you will only need to pick that form on the main Grid View and it will include all the sub-form table data in a zip file.

Save the Exported Data Pack

A Save File Window will appear after clicking the Export button. Click OK to Open or Save the File to your computer. The following figure shows how to save the Exported Data Package to your computer or device.

 

Exporting all Subject and Site/Study Data (Metadata)

The following screen of options is seen when exporting all data.  

Prerequisite: User has access to Extract All Study Data

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Field blinding is enforced in the data outputs, based on the user role executing the export.

If the user accessing the exports is a site-level user, the date exported will only be for the site(s) they belong to, or a single site can be selected to export. This saves needing to filter out that site’s data across every data set. 

The following screen of options is seen when exporting all data.  

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Option Descriptions

Include Archived Records

Archived records are past versions of records over time as data changes were made and records were resaved by users.

Include Deleted Records

Records that have been deleted from the study can still be accessed in the exports

Include Draft Records

Draft records are non-final versions of a record. This depends on the study function of draft saving having been enabled.

Include Administrative Site  Records

Check this to INCLUDE admin site data in export.  This is good for testing and validation.

Split Date fields into 3 parts

This option will take any date field and create three separate columns of data with "FIELDNAME_day", "FIELDNAME_month",  and "FIELDNAME_year"

Use Labels as Headers

This will use the reporting label for each field - defined in the form builder - in place of the default field name.

Version

It is necessary to select which version of the study to export. If multiple sites/subjects are on different versions, they will need to be exported separately. The reason exports are separated by version, is due to the extensive study design changes that can be made from one version to the next. Combining versions into a single export would lead to an inaccurate reflection of data.

Export Formats

Background versus Direct Download

These options will produce the same results. The only difference is how they get processed.

Direct Download will require the user to wait for the file to process while the status bar indicates progress. Once complete it will automatically download. Navigating away from the screen will stop the export.

The background option is helpful for larger data volumes to avoid waiting on the screen for the download to finish. You can return later on to the background exports screen to retrieve the file.

CDISC ODM

The CDISC ODM (Operational Data Model) XML is a Snapshot format that supports version 1.3 of the specification as published at http://www.cdisc.org. There are 3 options for the ODM export in TrialKit: Metadata Only export, the Data Only export, and Metadata and Data in one file export.

Metadata Only Export

The Metadata Only export defines events, forms, and questions that make up a study.  The metadata can be downloaded by clicking on the Click here to Export Metadata to ODM link as shown in the figure below.

Data Only Export

The Data Only export provides a data transport and storage mechanism for the actual clinical data as entered in the CRFs. The data can be downloaded by clicking on the Click Here to Export Data To ODM link as shown in the figure below.

Metadata and Data Export

The Metadata and Data export option combines both the Metadata and Data in one ODM export file. The data can be the system's unique file ID which is also seen in the file repository, to help with identifying files.