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Using REDx to convert NCI Content to REDCap Data Dictionary

 

Table of Contents

Introduction .............................................................................................................................................

Converting NCI CDEs to REDCap Data Dictionary .......................................................................

Skip to “ Running REDx using an XML Editor

Converting NCI CRFs/Forms to REDCap: ........................................................................................

Running REDx using an XML Editor .................................................................................................

Introduction

This document describes how to download and convert NCI CDEs and CRFs into a REDCap Data Dictionary.

 

Problems running the REDxCRF or REDxCDE utility should be reported to the NCI Help Desk, attention of the caDSR team.

 

Converting NCI CDEs to REDCap Data Dictionary

Use NCI caDSR CDE Browser to find the CDEs you are interested in using in REDCap.

https://cdebrowser.nci.nih.gov

 

Download the REDxCDEv1 utility from the NCI Wiki and save it on your desktop to use in the XSLT processing step. https://wiki.nci.nih.gov/display/caDSR/caDSR+Downloads

 

1. Visit the CDE Browser and search for NCI CDEs

 

Find the CDEs you are interested in using the CDE Browser using any of the following searches:

 

a) to get the CDEs associated with caDSR forms published to the CDE Browser, you can in the CDE Browser caBIG "Catalogue of Forms" node, click on the note to return the CDEs associated with the form.

Click: "Download to XML"

CDE Browser just downloads the CDE’s metadata, without the form branching logic or other form specific details, such as restrictions on the list of permitted values. To get the form specific details, visit the caDSR Form Builder and use the REDxCRF utility to transform the form.

 

Or

b) Search for CDEs using any of the "Classifications" nodes in any of the Contexts.

Or

c) Search for CDEs using "Advanced Search" and "Classifications" to retreive a collection

Click: "Download to XML"

Or

d) Search for an arbitrary collection of CDEs, add them into the CDE Cart, then

Click: "Download to XML" from the CDE Cart

Or

e) Find all forms in a CTEP study by clicking "CTEP>Protocol forms", select the desired node, when results are returned,

Click: "Download to XML" from search results page

 

2. Save the XML file to your desktop

 

3. Skip to “ Running REDx using an XML Editor

 

Converting NCI CRFs/Forms to REDCap:

Use NCI caDSR Form Builder to find the forms you are interested in using in REDCap.

http://formbuilder.nci.nih.gov

 

Download the REDxCRFv1 utility from the NCI Wiki and save it on your desktop to use in the XSLT processing step. https://wiki.nci.nih.gov/display/caDSR/caDSR+Downloads

 

1. Login to Form Builder using your caDSR account, or the Guest account (user id and passcode for the guest account are displayed on the Form Builder home page).

 

2. To find all the CRFs used by a particular group, click on the group name in the caDSR Context tree, or expand the group name and click on Classifications or Protocol Forms to find forms for a particular study. You will have to know the Protocol Id in order to locate forms for studies, the Protocol Names are not displayed in Form Builder.

 

To find NCI Standard CRFs, search for “*NCI Standard*”, with Context = “caBIG” or (“NCIP” Form Builder 4.1 or after), with Workflow status = “Released”. These forms have been preloaded in a form cart called “NCISTANDARD”. They can be copied from this cart following the instructions starting with Step 5.

 

screenshot of forms

 

3. Select the form(s) you are interested in by clicking the box in the first column, and then “Add to Form Cart”.

 

4. Go to FormCart (upper right of the UI) and be sure the form you are interested in is there, it will be at the bottom of the list. (You can delete forms in the Guest Cart you are not interested in if you want to, but it is not necessary).

 

screenshot of form cart

 

5. Go to the Object Cart Domain Class Browser: http://objcart.nci.nih.gov , click on “Continue” and click on: Domain Packages > gov.nih.nci.objectCart.domain > Cart

 

screenshot of object cart

 

screenshot of domain class browser with arrow pointing to Cart

 

6. Enter the caDSR userid for the Form Builder account that you signed in with to create the Form Cart. In this case userid = ‘dwarzel’.

 

If you want to download all the NCI Standard Templates, enter userid = “NCISTANDARD”. This cart contains all the standard templates.

 

screenhost of domain class browser and tree nodes

 

7. Click on “getCartObjectCollection” for the formCart row, shown in red in the next screenshot.

 

screenshot of form Cart row

 

8. View the object cart collection, highlight the row for the form you are interested in. Only copy one row at a time, each row is one form.

 

screenshot of rows

 

Running REDx using an XML Editor

  1. Open an XML Editor, such as Oxygen, crate a new XML document and paste the row into a new XML Document.

 

screenshot of xml document

 

  1. Delete any extraneous information at the end of the file after the closing tag, as highlighted in the next screenshot.

 

screenshot illustrating deleting extraneous information

 

  1. Make sure the file is a properly formed XML document, if the extraneous text has not been deleted as in the previous screenshot , the transform will fail. The first and last tag should be <form-transfer-object> ….</form-transfer-object> tag. You XML Editor will be able to format the document with indentations if it is properly formed, as shown in the next screenshot.

screenshot of XML document

 

  1. Run the XSLT processor inside the XML Editor using the REDxCRFv1.xsl downloaded from NCI

 

In the next screenshot in Oxygen, the “XML URL” is the name of the XML file from caDSR that you want to turn into a REDCap data dictionary. In this case the file is open in Oxygen so this interface is pointed to the ${currentFileURL}

 

The “XSL URL” is the REDxCRFv1.xsl you downloaded and saved on your desktop

 

screenshot of edit scenario

 

  1. Save the output of the transformation using .csv file extension

e.g. NCIDemographyCRF.csv and review for accuracy by opening using Excel, ensure columns are properly aligned

 

  1. Import the file into REDCap