NIH | National Cancer Institute | NCI Wiki  

Versions Compared

Old Version 243

changes.mady.by.user Warzel, Denise (NIH/NCI) [E]

Saved on

compared with

New Version 489

changes.mady.by.user Asafieva, Natalia (NIH/NCI) [C]

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Comment: Uploaded caDSR Community Released CDEs as of May 4 2022.
Wiki Markup
{scrollbar:icons=false}

...

caDSR Wiki | caDSR Database and Tools | caDSR Documentation
Section
Column
width55

The NCI caDSR CDE Browser can be used to download collections of

...

metadata describing data held in repositories for cancer research and clinical trials.

...

There are currently no NCI Recommended CDEs for use other than the  CDEs marked as having a Registration Status of "Standard".  Any CDE in caDSR can be reused, but the ones marked "Standard" have been through a broader governance process. There communities within NCI who have agreed to use a set of CDEs for specific purposes, for example EDRN, TCGA, NCTN, and many others.  If you wish to collect data that is compatible with a specific group, you should begin by looking for the group's CDEs using the CDE Browser.  The Context name is an organizing principle for tree based navigation, and the "Advanced Search" provides a way to search for CDEs grouped by Classifications, or keywords.

Best Practices for creating CDEs  can be found here.

The caDSR Form Builder can be used to create, view and download the Case Report Forms (CRFs) designs. Each question on a caDSR Form is generally backed by a caDSR CDE, though we do have some forms that were bulk loaded without CDEs. When a CDE is associated with a form it is visible in the Form Builder web application, and is present in the XML or Excel download. Since each CDE has been annotated with semantic concepts for the question and each valid value, you can use this information to compare data that may be been represented differently, or to explore deeper meaning by traversing to the NCI Thesaurus for synonyms, related concepts, and other semantic information about each concept. The concept information for each valid value is not in the XML or Excel download, but we can produce a CRF Data Dictionary which will contain the concepts for each question and valid value for any associated CDE. Please sent the CRF public ID and version number to the NCI App Support desk and ask that the caDSR team help you with this request.

Include Page
wikicontent:Included Help Downloading Files Panel
wikicontent:Included Help Downloading Files Panel

Column
width45

 caDSR LogoImage Added

caDSR CDE Browser logoImage Added


caDSR Form Builder LogoImage Added

Currently, CDEs can be downloaded to Excel or XML Format. CRFs can be downloaded to Excel format. 

CDEs as ExcelImage Added

CDEs as XMLImage Added

 CRF as ExcelImage Added

CDEs as ExcelCDEs as XMLCRF as Excel
Info
titleDownloading Production CDEs
See Community Released Downloads to download production CDEs to Excel and XML  format and download DTDs from Github.

Attempting to download all the caDSR CDEs would result in a file size that is too large for an a single MS Excel download. The canned collections in the following list are provided for your convenience., and currently forms can only be downloaded one form at a time.

Therefore, "canned", or pre-downloaded collections of all the NCI "Released" CDEs, and CDEs by selected individual projects in is provided for your convenience. The NCI Preferred Standards have become too large to download in a single file, so they can be extracted from the "Released" CDE files.

Note that NCI added an FTP site where all "Released" CDEs as XML.

Panel
titleTable of Contents

Table of Contents
maxLevel4
minLevel2

...

Section
bordertrue



Column
width100%

Anchor
Community Released Downloads
Community Released Downloads

Download caDSR Community Released CDEs

  • For current list of all NCI Standards since the date of this download, visit the NCI caDSR CDE Browser and select "Search", or enter search criteria to filter the results.
  • All non-retired production CDEs (CDEs with Workflow status NOT = "RETIRED....") as of

...

...

...

Section

REDCap CDE and CRF Transformation Utilities - REDx

  • These are XSLT files that transform caDSR CDEs and Forms in XML format to

...

CDEs associated with Standard Case Report Forms (CRFs):

...

  • a REDCap Data Dictionary:
  • The transformation utility converts a single or multiple Form represented in XML to REDCap compatible csv format
    • for CDE XML, the file may contain multiple CDEs
    • for CRF XML, the file can contain one or more form per transform, please select the correct version of the utility below

  • REDxCDEv5

    • Transformation utility to convert caDSR CDE Browser 4.0.5 XML download format into REDCap Data Dictionary as of 2016/10/02
    • Version 5 - 2016-10-27: Change transform to pull Min/Max Value instead of Min/Max Length
    • Version 4 - 2016-10-02: Add CDE ID/Version as "Field Annotation". Export Valid Values in teh same format as exported for CRFs, ensuring that CDE values/choices will be consistent for the same CDE used across studies, whether as a CRFs, or imported as a list of CDEs.
    • Version 3 - 2015-08-05: Change field note to contain the CDE Question Text, the field does not need to be lower-case without spaces, that rule applies only to variable name
    • Version 2.1 - 2015-6-18: Add instruction for customizing Form name, Id and Version
    • Version 2.0 - 2015-6-10: Add a check for existing CDE PV Values. If already a numeric, use existing value. If not, generate a unique value based on the position in the value list.

  • REDxCRFV10

Current NCI Standard CRFs

The NCI develops and publishes standard CRF templates for use in creating new clinical trials protocol forms.  Each CRFs consists of CDEs organized into 3 sections: mandatory, optional, and conditional CDEs. To retrieve these and any other forms registered in caDSR since the dates listed below, please visit the caDSR Form Builder, where a Guest account and password are provided for your convenience.

There are currently over 70 Standard CRFs released for production use. 

There are 60 CRFs that have been converted to REDCap format and can be found in the Shared Library, and in the zip file attached here.

NCI Standard CRFs: REDCap format Zip

Section
bordertrue
Column
width50%

...

  • June 21st,

...

...

  • June 21st,

...

Column
width50%

...

  • June 21st,

...

...

  • RECIST NCI CRF Standards created on

...

  • May 11th,

...

  • 2015

...

...

  • June 21st,

...

...

  • June 21st,

...

...

CDEs

...

For other formats and prior versions of the files see the attachments listed at the end of this page.

...

Initiatives

CDEs initiatives are owned by individual NCI Divisions, Offices, and Centers, as well as by NCI stakeholder communities who have chosen to use NCI caDSR as a central repository for their CDEs. The CDEs are organized in the caDSR CDE Browser based on Context and Classification Scheme.  Contexts represent a community who have agreed to share CDEs and CRFs, within a Context end users create Classification Schemes within caDSR for various projects in their community, and use them to classify and organize CDEs. The classifications are a list of keywords and categories familiar to the community. Opening up a Context in the CDE Browser will reveal a "Classifications" node, that when opened will list all the projects in alphabetical order. Clicking on a project node will return a list of all the CDEs for that project.

For prior downloaded versions of these collections, see the Attachments listed at the end of this page.  The date of the download is listed as the "as-of" date for each collection of CDEs.

If importing caDSR content from a download into another ISO/IEC 11179 or other similar CDE or CRF metadata registry, please add the caDSR Registration Authority Identifier (RAI) 2.16.840.1.113883.3.26.2 to the metadata to keep the caDSR content distinct from the local repository. Per ISO/IEC 11179, the RAI is part of a globally unique identifier known as the IRID (Item Registry Identifier), and uniquely identifies registry content as being related to particular registrars. The IRID for all caDSR content is the <caDSR OID + Item public Id + item version>. For example, if the caDSR item public id = 2181292, version = 1.1, when importing you would add the RAI, and the result would be an IRID = 2.16.840.1.113883.3.26.2 + 2181292 + 1.1.

Coming soon! A link to cancerGrid UK cgMDR PTCRi (Particle Therapy Cancer Research) instance of cgMDR where you can download metadata elements in caDSR XML format, the native cgMDR format for importing into your own cgMDR instance, as well as an XML Schema annotated with W3C SAWSDL annotation tags.

The following lists the attachments to this page.

Attachments

 

...

Section
Column
width33%

TCGA Phase II meta data elements (CDEs)

TCGA (The Cancer Genome Atlas) is a project funded by the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI). A project overview can be found on the TCGA Home Page.

TCGA provides data element descriptions for the clinical data elements found in the TCGA data files.  The BCR on-line data dictionary displaying the essentials of the clinical CDEs as an HTML page is located here.  The files below contain all the caDSR metadata for these CDEs.  The HTML data dictionary was generated from the XML download of the TCGA CDEs. For more information or help creating your own HTML Data Dictionary from NCI registered CDEs, please contact the NCI Help Desk.

They are also available from the CDE Browser in the caBIG Context under the Classifications tab heading " TCGA 2.6 by Disease ".  New TCGA CDEs not yet in the BCR data dictionary can be found under the caBIG Classification "The Cancer Genome Atlas", sub-heading "New TCGA Data Elements"

Biomedical Research Integrated Domain Group (BRIDG) meta data elements (CDEs)

BRIDG is a model that was created by a collaborative effort engaging stakeholders from the Clinical Data Interchange Standards Consortium (CDISC), the HL7 BRIDG Work Group, the US National Cancer Institute (NCI), and the US Food and Drug Administration (FDA). A logical information model was developed to describe basic, pre-clinical, clinical, and translational research.  Please visit the BRIDG website for more information.

The CDEs in the BRIDG model are available from the CDE Browser in the BRIDG Context under the Classifications heading "Link to BRIDG 3.2", subheading "BRIDG 3.2". They have been downloaded and made available here for convenience.

 BRIDG 3.0.2 is also available in the Attachments section of this page and in the CDE Browser.

Column
width34%
Column
width50%

North American Central Cancer Registries (NAACCR) meta data elements (CDEs)

NAACCR develops and promotes uniform data standards for cancer registration, and aggregates and publishes data from central cancer registries. It promotes the use of cancer surveillance data and systems for cancer control and epidemiological research. See their website for more information about NAACCR.

NCI has registered several versions of the NAACCR data elements as CDE metadata in caDSR for discovery and use by those wishing to utilize the NAACCR data, or create data repositories of compatible data.

The following versions of NAACCR have been recorded in caDSR, are available from the CDE Browser in the PS&CC Context under the Classifications tab heading "Division of Cancer Control and Population Sciences ". They have been downloaded and made available here for convenience.

Column
width20%

NAACCR LogoImage Added

National Biomedical Imaging Archive (NBIA)(formerly NCIA)

The CDEs in the HINTS 2005 survey are available from the CDE Browser in the caBIG Context under the Classifications heading "NBIA". They have been downloaded and made available here for convenience.

Column
width33%

Surveillance, Epidemiology and End Results (SEER) meta data elements (CDEs)

The SEER program works to provide information on cancer statistics in an effort to reduce the burden of cancer among the U.S. population.  The data elements collected in cancer surveillance have been registered in the NCI caDSR, and are available from the CDE Browser in the PS&CC Context under the Classifications tab heading "caSEER", subheading " com.imsweb.caseer ". They have been downloaded and made available here for convenience.

Health Information National Trends Survey (HINTS2005)

The CDEs in the HINTS 2005 survey are available from the CDE Browser in the PS&CC Context under the Classifications heading "HINTS2005". They have been downloaded and made available here for convenience.

Column
width80%

Electronic Medical Records and Genomics (eMerge) Network CDEs       

The CDEs in the eMerge project are available from the CDE Browser in the caBIG Context under the Classifications heading "eMerge Data Variables". They have been downloaded and made available here for convenience.

Column
width20%

Merge Network LogoImage Added

Attachments
previewfalse

caDSR Wiki | caDSR Database and Tools | caDSR Documentation

Include Page
wikicontent:Included Help Downloading Files Panel
wikicontent:Included Help Downloading Files Panel