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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.

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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.

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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.

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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.

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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.

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Section

REDx - caDSR REDCap Transformation Utilities

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

  • Release Notes
    • User Guide
    • REDxCDE V3

      • Transformation utility to convert caDSR CDE Browser 4.0.5 XML download format into REDCap Data Dictionary as of 2014/11/10
      • 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.
    • REDxCRF Single V5.0

      • Transformation utility to convert a single caDSR Form Builder 4.0.3.1 formCart Version 1 XML format (retrieved from Objcart API) into REDCap Data Dictionary
      • Version 5  - 2015-07-29: Add a check for existing CDE PV Values.  If PV Value is already a numeric, use existing value. If not, generate unique value based on the position of the PV in the value list. 
      • Version 4 - 2014-11-10:
        • Change generation of Field Label to the original caDSR Preferred Question Text, without converting it to lower case and replacing spaces with underscores
        • See Version comments within the xslt for prior version release notes

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