NIH | National Cancer Institute | NCI Wiki  


Wynne, Robert    NIH/NCI [C]x
Bauer, Scott  Mayox
Stancl, Craig
Endle,  CoryMayox


Follow up value set workflow questions for Rob.

Review Value Set workflow process (Rob)


As part of the existing Value Set workflow process:
  • What additional artifacts are created and exposed via the process
  • What is provided/required for FDA/CDISC/?? as part of the value set artifacts

Discussion Points: 

Rob indicated that that following tasks are completed in his workflow:

  • Remove resolved value set script - This removes all existing value set coding schemes
  • Remove definitions script is generated
  • Load definitions script is generated (based on a flag)
  • Script to resolve all 770 value set definitions is called
    • This takes 2.5 days.
The following files and scripts are created as part of the workflow:
  • Value set definition xml file for each value set
  • Admin scripts
  • Load resolved value set script for all in value sets in the NCIT
Value Set Definition XML file: The only parts that change programmatically are:
  • Entity description
  • Source
Neoplasm.xml has a different association:
  • referencedAssociation="subClassOf"


NCI Report Writer

  • Creates an XLS report file
  • Generating these reports
    • Takes about 10 minutes
    • Uses NCI coding scheme, not the resolved value set
    • Released files are on the FTP site
  • Codebase:


Decision Points:

  • Investigate concept and subset - look at applying transitive closure here.
  • Determine if the Value Set Definition XML file is needed and consequences of removing it from their workflow.
  • Investigate loading resolved value sets - more than one at a time
    • Use a Java process instead of a script.



Value Set Issues Identified during 2016.12 Technical Face-To-Face

1Investigate ability to be able to determine if Resolved VS coding scheme has changed.
1Investigate ability to update as needed (not have to load all 700 at the same time). Decrease time it takes to publish/deploy.

Investigate ability to be able to determine if Value Set Definition has changed.

2Investigate ability to capture "Hierarchal Value Sets" as coding schemes with hierarchy. (inside value set)


  • No labels