1. Leveraging Value Sets from the Value Set Authority Center (VSAC) in a Standards-Based Clinical Data Repository
Richard Kiefer1, Luke V. Rasmussen2, Jennifer A. Pacheco2, Peter Speltz3, Joshua C. Denny3, William K. Thompson2, Jyotishman Pathak4, Guoqian Jiang1
1 Mayo Clinic College of Medicine, Rochester, MN; 2 Northwestern University, Chicago, IL; 3 Vanderbilt University, Nashville, TN; 4 Weill Cornell Medicine, New York City, NY
Introduction
Methods
Discussion
NLM (National Library of Medicine) VSAC (Value Set Authority Center)1 stores value sets used in Clinical Quality Measures.
OHDSI (Observational Health Data Sciences and Informatics)2 offers a wide range of tools for large-scale integration & analytics of observational health data
Objectives:
Develop an app to import VSAC-hosted value set definitions into an OHDSI repository (OMOP)
Facilitate the reuse of well-defined value sets from existing value set repositories
Retrieved 50 random value sets from a CTS23 enabled repository.
Posted the concept name & namespace (vocabulary identifier) to the vocabulary search service to retrieve concepts from OMOP.
Defined the name for a concept set container.
Populated the concept set with the list of concepts retrieved from the vocabulary search.
Manually verified that the concepts in the concept sets matched the original value sets.
We retrieved VSAC value sets based on OIDs using CTS2 and migrated them to an OMOP repository for use in OHDSI tools.
This allows users of OHDSI to easily adopt established value set definitions from any CTS2 compliant repository.
Although there were some value sets which could not be completely recreated as a concept set, the program allows the user to view what codes are missing and take corrective actions.
The code could be incorporated into the OHDSI WebAPI for use in applications.
Architecture
VSAC
CTS2
Migrator
WebAPI
OMOP 1 2 3 4
2. WebAPI call to OMOP returns matching concepts.
3. Create ConceptSet container and populate with concepts
4. WebAPI call stores the ConceptSet container in OMOP
1. CTS2 call to VSAC returns value set concepts.
Results
For the 50 value sets we randomly pulled from VSAC:
37 value sets found exact matches in OMOP for all concepts.
Value set “ProcedureActStatusCode” used concepts from ActStatus code system which is not present in OMOP.
Some concepts stored as ICD9CM in VSAC were from ICD9Proc in OMOP.
Value set “Detailed Ethnicity” uses codes from CDCREC. The concept ids are present, but match LOINC.
4 value sets contained SNOMED codes which are not in OMOP.
Missing codes , , ,
Value set “ACE Inhibitor or ARB Ingredient” has several RxNorm codes missing in OMOP.
Missing codes – , , , , , , , , , , , , ,
Retinal Vascular Occlusion
Example
OHDSI – created concept set
VSAC – original value set
PhEMA4
Future Work
Use the value set migration as part of a larger implementation to allow algorithms created by the PhEMA authoring tool to be run against an OHDSI installation to retrieve patient cohorts.
Identify the cause of some ICD9CM and ICD10CM concepts not finding a match using the program but are located when searching manually.
References
1. VSAC:
2. OHDSI:
3. CTS2:
4. PhEMA:
PPT Scientific Poster_4x4 Blue Template.ppt
This work has been supported in part by funding from PhEMA (R01 GM105688) and eMERGE (U01 HG006379, U01 HG and U01 HG006388).