Feasibility of using clinical element models (CEM) to standardize phenotype variables in the database of genotypes and phenotypes (dbGaP)

Ko Wei Lin, Melissa Tharp, Michael Conway, Mindy Ross, Alexander Hsieh, Hyeon Eui Kim

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

2 Scopus citations

Abstract

The database of Genotypes and Phenotypes (dbGaP) contains various types of data generated in Genome Wide Association Studies (GWAS). These data can be used to facilitate novel scientific discovery and to reduce cost and time for exploratory research. However, idiosyncrasies in variable names become a major barrier for reusing these data. We studied the problem of formalizing the phenotype variable descriptions using Clinical Element Models (CEM). Direct mapping of 379 phenotype names to existing CEM yielded a low rate of exact matches (N=25). However, the flexible and expressive underlying information models of CEM provided a robust means of representing 115 phenotype variable descriptions, indicating that CEMs can be successfully applied to standardize a large portion of the clinical variables contained in dbGaP.

Original languageEnglish
Title of host publicationProceedings - 2012 IEEE 2nd Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2012
Pages123
Number of pages1
DOIs
StatePublished - 2012
Externally publishedYes
Event2012 IEEE 2nd Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2012 - San Diego, CA, United States
Duration: Sep 27 2012Sep 28 2012

Publication series

NameProceedings - 2012 IEEE 2nd Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2012

Conference

Conference2012 IEEE 2nd Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2012
Country/TerritoryUnited States
CitySan Diego, CA
Period09/27/1209/28/12

Fingerprint

Dive into the research topics of 'Feasibility of using clinical element models (CEM) to standardize phenotype variables in the database of genotypes and phenotypes (dbGaP)'. Together they form a unique fingerprint.

Cite this