Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium. Academic Article uri icon



  • RESEARCH OBJECTIVE: To develop scalable informatics infrastructure for normalization of both structured and unstructured electronic health record (EHR) data into a unified, concept-based model for high-throughput phenotype extraction. MATERIALS AND METHODS: Software tools and applications were developed to extract information from EHRs. Representative and convenience samples of both structured and unstructured data from two EHR systems-Mayo Clinic and Intermountain Healthcare-were used for development and validation. Extracted information was standardized and normalized to meaningful use (MU) conformant terminology and value set standards using Clinical Element Models (CEMs). These resources were used to demonstrate semi-automatic execution of MU clinical-quality measures modeled using the Quality Data Model (QDM) and an open-source rules engine. RESULTS: Using CEMs and open-source natural language processing and terminology services engines-namely, Apache clinical Text Analysis and Knowledge Extraction System (cTAKES) and Common Terminology Services (CTS2)-we developed a data-normalization platform that ensures data security, end-to-end connectivity, and reliable data flow within and across institutions. We demonstrated the applicability of this platform by executing a QDM-based MU quality measure that determines the percentage of patients between 18 and 75 years with diabetes whose most recent low-density lipoprotein cholesterol test result during the measurement year was <100 mg/dL on a randomly selected cohort of 273 Mayo Clinic patients. The platform identified 21 and 18 patients for the denominator and numerator of the quality measure, respectively. Validation results indicate that all identified patients meet the QDM-based criteria. CONCLUSIONS: End-to-end automated systems for extracting clinical information from diverse EHR systems require extensive use of standardized vocabularies and terminologies, as well as robust information models for storing, discovering, and processing that information. This study demonstrates the application of modular and open-source resources for enabling secondary use of EHR data through normalization into standards-based, comparable, and consistent format for high-throughput phenotyping to identify patient cohorts.


  • Pathak, Jyotishman
  • Bailey, Kent R
  • Beebe, Calvin E
  • Bethard, Steven
  • Carrell, David C
  • Chen, Pei J
  • Dligach, Dmitriy
  • Endle, Cory M
  • Hart, Lacey A
  • Haug, Peter J
  • Huff, Stanley M
  • Kaggal, Vinod C
  • Li, Dingcheng
  • Liu, Hongfang
  • Marchant, Kyle
  • Masanz, James
  • Miller, Timothy
  • Oniki, Thomas A
  • Palmer, Martha
  • Peterson, Kevin J
  • Rea, Susan
  • Savova, Guergana K
  • Stancl, Craig R
  • Sohn, Sunghwan
  • Solbrig, Harold R
  • Suesse, Dale B
  • Tao, Cui
  • Taylor, David P
  • Westberg, Les
  • Wu, Stephen
  • Zhuo, Ning
  • Chute, Christopher G

publication date

  • November 4, 2013



  • Data Mining
  • Electronic Health Records
  • Medical Informatics Applications
  • Natural Language Processing
  • Phenotype


PubMed Central ID

  • PMC3861933

Scopus Document Identifier

  • 84890446404

Digital Object Identifier (DOI)

  • 10.1136/amiajnl-2013-001939

PubMed ID

  • 24190931

Additional Document Info


  • 20


  • e2