Annotating Cohort Data Elements with OHDSI Common Data Model to Promote Research Reproducibility

Yiqing Zhao, Yanshan Wang, Henry Wang, Benjamin Yan, Feichen Shen, Kevin J. Peterson, Walter A Rocca, Jennifer St. Sauver, Hongfang D Liu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Rapid increase in the implementation of electronic health records (EHRs) has led to an unprecedented expansion in the availability of dense longitudinal cohort datasets for clinical studies. However, there is a growing need to ensure data traceability, validity, and reproducibility for EHR-based clinical research. Applying common data models that standardize EHR data elements could reduce research discrepancies and improve research reproducibility. As a pilot study, we utilized the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) developed by the Observational Health Data Sciences and Informatics (OHDSI) community to annotate cohort data elements from the local Rochester Epidemiology Project (REP). We evaluated the data coverage of the OMOP CDM by manually annotating the cohorts from 92 REP publications. Next, we examined cohort similarities between different publications using OMOP elements. Evaluation results showed that the OMOP CDM covers 99.8% of the content that is associated with cohort attributes. It demonstrated that the OMOP CDM can be used for data element standardization when extracting information from EHR and clinical registries. The OMOP CDM also shows its potential to be used as a tool for retrospective examination of cohort definition consistencies and epidemiology model similarities.

Original languageEnglish (US)
Title of host publicationProceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
EditorsHarald Schmidt, David Griol, Haiying Wang, Jan Baumbach, Huiru Zheng, Zoraida Callejas, Xiaohua Hu, Julie Dickerson, Le Zhang
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1310-1317
Number of pages8
ISBN (Electronic)9781538654880
DOIs
StatePublished - Jan 21 2019
Event2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 - Madrid, Spain
Duration: Dec 3 2018Dec 6 2018

Publication series

NameProceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018

Conference

Conference2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
CountrySpain
CityMadrid
Period12/3/1812/6/18

Fingerprint

Informatics
Electronic Health Records
Data structures
Health
Epidemiology
Research
Publications
Registries
Standardization
Availability

Keywords

  • cohort study
  • Common Data Model
  • data standardization
  • electronic health record

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

Cite this

Zhao, Y., Wang, Y., Wang, H., Yan, B., Shen, F., Peterson, K. J., ... Liu, H. D. (2019). Annotating Cohort Data Elements with OHDSI Common Data Model to Promote Research Reproducibility. In H. Schmidt, D. Griol, H. Wang, J. Baumbach, H. Zheng, Z. Callejas, X. Hu, J. Dickerson, ... L. Zhang (Eds.), Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 (pp. 1310-1317). [8621269] (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2018.8621269

Annotating Cohort Data Elements with OHDSI Common Data Model to Promote Research Reproducibility. / Zhao, Yiqing; Wang, Yanshan; Wang, Henry; Yan, Benjamin; Shen, Feichen; Peterson, Kevin J.; Rocca, Walter A; St. Sauver, Jennifer; Liu, Hongfang D.

Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. ed. / Harald Schmidt; David Griol; Haiying Wang; Jan Baumbach; Huiru Zheng; Zoraida Callejas; Xiaohua Hu; Julie Dickerson; Le Zhang. Institute of Electrical and Electronics Engineers Inc., 2019. p. 1310-1317 8621269 (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Zhao, Y, Wang, Y, Wang, H, Yan, B, Shen, F, Peterson, KJ, Rocca, WA, St. Sauver, J & Liu, HD 2019, Annotating Cohort Data Elements with OHDSI Common Data Model to Promote Research Reproducibility. in H Schmidt, D Griol, H Wang, J Baumbach, H Zheng, Z Callejas, X Hu, J Dickerson & L Zhang (eds), Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018., 8621269, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, Institute of Electrical and Electronics Engineers Inc., pp. 1310-1317, 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, Madrid, Spain, 12/3/18. https://doi.org/10.1109/BIBM.2018.8621269
Zhao Y, Wang Y, Wang H, Yan B, Shen F, Peterson KJ et al. Annotating Cohort Data Elements with OHDSI Common Data Model to Promote Research Reproducibility. In Schmidt H, Griol D, Wang H, Baumbach J, Zheng H, Callejas Z, Hu X, Dickerson J, Zhang L, editors, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Institute of Electrical and Electronics Engineers Inc. 2019. p. 1310-1317. 8621269. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018). https://doi.org/10.1109/BIBM.2018.8621269
Zhao, Yiqing ; Wang, Yanshan ; Wang, Henry ; Yan, Benjamin ; Shen, Feichen ; Peterson, Kevin J. ; Rocca, Walter A ; St. Sauver, Jennifer ; Liu, Hongfang D. / Annotating Cohort Data Elements with OHDSI Common Data Model to Promote Research Reproducibility. Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. editor / Harald Schmidt ; David Griol ; Haiying Wang ; Jan Baumbach ; Huiru Zheng ; Zoraida Callejas ; Xiaohua Hu ; Julie Dickerson ; Le Zhang. Institute of Electrical and Electronics Engineers Inc., 2019. pp. 1310-1317 (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).
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