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Building an OMOP common data model-compliant annotated corpus for COVID-19 clinical trials

Yingcheng Sun, Alex Butler, LaToya A. Stewart, Hao Liu, Chi Yuan, Christopher T. Southard, Jae Hyun Kim,
Published: 1 June 2021
Journal of Biomedical Informatics , Volume 118, pp 103790-103790; doi:10.1016/j.jbi.2021.103790

Abstract: Clinical trials are essential for generating reliable medical evidence, but often suffer from expensive and delayed patient recruitment because the unstructured eligibility criteria description prevents automatic query generation for eligibility screening. In response to the COVID-19 pandemic, many trials have been created but their information is not computable. We included 700 COVID-19 trials available at the point of study and developed a semi-automatic approach to generate an annotated corpus for COVID-19 clinical trial eligibility criteria called COVIC. A hierarchical annotation schema based on the OMOP Common Data Model was developed to accommodate four levels of annotation granularity: i.e., study cohort, eligibility criteria, named entity and standard concept. In COVIC, 39 trials with more than one study cohorts were identified and labelled with an identifier for each cohort. 1,943 criteria for non-clinical characteristics such as “informed consent”, “exclusivity of participation” were annotated. 9767 criteria were represented by 18,161 entities in 8 domains, 7,743 attributes of 7 attribute types and 16,443 relationships of 11 relationship types. 17,171 entities were mapped to standard medical concepts and 1,009 attributes were normalized into computable representations. COVIC can serve as a corpus indexed by semantic tags for COVID-19 trial search and analytics, and a benchmark for machine learning based criteria extraction.
Keywords: Clinical trial / Eligibility criteria / COVID-19 / Structured text corpus / Machine readable dataset

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