将本地生物样本记录映射到OMOP通用数据模型。
Mapping Local Biospecimen Records to the OMOP Common Data Model.
作者信息
Michael Chelsea L, Sholle Evan T, Wulff Regina T, Roboz Gail J, Campion Thomas R
机构信息
Department of Health Informatics, Memorial Sloan Kettering Cancer Center, New York, NY.
Department of Healthcare Policy & Research, Weill Cornell Medicine, New York, NY.
出版信息
AMIA Jt Summits Transl Sci Proc. 2020 May 30;2020:422-429. eCollection 2020.
Research to support precision medicine for leukemia patients requires integration of biospecimen and clinical data. The Observational Medical Outcomes Partnership common data model (OMOP CDM) and its Specimen table presents a potential solution. Although researchers have described progress and challenges in mapping electronic health record (EHR) data to populate the OMOP CDM, to our knowledge no studies have described populating the OMOP CDM with biospecimen data. Using biobank data from our institution, we mapped 26% of biospecimen records to the OMOP Specimen table. Records failed mapping due to local codes for time point that were incompatible with the OMOP reference terminology. We recommend expanding allowable codes to encompass research data, adding foreign keys to leverage additional OMOP tables with data from other sources or to store additional specimen details, and considering a new table to represent processed samples and inventory.
支持白血病患者精准医疗的研究需要整合生物样本和临床数据。观察性医疗结局合作组织通用数据模型（OMOP CDM）及其样本表提供了一个潜在的解决方案。尽管研究人员已经描述了将电子健康记录（EHR）数据映射到OMOP CDM以进行填充的进展和挑战，但据我们所知，尚无研究描述如何使用生物样本数据填充OMOP CDM。利用我们机构的生物样本库数据，我们将26%的生物样本记录映射到了OMOP样本表。记录映射失败的原因是时间点的本地代码与OMOP参考术语不兼容。我们建议扩展允许的代码以涵盖研究数据，添加外键以利用来自其他来源的数据或存储额外的样本详细信息来利用其他OMOP表，并考虑使用新表来表示处理后的样本和库存。
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