Standardizing clinical laboratory data for secondary use.

Journal of Biomedical Informatics
Swapna AbhyankarClement J McDonald

Abstract

Clinical databases provide a rich source of data for answering clinical research questions. However, the variables recorded in clinical data systems are often identified by local, idiosyncratic, and sometimes redundant and/or ambiguous names (or codes) rather than unique, well-organized codes from standard code systems. This reality discourages research use of such databases, because researchers must invest considerable time in cleaning up the data before they can ask their first research question. Researchers at MIT developed MIMIC-II, a nearly complete collection of clinical data about intensive care patients. Because its data are drawn from existing clinical systems, it has many of the problems described above. In collaboration with the MIT researchers, we have begun a process of cleaning up the data and mapping the variable names and codes to LOINC codes. Our first step, which we describe here, was to map all of the laboratory test observations to LOINC codes. We were able to map 87% of the unique laboratory tests that cover 94% of the total number of laboratory tests results. Of the 13% of tests that we could not map, nearly 60% were due to test names whose real meaning could not be discerned and 29% represented tests that...Continue Reading

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Citations

May 17, 2013·Journal of the American Medical Informatics Association : JAMIA·Mustafa Fidahussein, Daniel J Vreeman
Dec 24, 2013·Journal of the American Medical Informatics Association : JAMIA·Li-Hui LeeErhard Rahm
Jul 4, 2012·Journal of Biomedical Informatics·Elizabeth S ChenIndra Neil Sarkar
May 15, 2016·Journal of the American Medical Informatics Association : JAMIA·Benjamin H SlovisJason S Shapiro
Oct 11, 2014·Health Informatics Journal·Guilan Kong, Zhichun Xiao
Aug 24, 2018·Journal of the American Medical Informatics Association : JAMIA·Sharidan K ParrMichael E Matheny
Jun 21, 2019·Archives of Pathology & Laboratory Medicine·Michelle StramLiron Pantanowitz
Oct 28, 2019·Archives of Pathology & Laboratory Medicine·Courtney BarryCharlene Bierl
Feb 17, 2019·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·Xavier GanselAlex van Belkum
May 25, 2016·Scientific Data·Alistair E W JohnsonRoger G Mark
Oct 19, 2016·Critical Care Medicine·David M MasloveJoon Lee
Oct 1, 2014·Statistical Analysis and Data Mining·Yolanda HagarNoémie Elhadad

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