TY - JOUR
T1 - Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery
AU - Zhang, Xingmin Aaron
AU - Yates, Amy
AU - Vasilevsky, Nicole
AU - Gourdine, J. P.
AU - Callahan, Tiffany J.
AU - Carmody, Leigh C.
AU - Danis, Daniel
AU - Joachimiak, Marcin P.
AU - Ravanmehr, Vida
AU - Pfaff, Emily R.
AU - Champion, James
AU - Robasky, Kimberly
AU - Xu, Hao
AU - Fecho, Karamarie
AU - Walton, Nephi A.
AU - Zhu, Richard L.
AU - Ramsdill, Justin
AU - Mungall, Christopher J.
AU - Köhler, Sebastian
AU - Haendel, Melissa A.
AU - McDonald, Clement J.
AU - Vreeman, Daniel J.
AU - Peden, David B.
AU - Bennett, Tellen D.
AU - Feinstein, James A.
AU - Martin, Blake
AU - Stefanski, Adrianne L.
AU - Hunter, Lawrence E.
AU - Chute, Christopher G.
AU - Robinson, Peter N.
N1 - Publisher Copyright:
© 2019, The Author(s).
PY - 2019/12/1
Y1 - 2019/12/1
N2 - Electronic Health Record (EHR) systems typically define laboratory test results using the Laboratory Observation Identifier Names and Codes (LOINC) and can transmit them using Fast Healthcare Interoperability Resource (FHIR) standards. LOINC has not yet been semantically integrated with computational resources for phenotype analysis. Here, we provide a method for mapping LOINC-encoded laboratory test results transmitted in FHIR standards to Human Phenotype Ontology (HPO) terms. We annotated the medical implications of 2923 commonly used laboratory tests with HPO terms. Using these annotations, our software assesses laboratory test results and converts each result into an HPO term. We validated our approach with EHR data from 15,681 patients with respiratory complaints and identified known biomarkers for asthma. Finally, we provide a freely available SMART on FHIR application that can be used within EHR systems. Our approach allows readily available laboratory tests in EHR to be reused for deep phenotyping and exploits the hierarchical structure of HPO to integrate distinct tests that have comparable medical interpretations for association studies.
AB - Electronic Health Record (EHR) systems typically define laboratory test results using the Laboratory Observation Identifier Names and Codes (LOINC) and can transmit them using Fast Healthcare Interoperability Resource (FHIR) standards. LOINC has not yet been semantically integrated with computational resources for phenotype analysis. Here, we provide a method for mapping LOINC-encoded laboratory test results transmitted in FHIR standards to Human Phenotype Ontology (HPO) terms. We annotated the medical implications of 2923 commonly used laboratory tests with HPO terms. Using these annotations, our software assesses laboratory test results and converts each result into an HPO term. We validated our approach with EHR data from 15,681 patients with respiratory complaints and identified known biomarkers for asthma. Finally, we provide a freely available SMART on FHIR application that can be used within EHR systems. Our approach allows readily available laboratory tests in EHR to be reused for deep phenotyping and exploits the hierarchical structure of HPO to integrate distinct tests that have comparable medical interpretations for association studies.
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U2 - 10.1038/s41746-019-0110-4
DO - 10.1038/s41746-019-0110-4
M3 - Article
AN - SCOPUS:85089606359
SN - 2398-6352
VL - 2
JO - npj Digital Medicine
JF - npj Digital Medicine
IS - 1
M1 - 32
ER -