Semantic Integration of Clinical Laboratory Tests from Electronic Health Records for Deep Phenotyping and Biomarker Discovery

Zhang, X. A.; Yates, A.; Vasilevsky, N.; Gourdine, J.; Carmody, L. C.; Danis, D.; Joachimiak, M. P.; Ravanmehr, V.; Pfaff, E. R.; Champion, J.; Robasky, K.; Xu, H.; Fecho, K.; Walton, N. A.; Zhu, R.; Ramsdill, J.; Mungall, C.; Kohler, S.; Haendel, M. A.; McDonald, C.; Vreeman, D. J.; Peden, D. B.; Chute, C. G.; Robinson, P. N.

doi:10.1101/519231

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bioRxiv · 10.1101/519231

Semantic Integration of Clinical Laboratory Tests from Electronic Health Records for Deep Phenotyping and Biomarker Discovery

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Abstract

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 the Human Phenotype Ontology (HPO) terms. We annotated the medical implications of 2421 commonly used laboratory tests with HPO terms. Using these annotations, a software assesses laboratory test results and converts each 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 reusing readily available laboratory tests in EHR for deep phenotyping and using the hierarchical structure of HPO for association studies with medical outcomes and genomics.\n\nOne Sentence SummaryWe present an approach to semantically integrating LOINC-encoded laboratory data with the Human Phenotype Ontology and show that the integrated LOINC data can be used to identify biomarkers for asthma from electronic health record data.

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Zhang, X. A., Yates, A., Vasilevsky, N., Gourdine, J., Carmody, L. C., Danis, D., Joachimiak, M. P., Ravanmehr, V., Pfaff, E. R., Champion, J., Robasky, K., Xu, H., Fecho, K., Walton, N. A., Zhu, R., Ramsdill, J., Mungall, C., Kohler, S., Haendel, M. A., McDonald, C., Vreeman, D. J., Peden, D. B., Chute, C. G., Robinson, P. N.. 2019-01-13. Semantic Integration of Clinical Laboratory Tests from Electronic Health Records for Deep Phenotyping and Biomarker Discovery. https://doi.org/10.1101/519231

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