title: An integrated, ontology-driven approach to constructing observational databases for research.
abstract: The electronic health record (EHR) contains a diverse set of clinical observations that are captured as part of routine care, but the incomplete, inconsistent, and sometimes incorrect nature of clinical data poses significant impediments for its secondary use in retrospective studies or comparative effectiveness research. In this work, we describe an ontology-driven approach for extracting and analyzing data from the patient record in a longitudinal and continuous manner. We demonstrate how the ontology helps enforce consistent data representation, integrates phenotypes generated through analyses of available clinical data sources, and facilitates subsequent studies to identify clinical predictors for an outcome of interest. Development and evaluation of our approach are described in the context of studying factors that influence intracranial aneurysm (ICA) growth and rupture. We report our experiences in capturing information on 78 individuals with a total of 120 aneurysms. Two example applications related to assessing the relationship between aneurysm size, growth, gene expression modules, and rupture are described. Our work highlights the challenges with respect to data quality, workflow, and analysis of data and its implications toward a learning health system paradigm.
authors.affiliation: Department of Radiological Sciences, UCLA David Geffen School of Medicine, Los Angeles, CA, United States. Electronic address: willhsu@mii.ucla.edu.
authors.forename: William
authors.initials: W
authors.lastname: Hsu
authors.affiliation: Department of Radiological Sciences, UCLA David Geffen School of Medicine, Los Angeles, CA, United States; Department of Neurosurgery, UCLA David Geffen School of Medicine, Los Angeles, CA, United States.
authors.forename: Nestor R
authors.initials: NR
authors.lastname: Gonzalez
authors.affiliation: Department of Radiological Sciences, UCLA David Geffen School of Medicine, Los Angeles, CA, United States.
authors.forename: Aichi
authors.initials: A
authors.lastname: Chien
authors.affiliation: Department of Radiological Sciences, UCLA David Geffen School of Medicine, Los Angeles, CA, United States.
authors.forename: J
authors.initials: J
authors.lastname: Pablo Villablanca
authors.affiliation: Department of Human Genetics, UCLA David Geffen School of Medicine, Los Angeles, CA, United States.
authors.forename: Päivi
authors.initials: P
authors.lastname: Pajukanta
authors.affiliation: Department of Radiological Sciences, UCLA David Geffen School of Medicine, Los Angeles, CA, United States.
authors.forename: Fernando
authors.initials: F
authors.lastname: Viñuela
authors.affiliation: Department of Radiological Sciences, UCLA David Geffen School of Medicine, Los Angeles, CA, United States.
authors.forename: Alex A T
authors.initials: AA
authors.lastname: Bui
mesh_terms: D017542:Aneurysm, Ruptured / Q000145:classification*; D035843:Biomedical Research / Q000379:methods / Q000458:organization & administration; D000068598:Data Accuracy; D057225:Data Mining / Q000379:methods*; D003628:Database Management Systems; D016208:Databases, Factual; D057286:Electronic Health Records / Q000458:organization & administration*; D006801:Humans; D002532:Intracranial Aneurysm / Q000145:classification*; D062527:Meaningful Use; D009323:Natural Language Processing; D018511:Systems Integration; D014584:User-Computer Interface; D018875:Vocabulary, Controlled
keywords: Biomedical ontology; Data extraction; Database; Image analysis; Intracranial aneurysm; Retrospective study
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