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Design patterns for the development of electronic health record-driven phenotype extraction algorithms.

ABSTRACT: Design patterns, in the context of software development and ontologies, provide generalized approaches and guidance to solving commonly occurring problems, or addressing common situations typically informed by intuition, heuristics and experience. While the biomedical literature contains broad coverage of specific phenotype algorithm implementations, no work to date has attempted to generalize common approaches into design patterns, which may then be distributed to the informatics community to efficiently develop more accurate phenotype algorithms.Using phenotyping algorithms stored in the Phenotype KnowledgeBase (PheKB), we conducted an independent iterative review to identify recurrent elements within the algorithm definitions. We extracted and generalized recurrent elements in these algorithms into candidate patterns. The authors then assessed the candidate patterns for validity by group consensus, and annotated them with attributes.A total of 24 electronic Medical Records and Genomics (eMERGE) phenotypes available in PheKB as of 1/25/2013 were downloaded and reviewed. From these, a total of 21 phenotyping patterns were identified, which are available as an online data supplement.Repeatable patterns within phenotyping algorithms exist, and when codified and cataloged may help to educate both experienced and novice algorithm developers. The dissemination and application of these patterns has the potential to decrease the time to develop algorithms, while improving portability and accuracy.

SUBMITTER: Rasmussen LV

PROVIDER: S-EPMC4194216 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature

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Design patterns for the development of electronic health record-driven phenotype extraction algorithms.

Rasmussen Luke V LV Thompson Will K WK Pacheco Jennifer A JA Kho Abel N AN Carrell David S DS Pathak Jyotishman J Peissig Peggy L PL Tromp Gerard G Denny Joshua C JC Starren Justin B JB

Journal of biomedical informatics 20140621

<h4>Background</h4>Design patterns, in the context of software development and ontologies, provide generalized approaches and guidance to solving commonly occurring problems, or addressing common situations typically informed by intuition, heuristics and experience. While the biomedical literature contains broad coverage of specific phenotype algorithm implementations, no work to date has attempted to generalize common approaches into design patterns, which may then be distributed to the informa ...[more]

PMID: 24960203

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Project description:ObjectiveElectronic health records (EHR) offer medical and pharmacogenomics research unprecedented opportunities to identify and classify patients at risk. EHRs are collections of highly inter-dependent records that include biological, anatomical, physiological, and behavioral observations. They comprise a patient's clinical phenome, where each patient has thousands of date-stamped records distributed across many relational tables. Development of EHR computer-based phenotyping algorithms require time and medical insight from clinical experts, who most often can only review a small patient subset representative of the total EHR records, to identify phenotype features. In this research we evaluate whether relational machine learning (ML) using inductive logic programming (ILP) can contribute to addressing these issues as a viable approach for EHR-based phenotyping.MethodsTwo relational learning ILP approaches and three well-known WEKA (Waikato Environment for Knowledge Analysis) implementations of non-relational approaches (PART, J48, and JRIP) were used to develop models for nine phenotypes. International Classification of Diseases, Ninth Revision (ICD-9) coded EHR data were used to select training cohorts for the development of each phenotypic model. Accuracy, precision, recall, F-Measure, and Area Under the Receiver Operating Characteristic (AUROC) curve statistics were measured for each phenotypic model based on independent manually verified test cohorts. A two-sided binomial distribution test (sign test) compared the five ML approaches across phenotypes for statistical significance.ResultsWe developed an approach to automatically label training examples using ICD-9 diagnosis codes for the ML approaches being evaluated. Nine phenotypic models for each ML approach were evaluated, resulting in better overall model performance in AUROC using ILP when compared to PART (p=0.039), J48 (p=0.003) and JRIP (p=0.003).DiscussionILP has the potential to improve phenotyping by independently delivering clinically expert interpretable rules for phenotype definitions, or intuitive phenotypes to assist experts.ConclusionRelational learning using ILP offers a viable approach to EHR-driven phenotyping.

Project description:Introduction:Electronic health record (EHR)-driven phenotyping is a critical first step in generating biomedical knowledge from EHR data. Despite recent progress, current phenotyping approaches are manual, time-consuming, error-prone, and platform-specific. This results in duplication of effort and highly variable results across systems and institutions, and is not scalable or portable. In this work, we investigate how the nascent Clinical Quality Language (CQL) can address these issues and enable high-throughput, cross-platform phenotyping. Methods:We selected a clinically validated heart failure (HF) phenotype definition and translated it into CQL, then developed a CQL execution engine to integrate with the Observational Health Data Sciences and Informatics (OHDSI) platform. We executed the phenotype definition at two large academic medical centers, Northwestern Medicine and Weill Cornell Medicine, and conducted results verification (n = 100) to determine precision and recall. We additionally executed the same phenotype definition against two different data platforms, OHDSI and Fast Healthcare Interoperability Resources (FHIR), using the same underlying dataset and compared the results. Results:CQL is expressive enough to represent the HF phenotype definition, including Boolean and aggregate operators, and temporal relationships between data elements. The language design also enabled the implementation of a custom execution engine with relative ease, and results verification at both sites revealed that precision and recall were both 100%. Cross-platform execution resulted in identical patient cohorts generated by both data platforms. Conclusions:CQL supports the representation of arbitrarily complex phenotype definitions, and our execution engine implementation demonstrated cross-platform execution against two widely used clinical data platforms. The language thus has the potential to help address current limitations with portability in EHR-driven phenotyping and scale in learning health systems.

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Design patterns for the development of electronic health record-driven phenotype extraction algorithms.

Publications

Design patterns for the development of electronic health record-driven phenotype extraction algorithms.

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