Australia. Some of the data set(s) used for the analyses described were obtained from Vanderbilt University Medical Center's Synthetic Derivative and BioVU, which are supported by numerous sources: institutional funding, private agencies, and federal grants. These include the National Institutes of Health (NIH)-funded Shared Instrumentation grant S10RR025141 and CTSA grants UL1TR002243, UL1TR000445, and UL1RR024975. Genomic data are also supported by investigator-led projects that include U01HG004798,

Background Electronic health records (EHRs) are increasingly used for clinical and translational research through the creation of phenotype algorithms. Currently, phenotype algorithms are most commonly represented as noncomputable descriptive documents and knowledge artifacts that detail the protocols for querying diagnoses, symptoms, procedures, medications, and/or text-driven medical concepts, and are primarily meant for human comprehension. We present desiderata for developing a computable phenotype representation model (PheRM).Methods A team of clinicians and informaticians reviewed common features for multisite phenotype algorithms published in PheKB.org and existing phenotype representation platforms. We also evaluated well-known diagnostic criteria and clinical decision-making guidelines to encompass a broader category of algorithms.Results We propose 10 desired characteristics for a flexible, computable PheRM: (1) structure clinical data into queryable forms; (2) recommend use of a common data model, but also support customization for the variability and availability of EHR data among sites; (3) support both human-readable and computable representations of phenotype algorithms; (4) implement set operations and relational algebra for modeling phenotype algorithms; (5) represent phenotype criteria with structured rules; (6) support defining temporal relations between events; (7) use standardized terminologies and ontologies, and facilitate reuse of value sets; (8) define representations for text searching and natural language processing; (9) provide interfaces for external software algorithms; and (10) maintain backward compatibility.Conclusion A computable PheRM is needed for true phenotype portability and reliability across different EHR products and healthcare systems. These desiderata are a guide to inform the establishment and evolution of EHR phenotype algorithm authoring platforms and languages.

The task of event coreference resolution plays a critical role in many natural language processing applications such as information extraction, question answering, and topic detection and tracking. In this article, we describe a new class of unsupervised, nonparametric Bayesian models with the purpose of probabilistically inferring coreference clusters of event mentions from a collection of unlabeled documents. In order to infer these clusters, we automatically extract various lexical, syntactic, and semantic features for each event mention from the document collection. Extracting a rich set of features for each event mention allows us to cast event coreference resolution as the task of grouping together the mentions that share the same features (they have the same participating entities, share the same location, happen at the same time, etc.).Some of the most important challenges posed by the resolution of event coreference in an unsupervised way stem from (a) the choice of representing event mentions through a rich set of features and (b) the ability of modeling events described both within the same document and across multiple documents. Our first unsupervised model that addresses these challenges is a generalization of the hierarchical Dirichlet process. This new extension presents the hierarchical Dirichlet process's ability to capture the uncertainty regarding the number of clustering components and, additionally, takes into account any finite number of features associated with each event mention. Furthermore, to overcome some of the limitations of this extension, we devised a new hybrid model, which combines an infinite latent class model with a discrete time series model. The main advantage of this hybrid model stands in its capability to automatically infer the number of features associated with each event mention from data and, at the same time, to perform an automatic selection of the most informative features for the task of event coreference. The evaluation performed for solving both within-and cross-document event coreference shows significant improvements of these models when compared against two baselines for this task.

We provide an efficient solution for mining homelessness and ACE information from EHRs, which can facilitate large clinical and genetic studies of these social determinants of health.

Postmarketing population pharmacokinetic (PK) and pharmacodynamic (PD) studies can be useful to capture patient characteristics affecting PK or PD in real‐world settings. These studies require longitudinally measured dose, outcomes, and covariates in large numbers of patients; however, prospective data collection is cost‐prohibitive. Electronic health records (EHRs) can be an excellent source for such data, but there are challenges, including accurate ascertainment of drug dose. We developed a standardized system to prepare datasets from EHRs for population PK/PD studies. Our system handles a variety of tasks involving data extraction from clinical text using a natural language processing algorithm, data processing, and data building. Applying this system, we performed a fentanyl population PK analysis, resulting in comparable parameter estimates to a prior study. This new system makes the EHR data extraction and preparation process more efficient and accurate and provides a powerful tool to facilitate postmarketing population PK/PD studies using information available in EHRs.