Dataset Information

MedExtractR: A targeted, customizable approach to medication extraction from electronic health records.

ABSTRACT:

Objective

We developed medExtractR, a natural language processing system to extract medication information from clinical notes. Using a targeted approach, medExtractR focuses on individual drugs to facilitate creation of medication-specific research datasets from electronic health records.

Materials and methods

Written using the R programming language, medExtractR combines lexicon dictionaries and regular expressions to identify relevant medication entities (eg, drug name, strength, frequency). MedExtractR was developed on notes from Vanderbilt University Medical Center, using medications prescribed with varying complexity. We evaluated medExtractR and compared it with 3 existing systems: MedEx, MedXN, and CLAMP (Clinical Language Annotation, Modeling, and Processing). We also demonstrated how medExtractR can be easily tuned for better performance on an outside dataset using the MIMIC-III (Medical Information Mart for Intensive Care III) database.

Results

On 50 test notes per development drug and 110 test notes for an additional drug, medExtractR achieved high overall performance (F-measures >0.95), exceeding performance of the 3 existing systems across all drugs. MedExtractR achieved the highest F-measure for each individual entity, except drug name and dose amount for allopurinol. With tuning and customization, medExtractR achieved F-measures >0.90 in the MIMIC-III dataset.

Discussion

The medExtractR system successfully extracted entities for medications of interest. High performance in entity-level extraction provides a strong foundation for developing robust research datasets for pharmacological research. When working with new datasets, medExtractR should be tuned on a small sample of notes before being broadly applied.

Conclusions

The medExtractR system achieved high performance extracting specific medications from clinical text, leading to higher-quality research datasets for drug-related studies than some existing general-purpose medication extraction tools.

SUBMITTER: Weeks HL

PROVIDER: S-EPMC7025369 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

medExtractR: A targeted, customizable approach to medication extraction from electronic health records.

Weeks Hannah L HL Beck Cole C McNeer Elizabeth E Williams Michael L ML Bejan Cosmin A CA Denny Joshua C JC Choi Leena L

Journal of the American Medical Informatics Association : JAMIA 20200301 3

<h4>Objective</h4>We developed medExtractR, a natural language processing system to extract medication information from clinical notes. Using a targeted approach, medExtractR focuses on individual drugs to facilitate creation of medication-specific research datasets from electronic health records.<h4>Materials and methods</h4>Written using the R programming language, medExtractR combines lexicon dictionaries and regular expressions to identify relevant medication entities (eg, drug name, strengt ...[more]

PMID: 31943012

Similar Datasets

Project description:BackgroundMulti-center electronic health records (EHR) can support quality improvement initiatives and comparative effectiveness research in stroke care. However, limitations of EHR-based research include challenges in abstracting key clinical variables from non-structured data at scale. This is further compounded by missing data. Here we develop a natural language processing (NLP) model that automatically reads EHR notes to determine the NIH stroke scale (NIHSS) score of patients with acute stroke.MethodsThe study included notes from acute stroke patients (>= 18 years) admitted to the Massachusetts General Hospital (MGH) (2015-2022). The MGH data were divided into training (70%) and hold-out test (30%) sets. A two-stage model was developed to predict the admission NIHSS. A linear model with the least absolute shrinkage and selection operator (LASSO) was trained within the training set. For notes in the test set where the NIHSS was documented, the scores were extracted using regular expressions (stage 1), for notes where NIHSS was not documented, LASSO was used for prediction (stage 2). The reference standard for NIHSS was obtained from Get With The Guidelines Stroke Registry. The two-stage model was tested on the hold-out test set and validated in the MIMIC-III dataset (Medical Information Mart for Intensive Care-MIMIC III 2001-2012) v1.4, using root mean squared error (RMSE) and Spearman correlation (SC).ResultsWe included 4,163 patients (MGH = 3,876; MIMIC = 287); average age of 69 [SD 15] years; 53% male, and 72% white. 90% patients had ischemic stroke and 10% hemorrhagic stroke. The two-stage model achieved a RMSE [95% CI] of 3.13 [2.86-3.41] (SC = 0.90 [0.88-0. 91]) in the MGH hold-out test set and 2.01 [1.58-2.38] (SC = 0.96 [0.94-0.97]) in the MIMIC validation set.ConclusionsThe automatic NLP-based model can enable large-scale stroke severity phenotyping from EHR and therefore support real-world quality improvement and comparative effectiveness studies in stroke.

Project description:BACKGROUND:Primary care needs to be patient-centered, integrated, and interprofessional to help patients with complex needs manage the burden of medication-related problems. Considering the growing problem of polypharmacy, increasing attention has been paid to how and when medication-related decisions should be coordinated across multidisciplinary care teams. Improved knowledge on how integrated electronic health records (EHRs) can support interprofessional shared decision-making for medication therapy management is necessary to continue improving patient care. OBJECTIVE:The objective of our study was to examine how physicians and pharmacists understand and communicate patient-focused medication information with each other and how this knowledge can influence the design of EHRs. METHODS:This study is part of a broader cross-Canada study between patients and health care providers around how medication-related decisions are made and communicated. We visited community pharmacies, team-based primary care clinics, and independent-practice family physician clinics throughout Ontario, Nova Scotia, Alberta, and Quebec. Research assistants conducted semistructured interviews with physicians and pharmacists. A modified version of the Multidisciplinary Framework Method was used to analyze the data. RESULTS:We collected data from 19 pharmacies and 9 medical clinics and identified 6 main themes from 34 health care professionals. First, Interprofessional Shared Decision-Making was not occurring and clinicians made decisions based on their understanding of the patient. Physicians and pharmacists reported indirect Communication, incomplete Information specifically missing insight into indication and adherence, and misaligned Processes of Care that were further compounded by EHRs that are not designed to facilitate collaboration. Scope of Practice examined professional and workplace boundaries for pharmacists and physicians that were internally and externally imposed. Physicians decided on the degree of the Physician-Pharmacist Relationship, often predicated by colocation. CONCLUSIONS:We observed limited communication and collaboration between primary care providers and pharmacists when managing medications. Pharmacists were missing key information around reason for use, and physicians required accurate information around adherence. EHRs are a potential tool to help clinicians communicate information to resolve this issue. EHRs need to be designed to facilitate interprofessional medication management so that pharmacists and physicians can move beyond task-based work toward a collaborative approach.

Project description:BackgroundIdentifying implausible clinical observations (e.g., laboratory test and vital sign values) in Electronic Health Record (EHR) data using rule-based procedures is challenging. Anomaly/outlier detection methods can be applied as an alternative algorithmic approach to flagging such implausible values in EHRs.MethodsThe primary objectives of this research were to develop and test an unsupervised clustering-based anomaly/outlier detection approach for detecting implausible observations in EHR data as an alternative algorithmic solution to the existing procedures. Our approach is built upon two underlying hypotheses that, (i) when there are large number of observations, implausible records should be sparse, and therefore (ii) if these data are clustered properly, clusters with sparse populations should represent implausible observations. To test these hypotheses, we applied an unsupervised clustering algorithm to EHR observation data on 50 laboratory tests from Partners HealthCare. We tested different specifications of the clustering approach and computed confusion matrix indices against a set of silver-standard plausibility thresholds. We compared the results from the proposed approach with conventional anomaly detection (CAD) approaches, including standard deviation and Mahalanobis distance.ResultsWe found that the clustering approach produced results with exceptional specificity and high sensitivity. Compared with the conventional anomaly detection approaches, our proposed clustering approach resulted in significantly smaller number of false positive cases.ConclusionOur contributions include (i) a clustering approach for identifying implausible EHR observations, (ii) evidence that implausible observations are sparse in EHR laboratory test results, (iii) a parallel implementation of the clustering approach on i2b2 star schema, and (3) a set of silver-standard plausibility thresholds for 50 laboratory tests that can be used in other studies for validation. The proposed algorithmic solution can augment human decisions to improve data quality. Therefore, a workflow is needed to complement the algorithm's job and initiate necessary actions that need to be taken in order to improve the quality of data.