Assessment of structured data elements for social risk factors.

OBJECTIVES: Computable social risk factor phenotypes derived from routinely collected structured electronic health record (EHR) or health information exchange (HIE) data may represent a feasible and robust approach to measuring social factors. This study convened an expert panel to identify and assess the quality of individual EHR and HIE structured data elements that could be used as components in future computable social risk factor phenotypes. STUDY DESIGN: Technical expert panel. METHODS: A 2-round Delphi technique included 17 experts with an in-depth knowledge of available EHR and/or HIE data. The first-round identification sessions followed a nominal group approach to generate candidate data elements that may relate to socioeconomics, cultural context, social relationships, and community context. In the second-round survey, panelists rated each data element according to overall data quality and likelihood of systematic differences in quality across populations (ie, bias). RESULTS: Panelists identified a total of 89 structured data elements. About half of the data elements (n = 45) were related to socioeconomic characteristics. The panelists identified a diverse set of data elements. Elements used in reimbursement-related processes were generally rated as higher quality. Panelists noted that several data elements may be subject to implicit bias or reflect biased systems of care, which may limit their utility in measuring social factors. CONCLUSIONS: Routinely collected structured data within EHR and HIE systems may reflect patient social risk factors. Identifying and assessing available data elements serves as a foundational step toward developing future computable social factor phenotypes.

Synergies between centralized and federated approaches to data quality: a report from the national COVID cohort collaborative.

OBJECTIVE: In response to COVID-19, the informatics community united to aggregate as much clinical data as possible to characterize this new disease and reduce its impact through collaborative analytics. The National COVID Cohort Collaborative (N3C) is now the largest publicly available HIPAA limited dataset in US history with over 6.4 million patients and is a testament to a partnership of over 100 organizations. MATERIALS AND METHODS: We developed a pipeline for ingesting, harmonizing, and centralizing data from 56 contributing data partners using 4 federated Common Data Models. N3C data quality (DQ) review involves both automated and manual procedures. In the process, several DQ heuristics were discovered in our centralized context, both within the pipeline and during downstream project-based analysis. Feedback to the sites led to many local and centralized DQ improvements. RESULTS: Beyond well-recognized DQ findings, we discovered 15 heuristics relating to source Common Data Model conformance, demographics, COVID tests, conditions, encounters, measurements, observations, coding completeness, and fitness for use. Of 56 sites, 37 sites (66%) demonstrated issues through these heuristics. These 37 sites demonstrated improvement after receiving feedback. DISCUSSION: We encountered site-to-site differences in DQ which would have been challenging to discover using federated checks alone. We have demonstrated that centralized DQ benchmarking reveals unique opportunities for DQ improvement that will support improved research analytics locally and in aggregate. CONCLUSION: By combining rapid, continual assessment of DQ with a large volume of multisite data, it is possible to support more nuanced scientific questions with the scale and rigor that they require.

Extracting social determinants of health from electronic health records using natural language processing: a systematic review.

OBJECTIVE: Social determinants of health (SDoH) are nonclinical dispositions that impact patient health risks and clinical outcomes. Leveraging SDoH in clinical decision-making can potentially improve diagnosis, treatment planning, and patient outcomes. Despite increased interest in capturing SDoH in electronic health records (EHRs), such information is typically locked in unstructured clinical notes. Natural language processing (NLP) is the key technology to extract SDoH information from clinical text and expand its utility in patient care and research. This article presents a systematic review of the state-of-the-art NLP approaches and tools that focus on identifying and extracting SDoH data from unstructured clinical text in EHRs. MATERIALS AND METHODS: A broad literature search was conducted in February 2021 using 3 scholarly databases (ACL Anthology, PubMed, and Scopus) following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A total of 6402 publications were initially identified, and after applying the study inclusion criteria, 82 publications were selected for the final review. RESULTS: Smoking status (n = 27), substance use (n = 21), homelessness (n = 20), and alcohol use (n = 15) are the most frequently studied SDoH categories. Homelessness (n = 7) and other less-studied SDoH (eg, education, financial problems, social isolation and support, family problems) are mostly identified using rule-based approaches. In contrast, machine learning approaches are popular for identifying smoking status (n = 13), substance use (n = 9), and alcohol use (n = 9). CONCLUSION: NLP offers significant potential to extract SDoH data from narrative clinical notes, which in turn can aid in the development of screening tools, risk prediction models, and clinical decision support systems.

A Comparative Analysis of the Respiratory Subscore of the Sequential Organ Failure Assessment Scoring System.

Rationale: The Sequential Organ Failure Assessment (SOFA) tool is a commonly used measure of illness severity. Calculation of the respiratory subscore of SOFA is frequently limited by missing arterial oxygen pressure (PaO2) data. Although missing PaO2 data are commonly replaced with normal values, the performance of different methods of substituting PaO2 for SOFA calculation is unclear. Objectives: The study objective was to compare the performance of different substitution strategies for missing PaO2 data for SOFA score calculation. Methods: This retrospective cohort study was performed using the Weill Cornell Critical Care Database for Advanced Research from a tertiary care hospital in the United States. All adult patients admitted to an intensive care unit (ICU) from 2011 to 2019 with an available respiratory SOFA score were included. We analyzed the availability of the PaO2/fraction of inspired oxygen (FiO2) ratio on the first day of ICU admission. In those without a PaO2/FiO2 ratio available, the ratio of oxygen saturation as measured by pulse oximetry to FiO2 was used to calculate a respiratory SOFA subscore according to four methods (linear substitution [Rice], nonlinear substitution [Severinghaus], modified respiratory SOFA, and multiple imputation by chained equations [MICE]) as well as the missing-as-normal technique. We then compared how well the different total SOFA scores discriminated in-hospital mortality. We performed several subgroup and sensitivity analyses. Results: We identified 35,260 unique visits, of which 9,172 included predominant respiratory failure. PaO2 data were available for 14,939 (47%). The area under the receiver operating characteristic curve for each substitution technique for discriminating in-hospital mortality was higher than that for the missing-as-normal technique (0.78 [0.77-0.79]) in all analyses (modified, 0.80 [0.79-0.81]; Rice, 0.80 [0.79-0.81]; Severinghaus, 0.80 [0.79-0.81]; and MICE, 0.80 [0.79-0.81]) (P < 0.01). Each substitution method had a higher accuracy for discriminating in-hospital mortality (MICE, 0.67; Rice, 0.67; modified, 0.66; and Severinghaus, 0.66) than the missing-as-normal technique. Model calibration for in-hospital mortality was less precise for the missing-as-normal technique than for the other substitution techniques at the lower range of SOFA and among the subgroups. Conclusions: Using physiologic and statistical substitution methods improved the total SOFA score's ability to discriminate mortality compared with the missing-as-normal technique. Treating missing data as normal may result in underreporting the severity of illness compared with using substitution. The simplicity of a direct oxygen saturation as measured by pulse oximetry/FiO2 ratio-modified SOFA technique makes it an attractive choice for electronic health record-based research. This knowledge can inform comparisons of severity of illness across studies that used different techniques.

Understanding enterprise data warehouses to support clinical and translational research.

OBJECTIVE: Among National Institutes of Health Clinical and Translational Science Award (CTSA) hubs, adoption of electronic data warehouses for research (EDW4R) containing data from electronic health record systems is nearly ubiquitous. Although benefits of EDW4R include more effective, efficient support of scientists, little is known about how CTSA hubs have implemented EDW4R services. The goal of this qualitative study was to understand the ways in which CTSA hubs have operationalized EDW4R to support clinical and translational researchers. MATERIALS AND METHODS: After conducting semistructured interviews with informatics leaders from 20 CTSA hubs, we performed a directed content analysis of interview notes informed by naturalistic inquiry. RESULTS: We identified 12 themes: organization and data; oversight and governance; data access request process; data access modalities; data access for users with different skill sets; engagement, communication, and literacy; service management coordinated with enterprise information technology; service management coordinated within a CTSA hub; service management coordinated between informatics and biostatistics; funding approaches; performance metrics; and future trends and current technology challenges. DISCUSSION: This study is a step in developing an improved understanding and creating a common vocabulary about EDW4R operations across institutions. Findings indicate an opportunity for establishing best practices for EDW4R operations in academic medicine. Such guidance could reduce the costs associated with developing an EDW4R by establishing a clear roadmap and maturity path for institutions to follow. CONCLUSIONS: CTSA hubs described varying approaches to EDW4R operations that may assist other institutions in better serving investigators with electronic patient data.

Challenges, alternatives, and paths to sustainability for health information exchange efforts.

Health information exchange (HIE) is a promising approach to improving the cost and quality of healthcare. We sought to identify the strengths and weaknesses of organizational models to achieve exchange, and what can be done to ensure the sustainability and effectiveness of exchange efforts. We interviewed state and national health informatics policy experts (n = 17). Data were collected as part of an evaluation of the Health Care Efficiency and Affordability Law for New Yorkers (HEAL NY) program and included respondents from both the private and public sectors. Data were analyzed using a general inductive and comparative approach with open coding of themes. Interviewees generally viewed HIE as a public or societal good to be valued. However, they identified challenges with the regional health information organization (RHIO) model of facilitating exchange including: economics, organizational issues, and geography. RHIOs were contrasted against alternative methods of exchange such as Direct, enterprise HIE, and vendor-mediated exchange. HIE is a difficult undertaking due to political and economic reasons. Alternatives to the RHIO model have features that may be more attractive to participants, but may be of less public benefit. Using states as intermediaries and mandating exchange under public health law may avoid the challenges facing exchange efforts. Moving forward, policies will have to address the shortcomings of each HIE model to ensure information is effectively shared between providers to maximize health benefits.