Mapping Clinical Documents to the Logical Observation Identifiers, Names and Codes (LOINC) Document Ontology using Electronic Health Record Systems Structured Metadata

As Electronic Health Record (EHR) systems increase in usage, organizations struggle to maintain and categorize clinical documentation so it can be used for clinical care and research. While prior research has often employed natural language processing techniques to categorize free text documents, there are shortcomings relative to computational scalability and the lack of key metadata within notes' text. This study presents a framework that can allow institutions to map their notes to the LOINC document ontology using a Bag of Words approach. After preliminary manual value- set mapping, an automated pipeline that leverages key dimensions of metadata from structured EHR fields aligns the notes with the dimensions of the document ontology. This framework resulted in 73.4% coverage of EHR documents, while also mapping 132 million notes in less than 2 hours; an order of magnitude more efficient than NLP based methods.

Avenues for Strengthening PCORnet's Capacity to Advance Patient-Centered Economic Outcomes in Patient-Centered Outcomes Research (PCOR)

PCORnet, the National Patient-Centered Clinical Research Network, provides the ability to conduct prospective and observational pragmatic research by leveraging standardized, curated electronic health records data together with patient and stakeholder engagement. PCORnet is funded by the Patient-Centered Outcomes Research Institute (PCORI) and is composed of 8 Clinical Research Networks that incorporate at total of 79 health system "sites." As the network developed, linkage to commercial health plans, federal insurance claims, disease registries, and other data resources demonstrated the value in extending the networks infrastructure to provide a more complete representation of patient's health and lived experiences. Initially, PCORnet studies avoided direct economic comparative effectiveness as a topic. However, PCORI's authorizing law was amended in 2019 to allow studies to incorporate patient-centered economic outcomes in primary research aims. With PCORI's expanded scope and PCORnet's phase 3 beginning in January 2022, there are opportunities to strengthen the network's ability to support economic patient-centered outcomes research. This commentary will discuss approaches that have been incorporated to date by the network and point to opportunities for the network to incorporate economic variables for analysis, informed by patient and stakeholder perspectives. Topics addressed include: (1) data linkage infrastructure; (2) commercial health plan partnerships; (3) Medicare and Medicaid linkage; (4) health system billing-based benchmarking; (5) area-level measures; (6) individual-level measures; (7) pharmacy benefits and retail pharmacy data; and (8) the importance of transparency and engagement while addressing the biases inherent in linking real-world data sources.

Disruption in Blood Pressure Control With the COVID-19 Pandemic: The PCORnet Blood Pressure Control Laboratory

OBJECTIVE

To explore trends in blood pressure (BP) control before and during the COVID-19 pandemic.

PATIENTS AND METHODS

Health systems participating in the National Patient-Centered Clinical Research Network (PCORnet) Blood Pressure Control Laboratory Surveillance System responded to data queries, producing 9 BP control metrics. Averages of the BP control metrics (weighted by numbers of observations in each health system) were calculated and compared between two 1-year measurement periods (January 1, 2019, through December 31, 2019, and January 1, 2020, through December 31, 2020).

RESULTS

Among 1,770,547 hypertensive persons in 2019, BP control to <140/<90 mm Hg varied across 24 health systems (range, 46%-74%). Reduced BP control occurred in most health systems with onset of the COVID-19 pandemic; the weighted average BP control was 60.5% in 2019 and 53.3% in 2020. Reductions were also evident for BP control to <130/<80 mm Hg (29.9% in 2019 and 25.4% in 2020) and improvement in BP (reduction of 10 mm Hg in systolic BP or achievement of systolic BP <140 mm Hg; 29.7% in 2019 and 23.8% in 2020). Two BP control process metrics exhibited pandemic-associated disruption: repeat visit in 4 weeks after a visit with uncontrolled hypertension (36.7% in 2019 and 31.7% in 2020) and prescription of fixed-dose combination medications among those with 2 or more drug classes (24.6% in 2019 and 21.5% in 2020).

CONCLUSION

BP control decreased substantially during the COVID-19 pandemic, with a corresponding reduction in follow-up health care visits among persons with uncontrolled hypertension. It is unclear whether the observed decline in BP control during the pandemic will contribute to future cardiovascular events.

Seasonal variation in blood pressure control across US health systems

OBJECTIVE

We aimed to characterize seasonal variation in US population-based blood pressure (BP) control and BP-related metrics and evaluate the association between outdoor temperature and BP control variation.

METHODS

We queried electronic health records (EHRs) from 26 health systems, representing 21 states, to summarize BP metrics by quarters of 12-month periods from January 2017 to March 2020. Patients with at least one ambulatory visit during the measurement period and a hypertension diagnosis during the first 6 months or prior to the measurement period were included. Changes in BP control, BP improvement, medication intensification, average SBP reduction after medication intensification across quarters and association with outdoor temperature were analyzed using weighted generalized linear models with repeated measures.

RESULTS

Among 1 818 041 people with hypertension, the majority were more than 65 years of age (52.2%), female (52.1%), white non-Hispanic (69.8%) and had stage 1/2 hypertension (64.8%). Overall, BP control and process metrics were highest in quarters 2 and 3, and lowest in quarters 1 and 4. Quarter 2 had the highest percentage of improved BP (31.95 ± 0.90%) and average SBP reduction after medication intensification (16 ± 0.23 mmHg). Quarter 3 had the highest percentage of BP controlled (62.25 ± 2.55%) and lowest with medication intensification (9.73 ± 0.60%). Results were largely consistent in adjusted models. Average temperature was associated with BP control metrics in unadjusted models, but associations were attenuated following adjustment.

CONCLUSION

In this large, national, EHR-based study, BP control and BP-related process metrics improved during spring/summer months, but outdoor temperature was not associated with performance following adjustment for potential confounders.

Preoperative Depression Status and 5 Year Metabolic and Bariatric Surgery Outcomes in the PCORnet Bariatric Study Cohort

OBJECTIVE

To examine whether depression status before metabolic and bariatric surgery (MBS) influenced 5-year weight loss, diabetes, and safety/utilization outcomes in the PCORnet Bariatric Study.

SUMMARY OF BACKGROUND DATA

Research on the impact of depression on MBS outcomes is inconsistent with few large, long-term studies.

METHODS

Data were extracted from 23 health systems on 36,871 patients who underwent sleeve gastrectomy (SG; n=16,158) or gastric bypass (RYGB; n=20,713) from 2005-2015. Patients with and without a depression diagnosis in the year before MBS were evaluated for % total weight loss (%TWL), diabetes outcomes, and postsurgical safety/utilization (reoperations, revisions, endoscopy, hospitalizations, mortality) at 1, 3, and 5 years after MBS.

RESULTS

27.1% of SG and 33.0% of RYGB patients had preoperative depression, and they had more medical and psychiatric comorbidities than those without depression. At 5 years of follow-up, those with depression, versus those without depression, had slightly less %TWL after RYGB, but not after SG (between group difference = 0.42%TWL, P = 0.04). However, patients with depression had slightly larger HbA1c improvements after RYGB but not after SG (between group difference = - 0.19, P = 0.04). Baseline depression did not moderate diabetes remission or relapse, reoperations, revision, or mortality across operations; however, baseline depression did moderate the risk of endoscopy and repeat hospitalization across RYGB versus SG.

CONCLUSIONS

Patients with depression undergoing RYGB and SG had similar weight loss, diabetes, and safety/utilization outcomes to those without depression. The effects of depression were clinically small compared to the choice of operation.

Community risks for SARS-CoV-2 infection among fully vaccinated US adults by rurality: A retrospective cohort study from the National COVID Cohort Collaborative

BACKGROUND

While COVID-19 vaccines reduce adverse outcomes, post-vaccination SARS-CoV-2 infection remains problematic. We sought to identify community factors impacting risk for breakthrough infections (BTI) among fully vaccinated persons by rurality.

METHODS

We conducted a retrospective cohort study of US adults sampled between January 1 and December 20, 2021, from the National COVID Cohort Collaborative (N3C). Using Kaplan-Meier and Cox-Proportional Hazards models adjusted for demographic differences and comorbid conditions, we assessed impact of rurality, county vaccine hesitancy, and county vaccination rates on risk of BTI over 180 days following two mRNA COVID-19 vaccinations between January 1 and September 21, 2021. Additionally, Cox Proportional Hazards models assessed the risk of infection among adults without documented vaccinations. We secondarily assessed the odds of hospitalization and adverse COVID-19 events based on vaccination status using multivariable logistic regression during the study period.

RESULTS

Our study population included 566,128 vaccinated and 1,724,546 adults without documented vaccination. Among vaccinated persons, rurality was associated with an increased risk of BTI (adjusted hazard ratio [aHR] 1.53, 95% confidence interval [CI] 1.42-1.64, for urban-adjacent rural and 1.65, 1.42-1.91, for nonurban-adjacent rural) compared to urban dwellers. Compared to low vaccine-hesitant counties, higher risks of BTI were associated with medium (1.07, 1.02-1.12) and high (1.33, 1.23-1.43) vaccine-hesitant counties. Compared to counties with high vaccination rates, a higher risk of BTI was associated with dwelling in counties with low vaccination rates (1.34, 1.27-1.43) but not medium vaccination rates (1.00, 0.95-1.07). Community factors were also associated with higher odds of SARS-CoV-2 infection among persons without a documented vaccination. Vaccinated persons with SARS-CoV-2 infection during the study period had significantly lower odds of hospitalization and adverse events across all geographic areas and community exposures.

CONCLUSIONS

Our findings suggest that community factors are associated with an increased risk of BTI, particularly in rural areas and counties with high vaccine hesitancy. Communities, such as those in rural and disproportionately vaccine hesitant areas, and certain groups at high risk for adverse breakthrough events, including immunosuppressed/compromised persons, should continue to receive public health focus, targeted interventions, and consistent guidance to help manage community spread as vaccination protection wanes.

Higher hospitalization and mortality rates among SARS-CoV-2-infected persons in rural America

PURPOSE

Rural communities are among the most underserved and resource-scarce populations in the United States. However, there are limited data on COVID-19 outcomes in rural America. This study aims to compare hospitalization rates and inpatient mortality among SARS-CoV-2-infected persons stratified by residential rurality.

METHODS

This retrospective cohort study from the National COVID Cohort Collaborative (N3C) assesses 1,033,229 patients from 44 US hospital systems diagnosed with SARS-CoV-2 infection between January 2020 and June 2021. Primary outcomes were hospitalization and all-cause inpatient mortality. Secondary outcomes were utilization of supplemental oxygen, invasive mechanical ventilation, vasopressor support, extracorporeal membrane oxygenation, and incidence of major adverse cardiovascular events or hospital readmission. The analytic approach estimates 90-day survival in hospitalized patients and associations between rurality, hospitalization, and inpatient adverse events while controlling for major risk factors using Kaplan-Meier survival estimates and mixed-effects logistic regression.

FINDINGS

Of 1,033,229 diagnosed COVID-19 patients included, 186,882 required hospitalization. After adjusting for demographic differences and comorbidities, urban-adjacent and nonurban-adjacent rural dwellers with COVID-19 were more likely to be hospitalized (adjusted odds ratio [aOR] 1.18, 95% confidence interval [CI], 1.16-1.21 and aOR 1.29, CI 1.24-1.1.34) and to die or be transferred to hospice (aOR 1.36, CI 1.29-1.43 and 1.37, CI 1.26-1.50), respectively. All secondary outcomes were more likely among rural patients.

CONCLUSIONS

Hospitalization, inpatient mortality, and other adverse outcomes are higher among rural persons with COVID-19, even after adjusting for demographic differences and comorbidities. Further research is needed to understand the factors that drive health disparities in rural populations.

COVID-19 patients with documented alcohol use disorder or alcohol-related complications are more likely to be hospitalized and have higher all-cause mortality

BACKGROUND

Coronavirus Disease 2019 (COVID-19) has affected every country globally, with hundreds of millions of people infected with the SARS-CoV-2 virus and over 6 million deaths to date. It is unknown how alcohol use disorder (AUD) affects the severity and mortality of COVID-19. AUD is known to increase the severity and mortality of bacterial pneumonia and the risk of developing acute respiratory distress syndrome. Our objective is to determine whether individuals with AUD have increased severity and mortality from COVID-19.

METHODS

We utilized a retrospective cohort study of inpatients and outpatients from 44 centers participating in the National COVID Cohort Collaborative. All were adult COVID-19 patients with and without documented AUDs.

RESULTS

We identified 25,583 COVID-19 patients with an AUD and 1,309,445 without. In unadjusted comparisons, those with AUD had higher odds of hospitalization (odds ratio [OR] 2.00, 95% confidence interval [CI] 1.94 to 2.06, p < 0.001). After adjustment for age, sex, race/ethnicity, smoking, body mass index, and comorbidities, individuals with an AUD still had higher odds of requiring hospitalization (adjusted OR [aOR] 1.51, CI 1.46 to 1.56, p < 0.001). In unadjusted comparisons, individuals with AUD had higher odds of all-cause mortality (OR 2.18, CI 2.05 to 2.31, p < 0.001). After adjustment as above, individuals with an AUD still had higher odds of all-cause mortality (aOR 1.55, CI 1.46 to 1.65, p < 0.001).

CONCLUSION

This work suggests that AUD can increase the severity and mortality of COVID-19 infection. This reinforces the need for clinicians to obtain an accurate alcohol history from patients hospitalized with COVID-19. For this study, our results are limited by an inability to quantify the daily drinking habits of the participants. Studies are needed to determine the mechanisms by which AUD increases the severity and mortality of COVID-19.

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.

Tracking Blood Pressure Control Performance and Process Metrics in 25 US Health Systems: The PCORnet Blood Pressure Control Laboratory

Background The National Patient-Centered Clinical Research Network Blood Pressure Control Laboratory Surveillance System was established to identify opportunities for blood pressure (BP) control improvement and to provide a mechanism for tracking improvement longitudinally. Methods and Results We conducted a serial cross-sectional study with queries against standardized electronic health record data in the National Patient-Centered Clinical Research Network (PCORnet) common data model returned by 25 participating US health systems. Queries produced BP control metrics for adults with well-documented hypertension and a recent encounter at the health system for a series of 1-year measurement periods for each quarter of available data from January 2017 to March 2020. Aggregate weighted results are presented overall and by race and ethnicity. The most recent measurement period includes data from 1 737 995 patients, and 11 956 509 patient-years were included in the trend analysis. Overall, 15% were Black, 52% women, and 28% had diabetes. BP control (<140/90 mm Hg) was observed in 62% (range, 44%-74%) but varied by race and ethnicity, with the lowest BP control among Black patients at 57% (odds ratio, 0.79; 95% CI, 0.66-0.94). A new class of antihypertensive medication (medication intensification) was prescribed in just 12% (range, 0.6%-25%) of patient visits where BP was uncontrolled. However, when medication intensification occurred, there was a large decrease in systolic BP (≈15 mm Hg; range, 5-18 mm Hg). Conclusions Major opportunities exist for improving BP control and reducing disparities, especially through consistent medication intensification when BP is uncontrolled. These data demonstrate substantial room for improvement and opportunities to close health equity gaps.

Comparative Effectiveness of Aspirin Dosing in Cardiovascular Disease

BACKGROUND

The appropriate dose of aspirin to lower the risk of death, myocardial infarction, and stroke and to minimize major bleeding in patients with established atherosclerotic cardiovascular disease is a subject of controversy.

METHODS

Using an open-label, pragmatic design, we randomly assigned patients with established atherosclerotic cardiovascular disease to a strategy of 81 mg or 325 mg of aspirin per day. The primary effectiveness outcome was a composite of death from any cause, hospitalization for myocardial infarction, or hospitalization for stroke, assessed in a time-to-event analysis. The primary safety outcome was hospitalization for major bleeding, also assessed in a time-to-event analysis.

RESULTS

A total of 15,076 patients were followed for a median of 26.2 months (interquartile range [IQR], 19.0 to 34.9). Before randomization, 13,537 (96.0% of those with available information on previous aspirin use) were already taking aspirin, and 85.3% of these patients were previously taking 81 mg of daily aspirin. Death, hospitalization for myocardial infarction, or hospitalization for stroke occurred in 590 patients (estimated percentage, 7.28%) in the 81-mg group and 569 patients (estimated percentage, 7.51%) in the 325-mg group (hazard ratio, 1.02; 95% confidence interval [CI], 0.91 to 1.14). Hospitalization for major bleeding occurred in 53 patients (estimated percentage, 0.63%) in the 81-mg group and 44 patients (estimated percentage, 0.60%) in the 325-mg group (hazard ratio, 1.18; 95% CI, 0.79 to 1.77). Patients assigned to 325 mg had a higher incidence of dose switching than those assigned to 81 mg (41.6% vs. 7.1%) and fewer median days of exposure to the assigned dose (434 days [IQR, 139 to 737] vs. 650 days [IQR, 415 to 922]).

CONCLUSIONS

In this pragmatic trial involving patients with established cardiovascular disease, there was substantial dose switching to 81 mg of daily aspirin and no significant differences in cardiovascular events or major bleeding between patients assigned to 81 mg and those assigned to 325 mg of aspirin daily. (Funded by the Patient-Centered Outcomes Research Institute; ADAPTABLE ClinicalTrials.gov number, NCT02697916.).

Impact of the Early Phase of the COVID-19 Pandemic on US Healthcare Workers: Results from the HERO Registry

BACKGROUND

The HERO registry was established to support research on the impact of the COVID-19 pandemic on US healthcare workers.

OBJECTIVE

Describe the COVID-19 pandemic experiences of and effects on individuals participating in the HERO registry.

DESIGN

Cross-sectional, self-administered registry enrollment survey conducted from April 10 to July 31, 2020.

SETTING

Participants worked in hospitals (74.4%), outpatient clinics (7.4%), and other settings (18.2%) located throughout the nation.

PARTICIPANTS

A total of 14,600 healthcare workers.

MAIN MEASURES

COVID-19 exposure, viral and antibody testing, diagnosis of COVID-19, job burnout, and physical and emotional distress.

KEY RESULTS

Mean age was 42.0 years, 76.4% were female, 78.9% were White, 33.2% were nurses, 18.4% were physicians, and 30.3% worked in settings at high risk for COVID-19 exposure (e.g., ICUs, EDs, COVID-19 units). Overall, 43.7% reported a COVID-19 exposure and 91.3% were exposed at work. Just 3.8% in both high- and low-risk settings experienced COVID-19 illness. In regression analyses controlling for demographics, professional role, and work setting, the risk of COVID-19 illness was higher for Black/African-Americans (aOR 2.32, 99% CI 1.45, 3.70, p < 0.01) and Hispanic/Latinos (aOR 2.19, 99% CI 1.55, 3.08, p < 0.01) compared with Whites. Overall, 41% responded that they were experiencing job burnout. Responding about the day before they completed the survey, 53% of participants reported feeling tired a lot of the day, 51% stress, 41% trouble sleeping, 38% worry, 21% sadness, 19% physical pain, and 15% anger. On average, healthcare workers reported experiencing 2.4 of these 7 distress feelings a lot of the day.

CONCLUSIONS

Healthcare workers are at high risk for COVID-19 exposure, but rates of COVID-19 illness were low. The greater risk of COVID-19 infection among race/ethnicity minorities reported in the general population is also seen in healthcare workers. The HERO registry will continue to monitor changes in healthcare worker well-being during the pandemic.

TRIAL REGISTRATION

ClinicalTrials.gov identifier NCT04342806.

Rationale and Design of the Aspirin Dosing-A Patient-Centric Trial Assessing Benefits and Long-term Effectiveness (ADAPTABLE) Trial

Importance

Determining the right dosage of aspirin for the secondary prevention treatment of atherosclerotic cardiovascular disease (ASCVD) remains an unanswered and critical question.

Objective

To report the rationale and design for a randomized clinical trial to determine the optimal dosage of aspirin to be used for secondary prevention of ASCVD, using an innovative research method.

Design, Setting, and Participants

This pragmatic, open-label, patient-centered, randomized clinical trial is being conducted in 15 000 patients within the National Patient-Centered Clinical Research Network (PCORnet), a distributed research network of partners including clinical research networks, health plan research networks, and patient-powered research networks across the United States. Patients with established ASCVD treated in routine clinical practice within the network are eligible. Patient recruitment began in April 2016. Enrollment was completed in June 2019. Final follow-up is expected to be completed by June 2020.

Interventions

Participants are randomized on a web platform in a 1:1 fashion to either 81 mg or 325 mg of aspirin daily.

Main Outcomes and Measures

The primary efficacy end point is the composite of all-cause mortality, hospitalization for nonfatal myocardial infarction, or hospitalization for a nonfatal stroke. The primary safety end point is hospitalization for major bleeding associated with a blood-product transfusion. End points are captured through regular queries of the health systems' common data model within the structure of PCORnet's distributed data environment.

Conclusions and Relevance

As a pragmatic study and the first interventional trial conducted within the PCORnet electronic data infrastructure, this trial is testing several unique and innovative operational approaches that have the potential to disrupt and transform the conduct of future patient-centered randomized clinical trials by evaluating treatments integrated in clinical practice while at the same time determining the optimal dosage of aspirin for secondary prevention of ASCVD.

Trial Registration

ClinicalTrials.gov Identifier: NCT02697916.

Cost of Unnecessary Amylase and Lipase Testing at Multiple Academic Health Systems

OBJECTIVES

To determine adherence to Choosing Wisely recommendations for using serum lipase to diagnose acute pancreatitis rather than amylase, avoiding concurrent amylase/lipase testing and avoiding serial measurements after the first elevated test as both are ineffective for tracking disease course.

METHODS

Deidentified laboratory data from four large health systems were analyzed to determine concurrent testing rates, serial testing rates, and provider-ordering patterns.

RESULTS

While most providers adhered to recommendations with 58,693 lipase-only tests ordered and performed, 86% of amylase tests were performed concurrently with lipase. Ambulatory, inpatient, and emergency department settings revealed concurrent rates of 51%, 41%, and 8%, respectively. Services with order sets containing both amylase and lipase were associated with higher rates of concurrent testing.

CONCLUSIONS

Concurrent amylase/lipase testing is an area of opportunity to improve compliance, especially in ambulatory settings. Revision of order sets and provider education could be interventions to reduce unnecessary testing and save costs.

Consensus Development of a Modern Ontology of Emergency Department Presenting Problems-The Hierarchical Presenting Problem Ontology (HaPPy)

OBJECTIVE

Numerous attempts have been made to create a standardized "presenting problem" or "chief complaint" list to characterize the nature of an emergency department visit. Previous attempts have failed to gain widespread adoption as they were not freely shareable or did not contain the right level of specificity, structure, and clinical relevance to gain acceptance by the larger emergency medicine community. Using real-world data, we constructed a presenting problem list that addresses these challenges.

MATERIALS AND METHODS

We prospectively captured the presenting problems for 180,424 consecutive emergency department patient visits at an urban, academic, Level I trauma center in the Boston metro area. No patients were excluded. We used a consensus process to iteratively derive our system using real-world data. We used the first 70% of consecutive visits to derive our ontology, followed by a 6-month washout period, and the remaining 30% for validation. All concepts were mapped to Systematized Nomenclature of Medicine-Clinical Terms (SNOMED CT).

RESULTS

Our system consists of a polyhierarchical ontology containing 692 unique concepts, 2,118 synonyms, and 30,613 nonvisible descriptions to correct misspellings and nonstandard terminology. Our ontology successfully captured structured data for 95.9% of visits in our validation data set.

DISCUSSION AND CONCLUSION

We present the HierArchical Presenting Problem ontologY (HaPPy). This ontology was empirically derived and then iteratively validated by an expert consensus panel. HaPPy contains 692 presenting problem concepts, each concept being mapped to SNOMED CT. This freely sharable ontology can help to facilitate presenting problem-based quality metrics, research, and patient care.

Incorporating a location-based socioeconomic index into a de-identified i2b2 clinical data warehouse

OBJECTIVE

Clinical research data warehouses are largely populated from information extracted from electronic health records (EHRs). While these data provide information about a patient's medications, laboratory results, diagnoses, and history, her social, economic, and environmental determinants of health are also major contributing factors in readmission, morbidity, and mortality and are often absent or unstructured in the EHR. Details about a patient's socioeconomic status may be found in the U.S. census. To facilitate researching the impacts of socioeconomic status on health outcomes, clinical and socioeconomic data must be linked in a repository in a fashion that supports seamless interrogation of these diverse data elements. This study demonstrates a method for linking clinical and location-based data and querying these data in a de-identified data warehouse using Informatics for Integrating Biology and the Bedside.

MATERIALS AND METHODS

Patient data were extracted from the EHR at Nebraska Medicine. Socioeconomic variables originated from the 2011-2015 five-year block group estimates from the American Community Survey. Data querying was performed using Informatics for Integrating Biology and the Bedside. All location-based data were truncated to prevent identification of a location with a population <20 000 individuals.

RESULTS

We successfully linked location-based and clinical data in a de-identified data warehouse and demonstrated its utility with a sample use case.

DISCUSSION

With location-based data available for querying, research investigating the impact of socioeconomic context on health outcomes is possible. Efforts to improve geocoding can readily be incorporated into this model.

CONCLUSION

This study demonstrates a means for incorporating and querying census data in a de-identified clinical data warehouse.

Empirical Study on the Impact of a Tactical Biosurveillance Information Visualization on Users' Situational Awareness

Decisions on antibiotic-resistant infection (ARI) prevention in dynamic health care settings should be agile and target the right process at the right time. Health information technologies can aid the recognition of high-risk situations for ARI transmission and timely facilitate operators' situational awareness (SA) in various military and civilian health care locations or transport platforms. High SA is one of the significant predictors of better performance. The objective of this study was to evaluate the impact of the developed health information visualization (VIZ) on the users' SA regarding situations when risks of ARI transmission and exposure are high. The enrolled 19 subjects assessed the proposed VIZ artifacts representing 1 scenario, compared the VIZ effectiveness against the currently employed local methods, and reported their SA (perception and comprehension) with the use of a pre- and post-self-rating questionnaire. The results showed that the VIZ significantly increased SA in the study subjects and revealed the importance of communicating the risk of exposure to ARIs. The VIZ enabled the participants to quickly acknowledge the high-risk individuals (super-spreaders), locations (hot spots), and biosafety (deficient infection prevention). The study concluded that SA-oriented technologies may be promising for promoting better infection prevention practices.

Comparing the German Emergency Department Medical Record with the US HL7 Data Elements for Emergency Department Systems

Interoperability between emergency department (ED) information systems requires a shared data specification. In 2013 Health Level Seven International, an international standards body, approved a specification for Data Elements for Emergency Department Systems (DEEDS) for use in the United States. A similar specification was created in Germany for national employment, defining data elements and forms. This study presents the first step in the efforts to harmonize the two data definitions for International approval by comparing the meaning of the German Emergency Department Medical Record (GEDMR) data element definitions with the US DEEDS using a methodology for terminology mapping from ISO/TR 12300. The comparison between GEDMR and DEEDS did show significant differences in certain domains. The results support development of an international standard for ED data elements.

Standard for improving emergency information interoperability: the HL7 data elements for emergency department systems

BACKGROUND

Emergency departments in the United States service over 130 million visits per year. The demands for information from these visits require interoperable data exchange standards. While multiple data exchange specifications are in use, none have undergone rigorous standards review. This paper describes the creation and balloting of the Health Level Seven (HL7) Data Elements for Emergency Department Systems (DEEDS).

METHODS

Existing data exchange specifications were collected and organized into categories reflecting the workflow of emergency care. The concepts were then mapped to existing standards for vocabulary, data types, and the HL7 information model. The HL7 community then processed the specification through the normal balloting process addressing all comments and concerns. The resulting specification was then submitted for publication as an HL7 informational standard.

RESULTS

The resulting specification contains 525 concepts related to emergency care required for operations and reporting to external agencies. An additional 200 of the most commonly ordered laboratory tests were included. Each concept was given a unique identifier and mapped to Logical Observation Identifiers, Names, and Codes (LOINC). HL7 standard data types were applied.

DISCUSSION

The HL7 DEEDS specification represents the first set of common ED related data elements to undergo rigorous standards development. The availability of this standard will contribute to improved interoperability of emergency care data.

Semantic analysis of SNOMED CT for a post-coordinated database of histopathology findings

Objective

This research investigated the use of SNOMED CT to represent diagnostic tissue morphologies and notable tissue architectures typically found within a pathologist's microscopic examination report to identify gaps in expressivity of SNOMED CT for use in anatomic pathology.

Methods

24 breast biopsy cases were reviewed by two board certified surgical pathologists who independently described the diagnostically important tissue architectures and diagnostic morphologies observed by microscopic examination. In addition, diagnostic comments and details were extracted from the original diagnostic pathology report. 95 unique clinical statements were extracted from 13 malignant and 11 benign breast needle biopsy cases.

Results

75% of the inventoried diagnostic terms and statements could be represented by valid SNOMED CT expressions. The expressions included one pre-coordinated expression and 73 post-coordinated expressions. No valid SNOMED CT expressions could be identified or developed to unambiguously assert the meaning of 21 statements (ie, 25% of inventoried clinical statements). Evaluation of the findings indicated that SNOMED CT lacked sufficient definitional expressions or the SNOMED CT concept model prohibited use of certain defined concepts needed to describe the numerous, diagnostically important tissue architectures and morphologic changes found within a surgical pathology microscopic examination.

Conclusions

Because information gathered during microscopic histopathology examination provides the basis of pathology diagnoses, additional concept definitions for tissue morphometries and modifications to the SNOMED CT concept model are needed and suggested to represent detailed histopathologic findings in computable fashion for purposes of patient information exchange and research.

Trial registration number

UNMC Institutional Review Board ID# 342-11-EP.

Quality and safety implications of emergency department information systems

The Health Information Technology for Economic and Clinical Health Act of 2009 and the Centers for Medicare & Medicaid Services "meaningful use" incentive programs, in tandem with the boundless additional requirements for detailed reporting of quality metrics, have galvanized hospital efforts to implement hospital-based electronic health records. As such, emergency department information systems (EDISs) are an important and unique component of most hospitals' electronic health records. System functionality varies greatly and affects physician decisionmaking, clinician workflow, communication, and, ultimately, the overall quality of care and patient safety. This article is a joint effort by members of the Quality Improvement and Patient Safety Section and the Informatics Section of the American College of Emergency Physicians. The aim of this effort is to examine the benefits and potential threats to quality and patient safety that could result from the choice of a particular EDIS, its implementation and optimization, and the hospital's or physician group's approach to continuous improvement of the EDIS. Specifically, we explored the following areas of potential EDIS safety concerns: communication failure, wrong order-wrong patient errors, poor data display, and alert fatigue. Case studies are presented that illustrate the potential harm that could befall patients from an inferior EDIS product or suboptimal execution of such a product in the clinical environment. The authors have developed 7 recommendations to improve patient safety with respect to the deployment of EDISs. These include ensuring that emergency providers actively participate in selection of the EDIS product, in the design of processes related to EDIS implementation and optimization, and in the monitoring of the system's ongoing success or failure. Our recommendations apply to emergency departments using any type of EDIS: custom-developed systems, best-of-breed vendor systems, or enterprise systems.

Multi-National, Multi-Institutional Analysis of Clinical Decision Support Data Needs to Inform Development of the HL7 Virtual Medical Record Standard

An important barrier to the widespread dissemination of clinical decision support (CDS) is the heterogeneity of information models and terminologies used across healthcare institutions, health information systems, and CDS resources such as knowledge bases. To address this problem, the Health Level 7 (HL7) Virtual Medical Record project (an open, international standards development effort) is developing community consensus on the clinical information exchanged between CDS engines and clinical information systems. As a part of this effort, the HL7 CDS Work Group embarked on a multinational, collaborative effort to identify a representative set of clinical data elements required for CDS. Based on an analysis of CDS systems from 20 institutions representing 4 nations, 131 data elements were identified as being currently utilized for CDS. These findings will inform the development of the emerging HL7 Virtual Medical Record standard and will facilitate the achievement of scalable, standards-based CDS.

A qualitative analysis of academic and private physicians and administrators' perceptions of health information technology

A qualitative analysis of extensive interviews with academic and private physicians and administrators at a large academic medical center reveals six major themes associated with the adoption of Health Information Technology (HIT). The differences between academic and private physicians perceptions and administrators perceptions of the benefits of HIT are highlighted.

Structuring order sets for interoperable distribution

A major portion of patient care planning occurs during the process of writing orders. Computerized order entry can present collections of predefined orders to the user during the ordering process. These order sets are useful for promoting standards of care, and provide one element of structured clinical knowledge to be used by Computerized Provider Order Entry (CPOE) systems at the point of care. Since the creation, confirmation and maintenance of order sets is resource intensive, sharing order sets is a useful goal. We describe a standard representation of order sets that supports maintenance, sharing and interoperation of pre-defined order sets. A dialogue within the HL7 community seeks to harmonize this proposal with the Clinical Document Architecture and the HL7 Reference Information Model.

Improved coding of the primary reason for visit to the emergency department using SNOMED

There are over 100 million visits to emergency departments in the United States annually that could be a source of data for multiple uses including disease surveillance, health services research, quality assurance activates, and research. The patients' motivations for seeking care or the reason for visit (RFV) are recorded in every case. Efforts to utilize this rich source of data are hampered by inconsistent data entry and coding. This study analyzes ICD-9-CM, SNOMED-RT, and SNOMED-CT encoding of the RFV for accuracy. Each encoded reason for visit was compared to the text entry recorded at the time of visit to determine the closeness of fit. Each coded entry was judged to be an exact lexical match, a synonym, a broader or narrower concept or no match. SNOMED-CT was a lexical match or synonym for 93% of the text entries, while SNOMED-RT matched 87%, and ICD-9-CM matched 40%. We demonstrate that SNOMED coding of the RFV is more accurate than ICD-9-CM coding.