Semantically enabling clinical decision support recommendations.

BACKGROUND: Clinical decision support systems have been widely deployed to guide healthcare decisions on patient diagnosis, treatment choices, and patient management through evidence-based recommendations. These recommendations are typically derived from clinical practice guidelines created by clinical specialties or healthcare organizations. Although there have been many different technical approaches to encoding guideline recommendations into decision support systems, much of the previous work has not focused on enabling system generated recommendations through the formalization of changes in a guideline, the provenance of a recommendation, and applicability of the evidence. Prior work indicates that healthcare providers may not find that guideline-derived recommendations always meet their needs for reasons such as lack of relevance, transparency, time pressure, and applicability to their clinical practice. RESULTS: We introduce several semantic techniques that model diseases based on clinical practice guidelines, provenance of the guidelines, and the study cohorts they are based on to enhance the capabilities of clinical decision support systems. We have explored ways to enable clinical decision support systems with semantic technologies that can represent and link to details in related items from the scientific literature and quickly adapt to changing information from the guidelines, identifying gaps, and supporting personalized explanations. Previous semantics-driven clinical decision systems have limited support in all these aspects, and we present the ontologies and semantic web based software tools in three distinct areas that are unified using a standard set of ontologies and a custom-built knowledge graph framework: (i) guideline modeling to characterize diseases, (ii) guideline provenance to attach evidence to treatment decisions from authoritative sources, and (iii) study cohort modeling to identify relevant research publications for complicated patients. CONCLUSIONS: We have enhanced existing, evidence-based knowledge by developing ontologies and software that enables clinicians to conveniently access updates to and provenance of guidelines, as well as gather additional information from research studies applicable to their patients' unique circumstances. Our software solutions leverage many well-used existing biomedical ontologies and build upon decades of knowledge representation and reasoning work, leading to explainable results.

Planning and Monitoring Equitable Clinical Trial Enrollment Using Goal Programming.

Randomized clinical trial (RCT) studies are the gold standard for scientific evidence on treatment benefits to patients. RCT outcomes may not be generalizable to clinical practice if the trial population is not representative of the patients for which the treatment is intended. Specifically, enrollment plans may not adequately include groups of patients with protected attributes, such as gender, race, or ethnicity. Inequities in RCTs are a major concern for funding agencies such as the National Institutes of Health (NIH) and for policy makers. We address this challenge by proposing a goal-programming approach, explicitly integrating measurable enrollment goals, to design equitable enrollment plans for RCTs. We evaluate our model in both single and multisite settings using the enrollment criteria and study population from the Systolic Blood Pressure Intervention Trial (SPRINT) study. Our model can successfully generate equitable enrollment plans that satisfy multiple goals such as sample representativeness and minimum total financial cost. Our model can detect deviations from a target plan during the enrollment process and update the plan to reduce deviations in the remaining process. Finally, through appropriate site selection in the planning stage, the model can demonstrate the possibility of enrolling a nationally representative study population if geographic constraints exist in multisite recruitment (e.g., clinical centers in a particular region). Our model can be used to prospectively produce and retrospectively evaluate how equitable enrollment plans are based on subjects' protected attributes, and it allows researchers to provide justifications on validity of scientific analysis and evaluation of subgroup disparities.

Assessing the Association Between Network-based Provider Communities and Patient Mortality in the Medicare Population with Multiple Chronic Conditions.

Understanding the complexity of care delivery and care coordination for patients with multiple chronic conditions is challenging. Network analysis can model the relationship between providers and patients to find factors associated with patient mortality. We constructed a network by connecting the providers through shared patients, which was then partitioned into tightly connected communities using a community detection algorithm. After adjusting for patient characteristics, the odds ratio of death for one standard deviation increase in degree centrality ratio between primary care providers (PCPs) and non-PCPs was 0.95 (0.92-0.98). Our result suggest that the centrality of PCPs may be a modifiable factor for improving care delivery. We demonstrated that network analysis can be used to find higher order features associated with health outcomes in addition to patient-level features.

An Audio Personal Health Library of Clinic Visit Recordings for Patients and Their Caregivers (HealthPAL): User-Centered Design Approach.

BACKGROUND: Providing digital recordings of clinic visits to patients has emerged as a strategy to promote patient and family engagement in care. With advances in natural language processing, an opportunity exists to maximize the value of visit recordings for patients by automatically tagging key visit information (eg, medications, tests, and imaging) and linkages to trustworthy web-based resources curated in an audio-based personal health library. OBJECTIVE: This study aims to report on the user-centered development of HealthPAL, an audio personal health library. METHODS: Our user-centered design and usability evaluation approach incorporated iterative rounds of video-recorded sessions from 2016 to 2019. We recruited participants from a range of community settings to represent older patient and caregiver perspectives. In the first round, we used paper prototypes and focused on feature envisionment. We moved to low-fidelity and high-fidelity versions of the HealthPAL in later rounds, which focused on functionality and use; all sessions included a debriefing interview. Participants listened to a deidentified, standardized primary care visit recording before completing a series of tasks (eg, finding where a medication was discussed in the recording). In the final round, we recorded the patients' primary care clinic visits for use in the session. Findings from each round informed the agile software development process. Task completion and critical incidents were recorded in each round, and the System Usability Scale was completed by participants using the digital prototype in later rounds. RESULTS: We completed 5 rounds of usability sessions with 40 participants, of whom 25 (63%) were women with a median age of 68 years (range 23-89). Feedback from sessions resulted in color-coding and highlighting of information tags, a more prominent play button, clearer structure to move between one's own recordings and others' recordings, the ability to filter recording content by the topic discussed and descriptions, 10-second forward and rewind controls, and a help link and search bar. Perceived usability increased over the rounds, with a median System Usability Scale of 78.2 (range 20-100) in the final round. Participants were overwhelmingly positive about the concept of accessing a curated audio recording of a clinic visit. Some participants reported concerns about privacy and the computer-based skills necessary to access recordings. CONCLUSIONS: To our knowledge, HealthPAL is the first patient-centered app designed to allow patients and their caregivers to access easy-to-navigate recordings of clinic visits, with key concepts tagged and hyperlinks to further information provided. The HealthPAL user interface has been rigorously co-designed with older adult patients and their caregivers and is now ready for further field testing. The successful development and use of HealthPAL may help improve the ability of patients to manage their own care, especially older adult patients who have to navigate complex treatment plans.

Quantifying representativeness in randomized clinical trials using machine learning fairness metrics.

OBJECTIVE: We help identify subpopulations underrepresented in randomized clinical trials (RCTs) cohorts with respect to national, community-based or health system target populations by formulating population representativeness of RCTs as a machine learning (ML) fairness problem, deriving new representation metrics, and deploying them in easy-to-understand interactive visualization tools. MATERIALS AND METHODS: We represent RCT cohort enrollment as random binary classification fairness problems, and then show how ML fairness metrics based on enrollment fraction can be efficiently calculated using easily computed rates of subpopulations in RCT cohorts and target populations. We propose standardized versions of these metrics and deploy them in an interactive tool to analyze 3 RCTs with respect to type 2 diabetes and hypertension target populations in the National Health and Nutrition Examination Survey. RESULTS: We demonstrate how the proposed metrics and associated statistics enable users to rapidly examine representativeness of all subpopulations in the RCT defined by a set of categorical traits (eg, gender, race, ethnicity, smoking status, and blood pressure) with respect to target populations. DISCUSSION: The normalized metrics provide an intuitive standardized scale for evaluating representation across subgroups, which may have vastly different enrollment fractions and rates in RCT study cohorts. The metrics are beneficial complements to other approaches (eg, enrollment fractions) used to identify generalizability and health equity of RCTs. CONCLUSION: By quantifying the gaps between RCT and target populations, the proposed methods can support generalizability evaluation of existing RCT cohorts. The interactive visualization tool can be readily applied to identified underrepresented subgroups with respect to any desired source or target populations.

Natural language processing for automated annotation of medication mentions in primary care visit conversations.

OBJECTIVES: The objective of this study is to build and evaluate a natural language processing approach to identify medication mentions in primary care visit conversations between patients and physicians. MATERIALS AND METHODS: Eight clinicians contributed to a data set of 85 clinic visit transcripts, and 10 transcripts were randomly selected from this data set as a development set. Our approach utilizes Apache cTAKES and Unified Medical Language System controlled vocabulary to generate a list of medication candidates in the transcribed text and then performs multiple customized filters to exclude common false positives from this list while including some additional common mentions of the supplements and immunizations. RESULTS: Sixty-five transcripts with 1121 medication mentions were randomly selected as an evaluation set. Our proposed method achieved an F-score of 85.0% for identifying the medication mentions in the test set, significantly outperforming existing medication information extraction systems for medical records with F-scores ranging from 42.9% to 68.9% on the same test set. DISCUSSION: Our medication information extraction approach for primary care visit conversations showed promising results, extracting about 27% more medication mentions from our evaluation set while eliminating many false positives in comparison to existing baseline systems. We made our approach publicly available on the web as an open-source software. CONCLUSION: Integration of our annotation system with clinical recording applications has the potential to improve patients' understanding and recall of key information from their clinic visits, and, in turn, to positively impact health outcomes.

Comparison of Methods to Reduce Bias From Clinical Prediction Models of Postpartum Depression.

Importance: The lack of standards in methods to reduce bias for clinical algorithms presents various challenges in providing reliable predictions and in addressing health disparities. Objective: To evaluate approaches for reducing bias in machine learning models using a real-world clinical scenario. Design, Setting, and Participants: Health data for this cohort study were obtained from the IBM MarketScan Medicaid Database. Eligibility criteria were as follows: (1) Female individuals aged 12 to 55 years with a live birth record identified by delivery-related codes from January 1, 2014, through December 31, 2018; (2) greater than 80% enrollment through pregnancy to 60 days post partum; and (3) evidence of coverage for depression screening and mental health services. Statistical analysis was performed in 2020. Exposures: Binarized race (Black individuals and White individuals). Main Outcomes and Measures: Machine learning models (logistic regression [LR], random forest, and extreme gradient boosting) were trained for 2 binary outcomes: postpartum depression (PPD) and postpartum mental health service utilization. Risk-adjusted generalized linear models were used for each outcome to assess potential disparity in the cohort associated with binarized race (Black or White). Methods for reducing bias, including reweighing, Prejudice Remover, and removing race from the models, were examined by analyzing changes in fairness metrics compared with the base models. Baseline characteristics of female individuals at the top-predicted risk decile were compared for systematic differences. Fairness metrics of disparate impact (DI, 1 indicates fairness) and equal opportunity difference (EOD, 0 indicates fairness). Results: Among 573 634 female individuals initially examined for this study, 314 903 were White (54.9%), 217 899 were Black (38.0%), and the mean (SD) age was 26.1 (5.5) years. The risk-adjusted odds ratio comparing White participants with Black participants was 2.06 (95% CI, 2.02-2.10) for clinically recognized PPD and 1.37 (95% CI, 1.33-1.40) for postpartum mental health service utilization. Taking the LR model for PPD prediction as an example, reweighing reduced bias as measured by improved DI and EOD metrics from 0.31 and -0.19 to 0.79 and 0.02, respectively. Removing race from the models had inferior performance for reducing bias compared with the other methods (PPD: DI = 0.61; EOD = -0.05; mental health service utilization: DI = 0.63; EOD = -0.04). Conclusions and Relevance: Clinical prediction models trained on potentially biased data may produce unfair outcomes on the basis of the chosen metrics. This study's results suggest that the performance varied depending on the model, outcome label, and method for reducing bias. This approach toward evaluating algorithmic bias can be used as an example for the growing number of researchers who wish to examine and address bias in their data and models.

Evaluating artificial intelligence in medicine: phases of clinical research.

Increased scrutiny of artificial intelligence (AI) applications in healthcare highlights the need for real-world evaluations for effectiveness and unintended consequences. The complexity of healthcare, compounded by the user- and context-dependent nature of AI applications, calls for a multifaceted approach beyond traditional in silico evaluation of AI. We propose an interdisciplinary, phased research framework for evaluation of AI implementations in healthcare. We draw analogies to and highlight differences from the clinical trial phases for drugs and medical devices, and we present study design and methodological guidance for each stage.

The Semantic Data Dictionary - An Approach for Describing and Annotating Data.

It is common practice for data providers to include text descriptions for each column when publishing datasets in the form of data dictionaries. While these documents are useful in helping an end-user properly interpret the meaning of a column in a dataset, existing data dictionaries typically are not machine-readable and do not follow a common specification standard. We introduce the Semantic Data Dictionary, a specification that formalizes the assignment of a semantic representation of data, enabling standardization and harmonization across diverse datasets. In this paper, we present our Semantic Data Dictionary work in the context of our work with biomedical data; however, the approach can and has been used in a wide range of domains. The rendition of data in this form helps promote improved discovery, interoperability, reuse, traceability, and reproducibility. We present the associated research and describe how the Semantic Data Dictionary can help address existing limitations in the related literature. We discuss our approach, present an example by annotating portions of the publicly available National Health and Nutrition Examination Survey dataset, present modeling challenges, and describe the use of this approach in sponsored research, including our work on a large NIH-funded exposure and health data portal and in the RPI-IBM collaborative Health Empowerment by Analytics, Learning, and Semantics project. We evaluate this work in comparison with traditional data dictionaries, mapping languages, and data integration tools.

Knowledge Extraction of Cohort Characteristics in Research Publications.

When healthcare providers review the results of a clinical trial study to understand its applicability to their practice, they typically analyze how well the characteristics of the study cohort correspond to those of the patients they see. We have previously created a study cohort ontology to standardize this information and make it accessible for knowledge-based decision support. The extraction of this information from research publications is challenging, however, given the wide variance in reporting cohort characteristics in a tabular representation. To address this issue, we have developed an ontology-enabled knowledge extraction pipeline for automatically constructing knowledge graphs from the cohort characteristics found in PDF-formatted research papers. We evaluated our approach using a training and test set of 41 research publications and found an overall accuracy of 83.3% in correctly assembling the knowledge graphs. Our research provides a promising approach for extracting knowledge more broadly from tabular information in research publications.

Development and Field Testing of a Long-Term Care Decision Aid Website for Older Adults: Engaging Patients and Caregivers in User-Centered Design.

BACKGROUND AND OBJECTIVES: Decisions about long-term care and financing can be difficult to comprehend, consider, and communicate. In a previous needs assessment, families in rural areas requested a patient-facing website; however, questions arose about the acceptability of an online tool for older adults. This study engaged older adults and family caregivers in (a) designing and refining an interactive, tailored decision aid website, and (b) field testing its utility, feasibility, and acceptability. RESEARCH DESIGN AND METHODS: Based on formative work, the research team engaged families in designing and iteratively revising paper drafts, then programmed a tailored website. The field test used the ThinkAloud approach and pre-/postquestionnaires to assess participants' knowledge, decisional conflict, usage, and acceptability ratings. RESULTS: Forty-five older adults, family members, and stakeholders codesigned and tested the decision aid, yielding four decision-making steps: Get the Facts, What Matters Most, Consider Your Resources, and Make an Action Plan. User-based design and iterative storyboarding enhanced the content, personal decision-making activities, and user-generated resources. Field-testing participants scored 83.3% correct on knowledge items and reported moderate/low decisional conflict. All (100%) were able to use the website, spent an average of 26.3 min, and provided an average 87.5% acceptability rating. DISCUSSION AND IMPLICATIONS: A decision aid website can educate and support older adults and their family members in beginning a long-term care plan. Codesign and in-depth interviews improved usability, and lessons learned may guide the development of other aging decision aid websites.

Hierarchical patient-centric caregiver network method for clinical outcomes study.

In clinical outcome studies, analysis has traditionally been performed using patient-level factors, with minor attention given to provider-level features. However, the nature of care coordination and collaboration between caregivers (providers) may also be important in determining patient outcomes. Using data from patients admitted to intensive care units at a large tertiary care hospital, we modeled the caregivers that provided medical service to a specific patient as patient-centric subnetwork embedded within larger caregiver networks of the institute. The caregiver networks were composed of caregivers who treated either a cohort of patients with particular disease or any patient regardless of disease. Our model can generate patient-specific caregiver network features at multiple levels, and we demonstrate that these multilevel network features, in addition to patient-level features, are significant predictors of length of hospital stay and in-hospital mortality.

Predicting Adverse Drug Reactions on Distributed Health Data using Federated Learning.

Using electronic health data to predict adverse drug reaction (ADR) incurs practical challenges, such as lack of adequate data from any single site for rare ADR detection, resource constraints on integrating data from multiple sources, and privacy concerns with creating a centralized database from person-specific, sensitive data. We introduce a federated learning framework that can learn a global ADR prediction model from distributed health data held locally at different sites. We propose two novel methods of local model aggregation to improve the predictive capability of the global model. Through comprehensive experimental evaluation using real-world health data from 1 million patients, we demonstrate the effectiveness of our proposed approach in achieving comparable performance to centralized learning and outperforming localized learning models for two types of ADRs. We also demonstrate that, for varying data distributions, our aggregation methods outperform state-of-the-art techniques, in terms of precision, recall, and accuracy.

Prescription fill rates for acute and chronic medications in claims-EMR linked data.

Nonadherence to prescribed medications poses a significant public health problem. Prescription data in electronic medical records (EMRs) linked with pharmacy claims data provides an opportunity to examine the prescription fill rates and factors associated with it.Using a claims-EMR linked data, patients who had a prescription for either an antibiotic, antihypertensive, or antidiabetic in EMR were identified (index prescription). Prescription fill was defined as a pharmacy claim found within the 90 days following the EMR prescription. For each medication group, patient characteristics and fill rates were examined using descriptive statistics. Multivariate logistic regression was used to evaluate the association between fill rates and factors such as age, race, brand vs generic, and prior treatment during 365 days before the index date.Among 77,996 patients with index antibiotic prescription, 78,462 with index antihypertensive prescription, and 24,013 with index antidiabetic prescription, the prescription fill rate was 73%, 74%, and 76%, respectively. Overall, African American race was negatively associated with fill rates (odds ratio [OR] 0.8 for all 3 groups). Prior treatment history was positively associated with antihypertensives (OR 5.6, 95% confidence interval [CI] 5.4-5.7) or antidiabetics (OR 4.1, CI 3.8-4.4) but negatively with antibiotics (OR 0.6, CI 0.6-0.6). Older age was an additional factor that was negatively associated with first time fill rate among patients without prior treatment.Significant proportions of patients, especially patients with no prior treatment history, did not fill prescriptions for antibiotics, antihypertensives, or antidiabetics. The association between patient factors and medication fill rates varied across different medication groups.

Differences in Antipsychotic-Related Adverse Events in Adult, Pediatric, and Geriatric Populations.

In recent years, antipsychotic medications have increasingly been used in pediatric and geriatric populations, despite the fact that many of these drugs were approved based on clinical trials in adult patients only. Preliminary studies have shown that the "off-label" use of these drugs in pediatric and geriatric populations may result in adverse events not found in adults. In this study, we utilized the large-scale U.S. Food and Drug Administration (FDA) Adverse Events Reporting System (AERS) database to look at differences in adverse events from antipsychotics among adult, pediatric, and geriatric populations. We performed a systematic analysis of the FDA AERS database using MySQL by standardizing the database using structured terminologies and ontologies. We compared adverse event profiles of atypical versus typical antipsychotic medications among adult (18-65), pediatric (age < 18), and geriatric (> 65) populations. We found statistically significant differences between the number of adverse events in the pediatric versus adult populations with aripiprazole, clozapine, fluphenazine, haloperidol, olanzapine, quetiapine, risperidone, and thiothixene, and between the geriatric versus adult populations with aripiprazole, chlorpromazine, clozapine, fluphenazine, haloperidol, paliperidone, promazine, risperidone, thiothixene, and ziprasidone (p < 0.05, with adjustment for multiple comparisons). Furthermore, the particular types of adverse events reported also varied significantly between each population for aripiprazole, clozapine, haloperidol, olanzapine, quetiapine, risperidone, and ziprasidone (Chi-square, p < 10-6). Diabetes was the most commonly reported side effect in the adult population, compared to behavioral problems in the pediatric population and neurologic symptoms in the geriatric population. We also found discrepancies between the frequencies of reports in AERS and in the literature. Our analysis of the FDA AERS database shows that there are significant differences in both the numbers and types of adverse events among these age groups and between atypical and typical antipsychotics. It is important for clinicians to be mindful of these differences when prescribing antipsychotics, especially when prescribing medications off-label.

Use of Gene Expression Profiling and Chemotherapy in Early-Stage Breast Cancer: A Study of Linked Electronic Medical Records, Cancer Registry Data, and Genomic Data Across Two Health Care Systems.

PURPOSE: The 21-gene recurrence score (RS) identifies patients with breast cancer who derive little benefit from chemotherapy; it may reduce unwarranted variability in the use of chemotherapy. We tested whether the use of RS seems to guide chemotherapy receipt across different cancer care settings. METHODS: We developed a retrospective cohort of patients with breast cancer by using electronic medical record data from Stanford University (hereafter University) and Palo Alto Medical Foundation (hereafter Community) linked with demographic and staging data from the California Cancer Registry and RS results from the testing laboratory (Genomic Health Inc., Redwood City, CA). Multivariable analysis was performed to identify predictors of RS and chemotherapy use. RESULTS: In all, 10,125 patients with breast cancer were diagnosed in the University or Community systems from 2005 to 2011; 2,418 (23.9%) met RS guidelines criteria, of whom 15.6% received RS. RS was less often used for patients with involved lymph nodes, higher tumor grade, and age < 40 or ≥ 65 years. Among RS recipients, chemotherapy receipt was associated with a higher score (intermediate v low: odds ratio, 3.66; 95% CI, 1.94 to 6.91). A total of 293 patients (10.6%) received care in both health care systems (hereafter dual use); although receipt of RS was associated with dual use (v University: odds ratio, 1.73; 95% CI, 1.18 to 2.55), there was no difference in use of chemotherapy after RS by health care setting. CONCLUSION: Although there was greater use of RS for patients who sought care in more than one health care setting, use of chemotherapy followed RS guidance in University and Community health care systems. These results suggest that precision medicine may help optimize cancer treatment across health care settings.

Chromosomal copy number alterations for associations of ductal carcinoma in situ with invasive breast cancer.

INTRODUCTION: Screening mammography has contributed to a significant increase in the diagnosis of ductal carcinoma in situ (DCIS), raising concerns about overdiagnosis and overtreatment. Building on prior observations from lineage evolution analysis, we examined whether measuring genomic features of DCIS would predict association with invasive breast carcinoma (IBC). The long-term goal is to enhance standard clinicopathologic measures of low- versus high-risk DCIS and to enable risk-appropriate treatment. METHODS: We studied three common chromosomal copy number alterations (CNA) in IBC and designed fluorescence in situ hybridization-based assay to measure copy number at these loci in DCIS samples. Clinicopathologic data were extracted from the electronic medical records of Stanford Cancer Institute and linked to demographic data from the population-based California Cancer Registry; results were integrated with data from tissue microarrays of specimens containing DCIS that did not develop IBC versus DCIS with concurrent IBC. Multivariable logistic regression analysis was performed to describe associations of CNAs with these two groups of DCIS. RESULTS: We examined 271 patients with DCIS (120 that did not develop IBC and 151 with concurrent IBC) for the presence of 1q, 8q24 and 11q13 copy number gains. Compared to DCIS-only patients, patients with concurrent IBC had higher frequencies of CNAs in their DCIS samples. On multivariable analysis with conventional clinicopathologic features, the copy number gains were significantly associated with concurrent IBC. The state of two of the three copy number gains in DCIS was associated with a risk of IBC that was 9.07 times that of no copy number gains, and the presence of gains at all three genomic loci in DCIS was associated with a more than 17-fold risk (P = 0.0013). CONCLUSIONS: CNAs have the potential to improve the identification of high-risk DCIS, defined by presence of concurrent IBC. Expanding and validating this approach in both additional cross-sectional and longitudinal cohorts may enable improved risk stratification and risk-appropriate treatment in DCIS.

An Associative Memory Model for Integration of Fragmented Research Data and Identification of Treatment Correlations in Breast Cancer Care.

A major challenge in advancing scientific discoveries using data-driven clinical research is the fragmentation of relevant data among multiple information systems. This fragmentation requires significant data-engineering work before correlations can be found among data attributes in multiple systems. In this paper, we focus on integrating information on breast cancer care, and present a novel computational approach to identify correlations between administered drugs captured in an electronic medical records and biological factors obtained from a tumor registry through rapid data aggregation and analysis. We use an associative memory (AM) model to encode all existing associations among the data attributes from both systems in a high-dimensional vector space. The AM model stores highly associated data items in neighboring memory locations to enable efficient querying operations. The results of applying AM to a set of integrated data on tumor markers and drug administrations discovered anomalies between clinical recommendations and derived associations.

Breast cancer treatment across health care systems: linking electronic medical records and state registry data to enable outcomes research.

BACKGROUND: Understanding of cancer outcomes is limited by data fragmentation. In the current study, the authors analyzed the information yielded by integrating breast cancer data from 3 sources: electronic medical records (EMRs) from 2 health care systems and the state registry. METHODS: Diagnostic test and treatment data were extracted from the EMRs of all patients with breast cancer treated between 2000 and 2010 in 2 independent California institutions: a community-based practice (Palo Alto Medical Foundation; "Community") and an academic medical center (Stanford University; "University"). The authors incorporated records from the population-based California Cancer Registry and then linked EMR-California Cancer Registry data sets of Community and University patients. RESULTS: The authors initially identified 8210 University patients and 5770 Community patients; linked data sets revealed a 16% patient overlap, yielding 12,109 unique patients. The percentage of all Community patients, but not University patients, treated at both institutions increased with worsening cancer prognostic factors. Before linking the data sets, Community patients appeared to receive less intervention than University patients (mastectomy: 37.6% vs 43.2%; chemotherapy: 35% vs 41.7%; magnetic resonance imaging: 10% vs 29.3%; and genetic testing: 2.5% vs 9.2%). Linked Community and University data sets revealed that patients treated at both institutions received substantially more interventions (mastectomy: 55.8%; chemotherapy: 47.2%; magnetic resonance imaging: 38.9%; and genetic testing: 10.9% [P < .001 for each 3-way institutional comparison]). CONCLUSIONS: Data linkage identified 16% of patients who were treated in 2 health care systems and who, despite comparable prognostic factors, received far more intensive treatment than others. By integrating complementary data from EMRs and population-based registries, a more comprehensive understanding of breast cancer care and factors that drive treatment use was obtained.

A semantic-based method for extracting concept definitions from scientific publications: evaluation in the autism phenotype domain.

BACKGROUND: A variety of informatics approaches have been developed that use information retrieval, NLP and text-mining techniques to identify biomedical concepts and relations within scientific publications or their sentences. These approaches have not typically addressed the challenge of extracting more complex knowledge such as biomedical definitions. In our efforts to facilitate knowledge acquisition of rule-based definitions of autism phenotypes, we have developed a novel semantic-based text-mining approach that can automatically identify such definitions within text. RESULTS: Using an existing knowledge base of 156 autism phenotype definitions and an annotated corpus of 26 source articles containing such definitions, we evaluated and compared the average rank of correctly identified rule definition or corresponding rule template using both our semantic-based approach and a standard term-based approach. We examined three separate scenarios: (1) the snippet of text contained a definition already in the knowledge base; (2) the snippet contained an alternative definition for a concept in the knowledge base; and (3) the snippet contained a definition not in the knowledge base. Our semantic-based approach had a higher average rank than the term-based approach for each of the three scenarios (scenario 1: 3.8 vs. 5.0; scenario 2: 2.8 vs. 4.9; and scenario 3: 4.5 vs. 6.2), with each comparison significant at the p-value of 0.05 using the Wilcoxon signed-rank test. CONCLUSIONS: Our work shows that leveraging existing domain knowledge in the information extraction of biomedical definitions significantly improves the correct identification of such knowledge within sentences. Our method can thus help researchers rapidly acquire knowledge about biomedical definitions that are specified and evolving within an ever-growing corpus of scientific publications.