Ontology-based categorization of clinical studies by their conditions.

OBJECTIVE: The free-text Condition data field in the ClinicalTrials.gov is not amenable to computational processes for retrieving, aggregating and visualizing clinical studies by condition categories. This paper contributes a method for automated ontology-based categorization of clinical studies by their conditions. MATERIALS AND METHODS: Our method first maps text entries in ClinicalTrials.gov's Condition field to standard condition concepts in the OMOP Common Data Model by using SNOMED CT as a reference ontology and using Usagi for concept normalization, followed by hierarchical traversal of the SNOMED ontology for concept expansion, ontology-driven condition categorization, and visualization. We compared the accuracy of this method to that of the MeSH-based method. RESULTS: We reviewed the 4,506 studies on Vivli.org categorized by our method. Condition terms of 4,501 (99.89%) studies were successfully mapped to SNOMED CT concepts, and with a minimum concept mapping score threshold, 4,428 (98.27%) studies were categorized into 31 predefined categories. When validating with manual categorization results on a random sample of 300 studies, our method achieved an estimated categorization accuracy of 95.7%, while the MeSH-based method had an accuracy of 85.0%. CONCLUSION: We showed that categorizing clinical studies using their Condition terms with referencing to SNOMED CT achieved a better accuracy and coverage than using MeSH terms. The proposed ontology-driven condition categorization was useful to create accurate clinical study categorization that enables clinical researchers to aggregate evidence from a large number of clinical studies.

Ethical Framework for Assessing Manual and Digital Contact Tracing for COVID-19.

The coronavirus disease 2019 (COVID-19) pandemic has challenged the traditional public health balance between benefiting the good of the community through contact tracing and restricting individual liberty. This article first analyzes important technical and ethical issues regarding new smartphone apps that facilitate contact tracing and exposure notification. It then presents a framework for assessing contact tracing, whether manual or digital: the effectiveness at mitigating the pandemic; acceptability of risks, particularly privacy; and equitable distribution of benefits and risks. Both manual and digital contact tracing require public trust, engagement of minority communities, prompt COVID-19 testing and return of results, and high adherence with physical distancing and use of masks.

Effect of Mobile Device-Assisted N-of-1 Trial Participation on Analgesic Prescribing for Chronic Pain: Randomized Controlled Trial.

OBJECTIVES: Opioids and non-steroidal anti-inflammatory drugs (NSAIDs) are frequently prescribed for chronic musculoskeletal pain, despite limited evidence of effectiveness and well-documented adverse effects. We assessed the effects of participating in a structured, personalized self-experiment ("N-of-1 trial") on analgesic prescribing in patients with chronic musculoskeletal pain. METHODS: We randomized 215 patients with chronic pain to participate in an N-of-1 trial facilitated by a mobile health app or to receive usual care. Medical records of participating patients were reviewed at enrollment and 6 months later to assess analgesic prescribing. We established thresholds of ≥ 50, ≥ 20, and > 0 morphine milligram equivalents (MMEs) per day to capture patients taking relatively high doses only, patients taking low-moderate as well as relatively high doses, and patients taking any dose of opioids, respectively. RESULTS: There was no significant difference between the N-of-1 and control groups in the percentage of patients prescribed any opioids (relative odds ratio (ROR) = 1.05; 95% confidence interval [CI] = 0.61 to 1.80, p = 0.87). There was a clinically substantial but statistically not significant reduction of the percentage of patients receiving ≥ 20 MME (ROR = 0.58; 95% CI = 0.33 to 1.04, p = 0.07) and also in the percentage receiving ≥ 50 MME (ROR = 0.50; 95% CI = 0.19 to 1.34, p = 0.17). There was a significant reduction in the proportion of patients in the N-of-1 group prescribed NSAIDs compared with control (relative odds ratio = 0.53; 95% CI = 0.29 to 0.96, p = 0.04), with no concomitant increase in average pain intensity. There was no significant change in use of adjunctive medications (acetaminophen, gabapentenoids, or topicals). DISCUSSION: These exploratory results suggest that participation in N-of-1 trials may reduce long-term use of NSAIDs; there is also a weak signal for an effect on use of opioids. Additional research is needed to confirm these results and elucidate possible mechanisms. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT02116621.

Why we need a small data paradigm.

BACKGROUND: There is great interest in and excitement about the concept of personalized or precision medicine and, in particular, advancing this vision via various 'big data' efforts. While these methods are necessary, they are insufficient to achieve the full personalized medicine promise. A rigorous, complementary 'small data' paradigm that can function both autonomously from and in collaboration with big data is also needed. By 'small data' we build on Estrin's formulation and refer to the rigorous use of data by and for a specific N-of-1 unit (i.e., a single person, clinic, hospital, healthcare system, community, city, etc.) to facilitate improved individual-level description, prediction and, ultimately, control for that specific unit. MAIN BODY: The purpose of this piece is to articulate why a small data paradigm is needed and is valuable in itself, and to provide initial directions for future work that can advance study designs and data analytic techniques for a small data approach to precision health. Scientifically, the central value of a small data approach is that it can uniquely manage complex, dynamic, multi-causal, idiosyncratically manifesting phenomena, such as chronic diseases, in comparison to big data. Beyond this, a small data approach better aligns the goals of science and practice, which can result in more rapid agile learning with less data. There is also, feasibly, a unique pathway towards transportable knowledge from a small data approach, which is complementary to a big data approach. Future work should (1) further refine appropriate methods for a small data approach; (2) advance strategies for better integrating a small data approach into real-world practices; and (3) advance ways of actively integrating the strengths and limitations from both small and big data approaches into a unified scientific knowledge base that is linked via a robust science of causality. CONCLUSION: Small data is valuable in its own right. That said, small and big data paradigms can and should be combined via a foundational science of causality. With these approaches combined, the vision of precision health can be achieved.

Role of Health Information Technology in Addressing Health Disparities: Patient, Clinician, and System Perspectives.

Over the last decade, health information technology (IT) has dramatically transformed medical practice in the United States. On May 11-12, 2017, the National Institute on Minority Health and Health Disparities, in partnership with the National Science Foundation and the National Health IT Collaborative for the Underserved, convened a scientific workshop, "Addressing Health Disparities with Health Information Technology," with the goal of ensuring that future research guides potential health IT initiatives to address the needs of health disparities populations. The workshop examined patient, clinician, and system perspectives on the potential role of health IT in addressing health disparities. Attendees were asked to identify and discuss various health IT challenges that confront underserved communities and propose innovative strategies to address them, and to involve these communities in this process. Community engagement, cultural competency, and patient-centered care were highlighted as key to improving health equity, as well as to promoting scalable, sustainable, and effective health IT interventions. Participants noted the need for more research on how health IT can be used to evaluate and address the social determinants of health. Expanding public-private partnerships was emphasized, as was the importance of clinicians and IT developers partnering and using novel methods to learn how to improve health care decision-making. Finally, to advance health IT and promote health equity, it will be necessary to record and capture health disparity data using standardized terminology, and to continuously identify system-level deficiencies and biases.

Multivariate analysis of the population representativeness of related clinical studies.

OBJECTIVE: To develop a multivariate method for quantifying the population representativeness across related clinical studies and a computational method for identifying and characterizing underrepresented subgroups in clinical studies. METHODS: We extended a published metric named Generalizability Index for Study Traits (GIST) to include multiple study traits for quantifying the population representativeness of a set of related studies by assuming the independence and equal importance among all study traits. On this basis, we compared the effectiveness of GIST and multivariate GIST (mGIST) qualitatively. We further developed an algorithm called "Multivariate Underrepresented Subgroup Identification" (MAGIC) for constructing optimal combinations of distinct value intervals of multiple traits to define underrepresented subgroups in a set of related studies. Using Type 2 diabetes mellitus (T2DM) as an example, we identified and extracted frequently used quantitative eligibility criteria variables in a set of clinical studies. We profiled the T2DM target population using the National Health and Nutrition Examination Survey (NHANES) data. RESULTS: According to the mGIST scores for four example variables, i.e., age, HbA1c, BMI, and gender, the included observational T2DM studies had superior population representativeness than the interventional T2DM studies. For the interventional T2DM studies, Phase I trials had better population representativeness than Phase III trials. People at least 65years old with HbA1c value between 5.7% and 7.2% were particularly underrepresented in the included T2DM trials. These results confirmed well-known knowledge and demonstrated the effectiveness of our methods in population representativeness assessment. CONCLUSIONS: mGIST is effective at quantifying population representativeness of related clinical studies using multiple numeric study traits. MAGIC identifies underrepresented subgroups in clinical studies. Both data-driven methods can be used to improve the transparency of design bias in participation selection at the research community level.

Visual aggregate analysis of eligibility features of clinical trials.

OBJECTIVE: To develop a method for profiling the collective populations targeted for recruitment by multiple clinical studies addressing the same medical condition using one eligibility feature each time. METHODS: Using a previously published database COMPACT as the backend, we designed a scalable method for visual aggregate analysis of clinical trial eligibility features. This method consists of four modules for eligibility feature frequency analysis, query builder, distribution analysis, and visualization, respectively. This method is capable of analyzing (1) frequently used qualitative and quantitative features for recruiting subjects for a selected medical condition, (2) distribution of study enrollment on consecutive value points or value intervals of each quantitative feature, and (3) distribution of studies on the boundary values, permissible value ranges, and value range widths of each feature. All analysis results were visualized using Google Charts API. Five recruited potential users assessed the usefulness of this method for identifying common patterns in any selected eligibility feature for clinical trial participant selection. RESULTS: We implemented this method as a Web-based analytical system called VITTA (Visual Analysis Tool of Clinical Study Target Populations). We illustrated the functionality of VITTA using two sample queries involving quantitative features BMI and HbA1c for conditions "hypertension" and "Type 2 diabetes", respectively. The recruited potential users rated the user-perceived usefulness of VITTA with an average score of 86.4/100. CONCLUSIONS: We contributed a novel aggregate analysis method to enable the interrogation of common patterns in quantitative eligibility criteria and the collective target populations of multiple related clinical studies. A larger-scale study is warranted to formally assess the usefulness of VITTA among clinical investigators and sponsors in various therapeutic areas.

The Ontology of Clinical Research (OCRe): an informatics foundation for the science of clinical research.

To date, the scientific process for generating, interpreting, and applying knowledge has received less informatics attention than operational processes for conducting clinical studies. The activities of these scientific processes - the science of clinical research - are centered on the study protocol, which is the abstract representation of the scientific design of a clinical study. The Ontology of Clinical Research (OCRe) is an OWL 2 model of the entities and relationships of study design protocols for the purpose of computationally supporting the design and analysis of human studies. OCRe's modeling is independent of any specific study design or clinical domain. It includes a study design typology and a specialized module called ERGO Annotation for capturing the meaning of eligibility criteria. In this paper, we describe the key informatics use cases of each phase of a study's scientific lifecycle, present OCRe and the principles behind its modeling, and describe applications of OCRe and associated technologies to a range of clinical research use cases. OCRe captures the central semantics that underlies the scientific processes of clinical research and can serve as an informatics foundation for supporting the entire range of knowledge activities that constitute the science of clinical research.

A Closed-Loop Falls Monitoring and Prevention App for Multiple Sclerosis Clinical Practice: Human-Centered Design of the Multiple Sclerosis Falls InsightTrack.

BACKGROUND: Falls are common in people with multiple sclerosis (MS), causing injuries, fear of falling, and loss of independence. Although targeted interventions (physical therapy) can help, patients underreport and clinicians undertreat this issue. Patient-generated data, combined with clinical data, can support the prediction of falls and lead to timely intervention (including referral to specialized physical therapy). To be actionable, such data must be efficiently delivered to clinicians, with care customized to the patient's specific context. OBJECTIVE: This study aims to describe the iterative process of the design and development of Multiple Sclerosis Falls InsightTrack (MS-FIT), identifying the clinical and technological features of this closed-loop app designed to support streamlined falls reporting, timely falls evaluation, and comprehensive and sustained falls prevention efforts. METHODS: Stakeholders were engaged in a double diamond process of human-centered design to ensure that technological features aligned with users' needs. Patient and clinician interviews were designed to elicit insight around ability blockers and boosters using the capability, opportunity, motivation, and behavior (COM-B) framework to facilitate subsequent mapping to the Behavior Change Wheel. To support generalizability, patients and experts from other clinical conditions associated with falls (geriatrics, orthopedics, and Parkinson disease) were also engaged. Designs were iterated based on each round of feedback, and final mock-ups were tested during routine clinical visits. RESULTS: A sample of 30 patients and 14 clinicians provided at least 1 round of feedback. To support falls reporting, patients favored a simple biweekly survey built using REDCap (Research Electronic Data Capture; Vanderbilt University) to support bring-your-own-device accessibility-with optional additional context (the severity and location of falls). To support the evaluation and prevention of falls, clinicians favored a clinical dashboard featuring several key visualization widgets: a longitudinal falls display coded by the time of data capture, severity, and context; a comprehensive, multidisciplinary, and evidence-based checklist of actions intended to evaluate and prevent falls; and MS resources local to a patient's community. In-basket messaging alerts clinicians of severe falls. The tool scored highly for usability, likability, usefulness, and perceived effectiveness (based on the Health IT Usability Evaluation Model scoring). CONCLUSIONS: To our knowledge, this is the first falls app designed using human-centered design to prioritize behavior change and, while being accessible at home for patients, to deliver actionable data to clinicians at the point of care. MS-FIT streamlines data delivery to clinicians via an electronic health record-embedded window, aligning with the 5 rights approach. Leveraging MS-FIT for data processing and algorithms minimizes clinician load while boosting care quality. Our innovation seamlessly integrates real-world patient-generated data as well as clinical and community-level factors, empowering self-care and addressing the impact of falls in people with MS. Preliminary findings indicate wider relevance, extending to other neurological conditions associated with falls and their consequences.

Making sense of mobile health data: an open architecture to improve individual- and population-level health.

Mobile phones and devices, with their constant presence, data connectivity, and multiple intrinsic sensors, can support around-the-clock chronic disease prevention and management that is integrated with daily life. These mobile health (mHealth) devices can produce tremendous amounts of location-rich, real-time, high-frequency data. Unfortunately, these data are often full of bias, noise, variability, and gaps. Robust tools and techniques have not yet been developed to make mHealth data more meaningful to patients and clinicians. To be most useful, health data should be sharable across multiple mHealth applications and connected to electronic health records. The lack of data sharing and dearth of tools and techniques for making sense of health data are critical bottlenecks limiting the impact of mHealth to improve health outcomes. We describe Open mHealth, a nonprofit organization that is building an open software architecture to address these data sharing and "sense-making" bottlenecks. Our architecture consists of open source software modules with well-defined interfaces using a minimal set of common metadata. An initial set of modules, called InfoVis, has been developed for data analysis and visualization. A second set of modules, our Personal Evidence Architecture, will support scientific inferences from mHealth data. These Personal Evidence Architecture modules will include standardized, validated clinical measures to support novel evaluation methods, such as n-of-1 studies. All of Open mHealth's modules are designed to be reusable across multiple applications, disease conditions, and user populations to maximize impact and flexibility. We are also building an open community of developers and health innovators, modeled after the open approach taken in the initial growth of the Internet, to foster meaningful cross-disciplinary collaboration around new tools and techniques. An open mHealth community and architecture will catalyze increased mHealth efficiency, effectiveness, and innovation.

Personalized Data Science and Personalized (N-of-1) Trials: Promising Paradigms for Individualized Health Care.

The term 'data science' usually refers to the process of extracting value from big data obtained from a large group of individuals. An alternative rendition, which we call personalized data science (Per-DS), aims to collect, analyze, and interpret personal data to inform personal decisions. This article describes the main features of Per-DS, and reviews its current state and future outlook. A Per-DS investigation is of, by, and for an individual, the Per-DS investigator, acting simultaneously as her own investigator, study participant, and beneficiary, and making personalized decisions for study design and implementation. The scope of Per-DS studies may include systematic monitoring of physiological or behavioral patterns, case-crossover studies for symptom triggers, pre-post trials for exposure-outcome relationships, and personalized (N-of-1) trials for effectiveness. Per-DS studies produce personal knowledge generalizable to the individual's future self (thus benefiting herself) rather than knowledge generalizable to an external population (thus benefiting others). This endeavor requires a pivot from data mining or extraction to data gardening, analogous to home gardeners producing food for home consumption-the Per-DS investigator needs to 'cultivate the field' by setting goals, specifying study design, identifying necessary data elements, and assembling instruments and tools for data collection. Then, she can implement the study protocol, harvest her personal data, and mine the data to extract personal knowledge. To facilitate Per-DS studies, Per-DS investigators need support from community-based, scientific, philanthropic, business, and government entities, to develop and deploy resources such as peer forums, mobile apps, 'virtual field guides,' and scientific and regulatory guidance.

Long COVID and Medicine's Two Cultures.

Medicine has separated the two cultures of biological science and social science in research, even though they are intimately connected in the lives of our patients. To understand the cause, progression, and treatment of long COVID , biology and biography, the patient's lived experience, must be studied together.