A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management.

OBJECTIVE:Develop a device-agnostic cloud platform to host diabetes device data and catalyze an ecosystem of software innovation for type 1 diabetes (T1D) management. MATERIALS AND METHODS:An interdisciplinary team decided to establish a nonprofit company, Tidepool, and build open-source software. RESULTS:Through a user-centered design process, the authors created a software platform, the Tidepool Platform, to upload and host T1D device data in an integrated, device-agnostic fashion, as well as an application ("app"), Blip, to visualize the data. Tidepool's software utilizes the principles of modular components, modern web design including REST APIs and JavaScript, cloud computing, agile development methodology, and robust privacy and security. DISCUSSION:By consolidating the currently scattered and siloed T1D device data ecosystem into one open platform, Tidepool can improve access to the data and enable new possibilities and efficiencies in T1D clinical care and research. The Tidepool Platform decouples diabetes apps from diabetes devices, allowing software developers to build innovative apps without requiring them to design a unique back-end (e.g., database and security) or unique ways of ingesting device data. It allows people with T1D to choose to use any preferred app regardless of which device(s) they use. CONCLUSION:The authors believe that the Tidepool Platform can solve two current problems in the T1D device landscape: 1) limited access to T1D device data and 2) poor interoperability of data from different devices. If proven effective, Tidepool's open source, cloud model for health data interoperability is applicable to other healthcare use cases

Health Figures: An Open Source JavaScript Library for Health Data Visualization

The way we look at data has a great impact on how we can understand it, particularly when the data is related to health and wellness. Due to the increased use of self-tracking devices and the ongoing shift towards preventive medicine, better understanding of our health data is an important part of improving the general welfare of the citizens. Electronic Health Records, self-tracking devices and mobile applications provide a rich variety of data but it often becomes difficult to understand. We implemented the hFigures library inspired on the hGraph visualization with additional improvements. The purpose of the library is to provide a visual representation of the evolution of health measurements in a complete and useful manner. We researched the usefulness and usability of the library by building an application for health data visualization in a health coaching program. We performed a user evaluation with Heuristic Evaluation, Controlled User Testing and Usability Questionnaires. In the Heuristics Evaluation the average response was 6.3 out of 7 points and the Cognitive Walkthrough done by usability experts indicated no design or mismatch errors. In the CSUQ usability test the system obtained an average score of 6.13 out of 7, and in the ASQ usability test the overall satisfaction score was 6.64 out of 7. We developed hFigures, an open source library for visualizing a complete, accurate and normalized graphical representation of health data. The idea is based on the concept of the hGraph but it provides additional key features, including a comparison of multiple health measurements over time. We conducted a usability evaluation of the library as a key component of an application for health and wellness monitoring. The results indicate that the data visualization library was helpful in assisting users in understanding health data and its evolution over time.Comment: BMC Medical Informatics and Decision Making 16.1 (2016

Identification of trends in racial/ethnic disparities of patients with diabtes mellitus using web-based tableau dashboard- a cross sectional study

Many ways of creating data visualizations using the Business Intelligence tools have been implemented and new ways are continuously evolving. In this project, I have used Tableau Public software to analyze the trends of Race and Ethnic disparities in Diabetes Mellites patients by creating individual dashboards. A desktop application was created using the web programming languages like HTML and CSS to create more interactive and application embedded dashboard. The dataset selected was Health Facts® database, which is contributed of day-to-day patient care encounters. Data preparation and data pre-processing and data visualization were the two major steps to get the required results. In Data pre-processing, data mining tools such as SQL and Python were used to create the final dataset with 7 variables. An infographic was created with a dashboard with three views embedded into web pages. These three dashboard views were created based their specific information like one dashboard view showing the insights about the distribution of Hispanic with Diabetes Mellitus, another dashboard view showing the trends of African American and Caucasian races and the third view showing the distribution of patients with Diabetes Mellitus and specific cancers based on race and ethnicity. All the data obtained were analyzed and compared with the CDC data and the results confirmed. Moreover, to measure the usability of the desktop application, SUS (System Usability Score) was used. The result of the application clearly indicated the way such application can be used strategize the programs and interventions to reduce the disparities for Diabetes Mellitus amongst the African American population

Modeling Faceted Browsing with Category Theory for Reuse and Interoperability

Faceted browsing (also called faceted search or faceted navigation) is an exploratory search model where facets assist in the interactive navigation of search results. Facets are attributes that have been assigned to describe resources being explored; a faceted taxonomy is a collection of facets provided by the interface and is often organized as sets, hierarchies, or graphs. Faceted browsing has become ubiquitous with modern digital libraries and online search engines, yet the process is still difficult to abstractly model in a manner that supports the development of interoperable and reusable interfaces. We propose category theory as a theoretical foundation for faceted browsing and demonstrate how the interactive process can be mathematically abstracted in order to support the development of reusable and interoperable faceted systems. Existing efforts in facet modeling are based upon set theory, formal concept analysis, and light-weight ontologies, but in many regards they are implementations of faceted browsing rather than a specification of the basic, underlying structures and interactions. We will demonstrate that category theory allows us to specify faceted objects and study the relationships and interactions within a faceted browsing system. Resulting implementations can then be constructed through a category-theoretic lens using these models, allowing abstract comparison and communication that naturally support interoperability and reuse. In this context, reuse and interoperability are at two levels: between discrete systems and within a single system. Our model works at both levels by leveraging category theory as a common language for representation and computation. We will establish facets and faceted taxonomies as categories and will demonstrate how the computational elements of category theory, including products, merges, pushouts, and pullbacks, extend the usefulness of our model. More specifically, we demonstrate that categorical constructions such as the pullback and pushout operations can help organize and reorganize facets; these operations in particular can produce faceted views containing relationships not found in the original source taxonomy. We show how our category-theoretic model of facets relates to database schemas and discuss how this relationship assists in implementing the abstractions presented. We give examples of interactive interfaces from the biomedical domain to help illustrate how our abstractions relate to real-world requirements while enabling systematic reuse and interoperability. We introduce DELVE (Document ExpLoration and Visualization Engine), our framework for developing interactive visualizations as modular Web-applications in order to assist researchers with exploratory literature search. We show how facets relate to and control visualizations; we give three examples of text visualizations that either contain or interact with facets. We show how each of these visualizations can be represented with our model and demonstrate how our model directly informs implementation. With our general framework for communicating consistently about facets at a high level of abstraction, we enable the construction of interoperable interfaces and enable the intelligent reuse of both existing and future efforts

Where can teens find health information? A survey of web portals designed for teen health information seekers

The Web is an important source for health information for most teens with access to the Web (Gray et al, 2005a; Kaiser, 2001). While teens are likely to turn to the Web for health information, research has indicated that their skills in locating, evaluating and using health information are weak (Hansen et al, 2003; Skinner et al, 2003, Gray et al, 2005b). This behaviour suggests that the targeted approach to finding health information that is offered by web portals would be useful to teens. A web portal is the entry point for information on the Web. It is the front end, and often the filter, that users must pass through in order to link to actual content. Unlike general search engines such as Google, content that is linked to a portal has usually been pre-selected and even created by the organization that hosts the portal, assuring some level of quality control. The underlying architecture of the portal is structured and thus offers an organized approach to exploring a specific health topic. This paper reports on an environmental scan of the Web, the purpose of which was to identify and describe portals to general health information, in English and French, designed specifically for teens. It answers two key questions. First of all, what portals exist? And secondly, what are their characteristics? The portals were analyzed through the lens of four attributes: Usability, interactivity, reliability and findability. Usability is a term that incorporates concepts of navigation, layout and design, clarity of concept and purpose, underlying architecture, in-site assistance and, for web content with text, readability. Interactivity relates to the type of interactions and level of engagement required by the user to access health information on a portal. Interaction can come in the form of a game, a quiz, a creative experience, or a communication tool such as an instant messaging board, a forum or blog. Reliability reflects the traditional values of accuracy, currency, credibility and bias, and in the web-based world, durabililty. Findability is simply the ease with which a portal can be discovered by a searcher using the search engine that is most commonly associated with the Web by young people - Google - and using terms related to teen health. Findability is an important consideration since the majority of teens begin their search for health information using search engines (CIBER, 2008; Hansen et al, 2003). The content linked to by the portals was not evaluated, nor was the portals’ efficacy as a health intervention. Teens looking for health information on the Web in English have a wide range of choices available but French-language portals are much rarer and harder to find. A majority of the portals found and reviewed originated from hospitals, associations specializing in a particular disease, and governmental agencies, suggesting that portals for teens on health related topics are generally reliable. However, only a handful of the portals reviewed were easy to find, suggesting that valuable resources for teens remain buried in the Web

COVID-19 Data Warehouse: A Systematic Literature Review

The coronavirus disease (COVID-19) affects the whole world and led clinicians to use the available knowledge to diagnose or predict the infection. Data Warehouse is one of the most crucial tools that may enhance decision-making (DW).In this paper, three main questions will be investigated according to using DW in the COVID-19 pandemic. The effect of using DW in the field of diagnosing and prediction will be investigated, besides, the most used architecture of DW will be explored. The sectors that faced a lot of researchers' attention such as diagnosing, predicting, and finding the correlations among features will be examined. The selected studies are explored where the papers that have been published between 2019-2022 in the digital libraries (ACM, IEEE, Springer, Science Direct, and Elsevier) in the field of DW that handle the COVID-19 are selected. During the research, many limitations have been detected, while some future works are presented. Enterprise DW is the most used architecture for COVID-19 DW while finding correlation among features and prediction are the sectors that had taken the researchers' attentio

Repeatable and reusable research - Exploring the needs of users for a Data Portal for Disease Phenotyping

Background: Big data research in the field of health sciences is hindered by a lack of agreement on how to identify and define different conditions and their medications. This means that researchers and health professionals often have different phenotype definitions for the same condition. This lack of agreement makes it hard to compare different study findings and hinders the ability to conduct repeatable and reusable research. Objective: This thesis aims to examine the requirements of various users, such as researchers, clinicians, machine learning experts, and managers, for both new and existing data portals for phenotypes (concept libraries). Methods: Exploratory sequential mixed methods were used in this thesis to look at which concept libraries are available, how they are used, what their characteristics are, where there are gaps, and what needs to be done in the future from the point of view of the people who use them. This thesis consists of three phases: 1) two qualitative studies, including one-to-one interviews with researchers, clinicians, machine learning experts, and senior research managers in health data science, as well as focus group discussions with researchers working with the Secured Anonymized Information Linkage databank, 2) the creation of an email survey (i.e., the Concept Library Usability Scale), and 3) a quantitative study with researchers, health professionals, and clinicians. Results: Most of the participants thought that the prototype concept library would be a very helpful resource for conducting repeatable research, but they specified that many requirements are needed before its development. Although all the participants stated that they were aware of some existing concept libraries, most of them expressed negative perceptions about them. The participants mentioned several facilitators that would encourage them to: 1) share their work, such as receiving citations from other researchers; and 2) reuse the work of others, such as saving a lot of time and effort, which they frequently spend on creating new code lists from scratch. They also pointed out several barriers that could inhibit them from: 1) sharing their work, such as concerns about intellectual property (e.g., if they shared their methods before publication, other researchers would use them as their own); and 2) reusing others' work, such as a lack of confidence in the quality and validity of their code lists. Participants suggested some developments that they would like to see happen in order to make research that is done with routine data more reproducible, such as the availability of a drive for more transparency in research methods documentation, such as publishing complete phenotype definitions and clear code lists. Conclusions: The findings of this thesis indicated that most participants valued a concept library for phenotypes. However, only half of the participants felt that they would contribute by providing definitions for the concept library, and they reported many barriers regarding sharing their work on a publicly accessible platform such as the CALIBER research platform. Analysis of interviews, focus group discussions, and qualitative studies revealed that different users have different requirements, facilitators, barriers, and concerns about concept libraries. This work was to investigate if we should develop concept libraries in Kuwait to facilitate the development of improved data sharing. However, at the end of this thesis the recommendation is this would be unlikely to be cost effective or highly valued by users and investment in open access research publications may be of more value to the Kuwait research/academic community

iCloudECG: A Mobile Cardiac Telemedicine System

With rising healthcare costs and a substantially growing number of patients 65 or over, the benefits of telemedicine and patient self-monitoring systems are becoming increasingly evident. Patients, physicians, hospitals, and even insurance providers benefit from vigilant, cost-effective patient monitoring systems. This thesis describes the development of a portable, smart-phone connected system for continuous cardiac monitoring. The system is capable of continuously monitoring the conditions of the heart, automated detection of cardiac arrhythmias, and real-time notifying patients and physicians of the detected abnormalities. The system consists of four main subsystems: 1) a Bluetooth capable chest-strap ECG, 2) an Android-enabled mobile device, 3) a cloud-based analysis, storage, and notification system, and 4) a web-application portal. Data is collected by the single-lead ECG device, and transmitted to the mobile device via Bluetooth. An application allows the patient to view their ECG output in real-time, view the last 24 hours of recordings, and receive notifications and details regarding any detected abnormalities. The mobile device transmits the ECG data to a remote server for pre-processing and analysis, and then stores the data in a database which the patient or physician can access via a web-interface. The developed system can be used as a telemedicine system for management of cardiovascular diseases

Computational Methods for Interactive and Explorative Study Design and Integration of High-throughput Biological Data

The increase in the use of high-throughput methods to gain insights into biological systems has come with new challenges. Genomics, transcriptomics, proteomics, and metabolomics lead to a massive amount of data and metadata. While this wealth of information has resulted in many scientific discoveries, new strategies are needed to cope with the ever-growing variety and volume of metadata. Despite efforts to standardize the collection of study metadata, many experiments cannot be reproduced or replicated. One reason for this is the difficulty to provide the necessary metadata. The large sample sizes that modern omics experiments enable, also make it increasingly complicated for scientists to keep track of every sample and the needed annotations. The many data transformations that are often needed to normalize and analyze omics data require a further collection of all parameters and tools involved. A second possible cause is missing knowledge about statistical design of studies, both related to study factors as well as the required sample size to make significant discoveries. In this thesis, we develop a multi-tier model for experimental design and a portlet for interactive web-based study design. Through the input of experimental factors and the number of replicates, users can easily create large, factorial experimental designs. Changes or additional metadata can be quickly uploaded via user-defined spreadsheets including sample identifiers. In order to comply with existing standards and provide users with a quick way to import existing studies, we provide full interoperability with the ISA-Tab format. We show that both data model and portlet are easily extensible to create additional tiers of samples annotated with technology-specific metadata. We tackle the problem of unwieldy experimental designs by creating an aggregation graph. Based on our multi-tier experimental design model, similar samples, their sources, and analytes are summarized, creating an interactive summary graph that focuses on study factors and replicates. Thus, we give researchers a quick overview of sample sizes and the aim of different studies. This graph can be included in our portlets or used as a stand alone application and is compatible with the ISA-Tab format. We show that this approach can be used to explore the quality of publicly available experimental designs and metadata annotation. The third part of this thesis contributes to a more statistically sound experiment planning for differential gene expression experiments. We integrate two tools for the prediction of statistical power and sample size estimation into our portal. This integration enables the use of existing data, in order to arrive at more accurate calculation for sample variability. Additionally, the statistical power of existing experimental designs of certain sample sizes can be analyzed. All results and parameters are stored and can be used for later comparison. Even perfectly planned and annotated experiments cannot eliminate human error. Based on our model we develop an automated workflow for microarray quality control, enabling users to inspect the quality of normalization and cluster samples by study factor levels. We import a publicly available microarray dataset to assess our contributions to reproducibility and explore alternative analysis methods based on statistical power analysis