Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

Computer-Aided Pharmacoepidemiology in Drug Use and Safety: Examining the Intersection between Data Science and Medicines Research

Pharmacoepidemiology is a relatively new area of study that focuses on research aimed at producing data about drugs’ usage and safety in well-defined populations. Its significant impact on patient safety has translated into improving health care systems worldwide, where it has been widely adopted. This field has developed to an extent that policy and guidelines makers have started using its evidence alongside that produced from randomised controlled clinical trials. Although this significant improvement has been partly attributed to the adoption of statistics and computer-aided models into the way pharmacoepidemiology studies are designed and conducted, certain gaps still exist. This chapter reports some of the significant developments made, along with the gaps observed so far, in the adoption of statistics and computing into pharmacoepidemiology research. The goal is to highlight efforts that have led to the new pharmacoepidemiology developments, while examining the intersection between data science and pharmacology through research narrative reviews of computer-aided pharmacology. The chapter shows the significant number of initiatives that have been applied/adopted to improve pharmacoepidemiology research. Nonetheless, further developments in integrating pharmacoepidemiology with computers and statistics are needed in order to enhance the research agenda

The Use of Routinely Collected Data in Clinical Trial Research

RCTs are the gold standard for assessing the effects of medical interventions, but they also pose many challenges, including the often-high costs in conducting them and a potential lack of generalizability of their findings. The recent increase in the availability of so called routinely collected data (RCD) sources has led to great interest in their application to support RCTs in an effort to increase the efficiency of conducting clinical trials. We define all RCTs augmented by RCD in any form as RCD-RCTs. A major subset of RCD-RCTs are performed at the point of care using electronic health records (EHRs) and are referred to as point-of-care research (POC-R). RCD-RCTs offer several advantages over traditional trials regarding patient recruitment and data collection, and beyond. Using highly standardized EHR and registry data allows to assess patient characteristics for trial eligibility and to examine treatment effects through routinely collected endpoints or by linkage to other data sources like mortality registries. Thus, RCD can be used to augment traditional RCTs by providing a sampling framework for patient recruitment and by directly measuring patient relevant outcomes. The result of these efforts is the generation of real-world evidence (RWE). Nevertheless, the utilization of RCD in clinical research brings novel methodological challenges, and issues related to data quality are frequently discussed, which need to be considered for RCD-RCTs. Some of the limitations surrounding RCD use in RCTs relate to data quality, data availability, ethical and informed consent challenges, and lack of endpoint adjudication which may all lead to uncertainties in the validity of their results. The purpose of this thesis is to help fill the aforementioned research gaps in RCD-RCTs, encompassing tasks such as assessing their current application in clinical research and evaluating the methodological and technical challenges in performing them. Furthermore, it aims to assess the reporting quality of published reports on RCD-RCTs

Supporting Pharmacovigilance Signal Validation and Prioritization with Analyses of Routinely Collected Health Data: Lessons Learned from an EHDEN Network Study

Introduction: Individual case reports are the main asset in pharmacovigilance signal management. Signal validation is the first stage after signal detection and aims to determine if there is sufficient evidence to justify further assessment. Throughout signal management, a prioritization of signals is continually made. Routinely collected health data can provide relevant contextual information but are primarily used at a later stage in pharmacoepidemiological studies to assess communicated signals. Objective: The aim of this study was to examine the feasibility and utility of analysing routine health data from a multinational distributed network to support signal validation and prioritization and to reflect on key user requirements for these analyses to become an integral part of this process. Methods: Statistical signal detection was performed in VigiBase, the WHO global database of individual case safety reports, targeting generic manufacturer drugs and 16 prespecified adverse events. During a 5-day study-a-thon, signal validation and prioritization were performed using information from VigiBase, regulatory documents and the scientific literature alongside descriptive analyses of routine health data from 10 partners of the European Health Data and Evidence Network (EHDEN). Databases included in the study were from the UK, Spain, Norway, the Netherlands and Serbia, capturing records from primary care and/or hospitals. Results: Ninety-five statistical signals were subjected to signal validation, of which eight were considered for descriptive analyses in the routine health data. Design, execution and interpretation of results from these analyses took up to a few hours for each signal (of which 15–60 minutes were for execution) and informed decisions for five out of eight signals. The impact of insights from the routine health data varied and included possible alternative explanations, potential public health and clinical impact and feasibility of follow-up pharmacoepidemiological studies. Three signals were selected for signal assessment, two of these decisions were supported by insights from the routine health data. Standardization of analytical code, availability of adverse event phenotypes including bridges between different source vocabularies, and governance around the access and use of routine health data were identified as important aspects for future development. Conclusions: Analyses of routine health data from a distributed network to support signal validation and prioritization are feasible in the given time limits and can inform decision making. The cost–benefit of integrating these analyses at this stage of signal management requires further research