The Infectious Disease Ontology in the Age of COVID-19

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research

Epidemiological Prediction using Deep Learning

Department of Mathematical SciencesAccurate and real-time epidemic disease prediction plays a significant role in the health system and is of great importance for policy making, vaccine distribution and disease control. From the SIR model by Mckendrick and Kermack in the early 1900s, researchers have developed a various mathematical model to forecast the spread of disease. With all attempt, however, the epidemic prediction has always been an ongoing scientific issue due to the limitation that the current model lacks flexibility or shows poor performance. Owing to the temporal and spatial aspect of epidemiological data, the problem fits into the category of time-series forecasting. To capture both aspects of the data, this paper proposes a combination of recent Deep Leaning models and applies the model to ILI (influenza like illness) data in the United States. Specifically, the graph convolutional network (GCN) model is used to capture the geographical feature of the U.S. regions and the gated recurrent unit (GRU) model is used to capture the temporal dynamics of ILI. The result was compared with the Deep Learning model proposed by other researchers, demonstrating the proposed model outperforms the previous methods.clos

Thirty years of artificial intelligence in medicine (AIME) conferences: A review of research themes

Over the past 30 years, the international conference on Artificial Intelligence in MEdicine (AIME) has been organized at different venues across Europe every 2 years, establishing a forum for scientific exchange and creating an active research community. The Artificial Intelligence in Medicine journal has published theme issues with extended versions of selected AIME papers since 1998

When Infodemic Meets Epidemic: a Systematic Literature Review

Epidemics and outbreaks present arduous challenges requiring both individual and communal efforts. Social media offer significant amounts of data that can be leveraged for bio-surveillance. They also provide a platform to quickly and efficiently reach a sizeable percentage of the population, hence their potential impact on various aspects of epidemic mitigation. The general objective of this systematic literature review is to provide a methodical overview of the integration of social media in different epidemic-related contexts. Three research questions were conceptualized for this review, resulting in over 10000 publications collected in the first PRISMA stage, 129 of which were selected for inclusion. A thematic method-oriented synthesis was undertaken and identified 5 main themes related to social media enabled epidemic surveillance, misinformation management, and mental health. Findings uncover a need for more robust applications of the lessons learned from epidemic post-mortem documentation. A vast gap exists between retrospective analysis of epidemic management and result integration in prospective studies. Harnessing the full potential of social media in epidemic related tasks requires streamlining the results of epidemic forecasting, public opinion understanding and misinformation propagation, all while keeping abreast of potential mental health implications. Pro-active prevention has thus become vital for epidemic curtailment and containment

A systematic review on integration mechanisms in human and animal health surveillance systems with a view to addressing global health security threats

Lymphatic filariasis and onchocerciasis are neglected tropical diseases (NTDs) targeted for elimination by mass (antifilarial) drug administration. These drugs are predominantly active against the microfilarial progeny of adult worms. New drugs or combinations are needed to improve patient therapy and to enhance the effectiveness of interventions in persistent hotspots of transmission. Several therapies and regimens are currently in (pre-)clinical testing. Clinical trial simulators (CTSs) project patient outcomes to inform the design of clinical trials but have not been widely applied to NTDs, where their resource-saving payoffs could be highly beneficial. We demonstrate the utility of CTSs using our individual-based onchocerciasis transmission model (EPIONCHO-IBM) that projects trial outcomes of a hypothetical macrofilaricidal drug. We identify key design decisions that influence the power of clinical trials, including participant eligibility criteria and post-treatment follow-up times for measuring infection indicators. We discuss how CTSs help to inform target product profiles

Coordinating Coronavirus Research: The COVID-19 Infectious Disease Ontology

Rapidly, accurately and easily interpreting generated data is of fundamental concern. Ontologies – structured controlled vocabularies – support interoperability and prevent the development of data silos which undermine interoperability. The Open Biological and Biomedical Ontologies (OBO) Foundry serves to ensure ontologies remain interoperable through adherence by its members to core ontology design principles. For example, the Infectious Disease Ontology (IDO) Core includes terminological content common to investigations of all infectious diseases. Ontologies covering more specific infectious diseases in turn extend from IDOCore, such as the Coronavirus Infectious Disease Ontology (CIDO). The growing list of virus-specific IDO extensions has motivated construction of a reference ontology covering content common to viral infectious disease investigations: the Virus Infectious Disease Ontology (VIDO). Additionally the present pandemic has motivated construction of a more specific extension of CIDO covering terminological contents specific to the pandemic: the COVID-19 Infectious Disease Ontology (IDO-COVID-19). We report here the development of VIDO and IDO-COVID-19. More specifically we examine newly minted terms for each ontology, showcase reuse of terms from existing OBO ontologies, motivate choicepoints for ontological decisions based on research from relevant life sciences, apply ontology terms to explicate viral pathogenesis, and discuss the annotating power of virus ontologies for use in machine-learning projects

The Biosurveillance Analytics Resource Directory (BARD): Facilitating the Use of Epidemiological Models for Infectious Disease Surveillance

Epidemiological modeling for infectious disease is important for disease management and its routine implementation needs to be facilitated through better description of models in an operational context. A standardized model characterization process that allows selection or making manual comparisons of available models and their results is currently lacking. A key need is a universal framework to facilitate model description and understanding of its features. Los Alamos National Laboratory (LANL) has developed a comprehensive framework that can be used to characterize an infectious disease model in an operational context. The framework was developed through a consensus among a panel of subject matter experts. In this paper, we describe the framework, its application to model characterization, and the development of the Biosurveillance Analytics Resource Directory (BARD; http://brd.bsvgateway.org/brd/), to facilitate the rapid selection of operational models for specific infectious/communicable diseases. We offer this framework and associated database to stakeholders of the infectious disease modeling field as a tool for standardizing model description and facilitating the use of epidemiological models