The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

Ong, Caroline In February 2014, the Belgian parliament passed an amendment to the Belgian Act on Euthanasia of May 28th, 2002 removing the age limit of those requesting euthanasia provided that they have discerning capabilities and their parents approve. After mentioning briefly the arguments against legalising euthanasia, this article questions the ethical validity of removing the age limit, as well as the presumption that ending lives prematurely allows people to die with dignity. Caring for people who are vulnerable in their (...) suffering is the proper goal of the healing professions, not terminating lives. (shrink)

Ong, Caroline As health systems become more complex, moral distress is increasingly being recognised as a significant phenomenon amongst health professionals. It can be described as the state of being distressed when one is unable to act according to what one believes to be morally right. It may compromise patient care, the health professional involved and the organisation. Cumulative experiences of incompletely resolved moral distress - a phenomenon which is called moral residue - may leave us susceptible to more frequent (...) and more severe moral distress. Clear open communication, respect, inclusivity, openness to differences, compassion, support, education and the capacity to grow in self-awareness are key aspects in minimising moral distress. Early recognition of its symptoms and addressing both personal and external constraints of actions can also minimise moral residue and build resilience to further distress. (shrink)

Ong, Caroline Whilst the reason and purpose of suffering may never be fully understood, there are ways of enduring, transcending and growing resilience to how it affects us. Our experience of suffering lies in the web of perceptions that involve our physical, spiritual and cosmological beliefs. Referencing Pain Seeking Understanding: Suffering, Medicine and Faith, edited by Margaret E. Mohrmann and Mark J. Hanson, this article gives a brief exploration of some propositions as to why an all-powerful, good God would allow (...) suffering to exist. From these various perspectives and using examples cited in the book, the article proposes that the healing art of medicine, honed through years of experience, knowledge and wisdom, can help individual patients endure and transcend suffering, and be whole once again. (shrink)

Ong, Caroline In the debate about euthanasia, it is important that we consider all views, including those which might not at first seem attractive to us. Whether we believe in God or not, the views of the Catholic Church make a significant contribution to this debate. The Church does not support the deliberate killing either of oneself or another person. It also emphasises our moral obligation to respect life and to uphold the dignity of each person.

Ong, Caroline There was once a strong belief amongst global HIV/AIDS organisations that the key to the prevention of the sexual transmission of HIV was condom use. Other measures such as abstinence and being loyal to one partner were seen as beneficial, but secondary. Thirty years later, the evidence is mounting that behavioural change is much more effective in halting the spread of HIV than condoms.