The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the (...) class='Hi'>Infectious Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

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. (shrink)

After motivating a framework for evaluating top-down, middle-out, middle-in, and bottom-up ontology development strategies, we apply our framework to investigate whether infectious disease ontologies - specifically, the Virus Infectious Disease Ontology (VIDO) and the Coronavirus Infectious Disease Ontology (CIDO) - effectively promote semantic interoperability.

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report (...) the development of the Virus Infectious Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

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)

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. (shrink)

This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples (...) for each combination of dispositions is given along with a specific use case in IDO. Description logic restrictions are used to formalize statements relating to these combinations. (shrink)

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy (...) for the construction of a new taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant (...) new insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (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 (...) class='Hi'>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)

This paper has two objectives 1) to study the influence of digital and new technology on COVID-19 diagnosis and healthcare 2) To propose the integral guideline solutions of the infectious disease for the future. COVID-19 stands for corona (CO), virus (VI), disease (D), or SARS-CoV-2, is a respiratory virus first identified in December 2019 in Wuhan, China(WHO, 2019). It is an epidemiological crisis that caused the deaths and sudden destruction of wealth and health of people (...) around the world. Many countries responded to the crisis with what could only be called urgent prevention and treatment. In the 21st century, our society is based on digital and new technology that can control and prevent the COVID-19 pandemics. However, these ways for solving the problem of COVID-19 pandemics are rising an epistemological crisis too. There are some problems with the COVID-19 diagnosis. From Buddhist philosophy perspective, COVID-19 teaches us the coronavirus is causing us to experience some heightened forms of the three marks of our existence which are the impermanence (aniccā), the suffering (duḥkha), and the non-self (anatta). The establishment of scientific expertise and innovation has shown its value and educating the public about testing, diagnosis, communication, treatment, and vaccine development technology for prevention the of infectious diseases in the future. (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)

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance (...) purposes. (shrink)

The paper begins with a retrospective of the debates on the origin of life: the virus or the cell? The virus needs a cell for replication, instead the cell is a more evolved form on the evolutionary scale of life. In addition, the study of viruses raises pressing conceptual and philosophical questions about their nature, their classification, and their place in the biological world. The subject of pandemics is approached starting from the existentialism of Albert Camus and Sartre, (...) the replacement of the exclusion ritual with the disciplinary mechanism of Michel Foucault, and about the Gaia hypothesis, developed by James Lovelock and supported in the current pandemic by Bruno Latour. The social dimensions of pandemics, their connection to global warming, which has led to an increase in infectious diseases, and the deforestation of large areas, which have caused viruses to migrate from their native area (their "reservoir") are highlighted below. The ethics of pandemics is approached from several philosophical points of view, of which the most important in a crisis of such global dimensions is utilitarianism which involves maximizing benefits for society in direct conflict with the usual (Kantian) view of respect for people as individuals. After a retrospective of the COVID-19 virus that caused the current pandemic, its life cycle and its history, with an emphasis on the philosophy of death, the concept of biopower initially developed by Foucault is discussed, with reference to the practice of modern states of control of the populations and the debate generated by Giorgio Agamben who states that what is manifested in this pandemic is the growing tendency to use the state of emergency as a normal paradigm of government. An interesting and much debated approach is the one generated by the works of Slavoj Žižek, who states that the current pandemic has led to the bankruptcy of the current "barbaric" capitalism, wondering if the path that humanity will take is a neo-communism. Another important negative effect is desocialization, with the conclusion of some philosophers that we cannot exist independently of our relationships with others, that a person's humanity depends on the humanity of those around him. The last section is dedicated to forecasting what the world will look like after the pandemic, and there are already signs of a paradigm shift, including the sudden disappearance of the "wall" ideology: a cough was enough to make it suddenly impossible to avoid the responsibility that every individual has it towards all living beings for the simple fact that he is part of this world, and of the desire to be part of it. The whole is always involved in part, because everything is, in a sense, in everything and in nature there are no autonomous regions that are an exception. The COVID-19 pandemic seems to restore the supremacy that once belonged to politics. One of the virtues of the virus is its ability to generate a more sober idea of ​​freedom: to be free means to do what needs to be done in a specific situation. -/- CONTENTS: -/- Abstract Introduction 1 Viruses 1.1 Ontology 2 Pandemics 2.1 Social dimensions 2.2 Ethics 3 COVID-19 3.1 Biopolitics 3.2 Neocommunism 3.3 Desocialising 4 Forecasting Bibliography -/- DOI: 10.13140/RG.2.2.31039.74405/1. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...) bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. (shrink)

As the Zika virus pandemic continues to bring worry and fear to health officials and medical scientists, Centers for Disease Control and Prevention (CDC) and World Health Organization (WHO) have recommended that residents of the Zika-infected countries, e.g., Brazil, and those who have traveled to the area should delay having babies which may involve artificial contraceptive, particularly condom. This preventive policy, however, is seemingly at odds with the Roman Catholic Church’s position on the contraceptive. As least since the (...) promulgation of Paul VI’s 1968 encyclical, Humanae Vitae, the Church has explicitly condemned artificial birth control as intrinsic evil. However, the current pontiff, Pope Francis, during his recent visit to Latin America, remarked that the use of artificial contraception may not be in contradiction to the teaching of Humanae Vitae while drawing a parallel between the current Zika Crisis and the 1960’s Belgian Congo Nun Controversy. The pope mentioned that the traditional ethical principle of the lesser of two evils may be the doctrine that justified the exceptions. The authors of this paper attempt to expand the theological rationale of the pope’s suggestion. In so doing, the authors rely on casuistical reasoning as an analytic tool that compares the Belgian Congo Nun case and the given Zika case, and suggest that the former is highly similar to, if not the same as, the latter in terms of normative moral feature. That is, in both cases the use of artificial contraception is theologically justified in reference to the criteria that the doctrine of the lesser of two evils requires. The authors wish that the paper would provide a solid theological-ethical ground based on which condom-use as the most immediate and effective preventive measure can be recommended in numerous Catholic hospitals as well as among Catholic communities in the world, particularly the most Zika-affected and largest Catholic community in the world, Brazil – 123 million present Brazilian citizens are reported to be Roman Catholic. (shrink)

The study investigated ethical considerations and science diplomacy on coronavirus disease (Covid-19) pandemic in Nigeria. The outbreak of the coronavirus disease (Covid-19) in Nigeria has spread quickly to about 34 states out of the 36 states and over 5000 persons have tested positive as at the time of this research after the first index case of an Italian and there is a projection that in coming days and weeks the number of infected persons and states will increase. The (...) study was guided by two objectives and also adopted the normative ethical theory. The study employed the methods of exposition and critical analysis to explain better the ethical issues and science diplomacy of Covid-19 pandemic in Nigeria. Data was sourced from secondary sources such as journal articles, newspaper, books and internet sources. The findings of the study showed that the citizens have some obligations that will aid the containment of the virus and as well as the government. The study also found out that science diplomacy was used, which has led to Nigeria collaborating with China to get medical aids to effectively fight the pandemic. Consequently, the study recommended amongst others that the Ministry of Health and the Nigeria Center for Disease Control (NCDC) should adopt and enforce the World Health Organization (WHO) Guidance for Managing Ethical Issues in Infectious Disease Outbreak as a working document in crisis like the Covid-19 pandemic that has ravaged Nigeria and the government should involve more in science diplomacy with other countries so that it will help in the fight against Covid-19 and other diseases that may occur in the future. (shrink)

Research in infection biology aims to understand the complex nature of host–pathogen interactions. While this knowledge facilitates strategies for preventing and treating diseases, it can also be intentionally misused to cause harm. Such dual-use risk is potentially high for highly pathogenic microbes such as Risk Group-3 (RG3) bacteria and RG4 viruses, which could be used in bioterrorism attacks. However, other pathogens such as influenza virus (IV) and enterohemorrhagic Escherichia coli (EHEC), usually classified as RG2 pathogens, also demonstrate high dual-use (...) risk. As the currently approved therapeutics against these pathogens are not satisfactorily effective, previous outbreaks of these pathogens caused enormous public fear, media attention and economic burden. In this interdisciplinary review, we summarize the current perspectives of dual-use research on IV and EHEC, and further highlight the dual-use risk associated with evolutionary experiments with these infectious pathogens. We support the need to carry out experiments pertaining to pathogen evolution, including to gain predictive insights on their evolutionary trajectories, which cannot be otherwise achieved with stand-alone theoretical models and epidemiological data. However, we also advocate for increased awareness and assessment strategies to better quantify the risks-versus-benefits associated with such evolutionary experiments. In addition to building public trust in dual-use research, we propose that these approaches can be extended to other pathogens currently classified as low risk, but bearing high dual-use potential, given the particular pressing nature of their rapid evolutionary potential. (shrink)

The global pandemic of COVID 19 has changed consumer behaviour to reduce the risk. This is common for all interpersonal interactions of individuals especially in maintaining the recommended interpersonal distance based on the recommendations from the health experts. Sri Lanka as a developing country affected by COVID 19, observed changes in individuals' day today’ consumption decision making due to pandemic. Importantly the retailing sector is highly influenced by the conditions since the frequency of interpersonal interactions and degree of interaction is (...) higher in the retailing sector. Interestingly the retailing sector with its largest contributor, the SMEs need to identify the unique changes that happen to the consumer behaviour in responding to them. Accordingly, the objective of the study is to examine the impact of infectious disease risk on the perceived retail crowding in two perspectives of human density and the spatial density. The study has used a quantitative survey in collecting data with the online self-administrated questionnaire with a sample of 100 consumers. Data analysis has been done by using a PLS-SEM with the support of SmartPLS version 3. The key findings of the study emphasize the significant positive influence of infectious disease risk on human density as well as on the spatial density. Based on the findings the study attempts to provide the implications for the retailing industry to cope with situational changes in the environment. (shrink)

Background: Earlier study without actual trial indicated that caregivers needed delivery of information about outbreak situations independently of their job status. This report describes, for about two months in winter, actual delivery outbreak information to families with preschool children. The study objective was to confirm the usefulness of this information delivery. Method: Participants receiving outbreak information were recruited from the Child Care Support Service in a ward in Tokyo, Japan. Outbreak information was obtained from the Nursery School Absenteeism Surveillance System (...) (NSASSy) covering approximately 40% of all nursery schools in Japan, prescription surveillance and other resources. Delivery of outbreak information started in December 2017 and ceased at the end of February in 2018. After the delivery period, a questionnaire survey was administered to participants. Results: For this area, NSASSy showed the most dominant disease was influenza, with 707 patients, followed by group A streptococcal pharyngitis with 98 patients. The outbreak peak was inferred to be as Monday, 22 January, and it was announced by e-mail on 23 January. Of the 202 persons joined this trial, 60 participants responded to the questionnaire survey after the delivery period. Of those respondents, 98% wanted delivery of that information to continue. Conclusion: We found that almost all respondents confirmed usefulness of the information about infectious diseases which was delivered. (shrink)

Antimicrobial resistance (AMR) is a global public health disaster driven largely by antibiotic use in human health care. Doctors considering whether to prescribe antibiotics face an ethical conflict between upholding individual patient health and advancing public health aims. Existing literature mainly examines whether patients awaiting consultations desire or expect to receive antibiotic prescriptions, but does not report views of the wider public regarding conditions under which doctors should prescribe antibiotics. It also does not explore the ethical significance of public views (...) or their sensitivity to awareness of AMR risks or the standpoint (self-interested or impartial) taken by participants. Methods: An online survey was conducted with a sample of the U.S. public (n = 158). Participants were asked to indicate what relative priority should be given to individual patients and society-at-large from various standpoints and in various contexts, including antibiotic prescription. Results: Of the participants, 50.3% thought that doctors should generally prioritize individual patients over society, whereas 32.0% prioritized society over individual patients. When asked in the context of AMR, 39.2% prioritized individuals whereas 45.5% prioritized society. Participants were significantly less willing to prioritize society over individuals when they themselves were the patient, both in general (p = .001) and in relation to AMR specifically (p = .006). Conclusions: Participants’ attitudes were more oriented to society and sensitive to collective responsibility when informed about the social costs of antibiotic use and when considered from a third-person rather than first-person perspective. That is, as participants came closer to taking the perspective of an informed and impartial “ideal observer,” their support for prioritizing society increased. Our findings suggest that, insofar as antibiotic policies and practices should be informed by attitudes that are impartial and well-informed, there is significant support for prioritizing society. (shrink)

A central tenet of medical ethics holds that it is permissible to perform a medical intervention on a competent individual only if that individual has given informed consent to the intervention. However, in some circumstances it is tempting to say that the moral reason to obtain informed consent prior to administering a medical intervention is outweighed. For example, if an individual’s refusal to undergo a medical intervention would lead to the transmission of a dangerous infectious disease to other (...) members of the community, one might claim that it would be morally permissible to administer the intervention even in the absence of consent. Indeed, as we shall discuss below, there are a number of examples of public health authorities implementing compulsory or coercive measures for the purposes of infectious disease control (IDC). The plausibility of the thought that non-consensual medical interventions might be justified when performed for the purpose of IDC raises the question of whether such interventions might permissibly be used to realize other public goods. In this article we focus on one possibility: whether it could be permissible to non-consensually impose certain interventions that alter brain states or processes through chemical or physical means on serious criminal offenders. We shall suggest that some such interventions might be permissible if they safely and effectively serve to facilitate the offender’s rehabilitation and thereby prevent criminal recidivism. (shrink)

On May 16, 2020, the Center for Academic Research and Training in Anthropogeny organized the symposium “Impact of Infectious Disease on Humans and Our Origins”. The symposium aimed to gather experts on infectious diseases in one place and discuss the interrelationship between different pathogens and humans in an evolutionary context. The talks discussed topics including SARS-CoV-2, dengue and Zika, the notion of human-specific diseases, streptococci, microbiome in the human reproductive tract, Salmonella enterica, malaria, and human immunological memory.

In the contemporary biomedical literature, every disease is considered genetic. This extension of the concept of genetic disease is usually interpreted either in a trivial or genocentrist sense, but it is never taken seriously as the expression of a genetic theory of disease. However, a group of French researchers defend the idea of a genetic theory of infectious diseases. By identifying four common genetic mechanisms (Mendelian predisposition to multiple infections, Mendelian predisposition to one infection, and major (...) gene and polygenic predispositions), they attempt to unify infectious diseases from a genetic point of view. In this article, I analyze this explicit example of a genetic theory, which relies on mechanisms and is applied only to a specific category of diseases, what we call “a regional genetic theory.” I have three aims: to prove that a genetic theory of disease can be devoid of genocentrism, to consider the possibility of a genetic theory applied to every disease, and to introduce two hypotheses about the form that such a genetic theory could take by distinguishing between a genetic theory of diseases and a genetic theory of Disease. Finally, I suggest that network medicine could be an interesting framework for a genetic theory of Disease. (shrink)

The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as (...) well as its clinical presentation including signs and symptoms. (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)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for (...) General Medical Science (OGMS) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

Definitive diagnosis of malaria requires the demonstration through laboratory tests of the presence within the patient of malaria parasites or their components. Since malaria parasites can be present even in the absence of malaria manifestations, and since symptoms of malaria can be manifested even in the absence of malaria parasites, malaria diagnosis raises important issues for the adequate understanding of disease, etiology and diagnosis. One approach to the resolution of these issues adopts a realist view, according to which the (...) needed clarifications will be derived from a careful representation of the entities on the side of the patient which form the ultimate truthmakers for clinical statements. We here address a challenge to this realist approach relating to the diagnosis of malaria, and show how this challenge can be resolved by appeal to Basic Formal Ontology (BFO) and to the Ontology for General Medical Science (OGMS) constructed in its terms. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO (...) Foundry ontology that provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

In this paper, I offer one example of conceptual change. Specifically, I contend that the discovery that viruses could cause cancer represents an excellent example of branch jumping, one of Thagard’s nine forms of conceptual change. Prior to about 1960, cancer was generally regarded as a degenerative, chronic, non-infectious disease. Cancer causation was therefore usually held to be a gradual process of accumulating cellular damage, caused by relatively non-specific component causes, acting over long periods of time. Viral infections, (...) on the other hand, were generally understood to be acute processes, whereby single, specific and necessary causal agents acted alone to produce disease. However, during the 1960s and 1970s, a number of cancers were discovered to have an infectious aetiology. Of particular note were two—Burkitt’s lymphoma and cervical cancer—which I will discuss in detail later in this piece. Together, these discoveries led, in the short term, to a tentative aetiological reclassification of some types of cancer as infectious diseases and, in the longer term, to a full-blown reclassification of cancer as an aetiological disease branch in its own right. This process of reclassification forms the empirical basis for my concluding remarks on the influence of classification upon causation in medicine. Through this, I aim to demonstrate that conceptual change, far from being a purely abstract concern of the philosopher of science, is of substantial import to scientific practitioners. (shrink)

Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such (...) a way that – once formulated in a suitable formal language – the ontologies can be used for sophisticated automated reasoning applications. Reference ontologies can be applied across different contexts in which different, and often mutually incompatible, domain-specific vocabularies have traditionally been used. In this contribution we describe the Mental Functioning Ontology (MF) and Mental Disease Ontology (MD), two realism-based ontologies currently under development for the description of humanmental functioning and disease. We describe the structure and upper levels of the ontologies and preliminary application scenarios, and identify some open questions. (shrink)

The study of viruses raises pressing conceptual and philosophical questions about their nature, their classification, and their place in the biological world. A major set of problems concerns the individuality and diachronic identity of a virus: what is the virus, the viral particle (virion) or the entire viral cycle? The correct identification of the virus has significant ontological consequences, also related to the place and time when biological entities begin and end. DOI: 10.13140/RG.2.2.35874.66241.

The viruses coexist for approx. 300 million years with the humans. Sometimes viruses can infect people on a large scale. But how was the current pandemic possible? Global warming is causing extreme weather events that have led to an increase in infectious diseases. The new climate can support epidemiological vectors for longer periods of time, creating more favorable conditions for replication and the emergence of new vectors. In the case of emerging infectious diseases, it is considered that there (...) is a border that has already been crossed. Viruses normally have a native area (their "reservoir") from which they should not be pushed out. This creates a dangerous intimacy, with "hotspots" that include locations such as markets, which become real hotbeds of epidemics. DOI: 10.13140/RG.2.2.26974.87364 . (shrink)

While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the (...) patient. We here present a view of mental disease that is based on ontological realism and which follows the principles embodied in Basic Formal Ontology and in the application of BFO in the Ontology of General Medical Science. We analyzed statements about what counts as a mental disease provided in the research agenda for the DSM-V, and in Pies' model. The results were used to assess whether the representational units of BFO and OGMS were adequate as foundations for a formal representation of the entities in reality that these statements attempt to describe. We then analyzed the representational units specific to mental disease and provided corresponding definitions. Our key contributions lie in the identification of confusions and conflations in the existing terminology of mental disease and in providing what we believe is a framework for the sort of clear and unambiguous reference to entities on the side of the patient that is needed in order to avoid these confusions in the future. (shrink)

Coronavirus disease (Covid-19) is an infectious disease caused by the SARS-CoV-2 virus. Spreading rate of mutated corona virus (delta variant) during second wave was very fast. Most of the people infected with the COVID-19 virus experienced mild to moderate to severe respiratory illness. Although patients in the second wave were younger but the duration of hospitalization and case fatality rate were lower than those in the first wave. During first wave of Covid-19 it was (...) observed that persons above 55 years of age and those with underlying medical problems like cardiovascular disease, diabetes, chronic respiratory disease and cancer were more susceptible to develop serious illness but in second it was observed that person between 30 to 55 years along with old age and younger people suffering from hypertension, diabetes and respiratory diseases were more susceptible to this covid-19 virus. The most frequent signs and symptoms in both waves were fever, dyspnea, pneumonia, and cough, and the most relevant comorbidities were cardiovascular diseases, type 2 diabetes mellitus, and chronic neurological diseases. Every country has lost its human resources due to covid-19 virus which not only disturb the social life but economic conditions are also very badly affected. Now we use the resources so rapidly that may create economic imbalance in future. The psychological effect is an essential component of disaster management of infectious pandemics. (shrink)

Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in (...) the form of a list of terms and definitions designed to provide a consistent starting point for the representation of both disease and diagnosis in information systems in the future. (shrink)

Abstract The quasispecies theory is a helpful concept in the explanation of RNA virus evolution and behaviour, with a relevant impact on methods used to fight viral diseases. It has undergone some adaptations to integrate new empirical data, especially the non-deterministic nature of mutagenesis, and the variety of behavioural motifs in cooperation, competition, communication, innovation, integration, and exaptation. Also, the consortial structure of quasispecies with complementary roles of memory genomes of minority populations better fits the empirical data than did (...) the original concept of a master sequence and its mutant spectra. The high productivity of quasispecies variants generates unique sequences that never existed before and will never exist again. In the present essay, we underline that such sequences represent really new ontological entities, not just error copies of previous ones. Their primary unique property, the incredible variant production, is suggested here as quasispecies productivity, which replaces the error-replication narrative to better fit into a new relationship between mankind and living nature in the twenty-first century. (shrink)

Whipple disease is a rare, infectious, disease first described from a single case by Whipple in 1907. As well as characterising the clinical and pathological features of the condition, Whipple made two suggestions regarding its aetiology. These were either than the disease was caused by an infectious agent, or that it was of metabolic origin. As the disease is now thought to be caused by infection with the bacterium Tropheryma whipplei, historical reviews of the (...) history of the disease typically mention only the first of these suggestions. In this paper, we therefore revisit Whipple’s other theory. We argue that a diverse and often successful research programme was developed around this mechanism of disease causation which gave rise to many useful findings on the condition. In the later parts of this article, we then turn to discuss the surprising neglect of this period of Whipple disease research in the current literature, and conclude by offering a brief reconstruction of this early history suitable for use in a technical context. (shrink)

Identifying the necessary and sufficient conditions for individuating and classifying diseases is a matter of great importance in the fields of law, ethics, epidemiology, and of course, medicine. In this paper, I first propose a means of achieving this goal, ensuring that no two distinct disease-types could correctly be ascribed to the same disease-token. I then posit a metaphysical ontology of diseases—that is, I give an account of what a disease is. This is essential to providing (...) the most effective means of interfering with disease processes. Following existing work in the philosophy of medicine and epidemiology (primarily Christopher Boorse; Caroline Whitbeck; Alexander Broadbent), philosophy of biology (Joseph LaPorte; D.L. Hull), conditional analyses of causation (J.L. Mackie; David Lewis), and recent literature on dispositional essentialism (Stephen Mumford and Rani Anjum; Alexander Bird), I endorse a dispositional conception of disease. Following discussion of various conceptions of disease-identity, their relations to the clinical and pathological effects of the diseases in question, and how diseases are treated, I conclude (i) that diseases should be individuated by their causes, and (ii) that diseases are causal processes best seen as simultaneously acting sequences of mutually manifesting dispositions. (shrink)

Viruses and related infectious genetic parasites are the most abundant biological agents on this planet. They invade all cellular organisms, are key agents in the generation of adaptive and innate immune systems, and drive nearly all regulatory processes within living cells.

This paper considers Bram Stoker’s novel Dracula, published in 1897, as a window into techno-scientific and sociocultural developments of the fin-de-siècle era, ranging from blood transfusion and virology up to communication technology and brain research, but focusing on the birth of psychoanalysis in 1897, the year of publication. Stoker’s literary classic heralds a new style of scientific thinking, foreshadowing important aspects of post-1900 culture. Dracula reflects a number of scientific events which surfaced in the 1890s but evolved into major research (...) areas that are still relevant today. Rather than seeing science and literature as separate realms, moreover, Stoker’s masterpiece encourages us to address the ways in which techno-scientific and psycho- cultural developments mutually challenge and mirror one another, so that we may use his novel to deepen our understanding of emerging research practices and vice versa (Zwart 2008, 2010). Psychoanalysis plays a double role in this. It is the research field whose genealogical constellation is being studied, but at the same time (Lacanian) psychoanalysis guides my reading strategy. Dracula, the infectious, undead Vampire has become an archetypal cinematic icon and has attracted the attention of numerous scholars (Browning & Picart 2009). The vampire complex built on various folkloristic and literary sources and culminated in two famous nineteenth-century literary publications: the story The Vampyre by John Polidori (published in 1819)2 and Stoker’s version. Most of the more than 200 vampire movies released since Nosferatu (1922) are based on the latter (Skal 1990; Browning & Picart 2009; Melton 2010; Silver & Ursini 2010). Yet, rather than on the archetypal cinematic image of the Vampire, I will focus on the various scientific ideas and instruments employed by Dracula’s antagonists to overcome the threat to civilisation he represents. Although the basic storyline is well-known, I will begin with a plot summary. (shrink)

The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and relations dedicated (...) to the salivaomics domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry. The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB. Background Saliva (oral fluid) is an emerging biofluid for non-invasive diagnostics used in the detection of human diseases. The need to advance saliva research is strongly emphasized by the National Institute of Dental and Craniofacial Research (NIDCR), and is included in the NIDCR's 2004- 2009 expert panel long-term research agenda [1]. The ability to monitor health status, disease onset, progression, recurrence and treatment outcome through noninvasive means is highly important to advancing health care management. Saliva is a perfect medium to be explored for personalized individual medicine including diagnostics, offering a non-invasive, easy to obtain means for detecting and monitoring diseases. Saliva testing potentially allows the patient to collect their own saliva samples at home, yielding convenience for the patient and savings in health costs, and facilitating multiple sampling. Specimen collection is less objectionable to patients and easier in children and elderly individuals. Due to these advantages. (shrink)

Last year saw the 20th anniversary edition of JECP, and in the introduction to the philosophy section of that landmark edition, we posed the question: apart from ethics, what is the role of philosophy ‘at the bedside’? The purpose of this question was not to downplay the significance of ethics to clinical practice. Rather, we raised it as part of a broader argument to the effect that ethical questions – about what we should do in any given situation – are (...) embedded within whole understandings of the situation, inseparable from our beliefs about what is the case, what it is that we feel we can claim to know, as well as the meaning we ascribe to different aspects of the situation or to our perception of it. Philosophy concerns fundamental questions: it is a discipline requiring us to examine the underlying assumptions we bring with us to our thinking about practical problems. Traditional academic philosophers divide their discipline into distinct areas that typically include logic: questions about meaning, truth and validity; ontology: questions about the nature of reality, what exists; epistemology: concerning knowledge; and ethics: how we should live and practice, the nature of value. Any credible attempt to analyse clinical reasoning will require us to think carefully about these types of question and the relationships between them, as they influence our thinking about specific situations and problems. So, the answers to the question we posed, about the role of philosophy at the bedside, are numerous and diverse, and that diversity is illustrated in the contributions to this thematic edition. (shrink)

All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNAmediated process. This is required for the development and growth of each individual cell. Thus, all known living organisms fundamentally depend on these RNA-mediated processes. In most cases, they are interconnected with other RNAs and their associated protein complexes and function in a strictly coordinated hierarchy of temporal and spatial steps (i.e., an RNA network). Clearly, all cellular life as we know it (...) could not function without these key agents of DNA replication, namely rRNA, tRNA, and mRNA. Thus, any definition of life that lacks RNA functions and their networks misses an essential requirement for RNA agents that inherently regulate and coordinate (communicate to) cells, tissues, organs, and organisms. The precellular evolution of RNAs occurred at the core of the emergence of cellular life and the question remained of how both precellular and cellular levels are interconnected historically and functionally. RNA-networks andRNA-communication can interconnect these levels.With the reemergence of virology in evolution, it became clear that communicating viruses and subviral infectious genetic parasites are bridging these two levels by invading, integrating, coadapting, exapting, and recombining constituent parts in host genomes for cellular requirements in gene regulation and coordination aims. Therefore, a 21st century understanding of life is of an inherently social process based on communicating RNA networks, in which viruses and cells continuously interact. (shrink)

Starting from the importance of the figure of the parrhesiastes — the political and therapeutic truth- teller— for Foucault’s understanding of the care of the self, this paper traces the political figuration of the analogy between philosophers and physicians on the one hand, and rhetors and disease on the other in Plato’s Gorgias. I show how rhetoric, in the form of ventriloquism, infects the text itself, and then ask how we account for the effect of the “ contaminated ” (...) philosophical dialogue on our readerly health. Is the text placebo, vaccine, or virus? All of these options, I argue, complicate Foucault’s prescription for parrhesia, requiring us to think anew the continuing political ramifications of the metaphor of care. (shrink)

Non-communicable diseases (NCDs) such as cardiovascular diseases and diabetes are reported to have caused significant deaths for more than a decade. Consequently, NCDs have posed as a threat to the socio-economic well-being of individuals and families, contributed to a rise in healthcare costs and largely undermined the attainment of the Sustainable Development Goals (SDGs) especially in developing countries. According to the World Health Organization (WHO), the prevalence of NCDs have compounded the problem of already ill equipped healthcare systems in these (...) countries as they are faced with constraints to deal with the burden of both infectious and non-communicable diseases. Informed largely by the rapid increase in NCDs and their subsequent threat to public health, we aimed to ascertain the various healthcare interventions that Ghana has fashioned out in her bid to prevent and control the incidence of NCDs, how these interventions were rolled out and examined past and present barriers to their implementation since 1990. We culled the data gathered for this paper from both primary and secondary sources to construct a coherent synthesis and to facilitate discussions on Ghana’s NCDs interventions from 1990 to 2018. A systematic analysis of the data gathered, revealed that Ghana’s healthcare system has by far tackled the NCDs burden in two folds; the clinical care aspect and the health promotion aspect. While certain healthcare interventions were purposively directed toward addressing NCDs, others were directed at promoting healthy lifestyles but had a bearing on the prevention and control of NCDs. Present challenges concerning shortfalls in interventions are a reflection of unresolved challenges in the past. We argue that despite the significant strides made for more than two decades, the interventions have addressed the burden of NCDs with limited success given the trends in NCDs mortality and morbidity. (shrink)

While Quine’s linguistic behaviorism is well-known, his Kant Lectures contain one of his most detailed discussions of behaviorism in psychology and the philosophy of mind. Quine clarifies the nature of his psychological commitments by arguing for a modest view that is against ‘excessively restrictive’ variants of behaviorism while maintaining ‘a good measure of behaviorist discipline…to keep [our mental] terms under control’. In this paper, I use Quine’s Kant Lectures to reconstruct his position. I distinguish three types of behaviorism in psychology (...) and the philosophy of mind: ontological behaviorism, logical behaviorism, and epistemological behaviorism. I then consider Quine’s perspective on each of these views and argue that he does not fully accept any of them. By combining these perspectives we arrive at Quine’s surprisingly subtle view about behaviorism in psychology. (shrink)

The interplay between the virus, infected cells and immune responses to SARS-CoV-2 is still under debate. By extending the basic model of viral dynamics, we propose here a formal approach to describe neutralisation versus weak (or non-)neutralisation scenarios and compare them with the possible effects of antibody-dependent enhancement (ADE). The theoretical model is consistent with the data available in the literature; we show that both weakly neutralising antibodies and ADE can result in final viral clearance or disease progression, (...) but that the immunodynamics are different in each case. As a significant proportion of the world’s population is already naturally immune or vaccinated, we also discuss the implications for secondary infections after vaccination or in the presence of immune system dysfunctions. (shrink)

Face-coverings were widely mandated during the Covid-19 pandemic, on the assumption that they limit the spread of respiratory viruses and are therefore likely to save lives. I examine the following ethical dilemma: if the use of face-masks in social settings can save lives then are we obliged to wear them at all times in those settings? I argue that by en-masking the face in a way that is phenomenally inconsistent with or degraded from what we are innately programmed to detect (...) as human likeness, we are degrading the social quality of our relations. Drawing on my previously published proof that Self is socially reflexive (mutually mirrored) rather than monadic in its constitution, I conclude that any widespread en-masking is also deleterious to humanity and therefore unethical. (shrink)