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)

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)

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)

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)

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. 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 Infectious (...) class='Hi'>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)

Recent scholarship in medical humanities has expressed strong concern over the ability of pharmaceuticals companies to medicalize discomfort and subsequently invent diseases. In this article, I explore the clinical debates over the ontology of the sinus headache as a possible counter-case. Extending Foucault’s concept of principles or rarefaction, this paper documents the efforts of clinicians to resist the pharmaceutically-provided understanding of the sinus headache. In so doing, it offers institutions of rarefaction and rarefactive assemblages as useful heuristics for the (...) exploration of disease legitimization discourse. (shrink)

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)

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)

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)

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)

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)

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)

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)

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)

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)

In 1949, Linus Pauling and collaborators published in Science a paper provocatively titled: 'Sickle cell anemia, a molecular disease'. What was actually meant by 'molecular disease'? We interpret the concept of molecular disease in the frame of the traditional positions about the nature of diseases: the ontological and the physiological positions. We conclude that the physiological does not give an adequate account of what molecular diseases are. The ontological position, when correctly reinterpreted, leads to an understanding of (...) molecular diseases where the macromolecule is seen as a symptom or as a part of a mechanism leading to the symptoms of the disease. We then show that the concept of molecular disease leads to a particular view of therapy, emphasizing eugenics as a way of eliminating disease. On the individual level, this concept leads to an increased power of diagnosis, and especially predictive diagnosis, but has little therapeutic consequence. Lastly, we examine how this concept of disease unifies two contemporary classifications of diseases, one based on the location of the diseases, the other on the cause of the diseases. (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)

The goal of this paper is two-fold: first, to emphasize causality in disease ontology and knowledge representation, presenting a general and cursory discussion of causality and causal chains; and second, to clarify and develop the River Flow Model of Diseases (RFM). The RFM is an ontological account of disease, representing the causal structure of pathology. It applies general knowledge of causality using the concept of causal chains. The river analogy of disease is explained, formal descriptions are (...) offered, and the RFM disease definition is refined by describing causal chains in terms of causal relations. The definition is updated to coincide with the actual RFM classes found in its upper-level ontology, YAMATO, which brings to light some challenges in developing both YAMATO and the RFM. The RFM is also discussed in relation to another ontological account of disease. Strategies are offered toward interoperability between these theories. (shrink)

The prevalence of dementia is increasing worldwide but there is still no hope of a cure. Huge resources go into biomedical research, whose reductive ‘enactment’ has severe consequences for women, who are predominantly affected by dementia. To challenge such tragic enactment, this article considers ‘multiple ontologies’ of the most common type of dementia – Alzheimer’s disease – in the popular fictional film adaptations Still Alice and A Song for Martin. Using a post-humanist account of feminist visual studies of technoscience, (...) this comparative film analysis reveals how gender supersedes AD oversteering the hierarchical dualisms between health and pathology, human and nonhuman, and biomedical and artistic modes of knowing about Alzheimer’s. The author argues that these films stress the potential of the arts, as a multisensorial post-humanist embodied state of becoming with AD, to challenge hierarchical dualisms and innovatively contribute to dementia care. (shrink)

The clinical empiricism of Thomas Sydenham (1624–1689) and his definition of especie morbosae represented a substantial turn in the medicine of his time. This turn supposed the shift towards an ontological conception of diseases, from a qualitative to quantitative interpretation. Sydenham’s clinical proposal had a great influence on empiricism philosophical thinking, particularly in John Locke and his delimitation of knowledge. The dialogue between medicine and philosophy, set out by Sydenham-Locke, reactivates the problem of the clinical and theoretical foundations of medical (...) thought, as well as the limits of scientific knowledge. Similar to problem exposed in the Hippocratic treatise On ancient medicine, seventeenth-century medicine seeks its epistemological foundations and the solution to its difficulties in clinical experience, probability and analogy. The aim of this work is to show the Sydenham’s contribution to one of the great controversies between medicine and philosophy. (shrink)

This paper provides an introduction to the history of the concept of “emerging infectious diseases” (EID) and reflects on how humanities and social science scholars have interacted with it. It starts with a chronological outline of the coinage of the concept in the early 1990s in the wake of the shocks provoked by Ebola and HIV/AIDS, which disrupted the idea that the West was transitioning from a period of infectious diseases to one of chronic diseases. We argue that humanities and (...) social science scholars in disciplines such as history, anthropology, STS, and literature studies have critically explored the concept, showing how entrenched it was in the perceptions of the US and Europe about threats posed by the rest of the globe. Moreover, we explore how scholars in the humanities have used the EID concept to comment on contemporary realities and mobilized it to create dialogues with scientists, especially during the COVID-19 pandemic. Subsequently, we explore how the growing contemporary interest in EID has pushed historians to research the ontological and epistemological factors that enabled the “emergence” of diseases long before the invention of the EID concept, such as plague, Chagas disease, and sleeping sickness, as well as the factors that transformed these and other emerging diseases into pandemics. We conclude by outlining a few neglected factors in the EID literature that could be addressed: the circulation and reception of the concept outside of the West, the examination of EID as a problem for wild animals and not just for humans, and global histories of disease emergence as an epistemological and social process. (shrink)

In this article, I draw on my fieldwork creating protein models of hepatitis B at a biotech laboratory to think through how to approach the body and disease from ontological and phenomenological perspectives. I subsequently draw on Mariella Pandolfi’s work on how bodies can be made to suffer history and Paul Farmer’s work on global tuberculosis disparities to explore ways of analysing embodied activity as a means of identifying and clinically addressing enactments of social inequality and disease. I (...) also introduce Merleau-Ponty’s phenomenological concept of ‘flesh’ as a conceptual heuristic that allows us to understand the meaningful structuring of ontological worlds beyond our own. As I argue, bringing these perspectives together not only allows us to re-envision what an effective disease treatment should be in diverse medical contexts, but also how to better understand health disparities and the nature of disease itself. (shrink)

Alzheimer’s disease is emerging into public view in unprecedented ways. Foremost among these is the embodied form of elderly men and women appearing in commercial imagery for patient advocacy groups or pharmaceutical advertisements, but scientific imagery also seeps into the visual media cultures that surround us. The recent reconfiguration of Alzheimer’s disease is due to expanding ageing populations, an aggressive biopharmaceutical industry becoming a fast-growing material-semiotic realm that is providing powerful images of both gendered and racialized embodiment. Such (...) a visual, and yet highly material, realm is in need of feminist interventions, engaging with the images and ideas that circulate around ageing, medicine, human and non-human embodiment. From a non-representationalist and posthumanist perspective identified as feminist visual studies of technoscience, the authors seek to further the discussion in the direction of understanding the ‘scattered ontologies’ of Alzheimer’s — in laboratory practice, the realm of medical media and in commercial appeals to coherent individuality and human cognition — as gendered domains of figural reality and performative matter. (shrink)

The following article presents preliminary reflections on a processual theory of health and disease. It does this by steering the discussion more toward an ontology of organisms rather than conceptual analysis of the semantic content of the terms “health” and “disease.” In the first section, four meta-theoretical assumptions of the traditional debate are identified and alternative approaches to the problems are presented. Afterwards, the view that health and disease are constituted by a dynamic relation between demands (...) imposed on an organism and individual presuppositions for adequate response is developed. In the last section, the paper takes stock of three possible objections to and clarifies some implications of this approach to the notions of health and disease. (shrink)

In this paper, I focus on life-threatening medical conditions and argue that from the point of view of natural properties, induction(s), and participation in laws, at least some of the ill organisms dealt with in somatic medicine form natural kinds in the same sense in which the kinds in the exact sciences are thought of as natural. By way of comparing two ‘divisions of nature’, viz., a ‘classical’ exact science kind (gold) and a kind of disease (Graves disease), (...) I show that there is no justifiable ‘ontological gap’ between disease kinds and exact sciences kinds. We have instead a difference of degree. (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)

I explore the role that values and interests, especially ideological interests, play in managing and balancing epistemic risks in medicine. I will focus in particular on how diseases are identified and operationalized. Before we can do biomedical research on a condition, it needs to be identified as a medical condition, and it needs to be operationalized in a way that lets us identify sufferers, measure progress, and so forth. I will argue that each time we do this, we engage in (...) epistemic risk balancing that inevitably draws upon values and interests, often including social and ideological values. My main interest here is in the conceptualization of infertility as a disease. Infertility is a rich test case for exploring the interplay between interests and epistemic risk management. There is no uncontested or standardized definition of infertility. The various definitions of it are internally ambiguous and tension-ridden, and in spectacular contradiction with one another. Many interest groups who are invested in framing infertility as a pressing problem deserving of social and medical redress are quick to insist that it is a legitimate ‘disease,’ but they cannot agree on which disease it is, what its symptoms or diagnostic markers are, or even what its basic ontology is. I suggest that there are political explanations for this epistemic mess. Indeed, I contend that there are good scientific and ethical reasons to reduce away the category of ‘infertility,’ especially understood as a scientific or medical category; I argue that we should excise the concept from our research and clinical practices. (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.

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)

In this paper we articulate a characterization of the concept of disease as a social problem. We argue that, from a social ontology point of view, diseases are problems that are identified and addressed within the framework of concrete social institutions and practices (those that shape medicine). This approach allows us to overcome the classical distinction between naturalist and normativist approaches in the philosophy of medicine, taking into account both the material and the symbolic factors that shape the (...) categories and determine the practices of medicine. (shrink)

The massive increase of data generated by heterogeneous sources requires the development of computer tools enabling their semantic interoperability. Applied ontologies aim at fulfilling such needs. We will show in this article the central role that philosophical ontology can play for applied ontology, with a focus on biomedical ontologies; and reciprocally, how applied ontology can enlighten some classical issues in philosophical ontology, by considering the following question: Is disease a natural kind?

The aim of the paper is to give an ontologically informed account of disease that can aid in the construction of disease ontologies. The paper begins by distinguishing cases of diseases from what are purely structural abnormalities, referred to as ‘disorders’. The paper then presents a causal model apt for the understanding of disease that distinguishes diseases from both their causes and their potential effects. The analysis of disease defended treats disease in terms of distortions (...) of standard cellular network processes, where those distortions are incapable of self remedy and produce biologically disadvantageous symptoms. (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)

The ontology of medicine—the question of whether disease entities are real or not—is an underdeveloped area of philosophical inquiry. This essay explains the primary question at issue in medical ontology, discusses why answering this question is important from both a philosophical and a practical perspective, and argues that the problem of medical ontology is unique, i.e., distinct, from the ontological problems raised by other sciences and therefore requires its own analysis.

The pursuit of health is one of the most basic and prevalent concerns of humanity. In order to better attain and preserve health, a fundamental and unified description of the concept is required. Using Paul Tillich's ontological framework, I introduce a complete characterization of health and disease is that is useful to the philosophy of medicine and for health-care workers. Health cannot be understood merely as proper functioning of the physical body or of the separated levels of body, mind, (...) and soul. Rather, the multidimensional unity that is the essence of human life requires a new understanding of health as balanced self-integration within the multiple human dimensions. The ontological description of health and disease has concrete implications for how health-care workers should approach healing. It calls for a multidimensional approach to healing in which particular healing is needed and helpful if it considers the other realms of the human. It reveals the importance of accepting limited health as well as the value of faith understood as an ultimate concern because of its ability to wholly integrate the person. (shrink)

Physico-chemical sciences are dominated by the deterministic interpretation. Scientific medicine has generally been assigned to the area of functional biology and thence to the physico-chemical sciences. In as much as diseases are alterations of physiological processes, they share the ontological status of the latter. However, many diseases cannot be accommodated within a deterministic interpretation. First, many diseases are initiated by errors in transmission of information and followed by natural selection. These diseases, such as tumoural transformations and autoimmune processes, behave as (...) evolutionary processes. Second, physiological processes do not cause irreversible changes while diseases may do so when not followed by restitutio ad integrum. The tendency of living organisms to maintain stationary states of great stability and minimum energy dissipation is largely due to intermolecular forces-stabilized structures, the information for which is selected during phylogenesis and decodified during ontogenesis. Diseases cause alterations of the biological structures, thereby shifting living organisms toward stationary states of lower stability and increased dissipation. The shift, reversible or irreversible, to less stable and efficient stationary states is a common thermodynamic feature of diseases. In spite of the uniqueness of their genotype, living organisms, during ontogenetic development, form spatio-temporal unrestricted classes of infinite membership. Neither stationarity nor environment-induced perturbations and consequent adaptations are sources of historicity because of the genomic programme constraint. Historicity is conferred, however, to each organism by the permanent record of such unique events as: a) the variation-selection processes occurring in the brain-mind and immunological systems; and b) irreversible alterations induced by diseases. The disease-induced changes have ontological and epistemological consequences. Since biological structures and functions are transformed into individual, historical entities, the laws of scientific medicine must be applied in clinical practice to higher levels of organization, namely to the ensembles or groups of individuals affected by the diseases. (shrink)

The status of risk factors and disease remains a disputed question in the theory and practice of medicine and healthcare, and so does the related question of delineating disease boundaries. I present a framework based on Bernard Lonergan’s account of emergent probability for differentiating (1) generically distinct levels of systematic function within organisms and between organisms and their environments and (2) the methods of functional, genetic, and statistical investigation. I then argue on this basis that it is possible (...) to understand disease in terms of biological or higher intra-level dysfunction, risk factors—including genetic risk factors—in terms of statistical inter-level conditioning of a given stage or developmental sequence of systematic functioning, and the empirical boundaries of disease in terms of the limits of both functional categorization (from an epistemic standpoint) and upper-level integration of lower-level processes and events (from an ontological standpoint). (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)

This paper furnishes a brand storytelling account of the Covid-19 pandemic. By adopting a fictional ontological standpoint, the virus’ narrative space is mapped out by recourse to metaphorical modeling. The disease imagery stems from global mainstream media in the context of Covid-19’s brand globalization, as increasing interconnectedness of and interdependence between social, cultural and economic discourses. The main narrative components (actors, settings, actions, relationships) are outlined as episodes that make up the virus’ brand personality, against the background of a (...) reading grid. Subsequently, a nexus of ontological (deep) metaphors is identified as the virus’ master narrative, by identifying transfers between the global mediascape and the brand’s narrative space. Deep metaphors are equivalent to cultural archetypes or mythopoetic structures which make up a collective structural unconscious. Deep metaphors stem from reducing surface metaphors to their most universal semantic dimensions by identifying permeating themes. Instead of ascribing primacy to the . (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a (...) PRotein Ontology (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of (...) the categories identified and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections. (shrink)

This open access book is a systematic update of the philosophical and scientific foundations of the biopsychosocial model of health, disease and healthcare. First proposed by George Engel 40 years ago, the Biopsychosocial Model is much cited in healthcare settings worldwide, but has been increasingly criticised for being vague, lacking in content, and in need of reworking in the light of recent developments. The book confronts the rapid changes to psychological science, neuroscience, healthcare, and philosophy that have occurred since (...) the model was first proposed and addresses key issues such as the model’s scientific basis, clinical utility, and philosophical coherence. The authors conceptualise biology and the psychosocial as in the same ontological space, interlinked by systems of communication-based regulatory control which constitute a new kind of causation. These are distinguished from physical and chemical laws, most clearly because they can break down, thus providing the basis for difference between health and disease. This work offers an urgent update to the model’s scientific and philosophical foundations, providing a new and coherent account of causal interactions between the biological, the psychological and social. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes (...) of making computers understand medical natural language. (shrink)