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)

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)

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)

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)

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)

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)

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)

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)

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, philosophy of biology, conditional analyses of causation, and recent literature on dispositional essentialism, I endorse a dispositional conception of disease whereby diseases are individuated by their causes, and diseases are causal processes best seen as simultaneously acting sequences of mutually manifesting dispositions - this, I claim, follows from the assumption that diseases should be classified by consideration of both their clinical and pathological effects, and importantly, events that can lead to the cessation of these symptoms. (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 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)

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)

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)

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)

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages (...) established ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (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)

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)

The aim of this essay is to elaborate philosophical and ethical underpinnings of posthumous diagnosis of famous historical figures based on literary and artistic products, or commonly called retrospective diagnosis. It discusses ontological and epistemic challenges raised in the humanities and social sciences, and attempts to systematically reply to their criticisms from the viewpoint of clinical medicine, philosophy of medicine, particularly the ontology of disease and the epistemology of diagnosis, and medical ethics. The ontological challenge focuses on the (...) doubt about the persistence of a disease over historical time, whereas the epistemic challenge disputes the inaccessibility of scientific verification of a diagnosis in the past. I argue that the critics are in error in conflating the taxonomy of disease and the act of diagnosing a patient. Medical diagnosis is fundamentally a hypothesis-construction and an explanatory device that can be generated under various degrees of uncertainty and limited amount of information. It is not an apodictic judgment as the critics presuppose, but a probabilistic judgment with varying degrees of plausibility under uncertainty. In order to avoid this confusion, I propose that retrospective diagnosis of a historical figure be syndromic without identifying underlying disease, unless there is justifiable reason for such specification. Moreover it should be evaluated not only from the viewpoint of medical science but also in a larger context of the scholarship of the humanities and social sciences by its overall plausibility and consistency. On the other hand, I will endorse their concerns regarding the ethics and professionalism of retrospective diagnosis, and call for the need for situating such a diagnosis in an interdisciplinary scope and the context of the scholarship of the historical figure. I will then enumerate several important caveats for interdisciplinary retrospective diagnosis using an example of the retrospective diagnosis of Socrates for his life-long intermittent neurologic symptoms. Finally, I will situate the present argument in a larger context of the major debate among the historians of medicine and paleopathologists, and discuss the similarities and differences. (shrink)

The notion of competence in A Philosophical Basis of Medcial Practice presents a problem concerning the ontology of the body. This paper will maintain that an ontology of the body can only be based upon Cartesian grounds whereby the scientific knowable order is supposed to be identical to the natural order of things. Moral questions are not a part of this order and depend upon free will. Foucault has demonstrated that such a dualism between nature and morality cannot (...) be warranted for contemporary medical practice. Medical science does not derive its foundation from a natural order but from the order of knowing which is present in the body of knowledge (episteme). This body of knowledge is the significative cultural force in the way of looking at problems of disease, life and death. Thus in contemporary medical practice, concepts of morality and competence which are based on notions of free will, shall be discarded as non-sensical, even for the patient. (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)

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)

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)

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 convergence of biomedical sciences with nanotechnology as well as ICT has created a new wave of biomedical technologies, resulting in visions of a ‘molecular medicine’. Since novel technologies tend to shift concepts of disease and health, this paper investigates how the emerging field of molecular medicine may shift the meaning of ‘disease’ as well as the boundary between health and disease. It gives a brief overview of the development towards and the often very speculative visions of (...) molecular medicine. Subsequently three views of disease often used in the philosophy of medicine are briefly discussed: the ontological or neo-ontological, the physiological and the normative/holistic concepts of disease. Against this background two tendencies in the field of molecular medicine are highlighted: (1) the use of a cascade model of disease and (2) the notion of disease as a deviation from an individual pattern of functioning. It becomes clear that molecular medicine pulls conceptualizations of disease and health in several, partly opposed directions. However, the resulting tensions may also offer opportunities to steer the future of medicine in more desirable directions. (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.

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)

What, for Galen, are powers, and how are they to be properly individuated? The notion of a power or capacity does a great deal of work in Galen. As in Aristotle, the concept of a dunamis is tightly linked with that of an energeia, but these are not simply logical abstractions. Rather the natural energeiai are the basic functional activities of the animal body and its parts, and just as health consists in proper functioning, so disease is defined as (...) ‘damage to one of the natural energeiai of the body’, and these activities are damaged when something interferes with its related dunamis. Here I try to make sense of the apparently very different things Galen says regarding dunameis. For example, he says that they do not inhabit our bodies as we do our houses; that is, presumably, they are not substantial or hypostasized; rather they are properties of us. Equally, he is perfectly clear that they are relational items: a power is a power for affecting something determinate in some determinate way. They. (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)

Christopher Boorse’s Health care ethics: an introduction, Temple University Press, Philadelphia, pp 359–393, 1987; in Humber, Almeder, Totowa What is disease?, Humana Press, New York City, pp 1–134, 1997; J Med Philos, 39:683–724, 2014) Bio-Statistical Theory comprehends diseases in terms of departures from natural norms, which involve an objectively describable deviation from the proper physiological or psychological functioning of parts of the human organism. I argue that while recent revisions and additional considerations shield the BST from a number of (...) issues raised by critics, they give rise to significant new challenges. These are related to the attribution of epistemic authority, the possibility of multiple concepts in the authoritative literature, and the framing of BST as “philosophical explication.” The conclusion is that, in its current form, the BST is unable to provide a robust framework for a naturalist classification. (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)

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)

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)

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)

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)

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.

Biomedical research is increasingly a matter of the navigation through large computerized information resources deriving from functional genomics or from the biochemistry of disease pathways. To make such navigation possible, controlled vocabularies are needed in terms of which data from different sources can be unified. One of the most influential developments in this regard is the so-called Gene Ontology, which consists of controlled vocabularies of terms used by biologists to describe cellular constituents, biological processes and molecular functions, organized (...) into hierarchies via the relation of class subsumption. Here we seek to provide a rigorous account of the logic of classification that underlies GO and similar biomedical ontologies. Drawing on Aristotle, we develop a system of axioms and definitions for the treatment of biological classes and instances. (shrink)

In this article, I argue that the history and philosophy of autism need to account for two kinds of autism. Contemporary autism research and practice is structured, directed and connected by an ‘ontological understanding of disease’. This implies that autism is understood as a disease like any other medical disease, existing independently of its particular manifestations in individual patients. In contrast, autism in the 1950s and 1960s was structured by a psychoanalytical framework and an ‘individual understanding of (...) disease’. This implied that autism was not a distinct disease but an idiosyncratic and meaningful response of the child to a disturbed development of the ego. These two kinds of autism are embedded in and reveal two very different ‘styles of psychiatric thought’. (shrink)

Disagreement about the nature of ‘addiction’, such as whether it is a brain disease, arises in part because the label is applied to a wide range of phenomena. This creates conceptual and definitional confusions and misunderstandings, often leading to researchers talking past one another. Ontologies have been successfully implemented in other fields to help solve these problems by creating unifying frameworks that can accommodate divergence while clarifying the basis for it. We argue that ontologies can help transform the way (...) we think and communicate about addiction as well, providing a basis for a shared understanding of the domain and a shared means for communicating and achieving that understanding. -/- We introduce the use of ontologies in science and medicine and show how they can unify differing perspectives on addiction. We also show how ontologies provide a practical tool for organizing our collective knowledge in this field, even, and especially, when that knowledge is garnered through distinct disciplinary approaches adopting disparate methodologies or perspectives (e.g., neurobiological, psychological, sociological, etc.). In the end, we believe that ontologies can help to avoid letting questions like “Is addiction a brain disease?” divide the field, hamper communication, or otherwise disrupt the ability to make meaningful progress. (shrink)

Dr Taylor's book analyses the disease concept as it developed in medical history and seeks to clarify it with the help of concepts largely derived from logical class theories. A solution is proposed to the problem of how to distinguish between the class of 'patients' and the class of 'healthy persons' which corresponds to the actual diagnostic practices of doctors. The earliest theories of disease postulated concrete entities which exist independently of the body. The notion of disease (...) entity has lost its original ontological connotations and instead its important feature has become the possession of a unitary and self-contained character. Dr Taylor describes the modern theories as essentially 'reactive' in character, that is the symptoms of a disease are the bodily reactions to the 'noxae'. After seeing the subject in its historical content, Dr Taylor goes on to discuss in detail the notion of the classification of diseases, making extensive use of modern views on the logic of classes. (shrink)

Zachar's commentary can be read as a sophisticated theoretical extension of the target article, and I am very pleased to see support for a relationalist turn in understanding mental disorders. Indeed, underlying causal properties are only an ingredient of essentialism and a more elaborate discussion of this issue brings us readily to the discourse on kinds and ontology. Zachar is an advocate for thinking of psychiatric constructs as practical kinds. This logically leads him to think that the problem with (...) categorical classification systems like the Diagnostic and Statistical Manual of Mental Disorders and the International Classification of Diseases are practical problems (lack of... (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)

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)

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.

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)

While it is well-established that poverty and disease are intimately connected, the nature of this connection and the role of poverty in disease causation remains contested in scientific and social studies of disease. Using the case of HIV/AIDS in South Africa and drawing on a theoretically grounded analysis, this paper reconceptualises disease and poverty as ontologically entangled. In the context of the South African HIV epidemic, this rethinking of the poverty-disease dynamic enables an account of (...) how social forces such as poverty become embodied in the very substance of disease to produce ontologies of HIV/AIDS unique to South Africa. (shrink)

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)