The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies (...) play in two multicentric research projects. Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies (...) play in two multicentric research projects. Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

In the clinical setting, not enough attention is paid to the role that emotion plays. It is at worst ignored or avoided, isolating those who are suffering, at best treated as something to help another to endure. This is the result, in part, of an impoverished idea that views emotion as mere feelings. However, emotions are not just feelings, they are cognitive. If we look beneath the surface, emotions can provide information about values and beliefs, some of which may (...) be false or unreasonable. When they are motivating decisions that seriously affect the lives of others, there is a moral obligation to ferret them out and correct or deal with them. Attention needs to be paid to the emotions of healthcare providers as well as to the emotions of patients and their loved ones, and more done to train healthcare providers to deal effectively and productively with emotion – their own and others’. A son tearfully requests everything be done for his dying father. He fears limiting treatment means his father will be ignored. A physician orders another course of chemotherapy because she cannot bear for this patient to die. The patient, fearing he will painfully suffocate to death, agrees. Paying attention to emotions and bringing to light the beliefs and values behind them can only enhance the care and consideration of all involved. (shrink)

The theory of granular partitions (TGP) is a new approach to the understanding of ontologies and other classificatory systems. The paper explores the use of this new theory in the treatment of task-based clinical guidelines as a means for better understanding the relations between different clinical tasks, both within the framework of a single guideline and between related guidelines. We used as our starting point a DAML+OIL-based ontology for the WHO guideline for hypertension management, comparing this with (...) related guidelines and attempting to show that TGP provides a flexible and highly expressive basis for the manipulation of ontologies of a sort which might be useful in providing more adequate Computer Interpretable Guideline Models (CIGMs) in the future. (shrink)

Clinical guidelines are special types of plans realized by collective agents. We provide an ontological theory of such plans that is designed to support the construction of a framework in which guideline-based information systems can be employed in the management of workflow in health care organizations. The framework we propose allows us to represent in formal terms how clinical guidelines are realized through the actions of are realized through the actions of individuals organized into teams. We provide various (...) levels of implementation representing different levels of conformity on the part of health care organizations. Implementations built in conformity with our framework are marked by two dimensions of flexibility that are designed to make them more likely to be accepted by health care professionals than standard guideline-based management systems. They do justice to the fact 1) that responsibilities within a health care organization are widely shared, and 2) that health care professionals may on different occasions be non-compliant with guidelines for a variety of well justified reasons. The advantage of the framework lies in its built-in flexibility, its sensitivity to clinical context, and its ability to use inference tools based on a robust ontology. One disadvantage lies in its complicated implementation. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, (...) ‘statistical data analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in (...) fact exist and (b) they do this in terms of the types and type-level relationships described in these ontologies. While much attention has been devoted to (1), work on (2), which is the topic of this paper, is comparatively rare. Using Referent Tracking as basis, we describe a technical data wrangling strategy which consists in creating for each dataset a template that, when applied to each particular record in the dataset, leads to the generation of a collection of Referent Tracking Tuples (RTT) built out of unique identifiers for the entities described by means of the data items in the record. The proposed strategy is based on (i) the distinction between data and what data are about, and (ii) the explicit descriptions of portions of reality which RTTs provide and which range not only over the particulars described by data items in a dataset, but also over these data items themselves. This last feature allows us to describe particulars that are only implicitly referred to by the dataset; to provide information about correspondences between data items in a dataset; and to assert which data items are unjustifiably or redundantly present in or absent from the dataset. The approach has been tested on a dataset collected from patients seeking treatment for orofacial pain at two German universities and made available for the NIDCR-funded OPMQoL project. (shrink)

There are a number of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications represent classes of entities which exist at various anatomical levels of granularity. We argue that in order to apply such representations to the Electronic Health Records one needs sound ontologies which take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal theory for addressing these issues (...) in a way that the ontologies can be used to support inferences relating to entities which exist at different anatomical levels of granularity. Our case study is the colon carcinoma, one of the most common carcinomas prevalent within the European population. (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)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to (...) describe a number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of of effort has been invested in the development of various tools which automate the representation and execution of the recommendations contained within such guidelines and protocols by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based on standard terminology systems like UMLS, form one of the core components of such a model. We have created DAML+OIL-based CTOs for the tasks mentioned (...) in the WHO guideline for hypertension management, drawing comparisons also with other related guidelines. The advantages of CTOs include: contextualization of ontologies, providing ontologies tailored to specific aspects of the phenomena of interest, dividing the complexity involved in creating ontologies into different levels, providing a methodology by means of which the task recommendations contained within guidelines can be integrated into the clinical practices of a health care set-up. (shrink)

Ontologies are being ever more commonly used in biomedical informatics and we provide a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonised. We argue that one key foundation for both ontology evaluation and harmonisation is the adoption (...) of a realist paradigm in ontology development. For science-based ontologies of the sort which concern us in the eHealth arena, it is reality that provides the common benchmark against which ontologies can be evaluated and aligned within larger frameworks. Given the current multitude of ontologies in the biomedical domain the need for harmonisation is becoming ever more urgent. We describe one example of such harmonisation within the ACGT project, which draws on ontology-based computing as a basis for sharing clinical and laboratory data on cancer research. (shrink)

Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is (...) linked to multiple clinical trials investigating Gleevec’s related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed. (shrink)

For decades, physicians, philosophers, theologians, lawyers, and the public considered brain death a settled issue. However, a series of recent cases in which individuals were declared brain dead yet physiologically maintained for prolonged periods of time has challenged the status quo. This signals a need for deeper reflection and reexamination of the underlying philosophical, scientific, and clinical issues at stake in defining death. In this paper, I consider four levels of philosophical inquiry regarding death: the ontological basis, actual states (...) of affairs, epistemological standards, and clinical criteria for brain death. I outline several candidates for the states of affairs that may constitute death, arguing that we should strive for a single, unified ontological definition of death as a loss of integrated functioning as a unified organism, while acknowledging that two states of affairs may satisfy this concept. I argue that the clinical criteria for determining whole-brain death should be bolstered to meet the epistemic demand of sufficient certainty in defining death by adding indicators of cerebro-somatic dis-integration to the traditional triad of loss of consciousness, loss of brainstem function, and absence of confounding explanations. (shrink)

The objective of this research programme is to contribute to the establishment of the emerging science of Formal Ontology in Information Systems via a collaborative project involving researchers from a range of disciplines including philosophy, logic, computer science, linguistics, and the medical sciences. The re­searchers will work together on the construction of a unified formal ontology, which means: a general framework for the construction of ontological theories in specific domains. The framework will be constructed using the axiomatic-deductive method of modern (...) formal ontology. It will be tested via a series of applications relating to on-going work in Leipzig on medical taxonomies and data dictionaries in the context of clinical trials. This will lead to the production of a domain-specific ontology which is designed to serve as a basis for applications in the medical field. (shrink)

Background: SNOMED CT is a large terminology system designed to represent all aspects of healthcare. Its current form and content result from decades of bottom-up evolution. Due to SNOMED CT’s formal descriptions, it can be considered an ontology. The Basic Formal Ontology (BFO) is a foundational ontology that proposes a small set of disjoint, hierarchically ordered classes, supported by relations and axioms. In contrast, as a typical top-down endeavor, BFO was designed as a foundational framework for domain ontologies in (...) the natural sciences and related disciplines. Whereas it is mostly assumed that domain ontologies should be created as extensions of foundational ontologies, a post-hoc harmonization of consolidated domain ontologies in use, such as SNOMED CT, is known to be challenging. Methods: We explored the feasibility of harmonizing SNOMED CT with BFO, with a focus on the SNOMED CT Clinical Finding hierarchy. With more than 100,000 classes, it accounts for about one third of SNOMED CT’s content. In particular, we represented typical SNOMED CT finding/disorder concepts using description logics under BFO. Three representational patterns were created and the logical entailments analyzed. Results: Under a first scrutiny, the clinical intuition that diseases, disorders, signs and symptoms form a homogeneous ontological upper-level class appeared incompatible with BFO’s upper-level distinction into continuants and occurrents. The Clinical finding class seemed to be an umbrella for all kinds of entities of clinical interest, such as material entities, processes, states, dispositions, and qualities. This suggests the conclusion that Clinical finding would not be a suitable upper-level class from an BFO perspective. On closer inspection of the taxonomic links within this hierarchy and the implicit meaning derived thereof, it became clear that Clinical finding classes do not characterize the entity (e.g. a fracture, allergy, tumor, pain, hemorrhage, seizure, fever) in a literal sense but rather the condition of a patient having that fracture, allergy, pain etc. This gives sense to the current characteristic of the Clinical Finding hierarchy, in which complex classes are modeled as subclasses of their constituents. Most of these taxonomic links are inferred, as the consequence of the ‘role group’ design pattern, which is ubiquitous in SNOMED CT and has often been subject of controversy regarding its semantics. Conclusion: Our analyses resulted in the proposal of (i) equating SNOMED CT’s ‘role group’ property with the reflexive and transitive BFO relation ‘has occurrent part’; and (ii) reinterpreting Clinical Findings as Clinical Occurrents, i.e. temporally extended entities in an organism, having one or more occurrents as temporal parts that occur in continuants. This re-interpretation was corroborated by a manual analysis of classes under Clinical Finding, as well as the identification of similar modeling patterns in other ontologies. As a result, SNOMED CT does not require any content redesign to establish compatibility with BFO, apart from this re-interpretation, and a suggested re-labeling. Regarding the feasibility of harmonizing terminologies with principled foundational ontologies post-hoc, our results provide support to the assumption that this does not necessarily require major redesign efforts, but rather a careful analysis of the implicit assumptions of terminology curators and users. (shrink)

The purpose of this study was to evaluate, revise, and extend the Informed Consent Ontology (ICO) for expressing clinical permissions, including reuse of residual clinical biospecimens and health data. This study followed a formative evaluation design and used a bottom-up modeling approach. Data were collected from the literature on US federal regulations and a study of clinical consent forms. Eleven federal regulations and fifteen permission-sentences from clinical consent forms were iteratively modeled to identify entities and their (...) relationships, followed by community reflection and negotiation based on a series of predetermined evaluation questions. ICO included fifty-two classes and twelve object properties necessary when modeling, demonstrating appropriateness of extending ICO for the clinical domain. Twenty-six additional classes were imported into ICO from other ontologies, and twelve new classes were recommended for development. This work addresses a critical gap in formally representing permissions clinical permissions, including reuse of residual clinical biospecimens and health data. It makes missing content available to the OBO Foundry, enabling use alongside other widely-adopted biomedical ontologies. ICO serves as a machine-interpretable and interoperable tool for responsible reuse of residual clinical biospecimens and health data at scale. (shrink)

My article, “Whole-brain death and integration: Realigning the ontological concept with clinical diagnostic tests”.

Outcomes research in healthcare has been a topic much addressed in recent years. Efforts in this direction have been supplemented by work in the areas of guidelines for clinical practice and computer-interpretable workflow and careflow models.In what follows we present the outlines of a framework for understanding the relations between organizations, guidelines, individual patients and patient-related functions. The derived framework provides a means to extract the knowledge contained in the guideline text at different granularities, in ways that can help (...) us to assign tasks within the healthcare organization and to assess clinical performance in realizing the guideline. It does this in a way that preserves the flexibility of the organization in the adoption of the guidelines. (shrink)

Intuition in medical and moral reasoning -- Moral intuitionism -- The place of Aristotelian phronesis in clinical reasoning -- Aristotle's practical syllogism: accounting for the individual through a theory of action and cognition -- Individual and statistical physiognomy: the art and science of making the invisible visible -- Clinical intuition versus statistical reasoning -- Contingency and correlation: the significance of modeling clinical reasoning on statistics -- Abduction: the intuitive support of clinical induction -- Conclusion: medical ethics (...) beyond ontology. (shrink)

In After God: Morality and Bioethics in a Secular Age, H. Tristram Engelhardt, Jr. explores the broad implications for moral reasoning once a culture has lost a God’s-eye perspective. In this paper, I focus on the implications of Engelhardt’s views for clinical ethics consultation. I begin by examining the question of whether clinical ethics consultants should advocate a particular viewpoint and/or process during consultations or adopt a neutral stance. I then examine the implications of Engelhardt’s views for this (...) question. Finally, I discuss some of Engelhardt’s foundational ontological, metaphysical, meta-ethical, and epistemological commitments and how these commitments connect to his views on clinical ethics consultation. (shrink)

General Ontological Language (GOL) is a formal framework for representing and building ontologies. The purpose of GOL is to provide a system of top-level ontologies which can be used as a basis for building domain-specific ontologies. The present paper gives an overview about the basic categories of the GOL-ontology. GOL is part of the work of the research group Ontologies in Medicine (Onto-Med) at the University of Leipzig which is based on the collaborative work of the (...) Institute of Medical Informatics (IMISE) and the Institute for Computer Science (IfI). It represents work in progress toward a proposal for an integrated family of top-level ontologies and will be applied to several fields of medicine, in particular to the field of Clinical Trials. (shrink)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Philosophy, Psychiatry, & Psychology 12.1 (2005) 1-7 [Access article in PDF] Clinical Practice, Science, and the Unconscious Douglas McConnell Neil Pickering Keywords psychotherapy, cognitive science, neuroscience, computational view of mind. This volume of Philosophy, Psychiatry, & Psychology is devoted to questions about the unconscious mind. The philosophical complexities and difficulties associated with the unconscious are many and, despite widespread confusion and disagreement as to the nature of the (...) unconscious mind, it is used as a concept informing psychotherapy. It is therefore not surprising that papers in a special edition on the unconscious might be weighted heavily toward uncovering a justifiable conceptual niche for the unconscious and elaborating on some of the main conceptual connections. Although this makes for a slightly more philosophical edition of PPP than usual, those perhaps less interested in philosophy and more interested in actual psychiatric practice can incorporate the concepts and insights developed in these papers into their practice as they see fit.The three main articles take three quite distinct approaches to the unconscious. Schechtman (2005) addresses the need for a theory of personal identity to incorporate the unconscious and presents one that does so by developing some central Lockian intuitions. Church (2005) investigates whether the kinds of things happening in the unconscious can be explained by cognitive operations not normally associated with consciousness, specifically, spatial structuring of experience. McConnell and Gillett (2005) clarify some of Lacan's ontology of the mind where the language encountered and used by the subject provides the structure for their unconscious.The aim of this introduction is to ask and try to answer a question that logically precedes those raised in the articles in the light of the therapeutic use of the unconscious. When dealing with psychoanalysis or psychoanalytic concepts in an Anglo-American context, the struggle that psychoanalysis has had and continues to have in a psychiatric domain ruled by science is never far from the spotlight. Indeed Hinshelwood (2005) also picks up the importance of this conflict when replying to McConnell and Gillett. It seems to be historically true that the unconscious has fallen out of favor in scientific and psychiatric circles (it is no surprise that psychiatric training is largely based in "hard," that is, biological and biochemical science) particularly over the last 50 years or so. But is the scientific skepticism to be found about the use of the unconscious well-founded? And how does the continued utilization [End Page 1] of the unconscious by the therapist fit into current practice given this skepticism? Psychotherapy and the Unconscious In psychotherapy, the therapist and the client together construct a story that explains why the client is having some form of difficulty in his or her life. The stated aim is to enable the client to overcome this difficulty by gaining an understanding of what has generated it. Doing so may be a first step to dealing with that conflict. For example, an office worker who is scared of the boss and whose life at work is a misery as result may come to think that the boss is a reminder of some threatening figure from childhood and that the reaction is a regression to infantile behavior. Knowing this, the fear of the boss can be revisited—perhaps reconfigured, perhaps overcome—and life may improve. In the process of therapy, the relation of the figure from childhood to the boss is made conscious. But it was still operative before it was made explicit, even though the client did not realize it and some would say that the client's unconscious had somehow buried the memory from childhood or hidden from the client the relation of this memory of a threatening figure to the boss.A description of the content of the unconscious is, then, an intentional description involving the client's thought life, one made to help an individual understand otherwise unintelligible (to that individual) feelings, beliefs, desires, actions, and so on. Subjects' intentions are their normatively structured mental representations of, and attitudes toward, the world (e.g., "He is my boss"; "I am afraid of him"). An intentional unconscious description then takes an intentional form... (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)

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy (...) to advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

Objectives: Medical decision support and other intelligent applications in the life sciences depend on increasing amounts of digital information. Knowledge bases as well as formal ontologies are being used to organize biomedical knowledge and data. However, these two kinds of artefacts are not always clearly distinguished. Whereas the popular RDF(S) standard provides an intuitive triple-based representation, it is semantically weak. Description logics based ontology languages like OWL-DL carry a clear-cut semantics, but they are computationally expensive, and they are often (...) misinterpreted to encode all kinds of statements, including those which are not ontological. Method: We distinguish four kinds of statements needed to comprehensively represent domain knowledge: universal statements, terminological statements, statements about particulars and contingent statements. We argue that the task of formal ontologies is solely to represent universal statements, while the non-ontological kinds of statements can nevertheless be connected with ontological representations. To illustrate these four types of representations, we use a running example from parasitology. Results: We finally formulate recommendations for semantically adequate ontologies that can efficiently be used as a stable framework for more context-dependent biomedical knowledge representation and reasoning applications like clinical decision support systems. (shrink)

This article introduces a novel theoretical framework for addressing epistemic injustice—a phenomenon where certain groups or individuals are systematically excluded from knowledge creation and dissemination processes—by employing ontological relativity and conceptual analysis. “Ontological relativity” refers to a philosophical perspective that posits our understanding of reality as being shaped by our toolbox of concepts, categories, language, and social practices; “conceptual analysis” is a method of inquiry that involves the rigorous examination and deconstruction of a particular concept or set of concepts in (...) order to uncover their constituent elements, relationships, and underlying assumptions. To exemplify the effectiveness of the ontology‐based approach, two paradigmatic applications are explored: (a) educational practices and (b) clinical practice and access to health care. Through the presentation of these applications and the step‐by‐step illustration of the applied methodology, the aim of the article is to showcase the efficacy of ontology in tackling epistemic injustices, suggesting innovative paths for future research in this domain. (shrink)

Phenomenology gives rise to certain ontological considerations that have far-reaching implications for standard conceptions of patient autonomy in medical ethics, and, as a result, the obligations of and to patients in clinical decision-making contexts. One such consideration is the phenomenological reduction in classical phenomenology, a core feature of which is the characterisation of our primary experiences as immediately and inherently meaningful. This paper builds on and extends the analyses of the phenomenological reduction in the works of Husserl, Heidegger, and (...) Merleau-Ponty in order to identify and explain its implications for our current understanding of the principle of respect for patient autonomy and the norms of clinical decision making. (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)

Background: Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is acomprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic healthdata. Some efforts have been made to capture the contents of SCT as Web Ontology Language (OWL), but theseefforts have been hampered by the size and complexity of SCT. Method: Our proposal here is to develop an upper-level ontology and to use it as the basis for defining the termsin SCT in a way that (...) will support quality assurance of SCT, for example, by allowing consistency checks ofdefinitions and the identification and elimination of redundancies in the SCT vocabulary. Our proposed upper-levelSCT ontology (SCTO) is based on the Ontology for General Medical Science (OGMS). Results: The SCTO is implemented in OWL 2, to support automatic inference and consistency checking. Theapproach will allow integration of SCT data with data annotated using Open Biomedical Ontologies (OBO) Foundryontologies, since the use of OGMS will ensure consistency with the Basic Formal Ontology, which is the top-levelontology of the OBO Foundry. Currently, the SCTO contains 304 classes, 28 properties, 2400 axioms, and 1555annotations. It is publicly available through the bioportal athttp://bioportal.bioontology.org/ontologies/SCTO/. Conclusion: The resulting ontology can enhance the semantics of clinical decision support systems and semanticinteroperability among distributed electronic health records. In addition, the populated ontology can be used forthe automation of mobile health applications. (shrink)

Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user-friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage? Methods: Our focus here is on two different sets of answers to these questions that have been proposed, on the one hand in medicine, by the (...) SNOMED CT community, and on the other hand in biology, by the OBO Foundry. We address more specifically the issue as to how adherence to certain development principles can advance the usability and effectiveness of an ontology or terminology resource, for example by allowing more accurate maintenance, more reliable application, and more efficient interoperation with other ontologies and information resources. Results: SNOMED CT and the OBO Foundry differ considerably in their general approach.Nevertheless, a general trend towards more formal rigor and cross-domain interoperability can be seen in both and we argue that this trend should be accepted by all similar initiatives in the future. Conclusions: Future efforts in ontology development have to address the need for harmonization and integration of ontologies across disciplinary borders, and for this, coherent formalization of ontologies is a prerequisite. (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)

In this essay, I argue that traditional medical views of illness systematically exclude intuitive knowledge from their description of disease and thus result in a functionally impressive but humanly ungrounded medicine. Physicians trained in a technologized anatomico-pathologic view of disease find themselves cut off from much of what they knew about illness when they began their training. Not only do they lack a rigorous or formal way to confront the non-technical aspects of medical practice, but many have even lost sight (...) of the motives for medicine. I argue here for an intuitively based humanly grounded ontology of illness. Such an ontology begins in an understanding of the experience of the sick person rather than in an "objective" description of pathology. It is only through a science of illness-as-lived that one may achieve a truly humanistic medicine. CiteULike Connotea Del.icio.us What's this? (shrink)

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...) paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

The Belmont Report’s distinction between research and the practice of accepted therapy has led various authors to suggest that these purportedly distinct activities should be governed by different ethical principles. We consider some of the ethical consequences of attempts to separate the two and conclude that separation fails along ontological, ethical, and epistemological dimensions. Clinical practice and clinical research, as with yin and yang, can be thought of as complementary forces interacting to form a dynamic system in which (...) the whole exceeds the sum of its parts. Just as effective clinical practice cannot exist without clinical research, meaningful clinical research requires the context of clinical practice. We defend this thesis by triangulation, that is, by outlining how multiple investigators have reached this conclusion on the basis of varied theoretical and applied approaches. More confidence can be placed in a result if different methods/viewpoints have led to that result. (shrink)

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data (...) relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. (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 automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the (...) naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable. (shrink)

The work of Gregory Bateson offers a metaphysical basis for a “process psychology,” that is, a view of psychological practice and research guided by an ontology of becoming—identifying change, difference, and relationship as the basic elements of a foundational metaphysics. This article explores the relevance of Bateson's recursive epistemology, his re-conception of the Great Chain of Being, a first-principles approach to defining the nature of mind, and understandings of interaction and difference, pattern and symmetry, interpretation and context. Bateson's philosophical contributions (...) will be drawn into relationship with Wittgenstein's philosophy of language as use, Melnyk's theory of causal levels of explanation, Korzybski's account of map and territory, the rejection of the heuristic rigidity of substantialist ontologies, and a cybernetics communication science-informed approach to contextual bi-directionality of causality. We thereby arrive at an understanding of Bateson's process psychology that, given its ecological-systemic nature, is explanatorily applicable across the mind sciences. This process psychology equips us to answer the question: What is mind? Not by explanatory appeal to substantial entities contained within mind, but instead by recourse to the contextually relevant patterns for understanding mind to a particular purpose. We have thereby attended to the gulf between heuristics and fundamentals, between psychological models and an onto-epistemic account of reality. Insufficient attention has been given to characterising the vital nature of Bateson's philosophical oeuvre to psychological practice. This article draws out Bateson's relevance to establishing foundational principles for a process psychology capable of reinvigorating psychological thought. (shrink)

The article examines the patient-doctor relationship, relying on Michel Foucault’s concept of the clinical gaze. We argue that during the last decades, a profound transformation of the social nature of medicine took place, one that Foucault’s understanding of the clinical gaze cannot adequately account for. First, the article offers an elaboration of the three-node network of clinical gaze, the clinic, and nosology to explain the positioning of the doctor and the patient within the specific social ontology generated (...) by the rise of medicine. We then discuss intensive but irresolute developments brought by technological advancements, especially the X-ray tube. Finally, we argue that in the contemporary clinic, equipped with a plethora of sophisticated devices, the position of the doctor endured the most radical transformation in comparison with Foucault’s proponent of the clinical gaze at the dawn of modern medicine. (shrink)

The purpose is to identify common and distinctive features of concepts and methodology of the problem of subject within different discourses, implicitly or explicitly relevant to the definition of "clinical" mode of human existence. The research methodology combines techniques of discourse analysis and basic principles of historical and philosophical studies. Originality of the research lies in definition of the clinical philosophical discourse as a special communicative process, where utterances not only focus on disease syndromes, and reveal phenomenology of (...) inner experience of a pathological self, but also structure a certain type of sociality. Clinical discourse represents the space where the patient is treated not as a subject but as an object of disease. Ontology of clinical discourse prevails over ontology of disease, since its structures determine the notion of disease as such. Categorization of the disease, the idea of disease as a phenomenon subdued to professional authority leads to the idea of the need for patient’s isolation from the natural environment and removing him to special social institutions. The clinicist doctrines share the intention to reduce the patient’s self to its bodily dimension, while ignoring social determinants of psychological deviations. Conclusions of the study are summarized in the following positions: the current clinical discourse is based on the positivist-biological trend in humanitarian knowledge and it is the basis for the production and reproduction of medical and pharmaceutical repressive ideology; criticism of philosophical clinical discourse opens the possibility of overcoming the dominance of purely clinicist discourse; such a transformation is possible only after a paradigm shift in understanding the category of subject. (shrink)

Although researchers in psychiatry have been trying for decades to elucidate the pathophysiology underlying mental disorders, relatively little progress has been made. One explanation for this failure is that diagnostic categories in psychiatry are unlikely to track underlying neurological mechanisms. Because of this, the US National Institutes of Mental Health has recently developed a novel ontology to guide research in biological psychiatry: the Research Domain Criteria. In this paper, I argue that while RDoC may lead to better neuroscientific explanations for (...) mental disorders, it is unlikely that this new knowledge will then lead to an improved diagnostic system. I therefore suggest that researchers in psychiatry should work toward the development of two new ontologies: one for research and one for clinical practice. (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)

Recent work on the quality assurance of the Gene Ontology (GO, Gene Ontology Consortium 2004) from the perspective of both linguistic and ontological organization has made it clear that GO lacks the kind of formalism needed to support logic-based reasoning. At the same time it is no less clear that GO has proven itself to be an excellent terminological resource that can serve to combine together a variety of biomedical database and information systems. Given the strengths of GO, it is (...) worth investigating whether, by overcoming some of its weaknesses from the point of view of formal-ontological principles, we might not be able to enhance a version of GO which can come even closer to serving the needs of the various communities of biomedical researchers and practitioners. It is accepted that clinical and bioinformatics need to find common ground if the results of data-intensive biomedical research are to be harvested to the full. It is also widely accepted that no single method will be sufficient to create the needed common framework. We believe that the principles-based approach to life-science data integration and knowledge representation must be one of the methods applied. Indeed in dealing with the ontological representation of carcinomas, and specifically of colon carcinomas, we have established that, had GO (and related biomedical ontologies) followed some of the basic formal-ontological principles we have identified (Smith et al. 2004, Ceusters et al. 2004), then the effort required to navigate successfully between clinical and bioinformatics systems would have been reduced. We point here to the sources of ontologically-related errors in GO, and also provide arguments as to why and how such errors need to be resolved. (shrink)

The article examines the patient-doctor relationship, relying on Michel Foucault’s concept of the clinical gaze. We argue that during the last decades, a profound transformation of the social nature of medicine took place, one that Foucault’s understanding of the clinical gaze cannot adequately account for. First, the article offers an elaboration of the three-node network of clinical gaze, the clinic, and nosology to explain the positioning of the doctor and the patient within the specific social ontology generated (...) by the rise of medicine. We then discuss intensive but irresolute developments brought by technological advancements, especially the X-ray tube. Finally, we argue that in the contemporary clinic, equipped with a plethora of sophisticated devices, the position of the doctor endured the most radical transformation in comparison with Foucault’s proponent of the clinical gaze at the dawn of modern medicine. (shrink)

We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices. If properly developed and extended, we believe the VSO (...) will find applications for the EMR, clinical informatics, and medical device communities. (shrink)