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)

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 Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in publicly available databases. Such (...) annotation enables several objectives, including searching, browsing and cross-database data integration. A key benefit conferred by realismbased ontology is that suitably annotated research results are able to be aggregated and compared in a fashion that is based on the underlying reality that the science is studying. This has the potential of increasing the power of statistical analysis and meta-analysis in data-driven science. This aspect has been fruitfully exploited in the investigation of the functions of genes in molecular biology. Cognitive neuroscience uses functional neuroimaging to investigate the brain correlates of areas of mental functioning such as memory, planning and emotion. The use of functional neuroimaging to study affective phenomena such as the emotions is called ‘affective neuroscience’. BrainMap is the largest curated database of coordinates and metadata for studies in cognitive neuroscience, including affective neuroscience (Laird et al., 2005). BrainMap data is already classified and indexed using a terminology for classification, called the ‘Cognitive Paradigm Ontology’ (CogPO), that has been developed to facilitate searching and browsing. However, CogPO has been developed specifically for the BrainMap database, and the data are thus far not annotated to a realism-based ontology which would allow the discovery of interrelationships between research results across different databases on the basis of what the research is about. In this contribution, we describe ongoing work that aims to annotate affective neuroscience data, starting with the BrainMap database, using the Emotion Ontology. We describe our objectives and technical approach to the annotation, and mention some of the challenges. (shrink)

Mental health research faces a suite of unresolved challenges that have contributed to a stagnation of research efforts and treatment innovation. One such challenge is how to reliably and validly account for the subjective side of patient symptomatology, that is, the patient’s inner experiences or patient phenomenology. Providing a structured, standardised semantics for patient phenomenology would enable future research in novel directions. In this contribution, we aim at initiating a standardized approach to patient phenomenology by sketching a tentative formalisation within (...) the framework of an applied ontology, in the broader context of existing open-source Open Biomedical Ontologies resources such as the Mental Functioning Ontology. We further discuss a number of prevailing challenges and observations bearing on this task. (shrink)

A thorough understanding of what needs are is fundamental for design- ing well-behaved information systems for many social applications and in partic- ular for public services. Talking about needs pervades indeed the jargon of Public Administrations when motivating their service offering. In this paper, we propose an ontological analysis of needs, aiming at a principled disentangling of the differ- ent uses of the term. We leverage philosophical tradition on intentionality, for its rich understanding of mental entities, we compare it with (...) the well-established BDI (Belief-Desire-Intention) tradition in knowledge representation, and we propose a formalisation of needs within the foundational ontology DOLCE. Throughout the paper, we motivate our analysis focusing on needs in public services. (shrink)

Advances in emotion and affective science have yet to translate routinely into psychiatric research and practice. This is unfortunate since emotion and affect are fundamental components of many psychiatric conditions. Rectifying this lack of interdisciplinary integration could thus be a potential avenue for improving psychiatric diagnosis and treatment. In this contribution, we propose and discuss an ontological framework for explicitly capturing the complex interrelations between affective entities and psychiatric disorders, in order to facilitate mapping and integration between affective science and (...) psychiatric diagnostics. We build on and enhance the categorisation of emotion, affect and mood within the previously developed Emotion Ontology, and that of psychiatric disorders in the Mental Disease Ontology. This effort further draws on developments in formal ontology regarding the distinction between normal and abnormal in order to formalize the interconnections. This operational semantic framework is relevant for applications including clarifying psychiatric diagnostic categories, clinical information systems, and the integration and translation of research results across disciplines. (shrink)

Festschrift in Honor of Barry Smith on the occasion of his 65th Birthday. Published as issue 4:4 of the journal Cosmos + Taxis: Studies in Emergent Order and Organization. Includes contributions by Wolfgang Grassl, Nicola Guarino, John T. Kearns, Rudolf Lüthe, Luc Schneider, Peter Simons, Wojciech Żełaniec, and Jan Woleński.

Many recent accounts of the ontology of groups, institutions, and practices have touched upon the normative or deontic dimensions of social reality (e.g., social obligations, claims, permissions, prohibitions, authority, and immunity), as distinct from any specifically moral values or obligations. For the most part, however, the ontology of such socio-deontic phenomena has not received the attention it deserves. In what sense might a social obligation or a claim exist? What is the ontological status of such an obligation (e.g., is it (...) an entity in its own right)? And how do people come to have social obligations or permissions in the first place? In this dissertation, I argue that such social-deontic phenomena can be accounted for ontologically in terms of the existence of shared prescriptive representational content that is backed by collectively held dispositions to monitor for compliance, and to punish (sanction, blame, chide, look unfavorably upon) those who fail to comply. (shrink)