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Toward an Ontological Treatment of Disease and Diagnosis

In Proceedings of the 2009 AMIA Summit on Translational Bioinformatics. American Medical Informatics Association (2009)

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  1. OAE: The Ontology of Adverse Events.Yongqun He, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao & Barry Smith - 2014 - Journal of Biomedical Semantics 5 (29):1-13.
    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 (...)
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  • Representing Mental Functioning: Ontologies for Mental Health and Disease.Janna Hastings, Werner Ceusters, Mark Jensen, Kevin Mulligan & Barry Smith - 2012 - In Towards an Ontology of Mental Functioning (ICBO Workshop), Proceeedings of the Third International Conference on Biomedical Ontology.
    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 (...)
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  • A Unified Framework for Biomedical Terminologies and Ontologies.Werner Ceusters & Barry Smith - 2010 - Studies in Health Technology and Informatics 160:1050-1054.
    The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not met by most existing biomedical terminologies, the latter may nonetheless support (...)
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  • Foundations for a Realist Ontology of Mental Disease.Werner Ceusters & Barry Smith - 2010 - Journal of Biomedical Semantics 1 (10):1-23.
    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. (...)
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  • Bioinformatics Advances in Saliva Diagnostics.Ji-Ye Ai, Barry Smith & David T. W. Wong - 2012 - International Journal of Oral Science 4 (2):85--87.
    There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva (...)
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  • Ontologies for the Study of Neurological Disease.Alexander P. Cox, Mark Jensen, William Duncan, Bianca Weinstock-Guttman, Kinga Szigeti, Alan Ruttenberg, Barry Smith & Alexander D. Diehl - 2012 - In Towards an Ontology of Mental Functioning (ICBO Workshop), Third International Conference on Biomedical Ontology. Graz:
    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 (...)
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  • Vital Sign Ontology.Albert Goldfain, Barry Smith, Sivaram Arabandi, Mathias Brochhausen & William R. Hogan - 2011 - In Proceedings of the Workshop on Bio-Ontologies, ISMB, Vienna, June 2011. Vienna: pp. 71-74.
    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 (...)
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  • Dealing with Elements of Medical Encounters: An Approach Based on Ontological Realism.Farinelli Fernanda, Almeida Mauricio, Elkin Peter & Barry Smith - 2016 - Proceedings of the Joint International Conference on Biological Ontology and Biocreative 1747.
    Electronic health records (EHRs) serve as repositories of documented data collected in a health care encounter. An EHR records information about who receives, who provides the health care and about the place where the encounter happens. We also observe additional elements relating to social relations in which the healthcare consumer is involved. To provide a consensus representation of common data and to enhance interoperability between different EHR repositories we have created a solution grounded in formal ontology. Here, we present how (...)
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  • A Plant Disease Extension of the Infectious Disease Ontology.Ramona Walls, Barry Smith, Elser Justin, Goldfain Albert & W. Stevenson Dennis - 2012 - In Proceeedings of the Third International Conference on Biomedical Ontology (CEUR 897). pp. 1-5.
    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 (...)
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  • An Evolutionary Approach to the Representation of Adverse Events.Werner Ceusters, Maria Capolupo, Barry Smith & Georges De Moor - 2009 - Studies in Health Technology and Informatics 150:537-541.
    One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.
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  • Guest Editorial: Ontologies for Clinical and Translational Research.Barry Smith & Richard H. Scheuermann - 2011 - Journal of Biomedical Informatics 44 (1):3--7.
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  • From Affective Science to Psychiatric Disorder: Ontology as Semantic Bridge.Rasmus Rosenberg Larsen & Janna Hastings - 2018 - Frontiers in Psychiatry 9 (487):1-13.
    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 (...)
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  • SNOMED CT Standard Ontology Based on the Ontology for General Medical Science.Shaker El-Sappagh, Francesco Franda, Ali Farman & Kyung-Sup Kwak - 2018 - BMC Medical Informatics and Decision Making 76 (18):1-19.
    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 (...)
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  • Representing Disease Courses: An Application of the Neurological Disease Ontology to Multiple Sclerosis Typology.Mark Jensen, Alexander P. Cox, Barry Smith & Alexander Diehl - 2013 - In Proceedings of the Fourth International Conference on Biomedical Ontology (ICBO), CEUR, vol. 1060.
    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 (...)
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  • Biomarkers in the Ontology for General Medical Science.Werner Ceusters & Barry Smith - 2015 - In Ronald Cornet (ed.), Digital Healthcare Empowering Europeans. IOS Press. pp. 155-159.
    Based on the Ontology for General Medical Science, we propose definitions for biomarkers of various types of. These definitions provide not only a complete formal representation of what biomarkers are according to the Institute of Medicine (IOM), but also remove the ambiguities and inconsistencies encountered in the documentation provided by the IOM.
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  • Analytic Metaphysics Versus Naturalized Metaphysics: The Relevance of Applied Ontology.Baptiste Le Bihan & Adrien Barton - 2018 - Erkenntnis:1-17.
    The relevance of analytic metaphysics has come under criticism: Ladyman & Ross, for instance, have suggested do discontinue the field. French & McKenzie have argued in defense of analytic metaphysics that it develops tools that could turn out to be useful for philosophy of physics. In this article, we show first that this heuristic defense of metaphysics can be extended to the scientific field of applied ontology, which uses constructs from analytic metaphysics. Second, we elaborate on a parallel by French (...)
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  • Representing Dispositions.Johannes Röhl & Ludger Jansen - 2011 - Journal of Biomedical Semantics 2 (4).
    Dispositions and tendencies feature significantly in the biomedical domain and therefore in representations of knowledge of that domain. They are not only important for specific applications like an infectious disease ontology, but also as part of a general strategy for modelling knowledge about molecular interactions. But the task of representing dispositions in some formal ontological systems is fraught with several problems, which are partly due to the fact that Description Logics can only deal well with binary relations. The paper will (...)
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  • Malaria Diagnosis and the Plasmodium Life Cycle: The BFO Perspective.Werner Ceusters & Barry Smith - 2010 - In Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting. Tokyo: Keio University Press. pp. 25-34.
    Definitive diagnosis of malaria requires the demonstration through laboratory tests of the presence within the patient of malaria parasites or their components. Since malaria parasites can be present even in the absence of malaria manifestations, and since symptoms of malaria can be manifested even in the absence of malaria parasites, malaria diagnosis raises important issues for the adequate understanding of disease, etiology and diagnosis. One approach to the resolution of these issues adopts a realist view, according to which the needed (...)
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  • On Defining Bruxism.W. Ceusters & B. Smith - 2018 - Studies in Health Technology and Informatics 247:551-555.
    In a series of recent publications, orofacial researchers have debated the question of how ‘bruxism’ should be defined for the purposes of accurate diagnosis and reliable clinical research. Following the principles of realism-based ontology, we performed an analysis of the arguments involved. This revealed that the disagreements rested primarily on inconsistent use of terms, so that issues of ontology were thus obfuscated by shortfalls in terminology. In this paper, we demonstrate how bruxism terminology can be improved by paying attention to (...)
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  • Functions, Roles and Dispositions Revisited. A New Classification of Realizables.Johannes Röhl & Ludger Jansen - 2012 - In M. Boeker, H. Herre, R. Hoehndorf & F. Loebe (eds.), OBML 2012. Workshop Proceedings. Dresden, September 27-28.
    The concept of a function is central both to biology and to technology. But there is an intricate debate how functions as well as related entities like dispositions and roles are to be represented in top level ontologies and how they are to be related. We review important philosophical accounts and ontological models for functions and roles and discuss three models for the relation of functions and dispositions. We conclude that mainly because of the need to account for malfunctioning, functions (...)
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  • What’s a “Disease”? Questions for Applied Ontologies of Diseases.Alan Rector - 2015 - Applied Ontology 10 (2):71-77.
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