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  1. Wearable Technologies for Healthy Ageing: Prospects, Challenges, and Ethical Considerations.Stefano Canali, Agara Ferretti, Viola Schiaffonati & Alessandro Blasimme - 2024 - Journal of Frailty and Aging 2024:1-8.
    Digital technologies hold promise to modernize healthcare. Such opportunity should be leveraged also to address the needs of rapidly ageing populations. Against this backdrop, this paper examines the use of wearable devices for promoting healthy ageing. Previous work has assessed the prospects of digital technologies for health promotion and disease prevention in older adults. However, to our knowledge, ours is one of the first attempts to specifically address the use of wearables for healthy ageing, and to offer ethical insights for (...)
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  2. Conoscere la medicina. Strumenti filosofici.Stefano Canali - 2024 - Rome: Carocci.
    Per conoscere la medicina sono necessari strumenti teorici, pratici, tecnologici e culturali, ma non solo: come mostra il volume, anche la riflessione filosofica può svolgere un ruolo cruciale sui suoi vari aspetti. Analizzando esempi concreti e grazie ai contributi di medici, epidemiologi e ingegneri, il libro fornisce strumenti filosofici per leggere le caratteristiche fondamentali della medicina contemporanea, i suoi recenti sviluppi e le sfide che è chiamata ad affrontare: una lente di grande utilità per la formazione dei medici e per (...)
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  3. A Wolf in Sheep's Clothing: Idealisations and the aims of polygenic scores.Davide Serpico - 2023 - Studies in History and Philosophy of Science Part A 102 (C):72-83.
    Research in pharmacogenomics and precision medicine has recently introduced the concept of Polygenic Scores (PGSs), namely, indexes that aggregate the effects that many genetic variants are predicted to have on individual disease risk. The popularity of PGSs is increasing rapidly, but surprisingly little attention has been paid to the idealisations they make about phenotypic development. Indeed, PGSs rely on quantitative genetics models and methods, which involve considerable theoretical assumptions that have been questioned on various grounds. This comes with epistemological and (...)
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  4. When data drive health: an archaeology of medical records technology.Colin Koopman, Paul D. G. Showler, Patrick Jones, Mary McLevey & Valerie Simon - 2022 - Biosocieties 17 (4):782-804.
    Medicine is often thought of as a science of the body, but it is also a science of data. In some contexts, it can even be asserted that data drive health. This article focuses on a key piece of data technology central to contemporary practices of medicine: the medical record. By situating the medical record in the perspective of its history, we inquire into how the kinds of data that are kept at sites of clinical encounter often depend on informational (...)
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  5. Challenges and recommendations for wearable devices in digital health: Data quality, interoperability, health equity, fairness.Stefano Canali, Viola Schiaffonati & Andrea Aliverti - 2022 - PLOS Digital Health 1 (10):e0000104.
    Wearable devices are increasingly present in the health context, as tools for biomedical research and clinical care. In this context, wearables are considered key tools for a more digital, personalised, preventive medicine. At the same time, wearables have also been associated with issues and risks, such as those connected to privacy and data sharing. Yet, discussions in the literature have mostly focused on either technical or ethical considerations, framing these as largely separate areas of discussion, and the contribution of wearables (...)
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  6. Equipoise, standard of care, and consent: Responding to the authorisation of new COVID-19 treatments in randomised controlled trials.Soren Holm, Jonathan Lewis & Rafael Dal-Ré - 2022 - Journal of Medical Ethics:1-6.
    In response to the COVID-19 pandemic, large-scale research and pharmaceutical regulatory processes have proceeded at a dramatically increased pace with new and effective, evidence-based COVID-19 interventions rapidly making their way into the clinic. However, the swift generation of high-quality evidence and the efficient processing of regulatory authorisation have given rise to more specific and complex versions of well-known research ethics issues. In this paper, we identify three such issues by focusing on the authorisation of Molnupiravir, a novel antiviral medicine aimed (...)
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  7. Microethics for healthcare data science: attention to capabilities in sociotechnical systems.Mark Graves & Emanuele Ratti - 2021 - The Future of Science and Ethics 6:64-73.
    It has been argued that ethical frameworks for data science often fail to foster ethical behavior, and they can be difficult to implement due to their vague and ambiguous nature. In order to overcome these limitations of current ethical frameworks, we propose to integrate the analysis of the connections between technical choices and sociocultural factors into the data science process, and show how these connections have consequences for what data subjects can do, accomplish, and be. Using healthcare as an example, (...)
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  8. Cultivating Moral Attention: a Virtue-Oriented Approach to Responsible Data Science in Healthcare.Emanuele Ratti & Mark Graves - 2021 - Philosophy and Technology 34 (4):1819-1846.
    In the past few years, the ethical ramifications of AI technologies have been at the center of intense debates. Considerable attention has been devoted to understanding how a morally responsible practice of data science can be promoted and which values have to shape it. In this context, ethics and moral responsibility have been mainly conceptualized as compliance to widely shared principles. However, several scholars have highlighted the limitations of such a principled approach. Drawing from microethics and the virtue theory tradition, (...)
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  9. <null>me<null>: Algorithmic Governmentality and the Notion of Subjectivity in Project Itoh's Harmony.Fatemeh Savaedi & Maryam Alavi Nia - 2021 - Journal of Science Fiction and Philosophy 4:1-19.
    Algorithmic governmentality is a new form of political governance interconnected with technology and computation. By coining the term “algorithmic governmentality,” Antoinette Rouvroy argues that this mode of governance reduces everything to data, and people are no longer individuals but dividuals (able to be divided) or readable data profiles. Implementing the concept of algorithmic governmentality, the current study analyses Project Itoh’s award-winning novel Harmony in terms of such relevant concepts as “subjectivity,” “infra-individuality” and “control,” as suggested by Rouvroy and colleagues. The (...)
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  10. Homesteading the noosphere: The ethics of owning biological information.Robert R. Wadholm - 2018 - Northern Plains Ethics Journal 6 (1):47-63.
    The idea of homesteading can be extended to the realm of biological entities, to the ownership of information wherein organisms perform artifactual functions as a result of human development. Can the information of biological entities be ethically “homesteaded”: should humans (or businesses) have ownership rights over this information from the basis of mere development and possession, as in Locke’s theory of private property? I offer three non-consequentialist arguments against such homesteading: the information makeup of biological entities is not commonly owned, (...)
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Biomedical Ontology
  1. Ontology Development Strategies and the Infectious Disease Ontology Ecosystem.Giacomo De Colle, Ali Hasanzadeh & John Beverley - 2023 - Proceedings of the International Conference on Biomedical Ontologies.
    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.
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  2. Coordinating virus research: The Virus Infectious Disease Ontology.John Beverley, Shane Babcock, Gustavo Carvalho, Lindsay G. Cowell, Sebastian Duesing, Yongqun He, Regina Hurley, Eric Merrell, Richard H. Scheuermann & Barry Smith - 2024 - PLoS ONE 1.
    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 Disease Ontology (...)
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  3. Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019).Alexander D. Diehl, William D. Duncan & Gloria Sansò (eds.) - 2021
    The 10th International Conference on Biomedical Ontology (ICBO 2019), was held at the Jacobs School of Medicine and Biomedical Sciences of the University at Buffalo, in Buffalo, NY, USA. It was the 10-year anniversary of the ICBO series, and the return of the conference to Buffalo after the first two ICBO conferences were held in Buffalo in 2009 and 2011. ICBO 2019 was well attended, with 115 registered attendees and additional walk-ins from the local academic community. The program included excellent (...)
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  4. Ontology and Information Systems (2004).Barry Smith - manuscript
    In a development that has still been hardly noticed by philosophers, a conception of ontology has been advanced in recent years in a series of extra-philosophical disciplines as researchers in linguistics, psychology, geography and anthropology have sought to elicit the ontological commitments (‘ontologies’, in the plural) of different cultures or disciplines. Exploiting the terminology of Quine, researchers in psychology and anthropology have sought to establish what individual human subjects, or entire human cultures, are committed to, ontologically, in their everyday cognition, (...)
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  5. Improving the Quality and Utility of Electronic Health Record Data through Ontologies.Asiyah Yu Lin, Sivaram Arabandi, Thomas Beale, William Duncan, Hicks D., Hogan Amanda, R. William, Mark Jensen, Ross Koppel, Catalina Martínez-Costa, Øystein Nytrø, Jihad S. Obeid, Jose Parente de Oliveira, Alan Ruttenberg, Selja Seppälä, Barry Smith, Dagobert Soergel, Jie Zheng & Stefan Schulz - 2023 - Standards 3 (3):316–340.
    The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...)
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  6. The future of ontologies.Barry Smith - 2023 - In Terminology, Ontology and their Implementations. Cham, Switzerland: Springer Nature.
    We have now reached the point at which cloud computing and other types of advanced infrastructure are bringing about a situation in which knowledge objects can be delivered in an efficient manner to hose who need to consume them. And just as highways were the infrastructure necessary for a manufacturing economy, serving as the arteries along which raw materials and manufactured goods coming in from all directions could flow, so we believe that ontologies will in the future provide an important (...)
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  7. "Death is a Disease": Cryopreservation, Neoliberalism, and Temporal Commodification in the U.S.Taylor R. Genovese - 2018 - Technology in Society 54:52-56.
    In this article, I will be focusing specifically on cryopreservation and two of the American biotechnomedical tenets introduced by Robbie Davis-Floyd and Gloria St. John in their technocratic model of medicine: the “body as machine” and “death as defeat.” These axioms are embraced by both the biotechnomedical establishment as well as the cryopreservation communities when they discuss the future of humankind. In particular, I will be focusing on the political economy of cryopreservation as an embodiment of American neoliberalism—as well as (...)
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  8. A new framework for host-pathogen interaction research.Hong Yu, Li Li, Anthony Huffman, John Beverley, Junguk Hur, Eric Merrell, Hsin-hui Huang, Yang Wang, Yingtong Liu, Edison Ong, Liang Cheng, Tao Zeng, Jingsong Zhang, Pengpai Li, Zhiping Liu, Zhigang Wang, Xiangyan Zhang, Xianwei Ye, Samuel K. Handelman, Jonathan Sexton, Kathryn Eaton, Gerry Higgins, Gilbert S. Omenn, Brian Athey, Barry Smith, Luonan Chen & Yongqun He - 2022 - Frontiers in Immunology 13.
    COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...)
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  9. A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili, Robert Hoehndorf, Zoë May Pendlington, Paola Roncaglia, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur, Gilbert S. Omenn, Brian Athey & Barry Smith - 2022 - Journal of Biomedical Semantics 13 (1):25.
    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 (...)
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  10. The Nature of Harm: A Wine-Dark Sea.Eli G. Schantz & Mark D. Fox - 2022 - American Journal of Bioethics 22 (10):63-65.
    In “Harmful Choices, the Case of C, and Decision-Making Competence,” Pickering and colleagues advance an argument in favor of externalism, a view in which the competence of a decision maker is judged relative to factors external to their cognition. In advancing this argument, Pickering and colleagues focus on the external factor of harm: In their view, it is the harmfulness of a considered or chosen action that provides evidence against the competence of the decision maker. However, the proper identification of (...)
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  11. How an Addiction Ontology Can Unify Competing Conceptualizations of Addiction.Robert M. Kelly, Robert West & Janna Hastings - 2022 - In Nick Heather, Matt Field, Anthony Moss & Sally Satel (eds.), Evaluating the Brain Disease Model of Addiction. New York, NY, USA: Routledge.
    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 (...)
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  12. The bridge between philosophy and information-driven science.Barry Smith - 2021 - Journal of Knowledge Structures and Systems 2 (2):47-55.
    This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.
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  13. Biomedical Ontologies.Barry Smith - 2023 - In Peter Elkin (ed.), Terminology, Ontology and their Implementations. Cham, Switzerland: Springer Nature Switzerland AG. pp. 125-169.
    We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...)
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  14. OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies.Rebecca C. Jackson, Nicolas Matentzoglu, James A. Overton, Randi Vita, James P. Balhoff, Pier Luigi Buttigieg, Seth Carbon, Melanie Courtot, Alexander D. Diehl, Damion Dooley, William Duncan, Nomi L. Harris, Melissa A. Haendel, Suzanna E. Lewis, Darren A. Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M. Schriml, Barry Smith, Christian J. Stoeckert, Nicole A. Vasilevsky, Ramona L. Walls, Jie Zheng, Christopher J. Mungall & Bjoern Peters - 2021 - BioaRxiv.
    Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...)
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  15. Ontology (Science).Barry Smith - 2008 - In Carola Eschenbach & Mike Grüninger (eds.), Formal Ontology in Information Systems. Proceedings of the Fifth International Conference (FOIS 2008). Amsterdam: IOS Press. pp. 21-35.
    Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some will find self-evident) (...)
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  16. CIDO: The Community-Based Coronavirus Infectious Disease Ontology.Yongqun He, Hong Yu, Edison Ong, Yang Wang, Yingtong Liu, Anthony Huffman, Hsin-hui Huang, Beverley John, Asiyah Yu Lin, Duncan William D., Sivaram Arabandi, Jiangan Xie, Junguk Hur, Xiaolin Yang, Luonan Chen, Gilbert S. Omenn, Brian Athey & Barry Smith - 2021 - Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) and 10th Workshop on Ontologies and Data in Life Sciences (ODLS).
    Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...)
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  17. CTO: A Community-Based Clinical Trial Ontology and Its Applications in PubChemRDF and SCAIViewH.Asiyah Yu Lin, Stephan Gebel, Qingliang Leon Li, Sumit Madan, Johannes Darms, Evan Bolton, Barry Smith, Martin Hofmann-Apitius, Yongqun Oliver He & Alpha Tom Kodamullil - 2021 - Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) and 10th Workshop on Ontologies and Data in Life Sciences (ODLS).
    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 (...)
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  18. Peer Review Report: Ontologies relevant to behaviour change interventions, version 3.Robert M. Kelly, David Limbaugh & Barry Smith - 2021 - Human Behaviour Change Project.
    In the present review we focus on what we take to be some remaining issues with the Behaviour Change Intervention Ontology (BCIO). We are in full agreement with the authors’ endorsement of the principles of best practice for ontology development In particular, we agree that an ontology should be “logically consistent and having a clear structures [sic], preferably a well-organised hierarchical structure,” and that “Maximising the new ontology’s interoperability with existing ontologies by reusing entities from existing ontologies where appropriate” is (...)
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  19. 本体:广谱的知识集成工具.Barry Smith - 2020 - In 基于基本形式化本体的本体构建. Beijing: pp. 4-8.
    Ontology: Tool for Broad Spectrum Knowledge Integration (Foreword to Chinese translation of Building Ontologies with Basic Formal Ontology).
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  20. 基于基本形式化本体的本体构建.Robert Arp, Barry Smith & Andrew D. Spear - 2020 - Beijing: People's Medical Publishing House.
    In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...)
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  21. Coordinating Coronavirus Research: The COVID-19 Infectious Disease Ontology.John Beverley, Shane Babcock, Barry Smith, Yongqun He, Eric Merrell, Lindsay Cowell, Regina Hurley & Sebastian Duesing - 2022 - Proceedings of the International Conference on Biomedical Ontologies.
    The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...)
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  22. Peer Review Report: Ontologies Relevant to Behaviour Change Interventions, version 1.Robert M. Kelly, David Limbaugh & Barry Smith - 2020 - Human Behaviour Change Project.
    In “Ontologies Relevant to behaviour change interventions: A Method for their Development” Wright, et al. outline a step by step process for building ontologies of behaviour modification – what the authors call the Refined Ontology Developmental Method (RODM) – and demonstrate its use in the development of the Behaviour Change Intervention Ontology (BCIO). RODM is based on the principles of good ontology building used by the Open Biomedical Ontology (OBO) Foundry in addition to those outlined in (Arp, Smith, and Spear (...)
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  23. CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis.Oliver He, John Beverley, Gilbert S. Omenn, Barry Smith, Brian Athey, Luonan Chen, Xiaolin Yang, Junguk Hur, Hsin-hui Huang, Anthony Huffman, Yingtong Liu, Yang Wang, Edison Ong & Hong Yu - 2020 - Scientific Data 181 (7):5.
    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, (...)
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  24. Interdyscyplinarne perspektywy rozwoju, integracji i zastosowań ontologii poznawczych.Janna Hastings, Gwen Frishkoff, Barry Smith, Mark Jensen, Russell Poldrack, Jane Lomax, Anita Bandrowski, Fahim Imam, Jessica Turner, Maryann Martone & Przemysław Nowakowski - 2016 - Avant: Trends in Interdisciplinary Studies 7 (3):101-117.
    We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...)
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  25. Ontology as Product-Service System: Lessons Learned from GO, BFO and DOLCE.Barry Smith - 2019 - In Proceedings of the 10th International Conference on Biomedical Ontology (ICBO), Buffalo, NY.
    This paper defends a view of the Gene Ontology (GO) and of Basic Formal Ontology (BFO) as examples of what the manufacturing industry calls product-service systems. This means that they are products (the ontologies) bundled with a range of ontology services such as updates, training, help desk, and permanent identifiers. The paper argues that GO and BFO are contrasted in this respect with DOLCE, which approximates more closely to a scientific theory or a scientific publication. The paper provides a detailed (...)
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  26. Warranted Diagnosis.David Limbaugh, David Kasmier, Werner Ceusters & Barry Smith - 2019 - In Proceedings of the International Conference on Biomedical Ontology (ICBO), Buffalo, NY. Buffalo: pp. 1-10.
    A diagnostic process is an investigative process that takes a clinical picture as input and outputs a diagnosis. We propose a method for distinguishing diagnoses that are warranted from those that are not, based on the cognitive processes of which they are the outputs. Processes designed and vetted to reliably produce correct diagnoses will output what we shall call ‘warranted diagnoses’. The latter are diagnoses that should be trusted even if they later turn out to have been wrong. Our work (...)
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  27. 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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  28. Toll-like receptor signaling in vertebrates: Testing the integration of protein, complex, and pathway data in the Protein Ontology framework.Cecilia Arighi, Veronica Shamovsky, Anna Maria Masci, Alan Ruttenberg, Barry Smith, Darren Natale, Cathy Wu & Peter D’Eustachio - 2015 - PLoS ONE 10 (4):e0122978.
    The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...)
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  29. The development of non-coding RNA ontology.Jingshan Huang, Karen Eilbeck, Barry Smith, Judith Blake, Deijing Dou, Weili Huang, Darren Natale, Alan Ruttenberg, Jun Huan, Michael Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison Strachan, Nisansa de Silva & Mohan Vamsi Kasukurthi - 2016 - International Journal of Data Mining and Bioinformatics 15 (3):214--232.
    Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...)
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  30. More about ontology: Response.Barry Smith, Louis Goldberg, Michael Glick & Alan Ruttenberg - 2011 - Journal of the American Dental Association 142 (3):252-254.
    Letter commenting on the paper Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick, "Ontology and the Future of Dental Research Informatics", Journal of the American Dental Association 141 2010;(10):1173-75 with responses by the authors of the paper.
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  31. Letter to the Editor: Dealing with socially constructed concepts in an ontology.David Koepsell & Barry Smith - 2009 - Journal of Empirical Research on Human Research Ethics 4 (2):75-76.
    Response to the paper “The Biomedical Ethics Ontology Proposal: Excellent Aims, Questionable Methods" by James DuBois, published in the Journal of Empirical Research on Human Research Ethics.
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  32. 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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  33. The Emotion Ontology: Enabling Interdisciplinary Research in the Affective Sciences.Janna Hastings, Werner Ceusters, Barry Smith & Kevin Mulligan - 2011 - In M. Beigl, H. Christiansen, T. Roth-Berghofer, A. Kofod-Petersen, K. R. Coventry & H. R. Schmidtke (eds.), CONTEXT, The Seventh International and Interdisciplinary Conference on Modeling and Using Context. Springer. pp. 119--123.
    Affective science conducts interdisciplinary research into the emotions and other affective phenomena. Currently, such research is hampered by the lack of common definitions of terms used to describe, categorise and report both individual emotional experiences and the results of scientific investigations of such experiences. High quality ontologies provide formal definitions for types of entities in reality and for the relationships between such entities, definitions which can be used to disambiguate and unify data across different disciplines. Heretofore, there has been little (...)
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  34. Towards an ontology of pain.Barry Smith, Werner Ceusters, Louis J. Goldberg & Richard Ohrbach - 2011 - In Proceedings of the Conference on Ontology and Analytical Metaphysics. Keio University Press.
    We present an ontology of pain and of other pain-related phenomena, building on the definition of pain provided by the International Association for the Study of Pain (IASP). Our strategy is to identify an evolutionarily basic canonical pain phenomenon, involving unpleasant sensory and emotional experience based causally in localized tissue damage that is concordant with that experience. We then show how different variant cases of this canonical pain phenomenon can be distinguished, including pain that is elevated relative to peripheral trauma, (...)
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Biomedical Information, Misc
  1. Narrativization of human population genetics: Two cases in Iceland and Russia.Vadim Chaly & Olga V. Popova - 2023 - Public Understanding of Science.
    Using the two cases of the Icelandic Health Sector Database and Russian initiatives in biobanking, the article criticizes the view of narratives and imaginaries as a sufficient and unproblematic means of shaping public understanding of genetics and justifying population-wide projects. Narrative representations of national biobanking engage particular imaginaries that are not bound by the universal normative framework of human rights, promote affective thinking, distract the public from recognizing and discussing tangible ethical and socioeconomic issues, and harm trust in science and (...)
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  2. Gender in Medical Records.Michal Pruski - 2023 - Catholic Medical Quarterly 73 (3):16-18.
  3. A practical checklist for return of results from genomic research in the European context.Danya F. Vears, Signe Mežinska, Nina Hallowell, Heidi Beate Hallowell, Bridget Ellul, Therese Haugdahl Nøst, , Berge Solberg, Angeliki Kerasidou, Shona M. Kerr, Michaela Th Mayrhofer, Elizabeth Ormondroyd, Birgitte Wirum Sand & Isabelle Budin-Ljøsne - 2023 - European Journal of Human Genetics 1:1-9.
    An increasing number of European research projects return, or plan to return, individual genomic research results (IRR) to participants. While data access is a data subject’s right under the General Data Protection Regulation (GDPR), and many legal and ethical guidelines allow or require participants to receive personal data generated in research, the practice of returning results is not straightforward and raises several practical and ethical issues. Existing guidelines focusing on return of IRR are mostly project-specific, only discuss which results to (...)
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  4. Biobanking and risk assessment: a comprehensive typology of risks for an adaptive risk governance.Kaya Akyüz, Olga Tzortzatou, Łukasz Kozera, Melanie Goisauf, Signe Mezinska, Gauthier Chassang & Michaela Th Mayrhofer - 2021 - Life Sciences, Society and Policy 17 (1):1-28.
    Biobanks act as the custodians for the access to and responsible use of human biological samples and related data that have been generously donated by individuals to serve the public interest and scientific advances in the health research realm. Risk assessment has become a daily practice for biobanks and has been discussed from different perspectives. This paper aims to provide a literature review on risk assessment in order to put together a comprehensive typology of diverse risks biobanks could potentially face. (...)
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  5. Normative framework of informed consent in clinical research in Germany, Poland, and Russia.Marcin Orzechowski, Katarzyna Woniak, Cristian Timmermann & Florian Steger - 2021 - BMC Medical Ethics 22 (1):1-10.
    Background: Biomedical research nowadays is increasingly carried out in multinational and multicenter settings. Due to disparate national regulations on various ethical aspects, such as informed consent, there is the risk of ethical compromises when involving human subjects in research. Although the Declaration of Helsinki is the point of reference for ethical conduct of research on humans, national normative requirements may diverge from its provisions. The aim of this research is to examine requirements on informed consent in biomedical research in Germany, (...)
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  6. On evidence fiascos and judgments in COVID-19 policy.Stefano Canali & Saana Jukola - 2021 - History and Philosophy of the Life Sciences 43 (2):1-4.
    Calls for evidence-based approaches to COVID-19 have sparked up discussions on the use of evidence for policy. In this note, we expand these discussions: while the debate has mostly focused on the types of evidence to be used for policy, we argue that the assessment of judgments involved in data practices and evidence production should play a central role in evaluating policy.
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