Biomedical Information

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 (...) to the collection, development, application of biomedical knowledge has only partially been discussed. To fill in these gaps, in this article we provide an epistemic (knowledgerelated) overview of the main functions of wearable technology for health: monitoring, screening, detection, and prediction. On this basis, we identify 4 areas of concern in the application of wearables for these functions: data quality, balanced estimations, health equity, and fairness. To move the field forward in an effective and beneficial direction, we present recommendations for the 4 areas: local standards of quality, interoperability, access, and representativity. (shrink)

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 (...) at reducing the ability of SARS-CoV-2 to multiply in the body, for clinical use by the National Health Service in England and the concomitant testing of Molnupiravir through the large-scale PANORAMIC randomised control trial. By analysing the ways in which the authorisation and clinical use of Molnupiravir complicate standard approaches to clinical equipoise, standard of care, and participant consent in the PANORAMIC randomised control trial we will explain some of ethical implications for clinical trials that aim to study the efficacy and safety of new COVID-19 and other therapeutics when conditional authorisation has already been granted and when such treatments have already been made available to patients by national health providers. (shrink)

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, (...) attention to sociocultural conversion factors relevant to health can help in navigating technical choices that require broader considerations of the sociotechnical system, such as metric tradeoffs in model validation, resulting in better ethical and technical choices. This approach promotes awareness of the ethical dimension of technical choices by data scientists and others, and that can foster the cultivation of 'ethical skills' as integral to data science. (shrink)

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, (...) in this paper, we formulate a different approach to ethics in data science which is based on a different conception of “being ethical” and, ultimately, of what it means to promote a morally responsible data science. First, we develop the idea that, rather than only compliance, ethical decision-making consists in using certain moral abilities, which are cultivated by practicing and exercising them in the data science process. An aspect of virtue development that we discuss here is moral attention, which is the ability of data scientists to identify the ethical relevance of their own technical decisions in data science activities. Next, by elaborating on the capability approach, we define a technical act as ethically relevant when it impacts one or more of the basic human capabilities of data subjects. Therefore, rather than “applying ethics”, data scientists should cultivate ethics as a form of reflection on how technical choices and ethical impacts shape one another. Finally, we show how this microethical framework concretely works, by dissecting the ethical dimension of the technical procedures involved in data understanding and preparation of electronic health records. (shrink)

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 (...) analysis further draws on Foucault’s ideas of “governmentality” and “neoliberalism” and Deleuze’s concepts of “dividuality” and “society of control.” In Itoh’s fictional world, the entire society is subject to the new medical government, which replaced the chaotic world with a perfect but harrowing benevolent society, eradicating disease, suicide and crime. As elucidated in this paper, despite the dominant controlling government, there is a hope for humans to regain and reestablish their subjectivity and give meaning to their own personality by defying the nihilistic computational system. (shrink)

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, (...) and thus is not available for homesteading; the value of the individual biological entity extends to the information whereby it is constituted, and includes inalienable rights of an entity over itself and its information; and use of life as an information artifact makes an organism an unending means to an end rather than an end itself. I conclude that the information space of biological entities is not open for homesteading, not liable to private ownership, and should not be available for perpetual exploitation. (shrink)

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 (...) a Durkheimian death ritual—in the twenty-first century. Finally, I will theorize on a future populated by human beings from “the past” and the implications and consequences that may be caused by contemporary humans experiencing a temporal shift from traveling in deep time vis-à-vis cryopreservation. (shrink)

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 (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

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 (...) harmful choices and outcomes remains a demanding task, largely because our understanding of what harm is remains deeply incomplete. Despite 50 years of tempestuous debate, the metaphysics of harm remains an unsettled question. The existence of such a debate does not, in and of itself, provide evidence against the externalist position; rather, it is the theories of harm themselves that pose meaningful challenges for the externalist. Our purpose, here, is to illuminate these challenges. (shrink)

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

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.

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 (...) the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

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 (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

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) (...) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology development work being undertaken in support of scientific research. The ontologies created by scientists must, of course, be associated with implementations satisfying the requirements of software engineering. But these ontologies are not themselves engineering artifacts, and to conceive them as such brings grievous consequences. Rather, we shall argue, ontologies such as the GO are comparable to scientific theories, to scientific databases, or to scientific journal publications. Such a view implies a radically new conception of what is involved in the authoring, maintenance and application of ontologies in scientific contexts, and therewith also a radically new approach to the evaluation of ontologies and to the training of ontologists. (shrink)

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). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (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)

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 (...) critically important (Wright et al., 2020, p. 17). Our remaining concerns with BCIO relate directly to these two principles. First, we identify a number of issues with some of the classifications and definitions in BCIO that seem to be in tension with the just-mentioned principle . Second, we note some reservations about the reuse of certain classes in BCIO, namely from the Gazetteer (GAZ), the Ontology of Medically Related Social Entities (OMRSE), and the Information Artifact Ontology (IAO). While the latter principle of “reuse” is important, it is also important not to let the reuse of existing classes (or their corresponding definitions) compromise the logical integrity or the realist nature of one’s ontology. (shrink)

Ontology: Tool for Broad Spectrum Knowledge Integration (Foreword to Chinese translation of Building Ontologies with Basic Formal Ontology).

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 (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

Rapidly, accurately and easily interpreting generated data is of fundamental concern. Ontologies – structured controlled vocabularies – support interoperability and prevent the development of data silos which undermine interoperability. The Open Biological and Biomedical Ontologies (OBO) Foundry serves to ensure ontologies remain interoperable through adherence by its members to core ontology design principles. For example, the Infectious Disease Ontology (IDO) Core includes terminological content common to investigations of all infectious diseases. Ontologies covering more specific infectious diseases in turn extend from (...) IDOCore, such as the Coronavirus Infectious Disease Ontology (CIDO). The growing list of virus-specific IDO extensions has motivated construction of a reference ontology covering content common to viral infectious disease investigations: the Virus Infectious Disease Ontology (VIDO). Additionally the present pandemic has motivated construction of a more specific extension of CIDO covering terminological contents specific to the pandemic: the COVID-19 Infectious Disease Ontology (IDO-COVID-19). We report here the development of VIDO and IDO-COVID-19. More specifically we examine newly minted terms for each ontology, showcase reuse of terms from existing OBO ontologies, motivate choicepoints for ontological decisions based on research from relevant life sciences, apply ontology terms to explicate viral pathogenesis, and discuss the annotating power of virus ontologies for use in machine-learning projects. (shrink)

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 (...) 2015). BCIO uses as its top-level ontology Basic Formal Ontology (BFO). The methods outlined in Wright, et al. are a valuable contribution to the field, especially the use of formal mechanisms for literature annotation and expert stakeholder review, and the BCIO will certainly play an important role in the extension of OBO Foundry ontologies into the behavioural domain. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

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 (...) overview of ontology services and concludes with a discussion of some implications of the product-service system approach for the understanding of the nature of applied ontology. Ontology developer communities are compared in this respect with developers of scientific theories and of standards (such as W3C). For each of these we can ask: what kinds of products do they develop and what kinds of services do they provide for the users of these products? (shrink)

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 (...) is based on the recently developed Cognitive Process Ontology and further develops the Ontology of General Medical Science. It also has applications in fields such as intelligence, forensics, and predictive maintenance, all of which rely on vetted processes designed to secure the reliability of their outputs. (shrink)

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 (...) the relationships between (1) particulars and types, and (2) continuants and occurrents. (shrink)

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 (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

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 (...) large amounts of ncRNA biological and clinical data. (shrink)

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.

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.

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.

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 (...) effort directed towards such formal representation for affective phenomena, in part because of widespread debates within the affective science community on matters of definition and categorization. To address this requirement, we are developing an Emotion Ontology (EMO). (shrink)

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, (...) pain that is caused neuropathically (thus with no necessary peripheral stimulus), and pain reports arising through deception either of self or of others. We describe how our approach can answer some of the objections raised against the IASP definition, and sketch how it can be used to support more sophisticated discrimination of different types of pain resulting in improved data analysis that can help in advancing pain research. (shrink)

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 (...) return, or were developed outside Europe. To address this gap, we analysed existing normative documents identified online using inductive content analysis. We used this analysis to develop a checklist of steps to assist European researchers considering whether to return IRR to participants. We then sought feedback on the checklist from an interdisciplinary panel of European experts (clinicians, clinical researchers, population-based researchers, biobank managers, ethicists, lawyers and policy makers) to refine the checklist. The checklist outlines seven major components researchers should consider when determining whether, and how, to return results to adult research participants: 1) Decide which results to return; 2) Develop a plan for return of results; 3) Obtain participant informed consent; 4) Collect and analyse data; 5) Confirm results; 6) Disclose research results; 7) Follow-up and monitor. Our checklist provides a clear outline of the steps European researchers can follow to develop ethical and sustainable result return pathways within their own research projects. Further legal analysis is required to ensure this checklist complies with relevant domestic laws. (shrink)

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. (...) Methodologically set as a typology, the conceptual approach used in this paper is based on the interdisciplinary analysis of scientific literature, the relevant ethical and legal instruments and practices in biobanking to identify how risks are assessed, considered and mitigated. Through an interdisciplinary mapping exercise, we have produced a typology of potential risks in biobanking, taking into consideration the perspectives of different stakeholders, such as institutional actors and publics, including participants and representative organizations. With this approach, we have identified the following risk types: economic, infrastructural, institutional, research community risks and participant’s risks. The paper concludes by highlighting the necessity of an adaptive risk governance as an integral part of good governance in biobanking. In this regard, it contributes to sustainability in biobanking by assisting in the design of relevant risk management practices, where they are not already in place or require an update. The typology is intended to be useful from the early stages of establishing such a complex and multileveled biomedical infrastructure as well as to provide a catalogue of risks for improving the risk management practices already in place. (shrink)

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, (...) Poland, and Russia to determine how each national regulatory framework relates to the provisions of the Declaration of Helsinki. Methods: For this analysis, we conducted a search of the legal databases “Gesetze im Internet” for Germany, “Internetowy System Aktow Prawnych” for Poland, and “ГAPAHT – Garant” for Russia. The search was complemented by a review of secondary literature contained in the databases Google Scholar, PubMed, Polish National Library, and eLibrary ru. We have identified 21 normative regulations containing provisions on informed consent in clinical research in all three countries. The content of these documents was systematically categorized and analyzed. Results: The normative framework in all three countries shows a strong commitment towards the core ethical principles of research envisaged in the Declaration of Helsinki. Nevertheless, provisions on informed consent vary between these three countries. The differences range from the method and language in which information should be provided, through the amount of information required to be disclosed, to the form of documenting consent or withdrawal. In the case of research on vulnerable groups, these differences are particularly visible. Conclusions: The identified differences can negatively impact the ethical conduct of international clinical studies. Attention needs to be paid that flexibilities within national regulations are not misused to undermine the protection of research subjects. Achieving global or regional legislative harmonization might prove impossible. Such lack of legal consensus reinforces the significance of the international ethical agreements. (shrink)

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.

Epidemiological crisis during recrudescence of pandemic like COVID-19 may stir fear and anxiety leading to prejudices against people and communities, social isolation and stigma. Such behavioral change may wind up into increased hostility, chaos and unnecessary social disruptions. A qualitative exploratory approach was utilized to conduct an extensive review of secondary literature. The case-studies were gathered from academic literature like articles, opinions and perspective pieces published in journals and in grey literature like publications in humanitarian agencies and media reports. Grey (...) literature was included in the scope as the COVID-19 situation is still evolving. I discuss some of the mechanisms of stigmatization and how social connectedness and empathetic understandings can be a way out of negative stereotyping and discrimination met out to the sufferer of the communicable diseases as COVID-19. Empathetic understanding paves a way to approach a problem from the perspective of ‘we’ not limiting one only to ‘I’. The moment when we make an approach from ‘I’ to ‘We’ actually then we embark on a journey of illness to wellness. Keywords: COVID-19, pandemic, stigma, discrimination, mental health, empathy, India, Face-to-face communication, social distancing, suicide. (shrink)

Our technological lifeworld has become an info-computational media populated by data and algorithms, an artificial environment for life and shared experiences. In this chapter, I tried to sketch three new assumptions for bioethics – it is hardly possible to substantiate ethical guidelines or an idea of normativity in an aprioristic manner; moral status is a function of data entities, not something solely human; agency is plural and thus is shared or sometimes delegated – in order to chart a proposal for (...) a posthuman bioethics. Posthuman is perhaps not the best expression available, but it covers the idea of a shift from a world centered on self-contained and exclusively human agency to a more comprehensive and relational way of thinking. The “posthuman” label should be understood as a rebuttal of biocentrism and anthropocentrism by moving closer to conceptions we encounter in population ethics or in discourse about biosocial and technical systems. Posthuman bioethics is “environmentalist” without losing the humanistic stance. The question regarding how suitable an infocentric bioethics is in practice remains to be settled. The moral principles in bioethics could be reconceived as relying on these new assumptions, in a postindividualistic manner that accepts formal primacy of causal digital artifacts in affording actions in a world of ambient algorithmic intelligence. (shrink)