Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

The Protein Ontology (PRO; https://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (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)

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 (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

We suggest that the emerging field of the conservation humanities can play a valuable role in biodiversity protection in Papua New Guinea (PNG), where most land remains under collective customary clan ownership. As a first step to mobilising this scholarly field in PNG and to support capacity development for PNG humanities academics, we conducted a landscape review of PNG humanities teaching and research relating to biodiversity conservation and customary land rights. We conducted a systematic literature review, a PNG teaching programme (...) review, and a series of online workshops between the authors (10 PNG-based, 7 UK-based). We found a small but notable amount of PNG research and teaching focused on biodiversity conservation or customary land rights. This included explicit discussion of these topics in 8 of 156 PNG-authored humanities texts published 2010-2020 and related teaching content in the curricula of several different humanities-based programmes. We discuss current barriers to PNG academic development. The growth of fully fledged in-country conservation humanities will require a joint collaborative effort by PNG researchers, who are best placed to carry out such work, and researchers from abroad who can access resources to support the process. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

In this paper we suggest a revisionist perspective on two significant figures in early modern life science and philosophy: William Harvey and John Locke. Harvey, the discoverer of the circulation of the blood, is often named as one of the rare representatives of the ‘life sciences’ who was a major figure in the Scientific Revolution. While this status itself is problematic, we would like to call attention to a different kind of problem: Harvey dislikes abstraction and controlled experiments (aside from (...) the ligature experiment in De Motu Cordis), tends to dismiss the value of instruments such as the microscope, and emphasizes instead the privileged status of ‘observed experience’. To use a contemporary term, Harvey appears to rely on, and chiefly value, ‘tacit knowledge’. Secondly, Locke’s project is often explained with reference to the image he uses in the Epistle to the Reader of his Essay, that he was an “underlabourer” of the sciences. In fact, despite the significant medical phase of his career, Locke’s ‘empiricism’ turns out to be above all a practical (i.e. ‘moral’) project, which focuses on the delimitation of our powers in order to achieve happiness, and rejects the possibility of naturalizing knowledge. When combined, these two cases suggest a different view of some canonical moments in early modern natural philosophy. (shrink)

Open theists deny that God knows future contingents. Most open theists justify this denial by adopting the position that there are no future contingent truths to be known. In this paper we examine some of the arguments put forward for this position in two recent articles in this journal, one by Dale Tuggy and one by Alan Rhoda, Gregory Boyd, and Thomas Belt. The arguments concern time, modality, and the semantics of ‘will’ statements. We explain why we find none (...) of these arguments persuasive. This wide road leads only to destruction. (shrink)

Some people claim that death makes our lives meaningless. Bernard Williams and Viktor Frankl have made the opposite claim that death gives meaning to life. Although there has been much scrutiny of the former claim, the latter claim has received very little attention. In this paper, I will explore whether and how death gives meaning to our lives. As I will argue, there is not sufficient support for the strong claim that death is necessary for one's life to be (...) meaningful. However, there is support for the more limited conclusion that our finitude enhances or upholds the meaning in the lives of some individuals in four different ways. (shrink)

The two books reviewed here are different efforts to embrace the vast subject called “social thought.” The second edition of The Blackwell Dictionary of Modern Social Thought, edited by William Outhwaite with Alain Touraine, contains numerous updates; yet it also has some disadvantages compared to the first edition. Social Thought: From the Enlightenment to the Present, edited by Alan Sica, is a bold but controversial attempt at gathering in one anthology as many social thinkers as possible.

Science has been under attack ever since William Blake and Romantic movement. In our time, criticisms of modern science have led to Alan Sokal's spoof, and the so-called science wars. Both sides missed the point. Science deserves to be criticized for seriously misrepresenting its highly problematic aims, which have metaphysical, value and political assumptions associated with them. Instead of repressing these problematic aims, science ought rather to make them explicit, so that they can be critically assessed and, we may (...) hope, improved. (shrink)

Numerous philosophers have tried to define modesty, but none of them succeeds in articulating the necessary and sufficient conditions for this virtue. Moreover, all existing accounts ignore the striking self-other asymmetry that is at the heart of modesty. Drawing on the analogy with the practice of giving presents, I clarify and further investigate this self-other asymmetry. In the process, I show why Bernard Williams is right in pointing out the notorious truth that a modest person does not act under (...) the title of modesty and why Alan Bennett is wrong in supposing that all modesty is false modesty. (shrink)

The chapter examines fifty years of philosophers working on lying - from the 1970s to the current day – focusing on how lying is defined (descriptively and normatively), whether lying involves an intention to deceive (Deceptionists) or not (Non-Deceptionists), why lying is wrong, and whether lying is worse than other forms of deception, including misleading with the truth. Philosophers discussed include Roderick Chisholm and Thomas Feehan, Alan Donagan, Sissela Boy, Charles Fried, David Simpson, David Simpson, Bernard Williams, Paul (...) Faulkner, Thomas Carson, Roy Sorensen, Don Fallis, Jennifer Saul, Andreas Stoke, Jonathan Webber and Clea Rees. (shrink)

Proceedings of the papers presented at the Symposium on "Revisiting Turing and his Test: Comprehensiveness, Qualia, and the Real World" at the 2012 AISB and IACAP Symposium that was held in the Turing year 2012, 2–6 July at the University of Birmingham, UK. Ten papers. - https://www.pt-ai.org/turing-test --- Daniel Devatman Hromada: From Taxonomy of Turing Test-Consistent Scenarios Towards Attribution of Legal Status to Meta-modular Artificial Autonomous Agents - Michael Zillich: My Robot is Smarter than Your Robot: On the Need for (...) a Total Turing Test for Robots - Adam Linson, Chris Dobbyn and Robin Laney: Interactive Intelligence: Behaviour-based AI, Musical HCI and the Turing Test - Javier Insa, Jose Hernandez-Orallo, Sergio España - David Dowe and M.Victoria Hernandez-Lloreda: The anYnt Project Intelligence Test (Demo) - Jose Hernandez-Orallo, Javier Insa, David Dowe and Bill Hibbard: Turing Machines and Recursive Turing Tests — Francesco Bianchini and Domenica Bruni: What Language for Turing Test in the Age of Qualia? - Paul Schweizer: Could there be a Turing Test for Qualia? - Antonio Chella and Riccardo Manzotti: Jazz and Machine Consciousness: Towards a New Turing Test - William York and Jerry Swan: Taking Turing Seriously (But Not Literally) - Hajo Greif: Laws of Form and the Force of Function: Variations on the Turing Test. (shrink)

Dinî tecrübe Friedrich Schleiermacher (ö.1768) ile önem kazanan ve William James’in (ö.1842) eserleriyle din felsefesinde teistik delillerin içine dahil olan bir delildir. Dini tecrübelerin birçok şekilde meydana geldiği iddia edilmektedir. Bunlardan biri de sezgidir. Bu bildirinin amacı sezgisel bilginin Tanrı’nın varlığına delil olup olmadığını ortaya koymaktır. Sezgisel yetenek, insanın fiziksel gelişimine (yani beyin) paralel olarak gelişen bir yetidir ve zihnin gelişmesiyle birlikte kapasitesi artmaktadır. Önce çocukta duygusal bir sezgi hakim iken (4-7 yaş), daha sonra çocuğun somut işlemlere geçmesiyle sezgisel yetenek (...) somutla ilişkili hale gelir. (7-11 yaş) Ve somut nesne ve durumlar (deney ve pratikler) çocuğun sezgisel yeteneğinin gelişmesine yol açar. En son aşamada yani soyut işlemler döneminde (11-17 yaş) çocuğun beyninde prefrontal lobun gelişmesine bağlı olarak akli muhakeme gelişir ve bunun etkisiyle sezgisel yetenek, akli verileri kullanarak soyut sezgiye yönelir. Sezgisel yetenek böylece üç dönemin özelliklerini gösterebilir; çocukluktan aldığı duygusal sezgi ve somut/nesnenin çağrıştırdığı somut sezgi ve aklın dış dünyadan aldığı bilgileri zihinsel süreçlerden geçirerek işlemesi sonucu gelişen akılcı sezgi. O nedenle insanlarda tek bir sezgiden bahsetmek yanlıştır. Sezginin üç türü birbiriyle eş güdümlü olarak bilgiyi elde etmek için çalışır. Bu üç sezgi türünden akılcı sezgiye önem veren İbn Sina, sezgi bilgisini rasyonel, epistemolojik alana dahil eder. Yaptığı ilim sınıflamasında sezgi bilgisini deneye dayalı bilgi türü olarak görür ve akla/deneye dayalı bir sezgi anlayışı geliştirir. Bu sezgi anlayışı, peygamberliği rasyonel bir temele oturtmak ve irrasyonel olmadığın açıklamak için de kullanır. Kudsi akla sahip peygamberler üstün zekalarının etkisiyle güçlü sezgiye sahip olurlar ve vahiy alırlar. Vahiy alan sezgisel yetenek diğer insanlarda ortaya çıkıp dini tecrübeleri şekillendirebilir mi? Peygamberlerin vahiy tecrübesini taklit ederek kendilerinde yüksek sezgisel yeti olduğunu savunan bazı kişiler (veli) ilham yoluyla bilgi elde ettiklerini iddia etmişlerdir. Dini tecrübe delilinde bu tür tecrübeler dini delil olarak sayılmaktadır. Fakat bu sezgisel bilginin kaynağı duygu mudur, somut bir gösterge (deney) midir yoksa akıl mıdır? İlham ürünü olan eserlerde her zaman duygu vardır ve bu tür ifadeler insanı duygunun hakim olduğu zihinsel bir duruma götürür. Fakat vahiy tecrübesinde duygunun yanında, somut dünyanın varlığı ve akla dayalı bir sezginin olduğu da vurgulanmaktadır. O nedenle sezgisel bilgi ürünü vahiy üç tür sezgi bilgisine dayalı iken, ilham ürünü olan sezgisel bilgi sadece duyguya dayalıdır. O nedenle ‘dini’ bir delil olarak değil ‘mistik’ bir delil olarak değerlendirmeyi hak eder. (shrink)

In this article, I seek to provide a philosophical elucidation of the thesis of open theism. This task will be performed by utilising the conception of open theism, Generic Open Theism, provided by Alan Rhoda (and precisified in part by William Hasker). This conception will then be further elucidated through the employment of the notion of libertarianism, as proposed by Robert Kane, which will enable the thesis of Generic Open Theism to be shown to not be subject to two (...) important challenges: the Prophecy Challenge and the Divine Bodgery Challenge—which are challenges that focus on showing the incompatibility of perfect being theism, scripture and providence with the central tenets of Open Theism. Thus, in the end, one will be able to affirm the veracity of Open Theism within a scripturally grounded, perfect being theistic framework. (shrink)

My topic is a certain view about mental images: namely, the ‘Multiple Use Thesis’. On this view, at least some mental image-types, individuated in terms of the sum total of their representational content, are potentially multifunctional: a given mental image-type, individuated as indicated, can serve in a variety of imaginative-event-types. As such, the presence of an image is insufficient to individuate the content of those imagination-events in which it may feature. This picture is argued for, or (more usually) just assumed (...) to be true, by Christopher Peacocke, Michael Martin, Paul Noordhof, Bernard Williams, Alan White, and Tyler Burge. It is also presupposed by more recent authors on imagination such as Amy Kind, Peter Kung and Neil Van Leeuwen. I reject various arguments for the Multiple Use Thesis, and conclude that instead we should endorse SINGLE: a single image-type, individuated in terms of the sum total of its intrinsic representational content, can serve in only one imagination event-type, whose content coincides exactly with its own, and is wholly determined by it. Plausibility aside, the interest of this thesis is also in its iconoclasm, as well as the challenge it poses for the diverse theories that rest on the truth of the Multiple Use Thesis. (shrink)

Her din ve mistik kültürde ortaya çıkan dinî tecrübelerin felsefe, kelam ve fıkıh gibi bilim alanlarında farklı açıklamaları yapılmış, akli olup olmadığı sorgulanmıştır. Vahiy, keramet, vecd, hulul, tecelli gibi kavramlara açıklamalar getirilmiştir. Fakat bu tür tecrübelerin insanın fizyolojik ve psikolojik mekanizmalarıyla ne tür bir bağlantısı olduğu İslam düşünce geleneğinde pek tartışılmamıştır. Bu tür tecrübe yaşayan kişilerin sorunlu olup olmadığı tıbbi açıdan değerlendirilmemiştir. Dini tecrübeleri tıbbî bir sorun olarak ele alıp bu tecrübeleri ‘deney’ konusu yaparak inceleyen ilk düşünür William James’tir (ö.1910). (...) O, The Varieties of Religious Experience adlı kitabında her türlü ‘dini’ olarak ifade edilen tecrübeleri ele alıp açıkladığı gibi, dini olmayan ama dini tecrübelere benzer mistik tecrübeleri de araştırıp, incelemiştir. Fakat James, araştırmasında dini ve mistik tecrübe ayırımı yapmamıştır. İkili bir ayırma tabi tutulmadan bütün tecrübelerin tek bir başlık altında incelenip ‘psikolojik durum’ olarak kabul edilmesi bu bildirinin ele aldığı ana sorundur. Bütün tecrübeler tek bir başlık altında ele alınırsa peygamberlerin tecrübeleri (vahiy) ile bunun dışında yer alan mistik tecrübelerin (vecd, keramet) bir farkı kalmayacaktır. Bu ikisini ayırmak için akli kriterleri ve tecrübelerinin ana iddialarını değerlendirip ele almak gerekir. Vahiy tecrübelerinin temel iddialarıyla mistik tecrübelerin iddialarını karşılaştırdığımızda vahiy tecrübelerinin akli kriterlere uygun olduğu ve tıbbi açıdan hastalıklı bir insanın tecrübesi olmadığı görülecektir. Mistik tecrübeler de ise durum bunun tersi görünmektedir. Mistik tecrübeler geçirenlerin çoğu zaman depresyon, manik ve çoğu zaman da uyuşturucu ile ortaya çıktığı, bunalımlı ve savaş dönemlerinde bu tür tecrübelerin arttığı görülür. Bu şekilde vahiy tecrübesinin doğruluğu ortaya konduğunda toplumu etkileyen dini inançların doğru kaynağına yönelmek mümkün olur. Mistik tecrübelerin ise hastalıklı zihnin ürünü olması nedeniyle insanları saptırıcı, dinden çıkarıcı ve akıl dışı olduğu ortaya çıkar. Bu şekilde dini inançların istikameti doğru bir şekilde çizilmiş olur. (shrink)

ArgumentIn the United States, scientific knowledge is brought before the courts by way of testimony – the testimony of scientific experts. We argue that this expertise is best understoodfirstas related to the quality of the underlying scienceand thenin terms of who delivers it. Bloodstain pattern analysis (BPA), a contemporary forensic science, serves as the vaulting point for our exploration of objectivity as a metric for the quality of a science in judicial contexts. We argue that BPA fails to meet the (...) minimal standard set by Helen Longino’s social-procedural account of objectivity (1990, 2002). In light of some pressing issues for social-procedural accounts, we offer an infrastructural account of objectivity. This account offers what amounts to a friendly amendment to Longino’s account and adds to the ways in which we might analyze social-procedural objectivity. Finally, we address an issue that is pressing in the legal context: given that scientific knowledge is delivered by individuals, not communities, at least in U.S. courts, we (may) need a way to evaluate individual scientific and epistemic agents. We suggest a means for making this evaluation that is derived from our infrastructural account of objectivity. (shrink)

Understanding the relationship between wilderness outings and the resulting experience has been a central theme in resource-based, outdoor recreation research for nearly 50 years. The authors provide a review and synthesis of literature that examines how people, over time, build relationships with wilderness places and express their identities as consequences of multiple, ongoing wilderness engagements (i.e., continued participation). The paper reviews studies of everyday places and those specifically protected for wilderness and backcountry qualities. Beginning with early origins and working through (...) contemporary research the authors synthesize what diverse social scientists have learned about the long-term and continual nature of wilderness participation and its impact on the formation of identity. The thrust of the paper points researchers, planners, and managers in non-traditional directions and reframes goals and objectives for visitor planning and management in wilderness and other protected areas. (shrink)

If the world itself is metaphysically indeterminate in a specified respect, what follows? In this paper, we develop a theory of metaphysical indeterminacy answering this question.

One theoretical charge (of Optimality Theory in its early conception) must have been to retain that sense of qualitative particularity as affecting as constraining theory relevant to a proscribed field when clearly a motivation was to divine in circumscriptions operational consequences conceived on a deferred abstractive level. An attraction of the theory's embodying results of constraint interactions as responsive to theory-internal qualitative implementation, as being in fact supplementarily transparent to co-ordinations of variously language specific implementations, qualitative identifications, was apparent naturalistic (...) coordination of defined features taken here—in OT—at one fell-swoop. Differently put, the uses of analyses of the relevant types of spaces (‘primitive from the viewpoint of linguistic theories’) will (latterly) involve a period of time-stretch or compression over a previously normal (I take it) process of embeddings in a new theorised and recursively enacted invocation/re-invocation of base as digestively present in results of corrected theories. Or as Prince and Smolensky have it -/- 'What we have done, in essence, is to replace the iterative procedure (act/evaluate, act/evaluate, . . . ) with a recursive scheme: collect the results of all possible actions, then sort recursively.' OT, 16. (shrink)

Surveillance programs supporting the management of One Health issues such as antibiotic resistance are complex systems in themselves. Designing ethical surveillance systems is thus a complex task (retroactive and iterative), yet one that is also complicated to implement and evaluate (e.g., sharing, collaboration, and governance). The governance of health surveillance requires attention to ethical concerns about data and knowledge (e.g., performance, trust, accountability, and transparency) and empowerment ethics, also referred to as a form of responsible self-governance. Ethics in reflexive governance (...) operates as a systematic critical-thinking procedure that aims to define its value: What are the “right” criteria to justify how to govern “good” actions for a “better” future? The objective is to lay the foundations for a methodological framework in empirical bioethics, the rudiments of which have been applied to a case study to building reflexive governance in One Health. This ongoing critical thinking process involves “mapping, framing, and shaping” the dynamics of interests and perspectives that could jeopardize a “better” future. This paper proposes to hybridize methods to combine insights from collective deliberation and expert evaluation through a reflexive governance functioning as a community-based action-ethics methodology. The intention is to empower individuals and associations in a dialogue with society, which operation is carried out using a case study approach on data sharing systems. We based our reasoning on a feasibility study conducted in Québec, Canada (2018–2021), envisioning an antibiotic use surveillance program in animal health for 2023. Using the adaptive cycle and governance techniques and perspectives, we synthesize an alternative governance model rooted in the value of empowerment. The framework, depicted as a new “research and design (R&D)” practice, is linking operation and innovation by bridging the gap between Reflexive, Evaluative, and Deliberative reasonings and by intellectualizing the management of democratizing critical thinking locally (collective ethics) by recognizing its context (social ethics). Drawing on the literature in One Health and sustainable development studies, this article describes how a communitarian and pragmatic approach can broaden the vision of feasibility studies to ease collaboration through public-private-academic partnerships. The result is a process that “reassembles” the One Health paradigm under the perspective of global bioethics to create bridges between the person and the ecosystem through pragmatic ethics. (shrink)

The concept of acting intentionally is an important nexus where ‘theory of mind’ and moral judgment meet. Preschool children’s judgments of intentional action show a valence-driven asymmetry. Children say that a foreseen but disavowed side-effect is brought about 'on purpose' when the side-effect itself is morally bad but not when it is morally good. This is the first demonstration in preschoolers that moral judgment influences judgments of ‘on-purpose’ (as opposed to purpose influencing moral judgment). Judgments of intentional action are usually (...) assumed to be purely factual. That these judgments are sometimes partly normative — even in preschoolers — challenges current understanding. Young children’s judgments regarding foreseen side-effects depend upon whether the children process the idea that the character does not care about the side-effect. As soon as preschoolers effectively process the ‘theory of mind’ concept, NOT CARE THAT P, children show the side-effect effect.idea.. (shrink)

Basic Formal Ontology (BFO) is a top-level ontology consisting of thirty-six classes, designed to support information integration, retrieval, and analysis across all domains of scientific investigation, presently employed in over 350 ontology projects around the world. BFO is a genuine top-level ontology, containing no terms particular to material domains, such as physics, medicine, or psychology. In this paper, we demonstrate how a series of cases illustrating common types of change may be represented by universals, defined classes, and relations employing the (...) BFO framework. We provide discussion of these cases to provide a template for other ontologists using BFO, as well as to facilitate comparison with the strategies proposed by ontologists using different top-level ontologies. (shrink)

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

We argue that, in order to explain the relative strengths of our reasons to contribute to different collective endeavours, approaches to the ethics of collective action must understand the strengths of our reasons to make a given contribution as proportional to its expected benefits, or its chances of bringing about benefits in proportion to their magnitudes. The view that most clearly meets this proportionality requirement is the expected consequences approach, which identifies our reasons to perform an act with its expected (...) benefits. We contend that views other than the expected consequences approach must similarly proportion the expected degrees of what they take to be reason-giving features of a contribution – such as its virtuousness, appropriate expression, support by considerations of fairness, or helping without making a difference – to the contribution’s expected benefits. The proportionality requirement explains why we should spend more time participating in strategic social, political, and labour movement activities, while avoiding unproductive conflicts and merely performative activities. We conclude that the proportionality requirement, and the ability of views other than the expected consequences approach to meet it, are important for thinking and communicating about the ethics of collective action in ways that are simultaneously most compelling and most strategic. (shrink)

Discussions concerning whether there is a natural right to health care may occur in various forms, resulting in policy recommendations for how to implement any such right in a given society. But health care policies may be judged by international standards including the UN Universal Declaration of Human Rights. The rights enumerated in the UDHR are grounded in traditions of moral theory, a philosophical analysis of which is necessary in order to adjudicate the value of specific policies designed to enshrine (...) rights such as a right to health care. We begin with an overview of the drafting of the UDHR and highlight the primary influence of natural law theory in validating the rights contained therein. We then provide an explication of natural law theory by reference to the writings of Thomas Aquinas, as well as elucidate the complementary “capabilities approach” of Martha Nussbaum. We conclude that a right to health care ought to be guaranteed by the state. (shrink)

The current prevailing view is that participation in biomedical research is above and beyond the call of duty. While some commentators have offered reasons against this, we propose a novel public goods argument for an obligation to participate in biomedical research. Biomedical knowledge is a public good, available to any individual even if that individual does not contribute to it. Participation in research is a critical way to support an important public good. Consequently, all have a duty to participate. The (...) current social norm is that individuals participate only if they have a good reason to do so. The public goods argument implies that individuals should participate unless they have a good reason not to. Such a shift would be of great aid to the progress of biomedical research, eventually making society significantly healthier and longer lived. (shrink)

Objective Our study sought to (1) describe the practices and preferences of Colombian adolescents in accessing sexual and reproductive health services: accompanied versus alone; (2) compare actual practices with stated preferences; and (3) determine age and gender differences regarding the practice and these stated preferences. -/- Methods 812 participants aged 11–24 years old answered a survey in two Profamilia clinics in the cities of Medellin and Cali in Colombia. A cross-sectional analysis was performed to compare participants’ answers based on the (...) variables of gender and age. -/- Results A quarter of participants visited the clinic alone (25.4%). Females were more likely to go alone in comparison to males (26.3% vs 14.1%; p = 0.031), and older participants went alone more often than younger participants (p < 0.001). Most participants – 72.7% (95 %CI: 69.3–75.9) – expressed a preference in being accompanied to the clinic, and more than 90% had their preferences met. The preferences of older participants were, however, less likely to be met than those of younger participants (p < 0.001), notably, because they predominantly wanted to be accompanied. -/- Conclusion Contemporary public health and bioethics literature advocates in favor of developing health services that better meet the preferences of adolescents. The present research highlights an apparent blind spot related to the role that others (e.g., parents, friends, partners) can or should play in accompanying adolescent patients when they access sexual and reproductive health services. Respecting adolescents’ preferences, and hence their autonomy, is not simply a matter of ensuring freedom from constraints (e.g., their right and ability to go alone). Rather, it should also consider the liberty to choose whether to be accompanied when accessing SHRS and by whom. (shrink)

Depuis 2020, le monde a connu une situation sanitaire exceptionnelle à la suite de la pandémie de Covid-19, faisant face à une incertitude dans le monde médical clinique, de la recherche et dans l’ensemble des domaines connexes en santé publique. Le caractère imprévisible et l’absence de données fiables en lien avec ce virus ont fait émerger une quantité d’enjeux éthiques concrets, cela a donc révélé un domaine particulier, la bioéthique, et plus particulièrement une profession, les bioéthiciens. Les « bioéthiciens » (...) se sont fait connaître du grand public en se dressant parfois comme des garde-fous contre des dérives sanitaires, à d’autres moments comme des lanceurs d’alertes face à des injustices naissantes, ou comme critiques, polémistes et parfois même militants dans les médias ou en tant qu’acteurs de première ligne dans les systèmes politico-sanitaires. Ces divers rôles et pratiques illustrent bien la diversité et l’hétérogénéité du domaine de la bioéthique. Toutefois, l’absence de professionnalisation traditionnelle et formelle de la bioéthique complexifie la compréhension de ce champ disciplinaire. Même en Amérique du Nord, où la pratique de la bioéthique est professionnalisée, il ne s’agit toujours pas d’une profession officiellement reconnue et le terme « bioéthicien » lui-même peut être controversé. La forte présence de cette profession durant la pandémie de Covid-19 a révélé l’importance de décrire ce qu’est un bioéthicien, les fonctions qu’il occupe et en quoi consistent ses interventions. Nous apportons cette clarification nécessaire en expliquant la nature de la bioéthique contemporaine dans toute sa diversité. Comme nous l’a démontré la pandémie de Covid-19, les bioéthiciens représentant un soutien et un guide indispensable de nos jours menés par leur esprit critique et leur réflexivité permanente. (shrink)

New media (highly interactive digital technology for creating, sharing, and consuming information) affords users a great deal of control over their informational diets. As a result, many users of new media unwittingly encapsulate themselves in epistemic bubbles (epistemic structures, such as highly personalized news feeds, that leave relevant sources of information out (Nguyen forthcoming)). Epistemically paternalistic alterations to new media technologies could be made to pop at least some epistemic bubbles. We examine one such alteration that Facebook has made in (...) an effort to fight fake news and conclude that it is morally permissible. We further argue that many epistemically paternalistic policies can (and should) be a perennial part of the internet information environment. (shrink)

Higher education institutions are mining and analyzing student data to effect educational, political, and managerial outcomes. Done under the banner of “learning analytics,” this work can—and often does—surface sensitive data and information about, inter alia, a student’s demographics, academic performance, offline and online movements, physical fitness, mental wellbeing, and social network. With these data, institutions and third parties are able to describe student life, predict future behaviors, and intervene to address academic or other barriers to student success (however defined). Learning (...) analytics, consequently, raise serious issues concerning student privacy, autonomy, and the appropriate flow of student data. We argue that issues around privacy lead to valid questions about the degree to which students should trust their institution to use learning analytics data and other artifacts (algorithms, predictive scores) with their interests in mind. We argue that higher education institutions are paradigms of information fiduciaries. As such, colleges and universities have a special responsibility to their students. In this article, we use the information fiduciary concept to analyze cases when learning analytics violate an institution’s responsibility to its students. (shrink)

We describe a strategy for integration of data that is based on the idea of semantic enhancement. The strategy promises a number of benefits: it can be applied incrementally; it creates minimal barriers to the incorporation of new data into the semantically enhanced system; it preserves the existing data (including any existing data-semantics) in their original form (thus all provenance information is retained, and no heavy preprocessing is required); and it embraces the full spectrum of data sources, types, models, and (...) modalities (including text, images, audio, and signals). The result of applying this strategy to a given body of data is an evolving Dataspace that allows the application of a variety of integration and analytic processes to diverse data contents. We conceive semantic enhancement (SE) as a lightweight and flexible process that leverages the richness of the structured contents of the Dataspace without adding storage and processing burdens to what, in the intelligence domain, will be an already storage- and processing-heavy starting point. SE works not by changing the data to which it is applied, but rather by adding an extra semantic layer to this data. We sketch how the semantic enhancement approach can be applied consistently and in cumulative fashion to new data and data-models that enter the Dataspace. (shrink)

BioéthiqueOnline was launched in March 2012 as a non-peer reviewed journal with the aim of providing a platform to facilitate and encourage the development of a bilingual bioethics community in Canada and internationally. In light of discussions amongst the Editorial Committee over the past few months regarding the growth of the journal, we have decided to move to a peer-reviewed process for articles submitted to the journal.

The comprehension of anaphoric relations may be guided not only by discourse, but also syntactic information. In the literature on online processing, however, the focus has been on audible pronouns and descriptions whose reference is resolved mainly on the former. This paper examines one relation that both lacks overt exponence, and relies almost exclusively on syntax for its resolution: adjunct control, or the dependency between the null subject of a non-finite adjunct and its antecedent in sentences such as Mickey talked (...) to Minnie before ___ eating. Using visual world eyetracking, we compare the time course of interpreting this null subject and overt pronouns (Mickey talked to Minnie before he ate). We show that when control structures are highly frequent, listeners are just as quick to resolve reference in either case. When control structures are less frequent, reference resolution based on structural information still occurs upon hearing the non-finite verb, but more slowly, especially when unaided by structural and referential predictions. This may be due to increased difficulty in recognizing that a referential dependency is necessary. These results indicate that in at least some contexts, referential expressions whose resolution depends on very different sources of information can be resolved approximately equally rapidly, and that the speed of interpretation is largely independent of whether or not the dependency is cued by an overt referring expression. (shrink)

Although the last decade has seen a proliferation of ontological approaches to arguments, many of them employ ad hoc solutions to representing arguments, lack interoperability with other ontologies, or cover arguments only as part of a broader approach to evidence. To provide a better ontological representation of arguments, we present the Arguments Ontology (ArgO), a small ontology for arguments that is designed to be imported and easily extended by researchers who work in different upper-level ontology frameworks, different logics, and different (...) approaches to argument evaluation. Unlike most ontological approaches to arguments, ArgO utilizes Basic Formal Ontology (BFO) as an upper-level ontology, and may be used alongside other commonly used ontologies in the BFO framework, including boththe Information Artifact Ontology (IAO), and the Information Entity Ontology (INFO). Critically, our proposal is principled, based on rigorous definitions and formal axioms out of which characterizations of arguments naturally fall. It is our hope that ArgO may assist researchers in many projects, including: integrating heterogeneous sources of evidence, structuring the content of semantic wikis, and enhancing semantic reasoning. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at https://pir.georgetown.edu/pro/. (shrink)

Bioethics experts played a key role in ensuring a coherent ethical response to the COVID-19 pandemic in the fields of healthcare, public health, and scientific research in Canada. In the province of Quebec, a group of academic and practicing bioethicists met periodically in the early months of the pandemic to discuss approaches and solutions to ethical dilemmas encountered during the crisis. These meetings created the opportunity for a national survey of bioethics practitioners from different fields. The survey, in which forty-five (...) Canadian bioethics practitioners (clinical ethicists, ethicist members of REBs and government health policy ethicists, or any bioethicist practicing outside of academia) participated, explored their concerns, challenges and opportunities during the first wave of the pandemic, with the objective of informing bioethics research about the difficulties experienced by bioethicists “in the field”. Participants reported increased stress levels, increased workloads, and a greater proportion of their work being devoted to public health ethics. Most of their concerns focused on groups other than themselves, such as health professionals, patients, research participants, and people in vulnerable socio-economic situations. An optimism about the future of bioethics was noted due to an increased awareness of the importance of bioethics by the public and by health and research institutions. (shrink)

This article identifies and compares meanings of wildfire risk mitigation for stakeholders in the Front Range of Colorado, USA. We examine the case of a collaborative partnership sponsored by government agencies and directed to decrease hazardous fuels in interface areas. Data were collected by way of key informant interviews and focus groups. The analysis is guided by the Circuit of Culture model in communication research. We found both shared and differing meanings between members of this partnership (the ‘‘producers’’) and other (...) stakeholders not formally in the partnership (the ‘‘consumers’’). We conclude that those promoting the partnership’s project to mitigate risk are primarily aligned with a discourse of scientific management. Stakeholders outside the partnership follow a discourse of community. We argue that failure to recognize and account for differences in the way risk mitigation is framed and related power dynamics could hamper the communicational efforts of the collaborative partnership and impact goals for fuels reduction. We recommend ways that both groups can capitalize on shared meanings and how agency managers and decision makers can build better working relationships with interface communities and other external stakeholders. (shrink)

In Québec, the Act Respecting Access to Documents Held by Public Bodies and the Protection of Personal Information provides an exception to transparency to most public institutions where public health research is conducted by allowing them to not disclose their uses of personal data. This exceptionalism is ethically problematic due to important concerns and we argue that all those who conduct research should be transparent and accountable for the work they do in the public interest.

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.

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)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

This précis summarizes the main topics, arguments and conclusions of the book. Many interesting arguments and critiques have, of course, been omitted in order to make this summary appropriately brief.

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

There are unusual challenges in ethics for RAS. Perhaps the issue can best be summarised as needing to consider “technically informed ethics”. The technology of RAS raises issues that have an ethical dimension, and perhaps uniquely so due to the possibility of moving human decision-making which is implicitly ethically informed to computer systems. Further, if seeking solutions to these problems – ethically aligned design, to use the IEEE’s terminology – then the solutions must be technically meaningful, capable of realisation, capable (...) of assurance, and suitable as a basis for regulation. Thus, ethics for RAS is a rich, complex multi-disciplinary concern, and perhaps more complex than many other ethical issues facing society today. It is also fast-moving. This paper has endeavoured to give an accessible introduction to some of the key issues, noting that many of them are quite subtle, and it is not possible to do them full justice in such a short document. However, we have sought to counterbalance this by giving an extensive list of initiatives, standards, etc. that focus on ethics of RAS and AI, see Annex A. (shrink)