Ontology engineering is mainly done by domain experts who are specialists in their domain but have, if at all, limited knowledge in logics, computer science, or analytic philosophy. The literature on formal ontologies and biomedical ontologies is neither suited nor intended to serve as an educational resource that would help domain experts to become good ontologists. Existing educational resources focus rather on ontology tools and languages than on good practice. The purpose of the GoodOD guideline is to pave the road (...) for domain experts who want (or need) to become ontology engineers. It pursues the openly pragmatic approach that ontology engineers only need to know ontology theory to the extent which supports the (measurable) outcome of their work. The GoodOD Guideline builds upon given philosophical and methodological principles as well as preexisting tools and resources. In particular (pragmatic) scientific realism, first order logics and its subset OWL-DL (description logics), set theory, an upper-level ontology with high-level categories and a canonic set of relations, constraints which limit the freedom of choice when building coordinate expressions, the ontology editor Protégé 4, a complete DL reasoner, such as HermIT, ontology design patterns, and naming conventions. -/- Given these precepts the guideline contains all the knowledge to be acquired by a user to be able to solve ontology engineering problems in a foreseeable and non-arbitrary way. The didactic concept is to convey the skills not only by theory but also by practical examples. (shrink)

BACKGROUND -/- The importance of ontologies in the biomedical domain is generally recognized. However, their quality is often too poor for large-scale use in critical applications, at least partially due to insufficient training of ontology developers. -/- OBJECTIVE -/- To show the efficacy of guideline-based ontology development training on the performance of ontology developers. The hypothesis was that students who received training on top-level ontologies and design patterns perform better than those who only received training in the basic principles of (...) formal ontology engineering. -/- METHODS -/- A curriculum was implemented based on a guideline for ontology design. A randomized controlled trial on the efficacy of this curriculum was performed with 24 students from bioinformatics and related fields. After joint training on the fundamentals of ontology development the students were randomly allocated to two groups. During the intervention, each group received training on different topics in ontology development. In the assessment phase, all students were asked to solve modeling problems on topics taught differentially in the intervention phase. Primary outcome was the similarity of the students’ ontology artefacts compared with gold standard ontologies developed by the authors before the experiment; secondary outcome was the intra-group similarity of group members’ ontologies. -/- RESULTS -/- The experiment showed no significant effect of the guideline-based training on the performance of ontology developers (a) the ontologies developed after specific training were only slightly but not significantly closer to the gold standard ontologies than the ontologies developed without prior specific training; (b) although significant differences for certain ontologies were detected, the intra-group similarity was not consistently influenced in one direction by the differential training. -/- CONCLUSION -/- Methodologically limited, this study cannot be interpreted as a general failure of a guideline-based approach to ontology development. Further research is needed to increase insight into whether specific development guidelines and practices in ontology design are effective. (shrink)

Ontology engineering is mainly done by domain experts who are specialists in their domain but have, if at all, limited knowledge in logics, computer science, or analytic philosophy. The literature on formal ontologies and biomedical ontologies is neither suited nor intended to serve as an educational resource that would help domain experts to become good ontologists. Existing educational resources focus rather on ontology tools and languages than on good practice. The purpose of the GoodOD guideline is to pave the road (...) for domain experts who want (or need) to become ontology engineers. It pursues the openly pragmatic approach that ontology engineers only need to know ontology theory to the extent which supports the (measurable) outcome of their work. The GoodOD Guideline builds upon given philosophical and methodological principles as well as preexisting tools and resources. In particular (pragmatic) scientific realism, first order logics and its subset OWL-DL (description logics), set theory, an upper-level ontology with high-level categories and a canonic set of relations, constraints which limit the freedom of choice when building coordinate expressions, the ontology editor Protégé 4, a complete DL reasoner, such as HermIT, ontology design patterns, and naming conventions. -/- Given these precepts the guideline contains all the knowledge to be acquired by a user to be able to solve ontology engineering problems in a foreseeable and non-arbitrary way. The didactic concept is to convey the skills not only by theory but also by practical examples. (shrink)

OBJECTIVE: (a) To measure the effect of a guideline-based training on the performance of ontology developers compared with the performance after unspecific training by a competency question based evaluation; and (b) to provide empirical evidence for the applicability of competency questions in formal ontology evaluation in general. BACKGROUND: A close connection between ontology development and ontology evaluation as quality management procedure can been attained with the use of competency questions. Competency questions are often used as a semi-formal specification of requirements (...) for an ontology under development. Hence they can also be used as evaluation instruments, in order to check how far an ontology fulfills these requirements. METHODS: A randomized controlled trial was conducted with two groups of 12 students each. The intervention consisted in a differential guideline-based training on ontology development vs. unspecific training. After a group-specific training focusing on three topics per group, performance of students was assessed with 12 exercises (2 exercises per topic), in which the students had to apply their skills. Different types of competency questions were elaborated for the analysis of the students' ontologies. We used the proportion of correct answers as a measure of ontology quality. RESULTS: On single topic level, the performance of ontology developers increased after guideline-based training for two out of the six topics: it increased from a proportion of 0.46 to 0.63 for the topic Process \& Participation and from 0.44 to 0.53 for the topic Collective Material Entity. In regression analysis, a positive correlation was shown between the performance of students on untrained topics and the performance after specific guideline-based training. Moreover, in multiple regression analysis an overall effect of specific training of 0.09 was calculated (p < 0.1). CONCLUSION: The results show an effect of a specific guideline-based training on the performance of ontology developers compared to the performance after unspecific training by an increase of about 10 \% on the rate of correct competency questions. In addition, this study has shown the general applicability of competency questions in a formal ontology evaluation scenario. However, the study also shows that the training of ontology developers and their performance evaluation is a tedious task. The resulting performance of ontology developers is more dependent on the a priori individual competencies than on the specific acquired skills after training. (shrink)

Background: In order to improve ontology quality, tool- and language-related tutorials are not sufficient. Care must be taken to provide optimized curricula for teaching the representational language in the context of a semantically rich upper level ontology. The constraints provided by rigid top and upper level models assure that the ontologies built are not only logically consistent but also adequately represent the domain of discourse and align to explicitly outlined ontological principles. Finally such a curriculum must take into account the (...) pre-existing skills and knowledge of the target audience. -/- Objective: To develop a well-structured curriculum aligned to the particular requirements of life science professionals, in order to enable them to create logically sound, domain adequate and predicable ontologies using the Web Ontology Language (OWL) in Protégè. -/- Methods: Content selection for the curriculum was based on the literature, pre-existing tutorials, and a guideline for good ontology development (i.e ontology design enhancing domain adequacy, sustainability and interoperability) that drew on the authors previous experiences with large ontology development projects. Learning objectives were formulated according to a needs assessment of the targeted learners, who were students trained in life sciences with basic knowledge and practical skills in computer science. As instructional format we choose an approach with a high amount of practical exercises. The curriculum was first implemented with 24 Students and 7 lecturers/ tutors over 5 full days. The curriculum was evaluated by gathering the participants feedback via a questionnaire. -/- Results: Curricular development produced 16 modules of approximately 2 hours each, which covered basic principles of Applied Ontology, description logic syntax and semantics, as well as best design practices outlined in ontology design patterns and variants of the BioTop upper ontology. An opinion survey based on questionnaires indicated that the participants took advantage from the teaching strategies applied, as they indicated good knowledge gain and acknowledged the relevance of the modules. The difficulty was rated slightly lower. -/- Conclusion: The development of teaching material for principled ontology design and best practices is of crucial importance in order to enhance the quality of biomedical ontologies. Here, we present a curriculum for a week long workshop, leveraging on current educational principles, focusing on interactive hands-on exercises, group interactions, and problem-oriented learning. Whereas evaluation clearly showed the success of this approach, in particular regarding student’s satisfaction, the objective measurement of traceable effects on the quality of the generated ontology, although of much higher interest, has just started. (shrink)

Background -/- Ontology Design Patterns (ODPs) are representational artifacts devised to offer solutions for recurring ontology design problems. They promise to enhance the ontology building process in terms of flexibility, re-usability and expansion, and to make the result of ontology engineering more predictable. In this paper, we analyze ODP repositories and investigate their relation with upper-level ontologies. In particular, we compare the BioTop upper ontology to the Action ODP from the NeOn an ODP repository. In view of the differences in (...) the respective approaches, we investigate whether the Action ODP can be embedded into BioTop. We demonstrate that this requires re-interpreting the meaning of classes of the NeOn Action ODP in the light of the precepts of realist ontologies. -/- Results -/- As a result, the re-design required clarifying the ontological commitment of the ODP classes by assigning them to top-level categories. Thus, ambiguous definitions are avoided. Classes of real entities are clearly distinguished from classes of information artifacts. The proposed approach avoids the commitment to the existence of unclear future entities which underlies the NeOn Action ODP. Our re-design is parsimonious in the sense that existing BioTop content proved to be largely sufficient to define the different types of actions and plans. -/- Conclusions -/- The proposed model demonstrates that an expressive upper-level ontology provides enough resources and expressivity to represent even complex ODPs, here shown with the different flavors of Action as proposed in the NeOn ODP. The advantage of ODP inclusion into a top-level ontology is the given predetermined dependency of each class, an existing backbone structure and well-defined relations. Our comparison shows that the use of some ODPs is more likely to cause problems for ontology developers, rather than to guide them. Besides the structural properties, the explanation of classification results were particularly hard to grasp for 'self-sufficient' ODPs as compared with implemented and 'embedded' upper-level structures which, for example in the case of BioTop, offer a detailed description of classes and relations in an axiomatic network. This ensures unambiguous interpretation and provides more concise constraints to leverage on in the ontology engineering process. (shrink)

Dialog is a joint action at different levels. At the highest level, the goal of interlocutors is to align their mental representations. This emerges from joint activity at lower levels, both concerned with linguistic decisions (e.g., choice of words) and nonlinguistic processes (e.g., alignment of posture or speech rate). Because of the high‐level goal, the interlocutors are particularly concerned with close coupling at these lower levels. As we illustrate with examples, this means that imitation and entrainment are particularly pronounced during (...) interactive communication. We then argue that the mechanisms underlying such processes involve covert imitation of interlocutors’ communicative behavior, leading to emulation of their expected behavior. In other words, communication provides a very good example of predictive emulation, in a way that leads to successful joint activity. (shrink)

Ethics and the Clinical Encounter explores the moral dimensions of clinical medicine and the phenomenon of illness, to determine what ethics must be in order to be fully responsive to clinical encounters. Written in a lively and conversational style with minimal technical terminology, and enhanced by actual experience or real clinical situations, this volume lays out a clinical ethics methodology both in practical and theoretical terms. Here's what the experts had to say: Professor Zaner has provided us with a remarkably (...) lucid and trenchant discussion of the interface of philosophy and the field of medicine. He brings into play an extraordinary range of historial knowledge, extensive observations based on firsthand experience with medical practices, and an acute sense of philosophical argumentation. This is a work that will be an exemplary and indispensable text in the philosophy of medicine for years to come. -- Calvin Schrag... it is a highly original contribution usable in a number of fields.... It really has no competition.... The genius of Zaner's approach is to ground ethics from the 'bottom up' and to direct us to the concrete particulars of therapeutic encounters wherein lie moral and ethical matters... meaty, challenging, and ultimately rewarding.... -- Paul R. Dokecki Richard M. Zaner founded the Center for Clinical and Research Ethics at Vanderbilt University Medical Center. Having established Vanderbilt's first Hospital Ethics Committee (1985), he served as co-chair of VUMC's Ethics Committee since its inception in 1990. Zaner has published five original books, edited ten, and translated four more, and has published more than 100 sections of books and professional journals. (shrink)

Much has been published about the ethical issues encountered by clinicians in genetics/genomics, but those experienced by clinical laboratory scientists are less well described. Clinical laboratory scientists now frequently face navigating ethical problems in their work, but how they should be best supported to do this is underexplored. This lack of attention is also reflected in the ethics tools available to clinical laboratory scientists such as guidance and deliberative ethics forums, developed primarily to manage issues arising within the clinic.We explore (...) what ethical issues are being experienced by clinical scientists, how they think such issues could be best analysed and managed, and whether their practice might be enhanced by more situated approaches to ethics deliberation and practice such as ethical preparedness. From thematic analysis of cases presented by clinical scientists at a specially convened meeting of the UK Genethics Forum, we derived three main ethical themes: (1) the redistribution of labour and responsibilities resulting from the practice of genomic medicine; (2) the interpretation and certainty of results and (3) the proposal that better standardisation and consistency of ethical approaches (for example, more guidelines and policy) could resolve some of the challenges arising.We argue that although standardisation is important for promoting shared understandings of good (including ethical) practice, supplementary approaches to enhance and sustain ethical preparedness will be important to help clinical scientists and others in the recently expanded genetic/genomic medicine environment foster quality ethical thinking. (shrink)

Citizens today are increasingly expected to be knowledgeable about and prepared to engage with biomedical knowledge. In this article, I wish to reframe this ‘public understanding of science’ project, and place fresh emphasis on public understandings of research: an engagement with the everyday laboratory practices of biomedicine and its associated ethics, rather than with specific scientific facts. This is not based on an assumption that non-scientists are ‘ignorant’ and are thus unable to ‘appropriately’ use or debate science; rather, it is (...) underpinned by an empirically-grounded observation that some individuals may be unfamiliar with certain specificities of particular modes of research and ethical frameworks, and, as a consequence, have their autonomy compromised when invited to participate in biomedical investigations. Drawing on the perspectives of participants in my own sociological research on the social and ethical dimensions of neuroscience, I argue that public understanding of biomedical research and its ethics should be developed both at the community level and within the research moment itself in order to enhance autonomy and promote more socially robust science. Public bioethics will have to play a key role in such an endeavour, and indeed will contribute in important ways to the opening up of new spaces of symmetrical engagement between bioethicists, scientists and wider publics—and hence to the democratisation of the bioethical enterprise. (shrink)

This book defends antitheodicism, arguing that theodicies, seeking to excuse God for evil and suffering in the world, fail to ethically acknowledge the victims of suffering. The authors argue for this view using literary and philosophical resources, commencing with Immanuel Kant's 1791 "Theodicy Essay" and its reading of the Book of Job. Three important twentieth century antitheodicist positions are explored, including "Jewish" post-Holocaust ethical antitheodicism, Wittgensteinian antitheodicism exemplified by D.Z. Phillips and pragmatist antitheodicism defended by William James. The authors argue (...) that these approaches to evil and suffering are fundamentally Kantian. Literary works such as Franz Kafka'sThe Trial, Samuel Beckett's Waiting for Godot, and George Orwell's Nineteen Eighty-Four, are examined in order to crucially advance the philosophical case for antitheodicism. (shrink)

Pragmatism mediates rival extremes, and religion is no exception: The problems of realism versus antirealism, evidentialism versus fideism, and science versus religion, along with other key issues in the philosophy of religion, receive new interpretations when examined from a pragmatist point of view. Religion is then understood as a human practice with certain inherent aims and goals, responding to specific human needs and interests, serving certain important human values, and seeking to resolve problematic situations that naturally arise from our practices (...) themselves, especially our need to live with our vulnerability, finitude, guilt, and mortality. (shrink)

This book integrates pragmatism and transcendental philosophy in examining the most serious problem defining the human condition, death and mortality. Its analysis of human limits and finitude is intended to be relevant to the concerns of philosophers specializing in, for example, transcendental philosophy, philosophical anthropology, pragmatism, Wittgenstein, and the philosophy of religion. Mortality is studied as providing a necessary framework within which questions concerning the meaningfulness or meaninglessness of human life become possible.

Davidson's anomalous monism, his argument for the identity between mental and physical event tokens, has been frequently attacked, usually demanding a higher degree of physicalist commitment. My objection runs in the opposite direction: the identities inferred by Davidson from mental causation, the nomological character of causality and the anomaly of the mental are philosophically problematic and, more dramatically, incompatible with his famous argument against the third dogma of empiricism, the separation of content from conceptual scheme. Given the anomaly of the (...) mental and the absence of psychophysical laws, there are no conceptual resources to relate mental and physical predicates. We fall in the third dogma if we claim that the very same token event is mental and physical. One of the premises must be rejected: I will claim that we do not need a law to subsume cause and effect to be entitled to speak of causation. Davidson has never offered an argument to back this premise. Against such a dogma I will sketch some ideas pointing towards a different conception of causality, singularist and undetachable from explanatory practices. (shrink)

_Pragmatism and Objectivity_ illuminates the nature of contemporary pragmatism against the background of Rescher’s work, resulting in a stronger grasp of the prospects and promises of this philosophical movement. The central insight of pragmatism is that we must start from where we find ourselves and deflate metaphysical theories of truth in favor of an account that reflects our actual practices of the concept. Pragmatism links truth and rationality to experience, success, and action. While crude versions of pragmatism state that truth (...) is whatever works for a person or a community, Nicholas Rescher has been at the forefront of arguing for a more sophisticated pragmatist position. According to his position, we can illuminate a robust concept of truth by considering its links with inquiry, assertion, belief, and action. His brand of pragmatism is objective and organized around truth and inquiry, rather than other forms of pragmatism that are more subjective and lenient. The contingency and fallibility of knowledge and belief formation does not mean that our beliefs are simply what our community decides, or that truth and objectivity are spurious notions. Rescher offers the best chance of understanding how it is that beliefs can be the products of human inquiry yet aim at the truth nonetheless. The essays in this volume, written by established and up-and-coming scholars of pragmatism, touch on themes related to epistemology, philosophy of mind, philosophy of science, and ethics. (shrink)

Ilkka Niiniluoto, a distinguished philosopher of science, has been a tirelesspokesman for scientific realism and reason more generally. Trained in the tradition of the Finnish school of inductive logic he has refined the notion of truthlikeness (verisimilitude) to make the realist idea scientific progress mathematically exact. Niiniluotos main technical works are included in his books Is Science Progressive? (1984) and Truthlikeness (1987), but his most recent general defense of scientific realism culminated in his Critical Scientific Realism (1999). Niiniluoto is, since (...) 1981, Professor of Theoretical Philosophy at the University of Helsinki, and since 2003 the Rector of the University. He has for a long time been one of the most prominent public intellectuals in Finland. This Festschrift brings about a selection of philosophical essays on Niiniluotos philosophy by prominent member of the international community. The contributions are grouped around three themes. The first ones deal with philosophy of logic, the philosophy of language, and the philosophy of mathematics, and the second group consists of papers on induction, truthlikeness, and scientific progress. The third part collects essays on the history of logical empiricism, the ontology of social groups, and the dispute between theism and atheism. This book is a tribute to Ilkka Niiniluoto on his 60th birthday, and it also contains Niiniluoto's replies to comments, queries and criticisms. (shrink)

Lots of Websites offer the possibility to donate human beings. Another problem of ethics of communications.

While moral philosophy has traditionally been understood as an examination of the good life, this book argues that ethical inquiry should, rather, begin from an examination of evil and other 'negative' moral concepts, such as guilt and suffering.

With disparate rates of morbidity and mortality among minoritized communities, COVID-19 illuminated the need for equity-informed practices in public health. Pacia et al posit FQHCs as entities that addressed inequity when others failed. This commentary further situates how FQHCs address the public health crisis of institutional racism and related health inequities every day and presents a FQHC-led Ethics and Equity Framework and Workflow Checklist to guide ethical and equitable engagement with FQHCs.

Despite its uniform appearance, the cerebellar cortex is highly heterogeneous in terms of structure, genetics and physiology. Purkinje cells (PCs), the principal and sole output neurons of the cerebellar cortex, can be categorized into multiple populations that differentially express molecular markers and display distinctive physiological features. Such features include action potential rate, but also their propensity for synaptic and intrinsic plasticity. However, the precise molecular and genetic factors that correlate with the differential physiological properties of PCs remain elusive. In this (...) article, we provide a detailed overview of the cellular mechanisms that regulate PC activity and plasticity. We further perform a pathway analysis to highlight how molecular characteristics of specific PC populations may influence their physiology and plasticity mechanisms. (shrink)

BackgroundMoral distress (MD) is the psychological damage caused when people are forced to witness or carry out actions which go against their fundamental moral values. The main objective was to evaluate the prevalence and predictive factors associated with MD among health professionals during the pandemic and to determine its causes.MethodsA regional, observational and cross-sectional study in a sample of 566 professionals from the Public Health Service of Andalusia (68.7% female; 66.9% physicians) who completed the MMD-HP-SPA scale to determine the level (...) of MD (0-432 points). Five dimensions were used: i) Health care; ii) Therapeutic obstinacy-futility, iii) Interpersonal relations of the Healthcare Team, iv) External pressure; v) Covering up of medical malpractice.ResultsThe mean level of MD was 127.3 (SD=66.7; 95% CI 121.8-132.8), being higher in female (135 vs. 110.3; p<0.01), in nursing professionals (137.8 vs. 122; p<0.01) and in the community setting (136.2 vs. 118.3; p<0.001), with these variables showing statistical significance in the multiple linear regression model (p<0.001; r2=0.052). With similar results, the multiple logistic regression model showed being female was a higher risk factor (OR=2.27; 95% CI 1.5-3.4; p<0.001). 70% of the sources of MD belonged to the dimension "Health Care" and the cause "Having to attend to more patients than I can safely attend to" obtained the highest average value (Mean=9.8; SD=4.9).ConclusionsFemale, nursing professionals, and those from the community setting presented a higher risk of MD. The healthcare model needs to implement an ethical approach to public health issues to alleviate MD among its professionals. (shrink)

It has been argued that organizational structures (the way tasks are defined, allocated, and coordinated) can influence moral agency in organizations. In particular, low values on different structural parameters (functional concentration, specialization, separation, and formalization) are said to foster an organizational context (allowing for relating to the goals and output of the organization, moral deliberation, and social connectedness) that is conducive to moral agency. In this paper, we investigate the relation between the organizational structure and moral agency in the case (...) of a.s.r. (a large Dutch insurance company). While our empirical results fit the thesis that low values on structural parameters positively relate to moral agency, they also refine our understanding of the influence of structural parameters. In particular, our data suggest that the influence of functional concentration not only depends on whether it is low, but also on the type of criterion used for identifying business units; they suggest that the specific organizational context may put a limit to lowering design parameters and points at several non-structural factors that have an influence on the relation between structure and moral agency. In all, the paper contributes to a more detailed understanding of the conditions conducive to moral agency in organizations. (shrink)