Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (shrink)

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which (...) semantic similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results. (shrink)

The construction of complex ontologies can be facilitated by adapting existing vocabularies. There is little clarity and in fact little consensus as to what modifications of vocabularies are necessary in order to re-engineer them into ontologies. In this paper we present a method that provides clear steps to follow when re-engineering a thesaurus. The method makes use of top-level ontologies and was derived from the structural differences between thesauri and ontologies as well as from best practices in modeling, some (...) of which have been advocated in the biomedical domain. We illustrate each step of our method with examples from a re-engineering case study about agricultural fertilizers based on the AGROVOC thesaurus. Our method makes clear that re-engineering thesauri requires far more than just a syntactic conversion into a formal language or other easily automatable steps. The method can not only be used for re-engineering thesauri, but does also summarize steps for building ontologies in general, and can hence be adapted for the re-engineering of other types of vocabularies or terminologies. (shrink)

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We (...) advance a proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

Publication ethics is an important aspect of both the research and publication enterprises. It is particularly important in the field of biomedical science because published data may directly affect human health. In this article, we examine publication ethics policies in biomedical journals published in Central and Eastern Europe. We were interested in possible differences between East European countries that are members of the European Union (Eastern EU) and South-East European countries (South-East Europe) that are not members of the (...) European Union.The most common ethical issues addressed by all journals in the region were redundant publication, peer review process, and copyright or licensing details. Image manipulation, editors’ conflicts of interest and registration of clinical trialswere the least common ethical policies. Three aspects were significantly morecommon in journals published outside the EU: statements on the endorsement of international editorial standards, contributorship policy, and image manipulation.On the other hand, copyright or licensing information were more prevalent in journals published in the Eastern EU. The existence of significant differences amongbiomedical journals’ ethical policies calls for further research and active measuresto harmonize policies across journals. On the other hand, copyright or licensing information were more prevalent in journals published in the Eastern EU. The existence of significant differences among biomedical journals’ ethical policies calls for further research and active measures to harmonize policies across journals. (shrink)

The recent progression in AI, nanomedicine and robotics have increased concerns about ethics, policy and law. The increasing complexity and hybrid nature of AI and nanotechnologies impact the functionality of “law in action” which can lead to legal uncertainty and ultimately to a public distrust. There is an immediate need of collaboration between Central Asian biomedical scientists, AI engineers and academic lawyers for the harmonization of AI, nanomedicines and robotics in Central Asian legal system.

Statements about the behavior of biochemical entities (e.g., about the interaction between two proteins) abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that have to be taken into account in the practice of biomedical ontology engineering: Such statements can not only be understood as event reporting statements, but also as (...) ascriptions of dispositions or tendencies that may or may not refer to collectives of interacting molecules or even to collectives of interaction events. (shrink)

Statements about the behavior of biological entities, e.g. about the interaction between two proteins, abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that is necessary to take into account in the practice of biomedical ontology engineering. Several concurring formalizations are proposed. Emphasis is laid on the discussion of biological dispositions.

The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the ‘‘blueprint’’ of an organism, organisms are ‘‘reverse engineered’’ to discover their func- tionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adapta- tions, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. (...) In particular, the analogy with human-made machines falters when we move down to the level of molecular biology and genetics. Living organisms are far more messy and less transparent than human-made machines. Notoriously, evolution is an oppor- tunistic tinkerer, blindly stumbling on ‘‘designs’’ that no sensible engineer would come up with. Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with ‘‘programming’’ the right ‘‘software’’ would sug- gest. The idea of applying straightforward engineering approaches to living systems and their genomes— isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms—pushes the analogy with human artifacts beyond its limits. In the absence of a one-to-one correspondence between genotype and phenotype, there is no straightforward way to imple- ment novel biological functions and design new life forms. Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for ‘‘engi- neering’’ a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic ‘‘instructions’’ is probably intractable for any but the most simple phenotypes. Recent developments in the field of bio-engineering and synthetic biology reflect these limitations. Instead of genetically engi- neering a desired trait from scratch, as the machine/engineering metaphor promises, researchers are making greater strides by co-opting natural selection to ‘‘search’’ for a suitable genotype, or by borrowing and recombining genetic material from extant life forms. (shrink)

Recent advancements in artificial intelligence have fueled widespread academic discourse on the ethics of AI within and across a diverse set of disciplines. One notable subfield of AI ethics is machine ethics, which seeks to implement ethical considerations into AI systems. However, since different research efforts within machine ethics have discipline-specific concepts, practices, and goals, the resulting body of work is pestered with conflict and confusion as opposed to fruitful synergies. The aim of this paper is to explore ways to (...) alleviate these issues, both on a practical and theoretical level of analysis. First, we describe two approaches to machine ethics: the philosophical approach and the engineering approach and show how tensions between the two arise due to discipline specific practices and aims. Using the concept of disciplinary capture, we then discuss potential promises and pitfalls to cross-disciplinary collaboration. Drawing on recent work in philosophy of science, we finally describe how metacognitive scaffolds can be used to avoid epistemological obstacles and foster innovative collaboration in AI ethics in general and machine ethics in particular. (shrink)

Deep brain stimulation (DBS), a surgical procedure involving the implantation of electrodes in the brain, has rekindled the medical community’s interest in psychosurgery. Whereas many researchers argue DBS is substantially different from psychosurgery, we argue psychiatric DBS—though a much more precise and refined treatment than its predecessors—is nevertheless a form of psychosurgery, which raises both old and new ethical and legal concerns that have not been given proper attention. Learning from the ethical and regulatory failures of older forms of psychosurgery (...) can help shed light on how to address the regulatory gaps that exist currently in DBS research. To show why it is important to address the current regulatory gaps within psychiatric DBS, we draw on the motivations underlying the regulation of earlier forms of psychosurgery in the US. We begin by providing a brief history of psychosurgery and electrical brain stimulation in the US. Against this backdrop, we introduce psychiatric DBS, exploring current research and ongoing clinical trials. We then draw out the ethical and regulatory similarities between earlier forms of psychosurgery and psychiatric DBS. As we will show, the factors that motivated strict regulation of earlier psychosurgical procedures mirror concerns with psychiatric DBS today. We offer three recommendations for psychiatric DBS regulation, which echo earlier motivations for regulating psychosurgery, along with new considerations that reflect the novel technologies used in DBS. (shrink)

This article argues for a task-based approach to identifying and individuating cognitive systems. The agent-based extended cognition approach faces a problem of cognitive bloat and has difficulty accommodating both sub-individual cognitive systems ("scaling down") and some supra-individual cognitive systems ("scaling up"). The standard distributed cognition approach can accommodate a wider variety of supra-individual systems but likewise has difficulties with sub-individual systems and faces the problem of cognitive bloat. We develop a task-based variant of distributed cognition designed to scale up and (...) down smoothly while providing a principled means of avoiding cognitive bloat. The advantages of the task-based approach are illustrated by means of two parallel case studies: re-representation in the human visual system and in a biomedical engineering laboratory. (shrink)

In the graphical representation of ontologies, it is customary to use graph theory as the representational background. We claim here that the standard graph-based approach has a number of limitations. We focus here on a problem in the graph-based representation of ontologies in complex domains such as biomedical, engineering and manufacturing: lack of mereotopological representation. Based on such limitation, we proposed a diagrammatic way to represent an entity’s structure and various forms of mereotopological relationships between the entities.

This is the third volume of the Encyclopedia of Neutrosophic Researchers, edited from materials offered by the authors who responded to the editor’s invitation. The authors are listed alphabetically. The introduction contains a short history of neutrosophics, together with links to the main papers and books. Neutrosophic set, neutrosophic logic, neutrosophic probability, neutrosophic statistics, neutrosophic measure, neutrosophic precalculus, neutrosophic calculus and so on are gaining significant attention in solving many real life problems that involve uncertainty, impreciseness, vagueness, incompleteness, inconsistent, and (...) indeterminacy. In the past years the fields of neutrosophics have been extended and applied in various fields, such as: artificial intelligence, data mining, soft computing, decision making in incomplete / indeterminate / inconsistent information systems, image processing, computational modelling, robotics, medical diagnosis, biomedical engineering, investment problems, economic forecasting, social science, humanistic and practical achievements. (shrink)

This is the first volume of the Encyclopedia of Neutrosophic Researchers, edited from materials offered by the authors who responded to the editor’s invitation. The authors are listed alphabetically. The introduction contains a short history of neutrosophics, together with links to the main papers and books. Neutrosophic set, neutrosophic logic, neutrosophic probability, neutrosophic statistics, neutrosophic measure, neutrosophic precalculus, neutrosophic calculus and so on are gaining significant attention in solving many real life problems that involve uncertainty, impreciseness, vagueness, incompleteness, inconsistent, and (...) indeterminacy. In the past years the fields of neutrosophics have been extended and applied in various fields, such as: artificial intelligence, data mining, soft computing, decision making in incomplete / indeterminate / inconsistent information systems, image processing, computational modelling, robotics, medical diagnosis, biomedical engineering, investment problems, economic forecasting, social science, humanistic and practical achievements. (shrink)

This is the fourth volume of the Encyclopedia of Neutrosophic Researchers, edited from materials offered by the authors who responded to the editor’s invitation. The authors are listed alphabetically. The introduction contains a short history of neutrosophics, together with links to the main papers and books. Neutrosophic set, neutrosophic logic, neutrosophic probability, neutrosophic statistics, neutrosophic measure, neutrosophic precalculus, neutrosophic calculus and so on are gaining significant attention in solving many real life problems that involve uncertainty, impreciseness, vagueness, incompleteness, inconsistent, and (...) indeterminacy. In the past years the fields of neutrosophics have been extended and applied in various fields, such as: artificial intelligence, data mining, soft computing, decision making in incomplete / indeterminate / inconsistent information systems, image processing, computational modelling, robotics, medical diagnosis, biomedical engineering, investment problems, economic forecasting, social science, humanistic and practical achievements. (shrink)

This is the first volume of the Encyclopedia of Neutrosophic Researchers, edited from materials offered by the authors who responded to the editor’s invitation. The 78 authors are listed alphabetically. The introduction contains a short history of neutrosophics, together with links to the main papers and books. -/- Neutrosophic set, neutrosophic logic, neutrosophic probability, neutrosophic statistics, neutrosophic measure, neutrosophic precalculus, neutrosophic calculus and so on are gaining significant attention in solving many real life problems that involve uncertainty, impreciseness, vagueness, incompleteness, (...) inconsistent, and indeterminacy. -/- In the past years the fields of neutrosophics have been extended and applied in various fields, such as: artificial intelligence, data mining, soft computing, decision making in incomplete / indeterminate / inconsistent information systems, image processing, computational modelling, robotics, medical diagnosis, biomedical engineering, investment problems, economic forecasting, social science, humanistic and practical achievements. (shrink)

Neutrosophic set, neutrosophic logic, neutrosophic probability, neutrosophic statistics, neutrosophic measure, neutrosophic precalculus, neutrosophic calculus and so on are gaining significant attention in solving many real life problems that involve uncertainty, impreciseness, vagueness, incompleteness, inconsistent, and indeterminacy. In the past years the fields of neutrosophics have been extended and applied in various fields, such as: artificial intelligence, data mining, soft computing, decision making in incomplete / indeterminate / inconsistent information systems, image processing, computational modelling, robotics, medical diagnosis, biomedical engineering, (...) investment problems, economic forecasting, social science, humanistic and practical achievements. There are about 7,000 neutrosophic researchers, within 89 countries around the globe, that have produced about 4,000 publications and tenths of PhD and MSc theses, within more than two decades. This is the sixth volume of the Encyclopedia of Neutrosophic Researchers, edited from materials offered by the authors who responded to the editor’s invitation, with an introduction contains a short history of neutrosophics, together with links to the main papers and books. -/- ES: Este es el Sexto volumen de la Enciclopedia de Investigadores Neutróficos, editados a partir de materiales ofrecidos por los autores que respondieron a la invitación del editor. Los autores se enumeran alfabéticamente. La introducción contiene una breve historia de la neutrosófica, y en especial se sus impacto en latinoamérica junto con enlaces a los principales artículos y libros. Conjunto neutrosófico, lógica neutrosófica, probabilidad neutrosófica, estadística neutrosófica, medida neutrosófica, precálculo neutrosófico, cálculo neutrosófico, psicología neutrosófica, sociología neutrosófica etc., están ganando una atención significativa en resolver muchos problemas de la vida real que implican incertidumbre, imprecisión, vaguedad, incompletitud, inconsistencia e indeterminación. En los últimos años, los campos de la neutrosófica se han ampliado y aplicado en diversos campos, tales como: inteligencia artificial, minería de datos, software informática, toma de decisiones en forma incompleta / indeterminada / inconsistente sistemas de información, procesamiento de imágenes, modelado computacional, robótica, diagnóstico médico, ingeniería biomédica, problemas de inversión, previsión económica, ciencias sociales, humanística y la validación y consolidación del conocimiento científico. (shrink)

Neutrosophic set, neutrosophic logic, neutrosophic probability, neutrosophic statistics, neutrosophic measure, neutrosophic precalculus, neutrosophic calculus and so on are gaining significant attention in solving many real life problems that involve uncertainty, impreciseness, vagueness, incompleteness, inconsistent, and indeterminacy. In the past years the fields of neutrosophics have been extended and applied in various fields, such as: artificial intelligence, data mining, soft computing, decision making in incomplete / indeterminate / inconsistent information systems, image processing, computational modelling, robotics, medical diagnosis, biomedical engineering, (...) investment problems, economic forecasting, social science, humanistic and practical achievements. There are about 7,000 neutrosophic researchers, within 89 countries around the globe, that have produced about 4,000 publications and tenths of PhD and MSc theses, within more than two decades. This is the fifth volume of the Encyclopedia of Neutrosophic Researchers, edited from materials offered by the authors who responded to the editor’s invitation, with an introduction contains a short history of neutrosophics, together with links to the main papers and books. (shrink)

In this paper, I examine the ethics of e - trust and e - trustworthiness in the context of health care, looking at direct computer-patient interfaces (DCPIs), information systems that provide medical information, diagnosis, advice, consenting and/or treatment directly to patients without clinicians as intermediaries. Designers, manufacturers and deployers of such systems have an ethical obligation to provide evidence of their trustworthiness to users. My argument for this claim is based on evidentialism about trust and trustworthiness: the idea that trust (...) should be based on sound evidence of trustworthiness. Evidence of trustworthiness is a broader notion than one might suppose, including not just information about the risks and performance of the system, but also interactional and context-based information. I suggest some sources of evidence in this broader sense that make it plausible that designers, manufacturers and deployers of DCPIs can provide evidence to users that is cognitively simple, easy to communicate, yet rationally connected with actual trustworthiness. (shrink)

The bruxism is a medical sleep syndrome it is the remedial span for crushing the tines and gritting the jowl. Human rarely chore their tines and jowl, slightly than crushing their teeth lacking it producing any signals. The symptoms of bruxism are arduousness in the jowl joint, breakable teeth, headache, earache and difficulty in open in mouth etc. The causes of bruxism are snooze sickness, pressure and nervousness. The REM is a rapid eye movement its a stages of sleep. The (...) EEG signal are used in the measurement of neuron, the alpha, beta, gamma, theta and delta wave are used in the prognostic of bruxism syndrome. Its used in MATLAB coding by the six steps in prognostic in bruxism. Md Belal Bin Heyat | Faijan Akhtar | Shadab Azad "Comparative Analysis of Original Wave & Filtered Wave of EEG signal Used in the Prognostic of Bruxism medical Sleep syndrome" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-1 | Issue-1 , December 2016,. (shrink)

The bruxism is a medical sleep syndrome it is the remedial span for crushing the tines and gritting the jowl. Human rarely chore their tines and jowl, slightly than crushing their teeth lacking it producing any signals. The symptoms of bruxism are arduousness in the jowl joint, breakable teeth, headache, earache and difficulty in open in mouth etc. The causes of bruxism are snooze sickness, pressure and nervousness. The REM is a rapid eye movement it's a stages of sleep. The (...) EEG signal are used in the measurement of neuron, the alpha, beta, gamma, theta and delta wave are used in the prognostic of bruxism syndrome. It's used in MATLAB coding by the six steps in prognostic in bruxism. Md Belal Bin Heyat | Faijan Akhtar | Shadab Azad "Comparative Analysis of Original Wave & Filtered Wave of EEG signal Used in the Prognostic of Bruxism medical Sleep syndrome" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-1 | Issue-1 , December 2016,. (shrink)

In this new post-genomic age of medicine and biomedical technology, there will be novel approaches to understanding disease, and to finding drugs and cures for diseases. Hundreds of new “disease genes” thought to be the causative agents of various genetic maladies will be identified and added to the list of hundreds of such genes already identified. Based on this knowledge, many new genetic tests will be developed and used in genetic screening programs. Genetic screening is the foundation upon which (...) reproductive technologies such as pre-natal diagnosis (PND) and preimplantation genetic diagnosis (PGD) are based. Genetic information arising from the human genome may also be used in attempts to redesign the human genetic inheritance by engineering the human germline (germline engineering). In each of these technologies—PND, PGD, and germline engineering—there are serious ethical and social concerns. Moreover, all three are eugenic in nature because they strive to control which genes are passed down to future generations. The goals of this article are threefold: 1) to introduce the science behind the three technologies; 2) to give a brief overview of eugenics in the past century and show how these genetic technologies are eugenic; and 3) to present a vision of social justice that rejects the genetic determinism upon which eugenics is based and embraces a holistic, ecological view of nature and humanity. (shrink)

Ontology is currently perceived as the solution of first resort for all problems related to biomedical terminology, and the use of description logics is seen as a minimal requirement on adequate ontology-based systems. Contrary to common conceptions, however, description logics alone are not able to prevent incorrect representations; this is because they do not come with a theory indicating what is computed by using them, just as classical arithmetic does not tell us anything about the entities that are added (...) or subtracted. In this paper we shall show that ontology is indeed an essential part of any solution to the problems of medical terminology – but only if it is understood in the right sort of way. Ontological engineering, we shall argue, should in every case go hand in hand with a sound ontological theory. (shrink)

In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous sources. In this position paper, we present a set of principles learned (...) from the successful Open Biomedical Ontologies (OBO) Foundry initiative to guide the design and development of the Industrial Ontologies Foundry (IOF), which is a counterpart to the OBO Foundry initiative for the manufacturing industry. We also illustrate the potential utility of these principles by sketching the conceptual design of a framework for sustainable IOF development. (shrink)

The development of manufacturing technologies for new materials involves the generation of a large and continually evolving volume of information. The analysis, integration and management of such large volumes of data, typically stored in multiple independently developed databases, creates significant challenges for practitioners. There is a critical need especially for open-sharing of data pertaining to engineering design which together with effective decision support tools can enable innovation. We believe that ontology applied to engineering (OE) represents a viable strategy (...) for the alignment, reconciliation and integration of diverse and disparate data. The scope of OE includes: consistent capture of knowledge pertaining to the types of entities involved; facilitation of cooperation among diverse group of experts; more effective ongoing curation, and update of manufacturing data; collaborative design and knowledge reuse. As an illustrative case study we propose an ontology focused on the representation of composite materials focusing in particular on the class of Functionally Graded Materials (FGM) in particular. The scope of the ontology is to provide information about the components of such materials, the manufacturing processes involved in creation, and diversity of application ranging from additive manufacturing to restorative dentistry. The ontology is developed using Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). (shrink)

Some types of solar radiation management (SRM) research are ethically problematic because they expose persons, animals, and ecosystems to significant risks. In our earlier work, we argued for ethical norms for SRM research based on norms for biomedical research. Biomedical researchers may not conduct research on persons without their consent, but universal consent is impractical for SRM research. We argue that instead of requiring universal consent, ethical norms for SRM research require only political legitimacy in decision-making about global (...) SRM trials. Using Allen Buchanan & Robert Keohane's model of global political legitimacy, we examine several existing global institutions as possible analogues for a politically legitimate SRM decision-making body. (shrink)

Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those who (...) created them, and unable to serve as inputs for automated reasoning. This volume shows, in a nontechnical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends. (shrink)

Much of contemporary research ethics was developed in the latter half of the twentieth century as a response to the unethical treatment of human beings in biomedical research. Research ethical considerations have subsequently been extended to cover topics in the sciences and technology such as data handling, precautionary measures, engineering codes of conduct, and more. However, moral issues in the humanities have gained less attention from research ethicists. This article proposes an ethical principle for reading for research purposes: (...) Respect the author. (shrink)

This article critically examines one of the most prevalent metaphors in modern biology, namely the machine conception of the organism (MCO). Although the fundamental differences between organisms and machines make the MCO an inadequate metaphor for conceptualizing living systems, many biologists and philosophers continue to draw upon the MCO or tacitly accept it as the standard model of the organism. This paper analyses the specific difficulties that arise when the MCO is invoked in the study of development and evolution. In (...) developmental biology the MCO underlies a logically incoherent model of ontogeny, the genetic program, which serves to legitimate three problematic theses about development: genetic animism, neo-preformationism, and developmental computability. In evolutionary biology the MCO is responsible for grounding unwarranted theoretical appeals to the concept of design as well as to the interpretation of natural selection as an engineer, which promote a distorted understanding of the process and products of evolutionary change. Overall, it is argued that, despite its heuristic value, the MCO today is impeding rather than enabling further progress in our comprehension of living systems. (shrink)

Automatic detection of diseases and anatomical landmarks in medical images by the use of computers is important and considered a challenging process that could help medical diagnosis and reduce the cost and time of investigational procedures and refine health care systems all over the world. Recently, gastrointestinal (GI) tract disease diagnosis through endoscopic image classification is an active research area in the biomedical field. Several GI tract disease classification methods based on image processing and machine learning techniques have been (...) proposed by diverse research groups in the recent past. However, yet effective and comprehensive deep ensemble neural network-based classification model with high accuracy classification results is not available in the literature. In this thesis, we review ways and mechanisms to use deep learning techniques to research on multi-disease computer-aided detection about gastrointestinal and identify these images. We re-trained five state-of-the-art neural network architectures, VGG16, ResNet, MobileNet, Inception-v3, and Xception on the Kvasir dataset to classify eight categories that include an anatomical landmark (pylorus, z-line, cecum), a diseased state (esophagitis, ulcerative colitis, polyps), or a medical procedure (dyed lifted polyps, dyed resection margins) in the Gastrointestinal Tract. Our models have showed results with a promising accuracy which is a remarkable performance with respect to the state-of-the-art approaches. The resulting accuracies achieved using VGG, ResNet, MobileNet, Inception-v3, and Xception were 98.3%, 92.3%, 97.6%, 90% and 98.2%, respectively. As it appears, the most accurate result has been achieved when retraining VGG16 and Xception neural networks with accuracy reache to 98% due to its high performance on training on ImageNet dataset and internal structure that support classification problems. (shrink)

Health Level 7 (HL7) is an international standards development organisation in the domain of healthcare information technology. Initially the mission of HL7 was to enable data exchange via the creation of syntactic standards which supported point-to-point messaging. Currently HL7 sees its mission as one of creating standards for semantic interoperability in healthcare IT on the basis of its flagship “version 3” (v3). Unfortunately, v3 has been plagued by quality and consistency issues, and it has not been able to keep pace (...) with recent developments either in semantics and ontology or in computer science and engineering. HL7’s response has been to develop its “Services-Aware Interoperability Framework” (SAIF), which is intended to provide a foundation for work on all aspects of standardization in HL7 henceforth. We here summarise the major design principles that must be satisfied by a semantic interoperability framework – principles relating both to static semantics and to computational behaviour. We then assess the SAIF in light of these principles. We conclude that the SAIF is not in a position to support the needed reform of the HL7 v3 family of standards. (shrink)

When humanism is thought, especially within the borders of 20th century philosophy, one of the things that first comes to mind is the statements which have occurred in 1950s between Martin Heidegger and Jean-Paul Sartre, can be named as Heidegger-Sartre Controversy on Humanism and mainly based on two texts. Sartre, in one of his speeches, builds an essential connection between humanism and existentialism and in here he defines Heidegger as an existentialist like himself. In return, Heidegger, probably as a criticism (...) to Sartre's attribution to him, told about his thoughts on humanism within the expanded version of one of his earlier letters. By this controversy the context and content humanism had been expanded, the understanding of humanism is deepened. The aim of this article is to manifest if there are some things that the controversy between Heidegger and Sartre could contribute to the terms -as a problematic humanism has nowadays- like post-humanism, trans-humanism, meta-humanism, super-humanism, alter-humanism whose terminological meanings aren't quite well-defined. It is to investigate if there are any solutions that humanism -which is being shaped again and obtaining new contexts through these terms- could gain by this controversy against this current terminology problem. (shrink)

In here, philosophical-literate thinking on the way is mainly tried. On one side, making a philosophical analysis of Heraclitus’ fragment 60 is aimed. The different views on what Heraclitus might have meant in this article which is generally translated as the way up and the way down are one and the same are examined. On the other side, with a reading of Robert Frost’s famous poem of Road Not Taken, it has been tried whether a phenomenological interpretation of the way (...) based on passenger is possible or not. It has been researched if there is a common ground or not where this fragment and poem -which exhibit two different views on the way- have met each other. This fragment and poem has been linked together on the context of essentiality of the passenger for the way. (shrink)

In this work, it has been mainly aimed to make a research on origin, meaning and context of two terms [Apophasis and Aphairesis]. These two terms which have an important place within the negative theology that has been thought explicitly appeared first with Pseudo-Dionysos Areopagita –but if required, it can be started in Plotinus, Aristotle, Plato or Parmenides– in history of philosophy [terms which also have been a subject to a misunderstanding, to a problem due to their being understood as (...) synonymous with each other], are tried to be traced back within Greek thinking, culture and especially in Aristotle. With putting forth which sense and context these two terms were used and understood in Aristotle, the meaning and context changes these two terms had historically have been tried to be revealed. (shrink)

The article which is presented here includes an analysis of concept of “care” which mostly has found itself a place in history of philosophy in different forms. Even though thinkers who gave a place to this concept in their works, the main interest is about what Herder and Heidegger said. It has been tried to show how concept of “care” is understood throughout the history of philosophy. Lastly, it has been tried if there is a possible and genuine interpretation.

In this text presented here, it has been tried to Show the difference between Heidegger’s first and second era understanding of language. In his first era, to manifest Heidegger’s understanding of language, outlines of Being and Time has been discussed and concerned chapter is read carefully. To manifest his understanding of language in second era, the work of On the Way to the Language has been taken as a base. With this comparative study, it has been tried to shown the (...) change that “language” has undergone in Heidegger philosophy. (shrink)

In this article, it has been searched if the language and consciousness have a co-origin or not. This origin of language and consciousness problem which draws interest in areas especially like anthropology, biology and evolutionary linguistics and evolutionary psychology is tried to be handled from a philosophical point of view. By presenting the theories about the relation between language and consciousness, theories that are well-accepted but contradicted to another from certain aspects, a thinking -which tries to go beyond this contradiction- (...) about the origin of language and consciousness has been attempted. With paying regard to different approaches represented by names like Piaget, Vygotsky, Chomsky, Whorf, an investigation has been made about what the meaning of language and consciousness having a not historical but elementarily philosophical co-origin can mean. It has been aimed to present a compiling point of view with this investigation. (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 this article, the difference between human and animal in philosophy is mainly handled. This difference is thought over the concept of “the other” and Heidegger’s phenomenological distinction between human and animal. With respect to especially the views of Derrida and Levinas regarding to this matter, it has been attempted to exhibit this difference. Therefore, the two approaches -which were represented as the opposition of Derrida and Levinas- have been tried to clarify. After this, as a new approach to this (...) opposition, the concept of “embrace” is philosophically problematized. This examination which also can be read under the main heading of philosophy of body makes especially the dorsal and more generally the whole back surface of human body subject matter of philosophical interpretation. The concepts of dorsal and embracing which can also be considered from the angle of phenomenology of the body- are approached from evolutionary and psychologically. With this, the concept of embracing deepens the thought of being-together-with-others in a specific context. A special relation is constructed between the meaning that is giving to embracing and rubbing of the back and existing. (shrink)

This article mainly aims to make an examination over the holy. It has been inquired into how something being ascribed holy can have a meaning in philosophy. As the article's research area, the differences in both opinion and execution which have later divided Christianity into two as Catholic and Orthodox Churches have been selected. The separation of these two churches under the subject titles such as Filioque controversy, the idea of First Among Equals (primas inter pares), and ritual of Transubstantiation (...) have also shaped how they perceived and thought the holy. With these divergences being investigated, it has been tried to present how much of a share these had in giving meaning for the holy. It has been labored to manifest the role of these two Churches' -which belong to and come from the same celestial tradition- divergences in the metamorphosis and paradigm shift that the holy underwent. For the last, through the Church Fathers' opinions and views which have been seen related to subject matter, with moving beyond the divergences, it has been searched whether there is a possibility of meeting on the common ground or not . (shrink)

In this article, it has been aimed to examine Nietzsche’s main critique towards different understandings of morals in his era. With this criticism, it is aimed to integrally understand the opinions -which are articulated directly or metaphorically- towards morals which have been encountered. In here, while keeping in mind the difference between the concepts of immoralism and amoralism, Nietzsche’s views are interpreted. Being parallel to that aim mentioned above, it has been investigated if there is a thinking in Nietzsche which (...) can be seen as a kind of understanding of morals (maybe as the understanding of morals without morals) or not. And finally, it has been thought that if Nietzsche’s views on morals have any value for the 21st century and upcoming 22nd century human or not, whether there’s something left to learn for this human from his critiques or not. (shrink)

In this article, some theories about evolutionary progress of human mind are examined and criticised. Through a comparative reading of these theories -which are sometimes contradictory to each other- it has been tried to present the common missing parts of these theories. The meaning of these theories for philosophy has been thought and the presupposition of linearity in these theories is criticised. The relation of the concept of emotion with the terms like cognition, apprehension, comprehension, intellect, self-awareness, consciousness -which stand (...) forward within these theories- is emphasized. Through the visual cliff experiment, it has been attempted to clarify this relation. (shrink)

When discussing the safety of research subjects, including their exploitation and vulnerability as well as failures in clinical research, recent commentators have focused mostly on countries with low or middle-income economies. High-income countries are seen as relatively safe and well-regulated. This article presents irregularities in clinical trials in an EU member state, Poland, which were revealed by the Supreme Audit Office of Poland (the NIK). Despite adopting many European Union regulations, including European Commission directives concerning Good Clinical Practice, these irregularities (...) occurred. Causes as well as potential solutions to make clinical trials more ethical and safer are discussed. (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)

Review of: Sophia Roosth, Synthetic: How Life Got Made (University of Chicago Press, 2017); and Andrew S. Balmer, Katie Bulpin, and Susan Molyneux-Hodgson, Synthetic Biology: A Sociology of Changing Practices (Palgrave Macmillan, 2016).

According to a prevailing view, conceptual engineering introduces a revolutionary philosophical methodology, challenging traditional conceptual analysis. However, in our paper, we argue that closer scrutiny reveals not only the falsity but also the inherent ambiguity of this narrative. We explore four interpretations of the "Anti-Novelty Claim", the claim that conceptual engineering is not a new way of doing philosophy. Discussing the Anti-Novelty Claim from the perspective of a text’s producer, the text’s consumers, and the exegetical potential of the (...) text, we examine each perspective’s metaphilosophical implications and demonstrate that taking each perspective requires different methods. Adopting these different methods, we argue that the different interpretations of the Anti-Novelty Claim range from nearly trivially true to unlikely but untested. Importantly, we emphasize that each interpretation offers unique philosophical insights, yet addressing them requires diverse types of evidence, preventing a singular, straightforward answer to whether conceptual engineering is new. (shrink)