As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to extend (...) or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (shrink)

This collection of essays on themes in the work of John Locke , George Berkeley , and David Hume , provides a deepened understanding of major issues raised in the Empiricist tradition. In exploring their shared belief in the experiential nature of mental constructs, The Empiricists illuminates the different methodologies of these great Enlightenment philosophers and introduces students to important metaphysical and epistemological issues including the theory of ideas, personal identity, and skepticism. It will be especially useful in courses devoted (...) to the history of modern philosophy. (shrink)

The Matrix exposes us to the uncomfortable worries of philosophical skepticism in an especially compelling way. However, with a bit more reflection, we can see why we need not share the skeptic’s doubts about the existence of the world. Such doubts are appropriate only in the very special context of the philosophical seminar. When we return to normal life we see immediately that they are groundless. Furthermore, we see also the drastic mistake that Cypher commits in turning his back upon (...) reality and re-entering the matrix. Not only does reason compel us to admit the existence of the external world, it also requires us to face this world, to build for ourselves meaningful lives within it, and to engage, as adults, in the serious business of living. (shrink)

Embryogenesis requires the precise movement and reorganization of many cell and tissue types. Presumably, cell surface receptors allow cells to interact selectively with adjacent cells and with the extracellular environment, as well as initiate differentiative events by transducing appropriate signals across the plasma membrane. One cell surface component that serves as a receptor during a variety of cellular interactions is β1,4‐galactosyltransferase. Cell surface galactosyltransferase participates in diverse cellular interactions by binding its specific glycoconjugate substrate on adjacent cell surfaces or in (...) the extracellular matrix. Biochemical, immunological, and molecular probes are being used to better define cell surface galactosyl‐transferase functional in cellular interactions during fertilization, intercellular adhesion, cell migration, and growth control. (shrink)

The dynamics of knowledge transmission and acquisition, or how different aspects of culture are passed from one individual to another and how they are acquired and embodied by individuals, are central to understanding cultural evolution. In small-scale societies, cultural knowledge is largely acquired early in life through observation, imitation, and other forms of social learning embedded in daily experiences. However, little is known about the pathways through which such knowledge is transmitted, especially during middle childhood and adolescence. This study presents (...) new empirical data on cultural knowledge transmission during childhood. Data were collected among the Baka, a forager-farmer society in southeastern Cameroon. We conducted structured interviews with children between 5 and 16 years of age about group composition during subsistence activities. Children’s groups were generally diverse, although children tended to perform subsistence activities primarily without adults and with same-sex companions. Group composition varied from one subsistence activity to another, which suggests that the flow of knowledge might also vary according to the activity performed. Analysis of the social composition of children’s subsistence groups shows that vertical and oblique transmission of subsistence-related knowledge might not be predominant during middle childhood and adolescence. Rather, horizontal transmission appears to be the most common knowledge transmission strategy used by Baka children during middle childhood and adolescence, highlighting the importance of other children in the transmission of knowledge. (shrink)

Introduction of O2 to Earth's early biosphere stimulated remarkable evolutionary adaptations, and a wide range of electron acceptors allowed diverse, energy-yielding metabolic pathways. Enzymatic reduction of O2 yielded a several-fold increase in energy production, enabling evolution of multi-cellular animal life. However, utilization of O2 also presented major challenges as O2 and many of its derived reactive oxygen species are highly toxic, possibly impeding multicellular evolution after the Great Oxidation Event. Remarkably, ROS, and especially hydrogen peroxide, seem to play a major (...) part in early diversification and further development of cellular respiration and other oxygenic pathways, thus becoming an intricate part of evolution of complex life. Hence, although harnessing of chemical and thermo-dynamic properties of O2 for aerobic metabolism is generally considered to be an evolutionary milestone, the ability to use ROS for cell signaling and regulation may have been the first true breakthrough in development of complex life. The importance of Earth's oxygen cycle and reactive oxygen species produced on the evolution of complex life. The ability to detoxify oxygen species is not a trait that emerged as a response to increased O2 levels but rather crucial adaptation to the early Earth's weakly oxic microenvironments. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, we aim to move beyond the level (...) of controlled vocabularies to yield an ontology with the ability to support reasoning applications. (shrink)

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

When the COVID-19 surge hit New York City hospitals, the Division of Medical Ethics at Weill Cornell Medical College, and our affiliated ethics consultation services, faced waves of ethical issues sweeping forward with intensity and urgency. In this article, we describe our experience over an eight-week period (16 March through 10 May 2020), and describe three types of services: clinical ethics consultation (CEC); service practice communications/interventions (SPCI); and organizational ethics advisement (OEA). We tell this narrative through the prism of time, (...) describing the evolution of ethical issues and trends as the pandemic unfolded. We delineate three phases: anticipation and preparation, crisis management, and reflection and adjustment. The first phase focused predominantly on ways to address impending resource shortages and to plan for remote ethics consultation, and CECs focused on code status discussions with surrogates. The second phase was characterized by the dramatic convergence of a rapid increase in the number of critically ill patients, a growing scarcity of resources, and the reassignment/ redeployment of staff outside their specialty areas. The third phase was characterized by the recognition that while the worst of the crisis was waning, its medium- and long-term consequences continued to pose immense challenges. We note that there were times during the crisis that serving in the role of clinical ethics consultant created a sense of dis-ease as novel as the coronavirus itself. In retrospect we learned that our activities far exceeded the familiar terrain of clinical ethics consultation and extended into other spheres of organizational life in novel ways that were unanticipated before this pandemic. To that end, we defined and categorized a middle level of ethics consultation, which we have termed service practice communication intervention (SPCI). This is an underappreciated dimension of the work that ethics consult services are capable of in times of crisis. We believe that the pandemic has revealed the many enduring ways that ethics consultation services can more robustly contribute to the ethical life of their institutions moving forward. (shrink)

Consent remains a crucial, yet challenging, cornerstone of clinical practice. The ethical, legal and professional understandings of this construct have evolved away from a doctor-centred act to a patient-centred process that encompasses the patient’s values, beliefs and goals. This alignment of consent with the philosophy of shared decision-making was affirmed in a recent high-profile Supreme Court ruling in England. The communication of information is central to this model of health care delivery but it can be difficult for doctors to gauge (...) the information needs of the individual patient. The aim of this paper is to describe ‘core information sets’ which are defined as a minimum set of consensus-derived information about a given procedure to be discussed with all patients. Importantly, they are intended to catalyse discussion of subjective importance to individuals. The model described in this paper applies health services research and Delphi consensus-building methods to an idea orginally proposed 30 years ago. The hypothesis is that, first, large amounts of potentially-important information are distilled down to discrete information domains. These are then, secondly, rated by key stakeholders in multiple iterations, so that core information of agreed importance can be defined. We argue that this scientific approach is key to identifying information important to all stakeholders, which may otherwise be communicated poorly or omitted from discussions entirely. Our methods apply systematic review, qualitative, survey and consensus-building techniques to define this ‘core information’. We propose that such information addresses the ‘reasonable patient’ standard for information disclosure but, more importantly, can serve as a spring board for high-value discussion of importance to the individual patient. The application of established research methods can define information of core importance to informed consent. Further work will establish how best to incorporate this model in routine practice. (shrink)

In an effort to explain the Yoruba concept of "emi" or self, an elder uses the metaphor of a house with many tenants--such as memory and imagination, and then says the 'key' to accessing them is self-consciousness. A consideration of impressive contextual dexterity.

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

A series of papers on different aspects of practical knowledge by Roderick Chisholm, Rudolf Haller, J. C. Nyiri, Eva Picardi, Joachim Schulte Roger Scruton, Barry Smith and Johan Wrede.

Several lines of evidence have underscored the remarkable neuroplasticity of the primate sensorimotor cortex, characterizing these cortical areas as dynamic constructs that are modelled in a use-dependent manner by behaviourally significant experiences. Their plasticity likely provides a neural substrate that may contribute to the dynamic systems paradigm argued by Shanker & King (S&K) as crucial for development of communication skills.

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...) life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from The Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. (shrink)

Objectives“Attachment difficulties” is an umbrella term often used to describe various forms of non-secure attachment. Differentiating “attachment difficulties” from autism spectrum disorder and attention deficit hyperactivity disorder has been characterized as challenging. Few studies have explored how this happens in practice, from the perspective of professionals.DesignQualitative study.MethodsWe conducted in-depth semi-structured interviews with healthcare professionals from five NHS Foundation Trusts in the United Kingdom. Participants were recruited using a combination of snowballing, convenience and purposive sampling. Data were analyzed using a thematic (...) approach.ResultsWe identified six interrelated themes that might reflect difficulties with differential conceptualization. These include: a clinical lexicon of attachment; approaching attachment with caution; contextual factors; perceived characteristic behaviors; assessing attachment and adjacent supports; spotlighting intervention and dual conceptualization.ConclusionOur results indicate some of the ways suspicions around attachment are raised in practice. We advocate for more dialogue between research and practice communities on issues of differential conceptualization. We call for collaboration between a panel of experts consisting of attachment and neurodevelopmental orientated practitioners and researchers, to clarify issues around differentiating between attachment difficulties, ASD, and ADHD. (shrink)

Screening for prostate cancer with the prostate-specific antigen blood test is controversial, as evidence to date has not demonstrated such screening does more good than harm. While the potential benefit of PSA screening on reducing prostate cancer mortality has not been documented in randomized trials, many risks of PSA screening have been well documented. These risks include a substantially higher risk of a prostate cancer diagnosis over a screenee’s lifetime, false-positive and false-negative test results, possible complications from biopsies done in (...) response to suspicious test results, and substantial risks of side effects from subsequent prostate cancer treatments. Nevertheless, PSA screening is widespread in the United States, and many physicians in a national survey reported supporting routine PSA screening as well as getting PSA tests themselves, despite the lack of evidence. (shrink)

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

Basic Formal Ontology (BFO) is a top-level ontology used in hundreds of active projects in scientific and other domains. BFO has been selected to serve as top-level ontology in the Industrial Ontologies Foundry (IOF), an initiative to create a suite of ontologies to support digital manufacturing on the part of representatives from a number of branches of the advanced manufacturing industries. We here present a first draft set of axioms and definitions of an IOF upper ontology descending from BFO. The (...) axiomatization is designed to capture the meanings of terms commonly used in manufacturing and is designed to serve as starting point for the construction of the IOF ontology suite. (shrink)

The Matrix exposes us to the uncomfortable worries of philosophical skepticism in an especially compelling way. However, with a bit more reflection, we can see why we need not share the skeptic’s doubts about the existence of the world. Such doubts are appropriate only in the very special context of the philosophical seminar. When we return to normal life we see immediately that they are groundless. Furthermore, we see also the drastic mistake that Cypher commits in turning his back upon (...) reality and re-entering the matrix. Not only does reason compel us to admit the existence of the external world, it also requires us to face this world, to build for ourselves meaningful lives within it, and to engage, as adults, in the serious business of living. (shrink)

In the developing world, the dramatic male bias in tobacco use is usually ascribed to pronounced gender disparities in social, political, or economic power. This bias might also reflect under-reporting by woman and/or over-reporting by men. To test the role of gender inequality on gender differences in tobacco use we investigated tobacco use among the Aka, a Congo Basin foraging population noted for its exceptionally high degree of gender equality. We also tested a sexual selection hypothesis—that Aka men’s tobacco use (...) is related to risk taking. Tobacco use, income, tobacco purchases, tobacco sharing, reasons for using tobacco, risk taking, and other variables were measured using structured surveys and peer reports. Tobacco use was verified by testing for salivary cotinine, a nicotine metabolite. Contrary to expectations, we found a very large male bias in tobacco use. Low levels of use among females appeared to be explained by aversions to tobacco, concerns over its negative effects on fetal health, and a desire to attract husbands, who prefer nonsmoking wives. High male use appeared to be related to a desire to enhance hunting abilities and attract and/or retain wives, who prefer husbands that smoke. We conclude that low levels of smoking by Aka women are better explained by the hypothesis that women evolved to avoid plant toxins to protect their fetuses and nursing infants. High male use might be better explained by sexual selection. We also highlight the important role that recreational drugs appear to play in hunter-gatherer sharing relationships. (shrink)

In this paper I wish to propose and defend a form of the Representative Theory of Perception. According to this version of the theory, when a subject perceives some object x to be in a state P1 he does so by being aware of some modfication M1 of some object E. The subject's way of perceiving any one of a range of objects x,y,z, … is that of being aware of some modification of E. It will be a necessary condition (...) of someone's perceiving x to have property P1 that E be modified in some way. And in order for the modifications of E to be representations, a given property P1 will need to be causally related, characteristically, to one or more specific modifications, M1,M2, … Mn, of E. symbolized by ‘X'.). (shrink)

The chief sources of groundwater contamination on farms come from point sources and diffuse sources. Possible point sources are feedlots, poorly-sited manure piles, septic sewage-treatment systems—all of which can release nitrate, phosphates and bacteria— and sites of chemical spills. Diffuse sources are typified by excess fertilizer leaching from a number of arable fields. The basis of quality standards for drinking-water is discussed in relation to common contaminants present on farms. Samples of drinking-water were collected in 1991–1992 from wells on about (...) 1,200 farms in order to study the quality of rural groundwater in Ontario. Analysis showed that approximately one third of wells were contaminated with bacteria, 14% were contaminated with nitrate, two wells were contaminated with pesticide, but 40% were considered unsafe because of the presence of at least one contaminant. These values were similar to those reported for similar regions in the U.S. There was no significant effect of agricultural practice on the proportion of contaminated samples. One response of Ontario's farmers to information on water quality has been to initiate their own program, the Environmental Farm Plan, which has 23 modules by which the risk of environmental contamination can be assessed. Government policies for agriculture can be expected to influence farming practices. However, the literature suggests that the consequences of policies aimed at reducing environmental contamination are poorly understood, not least because the instruments used for implementation can have widely differing impacts. The need for discussions on the ethics surrounding the relationship between food producers and consumers with regard to environmental contamination is identified. (shrink)

Understanding spoken words involves a rapid mapping from speech to conceptual representations. One distributed feature-based conceptual account assumes that the statistical characteristics of concepts’ features—the number of concepts they occur in and likelihood of co-occurrence —determine conceptual activation. To test these claims, we investigated the role of distinctiveness/sharedness and correlational strength in speech-to-meaning mapping, using a lexical decision task and computational simulations. Responses were faster for concepts with higher sharedness, suggesting that shared features are facilitatory in tasks like lexical decision (...) that require access to them. Correlational strength facilitated responses for slower participants, suggesting a time-sensitive co-occurrence-driven settling mechanism. The computational simulation showed similar effects, with early effects of shared features and later effects of correlational strength. These results support a general-to-specific account of conceptual processing, whereby early activation of shared features is followed by the gradual emergence of a specific target representation. (shrink)

ABSTRACTDifficulties with inhibiting fear have been associated with the emergence of anxiety problems and poor response to cognitive–behavioural treatment. Fear inhibition problems measured using experimental paradigms involving aversive stimuli may be inappropriate for vulnerable samples and may not capture fear inhibition problems evident in everyday life. We present the Fear Inhibition Questionnaire, a self-report measure of fear inhibition abilities. We assess the FIQ’s factor structure across two cultures and how well it correlates with fear inhibition indices derived experimentally. Adolescent participants (...) from Hong Kong and England completed the FIQ, with the English participants also completing a conditioning and extinction task to assess fear inhibition problems. Across both cultures, the FIQ showed a single factor structure and low FIQ scores, or worse fear inhibition problems, were associated with self-reports of heightened anxiety. Correlation of FIQ scores with experimental indices, whi... (shrink)

Thomas' theory of sin is a specification of his general theory of metaphysical evil. Both his theory of evil in general and his theory of moral evil specifically provide an understanding that constitutes a scientia, for both theories consist of an explanation of the four causes of evil. As a contrary of good, evil can be explained by means of its causes, for the scientia of good includes the understanding of the contrary of good. Thus sin can be understood precisely (...) as it is opposed to the good proper to rational creatures. ;The fact that Thomas's theory of evil consists of an explanation of its four causes is most evident in his Disputed Questions De malo. Thomas' explanation of moral evil parallels his explanation of metaphysical evil, as it demonstrates the four causes of sin in a similar fashion. Further, Thomas' theory of metaphysical evil provides the foundation for his explanation of moral evil; thus Thomas will apply the principles established concerning evil in general to the particular difficulties that arise in regard to the evil found in the rational creature. ;In his general theory of evil, Thomas determined that evil itself was not a thing, for there is no form or end proper to an evil nature. Evil can be understood according to the form that it opposes, and it is only found in some subject that properly possesses that form. Something that acts according to its end as a final cause may be the efficient cause of evil, either deficiently as it or the matter it acts upon is deficient, or as the good it acts for is accidentally an evil to another. The particular good that the efficient cause of evil intends or acts for, then, is a particular good that is in some way contrary to the particular good of some creature. In the case of sin, the will is the efficient cause of evil, as it intends something good, but there is some evil joined to it either accidentally or through its deficiency. Moral evil, then, is known by way of these causes. (shrink)