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

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

There are two opposing views concerning intuitive cases of wage exploitation. The first denies that they are cases of exploitation at all. It is based on the nonworseness claim: there is nothing wrong with a discretionary mutually beneficial employment relationship. The second is the reasonable view: some employment relationships can be exploitative even if employers have no duty towards their employees. This article argues that the reasonable view does not completely defeat defences of wage exploitation, because these do not rely (...) solely on the nonworseness claim. They also rely on the idea, popularised by Alan Wertheimer, that exploitation is a form of disequilibrium price occurring in defective markets. The article then proceeds to criticise Wertheimer’s account through neoclassical, new institutional, and Austrian economics. It concludes that considerations for economic efficiency are irrelevant to assessing intuitions regarding exploitation. (shrink)

In 1949, the Department of Philosophy at the University of Manchester organized a symposium “Mind and Machine” with Michael Polanyi, the mathematicians Alan Turing and Max Newman, the neurologists Geoff rey Jeff erson and J. Z. Young, and others as participants. Th is event is known among Turing scholars, because it laid the seed for Turing’s famous paper on “Computing Machinery and Intelligence”, but it is scarcely documented. Here, the transcript of this event, together with Polanyi’s original statement and (...) his notes taken at a lecture by Jeff erson, are edited and commented for the fi rst time. Th e originals are in the Regenstein Library of the University of Chicago. Th e introduction highlights elements of the debate that included neurophysiology, mathematics, the mind-body-machine problem, and consciousness and shows that Turing’s approach, as documented here, does not lend itself to reductionism. (shrink)

Saul Kripke once noted that there is a tight connection between computation and de re knowledge of whatever the computation acts upon. For example, the Euclidean algorithm can produce knowledge of which number is the greatest common divisor of two numbers. Arguably, algorithms operate directly on syntactic items, such as strings, and on numbers and the like only via how the numbers are represented. So we broach matters of notation. The purpose of this article is to explore the relationship between (...) the notations acceptable for computation, the usual idealizations involved in theories of computability, flowing from Alan Turing’s monumental work, and de re propositional attitudes toward numbers and other mathematical objects. (shrink)

To justify inductive inference and vanquish classical skepticisms about human memory, external world realism, etc., Richard Fumerton proposes his “inferential internalism,” an epistemology whereby humans ‘see’ by Russellian acquaintance Keynesian probable relations (PRs) between propositions. PRs are a priori necessary relations of logical probability, akin to but not reducible to logical entailments, such that perceiving a PR between one’s evidence E and proposition P of unknown truth value justifies rational belief in P to an objective degree. A recent critic of (...) inferential internalism is Alan Rhoda, who questions its psychological plausibility. Rhoda argues that in order to see necessary relations between propositions E and P, one would need acquaintance with too many propositions at once, since our evidence E is often complex. In this paper, I criticize Rhoda’s implausibility objection as too quick. Referencing the causal status effect (CSE) from psychology, I argue that some of the complex features of evidence E contribute to our type-categorizing it as E-type, and thus we do not need to ‘see’ all of the complex features when we see the PR between E and P. My argument leaves unchanged Fumerton’s justificatory role for the PR, but enhances its psychological plausibility. (shrink)

Bu makalede, bilim felsefecisi kimliğiyle tanınan Thomas Kuhn’un eğitim ve özellikle fen eğitimi alanındaki görüşlerine değinilmektedir. Fen eğitimi, bilim, bilimin doğası ve bilim uygulamaları hakkında düşünceler geliştirmeye odaklanarak fen öğrenimi için gerekli olan beceri ve anlayışın geliştirilmesini amaçlamaktadır. Fen eğitiminin temel amaçlarından biri bilimin gerçek doğasının tespit edilmesi ve bu doğrultuda bir eğitim modelinin belirlenmesidir. Bu çerçevede Kuhn’un bilim tarihine yönelik incelemeleri neticesinde ileri sürdüğü paradigma kavramı bilimin doğası ve fen eğitimi konusundaki görüşlerin değişimine yol açmıştır. Kuhn açısından fen eğitimi (...) yürürlükteki bilim yapma tarzının temelinde yatan paradigma ve öğretilerinin bilim insanlarına ve öğrencilere aktarılması sürecidir, bu nedenle fen eğitimi yalnızca olağan bilim döneminde mümkündür. Kuhn’un eğitim modeli, mevcut paradigmayla ilişkili olarak karşılaşılan bulmaca ya da sorunları çeşitli örneklerden hareketle tekrar tekrar çözmeye çalışan öğrenciler aracılığıyla gerçekleştirilir. Kuhn’un olağan bilimin sınırları içerisinde kalarak değerlendirdiği fen eğitimi anlayışı eleştirel düşünceyi engellediği iddiasıyla Karl Popper, John Watkins ve Richard Bailey tarafından katı, tutucu, dogmatik ve endoktrinasyonu vurgulayan bir eğitim anlayışı olarak görülmektedir. Bu çerçevede makalede, öncelikli olarak Kuhn’un bilimin doğası ve bilimin gelişim tarzına yönelik belirlemeleri doğrultusunda fen eğitimine yönelik düşünceleri ve bu düşüncelerin eğitim alanındaki yansımaları incelenmektedir. Ardından, Kuhn’un fen eğitimi üzerine görüşlerinin iddia edildiği gibi dogmatik bir yapıda olmadığı, endoktrinasyonu ya da zorla öğretimi vurgulamadığı, bu tür yorumların radikal bir yaklaşımdan öteye gidemediği ileri sürülmektedir. Son olarak makalede, Kuhn’un fen eğitimi anlayışının yalnızca bir durum tespiti ya da bir fen eğitimi tasviri olarak değerlendirilmesi gerektiği düşüncesi ön plana çıkarılmaktadır. -/- In this article, Thomas Kuhn’s impact, who is known as a philosopher of science, on science education are mentioned. Science education aims to develop the skills and understanding necessary for science learning, with a focus on developing ideas about science and the nature of science. One of the main purposes of science education is to determine the true nature of science and to determine an education model in this direction. In this context, the concept of paradigm, which Kuhn put forward as a result of his studies on the history of science, has led to a change in views on the nature of science and science education. For Kuhn, science education is the process of conveying the paradigm underlying the current way of doing science to scientists and students because science education is possible only in the normal science period. Kuhn’s educational model is carried out through students who repeatedly try to solve puzzles or problems encountered in relation to the current paradigm. Kuhn’s understanding of science education is seen by Karl Popper, John Watkins and Richard Bailey as a rigid, conservative, dogmatic and indoctrinational education approach with the claim that it prevents critical thinking. In this context, the article primarily examines Kuhn’s thoughts on science education and the reflections of these thoughts in the field of education. Then, it is argued that Kuhn’s views on science education are not dogmatic as claimed, he does not emphasize indoctrination, and that such interpretations cannot go beyond a radical approach. Finally, in the article, it is emphasized that Kuhn’s understanding of science education should be evaluated only as a description of science education. (shrink)

In 1951 John Rawls expressed these convictions about the fundamental issues in metaethics: [T]he objectivity or the subjectivity of moral knowledge turns, not on the question whether ideal value entities exist or whether moral judgments are caused by emotions or whether there is a variety of moral codes the world over, but simply on the question: does there exist a reasonable method for validating and invalidating given or proposed moral rules and those decisions made on the basis of them? For (...) to say of scientific knowledge that it is objective is to say that the propositions expressed therein may be evidenced to be true by a reasonable and reliable method, that is, by the rules and procedures of what we may call "inductive logic"; and, similarly, to establish the objectivity of moral rules, and the decisions based upon them, we must exhibit the decision procedure, which can be shown to be both reasonable and reliable, at least in some cases, for deciding between moral rules and lines of conduct consequent to them.1 In this passage Rawls reconfigured the issue of moral objectivity and so reoriented the practice of metaethics from linguistic analysis to rational methodology. In so doing, his work has provided inspiration to philosophers as disparate in normative views as Thomas Nagel,2 Richard Brandt3, Alan Gewirth4, and David Gauthier.5 Rawls replaced the Moorean question, Do moral terms refer? with the Rawlsian question, Can moral judgments be the outcome of a rational and reliable procedure? He later gave a resoundingly positive answer to this question6 and later still, a more tentative one.7 Rawls' considered qualification of his earlier enthusiasm about the extent to which moral philosophy could be "part of the theory of rational choice"8 is a tribute to the seriousness with which he took his critics' objections. (shrink)

Several scholars, including Martin Hengel, R. Alan Culpepper, and Richard Bauckham, have argued that Papias had knowledge of the Gospel of John on the grounds that Papias’s prologue lists six of Jesus’s disciples in the same order that they are named in the Gospel of John: Andrew, Peter, Philip, Thomas, James, and John. In “A Note on Papias’s Knowledge of the Fourth Gospel” (JBL 129 [2010]: 793–794), Jake H. O’Connell presents a statistical analysis of this argument, according to which (...) the probability of this correspondence occurring by chance is lower than 1%. O’Connell concludes that it is more than 99% probable that this correspondence is the result of Papias copying John, rather than chance. I show that O’Connell’s analysis contains multiple mistakes, both substantive and mathematical: it ignores relevant evidence, overstates the correspondence between John and Papias, wrongly assumes that if Papias did not know John he ordered the disciples randomly, and conflates the probability of A given B with the probability of B given A. In discussing these errors, I aim to inform both Johannine scholarship and the use of probabilistic methods in historical reasoning. (shrink)

Using artificial intelligence (AI) to make decisions in human resource management (HRM) raises questions of how fair employees perceive these decisions to be and whether they experience respectful treatment (i.e., interactional justice). In this experimental survey study with open-ended qualitative questions, we examine decision making in six HRM functions and manipulate the decision maker (AI or human) and decision valence (positive or negative) to determine their impact on individuals’ experiences of interactional justice, trust, dehumanization, and perceptions of decision-maker role appropriate- (...) ness. In terms of decision makers, the use of human decision makers over AIs generally resulted in better perceptions of respectful treatment. In terms of decision valence, people experiencing positive over negative decisions generally resulted in better perceptions of respectful treatment. In instances where these cases conflict, on some indicators people preferred positive AI decisions over negative human decisions. Qualitative responses show how people identify justice concerns with both AI and human decision making. We outline implications for theory, practice, and future research. (shrink)

In this essay, I look at some extraordinary actors who never got their due—actors who had distinguished careers, but never won an Academy Award for acting. I review the work of: Joseph Cotten; Orson Welles; Edward G. Robinson; Cary Grant; James Mason; Richard Burton; Claude Rains; Alan Ladd: Robert Mitchum; and Fred MacMurray. In each case, I explore the actor’s best work, what made his acting outstanding, and offer possible explanations why he was not so honored.

This out-of-print collection in the area of the history, politics, ethics, and theory of privacy includes selections from Peter Gay, Alan Westin, Walter Benjamin, Catharine MacKinnon, Seyla Benhabib, Anita Allen, Ann Jennings, Charles Taylor, Richard Sennett, Mark Wicclair, Martha Nussbaum, and Robert Nozick.

Is the societal-level of analysis sufficient today to understand the values of those in the global workforce? Or are individual-level analyses more appropriate for assessing the influence of values on ethical behaviors across country workforces? Using multi-level analyses for a 48-society sample, we test the utility of both the societal-level and individual-level dimensions of collectivism and individualism values for predicting ethical behaviors of business professionals. Our values-based behavioral analysis indicates that values at the individual-level make a more significant contribution to (...) explaining variance in ethical behaviors than do values at the societal-level. Implicitly, our findings question the soundness of using societal-level values measures. Implications for international business research are discussed. (shrink)

Forms of Artificial Intelligence (AI) are already being deployed into clinical settings and research into its future healthcare uses is accelerating. Despite this trajectory, more research is needed regarding the impacts on patients of increasing AI decision making. In particular, the impersonal nature of AI means that its deployment in highly sensitive contexts-of-use, such as in healthcare, raises issues associated with patients’ perceptions of (un) dignified treatment. We explore this issue through an experimental vignette study comparing individuals’ perceptions of being (...) treated in a dignified and respectful way in various healthcare decision contexts. Participants were subject to a 2 (human or AI decision maker) x 2 (positive or negative decision outcome) x 2 (diagnostic or resource allocation healthcare scenario) factorial design. We found evidence of a “human bias” (i.e., a preference for human over AI decision makers) and an “outcome bias” (i.e., a preference for positive over negative outcomes). However, we found that for perceptions of respectful and dignified interpersonal treatment, it matters more who makes the decisions in diagnostic cases and it matters more what the outcomes are for resource allocation cases. We also found that humans were consistently viewed as appropriate decision makers and AI was viewed as dehumanizing, and that participants perceived they were treated better when subject to diagnostic as opposed to resource allocation decisions. Thematic coding of open-ended text responses supported these results. We also outline the theoretical and practical implications of these findings. (shrink)

This paper reports on an ongoing ARC Discovery Project that is conducting design research into learning in collaborative virtual worlds (CVW).The paper will describe three design components of the project: (a) pedagogical design, (b)technical and graphics design, and (c) learning research design. The perspectives of each design team will be discussed and how the three teams worked together to produce the CVW. The development of productive failure learning activities for the CVW will be discussed and there will be an interactive (...) demonstration of the project's CVW. (shrink)

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

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

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

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

Attention Deficit Hyperactivity Disorder (ADHD) continues to be controversial with arguments for and against its veracity being waged by individuals representing a variety of disciplines from behavioral scientists to philosophers. Our perspective focuses on the epistemological underpinnings of what is now commonly known as ADHD. Its ignominious history and current disputes may stem from a "pessimistic" epistemology, meaning that truth is only the province of persons in authority and power. The authoritative organizations that govern the diagnostic labels and criteria are (...) the American Psychiatric Association and their Diagnostic and Statistical Manual and the World Health Organization that sponsors the International Classification of Disease. We contrast the pessimistic epistemology with criteria for truth from the scientific method. Although scientific scrutiny has been and is being applied subsequent to "authoritarian edicts" of the disorder, we opine that ADHD currently does not have status beyond that of the "hypothetical construct." Moreover, current brain-based causal models have failed to provide rigorous supporting data that comes from testing falsifiable hypotheses. (shrink)

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

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

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

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

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

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

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

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

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

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

We consider the varieties and directions of influence that the source and target domains involved in a conceptual metaphor can have on each other during the course of understanding metaphorical utterances based on the metaphor. Previous studies have been restricted both as to direction of influence and as to type of influence. They have been largely confined to the “forward” (source to target) direction of influence, and they have concentrated on the transfer of features or propositions and (to some extent) (...) the highlighting of aspects of a domain. By contrast, this article stresses the importance both of other varieties of influence (e.g., transfer of queries and uncertainty effects) and of “reverse” influence (target to source). We seek to curb the natural tendency to think that, because metaphor involves an overall move from source to target, therefore all inter-domain influences in the course of understanding go in that direction. The bulk of the article explores the theoretical issues involved. These issues have arisen out of a reasoning-based approach to metaphor, seeking to make best use of information from metaphorical utterance, context, source and target domains, and known metaphorical mappings, by applying a complex overall reasoning process. The article briefly explains the thorough implementation of reverse influence in a computer program for metaphorical reasoning called ATT-Meta, although the theoretical considerations are relevant to all disciplines concerned with metaphor. We make some suggestions for further computational and psychological research on metaphor. (shrink)

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

Letter commenting on the paper Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick, "Ontology and the Future of Dental Research Informatics", Journal of the American Dental Association 141 2010;(10):1173-75 with responses by the authors of the paper.

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...) large amounts of ncRNA biological and clinical data. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...) the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)

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

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...) advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

"We wish this volume to be a sure companion to the study of free will, broadly construed to include action theory, moral and legal responsibility, and cohort studies feathering off into adjacent fields in the liberal arts and sciences. In addition to general coverage of the discipline, this volume attempts a more challenging and complementary accompaniment to many familiar narratives about free will. In order to map out some directions such accompaniment will take, in this introduction we anchor the thirty (...) contributions to this volume in some common history from which they arise, and attempt to indicate where future work in free will and moral responsibility will–and has already begun to–depart from that history." -Excerpt from Introduction. ... ... To read full introduction, (1) download attached file or (2) follow wiley_dot_com link below, click "Read An Excerpt", then click :Excerpt 3:(pdf)". (shrink)

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

I argue that most counterfactuals are false.

Bayesianism is our leading theory of uncertainty. Epistemology is defined as the theory of knowledge. So “Bayesian Epistemology” may sound like an oxymoron. Bayesianism, after all, studies the properties and dynamics of degrees of belief, understood to be probabilities. Traditional epistemology, on the other hand, places the singularly non-probabilistic notion of knowledge at centre stage, and to the extent that it traffics in belief, that notion does not come in degrees. So how can there be a Bayesian epistemology?

So-called “traditional epistemology” and “Bayesian epistemology” share a word, but it may often seem that the enterprises hardly share a subject matter. They differ in their central concepts. They differ in their main concerns. They differ in their main theoretical moves. And they often differ in their methodology. However, in the last decade or so, there have been a number of attempts to build bridges between the two epistemologies. Indeed, many would say that there is just one branch of philosophy (...) here—epistemology. There is a common subject matter after all. In this paper, we begin by playing the role of a “bad cop,” emphasizing many apparent points of disconnection, and even conflict, between the approaches to epistemology. We then switch role, playing a “good cop” who insists that the approaches are engaged in common projects after all. We look at various ways in which the gaps between them have been bridged, and we consider the prospects for bridging them further. We conclude that this is an exciting time for epistemology, as the two traditions can learn, and have started learning, from each other. (shrink)

There have long been calls from industry for guidance in implementing strategies for sustainable development. The Circular Economy represents the most recent attempt to conceptualize the integration of economic activity and environmental wellbeing in a sustainable way. This set of ideas has been adopted by China as the basis of their economic development, escalating the concept in minds of western policymakers and NGOs. This paper traces the conceptualisations and origins of the Circular Economy, tracing its meanings, and exploring its antecedents (...) in economics and ecology, and discusses how the Circular Economy has been operationalized in business and policy. The paper finds that while the Circular Economy places emphasis on the redesign of processes and cycling of materials, which may contribute to more sustainable business models, it also encapsulates tensions and limitations. These include an absence of the social dimension inherent in sustainable development that limits its ethical dimensions, and some unintended consequences. This leads us to propose a revised definition of the Circular Economy as “an economic model wherein planning, resourcing, procurement, production and reprocessing are designed and managed, as both process and output, to maximize ecosystem functioning and human well-being”. (shrink)

Pascal’s Wager involves expected utilities. In this chapter, we examine the Wager in light of two main features of expected utility theory: utilities and probabilities. We discuss infinite and finite utilities, and zero, infinitesimal, extremely low, imprecise, and undefined probabilities. These have all come up in recent literature regarding Pascal’s Wager. We consider the problems each creates and suggest prospects for the Wager in light of these problems.

When agents insert technological systems into their decision-making processes, they can obscure moral responsibility for the results. This can give rise to a distinct moral wrong, which we call “agency laundering.” At root, agency laundering involves obfuscating one’s moral responsibility by enlisting a technology or process to take some action and letting it forestall others from demanding an account for bad outcomes that result. We argue that the concept of agency laundering helps in understanding important moral problems in a number (...) of recent cases involving automated, or algorithmic, decision-systems. We apply our conception of agency laundering to a series of examples, including Facebook’s automated advertising suggestions, Uber’s driver interfaces, algorithmic evaluation of K-12 teachers, and risk assessment in criminal sentencing. We distinguish agency laundering from several other critiques of information technology, including the so-called “responsibility gap,” “bias laundering,” and masking. (shrink)

A comprehensive introduction to the ways in which meaning is conveyed in language. Alan Cruse covers semantic matters, but also deals with topics that are usually considered to fall under pragmatics. A major aim is to highlight the richness and subtlety of meaning phenomena, rather than to expound any particular theory.

Algorithmic systems and predictive analytics play an increasingly important role in various aspects of modern life. Scholarship on the moral ramifications of such systems is in its early stages, and much of it focuses on bias and harm. This paper argues that in understanding the moral salience of algorithmic systems it is essential to understand the relation between algorithms, autonomy, and agency. We draw on several recent cases in criminal sentencing and K–12 teacher evaluation to outline four key ways in (...) which issues of agency, autonomy, and respect for persons can conflict with algorithmic decision-making. Three of these involve failures to treat individual agents with the respect they deserve. The fourth involves distancing oneself from a morally suspect action by attributing one’s decision to take that action to an algorithm, thereby laundering one’s agency. (shrink)