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)

Medical science conceives the human body as a system comprised of many subsystems at a variety of levels. At the highest level are bodily systems proper, such as the endocrine system, which are central to our understanding of human anatomy, and play a key role in diagnosis and in dynamic modeling as well as in medical pedagogy and computer visualization. But there is no explicit definition of what a bodily system is; such informality is acceptable in documentation created for human (...) beings, but falls short of what is needed for computer representations. Our analysis is intended as a first step towards filling this gap. (shrink)

It is argued that medical science requires a classificatory system that (a) puts functions in the taxonomic center and (b) does justice ontologically to the difference between the processes which are the realizations of functions and the objects which are their bearers. We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences.

Background: Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. Results: We present (...) computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Conclusion: Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation. (shrink)

It is argued that medical science requires a classificatory system that (a) puts functions in the taxonomic center and (b) does justice ontologically to the difference between the processes which are the realizations of functions and the objects which are their bearers. We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences.

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)

In her ‘On the apparent paradox of ideal theory’, Laura Valentini combines three supposedly plausible premises to derive the paradoxical result that ideal theory is both unable to, and indispensable for, guiding action. Her strategy is to undermine one of the three premises by arguing that there are good and bad kinds of ideal theory, and only the bad kinds are vulnerable to the strongest version of their opponents’ attack. By undermining one of the three premises she releases ideal (...) theorists from the paradox, which is as follows. (1) Any sound theory of justice is action-guiding. (2) Any sound theory of justice is ideal. (3) Any ideal theory fails to be action-guiding. Here I shall respond to Valentini in two ways. First, I shall show that both (1) and (2) are false. The falsity of either is sufficient to release ideal theorists from the paradox. Second, I shall show that Valentini’s response to (3) can be extended, because her bad kinds of ideal theory do not necessarily fail to guide action. The cumulative effect of my arguments further strengthens Valentini’s support of ideal theory. I will deal with premises (1) and (2) in Sections I and II, and (3) in Section III. (shrink)

This volume brings together a range of influential essays by distinguished philosophers and political theorists on the issue of global justice. Global justice concerns the search for ethical norms that should govern interactions between people, states, corporations and other agents acting in the global arena, as well as the design of social institutions that link them together. The volume includes articles that engage with major theoretical questions such as the applicability of the ideals of social and economic equality to the (...) global sphere, the degree of justified partiality to compatriots, and the nature and extent of the responsibilities of the affluent to address global poverty and other hardships abroad. It also features articles that bring the theoretical insights of global justice thinkers to bear on matters of practical concern to contemporary societies, such policies associated with immigration, international trade, and climate change. -/- Contents: Introduction; Part I Standards of Global Justice: (i) Assistance-Based Responsibilities to the Global Poor: Famine, affluence and mortality, Peter Singer; We don't owe them a thing! A tough-minded but soft-hearted view of aid to the faraway needy, Jan Narveson; Does distance matter morally to the duty to rescue? Frances Myrna Kamm. (ii) Contribution-Based Responsibilities to the Global Poor: 'Assisting' the global poor, Thomas Pogge; Should we stop thinking about poverty in terms of helping the poor?, Alan Patten; Poverty and the moral significance of contribution, Gerhard Øverland. (iii)Cosmopolitans, Global Egalitarians, and its Critics: The one and the many faces of cosmopolitanism, Catherine Lu; Cosmopolitan justice and equalizing opportunities, Simon Caney; The problem of global justice, Thomas Nagel; Against global egalitarianism, David Miller; Egalitarian challenges to global egalitarianism: a critique, Christian Barry and Laura Valentini. Part II Pressing Global Socioeconomic Issues: (i) Governing the Flow of People: Immigration and freedom of association, Christopher Wellman; Democratic theory and border coercion: no right to unilaterally control your own borders, Arash Abizadeh; Justice in migration: a closed borders utopia?, Lea Ypi. (ii) Climate Change: Global environment and international inequality, Henry Shue; Valuing policies in response to climate change: some ethical issues, John Broome; Saved by disaster? Abrupt climate change, political inertia, and the possibility of an intergenerational arms race, Stephen M. Gardiner; Polycentric systems for coping with collective action and global environmental change, Elinor Ostrom. (iii) International Trade: Responsibility and global labor justice, Iris Marion Young; Property rights and the resource curse, Leif Wenar; Fairness in trade I: obligations arising from trading and the pauper-labor argument, Mathias Risse; Name index. -/- See: www.ashgate.com/default.aspx?page=637&calctitle=1&pageSubject=483&sort=pubdate&forthcoming=1&title_i d=9958&edition_id=13385. (shrink)

Over the years a few authors have argued that Rawls’s ideal theory of justice is useless for the real world. This criticism has been largely ignored by Rawlsians, but in the light of a recent accumulation of such criticisms, some authors (in particular Holly Lawford-Smith, A. John Simmons, Zofia Stemplowska and Laura Valentini) have tried to defend ideal theory. In this article I will recapitulate the precise problem with Rawls’s ideal theory, argue that some of Rawls’s defenders misconceive (...) it, and show that recent attempts to rescue Rawls’s ideal theory from the charge of being useless fail. While there are useful kinds of ideal theory, Rawls’s is not one of them. In addition, Rawls’s very tentative suggestions for some kind of bridge between ideal and non-ideal theory are contradictory insofar as they implicitly presuppose the non-existence of the problem they are meant to solve. Thus, Rawls’s “non-ideal theory” too, is useless, and not so much a theory at all but a set of ad hoc stipulations. Finally, I will show that certain attempts within the global justice debate to use some variation of the original position to directly derive guidelines for the real world are misguided and yield no useful results. (shrink)

Corcoran’s 27 entries in the 1999 second edition of Robert Audi’s Cambridge Dictionary of Philosophy [Cambridge: Cambridge UP]. -/- ancestral, axiomatic method, borderline case, categoricity, Church (Alonzo), conditional, convention T, converse (outer and inner), corresponding conditional, degenerate case, domain, De Morgan, ellipsis, laws of thought, limiting case, logical form, logical subject, material adequacy, mathematical analysis, omega, proof by recursion, recursive function theory, scheme, scope, Tarski (Alfred), tautology, universe of discourse. -/- The entire work is available online free at more than (...) one website. Paste the whole URL. http://archive.org/stream/RobertiAudi_The.Cambridge.Dictionary.of.Philosophy/Robert.Audi_The.Cambrid ge.Dictionary.of.Philosophy -/- The 2015 third edition will be available soon. Before you think of buying it read some reviews on Amazon and read reviews of its competition: For example, my review of the 2008 Oxford Companion to Philosophy, History and Philosophy of Logic,29:3,291-292. URL: http://dx.doi.org/10.1080/01445340701300429 -/- Some of the entries have already been found to be flawed. For example, Tarski’s expression ‘materially adequate’ was misinterpreted in at least one article and it was misused in another where ‘materially correct’ should have been used. The discussion provides an opportunity to bring more flaws to light. -/- Acknowledgements: Each of these entries was presented at meetings of The Buffalo Logic Dictionary Project sponsored by The Buffalo Logic Colloquium. The members of the colloquium read drafts before the meetings and were generous with corrections, objections, and suggestions. Usually one 90-minute meeting was devoted to one entry although in some cases, for example, “axiomatic method”, took more than one meeting. Moreover, about half of the entries are rewrites of similarly named entries in the 1995 first edition. Besides the help received from people in Buffalo, help from elsewhere was received by email. We gratefully acknowledge the following: José Miguel Sagüillo, John Zeis, Stewart Shapiro, Davis Plache, Joseph Ernst, Richard Hull, Concha Martinez, Laura Arcila, James Gasser, Barry Smith, Randall Dipert, Stanley Ziewacz, Gerald Rising, Leonard Jacuzzo, George Boger, William Demopolous, David Hitchcock, John Dawson, Daniel Halpern, William Lawvere, John Kearns, Ky Herreid, Nicolas Goodman, William Parry, Charles Lambros, Harvey Friedman, George Weaver, Hughes Leblanc, James Munz, Herbert Bohnert, Robert Tragesser, David Levin, Sriram Nambiar, and others. -/- . (shrink)

We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new kinds of (...) situations and thematic roles, (e.g., roles such as agent, patient and instrument), based on new compositions of existing representations. We applied our prototype in an intelligence analysis use case to test the hypothesis that a framework of this sort can produce usefully structured information from combined natural language and sensor data inputs. We further tested our hypothesis by adding an enhanced US Air Force ontology framework to our ODIS in order to (1) process a collection of sensor data, intel reports, and mission plans; (2) build composite POR representations from these data; and (3) machine analyze the fused results to infer mission threats. (shrink)

Background: The United States symbolizes democracy in the new world and contributes to global prosperity. Nevertheless, incrementalism is a historically dominant national approach to public policy implementation that delays democracy and undermines human dignity. Human flourishing and national development are endangered by slow-moving democratic changes. This necessitates a social justice framework that traces the exploitation of incrementalism and the consequences of opportunity gaps. Objectives: This study aims to construct a grounded theory to address and answer the following research question: Are (...) anti-democratic concepts part of a process or strategy that hinders democratic change, and what reinforces it, if anything? Methods: Two categories emerged from a grounded theory of democratic social change. This combination of anti-democratic tenets and democratic principles led to abductive reasoning to fill the research gap. Results: The key finding was the existence of a systematic approach that led to democracy while simultaneously disempowering the same group through legal and extralegal means. Two processes hinder democracy: incrementalism and an anti-democratic demoralizing process. A constructivist social justice grounded theory was developed to analyze and evaluate public policy for barriers and facilitators of democracy. A thorough analysis and evaluation of the impact and consequences of public policy is recommended to better understand how such policies impede democracy and influence American perceptions of justice. (shrink)

During the realist revival in the early years of this century, philosophers of various persuasions were concerned to investigate the ontology of truth. That is, whether or not they viewed truth as a correspondence, they were interested in the extent to which one needed to assume the existence of entities serving some role in accounting for the truth of sentences. Certain of these entities, such as the Sätze an sich of Bolzano, the Gedanken of Frege, or the propositions of Russell (...) and Moore, were conceived as the bearers of the properties of truth and falsehood. Some thinkers however, such as Russell, Wittgenstein in the Tractatus, and Husserl in the Logische Untersuchungen, argued that instead of, or in addition to, truth-bearers, one must assume the existence of certain entities in virtue of which sentences and/or propositions are true. Various names were used for these entities, notably 'fact', 'Sachverhalt', and 'state of affairs'. (1) In order not to prejudge the suitability of these words we shall initially employ a more neutral terminology, calling any entities which are candidates for this role truth-makers. (shrink)

Intelligent defence support systems are confronted with the need to manage ever-increasing floods of data in a way that raises significant challenges because the data are described and presented using different terminologies and formats. How, on this basis, is it possible to reach a common understanding of the information content of these data among people and software agents? How is it possible to ensure that domain knowledge is reused in consistent fashion in a way that makes this information available for (...) integration and analysis? How can we support the identification, selection, composition, and orchestration of services based on such diverse data providing homogeneous support by a service-oriented architecture? This collection is devoted to the use of ontologies to answer questions such as these. (shrink)

Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques such as ontology-based (...) multi-database querying, automated ontology alignment and ontology-based text-mining. These theses are illustrated by means of a case study of the Gene Ontology, a project of increasing importance within the field of biomedical data integration. (shrink)

Individuals have various kinds of obligations: keep promises, don’t cause harm, return benefits received from injustices, be partial to loved ones, help the needy and so on. How does this work for group agents? There are two questions here. The first is whether groups can bear the same kinds of obligations as individuals. The second is whether groups’ pro tanto obligations plug into what they all-things-considered ought to do to the same degree that individuals’ pro tanto obligations plug into what (...) they all-things-considered ought to do. We argue for parity on both counts. (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)

Formalisms such as description logics (DL) are sometimes expected to help terminologies ensure compliance with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) complies with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of SNOMED CT classes with respect to these principles. Our major results are: 31% of (...) the classes have a single child; 27% have multiple parents; 51% do not exhibit any differentiae between the description of the parent and that of the child. The applications of this study to quality assurance for ontologies are discussed and suggestions are made for dealing with multiple inheritance. (shrink)

The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad scope. (...) We argue here, however, that its organization manifests certain structural problems, and we describe revisions which we believe are needed if the network is to be maximally successful in realizing its goals of supporting terminology integration. (shrink)

Referent tracking (RT) is a new paradigm, based on unique identification, for representing and keeping track of particulars. It was first introduced to support the entry and retrieval of data in electronic health records (EHRs). Its purpose is to avoid the ambiguity that arises when statements in an EHR refer to disorders or other entities on the side of the patient exclusively by means of compound descriptions utilizing general terms such as ‘pimple on nose’ or ‘small left breast tumor’. In (...) this paper, we describe the theoretical foundations of this paradigm and show how it is being applied to the solution of analogous problems of ambiguous identification in the fields of digital rights management, corporate memories and decision algorithms. (shrink)

that can serve as a foundation for more refined ontologies in the field of proteomics. Standard data sources classify proteins in terms of just one or two specific aspects. Thus SCOP (Structural Classification of Proteins) is described as classifying proteins on the basis of structural features; SWISSPROT annotates proteins on the basis of their structure and of parameters like post-translational modifications. Such data sources are connected to each other by pairwise term-to-term mappings. However, there are obstacles which stand in the (...) way of combining them together to form a robust meta-classification of the needed sort. We discuss some formal ontological principles which should be taken into account within the existing datasources in order to make such a metaclassification possible, taking into account also the Gene Ontology (GO) and its application to the annotation of proteins. (shrink)

El presente ensayo plantea la posibilidad de considerar nuevamente al diseño editorial como una actividad artística. Este campo no pudo escapar al fenómeno de la sociedad del espectáculo que hoy envuelve a casi toda actividad humana. Ello indiscutiblemente afecta la manera en que se valora esta actividad actualmente, vista las más de las veces como un simple aditamento utilitario con más fines comerciales que artísticos. A pesar de ello no deja de ser loable una revaloración de la disciplina que la (...) considere como una producción también transutilitaria, un fenómeno a la vez estético y extraestético y una actividad que, a través de su propia praxis, construye al ser histórico... (shrink)

Als zu Beginn des Jahrhunderts der Realismus wieder ernst genommen wurde, gab es viele Philosophen, die sich mit der Ontologie der Wahrheit befaßten. Unabhängig von der Bestimmung der Wahrheit als Korrespondenzbeziehung wollten sie herausfinden, inwieweit zur Erklärung der Wahrheit von Sätzen besondere Entitäten herangezogen werden müssen. Einige dieser Entitäten, so zum Beispiel Bolzanos ‘Sätze an sich’, Freges ‘Gedanken’ oder die ‘propositions’ von Russell und Moore, wurden als Träger der Eigenschaften Wahrheit und Falschheit aufgefaßt. Einige Philosophen jedoch, wie Russell, Wittgenstein im (...) ›Tractatus‹ und Husserl in den ›Logischen Untersuchungen‹, argumentierten, zusätzlich zu den Wahrheitsträgern bzw. an ihrer Stelle müßten Entitäten angenommen werden, auf Grund deren Sätze und/oder ‘Propositionen’ wahr sind. Solchen Entitäten gab man verschiedene Namen, insbesondere ‘fact’, ‘Tatsache’, ‘state of affairs’ und ‘Sachverhalt’. 1 Wir wollen einer Entscheidung über die Angebrachtheit dieser Ausdrücke nicht vorgreifen und daher zunächst eine neutralere Terminologie verwenden: Alle Entitäten, die für diese zweite Rolle in Frage kommen, wollen wir ‘Wahrmacher’ nennen. (shrink)

We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices. If properly developed and extended, we believe the VSO (...) will find applications for the EMR, clinical informatics, and medical device communities. (shrink)

The theory of granular partitions (TGP) is a new approach to the understanding of ontologies and other classificatory systems. The paper explores the use of this new theory in the treatment of task-based clinical guidelines as a means for better understanding the relations between different clinical tasks, both within the framework of a single guideline and between related guidelines. We used as our starting point a DAML+OIL-based ontology for the WHO guideline for hypertension management, comparing this with related guidelines and (...) attempting to show that TGP provides a flexible and highly expressive basis for the manipulation of ontologies of a sort which might be useful in providing more adequate Computer Interpretable Guideline Models (CIGMs) in the future. (shrink)

Where humans can manipulate and integrate the information they receive in subtle and ever-changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, chemistry, mathematics, medicine (...) and many other areas, and all of these dimensions, as well as fundamental philosophical issues, must be taken into account in the construction of a domain ontology. Here we describe the basic features of domain ontologies in the life sciences and show how they can be used. (shrink)

Published in extended form as "Endurants and Perdurants in Directly Depicting Ontologies", -/- We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes and the enduring entities that participate in such processes. For this purpose we distinguish between ontologies and metaontology. Ontologies are based on very simple directly depicting languages and fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct (...) though compatible systems of categories. In a SNAP (snapshot) ontology we have the enduring entities in a given domain as they exist to be inventoried at some given moment of time. In a SPAN ontology we have perduring entities such as processes and their parts and aggregates. We argue that both kinds of ontology are required, together with the meta-ontology which joins them together. On the level of meta-ontology we are able to impose constraints on ontologies of a sort which can support efficient processing of large amounts of data. (shrink)

It is widely understood that protein functions can be exhaustively described in terms of no single parameter, whether this be amino acid sequence or the three-dimensional structure of the underlying protein molecule. This means that a number of different attributes must be used to create an ontology of protein functions. Certainly much of the required information is already stored in databases such as Swiss-Prot, Protein Data Bank, SCOP and MIPS. But the latter have been developed for different purposes and the (...) separate data-structures which they employ are not conducive to the needed data integration. When we attempt to classify the entities in the domain of proteins, we find ourselves faced with a number of cross-cutting principles of classification. Our question here is: how can we bring together these separate taxonomies in order to describe protein functions? Our proposed answer is: via a careful top-level ontological analysis of the relevant principles of classification, combined with a new framework for the simultaneous manipulation of classifications constructed for different purposes. (shrink)

Information may be defined as the conceptual or communicable part of the content of mental acts. The content of mental acts includes sensory data as well as concepts, particular as well as general information. An information system is an external (non-mental) system designed to store such content. Information systems afford indirect transmission of content between people, some of whom may put information into the system and others who are among those who use the system. In order for communication to happen, (...) the conceptual systems of the originators and users of the information must be sufficiently similar. A formal conceptual framework that can provide the basis for exchange of information is termed an ontology. In its most fundamental form, ontology studies the most basic constituents of reality. Traditionally, ontology seeks to reflects structures that are independent of thought and cognition. The term ontology is used more broadly in artificial intelligence and software engineering, to refer to the conceptual basis for an information system. (shrink)

We present some ideas on logical process descriptions, using relations from the DIO (Drug Interaction Ontology) as examples and explaining how these relations can be naturally decomposed in terms of more basic structured logical process descriptions using terms from linear logic. In our view, the process descriptions are able to clarify the usual relational descriptions of DIO. In particular, we discuss the use of logical process descriptions in proving linear logical theorems. Among the types of reasoning supported by DIO one (...) can distinguish both (1) basic reasoning about general structures in reality and (2) the domain-specific reasoning of experts. We here propose a clarification of this important distinction between (realist) reasoning on the basis of an ontology and rule-based inferences on the basis of an expert’s view. (shrink)

The report describes an application of ontologies to the analysis of wind turbine manufacturing data. We show how applying ontologies to composite materials data may facilitate the discovery of optimum composite material designs that will deliver maximum wind turbine blade performance within environmental constraints.

Equipped with the ultimate query answering system, computers would finally be in a position to address all our information needs in a natural way. In this paper, we describe how Language and Computing nv (L&C), a developer of ontology-based natural language understanding systems for the healthcare domain, is working towards the ultimate Question Answering (QA) System for healthcare workers. L&C’s company strategy in this area is to design in a step-by-step fashion the essential components of such a system, each component (...) being designed to solve some one part of the total problem and at the same time reflect well-defined needs on the prat of our customers. We compare our strategy with the research roadmap proposed by the Question Answering Committee of the National Institute of Standards and Technology (NIST), paying special attention to the role of ontology. (shrink)

Despite the recent advances in information and communication technology that have increased our ability to store and circulate information, the task of ensuring that the right sorts of information gets to the right sorts of people remains. We argue that the many efforts underway to develop efficient means for sharing information across healthcare systems and organizations would benefit from a careful analysis of human action in healthcare organizations. This in turn requires that the management of information and knowledge within healthcare (...) organizations be combined with models of resources and processes of patient care that are based on a general ontology of social interaction. The Health Level 7 (HL7) is one of several ANSI-accredited Standards Developing Organizations operating in the healthcare arena. HL7 has advanced a widely used messaging standard that enables healthcare applications to exchange clinical and administrative data in digital form. HL7 focuses on the interface requirements of the entire healthcare system and not exclusively on the requirements of one area of healthcare such as pharmacy, medical devices, imaging or insurance transactions. This has inspired the development of a powerful abstract model of patient care called the Reference Information Model (RIM). The present paper begins with an overview of the core classes of the HL7 (Version 3) RIM and a brief discussion of its “actcentered” view of healthcare. Central to this account is what is called the life cycle of events. A clinical action may progress from defined, through planned and ordered, to executed. These modalities of an action are represented as the mood of the act. We then outline the basis of an ontology of organizations, starting from the theory of speech Acts, and apply this ontology to the HL7 RIM. Special attention is given to the sorts of preconditions that must be satisfied for the successful performance of a speech act and to the sorts of entities to which speech acts give rise (e.g. obligations, claims, commitments, etc.). Finally we draw conclusions for the efficient communication and management of medical information and knowledge within and between healthcare organizations, paying special attention to the role that medical documents play in such organizations. (shrink)

Semantic interoperability can be defined as the ability of two or more computer systems to exchange information in such a way that the meaning of that information can be automatically interpreted by the receiving system accurately enough to produce useful results to the end users of both systems. Several activities are currently being performed by a variety of stakeholders to achieve semantic interoperability in healthcare. Many of these activities are not beneficial, because they place too great a focus on business (...) aspects and not enough on involvement of the right sorts of researchers, in particular those that are able to see how the data and information relate to the entities of concern on the side of the patient. The lack of a central focus on the patient, and the associated focus on ‘concepts’, have spawned a variety of mutually incompatible terminologies exhibiting non-resolvable overlap. The predominance of the healthcare IT industry in the writing and selection of semantic interoperability standards mitigates against the benefits that standards, when well designed, can bring about. (shrink)

An important part of the Unified Medical Language System (UMLS) is its Semantic Network, consisting of 134 Semantic Types connected to each other by edges formed by one or more of 54 distinct Relation Types. This Network is however for many purposes overcomplex, and various groups have thus made attempts at simplification. Here we take this work further by simplifying the relations which involve the three Semantic Types – Diagnostic Procedure, Laboratory Procedure and Therapeutic or Preventive Procedure. We define operators (...) which can be used to generate terms instantiating types from this selected set when applied to terms designating certain other Semantic Types, including almost all the terms specifying clinical tasks. Usage of such operators thus provides a useful and economical way of specifying clinical tasks. The operators allow us to define a mapping between those types within the UMLS which do not represent clinical tasks and those which do. This mapping then provides a basis for an ontology of clinical tasks that can be used in the formulation of computer-interpretable clinical guideline models. (shrink)

Outcomes research in healthcare has been a topic much addressed in recent years. Efforts in this direction have been supplemented by work in the areas of guidelines for clinical practice and computer-interpretable workflow and careflow models.In what follows we present the outlines of a framework for understanding the relations between organizations, guidelines, individual patients and patient-related functions. The derived framework provides a means to extract the knowledge contained in the guideline text at different granularities, in ways that can help us (...) to assign tasks within the healthcare organization and to assess clinical performance in realizing the guideline. It does this in a way that preserves the flexibility of the organization in the adoption of the guidelines. (shrink)

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (shrink)

Fear generalisation is a psychological phenomenon that occurs when fear that is elicited in response to a frightening stimulus spreads to similar or related stimuli. The practical harms of pathological fear generalisation related to trauma are well-documented, but little or no attention has been given so far to its epistemic harms. This paper fills this gap in the literature. It shows how the psychological phenomenon, when it becomes pathological, substantially curbs the epistemic agency of those who experience the fear that (...) generalizes, limiting their ability to respond to evidence, and substantially limiting their epistemic horizons. It is argued that when these epistemic harms are caused by wrongful actions and decisions of individuals or institutions, because the fear is elicited in response to a traumatic experience inflicted by them, the harms should be considered epistemic wrongs. The epistemic wrongs are closely akin to agential epistemic injustice, a variety of distributive epistemic injustice, and sometimes also involve epistemic exclusion. The paper thereby identifies a previously underexplored psychological mechanism that can be a vehicle through which both individuals and institutions can epistemically wrong others. The argument has implications for how both epistemic wrongs and epistemic injustice should be conceived, suggesting that both can occur without being caused by primarily epistemic flaws or errors, or a bad epistemic character. Finally, it highlights the advantage of taking a victim-centred approach to understanding epistemic harm. (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

Although the principle of fair subject selection is a widely recognized requirement of ethical clinical research, it often yields conflicting imperatives, thus raising major ethical dilemmas regarding participant selection. In this paper, we diagnose the source of this problem, arguing that the principle of fair subject selection is best understood as a bundle of four distinct sub-principles, each with normative force and each yielding distinct imperatives: (1) fair inclusion; (2) fair burden sharing; (3) fair opportunity; and (4) fair distribution of (...) third-party risks. We first map out these distinct sub-principles, and then identify the ways in which they yield conflicting imperatives for the design of inclusion and exclusion criteria, and the recruitment of participants. We then offer guidance for how decision makers should navigate these conflicting imperatives to ensure that participants are selected fairly. (shrink)

Findings from the cognitive sciences suggest that the cognitive mechanisms responsible for some memory errors are adaptive, bringing benefits to the organism. In this paper we argue that the same cognitive mechanisms also bring a suite of significant epistemic benefits, increasing the chance of an agent obtaining epistemic goods like true belief and knowledge. This result provides a significant challenge to the folk conception of memory beliefs that are false, according to which they are a sign of cognitive frailty, indicating (...) that a person is less reliable than others or their former self. Evidence of memory errors can undermine a person’s view of themselves as a competent epistemic agent, but we show that false memory beliefs can be the result of the ordinary operation of cognitive mechanisms found across the species, which bring substantial epistemic benefits. This challenge to the folk conception is not adequately captured by existing epistemological theories. However, it can be captured by the notion of epistemic innocence, which has previously been deployed to highlight how beliefs which have epistemic costs can also bring significant epistemic benefits. We therefore argue that the notion of epistemic innocence should be expanded so that it applies not just to beliefs but also to cognitive mechanisms. (shrink)

Scientific researchers welcome disagreement as a way of furthering epistemic aims. Religious communities, by contrast, tend to regard it as a potential threat to their beliefs. But I argue that religious disagreement can help achieve religious epistemic aims. I do not argue this by comparing science and religion, however. For scientific hypotheses are ideally held with a scholarly neutrality, and my aim is to persuade those who arecommittedto religious beliefs that religious disagreement can be epistemically beneficial for them too.

Some language encourages essentialist thinking. While philosophers have largely focused on generics and essentialism, I argue that nouns as a category are poised to refer to kinds and to promote representational essentializing. Our psychological propensity to essentialize when nouns are used reveals a limitation for anti-essentialist ameliorative projects. Even ameliorated nouns can continue to underpin essentialist thinking. I conclude by arguing that representational essentialism does not doom anti-essentialist ameliorative projects. Rather it reveals that would-be ameliorators ought to attend to the (...) propensities for our representational devices to essentialize and to the complex relationship between essentialism and prejudice. (shrink)

In this chapter, I examine Lewis's ideas about ontological innocence, ontological commitment and double-counting, in his discussion of composition as identity in Parts of Classes. I attempt to understand these primarily as epistemic or methodological claims: how far can we get down this route without adopting radical metaphysical theses about composition as identity?

This article provides a conceptual map of the debate on ideal and non‐ideal theory. It argues that this debate encompasses a number of different questions, which have not been kept sufficiently separate in the literature. In particular, the article distinguishes between the following three interpretations of the ‘ideal vs. non‐ideal theory’ contrast: (i) full compliance vs. partial compliance theory; (ii) utopian vs. realistic theory; (iii) end‐state vs. transitional theory. The article advances critical reflections on each of these sub‐debates, and highlights (...) areas for future research in the field. (shrink)

If you love someone, is it good to believe better of her than epistemic norms allow? The partiality view says that it is: love, on this view, issues norms of belief that clash with epistemic norms. The partiality view is supposedly supported by an analogy between beliefs and actions, by the phenomenology of love, and by the idea that love commits us to the loved one’s good character. I argue that the partiality view is false, and defend what I call (...) the epistemic view. On the epistemic view, love also issues norms of belief. But these say simply that you should adhere to epistemic norms in forming and maintaining beliefs about loved ones. I offer two arguments for the epistemic view. The first appeals to the emotional responses of love, which, when sensitive to what the loved one is really like, can make love great and be morally transformative. The second is a new argument for why caring for a loved one requires true beliefs about him. We see that there may be some boundaries, such as stuffy traditions, that love is right to defy, but that epistemic boundaries are not among them. (shrink)

Gatekeeping, or determining membership of your group, is crucial to science: the moniker ‘scientific’ is a stamp of epistemic quality or even authority. But gatekeeping in science is fraught with dangers. Gatekeepers must exclude bad science, science fraud and pseudoscience, while including the disagreeing viewpoints on which science thrives. This is a difficult tightrope, not least because gatekeeping is a human matter and can be influenced by biases such as groupthink. After spelling out these general tensions around gatekeeping in science, (...) we shed light on them with a case study from psychology. This concerns whether academic psychologists rightly or wrongly classify the applied-psychology framework of NLP (‘neuro-linguistic programming’) as unscientific and even pseudoscientific. This example of gatekeeping is particularly instructive because both the NLP community and the psychology community, we argue, make legitimate but also illegitimate moves. This case gives rise to several general insights about gatekeeping in science more generally. (shrink)

Where there is trust, there is also vulnerability, and vulnerability can be exploited. Epistemic trust is no exception. This chapter maps the phenomenon of the exploitation of epistemic trust. I start with a discussion of how trust in general can be exploited; a key observation is that trust incurs vulnerabilities not just for the party doing the trusting, but also for the trustee (after all, trust can be burdensome), so either party can exploit the other. I apply these considerations to (...) epistemic trust, specifically in testimonial relationships. There, we standardly think of a hearer trusting a speaker. But we miss an important aspect of this relationship unless we consider too that the speaker standardly trusts the hearer. Given this mutual trust, and given that both trustees and trusters can exploit each other, we have four possibilities for exploitation in epistemic-trust relationships: a speaker exploiting a hearer (a) by accepting his trust or (b) by imposing her trust on him, and a hearer exploiting a speaker (c) by accepting her trust or (d) by imposing his trust on her. One result is that you do not need to betray someone to exploit him – you can exploit him just as easily by doing what he trusts you for. (shrink)

Resolving religious disagreements is difficult, for beliefs about religion tend to come with strong biases against other views and the people who hold them. Evidence can help, but there is no agreed-upon policy for weighting it, and moreover bias affects the content of our evidence itself. Another complicating factor is that some biases are reliable and others unreliable. What we need is an evidence-weighting policy geared toward negotiating the effects of bias. I consider three evidence-weighting policies in the philosophy of (...) religion and advocate one of them as the best for promoting the resolution of religious disagreements. (shrink)