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

People have an “anomalous-is-bad” stereotype whereby they make negative inferences about the moral character of people with craniofacial anomalies like scars. This stereotype is hypothesized to be a byproduct of adaptations for avoiding pathogens. However, evidence for the anomalous-is-bad stereotype comes from studies of European and North American populations; the byproduct hypothesis would predict universality of the stereotype. We presented 123 Hadza across ten camps pairs of morphed Hadza faces—each with one face altered to include a scar—and asked who they (...) expected to be more moral and a better forager. Hadza with minimal exposure to other cultures chose at chance for both questions. Hadza with greater exposure to other cultures, however, expected the scarred face to be less moral and a better forager. These results suggest the anomalous-is-bad stereotype may be culturally shared or learned erroneously through associations with population-level differences, providing evidence against a universal pathogen avoidance byproduct hypothesis. (shrink)

Numerous research groups are now utilizing Basic Formal Ontology as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three existing BFO subcategories of realizable entity, namely function, role, and disposition. It proposes one further sub-category of tendency, and considers the merits of recognizing two sub-categories of function for domain ontologies, namely, artifactual and biological function. The motivation is to help advance the coherent ontological treatment of functions, roles, and dispositions, (...) to help provide the potential for more detailed classification, and to shed light on BFO’s general make-up and use. (shrink)

The goal of referent tracking is to create an ever-growing pool of data relating to the entities existing in concrete spatiotemporal reality. In the context of Electronic Healthcare Records (EHRs) the relevant concrete entities are not only particular patients but also their parts, diseases, therapies, lesions, and so forth, insofar as these are salient to diagnosis and treatment. Within a referent tracking system, all such entities are referred to directly and explicitly, something which cannot be achieved when familiar concept-based systems (...) are used in what is called “clinical coding”. In this paper we describe the components of a referent tracking system in an informal way and we outline the procedures that would have to be followed by healthcare personnel in using such a system. We argue that the referent tracking paradigm can be introduced with only minor – though nevertheless ontologically important – technical changes to existing EHR infrastructures, but that it will require a radically different mindset on the part of those involved in clinical coding and terminology development from that which has prevailed hitherto. (shrink)

Editor’s NoteThanks to the initiative of Alan Norrie, we are pleased to present here a symposium on Nick Wilson’s book The Space that Separates: A Realist Theory of Art. Several authors have contri...

Three-dimensionalists , sometimes referred to as endurantists, think that objects persist through time by being “wholly present” at every time they exist. But what is it for something to be wholly present at a time? It is surprisingly difficult to say. The threedimensionalist is free, of course, to take ‘is wholly present at’ as one of her theory’s primitives, but this is problematic for at least one reason: some philosophers claim not to understand her primitive. Clearly the three-dimensionalist would be (...) better off if she could state her theory in terms accessible to all. We think she can. What is needed is a definition of ‘is wholly present at’ that all can understand. in this paper, we offer one. (shrink)

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

Ernst Mach's atomistic theory of sensation faces problems in doing justice to our ability to perceive and remember complex phenomena such as melodies and shapes. Christian von Ehrenfels attempted to solve these problems with his theory of "Gestalt qualities", which he sees as entities depending one-sidedly on the corresponding simple objects of sensation. We explore the theory of dependence relations advanced by Ehrenfels and show how it relates to the views on the objects of perception advanced by Husserl and by (...) the Gestalt psychologists. (shrink)

In this paper we propose a formal theory of partitions (ways of dividing up or sorting or mapping reality) and we show how the theory can be applied in the geospatial domain. We characterize partitions at two levels: as systems of cells (theory A), and in terms of their projective relation to reality (theory B). We lay down conditions of well-formedness for partitions and we define what it means for partitions to project truly onto reality. We continue by classifying well-formed (...) partitions along three axes: (a) degree of correspondence between partition cells and objects in reality; (b) degree to which a partition represents the mereological structure of the domain it is projected onto; and (c) degree of completeness and exhaustiveness with which a partition represents reality. This classification is used to characterize three types of partitions that play an important role in spatial information science: cadastral partitions, categorical coverages, and the partitions involved in folk categorizations of the geospatial domain. (shrink)

This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each combination of dispositions is given (...) along with a specific use case in IDO. Description logic restrictions are used to formalize statements relating to these combinations. (shrink)

Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (i.e., (...) they belong to the domain of epistemology). We analyze terms from several biomedical vocabularies in order to throw light on the interactions between ontological and epistemological components of these terminologies. We identify four cases: 1) terms containing classification criteria, 2) terms reflecting detectability, modality, uncertainty, and vagueness, 3) terms created in order to obtain a complete partition of a given domain, and 4) terms reflecting mere fiat boundaries. We show that epistemology-loaded terms are pervasive in biomedical vocabularies, that the “classes” they name often do not comply with sound classification principles, and that they are therefore likely to cause problems in the evolution and alignment of terminologies and associated ontologies. (shrink)

We present the details of a methodology for quality assurance in large medical terminologies and describe three algorithms that can help terminology developers and users to identify potential mistakes. The methodology is based in part on linguistic criteria and in part on logical and ontological principles governing sound classifications. We conclude by outlining the results of applying the methodology in the form of a taxonomy different types of errors and potential errors detected in SNOMED-CT.

The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not met by most existing biomedical terminologies, the latter may nonetheless support (...) the Foundry’s goal of consistent and non-redundant annotation if appropriate mappings of data annotated with their aid can be achieved. To construct such mappings in reliable fashion, however, it is necessary to analyze terminological resources from an ontologically realistic perspective in such a way as to identify the exact import of the ‘concepts’ and associated terms which they contain. We propose a framework for such analysis that is designed to maximize the degree to which legacy terminologies and the data coded with their aid can be successfully used for information-driven clinical and translational research. (shrink)

The paradigm of referent tracking is based on a realist presupposition which rejects so-called negative entities (congenital absent nipple, and the like) as spurious. How, then, can a referent tracking-based Electronic Health Record deal with what are standardly called ‘negative findings’? To answer this question we carried out an analysis of some 748 sentences drawn from patient charts and containing some form of negation. Our analysis shows that to deal with these sentences we need to introduce a new ontological relationship (...) between a particular and a universal, which holds when no instance of the universal has a specific qualified ontological relation with the particular. This relation is found to be able to accommodate nearly all occurrences of negative findings in the examined sample, in ways which involve no reference to negative entities. (shrink)

This paper presents an axiomatic formalization of a theory of top-level relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the sub-universal relation among universals and the parthood relation among individuals, as well as cross-categorial relations such as instantiation and membership. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical for (...) geographic information processing. The axiomatic theory is developed using Isabelle, a computational system for implementing logical formalisms. All proofs are computer verified and the computational representation of the theory is available online. (shrink)

Ingarden distinguishes four strata making up the structure of the literary work of art: the stratum of word sounds and sound-complexes; the stratum of meaning units; the stratum of represented objectivities (characters, actions, settings, and so forth); and the stratum of schematized aspects (perspectives under which the represented objectivities are given to the reader). It is not only works of literature which manifest this four-fold structure but also certain borderline cases such as newspaper articles, scientific works, biographies, and so forth. (...) Ingarden specifies what is characteristic of a work of literature by asserting that all declarative sentences appearing in the stratum of meaning units of such work possess what he calls a quasi-judgmental character. We discuss here Ingarden’s theory of quasi-judgments and draw out its implication that all works of literature are works of fiction through and through. (shrink)

The dominant theory of judgment in 1870 was one or other variety of combination theory: the act of judgment is an act of combining concepts or ideas in the mind of the judging subject. In the decades to follow a succession of alternative theories arose to address defects in the combination theory, starting with Bolzano’s theory of propositions in themselves, Brentano’s theory of judgment as affirmation or denial of existence, theories distinguishing judgment act from judgment content advanced by Brentano’s students (...) Twardowski, Husserl and Meinong, and finally, Adolf Reinach’s addition of a linguistic dimension to the Brentano-Husserlian theory of judgment – an account of judgments as ways of doing things with words in what Reinach called ‘social acts’. (shrink)

There are some who defend a view of vagueness according to which there are intrinsically vague objects or attributes in reality. Here, in contrast, we defend a view of vagueness as a semantic property of names and predicates. All entities are crisp, on this view, but there are, for each vague name, multiple portions of reality that are equally good candidates for being its referent, and, for each vague predicate, multiple classes of objects that are equally good candidates for being (...) its extension. We provide a new formulation of these ideas in terms of a theory of granular partitions. We show that this theory provides a general framework within which we can understand the relation between vague terms and concepts on the one hand and correlated portions of reality on the other. We also sketch how it might be possible to formulate within this framework a theory of vagueness which dispenses with the notion of truth-value gaps and other artifacts of more familiar approaches. (shrink)

For corporate memory and enterprise ontology systems to be maximally useful, they must be freed from certain barriers placed around them by traditional knowledge management paradigms. This means, above all, that they must mirror more faithfully those portions of reality which are salient to the workings of the enterprise, including the changes that occur with the passage of time. The purpose of this chapter is to demonstrate how theories based on philosophical realism can contribute to this objective. We discuss how (...) realism-based ontologies (capturing what is generic) combined with referent tracking (capturing what is specific) can play a key role in building the robust and useful corporate memories of the future. (shrink)

Formalisms based on one or other flavor of Description Logic (DL) are sometimes put forward as helping to ensure that terminologies and controlled vocabularies comply with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) does indeed comply 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 these 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 the phenomenon of multiple inheritance. The advantages and limitations of our approach are also discussed. (shrink)

There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva (...) diagnostics made possible by the Saliva Ontology and SDxMart. (shrink)

The dominant theory of judgment in 1870 was one or other variety of combination theory: the act of judgment is an act of combining concepts or ideas in the mind of the judging subject. In the decades to follow a succession of alternative theories arose to address defects in the combination theory, starting with Bolzano’s theory of propositions in themselves, Brentano’s theory of judgment as affirmation or denial of existence, theories distinguishing judgment act from judgment content advanced by Brentano’s students (...) Twardowski, Husserl and Meinong, and finally, Adolf Reinach’s addition of a linguistic dimension to the Brentano-Husserlian theory of judgment – an account of judgments as ways of doing things with words in what Reinach called ‘social acts’. (shrink)

It is now increasingly accepted that many existing biological and medical ontologies can be improved by adopting tools and methods that bring a greater degree of logical and ontological rigor. In this chapter we will focus on the merits of a logically sound approach to ontologies from a methodological point of view. As we shall see, one crucial feature of a logically sound approach is that we have clear and functional definitions of the relational expressions such as ‘is a’ and (...) ‘part of ’. (shrink)

The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical principles that is designed to (...) comprehend the basic formal relationships that structure both reality and the ways humans perceive and communicate about reality. (shrink)

A comparison of six alternative definitions of the term 'cellular pathway' against the background of ontological realism.

This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to develop a simple temporal theory.

Affective science conducts interdisciplinary research into the emotions and other affective phenomena. Currently, such research is hampered by the lack of common definitions of terms used to describe, categorise and report both individual emotional experiences and the results of scientific investigations of such experiences. High quality ontologies provide formal definitions for types of entities in reality and for the relationships between such entities, definitions which can be used to disambiguate and unify data across different disciplines. Heretofore, there has been little (...) effort directed towards such formal representation for affective phenomena, in part because of widespread debates within the affective science community on matters of definition and categorization. To address this requirement, we are developing an Emotion Ontology (EMO). (shrink)

The three young philosophers Kevin Mulligan, Peter Simons and Barry Smith have become well-known in the last few years especially in German-speaking analytical philosophy and phenomenology circles. This is on the one hand as a result of their historical and systematic philosophical work; but it is also because of the provocative way in which they represent their philosophy. Because they often appear in threes, they have become known as the "gang of three" or "three musketeers" or even – and (...) this in an admiring sense – "mafiosi" (Rescher). They are known primarily for the small workshops they have been organizing in uncomplicated Anglo-Saxon manner all over Europe. Their goal has been to show that analytic philosophy as it has been pursued up to now is in need of reform and also that the history of scientific philosophizing is not identical to the history of Anglo-Saxon analytic philosophy. Above all, they have tried to make more well known the Austrian tradition of scientific philosophy, and they can be given credit for having done much to promote the current interest in this tradition, which means: the history of Austrian philosophy of the 19th and early 20th centuries and its historical context in the Austro-Hungarian Empire. (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)

On the consequences of the interplay between the diversity of ethnic, national, cultural and linguistic groupings in the Austro-Hungarian Empire.

Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ is often used by philosophers as a synonym for ‘metaphysics’ (literally: ‘what comes after the Physics’), a term which was used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. The term ‘ontology’ (or ontologia) was itself coined in 1613, independently, by two philosophers, Rudolf Göckel (...) (Goclenius), in his Lexicon philosophicum and Jacob Lorhard (Lorhardus), in his Theatrum philosophicum. The first occurrence in English recorded by the OED appears in Bailey’s dictionary of 1721, which defines ontology as ‘an Account of being in the Abstract’. (shrink)

The objective of this research programme is to contribute to the establishment of the emerging science of Formal Ontology in Information Systems via a collaborative project involving researchers from a range of disciplines including philosophy, logic, computer science, linguistics, and the medical sciences. The re­searchers will work together on the construction of a unified formal ontology, which means: a general framework for the construction of ontological theories in specific domains. The framework will be constructed using the axiomatic-deductive method of modern (...) formal ontology. It will be tested via a series of applications relating to on-going work in Leipzig on medical taxonomies and data dictionaries in the context of clinical trials. This will lead to the production of a domain-specific ontology which is designed to serve as a basis for applications in the medical field. (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)

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)

Clinical guidelines are special types of plans realized by collective agents. We provide an ontological theory of such plans that is designed to support the construction of a framework in which guideline-based information systems can be employed in the management of workflow in health care organizations. The framework we propose allows us to represent in formal terms how clinical guidelines are realized through the actions of are realized through the actions of individuals organized into teams. We provide various levels of (...) implementation representing different levels of conformity on the part of health care organizations. Implementations built in conformity with our framework are marked by two dimensions of flexibility that are designed to make them more likely to be accepted by health care professionals than standard guideline-based management systems. They do justice to the fact 1) that responsibilities within a health care organization are widely shared, and 2) that health care professionals may on different occasions be non-compliant with guidelines for a variety of well justified reasons. The advantage of the framework lies in its built-in flexibility, its sensitivity to clinical context, and its ability to use inference tools based on a robust ontology. One disadvantage lies in its complicated implementation. (shrink)

Hintergrund: Biomedizinische Ontologien existieren unter anderem zur Integration von klinischen und experimentellen Daten. Um dies zu erreichen ist es erforderlich, dass die fraglichen Ontologien von einer großen Zahl von Benutzern zur Annotation von Daten verwendet werden. Wie können Ontologien das erforderliche Maß an Benutzerfreundlichkeit, Zuverlässigkeit, Kosteneffektivität und Domänenabdeckung erreichen, um weitreichende Akzeptanz herbeizuführen? -/- Material und Methoden: Wir konzentrieren uns auf zwei unterschiedliche Strategien, die zurzeit hierbei verfolgt werden. Eine davon wird von SNOMED CT im Bereich der Medizin vertreten, die (...) andere im Bereich der Biologie und Biomedizin von der OBO Foundry. Es soll aufgezeigt werden, wie die Verpflichtung zu speziellen Kriterien der Ontologieentwicklung die Nützlichkeit und Effektivität der Ontologien positiv beeinflusst, indem die Pflege der terminologischen Systeme und ihre Interoperabilität vereinfacht werden. -/- Ergebnisse: SNOMED CT und die OBO Foundry unterscheiden sich grundlegend in ihren Ansätzen und Zielen. Unabhängig davon kann jedoch ein allgemeiner Trend zur strengeren Formalisierung und Fokussierung auf Interoperabilität zwischen unterschiedlichen Domänen und ihren Repräsentationen beobachtet werden. (shrink)

Neo-Kantianism is common conceived as a philosophy ‘from above’, excelling in speculative constructions – as opposed to the attitude of patient description which is exemplified by the phenomenological turn ‘to the things themselves’. When we study the work of Emil Lask in its relation to that of Husserl and the phenomenologists, however, and when we examine the influences moving in both directions, then we discover that this idea of a radical opposition is misconceived. Lask himself was influenced especially by Husserl’s (...) Logical Investigations, and Husserl, especially in his later writings, was in some respects closer to Kant than were the Neo-Kantians. The contrast between the two philosophers can be illustrated by looking at their view of the objects of judgment; for Lask, as for Kant, judgment can relate to the thing as such only in an indirect way. The world of judgment is a collection of ‘imitations holding a secondary position’. It is cut apart from the plain world of real things by what Lask calls a ‘chasm of artificiality and imagery’. For Husserl, in contrast, the object of judgment is a ‘Sachverhalt’ or state of affairs, something ontologically ‘positive’ in the sense that it is an entity in its own right and does not point beyond itself in the manner of a mere sign or proxy for something else. (shrink)

Semantic interoperability requires the use of standards, not only for Electronic Health Record (EHR) data to be transferred and structurally mapped into a receiving repository, but also for the clinical content of the EHR to be interpreted in conformity with the original meanings intended by its authors. Accurate and complete clinical documentation, faithful to the patient’s situation, and interoperability between systems, require widespread and dependable access to published and maintained collections of coherent and quality-assured semantic resources, including models such as (...) archetypes and templates that would (1) provide clinical context, (2) be mapped to interoperability standards for EHR data, (3) be linked to well specified, multi-lingual terminology value sets, and (4) be derived from high quality ontologies. Wide-scale engagement with professional bodies, globally, is needed to develop these clinical information standards. (shrink)

The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of data. To provide effective solutions computers need to integrate data deriving from myriad heterogeneous sources by bringing the data together within a single framework. The meeting brought together leaders in the field of what are called "top-level ontologies" to address this issue, and to establish strategies among leaders in (...) the field of biomedical ontology for the creation of interoperable biomedical ontologies which will serve the goal of useful data integration. (shrink)

Response to the paper “The Biomedical Ethics Ontology Proposal: Excellent Aims, Questionable Methods" by James DuBois, published in the Journal of Empirical Research on Human Research Ethics.

Description logics and other formal devices are frequently used as means for preventing or detecting mistakes in ontologies. Some of these devices are also capable of inferring the existence of inter-concept relationships that have not been explicitly entered into an ontology. A prerequisite, however, is that this information can be derived from those formal definitions of concepts and relationships which are included within the ontology. In this paper, we present a novel algorithm that is able to suggest relationships among existing (...) concepts in a formal ontology that are not derivable from such formal definitions. The algorithm exploits cross-lingual information that is implicitly present in the collection of terms used in various languages to denote the concepts and relationships at issue. By using a specific experimental design, we are able to quantify the impact of cross-lingual information in coping with underspecification in formal ontologies. (shrink)

The theory of granular partitions is designed to capture in a formal framework important aspects of the selective character of common-sense views of reality. It comprehends not merely the ways in which we can view reality by conceiving its objects as gathered together not merely into sets, but also into wholes of various kinds, partitioned into parts at various levels of granularity. We here represent granular partitions as triples consisting of a rooted tree structure as first component, a domain satisfying (...) the axioms of Extensional Mereology as second component, and a mapping (called ’projection’) of the first into the second as a third component. We define ordering relations among granular partitions the resulting structures are called partition frames. We then introduce an axiomatic theory which sentences are interpreted in partition frames. (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)

When does a human being begin to exist? We argue that it is possible, through a combination of biological fact and philosophical analysis, to provide a definitive answer to this question. We lay down a set of conditions for being a human being, and we determine when, in the course of normal fetal development, these conditions are first satisfied. Issues dealt with along the way include: modes of substance-formation, twinning, the nature of the intra-uterine environment, and the nature of the (...) relation between fetus and mother. (shrink)

In the specific case of geography, the real world consists on the one hand of physical geographic features (bona fide objects) and on the other hand of various fiat objects, for example legal and administrative objects, including parcels of real estate, areas of given soil types, census tracts, and so on. It contains in addition the beliefs and actions of human beings directed towards these objects (for example, the actions of those who work in land registries or in census bureaux), (...) and the relations between these beliefs and actions and their targets. The document is a Report of the Specialist Meeting held under the auspices of the Varenius Project. (shrink)

The dominant theory of judgment in 1870 was one or other variety of combination theory: the act of judgment is an act of combining concepts or ideas in the mind of the judging subject. In the decades to follow a succession of alternative theories arose to address defects in the combination theory, starting with Bolzano’s theory of propositions in themselves, Brentano’s theory of judgment as affirmation or denial of existence, theories distinguishing judgment act from judgment content advanced by Brentano’s students (...) Twardowski, Husserl and Meinong, and finally, Adolf Reinach’s addition of a linguistic dimension to the Brentano-Husserlian theory of judgment – an account of judgments as ways of doing things with words in what Reinach called ‘social acts’. (shrink)

This paper offers an overview of the philosophical work on epistemic injustices as it relates to psychiatry. After describing the development of epistemic injustice studies, we survey the existing literature on its application to psychiatry. We describe how the concept of epistemic injustice has been taken up into a range of debates in philosophy of psychiatry, including the nature of psychiatric conditions, psychiatric practices and research, and ameliorative projects. The final section of the paper indicates future directions for philosophical research (...) of epistemic injustices and psychiatry, concerning neurocognitive disorders, identity prejudices in psychiatric illness, concepts of epistemic privilege in psychiatry, and the prospects for combining phenomenological psychopathology and epistemic justice. We argue that much remains to be done in the conceptualization of these epistemic injustices and suggest that this future work should be multidisciplinary in character and sensitive to the phenomenology of psychiatric conditions. (shrink)

A dealbreaker, in the sense developed in this essay, is a relationship between a person's psychology and an aspect of an artwork to which they are exposed. When a person has a dealbreaking aversion to an aspect of a work, they are blocked from embracing the work's aesthetically positive features. I characterize dealbreakers, distinguish this response from other negative responses to an artwork, and argue that the presence or absence of a dealbreaker is in some cases an appropriate target of (...) moral evaluation. I then use the concept of dealbreakers to develop a new approach to the question of our moral obligations with respect to the work of immoral artists, arguing that there is no general obligation binding us to cultivate or eliminate a dealbreaking aversion to their work. I conclude by suggesting several other philosophical debates that could benefit from a focus on dealbreakers. (shrink)

Linda Martín Alcoff and others have emphasised that the discipline of philosophy suffers from a ‘demographic problem’. The persistence of this problem is partly the consequence of various forms of resistance to efforts to address the demographic problem. Such resistance is complex and takes many forms and could be responded to in different ways. In this paper, I argue that our attempts to explain and understand the phenomenon of resistance should use a kind of explanatory pluralism that, following Quassim Cassam, (...) I call multidimensionalism. I describe four general kinds of resistance and consider varying explanations, focusing on those focused on vices and social structures. I argue that vice-explanations and structural- explanations are both mutually consistent and mutually entailing. If so, there is no need to choose between vice explanations and structural explanations or any other kinds of explanation. We can and should be multidimensionalists: using many together is better. (shrink)