Barry Smith (forthcoming). Document Acts. In Anita Konzelmann-Ziv & Hans Bernhard Schmid (eds.), Institutions, Emotions, and Group Agents. Contributions to Social Ontology. Springer.
The theory of document acts is an extension of the more traditional theory of speech acts advanced by Austin and Searle. It is designed to do justice to the ways in which documents can be used to bring about a variety of effects in virtue of the fact that, where speech is evanescent, documents are continuant entities. This means that documents can be preserved in such a way that they can be inspected and modified at successive points in time and (...) grouped together into enduring document complexes. We outline some components of a theory of document acts, and show how it can throw light on certain problems in Searle’s ontology of social reality. (shrink)
If we are to develop efficient, reliable and secure means for sharing information across healthcare systems and organizations, then a careful analysis of human actions will be needed. To address this need, the HL7 organization has proposed its Reference Information Model (RIM), which is designed to provide a comprehensive representation of the entire domain of healthcare centered around the phenomenon of human action. Taking the Basic Formal Ontology as our starting point, we examine the RIM from an ontological point of (...) view, describing how it fails to provide a representation of the healthcare domain which would enjoy the sort of clarity, coherence, rigor and completeness that is claimed on its behalf. (shrink)
Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such (...) a way that – once formulated in a suitable formal language – the ontologies can be used for sophisticated automated reasoning applications. Reference ontologies can be applied across different contexts in which different, and often mutually incompatible, domain-specific vocabularies have traditionally been used. In this contribution we describe the Mental Functioning Ontology (MF) and Mental Disease Ontology (MD), two realism-based ontologies currently under development for the description of humanmental functioning and disease. We describe the structure and upper levels of the ontologies and preliminary application scenarios, and identify some open questions. (shrink)
Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...) needs to be integrated in order to promote a more comprehensive understanding of underlying processes and mechanisms, and this need for integration only becomes more pressing with our increase in understanding of differences among individuals and populations at the molecular level concerning susceptibility to specific illnesses. Substance addiction is a particularly relevant public health challenge in the developed world, affecting a substantial percentage of the population, often co-morbid with other illnesses such as mood disorders. Currently, however, there is no straightforward automated method to combine data of relevance to the study of substance addiction across multiple disciplines and populations. In this contribution, we describe a framework of interlinked, interoperable bio-ontologies for the annotation of primary research data relating to substance addiction, and discuss how this framework enables easy integration of results across disciplinary boundaries. We describe entities and relationships relevant for the description of addiction within the Mental Functioning Ontology, Chemical Entities of Biological Interest Ontology, Protein Ontology, Gene Ontology and the Neuroscience Information Framework ontologies. (shrink)
We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) perspectives within a single framework. We (...) examine how BFO-conformant domain ontologies can deal with the consistent representation of scientific data deriving from the measurement of processes of different types, and we outline on this basis the first steps of an approach to the classification of such processes within the BFO framework. (shrink)
We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping of intelligence data, and (...) describe how it can be applied in an agile fashion to new data resources in ways that address immediate needs of intelligence analysts. (shrink)
This essay is a contribution to social ontology, drawing on the work of John Searle and of Hernando de Soto. At the center of the argument is the proposition advanced by de Soto in his Mystery of Capital to the effect that many of the entities which structure our contemporary social reality are entities which exist in virtue of the fact that there are (paper or digital) documents which support their existence. I here develop de Soto’s argument further, focusing specifically (...) on the ontological problems raised by a family of new types of social phenomena – exemplified most dramatically in the domain of finance for example in the form of what are called ‘structured investment vehicles’ – made possible as a result of the employment of computer technology in entity creation. I address also Searle’s most recent work on social ontology, and conclude with an appendix on the theory of documentality advanced by Maurizio Ferraris. (shrink)
As available intelligence data and information expand in both quantity and variety, new techniques must be deployed for search and analytics. One technique involves the semantic enhancement of data through the creation of what are called ‘ontologies’ or ‘controlled vocabularies.’ When multiple different bodies of heterogeneous data are tagged by means of terms from common ontologies, then these data become linked together in ways which allow more effective retrieval and integration. We describe a simple case study to show how these (...) benefits are being achieved, and we describe our strategy for developing a suite of ontologies to serve the needs of the war-fighter in the ever more complex battlespace environments of the future. (shrink)
ABSTRACT: Differences of evaluative judgments are often assumed to be a reason to prefer pluralism, relativism or subjectivism to objectivism, and this preference is even more pronounced in the case of judgements of taste. A comparison between perceptual and moral disagreements, however, enables us to understand that differences in judgments may be due to a difference in access to the situation or object, and not necessarily to a difference in value. The feeling of irresolvable differences that sometimes arises in situations (...) of evaluation, may not hold in the absence of objective values and / or common values, but be due to a difficulty or inability to capture the perspective, or circumstances of assessment wherein the other agents are placed. (shrink)
Can we test philosophical thought experiments, such as whether people would enter an experience machine or would leave one once they are inside? Dan Weijers, responding to me "Can We Test the Experience Machine?" suggests that since “rational” subjects (e.g. students taking surveys in class) are believable, we can do so. By contrast, I argue that because such subjects have the wrong affect (i.e. emotional state), such tests are worthless. Moreover, understood as a general policy, such pretend testing would ruin (...) the results of most psychological tests, such as those of helping behavior, attitudes to authority, moral transgressions, etc. However, I argue that certain philosophical thought experiments do not require us to have any affect to understand them, and so can be tested. Generally, experimental philosophy must adhere to this limit, on pain of offering vacuous results. (shrink)
When Huxley quotes the famous Jefferson line in Brave New World Revisited—"If a nation expects to be ignorant and free . . . it expects what never was and never will be"2—there is something, on the face, humorously explicit to it. The state of civilization the brave new world is in seems to speak directly to this point. Brave new worlders are ignorant and conspicuously not free; they "[like] what [they've] got to do"3 because they have been decanted and conditioned (...) by the corporate government, the World State (an ironical reversal of government by the people to a people by the government). This cursory assessment, however, obscures another possibility, one that touches on the satirical poignancy and relevance of .. (shrink)
This article looks at the ways in which globalization and modernization have led to a number of changes in Buddhism. These include both the cultures in which it is practiced as well as the form that this practice takes. One consequence of existing within new cultures is that a religion that has been the majority faith for over 1000 years in many Asian countries is now a minority faith in the West. This study tests the hypothesis that religious doctrinal differences (...) are relative and the borders between religious organizations are malleable. In order to overcome inherent difficulties in studying small atypical organizations, these analyses rely on new methodological techniques by building on the internet and website links as a sociological tool. This study examines the use of websites by American Buddhists, both to determine the networks they are part of and what content they use. Comparisons are drawn to the similarities between American Buddhism as a small foreign religion and independent non-denominational Christian congregations. Consequences for studying Buddhism and future avenues of research involving the internet are discussed. (shrink)
We describe an ontology of philosophy that is designed to aid navigation through philosophical literature, including literature in the form of encyclopedia articles and textbooks and in both printed and digital forms. The ontology is designed also to serve integration and structuring of data pertaining to the philosophical literature, and in the long term also to support reasoning about the provenance and contents of such literature, by providing a representation of the philosophical domain that is oriented around what philosophical literature (...) is about. (shrink)
Affective science conducts interdisciplinary research into the emotions and other affective phenomena. Currently, such research is hampered by the lack of common definitions of te rms 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. We describe our efforts towards developing an Emotion Ontology (EMO) to serve the affective science community. We here focus on conformity to the BFO upper ontology and disambiguation of polysemous terminology. (shrink)
We describe a strategy for integration of data that is based on the idea of semantic enhancement. The strategy promises a number of benefits: it can be applied incrementally; it creates minimal barriers to the incorporation of new data into the semantically enhanced system; it preserves the existing data (including any existing data-semantics) in their original form (thus all provenance information is retained, and no heavy preprocessing is required); and it embraces the full spectrum of data sources, types, models, and (...) modalities (including text, images, audio, and signals). The result of applying this strategy to a given body of data is an evolving Dataspace that allows the application of a variety of integration and analytic processes to diverse data contents. We conceive semantic enhancement (SE) as a lightweight and flexible process that leverages the richness of the structured contents of the Dataspace without adding storage and processing burdens to what, in the intelligence domain, will be an already storage- and processing-heavy starting point. SE works not by changing the data to which it is applied, but rather by adding an extra semantic layer to this data. We sketch how the semantic enhancement approach can be applied consistently and in cumulative fashion to new data and data-models that enter the Dataspace. (shrink)
We present an ontology of pain and of other pain-related phenomena, building on the definition of pain provided by the International Association for the Study of Pain (IASP). Our strategy is to identify an evolutionarily basic canonical pain phenomenon, involving unpleasant sensory and emotional experience based causally in localized tissue damage that is concordant with that experience. We then show how different variant cases of this canonical pain phenomenon can be distinguished, including pain that is elevated relative to peripheral trauma, (...) pain that is caused neuropathically (thus with no necessary peripheral stimulus), and pain reports arising through deception either of self or of others. We describe how our approach can answer some of the objections raised against the IASP definition, and sketch how it can be used to support more sophisticated discrimination of different types of pain resulting in improved data analysis that can help in advancing pain research. (shrink)
Robert Nozick famously asks us whether we would plug in to an experience machine, or whether we would insist upon ‘living in contact with reality’. Felipe De Brigard, after conducting a series of empirical ‘inverted’ experience machine studies, suggests that this is a false dilemma. Rather, he says, '…the fact is that people tend to prefer the state of affairs they are in currently,' or the status quo. In this paper, I argue that these studies are a test case for (...) ‘experimental philosophy’ as such. Specifically, I argue that De Brigard offers a series of faulty studies, and so, reaches unfounded conclusions. More generally, I argue that certain philosophical thought experiments cannot be tested empirically at all, and this limits what experimental philosophy can do. (shrink)
Book review of Maxine Sheets-Johnstone’s The Roots of Morality Content Type Journal Article Pages 1-4 DOI 10.1007/s11097-011-9206-2 Authors Benedict Smith, Department of Philosophy, Durham University, 50 Old Elvet, Durham, DH1 3HN UK Journal Phenomenology and the Cognitive Sciences Online ISSN 1572-8676 Print ISSN 1568-7759.
Aircraft with increasingly high performance were important to the war effort in World War II. Changes in technology allowed aircraft to reach faster speeds and to complete missions at higher altitudes. With these changes came new obstacles for pilots who had to tolerate these stresses. Of primary concern to the U.S. War Department was the loss of consciousness that often occurred with high-speed maneuvers and especially during pull-up after dive-bombing missions. In some cases, pilots would experience up to 9G of (...) force during rapid ascent, much more than the 6G threshold that typically leads to loss of consciousness. In 1941, a research team in Red Wing, MN, proposed experiments to elucidate the mechanism .. (shrink)
While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. (...) We here present a view of mental disease that is based on ontological realism and which follows the principles embodied in Basic Formal Ontology (BFO) and in the application of BFO in the Ontology of General Medical Science (OGMS). We analyzed statements about what counts as a mental disease provided (1) in the research agenda for the DSM-V, and (2) in Pies' model. The results were used to assess whether the representational units of BFO and OGMS were adequate as foundations for a formal representation of the entities in reality that these statements attempt to describe. We then analyzed the representational units specific to mental disease and provided corresponding definitions. Our key contributions lie in the identification of confusions and conflations in the existing terminology of mental disease and in providing what we believe is a framework for the sort of clear and unambiguous reference to entities on the side of the patient that is needed in order to avoid these confusions in the future. (shrink)
This is the third draft of a paper that aims to clarify the apparent contradictions in the views presented in certain standards and other specifications of health informatics systems, contradictions which come to light when the latter are evaluated from the perspective of realist philosophy. One of the origins of this document was Klein’s discussion paper of 2005-07-02 entitled “Conceptology vs Reality” and the responses from Smith, as well as the several hours of discussions during the 2005 MIE meeting in (...) Geneva. (shrink)
Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)
In uttering a sentence we are often taken to assert more than its literal meaning — though we sometimes assert less. Robyn Carston and others take this phenomenon to show that what is said or asserted by a speaker on an occasion of utterance is usually a contextuallyenriched version of the semantic content of the sentence. I shall argue that we can resist this conclusion if we recognize that what we think we are asserting, or take others to be asserting, (...) involves selective attention to one of the ways a sentence could be true and neglects others. Most of the time people converge in their selective attention and so communication is not impaired. Though in the case of sentences involving predicates of taste, people’s attention to different aspect of the truth conditions leads to seemingly intractable disputes. I will propose a treatment of such cases on which speakers mean the same by a sentence, assert no more than its semantic content, hold conflicting opinions about its truth-value, and are both right. (shrink)
Machine generated contents note: Introduction -- Moral Philosophy and Experience -- Moral Particularism -- Perception and The Myth of the Moral Given -- Moral Judgement -- Moral Phenomenology -- The Space of Moral Reasons -- Conclusion -- Index.
Political life is and ought to be entirely autonomous from theology; religion belongs to the private sphere and political community is ruled by the sovereign power of the state in accordance with “secular reasons.” This is commonly referred to as the modern settlement over the vexed relationship between politics and religious faith, and many have characterized it as one of the greatest legacies of the Enlightenment. Against this positive assessment, I shall argue that in hisearly De Regno, Thomas Aquinas offers (...) compelling theological and philosophical reasons to doubt the coherence of the modern settlement and its compatibility with Christian tradition. According to this view, political practice must be reinterpreted according to a distinctly Christian understanding of the human person. Political life is not autonomous; rather it essentially requires theological reorientation. (shrink)
The Joint Battle Management Language (JBML) is an XML-based language designed to allow Command and Control (C2) systems to interface easily with Modeling and Simulation (M&S) systems. While some of the XML-tags defined in this language correspond to types of entities that exist in reality, others are mere syntactic artifacts used to structure the messages themselves. Because these two kinds of tags are not formally distinguishable, JBML messages in effect confuse data with what the data represent. In this paper we (...) show how a realism-based ontology combined with a rule language can be used to make these distinctions explicit. The approach allows storage of the contents of JBML messages in a Referent Tracking System in a format that mimics the structure of reality thereby providing an aid to message validation. (shrink)
Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in the (...) form of a list of terms and definitions designed to provide a consistent starting point for the representation of both disease and diagnosis in information systems in the future. (shrink)
The Universal Core (UCore) is a central element of the National Information Sharing Strategy that is supported by multiple U.S. Federal Government Departments, by the intelligence community, and by a number of other national and international institutions. The goal of the UCore initiative is to foster information sharing by means of an XML schema providing consensus representations for four groups of universally understood terms under the headings who, what, when, and where. We here describe a project to create an ontology-based (...) supporting layer for UCore, entitled ‘Universal Core Semantic Layer’ (UCore SL), and describe how UCore SL can be applied to further UCore’s information sharing goals. (shrink)
The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)
The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)
The Oxford Handbooks series is a major new initiative in academic publishing. Each volume offers an authoritative and up-to-date survey of original research in a particular subject area. Specially commissioned essays from leading figures in the discipline give critical examinations of the progress and direction of debates. Oxford Handbooks provide scholars and graduate students with compelling new perspectives upon a wide range of subjects in the humanities and social sciences. -/- Ernie Lepore and Barry Smith present the definitive reference work (...) for this diverse and fertile field of philosophy. A superb international team contribute more than forty brand-new essays covering topics from the nature of language to meaning, truth, and reference, and the interfaces of philosophy of language with linguistics, psychology, logic, epistemology, and metaphysics. It will be an essential resource for anyone working in the central areas of philosophy, for linguists interested in syntax, semantics, and pragmatics, and for psychologists and cognitive scientists working on language. (shrink)
This volume shows, in a non-technical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ...
Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some will find self-evident) (...) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology development work being undertaken in support of scientific research. Ontologies created by scientists must, of course, be associated with implementations satisfying the requirements of software engineering. But the ontologies are not themselves engineering artifacts, and to conceive them as such brings grievous consequences. Rather, ontologies such as the GO are in different respects comparable to scientific theories, to scientific databases, and to scientific journal publications. Such a view implies a new conception of what is involved in the authoring, maintenance and application of ontologies in scientific contexts, and therewith also a new approach to the evaluation of ontologies and to the training of ontologists. (shrink)
Consider a game of blind chess between two chess masters that is recorded in some standard chess notation. The recording is a representation of the game. But what is the game itself? We argue that it a special sort of quasi-abstract pattern, something that is:(i) like abstract entities such as numbers or forms, in that it is both nonphysical and nonpsychological; but at the same time, (ii) through its association with specific players and a specific occasion, tied to time and (...) history. We discover other abstract patterns of this sort especially in the domains of law and commerce. This essay draws on the work in social ontology, we of Hernando de Soto and of John Searle to develop an ontology of the social world based on an analysis of the peculiar interdependence between quasi-abstract patterns and their representations in documents of different sorts. (shrink)
The new Chomskian orthodoxy denies that our linguistic competence gives us knowledge *of* a language, and that the representations in the language faculty are representations *of* anything. In reply, I have argued that through their intuitions speaker/hearers, (but not their language faculties) have knowledge of language, though not of any externally existing language. In order to count as knowledge, these intuitions must track linguistic facts represented in the language faculty. I defend this idea against the objections Collins has raised to (...) such an account. (shrink)
Qualitative research methods in sport often advocate that to understand others, obtain significant knowledge and do ethically admirable research we should empathise with our participants by imagining being them. In philosophy, it is likewise often assumed that we can overcome differences between people through moral imagination: putting ourselves in the place of others, we can share their points of view, merge with them, and enter into their embodied worlds. Drawing partly on the view that imagination is embodied and the philosophy (...) of Bakhtin and Levinas, along with research on people's experiences of becoming disabled through playing sport, this paper problematises the assumption that we can imagine ourselves differently situated or being another person. It argues that our imagination and ability to put ourselves in the place of others is constrained partly by embodied experience and otherness. Some reflections on what this might mean for disability and sport research are then offered. (shrink)
Digital Rights Management (DRM) covers the description, identification, trading, protection, monitoring and tracking of all forms of rights over both tangible and intangible assets. The Digital Object Identifier (DOI) system provides a framework for the persistent identification of entities involved in this domain. Although the system has been very well designed to manage object identifiers, some important questions relating to the creation and assignment of identifiers are left open. The paradigm of a Referent Tracking System (RTS) recently advanced in the (...) healthcare and life sciences environment is able to fill these gaps. This is demonstrated by pointing out inconsistencies in the existing DOI models and by showing how they can be corrected using an RTS. (shrink)
Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway (http://pir.georgetown.edu/pro). (shrink)
The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)
The IPAP Schizophrenia Algorithm was originally designed in the form of a flow chart to help physicians optimise the treatment of schizophrenic patients. We examined the current version from the perspective of recent work on terminologies and ontologies thereby drawing on the resources of Basic Formal Ontology, and this with the objective to make the algorithm appropriate for Semantic Web applications. We found that Basic Formal Ontology is a rich enough theory to represent all the entities involved and that applying (...) the theory to the IPAP schizophrenia algorithm results in a representation that can be used by software agents to perform monitoring and control in a referent tracking environment. (shrink)
Ernie Lepore and Barry Smith present the definitive reference work for this diverse and fertile field of philosophy. A superb international team contribute forty brand-new essays covering topics from the nature of language to meaning, truth, and reference, and the interfaces of philosophy of language with linguistics, psychology, logic, epistemology, and metaphysics. It will be an essential resource for anyone working in the central areas of philosophy, for linguists interested in syntax, semantics, and pragmatics, and for psychologists and cognitive scientists (...) working on language. (shrink)
Philosophy in the West divides into three parts: Analytic Philosophy (AP), Continental Philosophy (CP), and History of Philosophy (HP). But all three parts are in a bad way. AP is sceptical about the claim that philosophy can be a science, and hence is uninterested in the real world. CP is never pursued in a properly theoretical way, and its practice is tailor-made for particular political and ethical conclusions. HP is mostly developed on a regionalist basis: what is studied is determined (...) by the nation or culture to which a philosopher belongs, rather than by the objective value of that philosopher’s work. Progress in philosophy can only be attained by avoiding these pitfalls. (shrink)
Introduction: Scandals of Knowledge -- Pre-Post-Modern Relativism -- Netting Truth: Ludwik Fleck's Constructivist Genealogy -- Cutting-Edge Equivocation: Conceptual Moves and Rhetorical Strategies in Contemporary Anti-Epistemology -- Disciplinary Cultures and Tribal Warfare: The Sciences and the Humanities Today -- Super Natural Science: The Claims of Evolutionary Psychology -- Animal Relatives, Difficult Relations.
The world of ontology development is full of mysteries. Recently, ISO Standard 15926 (“Lifecycle Integration of Process Plant Data Including Oil and Gas Production Facilities”), a data model initially designed to support the integration and handover of large engineering artefacts, has been proposed by its principal custodian for general use as an upper level ontology. As we shall discover, ISO 15926 is, when examined in light of this proposal, marked by a series of quite astonishing defects, which may however provide (...) general lessons for the developers of ontologies in the future. (shrink)
It is only by fixing on agreed meanings of terms in biomedical terminologies that we will be in a position to achieve that accumulation and integration of knowledge that is indispensable to progress at the frontiers of biomedicine. Standardly, the goal of fixing meanings is seen as being realized through the alignment of terms on what are called ‘concepts’. Part I addresses three versions of the concept-based approach – by Cimino, by Wüster, and by Campbell and associates – and surveys (...) some of the problems to which they give rise, all of which have to do with a failure to anchor the terms in terminologies to corresponding referents in reality. Part II outlines a new, realist solution to this anchorage problem, which sees terminology construction as being motivated by the goal of alignment not on concepts but on the universals (kinds, types) in reality and thereby also on the corresponding instances (individuals, tokens). We outline the realist approach, and show how on its basis we can provide a benchmark of correctness for terminologies which will at the same time allow a new type of integration of terminologies and electronic health records. We conclude by outlining ways in which the framework thus defined might be exploited for purposes of diagnostic decision-support. (shrink)
Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a (...) proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)
Right now my conscious experience is directed at part of the world. It takes in some aspects of things around me and not others. Some bits of the world occupy my attention, other worldly goings on condition or colour the character of my current perceptual experience. I experience buildings in view through the window, the clothes in the corner of the room, the colour of the walls, the plate with breads, the coffee mugs, the smell of fresh laundry, the muffled (...) sounds of someone in the kitchen, the sounds from the street: a sequence of things that in turn capture my attention moment to moment. And all the while thoughts occur to me, modulating my conscious awareness. I have no doubt that the world and my place in it, together with my recent past history, explains the particular form my consciousness takes right now. But what shape does that explanation take? Things out there beyond the boundaries of my skin enter into the conscious events I undergo. The inner is in this way shaped and determined by those outer things that impress themselves on the mind. What is it, though, for consciousness of this kind to go on at all? (shrink)
The critic Cyril Connolly once pointed out that diarists don’t make novelists. He went on to describe the problem for the would-be writer. “Writing for oneself: no public. Writing for others: no privacy” (Cyril Connolly, Journal). This paper addresses Connolly's worry about the public ad private: how can we reconcile the inner and conscious dimension of speech with its outer and public dimension? For if what people mean by their words involves, or consists in, what they have in mind when (...) they speak then how can what someone has in mind — the meaning she attaches to her words — be at the same time publicly accessible to others on the basis of her behaviour? The issue is whether there is a notion of the linguistic meaning of an expression that can do justice to both speakers’ inner experience of comprehension and to what is outwardly available in their public practice. (shrink)
Ernie Lepore and Barry Smith present the definitive reference work for this diverse and fertile field of philosophy. A superb international team contribute forty brand-new essays covering topics from the nature of language to meaning, truth, and reference, and the interfaces of philosophy of language with linguistics, psychology, logic, epistemology, and metaphysics. It will be an essential resource for anyone working in the central areas of philosophy, for linguists interested in syntax, semantics, and pragmatics, and for psychologists and cognitive scientists (...) working on language. (shrink)
EVERY speaker of a language knows a bewildering variety of linguistic facts, and will come to know many more. It is knowledge that connects sound and meaning. Questions about the nature of this knowledge cannot be separated from fundamental questions about the nature of language. The conception of language we should adopt depends on the part it plays in explaining our knowledge of language. This chapter explores options in accounting for language, and our knowledge of language, and defends the view (...) that individuals’ languages are constituted by the standing knowledge they carry from one speech situation to another. (shrink)
EVERY speaker of a language knows a bewildering variety of linguistic facts, and will come to know many more. It is knowledge that connects sound and meaning. Questions about the nature of this knowledge cannot be separated from fundamental questions about the nature of language. The conception of language we should adopt depends on the part it plays in explaining our knowledge of language. This chapter explores options in accounting for language, and our knowledge of language, and defends the view (...) that individuals’ languages are constituted by the standing knowledge they carry from one speech situation to another. (shrink)
In his latest book, Michael Devitt rejects Chomsky’s mentalist conception of linguistics. The case against Chomsky is based on two principal claims. First, that we can separate the study of linguistic competence from the study of its outputs: only the latter belongs to linguistic inquiry. Second, Chomsky’s account of a speaker’s competence as consisiting in the mental representation of rules of a grammar for his language is mistaken. I shall argue, fi rst, that Devitt fails to make a case for (...) separating the study of outputs from the study of competence, and second, that Devitt mis-characterises Chomsky’s account of competence, and so his objections miss their target. Chomsky’s own views come close to a denial that speaker’s have knowledge of their language. But a satisfactory account of what speakers are able to do will need to ascribe them linguistic knowledge that they use to speak and understand. I shall explore a conception of speaker’s knowledge of language that confi rms Chomsky’s mentalist view of linguistics but which is immune to Devitt’s criticisms. (shrink)
The Health Level 7 Reference Information Model (HL7 RIM) is lauded by its authors as ‘the foundation of healthcare interoperability’. Yet even after some 10 years of development work, the RIM is still subject to a variety of logical and ontological flaws, which has placed severe obstacles in the way of those who are called upon to develop implementations. We offer evidence that these obstacles are insurmountable and that the time has come to abandon an unworkable paradigm.
In this paper, I compare John Locke’s “memory theory” of personal identity and Memento (directed by Christopher Nolan). I argue that the plot of Memento is ambiguous, in that the main character (Leonard Shelby, played by Guy Pearce) seems to have two histories. As such, Memento is but a series of puzzle cases that intend to illustrate that, although our memories may not be chronologically related to one another, and may even be fused with the memories of other persons, those (...) memories still constitute personal identity. Just as Derek Parfit argues, perhaps there is no personal identity as such, since only survival (in some degree) matters to us. In Memento, Leonard Shelby is not identity to his former self, but survives to some extent. (shrink)
According to the most detailed articulation and defence of moral particularism, it is a metaphysical doctrine about the nature of reasons. This paper addresses aspects of particularist epistemology. In rejecting the existence and efficacy of principles in moral thinking and reasoning particularists typically appeal to a theory of moral knowledge which operates with a ‘perceptual’ metaphor. This is problematic. Holism about valence can give rise to a moral epistemology that is a metaethical variety of atomistic empiricism. To avoid what could (...) be called the Myth of the Moral Given, particularism has made use of a judgement-centred account of moral epistemology. This paper critically examines that account with reference to a proposed analogy between our moral knowledge and our knowledge of similarities. (shrink)
Abstract A meaningful life, we shall argue, is a life upon which a certain sort of valuable pattern has been imposed by the person in question?a pattern which involves in serious ways the person having an effect upon the world. Meaningfulness is thus a special kind of value which a human life can bear. Two interrelated difficulties face ths proposal. One concerns responsiblity: how are we to account for the fact that a life that satisfies the above criteria can have (...) more meaning than a life with the same positive outcomes but which lacks responsiblity on the part of the agent? The other turns on these outcomes themselves: how can the meaningfulness engendered by actions you perform now be affected by what those actions go on to produce in the future, perhaps even after your death? We provide a response to both of these difficulties. (shrink)
We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Version 04.08b of the NCI Thesaurus suffers from the same broad range (...) of problems that have been observed in other biomedical terminologies. For its further development, we recommend the use of a more principled approach that allows the Thesaurus to be tested not just for internal consistency but also for its degree of correspondence to that part of reality which it is designed to represent. (shrink)
