Based on the Ontology for General Medical Science, we propose definitions for biomarkers of various types of. These definitions provide not only a complete formal representation of what biomarkers are according to the Institute of Medicine (IOM), but also remove the ambiguities and inconsistencies encountered in the documentation provided by the IOM.

In this paper I want to show three things. First, that despite some similarities in their analyses of the history of philosophy there are substantial differences in the point or moral that Rorty and Heidegger want to draw. Secondly, that this difference derives from substantial differences, again despite some similarities, in their understanding of what it is to be human and in their conception of what philosophy is. Thirdly, as a consequence of these differences Heidegger should not be understood as (...) supporting Rorty’s proposals for the future of philosophy; and moreover, that from a Heideggerian perspective on philosophy we should be deeply suspicious of Rorty’s pragmatism. (shrink)

Presentation: Scientific misconduct and inappropriate behaviour – status and planned measures Authors: Werner Wegscheider (ETH); Aleksandra Radenovic (EPFL) .

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

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)

The Information Artifact Ontology (IAO) was created to serve as a domain‐neutral resource for the representation of types of information content entities (ICEs) such as documents, data‐bases, and digital im‐ages. We identify a series of problems with the current version of the IAO and suggest solutions designed to advance our understanding of the relations between ICEs and associated cognitive representations in the minds of human subjects. This requires embedding IAO in a larger framework of ontologies, including most importantly the Mental (...) Func‐tioning Ontology (MFO). It also requires a careful treatment of the aboutness relations between ICEs and associated cognitive representa‐tions and their targets in reality, which implies in turn a new treatment of the relation of truthmaking. (shrink)

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 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)

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 and in the application of BFO in the Ontology of General Medical Science. We analyzed statements about what counts as a mental disease provided in the research agenda for the DSM-V, and 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)

What makes science trustworthy to the public? This chapter examines one proposed answer: the trustworthiness of science is based at least in part on its independence from the idiosyncratic values, interests, and ideas of individual scientists. That is, science is trustworthy to the extent that following the scientific process would result in the same conclusions, regardless of the particular scientists involved. We analyze this "idiosyncrasy-free ideal" for science by looking at philosophical debates about inductive risk, focusing on two recent proposals (...) which offer different methods of avoiding idiosyncrasy: the high epistemic standards proposal and the democratic values proposal. (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)

Quality assurance in large terminologies is a difficult issue. We present two algorithms that can help terminology developers and users to identify potential mistakes. We demon­strate the methodology by outlining the different types of mistakes that are found when the algorithms are applied to SNOMED-CT. On the basis of the results, we argue that both formal logical and linguistic tools should be used in the development and quality-assurance process of large terminologies.

STIRNERs "Verdienst" geht im Grunde auf ein einziges Werk zurück: Der Einzige und sein Eigenthum erschienen 1844/45 in Leipzig. Hören wir also, was "berufene" Geister der Geschichte über ihn zu schreiben wußten: ARNOLD RUGE ein führender Kopf des sogenannten Vormärz der 48er Revolution des letzten Jahrhunderts, hat das Buch bei seinem ersten Erscheinen als "frischen Morgenruf im Lager der schlafenden Theoretiker" begrüßt. LUDWIG FEUERBACH nannte es, trotz einiger Einwände; das "Werk des genialsten und freiesten Schriftstellers, den er kenne". MAX NETTLAU (...) schreibt 1925, daß nur wenige Bücher so mißverstanden oder so verschiedenartig beurteilt werden wie dieses, "und viele Leser bleiben bei einem auf die Spitze getriebenen Individualismus oder Egoismus stehen, den sie herauslesen wollen". (shrink)

This essay argues that while the notion of collective responsibiility is incoherent if it is taken to be an application of the Kantian model of moral responsibility to groups, it is coherent -- and important -- if formulated in terms of the moral reactions that we can have to groups that cause harm in the world. I formulate collective responsibility as such and in doing so refocus attention from intentionality to the production of harm.

PURPOSE—A substantial fraction of the observations made by clinicians and entered into patient records are expressed by means of negation or by using terms which contain negative qualifiers (as in “absence of pulse” or “surgical procedure not performed”). This seems at first sight to present problems for ontologies, terminologies and data repositories that adhere to a realist view and thus reject any reference to putative non-existing entities. Basic Formal Ontology (BFO) and Referent Tracking (RT) are examples of such paradigms. The (...) purpose of the research here described was to test a proposal to capture negative findings in electronic health record systems based on BFO and RT. METHODS—We analysed a series of negative findings encountered in 748 sentences taken from 41 patient charts. We classified the phenomena described in terms of the various top-level categories and relations defined in BFO, taking into account the role of negation in the corresponding descriptions. We also studied terms from SNOMED-CT containing one or other form of negation. We then explored ways to represent the described phenomena by means of the types of representational units available to realist ontologies such as BFO. RESULTS—We introduced a new family of ‘lacks’ relations into the OBO Relation Ontology. The relation lacks_part, for example, defined in terms of the positive relation part_of, holds between a particular p and a universal U when p has no instance of U as part. Since p and U both exist, assertions involving ‘lacks_part’ and its cognates meet the requirements of positivity. CONCLUSION—By expanding the OBO Relation Ontology, we were able to accommodate nearly all occurrences of negative findings in the sample studied. (shrink)

This paper aims to build a bridge between two areas of philosophical research, the structure of kinds and metaphysical modality. Our central thesis is that kinds typically involve super-explanatory properties, and that these properties are therefore metaphysically essential to natural kinds. Philosophers of science who work on kinds tend to emphasize their complexity, and are generally resistant to any suggestion that they have “essences”. The complexities are real enough, but they should not be allowed to obscure the way that kinds (...) are typically unified by certain core properties. We shall show how this unifying role offers a natural account of why certain properties are metaphysically essential to kinds. (shrink)

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

This essay defends a pragmatic approach to transitional justice by arguing that it provides a convincing view of the relationships between theory and practice and is true to the nature of democratic justice itself.

Ontology is currently perceived as the solution of first resort for all problems related to biomedical terminology, and the use of description logics is seen as a minimal requirement on adequate ontology-based systems. Contrary to common conceptions, however, description logics alone are not able to prevent incorrect representations; this is because they do not come with a theory indicating what is computed by using them, just as classical arithmetic does not tell us anything about the entities that are added or (...) subtracted. In this paper we shall show that ontology is indeed an essential part of any solution to the problems of medical terminology – but only if it is understood in the right sort of way. Ontological engineering, we shall argue, should in every case go hand in hand with a sound ontological theory. (shrink)

Family members can provide crucial support to individuals participating in clinical trials. In research on the “newest frontier” of Deep Brain Stimulation (DBS)—the use of DBS for psychiatric conditions—family member support is frequently listed as a criterion for trial enrollment. Despite the significance of family members, qualitative ethics research on DBS for psychiatric conditions has focused almost exclusively on the perspectives and experiences of DBS recipients. This qualitative study is one of the first to include both DBS recipients and their (...) family members as interview participants. Using dyadic thematic analysis—an approach that takes both the individuals and the relationship as units of analyses—this study analyzes the complex ways in which family relationships can affect DBS trial participation, and how DBS trial participation in turn influences family relationships. Based on these findings, we propose ways to improve study designs to better take family relationships into account, and better support family members in taking on the complex, essential roles that they play in DBS trials for psychiatric conditions. (shrink)

Metaphysicians who are aware of modern physics usually follow Putnam (1967) in arguing that Special Theory of Relativity is incompatible with the view that what exists is only what exists now or presently. Partisans of presentism (the motto ‘only present things exist’) had very difficult times since, and no presentist theory of time seems to have been able to satisfactorily counter the objection raised from Special Relativity. One of the strategies offered to the presentist consists in relativizing existence to inertial (...) frames. This unfashionable strategy has been accused of counterfeiting, since the meaning of the concept of existence would be incompatible with its relativization. Therefore, existence could only be relativistically invariant. In this paper, I shall examine whether such an accusation hits its target, and I will do this by examining whether the different criteria of existence that have been suggested by the Philosophical Tradition from Plato onwards imply that existence cannot be relativized. (shrink)

Is there anything that members of each binary category of gender have in common? Even many non-essentialists find the lack of unity within a gender worrying as it undermines the basis for a common political agenda for women. One promising proposal for achieving unity is by means of a shared historical lineage of cultural reproduction with past binary models of gender. I demonstrate how such an account is likely to take on board different binary and also non-binary systems of gender. (...) This implies that all individuals construed as members of the category, “women” are in fact not members of the same historical kind after all! I then consider different possible means of modifying the account but conclude negatively: the problem runs deeper than has been appreciated thus far. (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.

Up until the present day, Confucianism has been a major factor in the normative discourses of East Asia. At first glance, it has sided with the preservation of the old and against innovation, according to Confucius’s self-declaration that he “only transmits and creates nothing new.” This also describes the historical role that Confucianism in distinction to other philosophies has actually played over long stretches of time. Nevertheless, Confucian ethics contains structural features, figures of thought and ideas which point beyond mere (...) traditionalism. They reflect the deep crisis of tradition against the background of which Confucianism came into existence and which has left its mark on it. They could set free a dynamic that made it possible to distance oneself from the Confucian tradition within this tradition itself and open it up to something new, if not in terms of its creation then at least in terms of its acceptance and support. This potential also intrinsically relates to the possibility of a “modern” Confucianism. The following three short essays do not claim to give a comprehensive account of the outlined problematique. It is only intended to throw a light upon some of the corresponding thought formations that developed in ancient China and explore by a few examples the extent to which the said potential has actually been realized in later Confucian discourse in Korea and Japan, assuming that border crossing might be among the factors to unleash it. (shrink)

If SNOMED CT is to serve as a biomedical reference terminology, then steps must be taken to ensure comparability of information formulated using successive versions. New releases are therefore shipped with a history mechanism. We assessed the adequacy of this mechanism for its treatment of the distinction between changes occurring on the side of entities in reality and changes in our understanding thereof. We found that these two types are only partially distinguished and that a more detailed study is required (...) to propose clear recommendations for enhancement along at least the following lines: (1) explicit representation of the provenance of a class; (2) separation of the time-period during which a component is stated valid in SNOMED CT from the period it is (or has been) valid in reality, and (3) redesign of the historical relationships table to give users better assistance for recovery in case of introduced mistakes. (shrink)

Electronic Health Records (EHRs) are organized around two kinds of statements: those reporting observations made, and those reporting acts performed. In neither case does the record involve any direct reference to what such statements are actually about. They record not: what is happening on the side of the patient, but rather: what is said about what is happening. While the need for a unique patient identifier is generally recognized, we argue that we should now move to an EHR regime in (...) which all clinically salient particulars – from the concrete disorder on the side of the patient and the body parts in which it occurs to the concrete treatments given – should be uniquely identified. This will allow us to achieve interoperability among different systems of records at the level where it really matters: in regard to what is happening in the real world. It will also allow us to keep track of particular disorders and of the effects of particular treatments in a precise and unambiguous way. We discuss the ontological and epistemological aspects of our claim and describe a scenario for implementation within EHR systems. (shrink)

Feminist social theory and female body experience are the twin themes of Iris Marion Young's twelve outstanding essays written over the past decade and brought together here. Her contributions to social theory raise critical questions about women and citizenship, the relations of capitalism and women's oppression, and the differences between a feminist theory that emphasizes women's difference and one that assumes a gender-neutral humanity. Loosely following a phenomenological method of description, Young's essays on female embodiment discuss female movement, pregnancy, (...) clothing, and the breasted body. In an introduction that situates her work in the context of shifts in feminist theory and politics over the past decade, Young emphasizes the rootedness of her theorizing in a dedicated and seasoned political activism. (shrink)

The focus on this contribution is on the ‘late-learners’ digression. In Sph. 251a8-c6, the Eleatic Stranger briefly discusses the view of some ‘young and old late-learners’ who hold that, from a logico-metaphysical point of view, unlike ‘a man is a man’ or ‘a good is good’, the statement ‘a man is good’ is neither a well-formed nor a grammatical sentence. Usually, modern commentators devote little energy to interpreting this passage since they are content to note that it suffices to discriminate (...) identity and predication to avoid the sophism. The aim of this paper is to show that the position of the ‘late-learners’ is in fact more subtle than it seems, since it is widely open to many readings, and that the chosen reading of the digression has a direct impact on the general interpretation of the rest of the dialogue (communication of kinds, semantic distinction between names and verbs, etc.). To this end, the view of the ‘late-learners’ will be compared with a similar position discussed in a quite different philosophical ecosystem: the White-Horse Paradox forged by Gōngsūn Lóng, a dialectician of the ‘School of Names’. This paradox states that the sentence ‘a white horse is not a horse’ is true. Many readings of the White-Horse Paradox have been offered: some of these readings are the same as those suggested for the ‘late-learners’ view, but others are absent from the scholarly literature, although they provide interesting insights into the interpretation of Sph. 251a8-c6. (shrink)

One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.

We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that (...) have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records. (shrink)

Natural kinds, real kinds, or, following J.S Mill simply, Kinds, are thought to be an important asset for scientific realists in the non-fundamental (or “special”) sciences. Essential natures are less in vogue. I show that the realist would do well to couple her Kinds with essential natures in order to strengthen their epistemic and ontological credentials. I argue that these essential natures need not however be intrinsic to the Kind’s members; they may be historical. I concentrate on assessing the merits (...) of historical essential natures in a paradigm case of Kinds in the non-fundamental sciences: species. I specify two basic jobs for essential natures: 1) offering individuation criteria, and 2) providing a causal explanation of the Kind’s multiple projectable properties. I argue that at least in the case of species historical essences are fit for both tasks. The principled resistance to Kinds with historical essences should also be cleared. (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)

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)

The question of ontological foundation has undergone a noteworthy revival in recent years: metaphysicians today quarrel about how exactly to understand the asymmetrical and hyperintensional relationship of grounding. One of the reasons for this revival is that the old quantificationalist meta-ontology inherited from Quine has been effectively criticised by leading philosophers favourable to a meta-ontology, the aim of which is to come to know “which facts/items ground (constitute the base of) which other facts/items”, thus to examine the relation of ontological (...) dependence between beings (e.g. chemical properties depend on physical properties, the economic situation on the behaviour of individuals etc.), i.e. to explore the hierarchical structure of reality. I shall not discuss here the relationship of grounding in itself, but make some historical-formal remarks on the properties of the ultimate ontological foundational item itself and its aporetic nature. To do so I explore various more or less exotic philosophical ecosystems in the following order: Heidegger (Seyn), Plato (ἕν), Wáng Bi (道, dào). On the way I shall propose a new interpretation both of certain hypotheses in the Parmenides and of the nature of the opposition between Wáng Bì and Guō Xiàng in regard to the logical grammar of the expression “nothing (無, wú)” (transl. J. Dudley). (shrink)

My aim in this paper is to explore the basis and implications of the disagreement between Sartre and de Beauvoir about love, indicating the points at which de Beauvoir implicitly challenges and moves away from Sartre’s theoretical framework. I will do this by first setting out the logic of Sartre’s analysis, and then by comparing it with de Beauvoir’s descriptions. I will conclude by offering some reasons for the tension between these two views of love, and suggesting how the tension (...) might be understood. (shrink)

Health Level 7 (HL7) is an organization seeking to provide universal standards for the exchange of healthcare information. In a document entitled ‘HL7 Version 3 Standard: Data Types’, the HL7 organization advances descriptions of data types recom- mended for use as identifiers. We will argue that the descriptions supplied provide insufficient guidance as to what exactly the entities are which these data types uniquely identify. Are they real things, such as persons or pieces of equipment? Or are they representations of (...) such real things in information artifacts? We here outline the problems faced by HL7 in providing answers to such questions, problems which arise because of the lack of anything like a coherent ontology in the HL7 standard, and we make some recommendations for future improvements. (shrink)

In “Analyzing COVID-19 Sex Difference Claims: The Harvard GenderSci Lab,” Marion Boulicault and Sarah Richardson summarize some of the groundbreaking work that they’re doing at the Harvard GenderSci Lab. Since March 2020, their lab has been analyzing, interrogating, and critiquing sex essentialist explanations of COVID-19 outcome disparities that are fairly ubiquitous in news media. Using interdisciplinary tools from feminist philosophy, science studies, and critical public health, they work collaboratively with two goals: (i) to critically examine COVID-19 sex difference research (...) and (ii) to explore and elevate the role of social variables in driving biological disparities. They argue that in public health research, media, and messaging, data on sex disparities must be contextualized both to avoid reinforcing harmful sex essentialist assumptions and also to help the public understand the complex ways in which social factors influence these patterns. They argue that within the context of COVID-19, doing so can both clarify risks and save lives. Their contribution to this issue describes their methods and shares some of their findings. (shrink)

Ontologies are today being applied in almost every field to support the alignment and retrieval of data of distributed provenance. Here we focus on new ontological work on dance and on related cultural phenomena belonging to what UNESCO calls the “intangible heritage.” Currently data and information about dance, including video data, are stored in an uncontrolled variety of ad hoc ways. This serves not only to prevent retrieval, comparison and analysis of the data, but may also impinge on our ability (...) to preserve the data that already exists. Here we explore recent technological developments that are designed to counteract such problems by allowing information to be retrieved across disciplinary, cultural, linguistic and technological boundaries. Software applications such as the ones envisaged here will enable speedier recovery of data and facilitate its analysis in ways that will assist both archiving of and research on dance. (shrink)

The aim of this paper is to provide some acquaintance with the exegetical history of ἐξαίφνης inside the Platonic Tradition, from Plato to Marsilio Ficino, by way of Middle Platonism and Greek Neoplatonism. (Since this is only a draft, several modifications should be made later, notably in order to improve the English.) Some part has been presented in Los Angeles: “Damascius’ Theodicy: Psychic Input of Disorder and Evil into the World”, 16th Annual ISNS (International Society for Neoplatonic Studies) Conference, Loyola (...) Marymount University, 14th June 2018. (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)

Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist and (b) (...) they do this in terms of the types and type-level relationships described in these ontologies. While much attention has been devoted to (1), work on (2), which is the topic of this paper, is comparatively rare. Using Referent Tracking as basis, we describe a technical data wrangling strategy which consists in creating for each dataset a template that, when applied to each particular record in the dataset, leads to the generation of a collection of Referent Tracking Tuples (RTT) built out of unique identifiers for the entities described by means of the data items in the record. The proposed strategy is based on (i) the distinction between data and what data are about, and (ii) the explicit descriptions of portions of reality which RTTs provide and which range not only over the particulars described by data items in a dataset, but also over these data items themselves. This last feature allows us to describe particulars that are only implicitly referred to by the dataset; to provide information about correspondences between data items in a dataset; and to assert which data items are unjustifiably or redundantly present in or absent from the dataset. The approach has been tested on a dataset collected from patients seeking treatment for orofacial pain at two German universities and made available for the NIDCR-funded OPMQoL project. (shrink)

The theme of this paper is Husserl’s concept of experience, through which I hope to show that and how Husserl’s description points the way toward a more adequate account of experience than traditional ones operating within realist-idealist and rationalist-empiricist frameworks.

Moral perceptualism is the theory that perception and perceptual experience is attuned to moral features in our environment. This idea has received renewed attention in the last 15–20 years, for its potential to do theoretical work in moral epistemology and moral psychology. In this paper, I review the main motivations and arguments for moral perceptualism, the variety of theories that go under the heading of “moral perception,” and the three biggest challenges to moral perception. https://youtu.be/9cc_1zykq80.

This essay argues that the concept of dependence now invoked in noramtive discussions of the welfare state is both incoherent and biased as a result of its conflation of four distinctly different notions of dependence, ranging from the purely causal to that associated with lower class identities.

The development of symbolic logic is often presented in terms of a cumulative story of consecutive innovations that led to what is known as modern logic. This narrative hides the difficulties that this new logic faced at first, which shaped its history. Indeed, negative reactions to the emergence of the new logic in the second half of the nineteenth century were numerous and we study here one case, namely logic at Oxford, where one finds Lewis Carroll, a mathematical teacher who (...) promoted symbolic logic, and John Cook Wilson, the Wykeham Professor of Logic who notoriously opposed it. An analysis of their disputes on the topic of logical symbolism shows that their opposition was not as sharp as it might look at first, as Cook Wilson was not so much opposed to the « symbolic » character of logic, but the intrusion of mathematics and what he perceived to be the futility of some of its problems, for logicians and philosophers alike. (shrink)

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

One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.

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)

Moral perception has made something of a comeback in recent work on moral epistemology. Many traditional objections to the view have been argued to fail upon closer inspection. But it remains an open question just how far moral perception might extend. In this paper, I provide the beginnings of an answer to this question by assessing the relationship between the metaphysical structure of different normative properties and a plausible constraint on which properties are eligible for perceptual awareness which I call (...) the Counterfactual Strengthening Test. Along the way I consider and reject a few other possible constraints on perceptual awareness. I defend the view that moral perception is restricted to the perception of evaluative and pro tanto deontic properties. I conclude with a few gestures toward what this limitation on moral perception may mean for broader moral epistemology. (shrink)