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 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)

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)

This thesis deals with Ernst Cassirer's work "Philosophie der Symbolischen Formen". The author analyses Cassirer's argumentation and examines how he understands the relationship between symbols and human thought. Cassirer argues that human thought is characterized by symbols, which are a kind of language. Symbols enable us to think about complex concepts and communicate about abstract ideas. Cassirer argues that language and symbols play a central role in understanding the world and human experience. Funke discusses Cassirer's ideas in the context of (...) contemporary philosophy and points out that his work has important implications for today's research. The author emphasizes that the study of the relationship between language, symbols and human thought can provide important insights into the workings of the human mind. In summary, the work provides a detailed analysis of Cassirer's work and emphasizes the importance of his ideas for modern philosophy. The study of the role of language and symbols in human thought is still an important field of research today that expands our understanding of human cognition. (shrink)

We defend a realistic attitude towards biological species. We argue that two species are not different species because they differ in intrinsic features, be they phenotypic or genomic, but because they are separated with regard to gene flow. There are no intrinsic species essences. However, there are relational ones. We argue that bearing a gene flow relation to conspecifics may serve as the essence of a species. Our view of the species as a Gene-Flow Community differs from Mayr’s definition of (...) the species as a reproductive community. In a reproductive community, each organism is able to successfully reproduce with each other. However, there are species in which geographically distant organisms lost their ability to successfully reproduce, due to strong genetic adaptations to the respective local environmental conditions. Despite this loss of the ability to mutually reproduce, they are still bound by gene flow via continuous intermediate populations. This replacement of Mayr’s notion of an interbreeding potential as a criterion for species membership has important implications for the treatment of populations in allopatry and sympatry. (shrink)

Jahrestage sind oft der Anlaß, um an Personen oder Ereignisse zu erinnern. Fritz Mauthner's Geburtstag jährt sich am 22. November zum 150-sten mal. Ich will diese Gelegenheit nutzen, um weniger seinen Namen, als sein Anliegen in Erinnerung zu rufen.

The thesis of Weak Unrestricted Composition says that every pair of objects has a fusion. This thesis has been argued by Contessa and Smith to be compatible with the world being junky and hence to evade an argument against the necessity of Strong Unrestricted Composition proposed by Bohn. However, neither Weak Unrestricted Composition alone nor the different variants of it that have been proposed in the literature can provide us with a satisfying answer to the special composition question, or so (...) we will argue. We will then go on to explore an alternative family of purely mereological rules in the vicinity of Weak Unrestricted Composition, Cardinal Composition: A plurality of pairwise non-overlapping objects composes an object iff the objects in the plurality are of cardinality smaller than $$\kappa $$ κ. As we will show, all the instances for infinite $$\kappa $$ κ s determine fusion and are compatible with junk, and every instance for a $$\kappa > \aleph _0$$ κ > ℵ 0 is furthermore compatible with gunk and dense chains of parthood. (shrink)

Non-naturalism is the view that normative properties are response-independent, irreducible to natural properties, and causally inefficacious. An underexplored question for non-naturalism concerns the metasemantics of normative terms. Ideally, the non-naturalist could remain ecumenical, but it appears they cannot. Call this challenge the metasemantic challenge. This chapter suggests that non-naturalists endorse an epistemic account of reference determination of the sort recently defended by Imogen Dickie, with some modifications. An important implication of this account is that, if correct, a fully fleshed out (...) moral epistemology will simultaneously rebut metasemantic objections to non-naturalism. Thus, both the metasemantic and the more widely discussed epistemological challenges in effect amount to one. Before setting out the positive view, the chapter considers why all of the traditional metasemantic theories cause trouble for the non-naturalist. This includes discussions of teleosemantics, conceptual role semantics, as well as Schroeter and Schroeter’s “connectedness” model. (shrink)

One of Plato’s aims in the Phaedrus seems to be to outline an ‘ideal’ form of rhetoric. But it is unclear exactly what the ‘true’ rhetorician really looks like, and what exactly his methods are. More broadly, just how does Plato see the relation between rhetoric and philosophy? I argue, in light of Plato’s epistemology, that the “true craft (techne) of rhetoric” which he describes in the Phaedrus is a regulative, but also an unattainable ideal. Consequently, the mythical palinode in (...) the dialogue is not (as some have claimed) an example of the true techne—and indeed it could not be. But neither is dialectic. Rather, dialectic is the closest approximation of the true techne of rhetoric which can be had; that is to say, dialectic is the best and highest kind of psychagogia (a ‘leading of the soul through words’). Plato’s purpose in describing the “true techne of rhetoric”, then, is not to reform or to rehabilitate rhetoric, but to urge us to abandon it in favor of the philosophical life. One implication of this is that Plato is just as hostile toward rhetoric as he is in the Gorgias. (shrink)

One important challenge for contingentists is that they seem to be unable to account for the meaning of some apparently meaningful modal discourse that is perfectly intelligible for necessitists. This worry is particularly pressing for higher-order contingentists, contingentists who hold that it is not only contingent which objects there are, but also contingent which semantic values there are for higher-order variables to quantify over. Objections against higher-order contingentism along these lines have been presented in Williamson (Mind 119(475):657–748, 2010; Modal logic (...) as metaphysics, Oxford University Press, 2013, ch. 7), and Fritz and Goodman (Mind 126(504):1063–1108, 2017). This paper presents a way for contingentists to respond to these challenges. The upshot is that the contingentist can account for the meaningfulness of the problematic modal claims by pretending necessitism to be true, but in some cases it turns out to be indeterminate whether they are true. I defend this strategy against the objections against pretence-strategies presented in Fritz and Goodman (Mind 126(504):1063–1108, 2017, §4). Furthermore, I defend the plausibility of the resulting indeterminacy from the contingentist’s perspective. (shrink)

The ending of the Phaedo is one of the most powerful and memorable moments in the entire Platonic corpus. It is not simply the end of a single dialogue, but a depiction of the end of the life of the man (Socrates) who is a looming presence in nearly everything that Plato wrote. In this article I offer an in-depth analysis of the final scene of the Phaedo. I argue that Plato very carefully constructs the scene for the sake of (...) specific philosophical, dramatic, and political ends. Plato uses it to unify the Phaedo as a singular text, while also provoking us to reflect on the nature of our lives, our deaths, and the possibilities and limits of philosophy itself. (shrink)

Moving beyond the piecemeal approach to the Euthyphro that has dominated much of the previous secondary literature, I aim in this article to understand the dialogue as an integrated whole. I argue that the question of myth underlies the philosophical and dialogical progression of the Euthyphro. It is an adherence to traditional myth that motivates each of Euthyphro’s definitions and that also accounts for their failure. The dialogue thus presents a broad criticism of traditional myth. But, as Socrates’s references to (...) Daedalus and Proteus show, myth can have a positive role and can be used for philosophical purposes. (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)

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified (...) and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections. (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)

It is commonly thought that there is a connection between love and death. But what can be said philosophically about the nature of that connection (if indeed it exists)? Plato's Symposium suggests at least three possible ways in which love and death might be connected: first, that love entails (or ought to entail) a willingness to die for one’s beloved; second, that love is a desire for (or perhaps itself is) a kind of death; and third, that love is linked (...) to human mortality and the desire for immortality. I argue that each of these three suggestions is problematic, and should not be accepted at face value. I am ultimately skeptical as to whether any one, overriding connection—be it moral or causal or metaphysical—between love and death exists. At the very least, the matter deserves more nuanced and multi-faceted reflection than what we find in the Symposium. (shrink)

Management of information is facilitated by unambiguously tracking portions of reality over time. To track the portions of reality, a referent tracking system is used. The referent tracking system is able to communicate with other tracking systems and/or tradition information systems. Errors in the referent tracking system are detected and corrected to maintain actual representations of the portions of reality.

SNODENT is a dental diagnostic vocabulary incompletely integrated in SNOMED-CT. Nevertheless, SNODENT could become the de facto standard for dental diagnostic coding. SNODENT's manageable size, the fact that it is administratively self-contained, and relates to a well-understood domain provides valuable opportunities to formulate and test, in controlled experiments, a series of hypothesis concerning diagnostic systems. Of particular interest are questions related to establishing appropriate quality assurance methods for its optimal level of detail in content, its ontological structure, its construction and (...) maintenance. This paper builds on previous–software-based methodologies designed to assess the quality of SNOMED-CT. When applied to SNODENT several deficiencies were uncovered. 9.52% of SNODENT terms point to concepts in SNOMED-CT that have some problem. 18.53% of SNODENT terms point to SNOMED-CT concepts do not have, in SNOMED, the term used by SNODENT. Other findings include the absence of a clear specification of the exact relationship between a term and a termcode in SNODENT and the improper assignment of the same termcode to terms with significantly different meanings. An analysis of the way in which SNODENT is structurally integrated into SNOMED resulted in the generation of 1081 new termcodes reflecting entities not present in the SNOMED tables but required by SNOMED's own description logic based classification principles. Our results show that SNODENT requires considerable enhancements in content, quality of coding, quality of ontological structure and the manner in which it is integrated and aligned with SNOMED. We believe that methods for the analysis of the quality of diagnostic coding systems must be developed and employed if such systems are to be used effectively in both clinical practice and clinical research. (shrink)

The last two decades have seen considerable efforts directed towards making Electronic Health Records interoperable through improvements in medical ontologies, terminologies and coding systems. Unfortunately, these efforts have been hampered by a number of influential ideas inherited from the work of Eugen Wüster, the father of terminology standardization and the founder of ISO TC 37. We here survey Wüster’s ideas – which see terminology work as being focused on the classification of concepts in people’s minds – and we argue that (...) they serve still as the basis for a series of influential confusions. We argue further that an ontology based unambiguously, not on concepts, but on the classification of entities in reality can, by removing these confusions, make a vital contribution to ensuring the interoperability of coding systems and healthcare records in the future. (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)

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (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 philosophy of the art of living asks the age-old question of orienting one’s own life: ‘How can I live well?’ An art of living is always called for when people do not know what to do and how to go on, when the ways of life are no longer self-evident, when traditions, conventions, rules, and norms lose their plausibility and individuals begin to worry about themselves. The art of living and of its philosophy has a practical aim: It is (...) not concerned with ethical principles, but with the concrete practice of people’s everyday life, with their individual and successful lives. Friedrich Nietzsche, as he often did, pushed the problem of the art of living to the extreme, making it palpable both in its dignity and in its force. For him, the modern uncertainty of human orientation caused by nihilism pointed to art and aesthetics, which, he supposed, makes life if not justifiable, at least bearable. The arts open up a multi-perspectival seeing and hearing, they experiment with alternative forms and techniques, and create the finest sensibilities for both – Nietzsche himself, with his rich forms of philosophical writing, is an outstanding example of this. -/- The volume we present here, entails contributions of German-speaking scholars on Nietzsche and the ways of living he proposes, especially, but not alone in Dawn. The papers are selected from a book series on the common issue “Critical Art of Living,” edited by Günter Gödde, Jörg Zirfas, and others, and translated on behalf of the Foundation for Philosophical Orientation. (shrink)

Werner Heisenberg made an important – and as yet insufficiently researched – contribution to the transformation of the modern conception of science. This transformation involved a reassessment of the status of scientific knowledge from certain to merely hypothetical – an assessment that is widely recognized today. I examine Heisenberg’s contribution in particular by taking his conception of “closed theories” as an example according to which the established physical theories have no universal and exclusive, but only a restricted validity. Firstly, (...) I characterize the historical process of hypothetization of claims to validity. Then, secondly, I reconstruct Heisenberg’s conception, as far as it can be derived from his popular writings, relating it to the process of hypothetization. Finally, I touch on the history of its reception and compare it with conceptions of science that emphasize the significance of the hypothetical for the modern theories of natural sciences. Compared to these conceptions, Heisenberg’s contribution turns out to be rather independent. (shrink)

Werner Sombart’s classic text "Luxury and Capitalism" is revisited in the light of recent economic historians’ works that have analyzed luxury’s role in the development of capitalism. Most of these works, as well as Sombart’s book itself, are focused on the eighteenth century, since it was then that the proliferation—and availability—of luxury manifested itself for the first time most conspicuously. By employing secondary texts by economic historians and primary sources from the debates on luxury in the eighteenth century—some of (...) which overlooked by a number of historians—the essay attempts a renewed outlook on a text that was controversial when written over a century ago and remains a prominent argument in the eternal discussion and dispute on the cause(s) of the rise of capitalism. (shrink)

I interpret the philosophical views of Werner Heisenberg as a pragmatism and non-metaphysical realism of a Wittgensteinian kind. The “closed theory” is a Wittgensteinian rule/concept.

This article is an introduction to the first English edition of Karl Kautsky's article series "The American Worker" (Karl Kautsky, “Der amerikanische Arbeiter”, Die neue Zeit, 24. 1905-1906, 1. Bd., 1906, H. 21, S. 676-683, H. 22, S. 717-727, H. 23, S. 740-752, H. 24, S. 773-787), which was a Marxist reply to Werner Somart's book Why Is There No Socialism in the United States? (Werner Sombart, Warum gibt es in den Vereinigten Staaten keinen Sozialismus?, Tübingen: J.C.B. Mohr, (...) 1906). (shrink)

Documentary film is that genre of filmmaking that lays bare the fact of all film, which is that it presents "a world past" (Cavell, The World Viewed). This fact of film seems to point to a paradox of time in our experience of movies: we are present at something that has happened, something that is over. But what if we were to take this fact to show that film has the power to place us outside our ordinary, unreflective relation to (...) time? In this essay I examine three pre-cinematic descriptions of relations to time – in Emerson, Thoreau, and Weil – that anticipate the paradox of time inherent in film. I then put that examination to use in a reading of Werner Herzog's Cave of Forgotten Dreams, a film ostensibly about prehistoric cave paintings but whose achievement is its declaration, not to document some past time, but to liberate the present moment. (shrink)

The conception that the world can be represented as a system of levels of being can be traced back to the beginnings of European philosophy and has lost little of its plausibility in the meantime. One of the important modern conceptions of levels was developed by Nicolai Hartmann. It exhibits remarkable similarities and contrasts with the classification of the real developed by Werner Heisenberg in his paper Ordnung der Wirklichkeit (Order of Reality). In my contribution I will introduce these (...) two conceptions of levels and compare their salient features. I will discuss them as variants of a scientific worldview that attempts to forge a link to the perspective of the lifeworld. Then I will go on to argue that the shortcomings of these conceptions can be remedied by extending them with the level of the very small and that of the very large. The introduction of these ontologically fundamental levels is based on scientific knowledge that for the most part eludes he intuitively representable character of lifeworld experience. Historical changes in science and the lifeworld could lead to the notion that reality can be represented as a system of levels being challenged in future. (shrink)

Příspěvek se zaměřuje na zavádějící příběh o tzv. kodaňské interpretaci kvantové mechaniky, již jako údajně nerozpornou či jednotnou vytvořili a sdíleli na základě tzv. kodaňského ducha kvantové teorie její tvůrci v roce 1927. Článek bude vycházet z role, kterou v tomto příběhu sehráli především N. Bohr a W. Heisenberg. První část příspěvku seznamuje s variacemi toho, co se v literatuře považuje za kodaňskou interpretaci. Druhá část odhaluje, že zatímco kvantová mechanika vznikla ve dvacátých letech 20. století, kodaňská interpretace je veskrze (...) problematickým a především Heisenbergovým produktem z let padesátých. Jednou z hlavních motivací, kvůli níž vystoupil s tzv. kodaňskou interpretací, byla obrana vůči množícím se kritikám obhájců kvantové teorie. Jelikož mezi členy tzv. kodaňské školy nepanovala žádná jednotná či nerozporná interpretace kvantové mechaniky, zaměřuje se poslední část příspěvku na několik vybraných rozdílů hlavně mezi Bohrovým a Heisenbergovým výkladem kvantové teorie. (shrink)

Я интерпретирую философские взгляды Вернера Гайзенберга как прагматизм и неметафизический реализм виттгенштайновского типа. «Замкнутая теория» – виттгенштайновское правило/концепт. В отличие от Бокулич, предпочитающей позицию Дирака относительно природы связей между различными физическими теориями, я отдаю предпочтение позиции Гайзенберга. Моя позиция, интерпретирующая Гайзенберга, также прямо противоположна позиции Поппера: критерием устоявшейся научной (замкнутой) теории является её нефальсифицируемость. -/- I interpret philosophical views of Werner Heisenberg as a pragmatism and non-metaphysical realism of a Wittgensteinian kind. The “closed theory” is a Wittgensteinian rule/concept. Unlike (...) Alisa Bokulich, favouring Dirac’s position about inter-theoretical relations, I favour Heisenberg’s one. My position, interpreting Heisenberg’s notion of a closed theory, is also in direct opposition to Popper’s one: the criterion of an established scientific (closed) theory is its non-falsifiability. (shrink)

Recent years saw the rise of an interest in the roles and significance of thought experiments in different areas of human thinking. Heisenberg's gamma ray microscope is no doubt one of the most famous examples of a thought experiment in physics. Nevertheless, this particular thought experiment has not received much detailed attention in the philosophical literature on thought experiments up to date, maybe because of its often claimed inadequacies. In this paper, I try to do two things: to provide an (...) interesting interpretation of the roles played by Heisenberg's gamma ray microscope in interpreting quantum mechanics – partly based on Thomas Kuhn’s views on the function of thought experiments – and to contribute to the ongoing discussions on the roles and significance of thought experiments in physics. (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 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)

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)

Though since Werner Jaeger's famous Studien zur Entstehungsgeschichte der Metaphysik des Aristoteles of 1912 remarkable observations were made, the topic "Composition of the Metaphysics" almost disappeared from the agenda. As, however, neglect of this philological task results in either selective reading or anachronistic systematization, the author has resumed it, extending it to the internal structure of the singular books.

Though since Werner Jaeger's famous Studien zur Entstehungsgeschichte der Metaphysik des Aristoteles of 1912 remarkable observations were made, the topic "Composition of the Metaphysics" almost disappeared from the agenda. As, however, neglect of this philological task results in either selective reading or anachronistic systematization, the author has resumed it, extendig it to the internal structure of the singular books.

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)

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.

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)

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)

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.

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.

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)

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)

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)

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)

Definitive diagnosis of malaria requires the demonstration through laboratory tests of the presence within the patient of malaria parasites or their components. Since malaria parasites can be present even in the absence of malaria manifestations, and since symptoms of malaria can be manifested even in the absence of malaria parasites, malaria diagnosis raises important issues for the adequate understanding of disease, etiology and diagnosis. One approach to the resolution of these issues adopts a realist view, according to which the needed (...) clarifications will be derived from a careful representation of the entities on the side of the patient which form the ultimate truthmakers for clinical statements. We here address a challenge to this realist approach relating to the diagnosis of malaria, and show how this challenge can be resolved by appeal to Basic Formal Ontology (BFO) and to the Ontology for General Medical Science (OGMS) constructed in its terms. (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)