In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular O/T as a (...) standard for data exchange purposes is often seen by the end-user as a function of the number of applications using that vocabulary (and, by extension, the size of the user base). Furthermore, the adoption of an O/T as an interoperability standard requires confidence in its stability and guaranteed continuity as a resource. (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)

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)

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)

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)

The idea of personalised medicine (PM) has gathered momentum recently, attracting funding and generating hopes as well as scepticism. As PM gives rise to differing interpretations, there have been several attempts to clarify the concept. In an influential paper published in this journal, Schleidgen and colleagues have proposed a precise and narrow definition of PM on the basis of a systematic literature review. Given that their conclusion is at odds with those of other recent attempts to understand PM, we consider (...) whether their systematic review gives them an edge over competing interpretations. We have found some methodological weaknesses and questionable assumptions in Schleidgen and colleagues’ attempt to provide a more specific definition of PM. Our perplexities concern the lack of criteria for assessing the epistemic strength of the definitions that they consider, as well as the logical principles used to extract a more precise definition, the narrowness of the pool from which they have drawn their empirical data, and finally their overlooking the fact that definitions depend on the context of use. We are also worried that their ethical assumption that only patients’ interests are legitimate is too simplistic and drives all other stakeholders’ interests—including those that are justifiable—underground, thus compromising any hope of a transparent and fair negotiation among a plurality of actors and interests. As an alternative to the shortcomings of attempting a semantic disciplining of the concept we propose a pragmatic approach. Rather than considering PM to be a scientific concept in need of precise demarcation, we look at it as an open and negotiable concept used in a variety of contexts including at the level of orienting research goals and policy objectives. We believe that since PM is still more an ideal than an achieved reality, a plurality of visions is to be expected and we need to pay attention to the people, reasons and interests behind these alternative conceptions. In other words, the logic and politics of PM cannot be disentangled and disagreements need to be tackled addressing the normative and strategic conflicts behind them. (shrink)

This original research hypothesises that the most fundamental building blocks of logical descriptions of cognitive, or knowledge, agents’ descriptions are expressible based on their conceptions (of the world). This article conceptually and logically analyses agents’ conceptions in order to offer a constructivist- based logical model for terminological knowledge. The most significant characteristic of [terminological] knowing is that there are strong interrelationships between terminological knowledge and the individualistic constructed, and to-be-constructed, models of knowledge. Correspondingly, I conceptually and logically analyse conception expressions (...) based on terminological knowledge, and I show how terminological knowledge may reasonably be assumed to be constructed based on the agents’ conceptions of the world. The focus of my model is on terminological knowledge structures, which may find applications in such diverse fields as the Semantic Web and educational/learning systems. (shrink)

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

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

Although formal thought disorder (FTD) has been for long a clinical label in the assessment of some psychiatric disorders, in particular of schizophrenia, it remains a source of controversy, mostly because it is hard to say what exactly the “formal” in FTD refers to. We see anomalous processing of terminological knowledge, a core construct of human knowledge in general, behind FTD symptoms and we approach this anomaly from a strictly formal perspective. More specifically, we present here a symbolic computational model (...) of storage in, and activation of, a human semantic network, or semantic memory, whose core element is logical form; this is normalized by description logic (DL), namely by CL, a DL-based language – Conception Language – designed to formalize conceptualization from the viewpoint of individual cognitive agency. In this model, disruptions in the rule-based implementation of the logical form account for the apparently semantic anomalies symptomatic of FTD, which are detected by means of a CL-based algorithmic assessment. (shrink)

This book offers substantial insight into students’ conceptualization of scientific terminology. The current book explores the commonalities and distinctions between Arabic and French physics terms, and the impact of the language disparities on students’ understanding of physics terms. This book adopts a novel approach to the problem of scientific terminology by exploring physics terms’ polysemy, prototypical meanings, and conceptual metaphor and metonymy, which motivates their extension of meaning. The book also investigates how the linguistic discrepancies and other variables (...) affect the learning of physics by Arab students (Moroccan students, in this book). Concepts in Physics: A Comparative Cognitive Analysis of Arabic and French Terminologies, whether you are a student of science, a science teacher or lecturer, a translator, or a linguist, is what you need. The book will help you comprehend the linguistic and cultural differences between western and non-western physics terminologies (in this book, French and Arabic physics terminologies) and the factors influencing the learning of physics concepts, and thus address the multiple challenges in learning scientific terms and concepts. (shrink)

Although scientific practice sometimes encounters philosophical dif- ficulties, it cannot shoulder the burden of resolving them. This can lead to controversies. An unavoidable difficulty is rooted in the linguistic attitude, i.e., in the fact that to a considerable extent we express our thoughts in words. I will attempt to illuminate some important characteristics of linguistic expres- sion which lead to paradoxical situations, identifiable thanks to philosophy. In my argument, I will investigate how the notion of consciousness has altered over the (...) course of philosophical investigation and how it relates to recent scientific practice. In conclusion, I will focus on a few recent so-called radical positions in philosophy with regard to a framework within which consciousness and more generally mental phenomena can be regarded in a new light, as well as on the barriers we face when trying to unify scientific results. (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 present article focuses on the conceptual structures of two Arabic words which are used in both everyday life and science: كَهْرَبَاء (kahrabāʾ) (electricity) and ضَوْء (ḍawʾ) (light). Under a cognitive linguistics approach, the polysemy of these terms, revealed in the citations extracted from ArabiCorpus, is studied. More specifically, the analysis of the terms involves the polysemy or ‘radial category’ along with its prototypical and peripheral meanings, and the main factors in projecting the idealised cognitive models (ICMs) where the radial (...) categories are formed: conceptual metaphor and conceptual metonymy. The results indicate that power and knowledge motivate the conceptualisations that underpin the categories كَهْرَبَاء (kahrabāʾ) (electricity) and ضَوْء (ḍawʾ) (light) respectively. Using such non-scientific conception in understanding the scientific senses of these terms leads to students’ confusion and failure to understand them. To ensure that students construe the scientific concepts correctly, they must be mindful of the inconsistency between their non-scientific and scientific meanings. (shrink)

Cognitive, or knowledge, agents, who are in some way aware of describing their own view of the world (based on their mental concepts), need to become concerned with the expressions of their own conceptions. My main supposition is that agents’ conceptions are mainly expressed in the form of linguistic expressions that are spoken, written, and represented based on e.g. letters, numbers, or symbols. This research especially focuses on symbolic conceptions (that are agents’ conceptions that are manifested in the form of (...) their symbols). I attempt to logically (and using ????LSYM) analyse symbolic conceptions in terminological systems. ????LSYM is an assertional fragment of my developed Conception Language (????L), which is utilised as a formal-logical system for representing and explicating agents’ conceptions of the world. Keywords: assertional logic; cognitive agent; knowledge agent; conception language; conception; symbol; symbolic conception. (shrink)

Biomedical terminologies are focused on what is general, Electronic Health Records (EHRs) on what is particular, and it is commonly assumed that the step from the one to the other is unproblematic. We argue that this is not so, and that, if the EHR of the future is to fulfill its promise, then the foundations of both EHR architectures and biomedical terminologies need to be reconceived. We accordingly describe a new framework for the treatment of both generals and particulars in (...) biomedical information systems that is designed: 1) to provide new opportunities for the sharing and management of data within and between healthcare institutions, 2) to facilitate interoperability among different terminology and record systems, and thereby 3) to allow new kinds of reasoning with biomedical data. (shrink)

Formalisms based on one or other flavor of Description Logic (DL) are sometimes put forward as helping to ensure that terminologies and controlled vocabularies comply with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) does indeed comply with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of (...) SNOMED CT classes with respect to these principles. Our major results are: 31% of these classes have a single child; 27% have multiple parents; 51% do not exhibit any differentiae between the description of the parent and that of the child. The applications of this study to quality assurance for ontologies are discussed and suggestions are made for dealing with the phenomenon of multiple inheritance. The advantages and limitations of our approach are also discussed. (shrink)

We present an algebraic account of the Tongan kinship terminology (TKT) that provides an insightful journey into the fabric of Tongan culture. We begin with the ethnographic account of a social event. The account provides us with the activities of that day and the centrality of kin relations in the event, but it does not inform us of the conceptual system that the participants bring with them. Rather, it is a slice in time of an ongoing dynamic process that (...) links behavior with a conceptual system of kin relations and vice versa. To understand this interplay, we need an account of the underlying conceptual system that is being activated during the event. Thus, we introduce a formal, algebraically based account of TKT. This account brings to the fore the underlying logic of TKT and allows us to distinguish between features of the kinship system that arise from the logic of TKT as a generative structure and features that must have arisen through cultural intervention. (shrink)

The paper deals with the problem of future biology teachers’ vocational preparation process and shaping in them of those capacities that contribute to the conservation and enhancement of our planet’s biodiversity as a reflection of the leading sustainable development goals of society. Such personality traits are viewed through the prism of forming the future biology teachers’ professional and terminological competence. The main aspects and categories that characterize the professional and terminological competence of future biology teachers, including terminology, nomenclature, term, (...) nomen and term element, have been explained. The criteria and stages of shaping the future biology teachers’ professional and terminological competence during the vocational training process have been fixed. Methods, techniques, technologies, guiding principles and forms of staged work on the forming of an active terminological dictionary of students have been described and specified. The content of the distant special course “Latin. Botanical Terminology”, which provides training for future teachers to study the professional subjects and to understand of international scientific terminology, has been presented. It is concluded that the proper level of formation of the future biology teachers’ professional and terminological competence will eventually ensure the qualitative preparation of pupils for life in a sustainable development era. (shrink)

Thomas Reid thinks of natural philosophy as a purely nomothetic enterprise but he maintains that it is proper for natural philosophers to employ causal terminology in formulating their explanatory claims. In this paper, I analyze this puzzle in light of Reid's distinction between efficient and physical causation – a distinction he grounds in his strict understanding of active powers. I consider several possible reasons that Reid may have for maintaining that natural philosophers ought to employ causal terminology and (...) suggest that the underlying rationale for his views is his understanding of the aims of explanation and their connection to the interests of human agents. The ultimate aim of knowing the causes of phenomena is to mollify the natural intellectual curiosity of human inquirers and provide guidance that insures successful action. The discovery of laws governing phenomena fulfills this aim and, as such, it is appropriate for natural philosophers to employ causal terminology. (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)

The current paper expands on previous work done on the influence of learners’ language and preexisting knowledge on understanding physics terminology by exploring the concept of ACCELERATION in Arabic and English. The study attempts to answer two questions: (1) what are the similarities and differences between the polysemy of Arabic تَسَارُع (tasāruʿ) (acceleration) and the polysemy of English acceleration, and (2) to what extent do prototypes and factors motivating the conceptualization of تَسَارُع (tasāruʿ) and the conceptualization of acceleration converge (...) or diverge? To this end, Arabic and English dictionaries and corpora, the ArabiCorpus (Arabic Corpus Search Tool) and the British National Corpus (BNC), were employed. The dictionaries were surveyed to explore the various meanings of تَسَارُع (tasāruʿ) and acceleration, while the ArabiCorpus and the BNC were employed to investigate the senses and to identify the most frequent collocates and so the prototypes of these terms. The meaning extension of the terms is examined on the basis of the cognitive mechanisms which appear in the corpora. Theoretically, the paper is informed by the prototype theory (Rosch, 1973; 1975), image schemas (Johnson, 1987), and conceptual metaphor (Lakoff & Johnson, 1980/2003). The results show that تَسَارُع (tasāruʿ) (acceleration) and acceleration generally overlap in terms of polysemy, prototype, and images schemas as well as conceptual metaphor that organize the conceptualization of these terms. It was also found that both Arab and English speakers mix ACCELERATION up with SPEED and so misunderstand them in a scientific setting. The present findings have several implications for science curriculum design, education, and research on universal and culture-specific properties of language. (shrink)

The present paper aims to broaden the current understanding of students’ misconception of scientific terminology by identifying the gaps between Arabic and English scientific terminologies and between everyday language and scientific language. The paper compares the polysemy, prototypes, and motivating factors of English energy with those of Arabic طَاقَة (ṭāqa), with more focus on students’ prior knowledge. The study employs Lakoff’s (1987) idealized cognitive models and Rosch’s (1975) prototype theory to reveal the radial members of both categories, i.e., energy (...) and طَاقَة (ṭāqa), and to explain the kinds of cognitive mechanisms that motivate the extension as well as understanding of the meanings of these terms. To this end, the study uses several English and Arabic dictionaries, lexical databases and corpora. This is to explore all the meanings, prototypes and motivating factors of the terms under investigation. The results show that the terms energy and طَاقَة (ṭāqa) overlap in prototypical meanings and motivating factors but differ in less prototypical and peripheral meanings. English and Arabic learners may then face similar issues in learning scientific concepts due to the difference between their pre-existing knowledge and scientific language. (shrink)

The terms ‘verification’ and ‘validation’ are widely used in science, both in the natural and the social sciences. They are extensively used in simulation, often associated with the need to evaluate models in different stages of the simulation development process. Frequently, terminological ambiguities arise when researchers conflate, along the simulation development process, the technical meanings of both terms with other meanings found in the philosophy of science and the social sciences. This article considers the problem of verification and validation in (...) social science simulation along five perspectives: The reasons to address terminological issues in simulation; the meaning of the terms in the philosophical sense of the problem of “truth”; the observation that some debates about these terms in simulation are inadvertently more terminological than epistemological; the meaning of the terms in the technical context of the simulation development process; and finally, a comprehensive outline of the relation between terminology used in simulation, different types of models used in the development process and different epistemological perspectives. (shrink)

The current paper expands on previous work done on the influence of learners’ language and preexisting knowledge on understanding physics terminology by exploring the concept of ACCELERATION in Arabic and English. The study attempts to answer two questions: (1) what are the similarities and differences between the polysemy of Arabic تَسَارُع (tasāruʿ) (acceleration) and the polysemy of English acceleration, and (2) to what extent do prototypes and factors motivating the conceptualization of تَسَارُع (tasāruʿ) and the conceptualization of acceleration converge (...) or diverge? To this end, Arabic and English dictionaries and corpora, the ArabiCorpus (Arabic Corpus Search Tool) and the British National Corpus (BNC), were employed. The dictionaries were surveyed to explore the various meanings of تَسَارُع (tasāruʿ) and acceleration, while the ArabiCorpus and the BNC were employed to investigate the senses and to identify the most frequent collocates and so the prototypes of these terms. The meaning extension of the terms is examined on the basis of the cognitive mechanisms which appear in the corpora. Theoretically, the paper is informed by the prototype theory (Rosch, 1973; 1975), image schemas (Johnson, 1987), and conceptual metaphor (Lakoff & Johnson, 1980/2003). The results show that تَسَارُع (tasāruʿ) (acceleration) and acceleration generally overlap in terms of polysemy, prototype, and images schemas as well as conceptual metaphor that organize the conceptualization of these terms. It was also found that both Arab and English speakers mix ACCELERATION up with SPEED and so misunderstand them in a scientific setting. The present findings have several implications for science curriculum design, education, and research on universal and culture-specific properties of language. (shrink)

Reconstructs the original Greek version of the confatalia-argument that Cicero attributes to Chrysippus in De fato and misrepresent in crucial ways. Compares this argument with Seneca's discussion of determinism in the Naturales quaestiones. Clarifies that Seneca makes a different distinction from that attested in Cicero's De fato. Argues that problems with interpreting both accounts derive from disregarding terminological distinctions harder to spot in the Latin versions and, related to this, insufficient attention to the ontological distinction between bodies (such as Fate) (...) and predicates (e.g. "what is fated"), which unfortunately does not square well with the modern ontological category "event." Contains some corrections to the author's earlier discussion of the topic in Seneca und die Stoa: Der Platz des Menschen in der Welt, De Gruyter 2006, ch. 3.3.4. (shrink)

In this paper I examine the ways in which our language and terminology predetermine how we approach, investigate and conceptualise mental illness. I address this issue from the standpoint of hermeneutic phenomenology, and my primary object of investigation is the phenomenon referred to as “mania”. Drawing on resources from classical phenomenology, I show how phenomenologists attempt to overcome their latent presuppositions and prejudices in order to approach “the matters themselves”. In other words, phenomenologists are committed to the idea that (...) in our everyday, natural attitude, we take for granted a number of prejudices and presuppositions that predetermine how we conceive of and understand what we experience. In order to properly approach the phenomena themselves, we need to find ways of neutralising our presuppositions and prejudices in order to develop new (and hopefully more accurate) accounts of the phenomena under investigation. One of the most popular examples of such an attempt at neutralisation is what Edmund Husserl calls the epoché, which is the practice of bracketing out or suspending presuppositions. However, later phenomenologists developed alternative approaches. Martin Heidegger, for instance, engaged in etymological analyses to discover latent meanings in our language and terminology. Hans-Georg Gadamer also engaged in historical analyses of how our traditions sediment into latent prejudices. After discussing the various ways in which phenomenologists have attempted to neutralise presuppositions and prejudices prior to engaging in their investigations, I apply some of these principles and methods to the domain of psychopathology, and discuss some of the prejudices inherent in contemporary discussions of the phenomenon of mania. I examine recent attempts to link the phenomenon that we today refer to as “mania” with the ancient Greek concept of “μανία” (mania), and argue that the practice of linking contemporary and historical concepts can be detrimental to attempts at reclassifying disorders. In addition, I consider the implications of the shift in terminology from “manic depressive illness” to “bipolar disorder” – especially how conceiving of mania as one of two “poles” predetermines its description by both clinicians and patients. Finally, I address the implications of the headings under which mania and bipolar disorder are discussed within diagnostic manuals. For example, I discuss the removal of the headings of affective and mood disorders in the DSM-5, and the explicit decision by the authors to place bipolar disorder between depressive disorders and schizophrenia. What I aim to accomplish in this paper is not so much a phenomenological investigation of mania as it is a pre-phenomenological investigation. In other words, I offer a preparatory investigation of the phenomenon (or phenomena) referred to as “mania” in contemporary discourse, with the intention of laying the groundwork for further phenomenological and psychological research. (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)

This article illustrates possible models and languages of morality, as well as the kinds of values, legitimations, and classifications that are connected to them. It takes Asian and European perspectives into account to reflect on the terminologies and taxonomies of doing or being good from a logical and semantical point of view. The argument is that mutual literacy of such terminologies and taxonomies is indispensable in order to achieve true ethical dialogue.

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.

Background: Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is acomprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic healthdata. Some efforts have been made to capture the contents of SCT as Web Ontology Language (OWL), but theseefforts have been hampered by the size and complexity of SCT. Method: Our proposal here is to develop an upper-level ontology and to use it as the basis for defining the termsin SCT in a way that (...) will support quality assurance of SCT, for example, by allowing consistency checks ofdefinitions and the identification and elimination of redundancies in the SCT vocabulary. Our proposed upper-levelSCT ontology (SCTO) is based on the Ontology for General Medical Science (OGMS). Results: The SCTO is implemented in OWL 2, to support automatic inference and consistency checking. Theapproach will allow integration of SCT data with data annotated using Open Biomedical Ontologies (OBO) Foundryontologies, since the use of OGMS will ensure consistency with the Basic Formal Ontology, which is the top-levelontology of the OBO Foundry. Currently, the SCTO contains 304 classes, 28 properties, 2400 axioms, and 1555annotations. It is publicly available through the bioportal athttp://bioportal.bioontology.org/ontologies/SCTO/. Conclusion: The resulting ontology can enhance the semantics of clinical decision support systems and semanticinteroperability among distributed electronic health records. In addition, the populated ontology can be used forthe automation of mobile health applications. (shrink)

The in­ten­tion of this pa­per is to po­int out a tr­o­u­ble­so­me si­tu­a­tion in con­tem­po­rary Ser­bian on­to­lo­gi­cal ter­mi­no­logy, and al­so to in­di­ca­te the ways and pre-con­di­ti­ons in terms of hi­story of phi­lo­sophy, hi­story of lan­gu­a­ge and met­ho­do­logy in se­ar­ching for pos­si­ble so­lu­ti­ons. We are al­so trying to cast so­me light on the pr­o­blem of re­la­ti­on­ship bet­we­en lan­gu­a­ge and phi­lo­sop­hi­cal thin­king.

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the (...) Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (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)

Definitions vary according to context of use and target audience. They must be made relevant for each context to fulfill their cognitive and linguistic goals. This involves adapting their logical structure, type of content, and form to each context of use. We examine from these perspectives the case of definitions in ontologies.

Recent developments in the field of forensic medicine and the judicial practice are both factors influencing considerably toward an increasing role of toxicologists in court hearings and litigation processes. The role of forensic toxicologist has been until a few decennia before a prerogative of the medico-legal specialists, but meanwhile a subspecialty of the general toxicology seems to have been created. Vis-à-vis the increasing presence of toxicologists in penal procedures of poisoning and intoxications, Albanian courts have created their own precedents and (...) bylaws, regulating the presence, the opinion taking, and the relative importance such an expert opinion will have on the final sentence. Due to a multiplicity of factors, legal terminology with regard to drugs of abuse needs to be revised and parallel to such a revision a better defining of the role of expert toxicologist as a collector and interpreter of the scientific proofs seems necessary. Overlapping competencies with judicial bodies and confusing legislative measures will do nothing else but complicate issues that should be and can be easily resolved, through simple and appropriate interventions at different levels. (shrink)

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies (...) in anatomy, physiology and pathology. (shrink)

This paper is an attempt to understand the content of, and motivation for, a popular form of physicalism, which I call ‘non-reductive physicalism’. Non-reductive physicalism claims although the mind is physical (in some sense), mental properties are nonetheless not identical to (or reducible to) physical properties. This suggests that mental properties are, in earlier terminology, ‘emergent properties’ of physical entities. Yet many non-reductive physicalists have denied this. In what follows, I examine their denial, and I argue that on a (...) plausible understanding of what ‘emergent’ means, the denial is indefensible: non-reductive physicalism is committed to mental properties being emergent properties. It follows that the problems for emergentism—especially the problems of mental causation—are also problems for non-reductive physicalism, and they are problems for the same reason. (shrink)

In this article, I critically reassess Iris Marion Young's late works, which centre on the distinction between liability and social connection responsibility. I concur with Young's diagnosis that structural injustices call for a new conception of responsibility, but I reject several core assumptions that underpin her distinction between two models and argue for a different way of conceptualising responsibility to address structural injustices. I show that Young's categorical separation of guilt and responsibility is not supported by the writings of Hannah (...) Arendt, which Young draws on, and that it is also untenable on independent systematic grounds. Furthermore, I argue that several of Young's other criteria fail to clearly demarcate two distinct phenomena. I therefore propose to transcend Young's distinction between two models in favour of a related, but conceptually different distinction between two forms of responsibility: interactional and structural. Embracing this terminology facilitates the conceptualisation of the general features of responsibility that are shared by both forms, including their retrospective and prospective time-direction and their applicability to individual, joint and group agency. The distinction between interactional and structural responsibility also yields a more compelling general account of the role of background structures, and of blame within ascriptions of political responsibility. (shrink)

The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of these (...) relations and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies. (shrink)

The term “Gettier Case” is a technical term frequently applied to a wide array of thought experiments in contemporary epistemology. What do these cases have in common? It is said that they all involve a justified true belief which, intuitively, is not knowledge, due to a form of luck called “Gettiering.” While this very broad characterization suffices for some purposes, it masks radical diversity. We argue that the extent of this diversity merits abandoning the notion of a “Gettier case” in (...) a favour of more finely grained terminology. We propose such terminology, and use it to effectively sort the myriad Gettier cases from the theoretical literature in a way that charts deep fault lines in ordinary judgments about knowledge. (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)

To understand something involves some sort of commitment to a set of propositions comprising an account of the understood phenomenon. Some take this commitment to be a species of belief; others, such as Elgin and I, take it to be a kind of cognitive policy. This paper takes a step back from debates about the nature of understanding and asks when this commitment involved in understanding is epistemically appropriate, or ‘acceptable’ in Elgin’s terminology. In particular, appealing to lessons from (...) the lottery and preface paradoxes, it is argued that this type of commitment is sometimes acceptable even when it would be rational to assign arbitrarily low probabilities to the relevant propositions. This strongly suggests that the relevant type of commitment is sometimes acceptable in the absence of epistemic justification for belief, which in turn implies that understanding does not require justification in the traditional sense. The paper goes on to develop a new probabilistic model of acceptability, based on the idea that the maximally informative accounts of the understood phenomenon should be optimally probable. Interestingly, this probabilistic model ends up being similar in important ways to Elgin’s proposal to analyze the acceptability of such commitments in terms of ‘reflective equilibrium’. (shrink)

Ontologies are being used increasingly to promote the reusability of scientific information by allowing heterogeneous data to be integrated under a common, normalized representation. Definitions play a central role in the use of ontologies both by humans and by computers. Textual definitions allow ontologists and data curators to understand the intended meaning of ontology terms and to use these terms in a consistent fashion across contexts. Logical definitions allow machines to check the integrity of ontologies and reason over data annotated (...) with ontology terms to make inferences that promote knowledge discovery. Therefore, it is important not only to include in ontologies multiple types of definitions in both formal and in natural languages, but also to ensure that these definitions meet good quality standards so they are useful. While tools such as Protégé can assist in creating well-formed logical definitions, producing good definitions in a natural language is still to a large extent a matter of human ingenuity supported at best by just a small number of general principles. For lack of more precise guidelines, definition authors are often left to their own personal devices. This paper aims to fill this gap by providing the ontology community with a set of principles and conventions to assist in definition writing, editing, and validation, by drawing on existing definition writing principles and guidelines in lexicography, terminology, and logic. (shrink)

I discuss Aristotle's anomalous terminology in Physics A.1 (involving "universals" and "particulars") and its coherence with Aristotle's notion of scientific demonstration.

It is widely alleged that metaphysical possibility is “absolute” possibility Conceivability and possibility, Clarendon, Oxford, 2002, p 16; Stalnaker, in: Stalnaker Ways a world might be: metaphysical and anti-metaphysical essays, Oxford University Press, Oxford, 2003, pp 201–215; Williamson in Can J Philos 46:453–492, 2016). Kripke calls metaphysical necessity “necessity in the highest degree”. Van Inwagen claims that if P is metaphysically possible, then it is possible “tout court. Possible simpliciter. Possible period…. possib without qualification.” And Stalnaker writes, “we can agree (...) with Frank Jackson, David Chalmers, Saul Kripke, David Lewis, and most others who allow themselves to talk about possible worlds at all, that metaphysical necessity is necessity in the widest sense.” What exactly does the thesis that metaphysical possibility is absolute amount to? Is it true? In this article, I argue that, assuming that the thesis is not merely terminological, and lacking in any metaphysical interest, it is an article of faith. I conclude with the suggestion that metaphysical possibility may lack the metaphysical significance that is widely attributed to it. (shrink)

Causalists and Evidentialists can agree about the right course of action in an (apparent) Newcomb problem, if the causal facts are not as initially they seem. If declining $1,000 causes the Predictor to have placed $1m in the opaque box, CDT agrees with EDT that one-boxing is rational. This creates a difficulty for Causalists. We explain the problem with reference to Dummett's work on backward causation and Lewis's on chance and crystal balls. We show that the possibility that the causal (...) facts might be properly judged to be non-standard in Newcomb problems leads to a dilemma for Causalism. One horn embraces a subjectivist understanding of causation, in a sense analogous to Lewis's own subjectivist conception of objective chance. In this case the analogy with chance reveals a terminological choice point, such that either (i) CDT is completely reconciled with EDT, or (ii) EDT takes precedence in the cases in which the two theories give different recommendations. The other horn of the dilemma rejects subjectivism, but now the analogy with chance suggests that it is simply mysterious why causation so construed should constrain rational action. (shrink)

In this paper, I claim that the personal/subpersonal distinction is first and foremost a distinction between two kinds of psychological theory or explanation: it is only in this form that we can understand why the distinction was first introduced, and how it continues to earn its keep. I go on to examine the different ontological commitments that might lead us from the primary distinction between personal and subpersonal explanations to a derivative distinction between personal and subpersonal states. I argue that (...) on one of the most common metaphysical interpretations of the explanatory distinction, talk of a distinction between personal and subpersonal states simply makes no sense. When people insist on applying the personal/subpersonal terminology to psychological states, I allow that they are often making a genuine distinction, but one that it is best understood in terms of Stich's (1978) distinction between doxastic and subdoxastic states. I end the paper by considering some other common misinterpretations of the personal/subpersonal distinction, such as those involving consciousness, normativity, or autonomy. (shrink)

Since 2016, there has been an explosion of academic work and journalism that fixes its subject matter using the terms ‘fake news’ and ‘post-truth’. In this paper, I argue that this terminology is not up to scratch, and that academics and journalists ought to completely stop using the terms ‘fake news’ and ‘post-truth’. I set out three arguments for abandonment. First, that ‘fake news’ and ‘post-truth’ do not have stable public meanings, entailing that they are either nonsense, context-sensitive, or (...) contested. Secondly, that these terms are unnecessary, because we already have a rich vocabulary for thinking about epistemic dysfunction. Thirdly, I observe that ‘fake news’ and ‘post-truth’ have propagandistic uses, meaning that using them legitimates anti-democratic propaganda, and runs the risk of smuggling bad ideology into conversations. (shrink)