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)

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 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)

It is only by fixing on agreed meanings of terms in biomedical terminologies that we will be in a position to achieve that accumulation and integration of knowledge that is indispensable to progress at the frontiers of biomedicine. Standardly, the goal of fixing meanings is seen as being realized through the alignment of terms on what are called ‘concepts’. Part I addresses three versions of the concept-based approach – by Cimino, by Wüster, and by Campbell and associates – and surveys (...) some of the problems to which they give rise, all of which have to do with a failure to anchor the terms in terminologies to corresponding referents in reality. Part II outlines a new, realist solution to this anchorage problem, which sees terminology construction as being motivated by the goal of alignment not on concepts but on the universals (kinds, types) in reality and thereby also on the corresponding instances (individuals, tokens). We outline the realist approach, and show how on its basis we can provide a benchmark of correctness for terminologies which will at the same time allow a new type of integration of terminologies and electronic health records. We conclude by outlining ways in which the framework thus defined might be exploited for purposes of diagnostic decision-support. (shrink)

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance (...) a proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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 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 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)

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)

Since its emergence in the 1960s, Artifcial Intelligence (AI) has grown to conquer many technology products and their felds of application. Machine learning, as a major part of the current AI solutions, can learn from the data and through experience to reach high performance on various tasks. This growing success of AI algorithms has led to a need for interpretability to understand opaque models such as deep neural networks. Various requirements have been raised from diferent domains, together with numerous tools (...) to debug, justify outcomes, and establish the safety, fairness and reliability of the models. This variety of tasks has led to inconsistencies in the terminology with, for instance, terms such as interpretable, explainable and transparent being often used interchangeably in methodology papers. These words, however, convey diferent meanings and are “weighted" diferently across domains, for example in the technical and social sciences. In this paper, we propose an overarching terminology of interpretability of AI systems that can be referred to by the technical developers as much as by the social sciences community to pursue clarity and efciency in the defnition of regulations for ethical and reliable AI development. We show how our taxonomy and defnition of interpretable AI difer from the ones in previous research and how they apply with high versatility to several domains and use cases, proposing a—highly needed—standard for the communication among interdisciplinary areas of AI. (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)

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)

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)

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)

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.

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)

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 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 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.

Recent research gives perspectivism the status of a stand-alone epistemological research program. As part of this development, it must be distinguished from other epistemologies, especially relativism. Not only do relativists and perspectivists use a similar vocabulary—even the supposed tenets (features of the doctrine) seem to partially overlap. To clarify the relation between these programs, I suggest drawing two important distinctions. The first is between the (1) terminological and (2) doctrinal components of epistemologies, the second between the (2a) analytical and (2b) (...) synthetical doctrinal elements. The method of the originalistic linguistic analysis that I introduce in this article shows that both relativism and perspectivism are using the same matrix of interconnected linguistic expressions that belong to what I call the universal epistemic language. Furthermore, this method reveals which doctrinal components necessarily follow from this linguistic basis and the terms “relativism” and “perspectivism” and which are a result of deliberate philosophical constructions. As for the linguistic basis and analytical doctrinal components, relativism and perspectivism are complementary members of one epistemology. Doctrinal additions that transform the original meaning of the terms “relativism” and “perspectivism”, such as “indifferentism” and “non-absolutism”, should be always explicitly mentioned to avoid confusion and strawmen debates in philosophy. (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)

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)

My aim in this chapter is to clarify the nature of the shift in Feyerabend’s philosophical thinking in the 1970s, focusing on issues of realism, relativism, and pluralism. Contra-Preston, I argue that realism-relativism is a misleading variable for characterizing Feyerabend’s shift in the 1970s. Rather, I characterize this shift as Feyerabend’s expansion of pluralism and suggest that this shift appears in Feyerabend’s publications starting in the late-1960s (e.g., Feyerabend 1968b, 1969b, 1970a, 1970c). Adopting the terminology of Brown and Kidd (...) (2016), this shift is characterized by a move from arguments for pluralism within science to broader arguments for pluralism in society. I argue that this shift was largely due to: (1) Feyerabend’s rejection of an empiricist demarcation criterion for science in the mid-1960s, and (2) Feyerabend’s incorporation of Mill’s arguments for pluralism into his own publications starting in 1970. This shift can be characterized as a broadening or expanding the scope of Feyerabend’s arguments for pluralism from contexts of scientific knowledge to the broader context of social or cultural (including ethical) knowledge. I articulate this argument with reference to the framework for classifying Feyerabend’s works formulated by Brown and Kidd (2016). Against Brown and Kidd (and Preston), I argue that realism-relativism is a red-herring as a variable for distinguishing Feyerabend’s early and middle works. Brown and Kidd’s distinction between pluralism within science and pluralism in society is a more useful variable for characterizing Feyerabend’s shift in thinking in the 1970s. Whereas Preston (1997) and Brown and Kidd (2016) identify the beginning of Feyerabend’s pluralism in society phase in 1978 with the publication of Science in a Free Society (Feyerabend 1978), I suggest that the relevant shift occurs much earlier, and it appears in Feyerabend’s publications starting in 1970 (Feyerabend 1970a, 1970b). On this understanding, Feyerabend’s philosophical shift (c. 1970) should be viewed as an expansion (or broadening) of the scope of application of his pluralist arguments, inspired by Mill’s ethical arguments for pluralism in society (Mill 1859/1977). (shrink)

Alexander Bird indicates that the significance of Thomas Kuhn in the history of philosophy of science is somehow paradoxical. On the one hand, Kuhn was one of the most influential and important philosophers of science in the second half of the twentieth century. On the other hand, nowadays there is little distinctively Kuhn’s legacy in the sense that most of Kuhn’s work has no longer any philosophical significance. Bird argues that the explanation of the paradox of Kuhn’s legacy is that (...) Kuhn took a direction opposite to that of the mainstream of the philosophy of science in his later academic career. This paper aims to provide a new way to understand and develop Kuhn’s legacy by revisiting the development of Kuhn’s philosophy of science in 1970s and proposing a new account of exemplar. Firstly, I propose my diagnosis of Kuhn’s “wrong turning” by identifying Kuhn’s two novel contributions: the introduction of paradigm and the proposal of the incommensurability thesis. Secondly, I argue that Kuhn made a conceptual/terminological turn from paradigm to theory, which undermined Kuhn’s novel contributions. Thirdly, I propose a new articulation of exemplar and propose an exemplar-based approach to analysing the history of science. Finally, I show how the exemplar-based approach can be applied to analyse the history of science by my case study of the early development of genetics. (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)

Observational and experimental discoveries of new factual entities such as objects, systems, or processes, are major contributors to some advances in the life sciences. Yet, whereas discovery of theories was extensively deliberated by philosophers of science, very little philosophical attention was paid to the discovery of factual entities. This paper examines historical and philosophical aspects of the experimental discovery by Carl Woese of archaea, prokaryotes that comprise one of the three principal domains of the phylogenetic tree. Borrowing Kuhn’s terminology, (...) this discovery of a major biological entity was made during a ‘normal science’ project of building molecular taxonomy for prokaryotes. Unexpectedly, however, an observed anomaly instigated the discovery of archaea. Substantiation of the existence of the new archaeal entity and consequent reconstruction of the phylogenetic tree prompted replacement of a long-held model of a prokarya and eukarya bipartite tree of life by a new model of a tripartite tree comprising of bacteria, archaea, and eukarya. This paper explores the history and philosophical implications of the progression of Woese’s project from normal science to anomaly-instigated model-changing discovery. It is also shown that the consequential discoveries of RNA splicing and of ribozymes were similarly prompted by unexpected irregularities during normal science activities. It is thus submitted that some discoveries of factual biological entities are triggered by unforeseen observational or experimental anomalies. (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)

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.

In a series of papers, Robin Jeshion has forcefully criticized both Donnellan's and Evans’ claims on the contingent a priori, and she has developed an “acquaintanceless” account of singular thoughts as an alternative view. Jeshion claims that one can fully grasp a singular thought expressed by a sentence including a proper name, even if its reference has been descriptively fixed and one’s access to the referent is “mediated” by that description. But she still wants to reject “semantic instrumentalism”, the view (...) that “there are no substantive conditions of any sort on having singular thought. We can freely generate singular thoughts at will by manipulating the apparatus of direct reference.” Her account of singular thoughts is a psychological one, rejecting any epistemic requirement. Having singular thoughts is for her a matter of deploying “mental files” or “dossiers” that play a significant role in the cognitive life of the individual. This paper elaborates on an alternative descriptivist-friendly view, which has important points of contact with Jeshion’s. It differs, particularly in that it is an epistemic view; it is only a broadly understood acquaintance view, as it will transpire, but this does not make it a mere terminological variation on Jeshion’s acquaintanceless one. To argue for it, the paper discusses some relevant aspects of the semantics of fictional discourse. (shrink)

In this paper we distinguish two issues that are often run together in discussions about physicalism. The first issue concerns levels. How do entities picked out by non-physical terminology, such as biological or psychological terminology, relate to physical entities? Are the former identical to, or metaphysically supervenient on, the latter? The second issue concerns physical parts and wholes. How do macroscopic physical entities relate to their microscopic parts? Are the former generally determined by the latter? We argue that (...) views on these two issues are independent of one another and should not be conflated. (shrink)

The correlation between dialogue and religion, both as conceptual apparatuses and as current practices, has had a long history. The purpose of this essay is to isolate one such instance – the “critical dialogue” taking place amongst scholars of religions – which involves also the dialogue scholars establish with their field of study and/or a given religious tradition. Following a brief clarification of terminology used, I will proceed to discuss concrete examples of critical dialogue within the Study of Religions (...) and how this might be enhanced. Finally, I will draw some partial conclusions which might pave the way for this critical dialogue to improve and continue. (shrink)

‘It is of the very nature of consciousness to be intentional’ said Jean-Paul Sartre, ‘and a consciousness that ceases to be a consciousness of something would ipso facto cease to exist’.1 Sartre here endorses the central doctrine of Husserl’s phenomenology, itself inspired by a famous idea of Brentano’s: that intentionality, the mind’s ‘direction upon its objects’, is what is distinctive of mental phenomena. Brentano’s originality does not lie in pointing out the existence of intentionality, or in inventing the terminology, (...) which derives from scholastic discussions of concepts or intentiones.2 Rather, his originality consists in his claim that the concept of intentionality marks out the subject matter of psychology: the mental. His view was that intentionality ‘is characteristic exclusively of mental phenomena. No physical phenomenon manifests anything like it’.3 This is Brentano’s thesis that intentionality is the mark of the mental. Despite the centrality of the concept of intentionality in contemporary philosophy of mind, and despite the customary homage paid to Brentano as the one who revived the terminology and placed the concept at the centre of philosophy, Brentano’s thesis is widely rejected by contemporary philosophers of mind. What is more, its rejection is not something which is thought to require substantial philosophical argument. Rather, the falsity of the thesis is taken as a starting-point in many contemporary discussions of intentionality, something so obvious that it only needs to be stated to be recognised as true. Consider, for instance, these remarks from the opening pages of Searle’s Intentionality: Some, not all, mental states and events have Intentionality. Beliefs, fears, hopes and desires are Intentional; but there are forms of nervousness, elation and undirected anxiety that are not Intentional.... My beliefs and desires must always be about something. But my nervousness and undirected anxiety need not in that way be about anything.4 Searle takes this as obvious, so obvious that it is not in need of further argument or elucidation. (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)

Empirical studies of the social lives of non-human primates, cetaceans, and other social animals have prompted scientists and philosophers to debate the question of whether morality and moral cognition exists in non-human animals. Some researchers have argued that morality does exist in several animal species, others that these species may possess various evolutionary building blocks or precursors to morality, but not quite the genuine article, while some have argued that nothing remotely resembling morality can be found in any non-human species. (...) However, these different positions on animal morality generally appear to be motivated more by different conceptions of how the term “morality” is to be defined than by empirical disagreements about animal social behaviour and psychology. After delving deeper into the goals and methodologies of various of the protagonists, I argue that, despite appearances, there are actually two importantly distinct debates over animal morality going on, corresponding to two quite different ways of thinking about what it is to define “morality”, “moral cognition”, and associated notions. Several apparent skirmishes in the literature are thus cases of researchers simply talking past each other. I then focus on what I take to be the core debate over animal morality, which is concerned with understanding the nature and phylogenetic distribution of morality conceived as a psychological natural kind. I argue that this debate is in fact largely terminological and non-substantive. Finally, I reflect on how this core debate might best be re-framed. (shrink)