Practical Ontology Research Articles

Ontology Driven Controlled Natural Language Clinical Decision Support System for the Cardiovascular Specialty

Abstract We present an end to end Question and Answering system to help the clinical practitioners in a cardiovascular healthcare environment. We introduce our proposed ontology framework, Ontology for General Clinical Practice, that we developed enhancing the currently available state-of-the-art ontologies for medical science and for the cardiovascular specialty, extending upon the OBO Foundry principles. It's shown the scientific and philosophical reasons of its present dual structure with a deeply expressive terminological base (TBox) and a highly computable assertions knowledge base (ABox). The knowledge base is automatically populated by means of a tutored acquisition from clinical reports using Controlled Natural Language rendering an ontology driven question answering system with high recall, precision and F-Measure that competes in its specific sub-domain with the more advanced current NLP systems developed in general for the healthcare domain.

Enrichment/Population of Customized CPR (Computer-Based Patient Record) Ontology from Free-Text Reports for CSI (Computer Semantic Interoperability)

CSI (Computer Semantic Interoperability) is a very important issue in healthcare. Ways for heterogeneous computer systems to “understand” important facts from the clinical process for clinical decision support are now beginning to be addressed. The authors present here comprehensive contributions to achieve CSI. EHR (Electronic Health Record) systems provide a way to extract reports of the clinicians activity. In order to formalize an automated acquisition from semi-structured, free-form, natural language texts in Portuguese into a Clinical Practice Ontology an important step is to develop the ability of decoding all the nicknames, acronyms and short-hand forms that each clinician tend to write down in their reports. The authors present the steps to develop clinical vocabularies extracting directly from clinical reports in Portuguese available in the SAM (Sistema de Apoio ao Médico) system. The presented techniques are easily further developed for any other natural language or knowledge representation framework with due adaptations.

The Expression of Espoused Humanizing Values in Organizational Practice: A Conceptual Framework and Case Study

We provide a conceptual framework and a case study of how an organization links its mission and espoused values with its operating practices. Conceptually, we locate this mission integration theme within Simons’ (1995, Levers of control. Harvard Business Review Press, Boston) management accounting and control framework, and then adapt Schatzki’s (2002, The site of the social. Pennsylvania State University Press, University Park) site ontology of social practice to develop general research expectations for case studies of espoused values/practice linkages. Empirically, we apply the conceptual framework to a case study of linkages among an actual company’s espoused values, human resource practices, and financial management during its 40-plus year history. The concluding section summarizes the study and discusses its implications, limitations, and opportunities for future research.

Hinterland's Who’s Who: Birding, Multiplicity, and Barn Owls

Hinterland's Who’s Who: Birding, Multiplicity, and Barn Owls

Social practices from the viewpoint of trans-subjective existentialism

The principal aim of this article is to examine the capacity of existential analytic to suggest alternatives to entrenched dichotomies and dilemmas in practice theory, and more generally, in social theory. In this regard, the doctrine of trans-subjective existentialism is developed. The underlying aim is to inform hermeneutic engagement with social practices’ potentiality-for-being in order to illuminate a possible existential ontology of practices. It is argued that the concept of chronotope should be central in this ontology. Thus, the possibility of hermeneutic realism about social practices becomes open to scrutiny.

More than trees! Understanding the agroforestry adoption gap in subsistence agriculture: Insights from narrative walks in Kenya

Agroforestry can contribute to the mitigation of climate change while delivering multiple benefits to sub-Saharan farmers who are exposed to climate variability, land degradation, water scarcity, high disease burden and persistent poverty. But adoption is slow. Based on a critical problem solving approach and grounded theory as a strategy, we study agroforestry and subsistence agriculture as integrated, yet separate, socio-ecological systems with different organisational logics and temporal dynamics. Using ‘narrative walks’ as a qualitative method to construct grounded data, we explore the social and natural dimensions of the complex, diverse and uncertain landscape and life-worlds of subsistence agriculture. In the grounded analysis, we clarify how social stratification constructs incentives and disincentives to adopt agroforestry. To exemplify, food secure and opportunity seeking farmers may invest land and labour in trees, nurseries and social networks while risk evading farmers are constrained by the ‘food imperative’, the ‘health imperative’ and poverty in and of itself. By recognising material, symbolic and relational aspects we show how the ontology of global policies focussing on the merits of agroforestry differs from the ontology of everyday practices and strategies in subsistence agriculture. Such ontological stratification constitutes another constraint to agroforestry adoption as a comprehensive form of socio-technological change.

Critical realism: a practical ontology to explain the complexities of smoking and tobacco control in different resource settings

BackgroundThis paper presents critical realism (CR) as an innovative system for research in tobacco prevention and control. CR argues that underlying mechanisms are considered and explored to ensure effective implementation of any program/policy or intervention. Any intervention or program/policy that is transposed from one country to another or one setting to another is complex.MethodsThe research was undertaken and analyzed through a critical ethnography lens using CR as a philosophical underpinning. The study relied upon the following components: original fieldwork in Nigeria including participant observation of smokers, in-depth interviews and focus groups with smokers, and in-depth interviews with health professionals working in the area of tobacco control in Nigeria.ResultsFindings from this small ethnographic study in Nigeria, suggest that Critical Realism holds promise for addressing underlying mechanism that links complex influences on smoking.ConclusionThis paper argues that understanding the underlying mechanisms associated with smoking in different societies will enable a platform for effective implementation of tobacco control policies that work in various settings.

Ontography: Investigating the production of things, deflating ontology

In this postscript to the special issue of Social Studies of Science on the ‘turn to ontology’ in science and technology studies, I discuss a tension that runs through many of the articles in the issue. This is a tension between adopting a general philosophical ontology and pursuing empirical studies of particular historical and contemporary practices. The general ontology highlights multiplicity and difference and rejects the idea that, for example, an identical disease entity underlies different practical enactments of that disease in different clinical and research circumstances. The empirical approach investigates how particular identities and differences are negotiated and instantiated in specific circumstances. The two approaches are not necessarily incompatible, but the first settles questions of identity and difference through a ‘pre-theoretical decision’, while the second remains open to distinct resolutions of what counts as identity and difference in the practical settings studied. In this postscript, I argue that a commitment to a general philosophical ontology confuses investigations of specific practical ontologies. To avoid such confusion, I recommend ‘ontography’: historical and ethnographic investigations of particular world-making and world-sustaining practices that do not begin by assuming a general picture of the world. Such investigations avoid making sharp distinctions between epistemology and ontology and take a symmetrical approach to concerns about identity and difference.

本体的盘诘及其思想视域

追求永恒是人类理性最根深蒂固的本能，形而上学研究难以回避本体论，确立本体的目的在于为人类思想提供坚实基础，然而人们对本体有着相近而又相互抵牾的观点，不同本体观念之间的盘诘暴露出本体认识的诸多悖谬，实体本体论、实践本体论、过程本体论代表了三种思维方式，其所蕴含的矛盾推动着本体论研究的深层进展，本体论绽放着新的可能性维度。 The pursuit of eternity is the most deep-rooted instinct of human reason. Metaphysical studies are difficult to avoid ontology. The purpose of the establishment of noumenon is to provide a solid foundation for thinking. However, people have similar and mutually contradictory views of noumenon. The cross-examination of different views about noumenon reveals many absurd ideas. Entity ontology, practice ontology and process ontology represent three ways of thinking. Their inherent contradictions push a deep progress in the study of ontology. In this sense, the dimension of ontology has new possibilities to be developed.

Ontology based Clinical Practice Justification in Natural Language

One of the most important contributions that any decision support system can make to achieve wide acceptance among any community is to be able to justify its own suggestions. When dealing with highly technical and scientifically advanced practitioners like medical doctors or any other related clinical workers, the ability to justify itself using the domain specialist usual terminology and technicalities is imperative. In this article we demonstrate the use of an ontological framework as inferencing basis for automatic sound clinical suggestions providing. Our work has two main contributions, consolidating the use of OGCP (Ontology for General Clinical Practice) as foundation and providing controlled English justifications of the extracted suggestions. We found that clinical practitioners feel as acceptable the Attempto Controlled English justifications generated from the knowledge base.

STRATEGY AS PRACTICE: A DISCUSSION OF THE EPISTEMOLOGICAL APPROPRIATION OF HISTORICAL-CULTURAL ACTIVITY THEORY BY THE ACTIVITY-BASED VIEW

As an approach in development, Strategy as Practice appropriates other theories with ontological and epistemological assumptions that converge for the construction of their analytical body. Therefore, in this discipline, the assumptions of the Structurationist and Historical-Cultural Activity Theory are to be found as grounded frameworks. This theoretical essay puts forward an argument concerning the appropriation of the Historical-Cultural Activity Theory by the Activity-Based View that figures as one of the analytical epistemological structures of Strategy as Practice. The analytical procedure is guided by the central aim of stimulating the debate about the ontological and epistemological assumptions of assimilation between one theory and the other added goal to dismantle an argument concerning the Ontology of Strategic Practice. The results of the analytical argument reveal that there is adequate ontological and epistemological coherence in the incorporation of the Historical-Cultural Activity Theory by the Activity-Based View.

Practice ‘in Talk’ and Talk ‘as Practice’: Dish Washing and the Reach of Language

The aim of this paper is to open up debate about the methodological implications of adopting practice theory in social research. Practice theory has become a much used analytical framework for researchers working on the question ‘what we do’ in relation to a diverse set of contemporary concerns, but discussion on the epistemological implications has thus far been limited. By looking at interview talk on dish washing through a practice-theoretical lens grounded in Schatzki's (1996 , 2002 ) ontology of practices, I set out to examine how language and talk form a resource and an obstruction when we want to think about mundane practices in scholarly ways. My concern is located within the broader questioning of qualitative interviews in debate in the social sciences. Acknowledging that interviews are ‘distinctive forms of social action’ ( Atkinson & Coffey 2003 ), I move on to consider how talk about washing up in interviews conveys the interaction between two practices; those of talking as the salient embodied practice wielded by human beings in interaction with each other, and dish washing as an integrated cleaning practice common in domestic kitchens. The analysis suggests that our qualitative interviews stimulated talk on the teleo-affective qualities of dish-washing. Rules and principles also appeared in the talk in specific ways. However, the talk was not so good for gaining understanding of the activity of dish washing. In conclusion, I argue that the standard qualitative interview brings out the human-to-human interactional concerns of practices, but that different research contexts need to be developed and employed for gaining greater understanding of the performance (or activity) of the practice of dish washing.

The Pitfall of Hypostatization/Reification and the Reality of Social Things

Hypostatization, (reification in one of its many senses) or the fallacy of misplaced concreteness refers to an abstraction being “treated as if it were a concrete, real event, or physical entity.” Hypostatization has occurred when concepts, frameworks, and theories freeze into pictures of reality that cannot be shaken by reality.There is a natural psychological tendency to assume that every word in language refers to something outside of language. Beliefs about the reality of the things of nature, such as gravity, heat, kinetic force, stones, and water, are usually unproblematic even though, as Kant demonstrated, these beliefs must involve an element of interpretation. Natural scientists are rarely concerned by the doubts of philosophers as to whether a real world exists. It is easy to grasp how the things existing in the natural world can kick back at the hypotheses scientists attempt to impose, and render them problematic.It is understandable that social scientists also tend to view the concepts they use, like the political system, elite, social class, interest group, bureaucracy, and capitalism as referring to real things in the real world, as do the concepts of stone, tree, and thunderstorm. This commonsense naive realist view of a reality existing independently of our knowledge has deep roots in the human psyche and in language. Few doubt the existence of a social world that can sometimes shatter our false beliefs about it. Yet it remains unclear just what it is that might kick back at the hypotheses social scientists make about it. When social scientists set about to study things like governments, markets, or power, they must have some idea of the nature of the things they wish to research. They make assumptions about the things they intend to investigate and these assumptions play a crucial role in determining what kinds of information to gather and how to gather it. Yet when the notions of social reality underlying social science research are scrutinized, it becomes clear how tenuous their representation can be.Without a clear sense of what is “out there” in the real world, concepts tend to create worlds of their own without protest from reality. Facts can always be found that fit the concepts. When a clear notion of social reality is present, that reality can kick back and shatter propositions that are made about it. This reduces the potential for hypostatization.This paper argues that a clear sense of social reality is usually missing in social science research, and that this accounts for the tendency to hypostatize. It attempts to develop a remedial approach to hypostatization by suggesting ways of developing an adequate, practical ontology of the social. Words are not simply labels for things. Improving our sense of real social world is the only effective means to combat reification. Research seeks to discover concrete sources of orderliness in social reality that can serve as objective constraints on the hypotheses the research seeks to impose.

Purity in danger: power, negotiation and ontology in medical practice

PurposeOrganizational analysts have long questioned the ways in which professional knowledge becomes powerful. The purpose of this paper is to extend that enquiry by examining two professional groups in the UK – doctors and veterinarians.Design/methodology/approachThe paper examines a selection of social interactions, tensions and disagreements between practitioners and non‐medical actors and draws on a range of qualitative research methods, particularly structured interview and participant observation, to analyse and interpret these as “epistemological conflicts”.FindingsHospital doctors and veterinary surgeons share a common belief that “truth” and “facts” are at the core of their clinical and surgical work. This positivist paradigm underpins a range of practical engagements with bodies and diseases and lends them a sense of ontological security when dealing with people from outside their professions, especially those without medical training. This paper examines the practical effects that such ontological tensions can have. In exposing some of these effects, this paper questions the often taken‐for‐granted divisions between science and arts, religion and medicine, and takes a more heterdox approach in analyzing social interactions.Originality/valueThe paper advocates philosophical, methodological and theoretical heterodoxy. The findings are viewed through a number of different theoretical lenses; from actor network theory and sociology of technology and science (STS) to deconstruction, frame theory and semiotics. The paper makes no attempt to choose between these approaches and instead argues that a “messy” and multiple understanding, both of theory and practice, is needed to gain insights into the tricky politics of knowledge and its effects in practical settings.

Practice-centred work analysis: towards ontology-based decision support in cross-boundary e-health

Ontologies are increasingly used as artefacts for representing human knowledge for problem solving and decision making. Studies have shown that the actual knowledge used in problem solving and decision-making often occurs at the work practice level – the level that typically goes beyond functional notions of work processes to include a wide range of contextual, socio-cultural, situated and dynamically changing factors through which individuals, in getting work done, seek to construct meaning out of their experiences and engagement with the environment. However, it still remains an open question how much of the issues encompassed by a notion of work practice is accommodated in current ontology design approaches in system design. In this paper, the creation and use of ontologies is analysed from a practice-theoretic perspective in order to understand the processes of shared conceptualisation and role of ontologies in explicating knowledge about actual clinical work processes and problem situations. We illustrate this using a clinical work practice ontology, which we refer to as WOPRON, and show its capability for representing clinical work practice knowledge for cross-boundary decision support in e-health.

Enrichment/Population of Customized CPR (Computer-based Patient Record) Ontology from Free-text Reports for CSI (Computer Semantic Interoperability)

CSI (Computer Semantic Interoperability) is a very important issue in healthcare. Ways for heterogeneous computer systems to “understand” important facts from the clinical process for clinical decision support are now beginning to be addressed. We present here comprehensive contributions to achieve CSI. EHR (Electronic Health Record) systems provide a way to extract reports of the clinicians activity. In order to formalize an automated acquisition from semi-structured, free-form, natural language texts in Portuguese into a Clinical Practice Ontology an important step is to develop the ability of decoding all the nicknames, acronyms and short-hand forms that each clinician tend to write down in their reports. We present the steps to develop clinical vocabularies extracting directly from clinical reports in Portuguese available in the SAM (Sistema de Apoio ao Médico) system. The presented techniques are easily further developed for any other natural language or knowledge representation framework with due adaptations.

Siting Praxeology. The Methodological Significance of “Public” in Theories of Social Practices

The concept of “site” is at the center of current debates in theories of social practices as well as in cultural anthropology. It is unclear, however, how to assess the associated methodological assumption that overriding social structures or cultural formations can manifest themselves in sites. The article draws on the conception of social practices and introduces the notion of “publicness” in order to explicate how and why sociality and social structures can be accessed through “siting”. Sites as well as social practices, it is claimed, have to be conceptualized as essentially public and thus principally observable phenomena. This assumption of publicness implicit to both site ontology and theories of social practices is unfolded on the basis of a praxeological reformulation of the paradigm of joint attention elaborated in developmental psychology. To avoid presentist misinterpretations, we then conceptualize sociality as chains of practices across time and space, drawing on the works of Theodore Schatzki, Ludwig Wittgenstein, Anthony Giddens and Bruno Latour. The public carriers of practices (artifacts, symbols, media, bodies) and the translocal structures they establish acquire particular significance in these approaches. In a further step, we present some methodological consequences of the “publicness assumption” and support our arguments by referring to Pierre Bourdieu's study on Distinction.

Conceptual challenges in the translation of research into practice: it's not just a matter of "communication".

This paper identifies key barriers to the translation of science into practice and policy and makes recommendations for addressing them. It focuses on the challenges of translation within the field of tobacco control, but we argue that the insights are widely generalisable. Actor-Network Theory is used to frame an analysis, supplemented by focussed discussions with international tobacco control practitioners (service delivery and advocacy) and researchers. The central challenge to translation is that researchers and practitioners have different "practical ontologies". Researchers use findings from specific contexts to generalise to universal principles, while practitioners try to use these generalisations to inform their work in what are typically a somewhat different set of specific contexts. Neglecting the need to translate back from the general to the particular means research syntheses are not framed to meet practitioners' needs. Traditional knowledge broking roles need to be extended to better align the needs of researchers and practitioners. This may be facilitated by more creative use of "social computing" to enable real-time input into research syntheses from all interested parties, including input to the questions that research addresses. To do this systematically requires that we construct "generalisation gradients" to help practitioners apply general research conclusions to their particular situation and researchers to identify the relevance of their work. Disadvantaged communities in particular need help, since there is typically less research directly applicable to their contexts; thus, they need to generalise more.

Bourdieu y Giddens: La superación de los dualismos y la ontología relacional de las prácticas sociales

Pierre Bourdieu (1930 ¿ 2002) y Anthony Giddens (1938- ) se constituyen en dos de los mejores exponentes de la síntesis superadora de los dualismos clásicos del pensamiento sociológico. En el artículo se mostrará cómo, a pesar de sus diferencias de enfoque teóricoempírico y de las tradiciones de pensamiento de las cuales provienen, ambos producen una ontología relacional de las prácticas sociales que se soporta en nociones básicas para la ciencia social actual como son las de habitus, campo, dualidad de la estructura e integración social y sistémica.

An Extension of the Environment for Building/Using Ontologies "Hozo" toward Practical Ontology Engineering - Focused on Practical Issues

Recently, ontology has attracted attention as an important technology for knowledge infrastructure and semantic processing, and a lot of ontologies have been constructed in various domains. At the same time, ontological theories, technologies, and ontology engineering tools have been developed by not only researchers but also practitioners. We also have been investigating ontological theories and developed a computer environment for building/using ontologies named ``Hozo'' which is based on the ontological theory of roles. Hozo has been used for practical ontology construction in various domains such as clinical medicine, bioinformatics, environmental engineering and so on. These practices of ontology development have raised many issues of ontology construction and utilization in both theoretical and technical points of view. We have solved them by extending our theories and functions of the system. It means we refined usability and reliability of Hozo through these practical experiences. In this paper, we focus on theoretical issues of ontology construction and discuss some extensions of ontological theories concerning representation of multiple inheritance and instances. First, we introduce IS-A relation which represents a relation weaker than is-a relation in the sense that it prohibits inheritance of identity, and we allow users to represent multiple inheritance using not usual strong is-a relation but IS-A relation. Then we investigate the validity of the representation using IS-A through ontological analysis of three utilization patterns of it. Next, we introduce two kinds of new representation of instances: ``simplified instance representation'' and ``#-(species) operator''. Users can use these representations for referring to instances in concept (class) definitions. These theoretical extensions would contribute to well-organized construction of ontologies in practical ontology engineering.