Can dissonance engineering improve risk analysis of human–machine systems?

The paper discusses dissonance engineering and its application to risk analysis of human–machine systems. Dissonance engineering relates to sciences and technologies relevant to dissonances, defined as conflicts between knowledge. The richness of the concept of dissonance is illustrated by a taxonomy that covers a variety of cognitive and organisational dissonances based on different conflict modes and baselines of their analysis. Knowledge control is discussed and related to strategies for accepting or rejecting dissonances. This acceptability process can be justified by a risk analysis of dissonances which takes into account their positive and negative impacts and several assessment criteria. A risk analysis method is presented and discussed along with practical examples of application. The paper then provides key points to motivate the development of risk analysis methods dedicated to dissonances in order to identify the balance between the positive and negative impacts and to improve the design and use of future human–machine system by reinforcing knowledge

Open biomedical pluralism : formalising knowledge about breast cancer phenotypes

We demonstrate a heterogeneity of representation types for breast cancer phenotypes and stress that the characterisation of a tumour phenotype often includes parameters that go beyond the representation of a corresponding empirically observed tumour, thus reflecting significant functional features of the phenotypes as well as epistemic interests that drive the modes of representation. Accordingly, the represented features of cancer phenotypes function as epistemic vehicles aiding various classifications, explanations, and predictions. In order to clarify how the plurality of epistemic motivations can be integrated on a formal level, we give a distinction between six categories of human agents as individuals and groups focused around particular epistemic interests. We analyse the corresponding impact of these groups and individuals on representation types, mapping and reasoning scenarios. Respecting the plurality of representations, related formalisms, expressivities and aims, as they are found across diverse scientific communities, we argue for a pluralistic ontology integration. Moreover, we discuss and illustrate to what extent such a pluralistic integration is supported by the distributed ontology language DOL, a meta-language for heterogeneous ontology representation that is currently under standardisation as ISO WD 17347 within the OntoIOp (Ontology Integration and Interoperability) activity of ISO/TC 37/SC 3. We particularly illustrate how DOL supports representations of parthood on various levels of logical expressivity, mapping of terms, merging of ontologies, as well as non-monotonic extensions based on circumscription allowing a transparent formal modelling of the normal/abnormal distinction in phenotypes

BIOMEDICAL ONTOLOGIES: EXAMINING ASPECTS OF INTEGRATION ACROSS BREAST CANCER KNOWLEDGE DOMAINS

The key ideas developed in this thesis lie at the intersection of epistemology, philosophy of molecular biology, medicine, and computer science. I examine how the epistemic and pragmatic needs of agents distributed across particular scientific disciplines influence the domain-specific reasoning, classification, and representation of breast cancer. The motivation to undertake an interdisciplinary approach, while addressing the problems of knowledge integration, originates in the peculiarity of the integrative endeavour of sciences that is fostered by information technologies and ontology engineering methods. I analyse what knowledge integration in this new field means and how it is possible to integrate diverse knowledge domains, such as clinical and molecular. I examine the extent and character of the integration achieved through the application of biomedical ontologies. While particular disciplines target certain aspects of breast cancer-related phenomena, biomedical ontologies target biomedical knowledge about phenomena that is often captured within diverse classificatory systems and domain-specific representations. In order to integrate dispersed pieces of knowledge, which is distributed across assorted research domains and knowledgebases, ontology engineers need to deal with the heterogeneity of terminological, conceptual, and practical aims that are not always shared among the domains. Accordingly, I analyse the specificities, similarities, and diversities across the clinical and biomedical domain conceptualisations and classifications of breast cancer. Instead of favouring a unifying approach to knowledge integration, my analysis shows that heterogeneous classifications and representations originate from different epistemic and pragmatic needs, each of which brings a fruitful insight into the problem. Thus, while embracing a pluralistic view on the ontologies that are capturing various aspects of knowledge, I argue that the resulting integration should be understood in terms of a coordinated social effort to bring knowledge together as needed and when needed, rather than in terms of a unity that represents domain-specific knowledge in a uniform manner. Furthermore, I characterise biomedical ontologies and knowledgebases as a novel socio-technological medium that allows representational interoperability across the domains. As an example, which also marks my own contribution to the collaborative efforts, I present an ontology for HER2+ breast cancer phenotypes that integrates clinical and molecular knowledge in an explicit way. Through this and a number of other examples, I specify how biomedical ontologies support a mutual enrichment of knowledge across the domains, thereby enabling the application of molecular knowledge into the clinics