Philosophers frequently struggle with the relation of metaphysics to the everyday world, with its practical value, and with its relation to empirical science. This paper distinguishes several different models of the relation between philosophical ontology and applied (scientific) ontology that have been advanced in the history of philosopy. Adoption of a strong participation model for the philosophical ontologist in science is urged, and requirements and consequences of the participation model are explored. This approach provides both a principled view and justification (...) of the role of the philosophical ontologist in contemporary empirical science as well as guidelines for integrating philosophers and philosophical contributions into the practice of science. (shrink)

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. (shrink)

This paper studies the structure of semantic theories over modular computational systems and applies the algebraic Theory of Institutions to provide a logical representation of such theories. A modular semantic theory is here defined by a cluster of semantic theories, each for a single program's module, and by a set of relations connecting models of different semantic theories. A semantic theory of a single module is provided in terms of the set of ∑‐models mapped from the category Th of ∑‐theories (...) and generating a hierarchy of structures from an abstract model to a concrete model of data. The collection of abstract models representing different modules of a program is formalised as the category of institutions INS, where theory morphisms express refinements, integrations, and compositions between couples of modules. Finally, it is required that a morphism in INS at any level occurs iff the same morphism occurs at the lower level alongside the Th hierarchy. (shrink)

We propose a functional view of ontologies that emphasises their role in determining answers to queries, irrespective of the formalism in which they are written. A notion of framework is introduced that captures the situation of a global language into which both an ontology language and a query language can be translated, in an abstract way. We then generalise existing notions of robustness from the literature, and relate these to interpolation properties that support modularisation of ontologies.