The collection and classification of data into meaningful categories is a key step in the process of knowledge making. In the life sciences, the design of data discovery and integration tools has relied on the premise that a formal classificatory system for expressing a body of data should be grounded in consensus definitions for classifications. On this approach, exemplified by the realist program of the Open Biomedical Ontologies Foundry, progress is maximized by grounding the representation and aggregation of data on (...) settled knowledge. We argue that historical practices in systematic biology provide an important and overlooked alternative approach to classifying and disseminating data, based on a principle of coordinative rather than definitional consensus. Systematists have developed a robust system for referring to taxonomic entities that can deliver high quality data discovery and integration without invoking consensus about reality or “settled” science. (shrink)

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)

Bio-ontologies are digital frameworks for handling biological and biomedical data. They consist of theoretical entities and relations with explicitly defined logical structures and precise definitions, whose purpose is to provide a shared language for representing information to be distributed and integrated across diverse scientific contexts. It is tempting to view bio-ontologies as clear and formal expressions of a scientific community’s ontological commitments about their domain of inquiry, and to view their integration as tantamount to the metaphysical unification of science that (...) some philosophers have envisaged. However, I argue that the local, practical, social and technological factors that influence their design prevent us from straightforwardly reading metaphysical conclusions from them. I discuss these complications and suggest how they can be overcome, revealing more general lessons for the development of a well-founded scientific metaphysics. (shrink)

Ontological realism is a philosophical stance that provides a definitional framework for ontologies and is referred to by various applied ontologists. From a computer science perspective, ontologies are often associated with formal languages for the representation of ontologies like the Web Ontology Language (OWL). It has, however, not been made explicit how the realist framework is related to the representation formalism. We analyse how the representational units of OWL can be used for modelling realist ontologies. While OWL is sufficiently close (...) to the realist framework of ontologies to describe them, there are categories in OWL that are alien to realist ontologies or duplicate categories in realist ontologies. This clarification allows separating talk about ontologies in general from talk about their specific representation. (shrink)

Many recent accounts of the ontology of groups, institutions, and practices have touched upon the normative or deontic dimensions of social reality (e.g., social obligations, claims, permissions, prohibitions, authority, and immunity), as distinct from any specifically moral values or obligations. For the most part, however, the ontology of such socio-deontic phenomena has not received the attention it deserves. In what sense might a social obligation or a claim exist? What is the ontological status of such an obligation (e.g., is it (...) an entity in its own right)? And how do people come to have social obligations or permissions in the first place? In this dissertation, I argue that such social-deontic phenomena can be accounted for ontologically in terms of the existence of shared prescriptive representational content that is backed by collectively held dispositions to monitor for compliance, and to punish (sanction, blame, chide, look unfavorably upon) those who fail to comply. (shrink)