Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those who (...) created them, and unable to serve as inputs for automated reasoning. This volume shows, in a nontechnical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends. (shrink)

The world of ontology development is full of mysteries. Recently, ISO Standard 15926 (“Lifecycle Integration of Process Plant Data Including Oil and Gas Production Facilities”), a data model initially designed to support the integration and handover of large engineering artefacts, has been proposed by its principal custodian for general use as an upper level ontology. As we shall discover, ISO 15926 is, when examined in light of this proposal, marked by a series of quite astonishing defects, which may however provide (...) general lessons for the developers of ontologies in the future. (shrink)

The thesis investigates how the notion of ‘ontology’ has been used in the field of medical informatics and knowledge representation. Partly to investigate what an ‘ontology’ can be said to represent and what requirements we can have on a good ‘ontology’. The author studies the already existing medical terminologies and ‘ontologies’ to elucidate what theories they are based on. The terminological theories of Eugen Wüster and his legacy in medical informatics are studied. It is noted that terminological theories handling linguistic (...) entities are not suited for describing and representing medical theories, since these are assumed to refer to the real world, which consists of more than linguistics entities. In order to find a metaphysical theory in accordance with the world view that medical theories describe, the author turn to the critical realism of Karl Popper, Roy Bhaskar and Ilkka Niiniluoto. These theories, taken together with the metaphysical theories regarding universals of David M Armstrong and Ingvar Johansson, are used as a basis to find out what an ‘ontology’ can be said to represent, and what criteria and requirements we can have on a good ‘ontology’. Among the requirements presented in the thesis are stability, interoperability and the requirement that a good ‘ontology’ must be in accordance with our best available theories. Finally, it is discussed how these requirements and criteria can come into conflict with one another, and how one should reason when handling these trade-offs. The author emphasises the importance of including the medical expertise in the process of creating ‘ontologies’, in order to produce as useful and relevant ‘ontologies’ as possible. (shrink)

Digital Rights Management (DRM) covers the description, identification, trading, protection, monitoring and tracking of all forms of rights over both tangible and intangible assets. The Digital Object Identifier (DOI) system provides a framework for the persistent identification of entities involved in this domain. Although the system has been very well designed to manage object identifiers, some important questions relating to the creation and assignment of identifiers are left open. The paradigm of a Referent Tracking System (RTS) recently advanced in the (...) healthcare and life sciences environment is able to fill these gaps. This is demonstrated by pointing out inconsistencies in the existing DOI models and by showing how they can be corrected using an RTS. (shrink)

A background piece on the role of ontology in technology research, focusing especially on the use-mention confusion.

For corporate memory and enterprise ontology systems to be maximally useful, they must be freed from certain barriers placed around them by traditional knowledge management paradigms. This means, above all, that they must mirror more faithfully those portions of reality which are salient to the workings of the enterprise, including the changes that occur with the passage of time. The purpose of this chapter is to demonstrate how theories based on philosophical realism can contribute to this objective. We discuss how (...) realism-based ontologies (capturing what is generic) combined with referent tracking (capturing what is specific) can play a key role in building the robust and useful corporate memories of the future. (shrink)