The current (still limited) use of the notion of informativeness in the domain of information system ontologies seems to indicate that such ontologies are informative if and only if they are understandable for their final recipients. This paper aims at discussing some theoretical issues emerging from that use which, as we will see, connects the informativeness of information system ontologies to their representational primitives, domains of knowledge, and final recipients. Firstly, we maintain that informativeness interacts not only with the actual (...) representational primitives, but also with their variability over time. Secondly, we discuss the correspondence between representational primitives and domains of knowledge of those ontologies. Finally, we explore the possibility of an epistemological discrepancy between human beings and software systems on the understanding of ontological contents. (shrink)

In the domain of information systems ontologies, the notion of completeness refers to ontological contents by demanding that they be exhaustive with respect to the domain that the ontology aims to represent. The purpose of this paper is to analyze such a notion, by distinguishing different varieties of completeness and by questioning its consistency with the open-world assumption, which formally assumes the incompleteness of conceptualizations on information systems ontologies.

Background: SNOMED CT is a large terminology system designed to represent all aspects of healthcare. Its current form and content result from decades of bottom-up evolution. Due to SNOMED CT’s formal descriptions, it can be considered an ontology. The Basic Formal Ontology (BFO) is a foundational ontology that proposes a small set of disjoint, hierarchically ordered classes, supported by relations and axioms. In contrast, as a typical top-down endeavor, BFO was designed as a foundational framework for domain ontologies in the (...) natural sciences and related disciplines. Whereas it is mostly assumed that domain ontologies should be created as extensions of foundational ontologies, a post-hoc harmonization of consolidated domain ontologies in use, such as SNOMED CT, is known to be challenging. Methods: We explored the feasibility of harmonizing SNOMED CT with BFO, with a focus on the SNOMED CT Clinical Finding hierarchy. With more than 100,000 classes, it accounts for about one third of SNOMED CT’s content. In particular, we represented typical SNOMED CT finding/disorder concepts using description logics under BFO. Three representational patterns were created and the logical entailments analyzed. Results: Under a first scrutiny, the clinical intuition that diseases, disorders, signs and symptoms form a homogeneous ontological upper-level class appeared incompatible with BFO’s upper-level distinction into continuants and occurrents. The Clinical finding class seemed to be an umbrella for all kinds of entities of clinical interest, such as material entities, processes, states, dispositions, and qualities. This suggests the conclusion that Clinical finding would not be a suitable upper-level class from an BFO perspective. On closer inspection of the taxonomic links within this hierarchy and the implicit meaning derived thereof, it became clear that Clinical finding classes do not characterize the entity (e.g. a fracture, allergy, tumor, pain, hemorrhage, seizure, fever) in a literal sense but rather the condition of a patient having that fracture, allergy, pain etc. This gives sense to the current characteristic of the Clinical Finding hierarchy, in which complex classes are modeled as subclasses of their constituents. Most of these taxonomic links are inferred, as the consequence of the ‘role group’ design pattern, which is ubiquitous in SNOMED CT and has often been subject of controversy regarding its semantics. Conclusion: Our analyses resulted in the proposal of (i) equating SNOMED CT’s ‘role group’ property with the reflexive and transitive BFO relation ‘has occurrent part’; and (ii) reinterpreting Clinical Findings as Clinical Occurrents, i.e. temporally extended entities in an organism, having one or more occurrents as temporal parts that occur in continuants. This re-interpretation was corroborated by a manual analysis of classes under Clinical Finding, as well as the identification of similar modeling patterns in other ontologies. As a result, SNOMED CT does not require any content redesign to establish compatibility with BFO, apart from this re-interpretation, and a suggested re-labeling. Regarding the feasibility of harmonizing terminologies with principled foundational ontologies post-hoc, our results provide support to the assumption that this does not necessarily require major redesign efforts, but rather a careful analysis of the implicit assumptions of terminology curators and users. (shrink)

This is a short editorial to introduce the double issue of Applied Ontology that celebrates the journal's tenth anniversary. At a time when information technology of all kinds depends on the use of explicit ontologies, our journal addresses the modeling issues that underlie the next generation of computational systems. As the editors of Applied Ontology, we are excited by how far we have come in the past decade and by the opportunities that await our research community.

In 2005, IOS Press published the first issue of applied Ontology. At the time, we argued that, at the core of the journal, there was “a desire to understand the nature of reality and how people construe their world”. We declared that ontology was both “fundamental to human thought” and “to translating our thoughts into computational artifacts” (Guarino & Musen,2005). With an editorial board of distinguished scholars representing the fields of computer science, informatics, information science, philosophy, linguistics, psychology, and social (...) science, we had the firm belief that applied Ontologywould fulfill an important academic niche, becoming an essential forum for discussion on topics such as ontological analysis, conceptual modeling, and the role of domain models in building and managing information systems. The facts now show that we were correct. (shrink)