Ontology as Product-Service System: Lessons Learned from GO, BFO and DOLCE

This paper defends a view of the Gene Ontology (GO) and of Basic Formal Ontology (BFO) as examples of what the manufacturing industry calls product-service systems. This means that they are products (the ontologies) bundled with a range of ontology services such as updates, training, help desk, and permanent identifiers. The paper argues that GO and BFO are contrasted in this respect with DOLCE, which approximates more closely to a scientific theory or a scientific publication. The paper provides a detailed overview of ontology services and concludes with a discussion of some implications of the product-service system approach for the understanding of the nature of applied ontology. Ontology developer communities are compared in this respect with developers of scientific theories and of standards (such as W3C). For each of these we can ask: what kinds of products do they develop and what kinds of services do they provide for the users of these products

Reasoning and Change Management in Modular Ontologies

The benefits of modular representations are well known from many areas of computer science. In this paper, we concentrate on the benefits of modular ontologies with respect to local containment of terminological reasoning. We define an architecture for modular ontologies that supports local reasoning by compiling implied subsumption relations. We further address the problem of guaranteeing the integrity of a modular ontology in the presence of local changes. We propose a strategy for analyzing changes and guiding the process of updating compiled information

Repairing Ontologies via Axiom Weakening.

Ontology engineering is a hard and error-prone task, in which small changes may lead to errors, or even produce an inconsistent ontology. As ontologies grow in size, the need for automated methods for repairing inconsistencies while preserving as much of the original knowledge as possible increases. Most previous approaches to this task are based on removing a few axioms from the ontology to regain consistency. We propose a new method based on weakening these axioms to make them less restrictive, employing the use of refinement operators. We introduce the theoretical framework for weakening DL ontologies, propose algorithms to repair ontologies based on the framework, and provide an analysis of the computational complexity. Through an empirical analysis made over real-life ontologies, we show that our approach preserves significantly more of the original knowledge of the ontology than removing axioms

An Ontological Framework for Characterizing Hydrological Flow Processes

The spatio-temporal processes that describe hydrologic flow - the movement of water above and below the surface of the Earth -- are currently underrepresented in formal semantic representations of the water domain. This paper analyses basic flow processes in the hydrology domain and systematically studies the hydrogeological entities, such as different rock and water bodies, the ground surface or subsurface zones, that participate in them. It identifies the source and goal entities and the transported water (the theme) as common participants in hydrologic flow and constructs a taxonomy of different flow patterns based on differences in source and goal participants. The taxonomy and related concepts are axiomatized in first-order logic as refinements of DOLCE\u27s participation relation and reusing hydrogeological concepts from the Hydro Foundational Ontology (HyFO). The formalization further enhances HyFO and contributes to improved knowledge integration in the hydrology domain

Orchestrating a Network of Mereo(topo)logical Theories

Parthood is used widely in ontologies across subject domains. Some modelling guidance can be gleaned from Ontology, yet it offers multiple mereological theories, and even more when combined with topology, i.e., mereotopology. To complicate the landscape, decidable languages put restrictions on the language features, so that only fragments of the mereo(topo)logical theories can be represented, yet during modelling, those full features may be needed to check correctness. We address these issues by specifying a structured network of theories formulated in multiple logics that are glued together by the various linking constructs of the Distributed Ontology Language, \DOL. For the KGEMT mereotopological theory and five sub-theories, together with the DL-based OWL species and first- and second-order logic, this network in \DOL orchestrates 28 ontologies. Further, we propose automated steps toward resolution of language feature conflicts when combining modules, availing of the new `OWL classifier' tool that pinpoints profile violations

On the role of automated proof-assistants in the formalization of upper ontologies

The use of formal languages in the specification of upper ontologies helps establishing precise and unambiguous definitions for its concepts and relations. In this context, the use of formal languages with support of proof-assistant software systems has potential of aiding the specification author in various aspects. We describe a study case in which the Isabelle/HOL language and the Isabelle proof-assistant environment are used to formalize a simplified version of the UFO-A ontology of endurants, to verify and correct the original axiomatization, and to optimize the specification theory's axioms and signature.</p