Ontological theory for ontological engineering: Biomedical systems information integration

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date

Formal ontology for biomedical knowledge systems integration

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, we aim to move beyond the level of controlled vocabularies to yield an ontology with the ability to support reasoning applications

The Divine Action Project, 1988–2003

This article explores the state of the art in theories of special divine action by means of a study of the Divine Action Project (DAP) co-sponsored by the Vatican Observatory and the Center for Theology and the Natural Sciences in Berkeley. The basic aim is to introduce the DAP and to summarize its results, especially as these were compiled in the final “capstone” meeting of the DAP, and drawing on the published output of the project where possible. The subsidiary aim is to evaluate criticisms of theories of special divine action developed within the DAP.ye

Some Issues on Ontology Integration

The word integration has been used with different meanings in the ontology field. This article aims at clarifying the meaning of the word “integration” and presenting some of the relevant work done in integration. We identify three meanings of ontology “integration”: when building a new ontology reusing (by assembling, extending, specializing or adapting) other ontologies already available; when building an ontology by merging several ontologies into a single one that unifies all of them; when building an application using one or more ontologies. We discuss the different meanings of “integration”, identify the main characteristics of the three different processes and proposethree words to distinguish among those meanings:integration, merge and use

Drawing Boundaries

In “On Drawing Lines on a Map” (1995), I suggested that the different ways we have of drawing lines on maps open up a new perspective on ontology, resting on a distinction between two sorts of boundaries: fiat and bona fide. “Fiat” means, roughly: human-demarcation-induced. “Bona fide” means, again roughly: a boundary constituted by some real physical discontinuity. I presented a general typology of boundaries based on this opposition and showed how it generates a corresponding typology of the different sorts of objects which boundaries determine or demarcate. In this paper, I describe how the theory of fiat boundaries has evolved since 1995, how it has been applied in areas such as property law and political geography, and how it is being used in contemporary work in formal and applied ontology, especially within the framework of Basic Formal Ontology

Who Cares about Axiomatization? Representation, Invariance, and Formal Ontologies

The philosophy of science of Patrick Suppes is centered on two important notions that are part of the title of his recent book (Suppes 2002): Representation and Invariance. Representation is important because when we embrace a theory we implicitly choose a way to represent the phenomenon we are studying. Invariance is important because, since invariants are the only things that are constant in a theory, in a way they give the “objective” meaning of that theory. Every scientific theory gives a representation of a class of structures and studies the invariant properties holding in that class of structures. In Suppes’ view, the best way to define this class of structures is via axiomatization. This is because a class of structures is given by a definition, and this same definition establishes which are the properties that a single structure must possess in order to belong to the class. These properties correspond to the axioms of a logical theory. In Suppes’ view, the best way to characterize a scientific structure is by giving a representation theorem for its models and singling out the invariants in the structure. Thus, we can say that the philosophy of science of Patrick Suppes consists in the application of the axiomatic method to scientific disciplines. What I want to argue in this paper is that this application of the axiomatic method is also at the basis of a new approach that is being increasingly applied to the study of computer science and information systems, namely the approach of formal ontologies. The main task of an ontology is that of making explicit the conceptual structure underlying a certain domain. By “making explicit the conceptual structure” we mean singling out the most basic entities populating the domain and writing axioms expressing the main properties of these primitives and the relations holding among them. So, in both cases, the axiomatization is the main tool used to characterize the object of inquiry, being this object scientific theories (in Suppes’ approach), or information systems (for formal ontologies). In the following section I will present the view of Patrick Suppes on the philosophy of science and the axiomatic method, in section 3 I will survey the theoretical issues underlying the work that is being done in formal ontologies and in section 4 I will draw a comparison of these two approaches and explore similarities and differences between them