Functions in Basic Formal Ontology

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections

Function, Role, and Disposition in Basic Formal Ontology

Numerous research groups are now utilizing Basic Formal Ontology (BFO) as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three BFO categories of function, role, and disposition, and considers two proposed sub-categories of artifactual function and bio-logical function. The motivation is to help advance the coherent treatment of functions, roles, and dispositions, to help provide the potential for more detailed classification, and to shed light on BFO’s general structure and use

Kind Instantiation and Kind Change - A Problem for Four-Category Ontology

In Lowe’s Four-Category Ontology, instantiation is a basic formal ontological relation between particulars (objects, modes) and their kinds (kinds, attributes). Therefore, instantiation must be considered as a metaphysically necessary relation, which also rules out the metaphysical possibility of kind change. Nevertheless, according to Lowe, objects obtain their identity conditions in a more general level than specific natural kinds, which allows for kind change. There also seems to be actual examples of kind change. The advocate of Four-Category Ontology is obliged to resolve the tension between these mutually incompatible claims. In this article, we argue that the only viable option for the advocate of Four-Category Ontology is to bite the bullet and stick to the necessity of each of the most specific natural kind to the object instantiating it. As a major drawback, the four-category ontologist does not have any credible means to allow for kind change or determination of the identity conditions in a more general level

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

Towards OWL-based Knowledge Representation in Petrology

This paper presents our work on development of OWL-driven systems for formal representation and reasoning about terminological knowledge and facts in petrology. The long-term aim of our project is to provide solid foundations for a large-scale integration of various kinds of knowledge, including basic terms, rock classification algorithms, findings and reports. We describe three steps we have taken towards that goal here. First, we develop a semi-automated procedure for transforming a database of igneous rock samples to texts in a controlled natural language (CNL), and then a collection of OWL ontologies. Second, we create an OWL ontology of important petrology terms currently described in natural language thesauri. We describe a prototype of a tool for collecting definitions from domain experts. Third, we present an approach to formalization of current industrial standards for classification of rock samples, which requires linear equations in OWL 2. In conclusion, we discuss a range of opportunities arising from the use of semantic technologies in petrology and outline the future work in this area.Comment: 10 pages. The paper has been accepted by OWLED2011 as a long presentatio

Using philosophy to improve the coherence and interoperability of applications ontologies: A field report on the collaboration of IFOMIS and L&C

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s LinKBase® is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates

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

From change to spacetime: an Eleatic journey

I present a formal ontological theory where the basic building blocks of the world can be either things or events. In any case, the result is a Parmenidean worldview where change is not a global property. What we understand by change manifests as asymmetries in the pattern of the world-lines that constitute 4-dimensional existents. I maintain that such a view is in accord with current scientific knowledge.Comment: 13 pages, accepted for publication in Foundations of Scienc

Instantiation and Characterization: Problems in Lowe's Four-Category Ontology

According to Lowe’s Four-Category Ontology, the general nature of the entities belonging to the four fundamental categories is determined by the basic formal ontological relations (instantiation and characterization) that they bear to other entities. I argue that, in closer analysis, instead of one formal relation of characterization, this category system introduces two, one connecting particulars and another universals. With regard to the characterization relation connecting particulars, it remains an open issue whether it would need further analysis. By contrast, the status of instantiation as an internal relation is comparatively clear. Nevertheless, because of holding by virtue of the essences of particulars, the holding of instantiation between universals and particulars rules out the possibility of kind change and entails that particulars are essentially rigidly dependent on universals. Finally, Lowe’s analysis of necessary exemplification gives us some reasons to suspect that some property universals need not have any instances in order to exist

Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain