Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such (...) a way that – once formulated in a suitable formal language – the ontologies can be used for sophisticated automated reasoning applications. Reference ontologies can be applied across different contexts in which different, and often mutually incompatible, domain-specific vocabularies have traditionally been used. In this contribution we describe the Mental Functioning Ontology (MF) and Mental Disease Ontology (MD), two realism-based ontologies currently under development for the description of humanmental functioning and disease. We describe the structure and upper levels of the ontologies and preliminary application scenarios, and identify some open questions. (shrink)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

The development of manufacturing technologies for new materials involves the generation of a large and continually evolving volume of information. The analysis, integration and management of such large volumes of data, typically stored in multiple independently developed databases, creates significant challenges for practitioners. There is a critical need especially for open-sharing of data pertaining to engineering design which together with effective decision support tools can enable innovation. We believe that ontology applied to engineering (OE) represents a viable strategy for the (...) alignment, reconciliation and integration of diverse and disparate data. The scope of OE includes: consistent capture of knowledge pertaining to the types of entities involved; facilitation of cooperation among diverse group of experts; more effective ongoing curation, and update of manufacturing data; collaborative design and knowledge reuse. As an illustrative case study we propose an ontology focused on the representation of composite materials focusing in particular on the class of Functionally Graded Materials (FGM) in particular. The scope of the ontology is to provide information about the components of such materials, the manufacturing processes involved in creation, and diversity of application ranging from additive manufacturing to restorative dentistry. The ontology is developed using Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). (shrink)

Festschrift in Honor of Barry Smith on the occasion of his 65th Birthday. Published as issue 4:4 of the journal Cosmos + Taxis: Studies in Emergent Order and Organization. Includes contributions by Wolfgang Grassl, Nicola Guarino, John T. Kearns, Rudolf Lüthe, Luc Schneider, Peter Simons, Wojciech Żełaniec, and Jan Woleński.

In this paper, we describe the conceptual elusiveness of the notion of function as used in engineering practice. We argue that it should be accepted as an ambiguous notion, and then review philosophical argumentations in which engineering functions occur in order to identify the consequences of this ambiguity. Function is a key notion in engineering, yet is used by engineers systematically in a variety of meanings. First, we demonstrate that this ambiguous use is rational for engineers by considering the role (...) of functions in design methods and by analysing the ambiguity in terms of Kuhn’s notion of methodological incommensurability. Second, we discuss ontological and mereological analyses of engineering functions and describe a proof that subfunctions cannot formally be taken as parts of the functions they decompose. Engineering functions figure sometimes in philosophical work and are then typically taken as having an unambiguous, well-defined meaning. Finally, we therefore revisit work in philosophy of technology on the dual nature of technical artefacts, in philosophy of science on functional and mechanistic explanations, and in philosophy of biology on biological functions, and explore the consequences of the fact that engineering function is an ambiguous notion. It is argued that one of these consequences may be that also the notion of biological function has an ambiguous meaning. (shrink)

In this paper, we describe the conceptual elusiveness of the notion of function as used in engineering practice. We argue that it should be accepted as an ambiguous notion, and then review philosophical argumentations in which engineering functions occur in order to identify the consequences of this ambiguity. Function is a key notion in engineering, yet is used by engineers systematically in a variety of meanings. First, we demonstrate that this ambiguous use is rational for engineers by considering the role (...) of functions in design methods and by analysing the ambiguity in terms of Kuhn’s notion of methodological incommensurability. Second, we discuss ontological and mereological analyses of engineering functions and describe a proof that subfunctions cannot formally be taken as parts of the functions they decompose. Engineering functions figure sometimes in philosophical work and are then typically taken as having an unambiguous, well-defined meaning. Finally, we therefore revisit work in philosophy of technology on the dual nature of technical artefacts, in philosophy of science on functional and mechanistic explanations, and in philosophy of biology on biological functions, and explore the consequences of the fact that engineering function is an ambiguous notion. It is argued that one of these consequences may be that also the notion of biological function has an ambiguous meaning. (shrink)

Basic Formal Ontology (BFO) is a top-level ontology consisting of thirty-six classes, designed to support information integration, retrieval, and analysis across all domains of scientific investigation, presently employed in over 350 ontology projects around the world. BFO is a genuine top-level ontology, containing no terms particular to material domains, such as physics, medicine, or psychology. In this paper, we demonstrate how a series of cases illustrating common types of change may be represented by universals, defined classes, and relations employing the (...) BFO framework. We provide discussion of these cases to provide a template for other ontologists using BFO, as well as to facilitate comparison with the strategies proposed by ontologists using different top-level ontologies. (shrink)

We describe an ontology of philosophy that is designed to aid navigation through philosophical literature, including literature in the form of encyclopedia articles and textbooks and in both printed and digital forms. The ontology is designed also to serve integration and structuring of data pertaining to the philosophical literature, and in the long term also to support reasoning about the provenance and contents of such literature, by providing a representation of the philosophical domain that is oriented around what philosophical literature (...) is about. (shrink)

This special issue of Applied Ontology is devoted to the foundation, the comparison and the application of functional theories in all areas, with particular attention to the biological and engineering domains. It includes theoretical and technical contributions related to the description, characterization, and application of functions.

Commonsense ontology often conflicts with the ontology of our best scientific and philosophical theories. However, commonsense ontology, and commonsense belief systems in general, seems to be remarkably efficient and cognitively fundamental. In cases of contrast, it is better to find a way to reconcile commonsense and ”theoretical” ontologies. Given that commonsense ontologies are typically expressed within natural language, a classical procedure of reconciliation is semantical. The strategy is that of individuating the ”ontologically problematic” expressions of natural language and paraphrasing the (...) sentences in which they appear in a (formal) language whose commitments are compatible with those of our best theories. We believe that this strategy of reconciliation, though quite standard, especially in the philosophical literature, is problematic: for a start, it forces us to conclude that the ”real content” of our commonsense expressions and beliefs is different from what it appears. Commonsense ontology becomes just an illusion. We will thus propose an alternative approach: according to our view, a commonsense ontology is reconciled with a theoretical ontology in case it is shown that the explanation of why we believe in the existence of a problematic entity is compatible with our best theories. We will call this kind of reconciliation ”epistemic”. The advantage of an epistemic reconciliation is that commonsense ontology is treated in its own right and could be taken prima facie. Another advantage of the view is that epistemic reconciliation can be analysed through the notion of explaining away: a commonsense ontology is epistemically reconciled with a theoretical ontology if and only if the problematic entities of the commonsense ontology are explained away by ”respectable” entities of the theoretical ontology. In the final part of the paper, we sketch a formal analysis of explaining away. (shrink)

This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to develop a simple temporal theory.

Ontologies aim to represent what is general, by means of universal statements. In contrast, dispositional predications capture knowledge about what is likely to happen if a certain set of circumstances obtain, which is crucial in investigative research such as in drug discovery and systems biology, where entities which are constitutionally dissimilar can nevertheless have similar behavior in a biological context. While such dispositional properties are increasingly included in biomedical ontologies, the circumstances under which the dispositions are realized are seldom explicitly (...) modeled, and doing so is problematic due to the necessary restriction to binary relations in OWL ontologies. In this paper we address this shortcoming, focusing on the bioactivity of small molecules at varying levels of concentration within a living organism as our problem domain, although our approach is generalizable to other problems. We discuss the ontological nature and representation of dispositions and their realization; consider the nature of concentrations and their representation; and finally we detail an approach to linking dispositions to the conditions for their realization which regards conditions as triggers for the process in which the disposition is realized. (shrink)

Dispositions and tendencies feature significantly in the biomedical domain and therefore in representations of knowledge of that domain. They are not only important for specific applications like an infectious disease ontology, but also as part of a general strategy for modelling knowledge about molecular interactions. But the task of representing dispositions in some formal ontological systems is fraught with several problems, which are partly due to the fact that Description Logics can only deal well with binary relations. The paper will (...) discuss some of the results of the philosophical debate about dispositions, in order to see whether the formal relations needed to represent dispositions can be broken down to binary relations. Finally, we will discuss problems arising from the possibility of the absence of realizations, of multi-track or multi-trigger dispositions and offer suggestions on how to deal with them. (shrink)

This dissertation focuses on teleology and functions in biology. More precisely, it focuses on the scientific legitimacy of teleofunctional attributions and explanations in biology. It belongs to a multi-faceted debate that can be traced back to at least the 1970s. One aspect of the debate concerns the naturalization of functions. Most authors try to reduce, translate or explain functions and teleology in terms of efficient causes so that they find their place in the framework of the natural sciences. Our approach (...) here is radically different, as we question the premise that teleological explanations are disguised causal explanations. On the contrary, we defend that they are acceptable in natural sciences and in biology in particular. We challenge the idea that teleological explanations are immature causal explanations, as well as the idea that teleology and functions are some sort of intentional explanations. We therefore reject the accusations of anthropomorphism, vitalism and finalism. On the contrary, we defend that teleology, causality and intentionality correspond to different, autonomous and complementary modes of representation of the outside world. -/- ———[FRANÇAIS]——— -/- Ce travail de thèse porte sur la téléologie et les fonctions en biologie. Plus précisément, il porte sur la légitimité scientifique des attributions et des explications téléofonctionnelles en biologie. Il s’inscrit dans le cadre d’un débat à plusieurs facettes que l’on peut faire remonter au moins jusqu’aux années 1970 et qui est encore très actif aujourd’hui. L’un des aspects du débat porte sur la naturalisation des fonctions, c’est-à-dire sur la manière de les réduire, de les traduire ou de les expliciter en termes de causes efficientes de sorte qu’elles trouvent leur place dans le cadre des sciences de la nature. Notre approche ici est radicalement différente, car nous remettons en question la prémisse selon laquelle les explications téléologiques seraient des explications causales déguisées. Nous défendons au contraire qu’elles sont acceptables en tant que telles aussi bien de façon générale que dans le domaine scientifique et en particulier en biologie. De façon générale, nous remettons en question l’idée selon laquelle la pensée téléologique serait une pensée causale immature, ainsi que sa dépendance présumée vis-à-vis de la psychologie, c’est-à-dire de l’intentionnalité. Nous rejetons donc les accusations d’anthropomorphisme, de vitalisme et de finalisme formulées contre elle. Nous défendons au contraire que la téléologie, la causalité et l’intentionnalité correspondent à des modes différents, autonomes et complémentaires de représentation du monde extérieur. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)