Few ontologies in the ecological domain exist, but their development can take advantage of gained experience in other domains and from existing modeling practices in ecology. Taxonomies do not suffice because more expressive modeling techniques are already available in ecology, and the perspective of flow with its centrality of events and processes cannot be represented adequately in a taxonomy. Therefore, formal ontologies are required for sufficient expressivity and to be of benefit to ecologists, which also enables future reuse. We (...) have created a formal mapping between the software-supported ecological modeling method and software tool STELLA and ontology elements, which simplifies bottom-up ontology development considerably and has excellent potential for semi-automated ontology development. However, the conducted experiments also revealed that ontology development for ecology is close to being part of ecological research that through the formalized representation of the knowledge more clearly points to lacunas and suggestions for further research in ecology. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant (...) to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (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)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of (...) the PO has been expanded to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Development of ontology development tools and ontology-enhanced software applications requires thorough understanding of ontology languages in order to implement them according to their specification. We present a formal specification of the ontologies part of the Web Services Modeling Language WSML documentation as a conceptual model in ORM2. Such an approach abstracts the semantics about ontological constructs, axioms, and properties from their implementation in arbitrary formats, thereby making the model easily understandable and reusable. This formal (...) model in ORM2, which is understandable by both logician and software developer, can be used as any other conceptual model to develop applications, thereby ensuring smooth transition from theory to implementations that are faithful to the theory. (shrink)

It is accepted that certain mereological concepts and phenomenological conceptualisations presented in Carl Stumpf’s Über den psychologischen Ursprung der Raumvorstellung and Tonpsychologie played an important role in the development of the Husserlian formal ontology. In the third Logical Investigation, which displays the formal relations between part and whole and among parts that make out a whole, one of the main concepts of contemporary formal ontology and metaphysics is settled: ontological dependence or foundation (Fundierung). My main objective is (...) to display Stumpf’s concepts of partial content, independent content, spatial wholes, sound wholes, and the different kinds of connection among parts, in particular, fusion (Verschmelzung). Second, I will show how Husserl improved this background, in particular with regards to the exact nature of the theory of manifolds (Mannigfaltigkeitslehre), in discussion with Georg Cantor, the father of set theory. Third, I will focus on Ingarden’s use of formal ontology and on the different modes of being that can be justified by appealing to the concept of ontological dependence in its Ingardenian variations. If my interpretation is adequate, it should be inferred that formal ontology is the operative theory of phenomenological philosophy, and this must be acknowledged in its full significance with respect to the supposed independence of the phenomenological method since 1913. A further consequence, not developed in this essay, is that formal ontology can be mathematised. (shrink)

The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical principles that is (...) designed to comprehend the basic formal relationships that structure both reality and the ways humans perceive and communicate about reality. (shrink)

This project was undertaken to develop a telelearning knowledge base aimed at making specialized telelearning knowledge accessible to non-specialized practitioners in the field. The challenge stems from a rationale related to a user-centered approach for the software design process, which is focused on learning in the context of professional practice, the bridge to be built between expert and practitioner knowledge, as well as the knowledge valorization of the latter. In order to take into account users and their situated actions, a (...) usage study was integrated in the analysis phase. This study allows the creation of procedural and contextual telelearning models, and also lists of needs. These results serve as a basis for formulating guidelines for the development of ontologies, for the design of the telelearning knowledge base user interface and telelearning knowledge base environmental description. This paper presents the guidelines and orientations derived from these models. (shrink)

Babylon Knowledge Explorer (BKE) is an integrated suite of tools and information sources developed in GlaxoSmithKline's Analysis, Applications, and Research Technologies Department to support the prototyping and implementation of ontology-driven information systems and ontology-enhanced knowledge applications. In this paper we describe the current state of BKE development and focus on some of its distinctive or novel approaches, highlighting -/- * How BKE makes use of multiple large pre-existing ontologies in support of text and data mining. * (...) The methodology employed for importing an ontology and making it immediately accessible to BKE's tools, interfaces, and API. * A formal description of BKE's ontology-based fact model and how this is employed in implementing information retrieval and data mining capabilities. * A sample application built on BKE that illustrates an ontologyenhanced machine learning tool. (shrink)

'Ontology and Metaontology: A Contemporary Guide' is a clear and accessible survey of ontology, focussing on the most recent trends in the discipline. -/- Divided into parts, the first half characterizes metaontology: the discourse on the methodology of ontological inquiry, covering the main concepts, tools, and methods of the discipline, exploring the notions of being and existence, ontological commitment, paraphrase strategies, fictionalist strategies, and other metaontological questions. The second half considers a series of case studies, introducing and (...) familiarizing the reader with concrete examples of the latest research in the field. The basic sub-fields of ontology are covered here via an accessible and captivating exposition: events, properties, universals, abstract objects, possible worlds, material beings, mereology, fictional objects. -/- The guide's modular structure allows for a flexible approach to the subject, making it suitable for both undergraduates and postgraduates looking to better understand and apply the exciting developments and debates taking place in ontology today. (shrink)

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by (...) taking account of certain organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

This article addresses ontological negotiations in the Global South through three case studies of community-based research in Brazil and Ghana. We argue that ontological perspectives of Indigenous people and local communities require an ontological pluralism that recognizes both the plurality of representational tools and of ways of being in the world. Locating these two readings of ontological pluralism in the politics of the Global South, the article highlights a wider dynamic from ontological paternalism to ontological diversity to ontological decolonization. (...) We conclude by arguing that this dynamic provides important lessons for the state for social ontology in academic philosophy and for the design of politically reflexive development interventions. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use (...) ontologies, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

An ontological approach as a tool for managing the processes of constructing mathematical models based on interval data and further use of these models for solving applied problems is proposed in this article. Mathematical models built using interval data analysis are quite effective in many applications, as they have “guaranteed” predictive properties, which are determined by the accuracy of experimental data. However, the application of mathematical modeling methods is complicated by the lack of software tools for the implementation of (...) procedures for constructing this type of mathematical models, creating an ontological model that operates by the categories of the subject area of mathematical modeling, regardless of the modeling object proposed in this article. This approach has made it possible to generate tools for mathematical modeling of various objects based on the interval data analysis for any software development environment selected by the user. The technology of creating the software on the basis of the developed ontological superstructure for mathematical modeling using the interval data for different objects, as well as various forms of user interface implementation, is presented in this article. A number of schemes, which illustrate the technology of using the ontological approach of mathematical modeling based on interval data, are presented, and the features of its interpretation when solving environmental monitoring problems are described. (shrink)

The relevance of analytic metaphysics has come under criticism: Ladyman & Ross, for instance, have suggested do discontinue the field. French & McKenzie have argued in defense of analytic metaphysics that it develops tools that could turn out to be useful for philosophy of physics. In this article, we show first that this heuristic defense of metaphysics can be extended to the scientific field of applied ontology, which uses constructs from analytic metaphysics. Second, we elaborate on a parallel (...) by French & McKenzie between mathematics and metaphysics to show that the whole field of analytic metaphysics, being useful not only for philosophy but also for science, should continue to exist as a largely autonomous field. (shrink)

The paper provides an OWL ontology for legal cases with an instantiation of the legal case Popov v. Hayashi. The ontology makes explicit the conceptual knowledge of the legal case domain, supports reasoning about the domain, and can be used to annotate the text of cases, which in turn can be used to populate the ontology. A populated ontology is a case base which can be used for information retrieval, information extraction, and case based reasoning. The (...) ontology contains not only elements for indexing the case (e.g. the parties, jurisdiction, and date), but as well elements used to reason to a decision such as argument schemes and the components input to the schemes. We use the Protégé ontology editor and knowledge acquisition system, current guidelines for ontology development, and tools for visual and linguistic presentation of the ontology. (shrink)

Current controversies about knowledge integration reflect conflicting ideas of what it means to “take Indigenous knowledge seriously”. While there is increased interest in integrating Indigenous and Western scientific knowledge in various disciplines such as anthropology and ethnobiology, integration projects are often accused of recognizing Indigenous knowledge only insofar as it is useful for Western scientists. The aim of this article is to use tools from philosophy of science to develop a model of both successful integration and integration failures. On (...) the one hand, I argue that cross-cultural recognition of property clusters leads to an ontological overlap that makes knowledge integration often epistemically productive and socially useful. On the other hand, I argue that knowledge integration is limited by ontological divergence. Adequate models of Indigenous knowledge will therefore have to take integration failures seriously and I argue that integration efforts need to be complemented by a political notion of ontological self-determination. (shrink)

FOIS is the flagship conference of the International Association for Ontology and its Applications, a non-profit organization which promotes interdisciplinary research and international collaboration at the intersection of philosophical ontology, linguistics, logic, cognitive science, and computer science. This book presents the papers delivered at FOIS 2023, the 13th edition of the Formal Ontology in Information Systems conference. The event was held as a sequentially-hybrid event, face-to-face in Sherbrooke, Canada, from 17 to 20 July 2023, and online from (...) 18 to 20 September 2023. In total, 62 articles from 19 different countries were submitted, out of which 25 were accepted for inclusion in the conference and for publication; corresponding to an acceptance rate of 40 percent. The contributions are separated into the book’s three sections: (1) Foundational ontological issues; (2) Methodological issues around the development, alignment, verification and use of ontologies; and (3) Domain ontologies and ontology-based applications. In these sections, ontological aspects from a wide variety of fields are covered, primarily from various engineering domains including cybersecurity, manufacturing, petroleum engineering, and robotics, but also extending to the humanities, social sciences, medicine, and dentistry. A noticeable trend among the contributions in this edition of the conference is the recognition that improving the tools to analyze, align, and improve ontologies is of paramount importance in continuing to advance the field of formal ontology. The book will be of interest to all formal and applied ontology researchers, and to those who use formal ontologies and information systems as part of their work. (shrink)

Words are indispensable linguistic tools for beings like us. However, there is not much philosophical work done about what words really are. In this paper, I develop a new ontology for words. I argue that words are abstract artifacts that are created to fulfill various kinds of purposes, and words are abstract in the sense that they are not located in space but they have a beginning and may have an end in time given that certain conditions are (...) met. What follows from this two-fold argument is that words, from an ontological point of view, are more like musical works, fictional characters or computer programs, than numbers or sets. (shrink)

Background: In order to improve ontology quality, tool- and language-related tutorials are not sufficient. Care must be taken to provide optimized curricula for teaching the representational language in the context of a semantically rich upper level ontology. The constraints provided by rigid top and upper level models assure that the ontologies built are not only logically consistent but also adequately represent the domain of discourse and align to explicitly outlined ontological principles. Finally such a curriculum must take into (...) account the pre-existing skills and knowledge of the target audience. -/- Objective: To develop a well-structured curriculum aligned to the particular requirements of life science professionals, in order to enable them to create logically sound, domain adequate and predicable ontologies using the Web Ontology Language (OWL) in Protégè. -/- Methods: Content selection for the curriculum was based on the literature, pre-existing tutorials, and a guideline for good ontology development (i.e ontology design enhancing domain adequacy, sustainability and interoperability) that drew on the authors previous experiences with large ontology development projects. Learning objectives were formulated according to a needs assessment of the targeted learners, who were students trained in life sciences with basic knowledge and practical skills in computer science. As instructional format we choose an approach with a high amount of practical exercises. The curriculum was first implemented with 24 Students and 7 lecturers/ tutors over 5 full days. The curriculum was evaluated by gathering the participants feedback via a questionnaire. -/- Results: Curricular development produced 16 modules of approximately 2 hours each, which covered basic principles of Applied Ontology, description logic syntax and semantics, as well as best design practices outlined in ontology design patterns and variants of the BioTop upper ontology. An opinion survey based on questionnaires indicated that the participants took advantage from the teaching strategies applied, as they indicated good knowledge gain and acknowledged the relevance of the modules. The difficulty was rated slightly lower. -/- Conclusion: The development of teaching material for principled ontology design and best practices is of crucial importance in order to enhance the quality of biomedical ontologies. Here, we present a curriculum for a week long workshop, leveraging on current educational principles, focusing on interactive hands-on exercises, group interactions, and problem-oriented learning. Whereas evaluation clearly showed the success of this approach, in particular regarding student’s satisfaction, the objective measurement of traceable effects on the quality of the generated ontology, although of much higher interest, has just started. (shrink)

This book puts forward a new role for mathematics in the natural sciences. In the traditional understanding, a strong viewpoint is advocated, on the one hand, according to which mathematics is used for truthfully expressing laws of nature and thus for rendering the rational structure of the world. In a weaker understanding, many deny that these fundamental laws are of an essentially mathematical character, and suggest that mathematics is merely a convenient tool for systematizing observational knowledge. The position developed in (...) this volume combines features of both the strong and the weak viewpoint. In accordance with the former, mathematics is assigned an active and even shaping role in the sciences, but at the same time, employing mathematics as a tool is taken to be independent from the possible mathematical structure of the objects under consideration. Hence the tool perspective is contextual rather than ontological. Furthermore, tool-use has to respect conditions like suitability, efficacy, optimality, and others. There is a spectrum of means that will normally differ in how well they serve particular purposes. The tool perspective underlines the inevitably provisional validity of mathematics: any tool can be adjusted, improved, or lose its adequacy upon changing practical conditions. (shrink)

In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous sources. In this position paper, we present a set (...) of principles learned from the successful Open Biomedical Ontologies (OBO) Foundry initiative to guide the design and development of the Industrial Ontologies Foundry (IOF), which is a counterpart to the OBO Foundry initiative for the manufacturing industry. We also illustrate the potential utility of these principles by sketching the conceptual design of a framework for sustainable IOF development. (shrink)

In the last decades ontology has been successfully developed in many directions and has fostered various approaches for depicting the contemporary ontological landscapes. An important task is to outline recent thought on the conceptual interfaces between science and philosophy. The present volume opens up a view onto the plurality of different ontological schemes. The papers collected here discuss the interfaces between ontology and empirical research that are created by the notions of a whole, a thought, a number, a (...) quality, an ability, a kind, notions of causation, dynamicity, and social objects, the application of relevant logical tools for the reconsideration of ontological paradigms, as well as the investigation of the consequences in cognitive sciences on the development of ontology. (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)

Reuse of elements from existing ontologies in the construction of new ontologies is a foundational principle in ontological design. It offers the benefits, among others, of consistency and interoperability between such knowledge structures as well as sharing resources. Reuse is widely found within important collections of established ontologies, such as BioPortal and the OBO Foundry. However, reuse comes with its own potential problems involving ontological commitment, granularity, and ambiguity. Guidelines are proposed to aid ontology developers and curators in their (...) prospective reuse of content. These guidelines have been gleaned over years of practice in the ontology field. The guidelines are couched in experiential reports on designing and curating particular ontologies (e.g., EXACT and EXACT2) and using generally accepted approaches (e.g., MIREOT) in doing so. Various software tools to assist in ontology reuse are surveyed and discussed. (shrink)

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...) life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from The Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. (shrink)

Ontologies have been successfully used to assign semantics in the Semantic Web context, to support integration of data from different systems or different sources, and to enable reasoning. However, building ontologies is not a trivial task. Ontology reuse can help in this matter. The search and selection of ontologies to be reused should consider the alignment between their scope and the scope of the ontology being developed. In this paper, we discuss how goal modeling can be helpful in (...) this context and we present GO-FOR, a framework in which goals are the central elements to promote ontology reuse. GO-FOR comprises a conceptual architecture, a goal-oriented ontology development process and a supporting tool. In GO-FOR we introduce Goal-Oriented Ontology Patterns as a new type of pattern to be applied to develop ontologies in a goal-oriented approach. Results of the use of GO-FOR to build an ontology used to integrate patient examination data are also shown in this paper. (shrink)

We propose a novel, ontological approach to studying mathematical propositions and proofs. By “ontological approach” we refer to the study of the categories of beings or concepts that, in their practice, mathematicians isolate as fruitful for the advancement of their scientific activity (like discovering and proving theorems, formulating conjectures, and providing explanations). We do so by developing what we call a “formal ontology” of proofs using semantic modeling tools (like RDF and OWL) developed by the computer science community. (...) In this article, (i) we describe this new approach and, (ii) to provide an example, we apply it to the problem of the identity of proofs. We also describe open issues and further applications of this approach (for example, the study of purity of methods). We lay some foundations to investigate rigorously and at large scale intellectual moves and attitudes that underpin the advancement of mathematics through cognitive means (carving out investigationally valuable concepts and techniques) and social means (like communication, collaboration, revision, and criticism of specific categories, inferential patterns, and levels of analysis). Our approach complements other types of analysis of proofs such as reconstruction in a deductive system and examination through a proof-assistant. (shrink)

The massive increase of data generated by heterogeneous sources requires the development of computer tools enabling their semantic interoperability. Applied ontologies aim at fulfilling such needs. We will show in this article the central role that philosophical ontology can play for applied ontology, with a focus on biomedical ontologies; and reciprocally, how applied ontology can enlighten some classical issues in philosophical ontology, by considering the following question: Is disease a natural kind?

Researchers in areas such as artificial intelligence, formal and computational linguistics, biomedical informatics, conceptual modeling, knowledge engineering and information retrieval have come to realise that a solid foundation for their research calls for serious work in ontology, understood as a general theory of the types of entities and relations that make up their respective domains of inquiry. In all these areas, attention is now being focused on the content of information rather than on just the formats and languages used (...) to represent information. The clearest example of this development is provided by the many initiatives growing up around the project of the Semantic Web. And, as the need for integrating research in these different fields arises, so does the realisation that strong principles for building well-founded ontologies might provide significant advantages over ad hoc, case-based solutions. The tools of formal ontology address precisely these needs, but a real effort is required in order to apply such philosophical tools to the domain of information systems. Reciprocally, research in the information sciences raises specific ontological questions which call for further philosophical investigations. The purpose of FOIS is to provide a forum for genuine interdisciplinary exchange in the spirit of a unified effort towards solving the problems of ontology, with an eye to both theoretical issues and concrete applications. This book contains a wide range of areas, all of which are important to the development of formal ontologies. (shrink)

We propose a logic of imagination, based on simulated belief revision, that intends to uncover the logical patterns governing the development of imagination in pretense. Our system complements the currently prominent logics of imagination in that ours in particular formalises (1) the algorithm that specifies what goes on in between receiving a certain input for an imaginative episode and what is imagined in the resulting imagination, as well as (2) the goal-orientedness of imagination, by allowing the context to determine, (...) what we call, the overall topic of the imaginative episode. To achieve this, we employ well-developed tools and techniques from dynamic epistemic logic and belief revision theory, enriched with a topicality component which has been exploited in the recent literature. As a result, our logic models a great number of cognitive theories of pretense and imagination [cf. Currie and Ravenscroft (Recreative minds, Oxford University Press, Oxford, 2002); Nichols and Stich (Mindreading: an integrated account of pretence, self-awareness, and understanding other minds, Oxford University Press, Oxford, 2003); Byrne (The rational imagination, The MIT Press, London, 2005); Williamson (The philosophy of philosophy, Blackwell Publishing, Oxford, 2007); Langland-Hassan (Philos Stud 159:155–179, 2012, in: Kind and Kung (eds) Knowledge through imaginaion, Oxford University Press, Oxford, 2016]. (shrink)

This dissertation aims to develop Martin Heidegger's famous analysis of equipment into an ontology of objects. Although numerous commentators have discussed the role of the tool in Heidegger's work, all have interpreted it too narrowly as a question of human practical activity, in connection with a limited range of familiar utensils such as chisels, jackhammers, and saws. Chapter One argues that Heidegger's analysis actually holds good of all possible entities, whether they be "useful" or not. The term 'tool-being' holds (...) good for grains of sand as much as saws, for angels as much as windmills. In truth, all entities are caught up in Heidegger's famous reversal between readiness-to-hand and presence-at-hand, a crippling global dualism from which nothing in the cosmos is immune. My related claim is that all of Heidegger's various attempts to discuss any sort of concrete subject matter quickly implode into a sheer repetition of the duel between tool and broken tool. His supposed discussions of "space," "truth," and "time" are nothing more than distracting code words for a repetitive duality that Heidegger tries to escape by means of his abortive project for a 'metontology.' His monotonous appeal to the drama of tool and broken tool is complicated by only one further dualism, one found in his work as early as the 1919 Freiburg course Zur Bestimmung der Philosophie. The interplay of these two principles is what leads Heidegger to his infamous notion of the fourfold , a concept too hastily ridiculed even by many of his admirers. Chapter Two offers a critical engagement with the secondary literature, focusing in particular on the concepts of Dasein, being, time, truth, Ereignis, language, and technology. Chapter Three attempts to develop the implications of this reading of Heidegger for a theory of the structure of objects in general. I argue in conclusion that Heidegger's holistic theory of the world, expressed in even clearer form in the works of Whitehead, leads to just as many perplexities as the substance-based theories of Aristotle and Leibniz. The concept of 'tool-being' requires some sort of compromise position between context and substance. (shrink)

This work aims to make tense logic a more robust tool for ontologists, philosophers, knowledge engineers and programmers by outlining a fusion of tense logic and ontology of time. In order to make tense logic better understandable, the central formal primitives of standard tense logic are derived as theorems from an informal and intuitive ontology of time. In order to make formulation of temporal propositions easier, temporal operators that were introduced by Georg Henrik von Wright are developed, and (...) mapped to the ontology of time. (shrink)

Applied ontology is the attempt to put to use the rigorous tools of philosophical ontology in the development of category systems which can be of use in the formalization and systematization of knowledge of a given domain. In what follows we shall sketch some elements of the ontology of legal and socio-political institutions, paying attention especially to the normativity involved in such institutions. We shall see that there is more than one type of normativity, but (...) that this fact that has often been ignored in standard attempts by philosophers to build ontologies of legal and other socio-political entities. In order to provide a sound system of categories for legal and socio-political institutions and entities, however, the manifold of normativity needs to be addressed. The classical examples of normative statements have been moral propositions; they do not merely describe states of affairs; they tell us how states of affairs ought to be. The distinction between how things are and how they ought to be is the basis of the distinction between fact and value. Analytic philosophers for a long time shunned discussions of normativity and ethics. They considered ethical statements as pseudo-propositions, or as expressions of pro- or con-attitudes of no theoretical significance.1 Nowadays, in contrast, prominent analytic philosophers discuss normative problems and there are important books written by such philosophers on topics such as law and justice. Here we pay attention to three seminal thinkers in this development: H. L. A. Hart, John Rawls, and John R. Searle in concerning ourselves especially with the way in which they deal with the issue of normativity. Hart is, within the context of recent analytic philosophy, the most important philosopher of law, Rawls the most.. (shrink)

Formal Ontology in Information Systems is the flagship conference of the International Association for Ontology and its Applications. Its interdisciplinary research focus lies at the intersection of philosophical ontology, linguistics, logic, cognitive science, and computer science, as well as in the applications of ontological analysis to conceptual modeling, knowledge engineering, knowledge management, information-systems development, library and information science, scientific research, and semantic technologies in general.As in previous years, FOIS 2014 was a nexus of interdisciplinary research and (...) communication. The current proceedings is divided into four main sections, dealing with: foundations; processes, agency and dispositions; methods and tools; and applications. The last of these covers a broad spectrum of areas, including in particular biology and medicine, engineering, and economy. For the first time in its history, the conference hosted a special track: an ontology competition, the aim of which was to encourage authors to make their ontologies publicly available and to allow them to be evaluated according to a set of predetermined criteria. Papers discussing these ontologies can also be found in this volume.The book will be of interest to all those whose work involves the application of ontologies, and who are looking for a current overview of developments in formal ontology. (shrink)

This article introduces the methodology of the ‘Ontology Explorer’, a semantic method and JavaScript-based open-source tool to analyse data models underpinning information systems. The Ontology Explorer has been devised and developed by the authors, who recognized a need to compare data models collected in different formats and used by diverse systems. The Ontology Explorer is distinctive firstly because it supports analyses of information systems that are not immediately comparable and, secondly, because it systematically and quantitatively supports discursive (...) analysis of ‘thin’ data models – also by detecting differences and absences through comparison. When applied to data models underpinning systems for population management, the Ontology Explorer enables the apprehension of how people are ‘inscribed’ in information systems: which assumptions are made about them, and which possibilities are excluded by design. The Ontology Explorer thus constitutes a methodology to capture authorities’ own imaginaries of populations and the ‘scripts’ through which they enact actual people. Furthermore, the method allows the comparison of scripts from diverse authorities. This is exemplified by illustrating its functioning with information systems for population management deployed at the European border. Our approach integrates a number of insights from early infrastructure studies and extends their methods and analytical depth to account for contemporary data infrastructures. By doing so, we hope to trigger a systematic discussion on how to extend those early methodical innovations at the semantic level to contemporary developments in digital methods. (shrink)

In a recent paper on realism and pragmatism published in this journal, Osmo Kivinen and Tero Piiroinen have been pleading for more methodological work in the philosophy of the social sciences—refining the conceptual tools of social scientists—and less philosophically ontological theories. Following this de-ontologizing approach, we scrutinize the debates on social explanation and contribute to the development of a pragmatic social science methodology. Analyzing four classic debates concerning explanation in the social sciences, we propose to shift the debate (...) away from (a) the ontologizing defenses of forms of social explanation, and (b) a winner-takes-all-approach. Instead, we advocate (c) a pragmatic approach towards social explanation, elaborating a rigorous framework for explanatory pluralism detached from the debates on social ontology. (shrink)

Ontology is doubtless the most important part of Roman Ingarden’s (1893-1970) philosophy. Contrary to Husserl, Ingarden always believed that any serious philosophical investigation must involve an ontological basis and he tried to formulate a solid ontological framework for his philosophy. There are several reasons why this ontology deserves our attention. For those who are interested in Husserl’s transcendental phenomenology, Ingarden’s ontology could be treated as an ingenious attempt to analyse the conceptual structure and hidden ontological assumptions of (...) Husserl’s transcendental idealism. For those who want to understand the immanent dialectics of the post-Brentanian development of the ontology of intentionality, Ingarden’s conception of the purely intentional object could be a very valuable tool. But Ingarden’s ontology has also independent value, and hence it is also interesting for those who pursue ontology for its own sake. In this paper, I will investigate the basic scheme of Ingarden’s ontology, including pure qualities, individual real objects, purely intentional objects and ideas. This schema will prove to be in many aspects generated by his phenomenological, i.e. descriptive and anti-reductionist, ideology. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a (...) PRotein Ontology (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

In a recent paper on realism and pragmatism published in this journal, Osmo Kivinen and Tero Piiroinen have been pleading for more methodological work in the philosophy of the social sciences—refining the conceptual tools of social scientists—and less philosophically ontological theories. Following this de-ontologizing approach, we scrutinize the debates on social explanation and contribute to the development of a pragmatic social science methodology. Analyzing four classic debates concerning explanation in the social sciences, we propose to shift the debate (...) away from (a) the ontologizing defenses of forms of social explanation, and (b) a winner-takes-all-approach. Instead, we advocate (c) a pragmatic approach towards social explanation, elaborating a rigorous framework for explanatory pluralism detached from the debates on social ontology. (shrink)

Applied technological developments are represented by (1) genetic engineering as management tools of biological evolution and (2) socio-economic engineering as management tools of civilizational and socio-cultural development. This binary structure logically follows from the postulated three-module organization of the sustainable evolutionary strategy of the sentient human being. Naturphilosophy once again acquires the status of the basis of the theory of evolution in an explicit way. There is a system of metaphysical postulates and ontological categories derived from the (...) anthropic principle of participation. For modern neoliberal political democracy, bio-power and biopolitics look like the most effective technology for stabilizing the scenarios and trends of the global evolutionary process that are optimal within this ideological system. Conclusions.Transbipolitics in our understanding is a political problematic related to the rationalization of the global evolutionary process. In the coming decades transbipolitics will become the carrier element of the global process of evolution of the noosphere with the consequent complication and increase of cohesion between the individual socio-cultural types that are part of the system of modern globalizing civilization. (shrink)

For over a decade now, a community of researchers has contributed to the development of the Unified Foundational Ontology (UFO) - aimed at providing foundations for all major conceptual modeling constructs. This ontology has led to the development of an Ontology-Driven Conceptual Modeling language dubbed OntoUML, reflecting the ontological micro-theories comprising UFO. Over the years, UFO and OntoUML have been successfully employed in a number of academic, industrial and governmental settings to create conceptual models in (...) a variety of different domains. These experiences have pointed out to opportunities of improvement not only to the language itself but also to its underlying theory. In this paper, we take the first step in that direction by revising the theory of types in UFO in response to empirical evidence. The new version of this theory shows that many of the meta-types present in OntoUML (differentiating Kinds, Roles, Phases, Mixins, etc.) should be considered not as restricted to Substantial types but instead should be applied to model Endurant Types in general, including Relator types, Quality types and Mode types. We also contribute a formal characterization of this fragment of the theory, which is then used to advance a metamodel for OntoUML 2.0. Finally, we propose a computational support tool implementing this updated metamodel. (shrink)

It is the aim of the present study to introduce the reader to the ways of thinking of those contemporary philosophers who apply the tools of symbolic logic to classical philosophical problems. Unlike the "conti nental" reader for whom this work was originally written, the English speaking reader will be more familiar with most of the philosophers dis cussed in this book, and he will in general not be tempted to dismiss them indiscriminately as "positivists" and "nominalists". But the (...) English version of this study may help to redress the balance in another respect. In view of the present emphasis on ordinary language and the wide spread tendency to leave the mathematical logicians alone with their technicalities, it seems not without merit to revive the interest in formal ontology and the construction of formal systems. A closer look at the historical account which will be given here, may convince the reader that there are several points in the historical develop ment whose consequences have not yet been fully assessed: I mention, e. g., the shift from the traditional three-level semantics of sense and deno tation to the contemporary two-level semantics of representation; the relation of extensional structure and intensional content in the extensional systems of Wittgenstein and Carnap; the confusing changes in labelling the different kinds of analytic and apriori true sentences; etc. Among the philosophically interesting tools of symbolic logic Lesniewski's calculus of names deserves special attention. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General (...) Medical Science (OGMS) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes (...) of making computers understand medical natural language. (shrink)

We classify two of Bertrand Russell's theories of events within the point-free ontology. The first of such approaches was presented informally by Russell in ‘The World of Physics and the World of Sense’ (Lecture IV in Our Knowledge of the External World of 1914). Based on this theory, Russell sketched ways to construct instants as collections of events. This paper formalizes Russell's approach from 1914. We will also show that in such a reconstructed theory, we obtain all axioms of (...) Russell's second theory from 1936 and all axioms of Thomason's theory of events from 1989. Russell's work certainly influenced the works of Stanisław Leśniewski, his student Alfred Tarski, and Czesław Lejewski – prominent members of the Lvov-Warsaw School (LWS). We see our work in the tradition of the research of Leśniewski and Tarski. Building on the technical tools developed in this environment and in the spirit of the traditional research of the LWS, we engage here, in particular, with two classic works by Russell on fundamental ontology. (shrink)

What is the best method for undertaking critical social theory, and what are its ontological and normative commitments? Andreas Reckwitz has developed compelling answers to these questions drawing on practice theory. As a practice theorist myself, I am very sympathetic to his approach. This paper sketches a social theory that extends the reach of practice theory to include non-human animals and allows us to discriminate between importantly different kinds of social formations. In doing so, I argue that a strongly normative (...) basis for differentiating social phenomena is compatible with the methods of social theory and critical social theorists need not shy away from first-order moral commitments. (shrink)

The development of computers as ‘mind tools’ has generated intriguing and provocative views about their potential human-like qualities. In this paper an attempt is made to explore the ‘real’ nature of computers by an examination of three widely different perspective, (1) the common-sense view of computers as tools; (2) the provocative view of computers as persons; and (3) the challenging view of computers as texts. In the course of the discussion an extended critique of the use of (...) anthropomorphic terms in relation to machines is conducted and the fundamental differences between human persons and machines is reasserted. (shrink)