Upper ontologies have traditionally arisen from the approach in which concepts that are common across a set of domains can be axiomatized at a general level. The rationale is that reuse across domains is to be supported through specialization of the general concepts from an upper ontology. Similarly, semantic integration between ontologies is to be achieved through the general concepts they specialize. The TUpper Ontology follows an alternative approach to the conventional upper ontology paradigm. Rather than think (...) of an upper ontology as a monolithic axiomatization centred on a taxonomy, the sideways approach considers an upper ontology to be a modular ontology composed of generic ontologies that cover concepts including those related to time, process, and space. TUpper is therefore composed of a set of generic ontologies, and each generic ontology axiomatizes a particular set of generic concepts. The TUpper Ontology is designed as a top-level ontology that contains modules from the ontologies within existing international standards. (shrink)

yamato sharply distinguishes itself from other existing upper ontologies in the following respects. Most importantly, yamato is designed with both engineering and philosophical minds. yamato is based on a sophisticated theory of roles, given that the world is full of roles. yamato has a tenable theory of functions which helps to deal with artifacts effectively. Information is a ‘content-bearing’ entity and it differs significantly from the entities that philosophers have traditionally discussed. Taking into account the modern society in which (...) a flood of information occurs, yamato has a sophisticated theory of informational objects. Quality and quantity are carefully organized for the sake of greater interoperability of real-world data. The philosophical contribution of yamato includes a theory of objects, processes, and events. Those features are illustrated with several case studies. These features lead to the intensive application of yamato in some domains such as biomedicine and learning engineering. (shrink)

Background -/- Ontology Design Patterns (ODPs) are representational artifacts devised to offer solutions for recurring ontology design problems. They promise to enhance the ontology building process in terms of flexibility, re-usability and expansion, and to make the result of ontology engineering more predictable. In this paper, we analyze ODP repositories and investigate their relation with upper-level ontologies. In particular, we compare the BioTop upper ontology to the Action ODP from the NeOn an ODP repository. In view of the (...) differences in the respective approaches, we investigate whether the Action ODP can be embedded into BioTop. We demonstrate that this requires re-interpreting the meaning of classes of the NeOn Action ODP in the light of the precepts of realist ontologies. -/- Results -/- As a result, the re-design required clarifying the ontological commitment of the ODP classes by assigning them to top-level categories. Thus, ambiguous definitions are avoided. Classes of real entities are clearly distinguished from classes of information artifacts. The proposed approach avoids the commitment to the existence of unclear future entities which underlies the NeOn Action ODP. Our re-design is parsimonious in the sense that existing BioTop content proved to be largely sufficient to define the different types of actions and plans. -/- Conclusions -/- The proposed model demonstrates that an expressive upper-level ontology provides enough resources and expressivity to represent even complex ODPs, here shown with the different flavors of Action as proposed in the NeOn ODP. The advantage of ODP inclusion into a top-level ontology is the given predetermined dependency of each class, an existing backbone structure and well-defined relations. Our comparison shows that the use of some ODPs is more likely to cause problems for ontology developers, rather than to guide them. Besides the structural properties, the explanation of classification results were particularly hard to grasp for 'self-sufficient' ODPs as compared with implemented and 'embedded' upper-level structures which, for example in the case of BioTop, offer a detailed description of classes and relations in an axiomatic network. This ensures unambiguous interpretation and provides more concise constraints to leverage on in the ontology engineering process. (shrink)

Philosophy for Children (P4C) provides educators with the process and structures to engage children in inquiring as a group into 'big' moral, ethical, and spiritual questions, while also considering curricular necessities and the demands of national and local standards. Based on the actual experiences of educators in diverse and global classroom contexts, this comprehensive guide gives you the tools you need to introduce philosophical thinking into your classroom, curriculum and beyond. Drawing on research-based educational and psychological models, this book highlights (...) the advantages gained by students who regularly participate in philosophical discussion: from building cognitive and social/emotional development, to becoming more informed citizens. Helpful tools and supplementary online resources offer additional frameworks for supporting and sustaining a higher level of thinking and problem-solving among your students. This practical guide is essential reading for teachers, coaches, and anyone wondering how you can effectively teach philosophy in your classroom. (shrink)

Basic Formal Ontology (BFO) is a top-level ontology used in hundreds of active projects in scientific and other domains. BFO has been selected to serve as top-level ontology in the Industrial Ontologies Foundry (IOF), an initiative to create a suite of ontologies to support digital manufacturing on the part of representatives from a number of branches of the advanced manufacturing industries. We here present a first draft set of axioms and definitions of an IOF upper ontology (...) descending from BFO. The axiomatization is designed to capture the meanings of terms commonly used in manufacturing and is designed to serve as starting point for the construction of the IOF ontology suite. (shrink)

The next generation of Geographic Information Systems is anticipated to automate some of the reasoning required for spatial analysis. An important step in the development of such systems is to gain a better understanding and corresponding modeling practice of when to apply arithmetic operations to quantities. The concept of extensivity plays an essential role in determining when quantities can be aggregated by summing them, and when this is not possible. This is of particular importance to geographic information systems, which serve (...) to quantify phenomena across space and time. However, currently, multiple contrasting definitions of extensivity exist, and none of these suffice for handling the different practical cases occurring in geographic information. As a result, analysts predominantly rely on intuition and ad hoc reasoning to determine whether two quantities are additive. In this paper, we present a novel approach to formalizing the concept of extensivity. Though our notion as such is not restricted to quantifications occurring within geographic information, it is particularly useful for this purpose. Following the idea of spatio-temporal controls by Sinton, we define extensivity as a property of measurements of quantities with respect to a controlling quantity, such that a sum of the latter implies a sum of the former. In our algebraic definition of amounts and other quantities, we do away with some of the constraints that limit the usability of older approaches. By treating extensivity as a relation between amounts and other types of quantities, our definition offers the flexibility to relate a quantity to many domains of interest. We show how this new notion of extensivity can be used to classify the kinds of amounts in various examples of geographic information. (shrink)

The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of data. To provide effective solutions computers need to integrate data deriving from myriad heterogeneous sources by bringing the data together within a single framework. The meeting brought together leaders in the field of what are called "top-level ontologies" to address this issue, and to establish (...) strategies among leaders in the field of biomedical ontology for the creation of interoperable biomedical ontologies which will serve the goal of useful data integration. (shrink)

Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general, domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, which is intended to be the basis of a knowledge modelling language GOL (for: 'General Ontological Language'). It turns out that the upper- level ontology underlying standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. Set theory has considerable (...) mathematical power and great flexibility as a framework for modelling different sorts of structures. At the same time it has the disadvantage that sets are abstract entities (entities existing outside the realm of time, space and causality), and thus a set-theoretical framework should be supplemented by some other machinery if it is to support applications in the ripe, messy world of concrete objects. In the present paper we partition the entities of the real world into sets and urelements, and then we introduce several new ontological relations between these urelements. In contrast to standard modelling and representation formalisms, the concepts of GOL provide a machinery for representing and analysing such ontologically basic relations. (shrink)

dolce, the first top-level ontology to be axiomatized, has remained stable for twenty years and today is broadly used in a variety of domains. dolce is inspired by cognitive and linguistic considerations and aims to model a commonsense view of reality, like the one human beings exploit in everyday life in areas as diverse as socio-technical systems, manufacturing, financial transactions and cultural heritage. dolce clearly lists the ontological choices it is based upon, relies on philosophical principles, is richly formalized, (...) and is built according to well-established ontological methodologies, e.g. OntoClean. Because of these features, it has inspired most of the existing top-level ontologies and has been used to develop or improve standards and public domain resources. Being a foundational ontology, dolce is not directly concerned with domain knowledge. Its purpose is to provide the general categories and relations needed to give a coherent view of reality, to integrate domain knowledge, and to mediate across domains. In these 20 years dolce has shown that applied ontologies can be stable and that interoperability across reference and domain ontologies is a reality. This paper briefly introduces the ontology and shows how to use it on a few modeling cases. (shrink)

The present research examines how narrative engagement, or the extent to which people immerse themselves into the world of a story, varies as a function of narrative perspective and individual differences in alexithymia. The authors hypothesised that narrative engagement would be higher when people assume a first-person (rather than third-person) perspective and for people lower (rather than higher) on alexithymia. In an online study (N = 541) and a lab study (N = 55), participants with varying levels of alexithymia read (...) first- and/or third-person narrated texts and then rated their narrative engagement. As expected, first-person stories evoked more narrative engagement than third-person stories, and global alexithymia was negatively correlated with narrative engagement. Narrative perspective did not interact with cognitive facets of alexithymia (i.e. difficulties identifying, verbalising, and understanding feelings). However, narrative perspective did interact with affective facets of alexithymia (i.e. emotionalising and fantasising): First-person (rather than third-person) stories elicited more narrative engagement at lower levels of affective alexithymia, but not at higher levels of affective alexithymia. The interaction effect was significant in Study 1; the interaction was significant in Study 2 after controlling for trait absorption. Together, these findings suggest that alexithymia is linked to difficulties in mentally simulating narrative worlds. (shrink)

The present research examines how narrative engagement, or the extent to which people immerse themselves into the world of a story, varies as a function of narrative perspective and individual differences in alexithymia. The authors hypothesised that narrative engagement would be higher when people assume a first-person (rather than third-person) perspective and for people lower (rather than higher) on alexithymia. In an online study (N = 541) and a lab study (N = 55), participants with varying levels of alexithymia read (...) first- and/or third-person narrated texts and then rated their narrative engagement. As expected, first-person stories evoked more narrative engagement than third-person stories, and global alexithymia was negatively correlated with narrative engagement. Narrative perspective did not interact with cognitive facets of alexithymia (i.e. difficulties identifying, verbalising, and understanding feelings). However, narrative perspective did interact with affective facets of alexithymia (i.e. emotionalising and fantasising): First-person (rather than third-person) stories elicited more narrative engagement at lower levels of affective alexithymia, but not at higher levels of affective alexithymia. The interaction effect was significant in Study 1; the interaction was significant in Study 2 after controlling for trait absorption. Together, these findings suggest that alexithymia is linked to difficulties in mentally simulating narrative worlds. (shrink)

What follows is a first step towards an ontology of conscious mental processes. We provide a theoretical foundation and characterization of conscious mental processes based on a realist theory of intentionality and using BFO as our top-level ontology. We distinguish three components of intentional mental process: character, directedness, and objective referent, and describe several features of the process character and directedness significant to defining and classifying mental processes. We arrive at the definition of representational mental process as a process (...) that is the bringing into being, sustaining, modifying, or terminating of a mental representation. We conclude by outlining some benefits and applications of this approach. (shrink)

Flow is a state of full task engagement that is accompanied with low-levels of self-referential thinking. Flow is considered highly relevant for human performance and well-being and has, therefore, been studied extensively. Yet, the neurocognitive processes of flow remain largely unclear. In the present mini-review we focus on how the brain's locus coeruleus-norepinephrine (LC-NE) system may be involved in a range of behavioral and subjective manifestations of flow. The LC-NE system regulates decisions regarding task engagement vs. disengagement. This is doneviadifferent (...) modes of baseline and stimulus-evoked norepinephrine release. We emphasize the theoretical and empirical overlap between the LC-NE system and flow. For both, a match between a person's skill and task challenge is important in order to induce high levels task-related attention. Moreover, psychophysiological indicators of LC-NE system activity, such as eye pupil diameter and arousal are also sensitive to flow states. Flow is related to arousal in an inverted U-shape. Similarly, in theories on the LC-NE system, task engagement is highest with intermediate levels of arousal. We argue that knowledge about the role of the LC-NE system in establishing the flow experience may help to gain fundamental knowledge of flow and can contribute to unifying various empirical findings on this topic. (shrink)

The concept of measurement is fundamental to a whole range of different disciplines, including not only the natural and engineering sciences, but also laboratory medicine and certain branches of the social sciences. This being the case, the concept of measurement has a particular relevance to the development of top-level ontologies in the area of knowledge engineering. For this reason, the present paper is concerned with ontological aspects of measurement. We are searching for a list of concepts that are (...) apt to characterize measurement methods in a general manner. To establish such means of characterization, we will primarily deal with the semantics of measurement values. (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)

In the last two decades we have witnessed considerable efforts directed towards making electronic healthcare records comparable and interoperable through advances in record architectures and (bio)medical terminologies and coding systems. Deep semantic issues in general, and ontology in particular, have received some interest from the research communities. However, with the exception of work on so-called ‘controlled vocabularies’, ontology has thus far played little role in work on standardization. The prime focus has been rather the rapid population of terminologies at the (...) level of fine detail. In this paper, we argue that more efforts are needed on the side of both research and standardization to ensure that the coding systems used in electronic healthcare records enjoy a semantics that is coherent with the semantics of the record. We propose realist ontology as a method to bring about this coherence by means of a robust system of top-level ontological categories. (shrink)

General Ontological Language (GOL) is a formal framework for representing and building ontologies. The purpose of GOL is to provide a system of top-level ontologies which can be used as a basis for building domain-specific ontologies. The present paper gives an overview about the basic categories of the GOL-ontology. GOL is part of the work of the research group Ontologies in Medicine (Onto-Med) at the University of Leipzig which is based on the collaborative work of (...) the Institute of Medical Informatics (IMISE) and the Institute for Computer Science (IfI). It represents work in progress toward a proposal for an integrated family of top-level ontologies and will be applied to several fields of medicine, in particular to the field of Clinical Trials. (shrink)

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. (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)

The goal of the paper is to analyse some specific features of a very central concept for top-level ontologies for information systems: i.e. the concept of artefact. Specifically, we analyse the relation to be a copy of that is strongly linked to the notion of artefact and—as we will demonstrate—could be useful to distinguish artefacts from objects of other kinds. Firstly, we outline some intuitive and commonsensical reasons for the need of a clarification of the notion of artefact (...) in ontologies for information systems, and we analyse some characterisations of the notion given by two top-level ontologies (Cyc and Wordnet). Secondly, we introduce and critically analyse Tzouvaras’ notion of copy. Thirdly, we try to complete an analysis of copy by distinguishing three kinds of copies: replicas (Tzouvaras’ notion of copy), rigid copies, and functional copies. With the help of these three notions we outline a first and preliminary distinction between artefacts, objects of art and natural objects. (shrink)

The General Formal Ontology is a top-level ontology that is being developed at the University of Leipzig since 1999. Besides introducing some of the basic principles of the ontology, we expound axiomatic fragments of its formalization and present ontological models of several use cases. GFO is a top-level ontology that integrates objects and processes into a unified framework, in a way that differs significantly from other ontologies. Another unique selling feature of GFO is its meta-ontological architecture, which (...) includes set theory into ontology and which accounts for its specific role in common representation approaches. The second level of that architecture starts from the distinction of categories and individuals, which forms the backbone of the world’s structure. Furthermore, GFO comprises several kinds of categories, among them universals and concepts, and it considers several ontological regions and levels. In the context of this special issue paper, we study five pre-determined use cases from the perspective of GFO. The results of these analyses yield insights into how the ontology treats several important notions. Very abridged, this covers material objects and their composition; roles and social entities; properties with their relations to objects and processes, and their changing; changes of processes, including a functional perspective; and, eventually, the nature and changing of concepts as well as terminology. A final part summarizes application projects that use GFO in various contexts. (shrink)

In “Ontologies Relevant to behaviour change interventions: A Method for their Development” Wright, et al. outline a step by step process for building ontologies of behaviour modification – what the authors call the Refined Ontology Developmental Method (RODM) – and demonstrate its use in the development of the Behaviour Change Intervention Ontology (BCIO). RODM is based on the principles of good ontology building used by the Open Biomedical Ontology (OBO) Foundry in addition to those outlined in (Arp, Smith, (...) and Spear 2015). BCIO uses as its top-level ontology Basic Formal Ontology (BFO). The methods outlined in Wright, et al. are a valuable contribution to the field, especially the use of formal mechanisms for literature annotation and expert stakeholder review, and the BCIO will certainly play an important role in the extension of OBO Foundry ontologies into the behavioural domain. (shrink)

We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) perspectives within (...) a single framework. We examine how BFO-conformant domain ontologies can deal with the consistent representation of scientific data deriving from the measurement of processes of different types, and we outline on this basis the first steps of an approach to the classification of such processes within the BFO framework. (shrink)

BACKGROUND -/- The importance of ontologies in the biomedical domain is generally recognized. However, their quality is often too poor for large-scale use in critical applications, at least partially due to insufficient training of ontology developers. -/- OBJECTIVE -/- To show the efficacy of guideline-based ontology development training on the performance of ontology developers. The hypothesis was that students who received training on top-level ontologies and design patterns perform better than those who only received training in the (...) basic principles of formal ontology engineering. -/- METHODS -/- A curriculum was implemented based on a guideline for ontology design. A randomized controlled trial on the efficacy of this curriculum was performed with 24 students from bioinformatics and related fields. After joint training on the fundamentals of ontology development the students were randomly allocated to two groups. During the intervention, each group received training on different topics in ontology development. In the assessment phase, all students were asked to solve modeling problems on topics taught differentially in the intervention phase. Primary outcome was the similarity of the students’ ontology artefacts compared with gold standard ontologies developed by the authors before the experiment; secondary outcome was the intra-group similarity of group members’ ontologies. -/- RESULTS -/- The experiment showed no significant effect of the guideline-based training on the performance of ontology developers (a) the ontologies developed after specific training were only slightly but not significantly closer to the gold standard ontologies than the ontologies developed without prior specific training; (b) although significant differences for certain ontologies were detected, the intra-group similarity was not consistently influenced in one direction by the differential training. -/- CONCLUSION -/- Methodologically limited, this study cannot be interpreted as a general failure of a guideline-based approach to ontology development. Further research is needed to increase insight into whether specific development guidelines and practices in ontology design are effective. (shrink)

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the (...) model organism communities to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (...) (3) testing, and (4) data exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

This book contains selected papers from the First International Conference on the Ontology of Spacetime. Its fourteen chapters address two main questions: first, what is the current status of the substantivalism/relationalism debate, and second, what about the prospects of presentism and becoming within present-day physics and its philosophy? The overall tenor of the four chapters of the book’s first part is that the prospects of spacetime substantivalism are bleak, although different possible positions remain with respect to the ontological status of (...) spacetime. Part II and Part III of the book are devoted to presentism, eternalism, and becoming, from two different perspectives. In the six chapters of Part II it is argued, in different ways, that relativity theory does not have essential consequences for these issues. It certainly is true that the structure of time is different, according to relativity theory, from the one in classical theory. But that does not mean that a decision is forced between presentism and eternalism, or that becoming has proved to be an impossible concept. It may even be asked whether presentism and eternalism really offer different ontological perspectives at all. The writers of the last four chapters, in Part III, disagree. They argue that relativity theory is incompatible with becoming and presentism. Several of them come up with proposals to go beyond relativity, in order to restore the prospects of presentism. · Space and time in present-day physics and philosophy · Relatively low level of technicality, easily accessible · Introduction from scratch of the debates surrounding time · Top authors explaining their positions · Broad spectrum of approaches, coherently represented. (shrink)

BACKGROUND -/- The need for detailed description and modeling of cells drives the continuous generation of large and diverse datasets. Unfortunately, there exists no systematic and comprehensive way to organize these datasets and their information. CELDA (Cell: Expression, Localization, Development, Anatomy) is a novel ontology for the association of primary experimental data and derived knowledge to various types of cells of organisms. -/- RESULTS -/- CELDA is a structure that can help to categorize cell types based on species, anatomical localization, (...) subcellular structures, developmental stages and origin. It targets cells in vitro as well as in vivo. Instead of developing a novel ontology from scratch, we carefully designed CELDA in such a way that existing ontologies were integrated as much as possible, and only minimal extensions were performed to cover those classes and areas not present in any existing model. Currently, ten existing ontologies and models are linked to CELDA through the top-level ontology BioTop. Together with 15.439 newly created classes, CELDA contains more than 196.000 classes and 233.670 relationship axioms. CELDA is primarily used as a representational framework for modeling, analyzing and comparing cells within and across species in CellFinder, a web based data repository on cells (http://cellfinder.org). -/- CONCLUSIONS -/- CELDA can semantically link diverse types of information about cell types. It has been integrated within the research platform CellFinder, where it exemplarily relates cell types from liver and kidney during development on the one hand and anatomical locations in humans on the other, integrating information on all spatial and temporal stages. CELDA is available from the CellFinder website: http://cellfinder.org/about/ontology. (shrink)

As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, (...) and functionally difficult to extend or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

PURPOSE—A substantial fraction of the observations made by clinicians and entered into patient records are expressed by means of negation or by using terms which contain negative qualifiers (as in “absence of pulse” or “surgical procedure not performed”). This seems at first sight to present problems for ontologies, terminologies and data repositories that adhere to a realist view and thus reject any reference to putative non-existing entities. Basic Formal Ontology (BFO) and Referent Tracking (RT) are examples of such paradigms. (...) The purpose of the research here described was to test a proposal to capture negative findings in electronic health record systems based on BFO and RT. METHODS—We analysed a series of negative findings encountered in 748 sentences taken from 41 patient charts. We classified the phenomena described in terms of the various top-level categories and relations defined in BFO, taking into account the role of negation in the corresponding descriptions. We also studied terms from SNOMED-CT containing one or other form of negation. We then explored ways to represent the described phenomena by means of the types of representational units available to realist ontologies such as BFO. RESULTS—We introduced a new family of ‘lacks’ relations into the OBO Relation Ontology. The relation lacks_part, for example, defined in terms of the positive relation part_of, holds between a particular p and a universal U when p has no instance of U as part. Since p and U both exist, assertions involving ‘lacks_part’ and its cognates meet the requirements of positivity. CONCLUSION—By expanding the OBO Relation Ontology, we were able to accommodate nearly all occurrences of negative findings in the sample studied. (shrink)

Against the background that the top-level semantic framework of Chinese traditional culture is not comprehensive and unified, this study aims to preserve and disseminate cultural heritage information about Chinese traditional culture through the development of a domain ontology which is constructed from ancient books. A combination of top-down and bottom-up approaches was used to construct the ontology for Chinese traditional culture. An investigation of historians’ needs, and LDA topic clustering model were conducted, understanding the specific needs of historians, collecting (...) the topic, concepts and relationships. CIDOC CRM was reused to construct the basic framework of CTCO. Ontology structure and function were adopted to evaluate the effectiveness of CTCO. Evaluation results show that the ontology meets all the quality criteria of OntoMetrics, and the experts agreed on content representation. CTCO contributes to the organization of traditional Chinese culture and the construction of related databases. The study also forms a common path and puts forward proposals for the construction of domain ontology, which has great social relevance. (shrink)

The construction of complex ontologies can be facilitated by adapting existing vocabularies. There is little clarity and in fact little consensus as to what modifications of vocabularies are necessary in order to re-engineer them into ontologies. In this paper we present a method that provides clear steps to follow when re-engineering a thesaurus. The method makes use of top-level ontologies and was derived from the structural differences between thesauri and ontologies as well as from best (...) practices in modeling, some of which have been advocated in the biomedical domain. We illustrate each step of our method with examples from a re-engineering case study about agricultural fertilizers based on the AGROVOC thesaurus. Our method makes clear that re-engineering thesauri requires far more than just a syntactic conversion into a formal language or other easily automatable steps. The method can not only be used for re-engineering thesauri, but does also summarize steps for building ontologies in general, and can hence be adapted for the re-engineering of other types of vocabularies or terminologies. (shrink)

Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is linked (...) to multiple clinical trials investigating Gleevec’s related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed. (shrink)

Background: Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is acomprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic healthdata. Some efforts have been made to capture the contents of SCT as Web Ontology Language (OWL), but theseefforts have been hampered by the size and complexity of SCT. Method: Our proposal here is to develop an upper-level ontology and to use it as the basis for defining the termsin SCT in a way that (...) will support quality assurance of SCT, for example, by allowing consistency checks ofdefinitions and the identification and elimination of redundancies in the SCT vocabulary. Our proposed upper-levelSCT ontology (SCTO) is based on the Ontology for General Medical Science (OGMS). Results: The SCTO is implemented in OWL 2, to support automatic inference and consistency checking. Theapproach will allow integration of SCT data with data annotated using Open Biomedical Ontologies (OBO) Foundryontologies, since the use of OGMS will ensure consistency with the Basic Formal Ontology, which is the top-levelontology of the OBO Foundry. Currently, the SCTO contains 304 classes, 28 properties, 2400 axioms, and 1555annotations. It is publicly available through the bioportal athttp://bioportal.bioontology.org/ontologies/SCTO/. Conclusion: The resulting ontology can enhance the semantics of clinical decision support systems and semanticinteroperability among distributed electronic health records. In addition, the populated ontology can be used forthe automation of mobile health applications. (shrink)

The Industrial Ontologies Foundry (IOF) was formed to create a suite of interoperable ontologies. Ontologies that would serve as a foundation for data and information interoperability in all areas of manufacturing. To ensure that each ontology is developed in a structured and mutually coherent manner, the IOF has committed to the tiered architecture of ontology building based on the Basic Formal Ontology (BFO) as top level. One of the critical elements of a successful tiered architecture build (...) is the domain mid-level ontologies. However, thus far there has been no mid-level manufacturing ontology that is based on BFO. The IOF has recently released the IOF Core version 1 beta to fill this gap. This paper documents the development process and gives an overview of the current content of the IOF Core. Finally, the paper describes how the IOF Core can be used as the basis for a more domain-specific Supply Chain Ontology. (shrink)

Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate representation (...) of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information. (shrink)

This paper presents an axiomatic formalization of a theory of top-level relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the sub-universal relation among universals and the parthood relation among individuals, as well as cross-categorial relations such as instantiation and membership. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical (...) for geographic information processing. The axiomatic theory is developed using Isabelle, a computational system for implementing logical formalisms. All proofs are computer verified and the computational representation of the theory is available online. (shrink)

The labor market is an area with diverse data structures and multiple applications, such as matching job seekers with the right training or job. For this reason, the multilingual classification of European Skills, Competences, Qualifications and Occupations (ESCO) is a good example of the central role of ontologies in this area. However, ESCO cannot provide all the details of local labor market needs and does not provide links to other hierarchies of competences. For example, other taxonomies of occupations and (...) skills are widely used in German-speaking countries, but they are not in a state where they are easily accessible for interoperability and reasoning. In this paper, we present a first version of a German Labor Market Ontology (GLMO) that uses ESCO as a top-level ontology for the target domain. This makes it highly interoperable and comparable to existing ontologies by providing details for the regional structures in German-speaking countries. In addition, we present a detailed evaluation of the provided data and applications, as well as an extensive discussion of future work. (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)

The ethics of artificial intelligence (AI) is a research topic with both theoretical and practical significance. However, the ethical and moral aspects of conceptual, ontological, semantic, and knowledge modeling, more specifically, and which are sometimes found in AI applications, is not being given sufficient attention. I argue that it should. Whether considering using or developing these meaning-focused models, there are ethical aspects. This paper offers a preliminary outline about this potentially new research field, discussing: some questions and areas of concern, (...) their significance; scenarios of ethical import, and initial ethical guidelines. A focus area, potential case study, and lens through which to see the ethical significance at hand, is ontologies, with emphasis on the most abstract ontologies (so-called generic, foundational, top-level or upper ontologies). This would aim to show the ethical import of highly abstract (often philosophical) ontological choices, assumptions, and their effects on data, developers, users, and society. In particular, I stress the need for critical examination of such models, their content, their intended meanings, assumptions, ideologies, as well as the development process. Both the ethics of, and ethics in, these activities are, therefore, of interest. Topics in the ethics of AI that are relevant include: transparency, bias, data-sharing, privacy, control over data, etc. This paper thereby contributes to the ethics of AI, as well as the ethics of information, of knowledge managment and relevant topics by developing and discussing the ethics of ontology (and similar systems). Future development will refine and add to the ideas expressed in this paper. (shrink)

We present a formal Arabic wordnet built on the basis of a carefully designed ontology hereby referred to as the Arabic Ontology. The ontology provides a formal representation of the concepts that the Arabic terms convey, and its content was built with ontological analysis in mind, and benchmarked to scientific advances and rigorous knowledge sources as much as this is possible, rather than to only speakers’ beliefs as lexicons typically are. A comprehensive evaluation was conducted thereby demonstrating that the current (...) version of the top-levels of the ontology can top the majority of the Arabic meanings. The ontology consists currently of about 1,800 well-investigated concepts in addition to 16,000 concepts that are partially validated. The ontology is accessible and searchable through a lexicographic search engine that also includes about 150 Arabic-multilingual lexicons, and which are being mapped and enriched using the ontology. The ontology is fully mapped with Princeton WordNet, Wikidata, and other resources. (shrink)

This paper proposes a formal top-level model of explaining the outputs of machine-learning-based decision-making applications and evaluates it experimentally with three data sets. The model draws on AI & law research on argumentation with cases, which models how lawyers draw analogies to past cases and discuss their relevant similarities and differences in terms of relevant factors and dimensions in the problem domain. A case-based approach is natural since the input data of machine-learning applications can be seen as cases. While (...) the approach is motivated by legal decision making, it also applies to other kinds of decision making, such as commercial decisions about loan applications or employee hiring, as long as the outcome is binary and the input conforms to this paper’s factor- or dimension format. The model is top-level in that it can be extended with more refined accounts of similarities and differences between cases. It is shown to overcome several limitations of similar argumentation-based explanation models, which only have binary features and do not represent the tendency of features towards particular outcomes. The results of the experimental evaluation studies indicate that the model may be feasible in practice, but that further development and experimentation is needed to confirm its usefulness as an explanation model. Main challenges here are selecting from a large number of possible explanations, reducing the number of features in the explanations and adding more meaningful information to them. It also remains to be investigated how suitable our approach is for explaining non-linear models. (shrink)

Ontological approaches to the arts have neglected art forms such as dance. This hinders analysis of the metaphysical similarities and differences between different art forms. In this paper, I develop a metaphysical realist ontological approach to dance and sport that is grounded in embodiment. I first examine the debate between descriptivism and metaontological realism in the philosophy of arts in the context of Thomasson’s descriptive approach and Dodd’s metaontological approach of folk-theoretic modesty. Following Dodd, I adopt a realist metaontological approach (...) to dance as an art form, drawing on philosophical debates within dance. I then review metaphysical approaches to sport and argue that most such approaches are based on abstract, top-down models. I therefore propose an ontological account of sport and dance based on metaontological realism and grounded in embodied movement knowledge. Drawing on Schaffer’s concept of ground functionalism, I use this approach to compare the aesthetic and bodily aspects of sport and dance in terms of elite-level movement knowledge. I describe how the embodiment of such movement knowledge through practice permits dancers and athletes to create expert movements. Drawing on findings from neuroscientific research, I argue that dancers and athletes, through the process of physiological plasticity, acquire embodied memories that are transformed into new bodily and behavioral dispositions. I believe that the metaphysical realist ontological approach presented here could help to broaden the focus in arts ontology to encompass movement disciplines such as sport and dance. This account may also engender cross-disciplinary research and encourage philosophers to explore the role of movement in arts such as music. (shrink)

I first explore the notion of the world's being such that everything in it is a proper part. I then explore the notion of the world's being such that everything in it both is and has a proper part. Given two well recognized assumptions, I argue that both notions represent genuine metaphysical possibilities. Finally I consider, but dismiss, some possible objections.

Given the assertion of a relation between two types, like: “Epidermis has part some Keratinocyte”, we define silent change as any kind of change of the instance-relata of the relation in question that does not change the truth-value of the respective type-level assertion. Such assertions are notoriously difficult to model in OWL 2. To address this problem, we distinguish different modes of type-level relatedness giving rise to this problem and describe a conservative extension to the BFO top-level (...) ontology that allows expressing these modes. (shrink)

It is widely understood that protein functions can be exhaustively described in terms of no single parameter, whether this be amino acid sequence or the three-dimensional structure of the underlying protein molecule. This means that a number of different attributes must be used to create an ontology of protein functions. Certainly much of the required information is already stored in databases such as Swiss-Prot, Protein Data Bank, SCOP and MIPS. But the latter have been developed for different purposes and the (...) separate data-structures which they employ are not conducive to the needed data integration. When we attempt to classify the entities in the domain of proteins, we find ourselves faced with a number of cross-cutting principles of classification. Our question here is: how can we bring together these separate taxonomies in order to describe protein functions? Our proposed answer is: via a careful top-level ontological analysis of the relevant principles of classification, combined with a new framework for the simultaneous manipulation of classifications constructed for different purposes. (shrink)

So far, we have focused on discourse reference to atomic individuals and specific times, events, and states. The basic point of the argument was that all types of discourse reference involve attention-guided anaphora (in the sense of Bittner 2012: Ch. 2). We now turn to discourses involving anaphora to and by quantificational expressions. Today, we focus on quantification over individuals but the analysis we develop will directly generalize to other semantic types. The basic idea is that quantification is one more (...) species of top-level anaphora--to wit, anaphora to top-ranked sets. (shrink)

Background: SNOMED CT is a large terminology system designed to represent all aspects of healthcare. Its current form and content result from decades of bottom-up evolution. Due to SNOMED CT’s formal descriptions, it can be considered an ontology. The Basic Formal Ontology (BFO) is a foundational ontology that proposes a small set of disjoint, hierarchically ordered classes, supported by relations and axioms. In contrast, as a typical top-down endeavor, BFO was designed as a foundational framework for domain ontologies in (...) the natural sciences and related disciplines. Whereas it is mostly assumed that domain ontologies should be created as extensions of foundational ontologies, a post-hoc harmonization of consolidated domain ontologies in use, such as SNOMED CT, is known to be challenging. Methods: We explored the feasibility of harmonizing SNOMED CT with BFO, with a focus on the SNOMED CT Clinical Finding hierarchy. With more than 100,000 classes, it accounts for about one third of SNOMED CT’s content. In particular, we represented typical SNOMED CT finding/disorder concepts using description logics under BFO. Three representational patterns were created and the logical entailments analyzed. Results: Under a first scrutiny, the clinical intuition that diseases, disorders, signs and symptoms form a homogeneous ontological upper-level class appeared incompatible with BFO’s upper-level distinction into continuants and occurrents. The Clinical finding class seemed to be an umbrella for all kinds of entities of clinical interest, such as material entities, processes, states, dispositions, and qualities. This suggests the conclusion that Clinical finding would not be a suitable upper-level class from an BFO perspective. On closer inspection of the taxonomic links within this hierarchy and the implicit meaning derived thereof, it became clear that Clinical finding classes do not characterize the entity (e.g. a fracture, allergy, tumor, pain, hemorrhage, seizure, fever) in a literal sense but rather the condition of a patient having that fracture, allergy, pain etc. This gives sense to the current characteristic of the Clinical Finding hierarchy, in which complex classes are modeled as subclasses of their constituents. Most of these taxonomic links are inferred, as the consequence of the ‘role group’ design pattern, which is ubiquitous in SNOMED CT and has often been subject of controversy regarding its semantics. Conclusion: Our analyses resulted in the proposal of (i) equating SNOMED CT’s ‘role group’ property with the reflexive and transitive BFO relation ‘has occurrent part’; and (ii) reinterpreting Clinical Findings as Clinical Occurrents, i.e. temporally extended entities in an organism, having one or more occurrents as temporal parts that occur in continuants. This re-interpretation was corroborated by a manual analysis of classes under Clinical Finding, as well as the identification of similar modeling patterns in other ontologies. As a result, SNOMED CT does not require any content redesign to establish compatibility with BFO, apart from this re-interpretation, and a suggested re-labeling. Regarding the feasibility of harmonizing terminologies with principled foundational ontologies post-hoc, our results provide support to the assumption that this does not necessarily require major redesign efforts, but rather a careful analysis of the implicit assumptions of terminology curators and users. (shrink)