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, and we outline an associated knowledge modelling language called GOL – for: General Ontological Language. It turns out that the upper-level ontology underlying well-known standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology (...) of sets. In a set theory which allows Urelements, however, there will be ontological relations between these Urelements which the set-theoretic machinery cannot capture. In contrast to standard modelling and representation formalisms, GOL provides a machinery for representing and analysing such ontologically basic relations. GOL is thus a genuine extension of KIF and of similar languages. In GOL entities are divided into sets and Urelements, the latter being divided in their turn into individuals and universals. Foremost among the individuals are things or substances, tropes or moments, and situoids: entities containing facts as components. (shrink)

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)

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)

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)

Willard van Orman Quine once said that he had a preference for a desert ontology. This was in an earlier day when concerns with logical structure and ontological simplicity reigned supreme. Ontological genocide was practiced upon whole classes of upper-level or ‘derivative’ entities in the name of elegance, and we were secure in the belief that one strayed irremediably into the realm of conceptual confusion and possible error the further one got from ontic fundamentalism. In those days, (...) one paid more attention to generic worries about possible errors than to actual errors derived from distancing oneself too far from the nitty-gritty details of actual theory, actual inferences from actual data, the actual conditions under which we posited and detected entities, calibrated and ‘burned in’ instruments, identified and rejected artifacts, debugged programs and procedures, explained the mechanisms behind regularities, judged correlations to be spurious, and in general, to the real complexities and richness of actual scientific practice. (shrink)

Basic Formal Ontology was created in 2002 as an upper-level ontology to support the creation of consistent lower-level ontologies, initially in the subdomains of biomedical research, now also in other areas, including defense and security. BFO is currently undergoing revisions in preparation for the release of BFO version 2.0. We summarize some of the proposed revisions in what follows, focusing on BFO’s treatment of material entities, and specifically of the category object.

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)

Changes in an upper level ontology have obvious conse-quences for the domain ontologies that use it at lower levels. It is therefore crucial to document the changes made between successive versions of ontologies of this kind. We describe and apply a method for tracking, explaining and measuring changes between successive versions of upper level ontologies such as the Basic Formal Ontology (BFO). The proposed change-tracking method extends earlier work on Realism-Based Ontology Versioning (RBOV) (...) and Evolutionary Terminology Auditing (ETA). We describe here the application of this evaluation method to changes between BFO 1.0, BFO 1.1, and BFO 2.0. We discuss the issues raised by this application and describe the extensions which we added to the original evaluation schema in order to account for changes in an ontology of this type. Our results show that BFO has undergone eight types of changes that can be systematically explained by the extended evaluation schema. Finally, we discuss problematic cases, possible pitfalls and certain limits of our study that we propose to address in future work. (shrink)

Although the last decade has seen a proliferation of ontological approaches to arguments, many of them employ ad hoc solutions to representing arguments, lack interoperability with other ontologies, or cover arguments only as part of a broader approach to evidence. To provide a better ontological representation of arguments, we present the Arguments Ontology (ArgO), a small ontology for arguments that is designed to be imported and easily extended by researchers who work in different upper-level ontology (...) frameworks, different logics, and different approaches to argument evaluation. Unlike most ontological approaches to arguments, ArgO utilizes Basic Formal Ontology (BFO) as an upper-level ontology, and may be used alongside other commonly used ontologies in the BFO framework, including boththe Information Artifact Ontology (IAO), and the Information Entity Ontology (INFO). Critically, our proposal is principled, based on rigorous definitions and formal axioms out of which characterizations of arguments naturally fall. It is our hope that ArgO may assist researchers in many projects, including: integrating heterogeneous sources of evidence, structuring the content of semantic wikis, and enhancing semantic reasoning. (shrink)

The goal of this paper is two-fold: first, to emphasize causality in disease ontology and knowledge representation, presenting a general and cursory discussion of causality and causal chains; and second, to clarify and develop the River Flow Model of Diseases (RFM). The RFM is an ontological account of disease, representing the causal structure of pathology. It applies general knowledge of causality using the concept of causal chains. The river analogy of disease is explained, formal descriptions are offered, and the (...) RFM disease definition is refined by describing causal chains in terms of causal relations. The definition is updated to coincide with the actual RFM classes found in its upper-level ontology, YAMATO, which brings to light some challenges in developing both YAMATO and the RFM. The RFM is also discussed in relation to another ontological account of disease. Strategies are offered toward interoperability between these theories. (shrink)

The world of ontology development is full of mysteries. Recently, ISO Standard 15926 (“Lifecycle Integration of Process Plant Data Including Oil and Gas Production Facilities”), a data model initially designed to support the integration and handover of large engineering artefacts, has been proposed by its principal custodian for general use as an upper level ontology. As we shall discover, ISO 15926 is, when examined in light of this proposal, marked by a series of quite astonishing defects, (...) which may however provide general lessons for the developers of ontologies in the future. (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)

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)

We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the (...) light of the interconnections between them. (shrink)

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

GUM is a linguistically-motivated ontology originally developed to support natural language processing systems by offering a level of representation intermediate between linguistic forms and domain knowledge. Whereas modeling decisions for individual domains may need to be responsive to domain-specific criteria, a linguistically-motivated ontology offers a characterization that generalizes across domains because its design criteria are derived independently both of domain and of application. With respect to this mediating role, the use of GUM resembles the adoption of (...) class='Hi'>upper ontologies as tools for mediating across domains and for supporting domain modeling. This paper briefly introduces the ontology, setting out its origins, design principles and applications. The example cases for this special issue are then described, illustrating particularly some of the principal differences and similarities of GUM to non-linguistically motivated upper ontologies. (shrink)

In this engaging and wide-ranging new book, Nikk Effingham provides an introduction to contemporary ontology - the study of what exists - and its importance for philosophy today. He covers the key topics in the field, from the ontology of holes, numbers and possible worlds, to space, time and the ontology of material objects - for instance, whether there are composite objects such as tables, chairs or even you and me. While starting from the basics, every chapter (...) is up-to-date with the most recent developments in the field, introducing both longstanding theories and cutting-edge advances. As well as discussing the latest issues in ontology, Effingham also helpfully deals in-depth with different methodological principles and introduces them alongside an example ontological theory that puts them into practice. This accessible and comprehensive introduction will be essential reading for upper-level undergraduate and post-graduate students, as well as any reader interested in the present state of the subject. (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 (...) class='Hi'>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)

Numerous research groups are now utilizing Basic Formal Ontology as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three existing BFO subcategories of realizable entity, namely function, role, and disposition. It proposes one further sub-category of tendency, and considers the merits of recognizing two sub-categories of function for domain ontologies, namely, artifactual and biological function. The motivation is to help advance the coherent ontological treatment of functions, (...) roles, and dispositions, to help provide the potential for more detailed classification, and to shed light on BFO’s general make-up and use. (shrink)

BACKGROUND -/- In biomedical ontologies, mereological relations have always been subject to special interest due to their high relevance in structural descriptions of anatomical entities, cells, and biomolecules. This paper investigates two important subrelations of has_proper_part, viz. the relation has_grain, which relates a collective entity to its multiply occurring uniform parts (e.g., water molecules in a portion of water), and the relation has_component, which relates a compound to its constituents (e.g., molecules to the atoms they consist of). -/- METHOD -/- (...) We distinguish between four kinds of complex entities and characterize them in first order logic. We then discuss whether similar characterizations could be given in description logics, and finally apply the results to mixtures. -/- RESULTS -/- At first sight, collectives and compounds seem to be disjoint categories. Their disjointness, however, relies on agreement about what are uniform entities, and thus on the granularity of description. For instance, the distinction between isomeric subtypes of a molecule can be important in one use case but might be neglected in another one. We demonstrate that, as implemented in the BioTop domain upper level ontology, equivalence or subsumption between different descriptions of same or similar entities cannot be achieved. Using OWL-DL, we propose a new design pattern that avoids primitive subrelations at the expense of more complex descriptions and thus supports the needed inferences. (shrink)

This article describes an ontological model of norms. The basic assumption is that a substantial part of a legal system is grounded on the concept of agency. Since a legal system aims at regulating a society, then its goal can be achieved only by affecting the behaviour of the members of the society. We assume that a society is made up of agents (which can be individuals, institutions, software programs, etc.), that agents have beliefs, goals and preferences, and that they (...) commit to intentions in order to choose a line of behaviour. The role of norms, within a legal system, is to specify how and when the chosen behaviour agrees with the basic principles of the legal system. In this article, we show how a model based on plans can be the basis for the ontological representation of norms, which are expressed as constraints on the possible plans an agent may choose to guide its behaviour. Moreover, the paper describes how the proposed model can be linked to the upper level of a philosophically well-founded ontology (DOLCE); in this way, the model is set in a wider perspective, which opens the way to further developments. (shrink)

The purpose of this article is to identify the most important factors and features in the evolution of thesauri and ontologies through a dialectic model. This model relies on a dialectic process or idea which could be discovered via a dialectic method. This method has focused on identifying the logical relationship between a beginning proposition, or an idea called a thesis, a negation of that idea called the antithesis, and the result of the conflict between the two ideas, called a (...) synthesis. During the creation of knowl­edge organization systems, the identification of logical relations between different ideas has been made possible through the consideration and use of the most influential methods and tools such as dictionaries, Roget’s Thesaurus, thesaurus, micro-, macro- and metathesauri, ontology, lower, middle and upper level ontologies. The analysis process has adapted a historical methodology, more specifically a dialectic method and documentary method as the reasoning process. This supports our arguments and synthesizes a method for the analysis of research results. Confirmed by the research results, the principle of unity has shown to be the most important factor in the development and evolution of the structure of knowl­edge organization systems and their types. There are various types of unity when considering the analysis of logical relations. These include the principle of unity of alphabetical order, unity of science, semantic unity, structural unity and conceptual unity. The results have clearly demonstrated a movement from plurality to unity in the assembling of the complex structure of knowl­edge organization systems to increase information and knowl­edge storage and retrieval performance. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease (...) Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (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)

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)

In most computational ontologies, information inheritance is based on the taxonomic relation is_a. A given type inherits from other type only if the latter subsumes the former. We assume, however, that inheritance can be related, not only to the taxonomic relation, but also to the meronymic relationship between parts and wholes. The main aim of this paper is to organise upper-level ontologies associated with lexical information by taking into account part-whole subsumption. As we consider that parts may subsume (...) wholes under specific conditions, ontologies can be defined in terms of systems in which wholes inherit information from its parts. In this article, we describe how part-whole subsumption and, then, meronymic inheritance can be used to deal with type mismatch and metonymic interpretation of polysemous nouns. For this purpose, we attempt to merge old assumptions from both formal ontology and lexical semantics into a homogeneous framework. (shrink)

Ontology engineering is mainly done by domain experts who are specialists in their domain but have, if at all, limited knowledge in logics, computer science, or analytic philosophy. The literature on formal ontologies and biomedical ontologies is neither suited nor intended to serve as an educational resource that would help domain experts to become good ontologists. Existing educational resources focus rather on ontology tools and languages than on good practice. The purpose of the GoodOD guideline is to pave (...) the road for domain experts who want (or need) to become ontology engineers. It pursues the openly pragmatic approach that ontology engineers only need to know ontology theory to the extent which supports the (measurable) outcome of their work. The GoodOD Guideline builds upon given philosophical and methodological principles as well as preexisting tools and resources. In particular (pragmatic) scientific realism, first order logics and its subset OWL-DL (description logics), set theory, an upper-level ontology with high-level categories and a canonic set of relations, constraints which limit the freedom of choice when building coordinate expressions, the ontology editor Protégé 4, a complete DL reasoner, such as HermIT, ontology design patterns, and naming conventions. -/- Given these precepts the guideline contains all the knowledge to be acquired by a user to be able to solve ontology engineering problems in a foreseeable and non-arbitrary way. The didactic concept is to convey the skills not only by theory but also by practical examples. (shrink)

The purpose of this article is to delineate the process of evolution of know­ledge organization systems (KOSs) through identification of principles of unity such as internal and external unity in organizing the structure of KOSs to achieve content storage and retrieval purposes and to explain a novel method used in ranking of KOSs by proposing the principle of rank unity. Different types of KOSs which are addressed in this article include dictionaries, Roget’s thesaurus, thesauri, micro, macro, and meta-thesaurus, ontologies, and (...) lower, middle, and upper-level ontologies. This article relied on dialectic models to clarify the ideas in Kant’s know­ledge theory. This is done by identifying logical relationships between categories (i.e., Thesis, antithesis, and synthesis) in the creation of data, information, and know­ledge in the human mind. The Analysis has adapted a historical methodology, more specifically a documentary method, as its reasoning process to propose a conceptual model for ranking KOSs. The study endeavors to explain the main elements of data, information, and know­ledge along with engineering mechanisms such as data, information, and know­ledge engineering in developing the structure of KOSs and also aims to clarify their influence on content storage and retrieval performance. KOSs have followed related principles of order to achieve an internal order, which could be examined by analyzing the principle of internal unity in know­ledge organizations. The principle of external unity leads us to the necessity of compatibility and interoperability between different types of KOSs to achieve semantic harmonization in increasing the performance of content storage and retrieval. Upon introduction of the principle of rank unity, a ranking method of KOSs utilizing cognition states as criteria could be considered to determine the position of each know­ledge organization with respect to others. The related criteria of the principle of rank unity- cognition states- are derived from Immanuel Kant’s epistemology. The research results showed that KOSs, while having defined positions in cognition states, specific principles of order, related operational mechanisms, and related principles of unity in achieving their specific purposes, have benefited from the developmental experiences of previous KOSs, and further, their developmental processes owe to the experiences and methods of their previous generations. (shrink)

This book explores both scientific and humanistic theoretical traditions in anthropology through the lens of ontology. The first part of the book examines different methods for generating valid anthropological knowledge, and proposes a shift in current consensus. Drawing on western scholars of antiquity and the medieval period and moving away from twentieth century theorists, it argues that we must first make ontological assumptions about the kinds of things that can exist (or not) before we can then develop epistemologies that (...) study those kinds of things. The book goes on to apply the ontology-first theory to a set of case studies in modern day conspiracy theories, misinformation, and magical thinking. It asserts that we need to move away from unneeded metaphysical assumptions of conspiracy theories being misinformation, and argues that reconstructing particular historical events can be a fruitful zone for application of quantitative methods to humanistic questions. Theorizing the Anthropology of Belief is an excellent supplementary suitable for upper-level undergraduate and graduate courses in anthropological theory. (shrink)

Ontologies are some of the most central constructs in today's large plethora of knowledge technologies, namely in the context of the semantic web. As their coinage indicates, they are direct heirs to the ontological investigations in the long Western philosophical tradition, but it is not easy to make bridges between them. Contemporary ontological commitments often take causality as a central aspect for the ur-segregation of entities, especially in scientific upper ontologies; theories of causality and philosophical ontological investigations often go (...) hand-in-hand, and were essentially inseparable in medieval thought. This constitutes the foundation for a bridge, and this article analyzes the causality-based ontology of the late medieval philosopher Dietrich of Freiberg from the viewpoint of today's upper-ontology engineering. In this bridging attempt, it offers a translation into English of the first part of Dietrich's De origine (abbreviated title) that is a compromise between traditional scholarly translations of medieval Latin philosophical texts and contemporary ontology. (shrink)

Scientists and philosophers frequently speak about levels of description, levels of explanation, and ontological levels. In this paper, I propose a unified framework for modelling levels. I give a general definition of a system of levels and show that it can accommodate descriptive, explanatory, and ontological notions of levels. I further illustrate the usefulness of this framework by applying it to some salient philosophical questions: (1) Is there a linear hierarchy of levels, with a fundamental level at the bottom? (...) And what does the answer to this question imply for physicalism, the thesis that everything supervenes on the physical? (2) Are there emergent properties? (3) Are higher-level descriptions reducible to lower-level ones? (4) Can the relationship between normative and non-normative domains be viewed as one involving levels? Although I use the terminology of “levels”, the proposed framework can also represent “scales”, “domains”, or “subject matters”, where these are not linearly but only partially ordered by relations of supervenience or inclusion. (shrink)

Scientists and philosophers frequently speak about levels of description, levels of explanation, and ontological levels. This paper presents a framework for studying levels. I give a general definition of a system of levels and discuss several applications, some of which refer to descriptive or explanatory levels while others refer to ontological levels. I illustrate the usefulness of this framework by bringing it to bear on some familiar philosophical questions. Is there a hierarchy of levels, with a fundamental level at (...) the bottom? And what does the answer to this question imply for physicalism, the thesis that everything supervenes on the physical? Are there emergent higher-level properties? Are higher-level descriptions reducible to lower-level ones? Can the relationship between normative and non-normative domains be viewed as one involving levels? And might a levelled framework shed light on the relationship between third-personal and first-personal phenomena? (shrink)

This collection of essays, first published two decades ago, presents central feminist critiques and analyses of natural and social sciences and their philosophies. Unfortunately, in spite of the brilliant body of research and scholarship in these fields in subsequent decades, the insights of these essays remain as timely now as they were then: philosophy and the sciences still presume kinds of social innocence to which they are not entitled. The essays focus on Plato, Aristotle, Descartes, Hobbes, Rousseau, and Marx; on (...) the 'adversary method' model of philosophic reasoning; on principles of individuation on philosophical ontology and philosophy of language; on individualistic assumptions in psychology; functionalism in sociological and biological theory; evolutionary theory; the methodology of political science; and conceptions of objective inquiry in the sciences. In taking insights of both Liberal and Marxian women's movements into the purportedly most abstract and value-free areas of Western thought, these essays chart sexist and androcentric assumptions, claims and practices in the cognitive, technical cores of Western sciences and their philosophies. They begin to identify the distinctive aspects of women's experiences and locations in male-supremacist social structures which can provide resources needed for the creation of post-androcentric thinking in research, scholarship, and public policy. Such uses of feminist insights remain controversial today, and even among some feminists. These authors were all junior researchers and scholars two decades ago; today many are among the most distinguished senior scholars in their fields. Their work here provides a splendid opportunity for upper-level undergraduate and graduate students in philosophy and the social sciences to explore some of the most intriguing and controversial challenges to disciplinary projects and to public policy today. (shrink)

Time: A Philosophical Introduction presents the philosophy of time as the central debate between being and the becoming.This core theme brings together the key topics, debates and thinkers, making ideas such as Zeno's paradoxes, the experience of change and temporal flow and the direction and shape of time and time travel, clear and understandable. Alongside a glossary and detailed timeline to further enhance study and understanding, each chapter features: • Extensive lists of further reading in both primary and secondary sources (...) • A chronological listing of key figures, brief biographical data and references • True/false questions, matching, multiple choice, and short answer questions Time is a central philosophical subject, impacting on all many different aspects of philosophy. More technical discussions of issues from mathematics, logic and physics are separated into Technical Interludes,allowing readers to choose their level of difficultly. As a result this comprehensive introduction is essential reading for upper-level undergraduates studying the philosophy of time,metaphysics or the philosophy of science. (shrink)

It is common in contemporary metaphysics to distinguish two levels of ontology: the ontology of ordinary objects and the ontology of fundamental reality. This papers argues that natural language reflects not only the ontology of ordinary objects, but also a language-driven ontology, which is involved in the mass-count distinction and part-structure-sensitive semantic selection, as well as perhaps the light ontology of pleonastic entities. The paper recasts my older theory of situated part structures without situations, (...) making use of a primitive notion of unity. (shrink)

What is mathematics about? Does the subject-matter of mathematics exist independently of the mind or are they mental constructions? How do we know mathematics? Is mathematical knowledge logical knowledge? And how is mathematics applied to the material world? In this introduction to the philosophy of mathematics, Michele Friend examines these and other ontological and epistemological problems raised by the content and practice of mathematics. Aimed at a readership with limited proficiency in mathematics but with some experience of formal logic it (...) seeks to strike a balance between conceptual accessibility and correct representation of the issues. Friend examines the standard theories of mathematics - Platonism, realism, logicism, formalism, constructivism and structuralism - as well as some less standard theories such as psychologism, fictionalism and Meinongian philosophy of mathematics. In each case Friend explains what characterises the position and where the divisions between them lie, including some of the arguments in favour and against each. This book also explores particular questions that occupy present-day philosophers and mathematicians such as the problem of infinity, mathematical intuition and the relationship, if any, between the philosophy of mathematics and the practice of mathematics. Taking in the canonical ideas of Aristotle, Kant, Frege and Whitehead and Russell as well as the challenging and innovative work of recent philosophers like Benacerraf, Hellman, Maddy and Shapiro, Friend provides a balanced and accessible introduction suitable for upper-level undergraduate courses and the non-specialist. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:Shopping for Meaningful Lives: The Religious Motive of Consumerism by Bruce P. RittenhouseIlsup AhnShopping for Meaningful Lives: The Religious Motive of Consumerism Bruce P. Rittenhouse eugene, or: cascade, 2013. 211 pp. $33.00Are there any theories of consumerism that characterize people’s lives on a global scale? What motivates them to choose a consumerist lifestyle? If possible, how can we overcome this lifestyle that entails destructive consequences? In this new (...) book, Shopping for Meaningful Lives, Bruce Rittenhouse answers these questions by critically appropriating Paul Tillich’s theological insights. He first diagnoses consumerism as “not only a pattern of behavior that characterizes an individual life, but a way in which an individual organizes his or her particular life to seek to give it meaning” (3). It is thus more insidious than the mere acquisition of goods and services in ever-increasing amounts because humans are not meant to be mere consuming animals. [End Page 196]In attempting to deconstruct consumerism, Rittenhouse first points out that it has been poorly understood despite its seeming ubiquity. He launches his own investigation to look for possible theories of consumerism, which he then evaluates according to a consistent set of empirical criteria. In chapter 3 he enumerates five main types that describe Western consumerism: “1, greed, i.e., consumers’ intemperate materialistic hedonism; 2, status signaling, i.e., consumers’ desire to communicate superior social status; 3, manipulation of consumer by the producers of economic goods through marketing and advertising; 4, imaginative hedonism, i.e., consumers’ seeking emotional pleasure through the imaginative identities; 5, parental concern, i.e., parents’ desire to maximize their children’s well-being” (47). According to Rittenhouse, these five theories of the motivations for consumerism provide anecdotal support to demonstrate their practical relevance, but they “fall short of demonstrating their theories’ empirical possibility, let alone their empirical superiority over the rival theories” (95).Rittenhouse’s alternative theory is then developed in chapter 5, after he provides empirical evidence (including economic charts and analyses) for his own critique in chapter 4. His years of experience as a professional economist aptly qualify him to develop his social-scientific argumentation. Rittenhouse’s constructive proposal is hinged upon his critical insight that consumerism’s motivation may best be understood as religious. By religious, he means that it “answers a question posed by the nature of human existence” (132). Consumerism is now newly understood both as existential and as religious matter, and here Rittenhouse critically appropriates Tillich’s ontotheological categories and concepts, such as the three pairs of ontological elements in the self-world structure of being (individuation and participation, dynamics and form, and freedom and destiny). Since consumerism’s motivation is existential and religious, Rittenhouse attempts to resolve the moral and religious failings of consumerism by demonstrating the “correlation between the existential question of meaning and the answer of existential Christian faith” (133).Rittenhouse concludes his book by calling for existential conversion through the means of grace—that is, “the means of conversion to existential Christian faith and of ongoing conversion within ambiguous existential Christian faith” (175). The strength of this book lies in his discovery that consumerism is a spurious form of religious life that only destroys those who are intoxicated by its lifestyle. Given that consumerism has taken root everywhere affected by ever rising globalization, Rittenhouse’s existential investigation and theological remedy are definitely a welcome voice in the field of Christian ethics. His expertise in social-scientific study and empirical analysis is also a rare strength in this important pursuit. This book is well suited for upper-level college students as well as seminarians and theological school students. It is also a wonderful text for adult Bible study groups in churches and religious communities. [End Page 197]Ilsup AhnNorth Park UniversityCopyright © 2015 Society of Christian Ethics... (shrink)

Functional reductionism characterises inter-theoretic reduction as the recovery of the upper-level behaviour described by the reduced theory in terms of the lower-level reducing theory. For instance, finding a statistical mechanical realiser that plays the functional role of thermodynamic entropy allows for establishing a reductive link between thermodynamics and statistical mechanics. This view constitutes a unique approach to reduction that enjoys a number of positive features, but has received limited attention in the philosophy of science. -/- This paper (...) aims to clarify the meaning of functional reductionism in science, with a focus on physics, to define both its place with respect to other approaches to reduction and its connection to ontology. To do so, we develop and explore two alternative frameworks for functional reduction, called Syntactic Functional Reductionism and Semantic Functional Reductionism. They represent two different possible stances on the view that expand and improve the basic functional reductionist approach along different lines, and make clear how the approach works in practice. The former elaborates on David Lewis’ account, is connected with the syntactic view of theories, is committed to a logical characterisation of functional roles, and is embedded within Nagelian reductionism. The latter adopts a semantic view of theories, spells out functional roles mainly in terms of mathematical roles within the models of theories, and is expressed in terms of the related structuralist approach to reduction. The development of these frameworks has the final goal of advancing functional reductionism, to make it a fully-fledged alternative account for reduction in science. (shrink)

An overview of the following three related papers in this issue presents the Emergence of Highly Complex Systems such as living organisms, man, society and the human mind from the viewpoint of the current Ontological Theory of Levels. The ontology of spacetime structures in the Universe is discussed beginning with the quantum level; then, the striking emergence of the higher levels of reality is examined from a categorical—relational and logical viewpoint. The ontological problems and methodology aspects discussed in (...) the first two papers are followed by a rigorous paper based on Category Theory, Algebraic Topology and Logic that provides a conceptual and mathematical basis for a Categorical Ontology Theory of Levels. The essential links and relationships between the following three papers of this issue are pointed out, and further possible developments are being considered. (shrink)

The status of risk factors and disease remains a disputed question in the theory and practice of medicine and healthcare, and so does the related question of delineating disease boundaries. I present a framework based on Bernard Lonergan’s account of emergent probability for differentiating (1) generically distinct levels of systematic function within organisms and between organisms and their environments and (2) the methods of functional, genetic, and statistical investigation. I then argue on this basis that it is possible to understand (...) disease in terms of biological or higher intra-level dysfunction, risk factors—including genetic risk factors—in terms of statistical inter-level conditioning of a given stage or developmental sequence of systematic functioning, and the empirical boundaries of disease in terms of the limits of both functional categorization (from an epistemic standpoint) and upper-level integration of lower-level processes and events (from an ontological standpoint). (shrink)

I present—in an extremely sketchy form—a model of two-level, open, plastic and multidimensional human nature. Due to the included attribute of multidimensionality this model opposes the reductive conceptions of man dominating in today’s philosophy. The main objective of the paper is the ontological status of man, especially the ontic foundation of multidimensional man. I demonstrate that this status remains a riddle; one only knows that from the ontological perspective man is a wholly exceptional object, not explainable by to-date ontological (...) constructions. -/- . (shrink)

On March 14-15, 2006, at the US National Institute of Standards and Technology (NIST) in Gaithersburg, MD there took place the first Upper Ontology Summit (UOS). This was a convening of custodians of several prominent upper ontologies, key technology participants, and interested other parties, with the purpose of finding a means to relate the different ontologies to each other. The result is reflected in a joint communiqué, directed to the larger ontology community and the general public, (...) and expressing a joint intent to build bridges among the existing upper ontologies in ways designed to increase and rationalize their utilization and to enhance their semantic interoperability. (shrink)

An overview of the following three related papers in this issue presents the Emergence of Highly Complex Systems such as living organisms, man, society and the human mind from the viewpoint of the current Ontological Theory of Levels. The ontology of spacetime structures in the Universe is discussed beginning with the quantum level; then, the striking emergence of the higher levels of reality is examined from a categorical—relational and logical viewpoint. The ontological problems and methodology aspects discussed in (...) the first two papers are followed by a rigorous paper based on Category Theory, Algebraic Topology and Logic that provides a conceptual and mathematical basis for a Categorical Ontology Theory of Levels. The essential links and relationships between the following three papers of this issue are pointed out, and further possible developments are being considered. (shrink)

An overview of the following three related papers in this issue presents the Emergence of Highly Complex Systems such as living organisms, man, society and the human mind from the viewpoint of the current Ontological Theory of Levels. The ontology of spacetime structures in the Universe is discussed beginning with the quantum level; then, the striking emergence of the higher levels of reality is examined from a categorical—relational and logical viewpoint. The ontological problems and methodology aspects discussed in (...) the first two papers are followed by a rigorous paper based on Category Theory, Algebraic Topology and Logic that provides a conceptual and mathematical basis for a Categorical Ontology Theory of Levels. The essential links and relationships between the following three papers of this issue are pointed out, and further possible developments are being considered. (shrink)