While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through (...) which semantic similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results. (shrink)

The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of (...) these relations and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies. (shrink)

Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (...) (i.e., they belong to the domain of epistemology). We analyze terms from several biomedical vocabularies in order to throw light on the interactions between ontological and epistemological components of these terminologies. We identify four cases: 1) terms containing classification criteria, 2) terms reflecting detectability, modality, uncertainty, and vagueness, 3) terms created in order to obtain a complete partition of a given domain, and 4) terms reflecting mere fiat boundaries. We show that epistemology-loaded terms are pervasive in biomedical vocabularies, that the “classes” they name often do not comply with sound classification principles, and that they are therefore likely to cause problems in the evolution and alignment of terminologies and associated ontologies. (shrink)

The goal of the Department of Defense Net-Centric Data Strategy is to improve data sharing throughout the DoD. Data sharing is a critical element of interoperability in the emerging system-of-systems. Achieving interoperability requires the elimination of two types of data heterogeneity: differences of syntax and differences of semantics. This paper builds a path toward semantic uniformity through application of a disciplined approach to ontology. An ontology is a consensus framework representing the types of entities within a given domain (...) and the relations between them. The construction of an ontology begins when a Community of Interest (COI) identifies its authoritative data sources (ADS), which are usually manifest in relevant doctrinal publications, glossaries, data dictionaries, and logical data models. The identified terms are then defined in relation to a common logical framework that has been designed to ensure interoperability with other ontologies created on the basis of the same strategy. As will be described, the Command and Control (C2) Ontology will include representations of a substantial number of entities within the Command and Control (C2) domain. If domain ontologies (e.g. Strike and Counterinsurgency) semantically align with the C2 Ontology, then a substantial barrier to systems interoperability is thereby crossed. (shrink)

The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and relations dedicated (...) to the salivaomics domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry. The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB. Background Saliva (oral fluid) is an emerging biofluid for non-invasive diagnostics used in the detection of human diseases. The need to advance saliva research is strongly emphasized by the National Institute of Dental and Craniofacial Research (NIDCR), and is included in the NIDCR's 2004- 2009 expert panel long-term research agenda [1]. The ability to monitor health status, disease onset, progression, recurrence and treatment outcome through noninvasive means is highly important to advancing health care management. Saliva is a perfect medium to be explored for personalized individual medicine including diagnostics, offering a non-invasive, easy to obtain means for detecting and monitoring diseases. Saliva testing potentially allows the patient to collect their own saliva samples at home, yielding convenience for the patient and savings in health costs, and facilitating multiple sampling. Specimen collection is less objectionable to patients and easier in children and elderly individuals. Due to these advantages. (shrink)

Ontological pluralism is the view that there are different ways of being. Historically, ways of being are aligned with the ontological categories. This paper is about to investigate why there is such a connection, and how it should be understood. Ontological pluralism suffers from an objection, according to which ontological pluralism collapses into ontological monism, i.e., there is only one way to be. Admitting to ontological categories can save ontological pluralism from this objection if ways of being ground ontological categories. (...) -/- . (shrink)

In conceptual modeling (CM) as a subdiscipline of software engineering, current proposed ontologies (categorical analysis of entities) are typically established through whole adoption of philosophical theories (e.g. Bunge’s). In this paper, we pursue an interdisciplinary research approach to develop a diagrammatic-based ontological foundation for CM using philosophical ontology as a secondary source. It is an endeavor to escape an offshore procurement of ontology from philosophy and implant it in CM. In such an effort, the CM diagrammatic language plays (...) an important role in contrast to dogmatic philosophical languages’ obsession with abstract entities. Specifically, this paper is about developing a descriptive (in contrast to formal) ontology that a modeler accepts as a supplementary account of reality when using thinging machines (TMs; i.e. a reality that uncovers the ontology of things that TM modeling discusses or “talks about,” akin to the ontology of natural language). Although existence is a well-established notion, we defend subsistence (Stoic term) as a supplementary mode of reality (e.g. reflection of event). The aim here is aligned toward developing CM notions and processes that are firm enough. Classical analysis of being per se (e.g. identity, substance, classes, objects) is de-emphasized in this work; nevertheless, philosophical concepts form an acknowledged authority to compare to. As a case study, such a methodology is applied to the notion of information that provides a common-sense understanding of the world. This application would enhance understanding of the TM methodology and clarify some of the issues that shed light on the question of the nature of information as an important concept in software engineering. Information is defined as about events; that is, it is about existing things. It is viewed as having a subsisting nature that exists only through being “carried on” by other things. The results seem to indicate a promising approach to define information and understand its nature. (shrink)

Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques (...) such as ontology-based multi-database querying, automated ontology alignment and ontology-based text-mining. These theses are illustrated by means of a case study of the Gene Ontology, a project of increasing importance within the field of biomedical data integration. (shrink)

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

Recent years have seen rapid progress in the development of ontologies as semantic models intended to capture and represent aspects of the real world. There is, however, great variation in the quality of ontologies. If ontologies are to become progressively better in the future, more rigorously developed, and more appropriately compared, then a systematic discipline of ontology evaluation must be created to ensure quality of content and methodology. Systematic methods for ontology evaluation will take into account representation of (...) individual ontologies, performance (in terms of accuracy, domain coverage and the efficiency and quality of automated reasoning using the ontologies) on tasks for which the ontology is designed and used, degree of alignment with other ontologies and their compatibility with automated reasoning. A sound and systematic approach to ontology evaluation is required to transform ontology engineering into a true scientific and engineering discipline. This chapter discusses issues and problems in ontology evaluation, describes some current strategies, and suggests some approaches that might be useful in the future. (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)

This article examines the ontology and politics of Peter Sloterdijk's Spheres trilogy, focusing in particular upon the notion of microspherical enclosure explicated in the first volume of this series. Noting Sloterdijk's unusual alignment of his philosophy with media theory, three main contentions are put forward. Firstly, that Sloterdijk's reconfiguration of Heidegger's fundamental ontology represents a largely unacknowledged renunciation of the primacy of Being-towards-death in the authentic existence of Dasein, foregrounding instead an originary co-belonging between mother and child. (...) Secondly, that Sloterdijk borrows from media theory a concern regarding the facticity of all communication, grounding philosophical discourse in the determinate locality of its origin, but does so while exalting a pre-natal communicative immediacy that would seem to disparage the everydayness of Dasein. Finally, that Sloterdijk's oft-justified scepticism regarding globalization often retreats into an anti-cosmopolitanism that, in its nostalgia for the comfort, security and immediacy of the matrixial co-belonging, evinces a covert but potentially noxious politics of exclusion. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical (...) data analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist (...) framework for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (shrink)

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

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational (...) modification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of (...) domain ontologies in anatomy, physiology and pathology. (shrink)

The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the (...) naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable. (shrink)

Ontologies are being ever more commonly used in biomedical informatics and we provide a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonised. We argue that one key foundation for both ontology evaluation and harmonisation is the adoption of a realist paradigm (...) in ontology development. For science-based ontologies of the sort which concern us in the eHealth arena, it is reality that provides the common benchmark against which ontologies can be evaluated and aligned within larger frameworks. Given the current multitude of ontologies in the biomedical domain the need for harmonisation is becoming ever more urgent. We describe one example of such harmonisation within the ACGT project, which draws on ontology-based computing as a basis for sharing clinical and laboratory data on cancer research. (shrink)

Ontologies are today being applied in almost every field to support the alignment and retrieval of data of distributed provenance. Here we focus on new ontological work on dance and on related cultural phenomena belonging to what UNESCO calls the “intangible heritage.” Currently data and information about dance, including video data, are stored in an uncontrolled variety of ad hoc ways. This serves not only to prevent retrieval, comparison and analysis of the data, but may also impinge on our (...) ability to preserve the data that already exists. Here we explore recent technological developments that are designed to counteract such problems by allowing information to be retrieved across disciplinary, cultural, linguistic and technological boundaries. Software applications such as the ones envisaged here will enable speedier recovery of data and facilitate its analysis in ways that will assist both archiving of and research on dance. (shrink)

When the U.S. conducts warfare, elements of a force are drawn from different services and work together as a single team to accomplish an assigned mission. To achieve such unified action, it is necessary that the doctrines governing the actions of members of specific services be both consistent with and subservient to joint Doctrine. Because warfighting today increasingly involves not only live forces but also automated systems, unified action requires that information technology that is used in joint warfare must be (...) aligned with joint doctrine. It requires also that the separate information systems used by the different elements of a joint force must be interoperable, in the sense that data and information that is generated by each element must be usable (understandable, processable) by all the other elements that need them. Currently, such interoperability is impeded by multiple inconsistencies among the different data and software standards used by warfighters. We describe here the on-going project of creating a Joint Doctrine Ontology (JDO), which uses joint doctrine to provide shared computer-accessible content valid for any field of military endeavor, organization, and information system. JDO addresses the two previously mentioned requirements of unified action by providing a widely applicable benchmark for use by developers of information systems that will both guarantee alignment with joint doctrine and support interoperability. (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)

Background: Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. Results: (...) We present computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Conclusion: Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation. (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and (...) challenging, agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

This article presents a simple derivation of optimization models for reaction networks leading to a generalized form of the mass-action law, and compares the formal structure of Minimum Information Divergence, Quadratic Programming and Kirchhoff type network models. These optimization models are used in related articles to develop and illustrate the operation of ontology alignment algorithms and to discuss closely connected issues concerning the epistemological and statistical significance of sharp or precise hypotheses in empirical science.

SNODENT is a dental diagnostic vocabulary incompletely integrated in SNOMED-CT. Nevertheless, SNODENT could become the de facto standard for dental diagnostic coding. SNODENT's manageable size, the fact that it is administratively self-contained, and relates to a well-understood domain provides valuable opportunities to formulate and test, in controlled experiments, a series of hypothesis concerning diagnostic systems. Of particular interest are questions related to establishing appropriate quality assurance methods for its optimal level of detail in content, its ontological structure, its construction and (...) maintenance. This paper builds on previous–software-based methodologies designed to assess the quality of SNOMED-CT. When applied to SNODENT several deficiencies were uncovered. 9.52% of SNODENT terms point to concepts in SNOMED-CT that have some problem. 18.53% of SNODENT terms point to SNOMED-CT concepts do not have, in SNOMED, the term used by SNODENT. Other findings include the absence of a clear specification of the exact relationship between a term and a termcode in SNODENT and the improper assignment of the same termcode to terms with significantly different meanings. An analysis of the way in which SNODENT is structurally integrated into SNOMED resulted in the generation of 1081 new termcodes reflecting entities not present in the SNOMED tables but required by SNOMED's own description logic based classification principles. Our results show that SNODENT requires considerable enhancements in content, quality of coding, quality of ontological structure and the manner in which it is integrated and aligned with SNOMED. We believe that methods for the analysis of the quality of diagnostic coding systems must be developed and employed if such systems are to be used effectively in both clinical practice and clinical research. (shrink)

As the international momentum of the school effectiveness movement continues, its exponents remain largely impervious to criticism. This paper argues that while they may not readily align themselves with the individualistic aspects of Conservative social philosophy, their methodology necessarily secretes an atomised social ontology. The charge of ideological commitment rests on the fact that the essentially positivist epistemology employed by school effectiveness researchers presupposes an ontology of closed systems and atomistic events. Thus any notion of the structuring of (...) life‐chances is automatically ruled out of court. The reciprocity of social ontology and methodology is explored in order to account for the myopia of the school effectiveness movement. (shrink)

Gender classifications often are controversial. These controversies typically focus on whether gender classifications align with facts about gender kind membership: Could someone really be nonbinary? Is Chris Mosier really a man? I think this is a bad approach. Consider the possibility of ontological oppression, which arises when social kinds operating in a context unjustly constrain the behaviors, concepts, or affect of certain groups. Gender kinds operating in dominant contexts, I argue, oppress trans and nonbinary persons in this way: they marginalize (...) trans men and women, and exclude nonbinary persons. As a result, facts about membership in dominant gender kinds should not settle gender classification practices. (shrink)

What justifies one interlocutor to challenge the conversational expectations of the other? Paul Grice approaches conversation as one instance of joint action that, like all such action, is governed by the Cooperative Principle. He thinks the expectations of the interlocutors must align, although he acknowledges that expectations can and do shift in the course of a conversation through a process he finds strange. Martin Heidegger analyzes discourse as governed by the normativity of care for self and for another. It is (...) the structure of care that warrants disrupting the presumed cooperative horizon of a conversation in order to occasion some new insight. The chapter expands Heidegger’s ontological conception of care to make sense of the exigencies of conversation. Conversation requires taking cognizance of (1) the human good, (2) the specifics of the conversational context, and (3) one’s responsibilities for the other. This threefold understanding can provide directives for subverting the interlocutor’s expectation for the purposes of a given conversation. (shrink)

Holobionts are symbiotic assemblages composed by a macrobe host plus its symbiotic microbiota. In recent years, the ontological status of holobionts has created a great amount of controversy among philosophers and biologists: are holobionts biological individuals or are they rather ecological communities of independent individuals that interact together? Chiu and Eberl have recently developed an eco-immunity account of the holobiont wherein holobionts are neither biological individuals nor ecological communities, but hybrids between a host and its microbiota. According to their account, (...) the microbiota is not a proper part of the holobiont. Yet, it should be regarded as a set of scaffolds that support the individuality of the host. In this paper, we approach Chiu and Eberl’s account from a metaphysical perspective and argue that, contrary to what the authors claim, the eco-immunity account entails that the microorganisms that compose the host’s microbiota are proper parts of the holobiont. Second, we argue that by claiming that holobionts are hybrids, and therefore, not biological individuals, the authors seem to be assuming a controversial position about the ontology of hybrids, which are conventionally characterized as a type of biological individual. In doing so, our paper aligns with the contemporary tendency to incorporate metaphysical resources to shed light on current biological debates and builds on that to provide additional support to the consideration of holobionts as biological individuals from an eco-immunity perspective. (shrink)

TWENTIETH-CENTURY ETHICS. AFTER NIETZSCHE -/- Preface This book tells the story of twentieth-century ethics or, in more detail, it reconstructs the history of a discussion on the foundations of ethics which had a start with Nietzsche and Sidgwick, the leading proponents of late-nineteenth-century moral scepticism. During the first half of the century, the prevailing trends tended to exclude the possibility of normative ethics. On the Continent, the trend was to transform ethics into a philosophy of existence whose self-appointed task was (...) that of describing the human condition as consisting of choices, as unavoidable as arbitrary, without any attempt at providing criteria for making such choices. In the Anglo-Saxon countries, the heir of ethics was a philosophy of morality, that is, an analysis of the language of morality that intended to clarify valuations without trying to justify them. 1958 was the year of the normative turn that led to the Rehabilitation of practical philosophy, a turn followed by decades of controversies between distinct kinds of normative ethics: utilitarian, Kantian, virtue ethics. While the controversy was raging, a quiet revolution took place, that of applied ethics which surprisingly dissolved the controversy's very subject matter by providing methods for making convergence possible on intermediate principles even when no agreement was available about first principles. The normative turn and the revolution of applied ethics have led us, at the turn of the century, to a goal that was quite far from the starting point. Instead of scepticism and relativism that was the fashion at the beginning of the century, at the beginning of the third millennium impartial and universal moral arguments seem to hold the spot being supported, if not by a final rational foundation, at least by reasonableness, the most precious legacy of the Enlightenment. -/- ● TABLE OF CONTENTS -/- ● I Anglo-Saxon philosophy: naturalism 1. Dewey beyond evolutionism and utilitarianism 2. Dewey and anti-essentialist moral epistemology 3. Dewey and naturalist moral ontology 4. Dewey and normative ethics of conduct and function 5. Perry and semantic naturalism -/- ● II Anglo-Saxon philosophy: ideal utilitarianism and neo-intuitionism 1. Moore's critique of utilitarian empiricism 2. Moore on the naturalistic fallacy 3. Moore on the nature of intrinsic value 4. Moore on ideal utilitarianism 5. Prichard on the priority of the right over the good 6. Ross's coherentist moral epistemology 7. Ross's moral ontology: realism, pluralism, and non-naturalism 8. Ross's normative ethics of prima facie duties -/- The chapter reconstructs the background of ideas, concerns and intentions out of which Moore's early essays, the preliminary version, and then the final version of Principia Ethica originated. It stresses the role of religious concerns, as well as that of the Idealist legacy. It argues that PE is more a patchwork of somewhat diverging contributions than a unitary work, not to say the paradigm of a new school in Ethics. -/- ●III Anglo-Saxon philosophy: non-cognitivism 1. The Scandinavian School, the Vienna circle and proto-emotivism 2. Wittgenstein and the ineffability of ethics 3. Russell's and Ayer's radical emotivism 4. Stevenson and moderate emotivism 5. Stevenson and the pragmatics of moral language 6. Stevenson and the methods for solving ethical disagreement 7. Hare and prescriptivism The chapter reconstructs first the discussion after Moore. The naturalistic-fallacy argument was widely accepted but twisted to prove instead that the intuitive character of the definition of 'good', its non-cognitive meaning, in a first phase identified with 'emotive' meaning. Alfred Julius Ayer is indicated as a typical proponent of such non-cognitivist meta-ethics. More detailed discussion is dedicated to Bertrand Russell's ethics, a more nuanced and sophisticated doctrine, arguing that non-cognitivism does not condemn morality to arbitrariness and that the project of rational normative ethics is still possible, heading finally to the justification of a kind of non-hedonist utilitarianism. Stevenson's theory, another moderate version of emotivism is discussed at some length, showing how the author comes close to the discovery of the role of a pragmatic dimension of language as a basis for ethical argument. A section reconstructs the discussion from the Forties about Hume's law, mentioning Karl Popper's argument and Richard Hare's early non-cognitivist but non-emotivist doctrine named prescriptivism. -/- ●IV Anglo-Saxon philosophy: critics of non-cognitivism 1. Neo-naturalism and its objections to the naturalistic fallacy argument 2. Objections to Hume's law 3. Clarence Lewis and the pragmatic contradiction 4. Toulmin and the good reasons approach 5. Baier and moral reasons 5. Baier, social moralities and the absolute morality 6. Baier and the moral point of view 7. Baier and the contents of absolute ethics -/- ● V Continental philosophy: the philosophy of values 1. Max Weber and the polytheism of values 2. Phenomenology against psychologism and rationalism 3. Reinach and the theory of social acts 4. Scheler and the material ethics of values 5. Hartmann and the ontology of values 6. Plessner, Gehlen and the Philosophische Anthropologie -/- The chapter illustrates first the idea of phenomenology and the Husserl's project of a phenomenological ethic as illustrated in his 1908-1914 lectures. The key idea is dismissing psychology and trying to ground a new science of the apriori of action, within which a more restricted field of inquiry will be the science of right actions. Then the chapter illustrates the criticism of modern moral philosophy conducted in the 1920 lectures, where the main target is naturalism, understood in the Kantian meaning of primacy of common sense. The third point illustrate is Adolph Reinach's theory of social acts as a key the grounding of norms, a view that sketches the ideas 'discovered' later by Clarence I. Lewis, John Searle, Karl-Otto Apel and Jürgen Habermas. A final section discusses Nicolai Hartman, who always refused to define himself a phenomenologist and yet developed a more articulated and detailed theory of 'values' – with surprising affinities with George E. Moore - than philosophers such as Max Scheler, who claimed to be Husserl's legitimate heirs. -/- ● VI Continental philosophy: the critics of the philosophy of values 1. Freud, the Superego and Civilization 2. Heidegger on original ethos against ethics 3. Sartre and de Beauvoir on authenticity and ambiguity 4. Adorno and Horkheimer on emancipation and immoralism -/- ●VII Post-liberal theologians and religious thinkers 1. Barth on the autonomy of faith from ethics 2. Developments of Reformed moral theology after Barth 3. Bonhoeffer on the concrete divine command and ethics of penultimate realities 4. Developments of Reformed and Catholic moral theology after world war II 5. Baeck and the transformation of liberal Judaism 6. Rosenzweig against liberal Judaism 7. Buber and religion as the vital lymph of morality 8. Heschel and Judaism as a science of actions -/- The chapter examines the main protagonists of Christian theology and Jewish religious thinking in the twentieth century. It stresses how the main dilemmas of contemporary philosophical ethics lie at the root of the various path of inquiry taken by these thinkers. -/- ● VIII Normative ethics: neo-Utilitarianism 1. The discussion on act and rule utilitarianism 2. Hare on two-tiered preference utilitarianism 3. Harsanyi, Gauthier and rational choice ethics 4. Parfit, utilitarianism and the idea of a person 5. Brandt and indirect conscience utilitarianism -/- The chapter addresses the issue of the complex process of self-transformation Utilitarianism underwent after Sidgwick's and Moore's fatal criticism and the unexpected Phoenix-like process of rebirth of a doctrine refuted. Two examples give the reader a glimpse at this uproarious process. The first is Roy Harrod Wittgensteinian transformation of utilitarianism in pure normative ethics depurated from hedonism as well as from whatsoever theory of the good. This transformation results in preference utilitarianism combined with a 'Kantian' version of rule utilitarianism. The second is Richard Hare's two-level preference utilitarianism, where act utilitarianism plays the function of the eventual rational justification of moral judgments and rule-utilitarianism that of an action-guiding practical device. -/- ● IX Normative ethics: neo-Aristotelianism and virtue ethics 1. Hannah Arendt, action and judgement 2. Hans-Georg Gadamer and phronesis 3. Alasdair MacIntyre on practices, virtues, and traditions 5. Stuart Hampshire on deliberation 6. Bernard Williams and moral complexity 7. Feminist ethics -/- Sect 1 reconstructs the post-war rediscovery of ethics by many German thinkers and its culmination in the Sixties in the movement named 'Rehabilitation of practical philosophy' is described. Heidegger's most brilliant disciples were the promoters of this Rehabilitation. Hans-Georg Gadamer is a paradigmatic example. His reading of Aristotle's lesson I reconstructed, starting with Heidegger's lesson but then subtly subverting its outcome thanks to the recovery of the significant role of the notion of phronesis. Sect 3 discusses the three theses defended by Anscombe in 'Modern Moral Philosophy'. It argues that: a) her answer to the question "why should I be moral?" requires a solution of the problem of theodicy, and ignores any attempts to save the moral point of view without recourse to divine retribution; b) her notion of divine law is an odd one more neo-Augustinian than Biblical or Scholastic; c) her image of Kantian ethics and intuitionism is the impoverished image manufactured by consequentialist opponents for polemical purposes and that she seems strangely accept it; d) the difficulty of identifying the "relevant descriptions" of acts is not an argument in favour of an ethics of virtue and against consequentialism or Kantian ethics, and indeed the role of judgment in the latter is a response to the difficulties raised by the case of judgment concerning future action. The chapter gives a short look at further developments in the neo-naturalist current trough a reconstruction of Philippa Foot's and Peter Geach's critiques to the naturalist-fallacy argument and Alasdair MacIntyre's grand reconstruction of the origins and allegedly inevitable failure of the Enlightenment project of an autonomous ethic. -/- ● X Normative ethics: Kantian and rights-based ethics 1. Dialogical constructivism 2. Apel, Habermas and discourse ethics 3. Gewirth and rights-based ethics 4. Nagel on agent-relative reasons 5. Donagan and persons as ends in themselves Parallel to the neo-Aristotelian trend, there was in the Rehabilitation of practical philosophy a Kantian current. This current started with the discovery of the pragmatic dimension of language carried out by Charles Peirce and the Oxford linguistic philosophy. On this basis, Karl-Otto Apel singled out as the decisive proponent of the linguistic and Kantian turn in German-speaking ethics, worked out the performative-contradiction argument while claiming that this was able to provide a new rational and universal basis for normative ethics. The chapter offers an examination of his argument in some detail, followed by a more cursory reconstruction of Jürgen Habermas's elaboration on Apel's theory. -/- ● XI The applied ethics renaissance 1. Elisabeth Anscombe on the atom bomb 2. From medical ethics to bioethics 3. Rawls and public ethics 3. Nozick, Dworkin and further developments of public ethics 5. Sen and the revival of economic ethics -/- The chapter presents the revolution of applied ethics while stressing its methodological novelty, exemplified primarily by Beauchamp and Childress principles approach and then by Jonsen and Toulmin's new casuistry. The chapter argues that Rawls's distinction between a "political" and a "metaphysical" approach to the theory of justice, one central part of ethical theory, is a formulation of the same basic idea at the root of both the principles approach and the new casuistry, both discussed in the following chapter. The idea is that it is possible to reach an agreement concerning positive moral judgments even though the discussion is still open – and in Rawls' view never will be close – on the essential criteria for judgment. -/- ● XII Fin-de-siècle metaethics 1. Deontic logics 2. Anti-realism 3. External realism 4. Internal realism 5. Kantian constructivism -/- The chapter illustrates the fresh start of meta-ethical discussion in the Eighties and Nineties and the resulting new alignments: metaphysical naturalism, internal realism, anti-realism, and constructivism. (shrink)

This paper aims to find, in Merleau-Ponty’s late thinking, a definition of the virtual which aligns with the latest advancements in digital technology while avoiding a reduction to the digital realm or a stark opposition to reality. The virtual is considered as a crucial characteristic in Merleau-Ponty’s late ontology, especially in The Visible and the Invisible, where a “virtual focus” or “virtual center” of the flesh is introduced. The argument posits that Merleau-Ponty’s monism of the flesh results in a (...) dynamic view of virtuality, with significant ontological implications that reshape the relationship between the digital and the analogue. Merleau-Ponty’s concept of the virtual is defined by several key features: it applies to a monist perspective on reality, to a dynamic relationality between dialectic poles, and to the fabric of reality. This interpretation of the virtual implies a divergence from the digital, as virtuality belongs to the whole spectrum of reality. (shrink)

This article presents a discursive critique of the Eurocentric paradigms of knowledge production that characterise much of the underlying logics in the age of neoliberal discourses on resilience, pointing out important areas not given sufficient attention. In particular, it highlights the limits of the modernist ontology of resilience, whereby extremely “vulnerable” African communities are encouraged “to become resilient” to climatic disruption and environmental catastrophe and to “bounce back” as rapidly as possible. The article moves the discussion forward, drawing from (...) critical decolonial approaches, in alignment with Indigenous knowledges, to question and rethink meaningful alternative ontologies, ways of knowing and being, in adaptive governance. I argue that the recognition of the plurality of many worlds, rather than one world, highlighted through critical decolonial understandings of epistemic forms with Indigenous knowledges, can be counterposed to Western universality as an innovative ontology to decentre the world order in the problematic dominant development of resilience thinking. Keywords: resilience; decolonisation; Africa; epistemology; pluriverse; Indigeneity. (shrink)

Adorno and Heidegger are frequently aligned because of apparent similarities in their critiques of modern epistemology. This alignment fails, however, to appreciate the substantial differences in the philosophical presuppositions that inform those very critiques. I distinguish Adorno's negative dialectic from Heidegger's fundamental ontology under the respective designations of critical versus phenomenological forms of transcendental philosophy. I argue that only by understanding Adorno's negative dialectic as a revised version of epistemology (namely a dialectical epistemology, committed to subject-object and transcendental (...) argument) can we make sense of, first, the profound differences between Adorno and Heidegger on the question of epistemology and, second, the philosophical motivations behind Adorno's trenchant rejection of Heidegger. Key Words: being-in-the-world • - dialectics • - empiricism • - epistemology • - idealism • - identity • - immediacy • - irrationalism • - mediation • - project • - subject • -object • - transcendental. (shrink)

John Wilkins and Malte Ebach respond to the dismissal of classification as something we need not concern ourselves with because it is, as Ernest Rutherford suggested, mere ‘‘stamp collecting.’’ They contend that classification is neither derivative of explanation or of hypothesis-making but is necessarily prior and prerequisite to it. Classification comes first and causal explanations are dependent upon it. As such it is an important (but neglected) area of philosophical study. Wilkins and Ebach reject Norwood Russell Hanson’s thesis that classification (...) relies on observation that is theory-laden and deny the need for aetiological assumptions and historical reconstruction to justify its arrangement. What they offer instead is a significant (albeit controversial) contribution to the philosophical literature on classification, a pre-theoretic natural classification based on the observation of patterns in data of ready-made phenomena. Their notion of ready-made phenomena rests on a conception of tacit knowledge or know-how. This is evident in their distinction between strong Theory-dependence and na ̈ıve theory-dependence. Their small t-theory-dependence permits patterns of observation that facilitate know-how but does not rely on a domain-specific explanatory theory of their aetiology. Wilkins and Ebach suggest classification differs from theory building in that it is passive (whereas theory building is active). Classification is possible just because it does not require the sieve of theory to capture classes that are ‘‘handed to you by your cognitive dispositions and the data that you observe’’ (p. 18). Finding regularities sans-theory is just something we do and can do without any prior theory about the underlying causes or origins of the resultant regularities. Luke Howard’s classification of clouds serves as an exemplar of a passive, theory-free classification system and the periodic table and the DSM help to illustrate this type of non-aetiological patterning. A recurrent theme is the nature of naturalness. For Wilkins and Ebach, the conception of naturalness is not one that is based on the generation or discovery of natural kind categories popular in both the traditional metaphysics of Mill and Wittgenstein as well as updated notions within philosophy of biology such as Boyd’s Homeostatic Property Cluster kinds. Instead, Wilkins and Ebach define the naturalness of classification as the falling into hierarchical patterns, aligning the search for natural arrangement with the aim of systematics, and as something that is grounded in a cognitive task or activity. However, they leave the question of realism v. antirealism open. ‘‘In natural classification...we must have real relations no matter how we might interpret ‘real’’’ (p. 70). There is tension with regard to their ontological commitments as they vacillate between constructive, operationalist, and realist approaches. Wilkins and Ebach initially define real as that which is causal and important (pp. 70–71), and later as that which ‘‘depends in no way upon a mind or observer’’ (p. 122). This makes their claim that there was ‘‘no real theory involved [in the pre-Darwinian classifications of Jussieu and Adanson]’’ (p. 64) difficult to interpret. Cont’d……. (shrink)

As the international momentum of the school effectiveness movement continues, its exponents remain largely impervious to criticism. This paper argues that while they may not readily align themselves with the individualistic aspects of Conservative social philosophy, their methodology necessarily secretes an atomised social ontology. The charge of ideological commitment rests on the fact that the essentially positivist epistemology employed by school effectiveness researchers presupposes an ontology of closed systems and atomistic events. Thus any notion of the structuring of (...) life-chances is automatically ruled out of court. The reciprocity of social ontology and methodology is explored in order to account for the myopia of the school effectiveness movement. (shrink)

This paper explores applying the truthmaker theory to address the challenge of divine simplicity and its alignment with Ibn Sina’s understanding of divine attributes. It proposes that God’s essence enables the predication of these attributes, eliminating the need for constituent properties. By adopting this approach, meaningful statements about God can be expressed without delving into ontological intricacies. The truthmaker account establishes a direct connection between God’s necessary existence and the truthfulness of statements about Him, overcoming the barrier of ineffability. (...) It offers a robust framework for understanding and expressing the truth of divine attributes while preserving divine simplicity. Ultimately, the truthmaker account provides a compelling resolution to the problem of ineffability in the realm of divine attributes in Ibn Sina’s philosophy. (shrink)

People inhabit a vast and intricate social network nowadays. In addition to our own decisions and actions, we confront those of various groups every day. Collective decisions and actions are more complex and bewildering compared to those made by individuals. As members of a collective, we contribute to its decisions, but our contributions may not always align with the outcome. We may also find ourselves excluded from certain groups and passively subjected to their influences without being aware of the source. (...) We are used to being in overlapping groups and may switch identities, supporting or opposing the claims of particular groups. But rarely do we pause to think: What do we talk about when we talk about groups and their decisions? At the heart of this dissertation is the question of collective agency, i.e., in what sense can we treat a group as a rational agent capable of its action. There are two perspectives we take: a philosophical and logical one. The philosophical perspective mainly discusses the ontological and epistemological issues related to collective agency, sorts out the relevant philosophical history, and argues that the combination of a relational view of collective agency and a dispositional view of collective intentionality provides a rational and realistic account. The logical perspective is associated with formal theories of groups, it disregards the psychological content involved in the philosophical perspective, establishes a logical system that is sufficiently formal and objective, and axiomatizes the nature of a collective. The first topic that is addressed is the ontology of collective agency, i.e., the question what exactly is collective agency. The philosophical discussion of collective agency centres around the reduction problem of the concept of a collective. Individualism and Cartesian internalism have long influenced orthodox theories and made them face the choice between an irreducible concept of a collective and ontological reductionism. Heterodox theories such as functionalism and interpretationism reinterpret the concept of agency and accept it as also realized on the level of a collective. To adequately explain social phenomena that are essentially relational in nature, we propose a relational, holistic account of collective agency and argue that functionalism and interpretationism can be integrated into such an account. While acknowledging the irreducibility of the concept of a collective, we find that there is a deep incompatibility between the concept of a collective and the concept of intentionality as the mark of the mental. To explain how collective intentionality nevertheless is possible and why we tend to use it analogously to how we use the concept of individual intentionality, we explore a dispositional account of intentionality which enables us to give an account of the concept of intentionality at both the individual and collective level. Specifically, we subdivide the dispositional account into three aspects: behavioral, purely mental, and cognitive. We then argue that collective intentionality is real by analyzing different forms of attributive judgments of intentionality and by introducing the perspective of indispensable collective responsibility. We also analyze how philosophical theories about collective agency relate to central features of formal theories about collective decisions, such as game theory. Although the two fields are both concerned with collectives, there are also differences that need to be addressed. For example, game theory is clearly anti-psychologistic since its aim is a formal and objective analysis. However, from the relational and dispositional perspective, intentionality at the individual level and collective intentionality as we analyze it, inevitably involve mental content. In order to explain this difference and identify where the boundary is, we analyze the relationships between the three basic concepts involved, namely intentionality, preference, and dependency, so as to provide a unified picture of collective theory across philosophical and formal theories. After paving the nexus between philosophical and formal perspectives, the logical perspective becomes the theme of our discussion. To be able to express game theoretical concepts and to connect them to our philosophical perspective, We present a logic of preference and functional dependence and its hybrid extension, and provide an axiomatization which is sound and strongly complete. The decidability of this logic is also proved. Its application to modeling non-cooperative and cooperative games in strategic form is explored. The resulting framework provides a unified view of Nash equilibrium, Pareto optimality, and the core. The philosophical relevance of these game-theoretical notions to discussions of collective agency is made explicit. Finally, we conclude and clarify the position of our theory in the broader field of research on the topics addressed in the thesis. Also, we point out many new questions and directions suggested by our analysis, including philosophical and logical open problems. (shrink)

False consciousness requires a general explanation for why, and how, oppressed individuals believe propositions against, as opposed to aligned with, their own well-being in virtue of their oppressed status. This involves four explanatory desiderata: belief acquisition, content prevalence, limitation, and systematicity. A social constructionist approach satisfies these by understanding the concept of false consciousness as regulating social research rather than as determining the exact mechanisms for all instances: the concept attunes us to a complex of mechanisms conducing oppressed individuals to (...) mistake social understandings of themselves as natural self-understandings—the limits lie where these overlap (sometimes), or are entirely absent. (shrink)

Modal idealism is a Theory of Everything, based on metaphysical abstractions of the physical principles of hidden symmetries, entanglement, and quantum field theory, considered in the context of the Many Worlds Interpretation of quantum mechanics. These abstractions are used to extend the scope of existing philosophical positions on idealism, consciousness and possible world semantics, to rationally explain the fundamental mysteries of our existence. While it conceptually aligns with the Many Minds Interpretation of quantum mechanics, modal idealism posits a more comprehensive (...) characterization of the mind, and thereby addresses many of the objections to MMI and MWI. Consequently, it can provide unequivocal, logical answers to our most enduring existential questions. To demonstrate the explanatory power of modal idealism, this article will present seven of our most meaningful physical and metaphysical questions, enumerate the principles of this framework, and use them to rationally answer these questions. (shrink)

De libero arbitrio presents one of the first arguments of God’s existence developed by a Christian thinker. Using the hierarchy of beings, St. Augustine establishes Reason as an instrument for seeking a reality that is supreme: that which, finding nothing more excellent, Reason itself would not hesitate to call “God”. The present paper demonstrates how this argument is aligned with Augustinian axiom that the rational search already presupposes a fiduciary adhesion. If on the one hand it offers a substrate upon (...) which other thinkers will develop their ontological arguments of divine existence, on the other hand, Augustine differs from them in his intention. For him, more than convincing doubters, this exercise finds its greatest value in strengthening by Reason the convictions of those who have already found, by faith, the God they now seek to know. (shrink)

Major Research Paper Abstract -/- A Part of This World: Deleuze & The Logic Of Creation. -/- Is there a particular danger in following Deleuze’s philosophy to its end result? According to Peter Hallward and Alain Badiou, Deleuze’s philosophy has some rather severe conclusions. Deleuze has been known as a vitalist thinker of life and affirmation. Hallward & Badiou seek to challenge the accepted view of Deleuze; showing that these accepted norms in Deleuzian scholarship should be challenged; and that initially (...) Deleuze calls for the evacuation of political action in order to remain firm in the realm of pure contemplation. I intend to investigate and defend Deleuze’s philosophy and against critics like Badiou and Hallward; and that not only is Deleuze’s philosophy creative and vital but also highly revolutionary and ‘a part of this world.’ I will look at several works in Deleuze’s corpus, as well as look at Deleuzian scholars whom defend Deleuze’s position -/- Hallward sees Deleuze as a theophantic thinker of the one and like Spinoza an individual mode must align oneself with the intellectual love of god, so that creativity and expressivity may mediate through them. Thus, according to Hallward the major theme of Deleuze’s philosophy is creativity; and a subject or a creature must tap into this vital spark of creation, which, is also a form of creatural confinement. Hallward states this creative act can only occur in the realm of the virtual, by lines of flight leading 'out of this world'. The subject is then re-introduced to an extra-worldly existence of contemplation and remains further away from decisions and lived experience. Deleuze, according to Hallward, falls prey to a cosmological pantheism. -/- Badiou has similar concerns. Deleuze’s philosophy is too systematic and abstract. The entirety of Deleuzes’ work is surrounded by metaphysics of the one; and essentially its repercussions lead to an overt asceticism. Badiou notes that Deleuze wants us all to surrender thought to a renewed concept of the one. Through the surrender of the one, the multiple is lost and incorporated into the realm of simulacra. Everything in this Deleuzian world is ‘always-already’ in the infinite and inhuman totality of the one. According to Badiou, this entire process is articulated in the power of inorganic life that operates through all of us. Like Hallward, Badiou sees Deleuze demolishing the subject, who is stuck between machinery and exteriority. Subjects are forced to transcend and go beyond their limits, slowly collapsing into an infinite virtuality. Badiou believes this is a powerful metaphor for a philosophy of death. Thus the conditions of Deleuzian thought are contingent upon asceticism, making a Deleuzian world a sort of ‘crowned anarchy’. Badiou sees Deleuze’s ascetic mission intimately linked with a philosophy of death, and like Hallward we should pay careful attention to the outcome of such an aristocratic philosophy. Death according to Badiou, symbolizes Deleuzian thought, not only making it dangerous, but also actualizing it as an ineffective position. Badiou also points out that Deleuze’s conceptual sources are not only limited but also repeated time and time again through a monotonous selection of concepts. Is this a fair critique and representation of Deleuzian thought? -/- Eugene Holland states, that both Hallward and Badiou have misrepresented Deleuze. Deleuze does invoke the creation of a new earth but one which we all fully believe in. The only world Deleuze wants to get out of is the world of habits, conformity, power; and forces that block creative being. According to Holland, Hallward presents us a Deleuze that inhibits an engagement with the world. However Deleuze’s creative enterprise is insistent on forming concepts that can change and transform our world. -/- So the question arises where does the problem of misrepresentation begin? It begins with both Badiou and Hallward having an erroneous account of the actual/virtual distinction in Deleuze’s Philosophy. According to Protevi, Hallward posits a dualism between the actual and the virtual, denying the role of the intensive. Hallward initially sees the relationship between the intensive and the virtual, ignoring the fact that the intensive has its own ontological register that mediates both the virtual and the actual. However, Protevi notes if one could not accept the intensive for an ontological register and had to place it with one or the other; you would have to accept an interrelationship between the actual and the intensive. Hallward places it in the realm of the virtual, thus, leading us to his major claim that Deleuze’s philosophy leads us out of the world. Protevi states, intensive processes happen in our world they are a part of this world. Hallward completely empties all creativity from the actual, thus depending on the virtual and its slippery slope. Both Hallward and Badiou have missed the point altogether. We live in an intensive/actual world and the main point about Deleuze’s politics has to do with experimentation and social interaction and the transformation and intervention of the concept. As Daniel W. Smith states, unlike Badiou, Deleuze is not searching for an axiomatic approach to the world, one that is prone to reductionism but rather with problematic, inventive and creative methods to transform a society. (shrink)

Van Gordon et al. outline the classification of their Ontological Addiction Theory (OAT), including its aetiology and treatment. In this review article I will from an appreciative perspective question some of its fundamental assumptions by presenting an alternative view on the ontology of ‘the person’, as distinct from its presently assumed conventional conflation with a contracted separate egoic self. I will propose this view as structurally and ethically significant for the ‘embodied’ experience of a reconstructed “dynamic and non-dual self”, (...) as cultivated in their treatment. Rather than this reconstructed self simply being socially desirable for functional purposes, I will underscore the meaning-generative case for ontological status, in the absence of which, a pervasive ‘sense of lack’ is evident, with all attendant individual, psychological, social, ecological and ethical implications. This article brings a developmental psychology perspective to bear in appreciating ‘personhood’ as an emergent, progressively realised and is thus similarly aligned with the intent of OAT in overcoming egoic addictive suffering. This mapping of the territory however populates a blind spot in OAT’s diagnosis by affirming unique personhood, a quality of ‘integrative presence’, meaningfully understood as a psycho-spiritual ontological reality. It offers, as with OAT’s stated intent, the merit of avoiding attendant mental health and developmental pitfalls, which can beset what we may discern as an implicit transcendental reductionist assumption operative in OAT, where ‘the many’ are reduced to ‘the One’ and there are, it is assumed, no real many. This framing is resonant with the lived experience of healthy ‘individuation’, a process distinct from the problematic phenomenon of ‘individualism’, evidenced by the empirical data on post-conventional human development, which potentially provides diagnostic markers for any optimal treatment discernment. It is also attuned to what many recognise as a contemporary Fourth Turning in Buddhism, in its conscious evolutionary recognition of the emergence in non-dual states of a ‘unique personal perspective’, and/or a relative individuation within the whole. This differentiation has formerly been interpreted through an ‘impersonal’ lens as an egoic holdover, and potentially inhibits ethical action in the world, as distinct from the ethical import and potential fruits stemming from the ontological affirmation of the person. Keywords: ego; unique personhood; ontology; epistemology; contemplative traditions; Western Enlightenment; developmental psychology; transcendental reductionism; Fourth Turning in Buddhism. (shrink)

Timothy Williamson has argued that in the debate on modal ontology, the familiar distinction between actualism and possibilism should be replaced by a distinction between positions he calls contingentism and necessitism. He has also argued in favor of necessitism, using results on quantified modal logic with plurally interpreted second-order quantifiers showing that necessitists can draw distinctions contingentists cannot draw. Some of these results are similar to well-known results on the relative expressivity of quantified modal logics with so-called inner and (...) outer quantifiers. The present paper deals with these issues in the context of quantified modal logics with generalized quantifiers. Its main aim is to establish two results for such a logic: Firstly, contingentists can draw the distinctions necessitists can draw if and only if the logic with inner quantifiers is at least as expressive as the logic with outer quantifiers, and necessitists can draw the distinctions contingentists can draw if and only if the logic with outer quantifiers is at least as expressive as the logic with inner quantifiers. Secondly, the former two items are the case if and only if all of the generalized quantifiers are first-order definable, and the latter two items are the case if and only if first-order logic with these generalized quantifiers relativizes. (shrink)

In this chapter, I examine Lewis's ideas about ontological innocence, ontological commitment and double-counting, in his discussion of composition as identity in Parts of Classes. I attempt to understand these primarily as epistemic or methodological claims: how far can we get down this route without adopting radical metaphysical theses about composition as identity?

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

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that (...) is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some will find (...) self-evident) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology development work being undertaken in support of scientific research. The ontologies created by scientists must, of course, be associated with implementations satisfying the requirements of software engineering. But these ontologies are not themselves engineering artifacts, and to conceive them as such brings grievous consequences. Rather, we shall argue, ontologies such as the GO are comparable to scientific theories, to scientific databases, or to scientific journal publications. Such a view implies a radically new conception of what is involved in the authoring, maintenance and application of ontologies in scientific contexts, and therewith also a radically new approach to the evaluation of ontologies and to the training of ontologists. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic (...) expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)