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

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

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (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)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (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)

This paper describes an AFOSR-supported basic research program that focuses on developing a new framework for combining hard with soft data in order to improve space situational awareness. The goal is to provide, in an automatic and near real-time fashion, a ranking of possible threats to blue assets (assets trying to be protected) from red assets (assets with hostile intentions). The approach is based on Conceptual Spaces models, which combine features from traditional associative and symbolic cognitive models. While Conceptual Spaces (...) are revolutionary, they lack an underlying mathematical framework. Several such frameworks have attempted to represent Conceptual Spaces, but by far the most robust is the model developed by Holender. His model utilizes integer linear programming in order to obtain an overall similarity value between observations and concepts that support the formation of hypotheses. This paper will describe a method for building Conceptual Spaces models for threats that utilizes ontologies as a means to provide a clear semantic foundation for this inferencing process; in particular threat ontologies and space domain ontologies are developed and employed in this approach. A space situational awareness use-case is presented involving a kinetic kill scenario and results are shown to assess the performance of this fusion-based inferencing framework. (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)

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

This introduction to the second international conference on Formal Ontology and Information Systems presents a brief history of ontology as a discipline spanning the boundaries of philosophy and information science. We sketch some of the reasons for the growth of ontology in the information science field, and offer a preliminary stocktaking of how the term ‘ontology’ is currently used. We conclude by suggesting some grounds for optimism as concerns the future collaboration between philosophical ontologists and information scientists.

First published in 1995. Routledge is an imprint of Taylor & Francis, an informa company.

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

The current industrial revolution is said to be driven by the digitization that exploits connected information across all aspects of manufacturing. Standards have been recognized as an important enabler. Ontology-based information standard may provide benefits not offered by current information standards. Although there have been ontologies developed in the industrial manufacturing domain, they have been fragmented and inconsistent, and little has received a standard status. With successes in developing coherent ontologies in the biological, biomedical, and financial domains, an effort called (...) Industrial Ontologies Foundry (IOF) has been formed to pursue the same goal for the industrial manufacturing domain. However, developing a coherent ontology covering the entire industrial manufacturing domain has been known to be a mountainous challenge because of the multidisciplinary nature of manufacturing. To manage the scope and expectations, the IOF community kicked-off its effort with a proof-of-concept (POC) project. This paper describes the developments within the project. It also provides a brief update on the IOF organizational set up. (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)

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

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data (...) from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (shrink)

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

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

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

This paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. Contextual data is (...) also taken into account, for example data about space weather effects, by drawing on the Space Domain Ontologies, a large system of ontologies designed to support all aspects of space situational awareness. The framework is coupled with a mathematical programming scheme that frames a mathematically optimal approach for decision support, providing a quantitative basis for ranking potential for collision across multiple satellite pairs. The goal is to provide the broadest possible information foundation for critical assessments of collision likelihood. (shrink)

The intuitions at the core of environmental ethics and of other neglected value realms put pressure on traditional anthropocentric ethics based on monistic value theories. Such pressure is so severe that it has led many to give up on the idea of monistic value theories altogether. I argue that value monism is still preferable to value pluralism and that, indeed, these new challenges are opportunities to vastly improve impoverished traditional theories. I suggest an alternative monistic theory, Richness Theory, and show (...) how it provides an opportunity to capture the needs of both environmental ethics and of our traditional ethics. (shrink)

Artificial intelligence is man's attempt to use software to emulate the intelligence of human beings. But the complexity of the human neurological system formed in the course of evolution is impossible to replicate: "Human languages and societies are complex systems, indeed complex systems of many complex systems," so much so that their mathematical modeling is impossible. Barry Smith, philosopher and professor at the University at Buffalo. shows no uncertainty about this. His latest book written with Jobst Landgrebe, a mathematician (...) and entrepreneur in the AI field, leaves no doubt – starting with the title: Why machines will never rule the world (Routledge 2023). The book was presented in Turin during an evening organized by the Fondazione CRT and the Bruno Leoni Institute, in which Smith was interviewed based on questions developed by generative Ai. We have accepted the challenge to conduct an interview parallel to the one done with GPT4. (shrink)

L.S. Vygotsky’s “regulative” account of the development of human thinking hinges on the centralization of “directive” speech acts (commands or imperatives). With directives, one directs the activity of another, and in turn begins to “self-direct” (or self-regulate). It’s my claim that Vygotsky’s reliance on directives de facto keeps his account stuck at Tomasello's level of individual intentionality. Directive speech acts feature prominently in Tomasello’s developmental story as well. But Tomasello has the benefit of accounting for a functional differentiation in directive (...) communication—i.e., in collaborative activity, the command gives way to both the request and informational assertion. Lacking such differentiation, Vygotsky’s account runs the risk of playing to a rather strident conception of the socius, one more Machiavellian than Marxist. (shrink)

The category of sympathy marks a number of basic divisions in early modern approaches to action explanations, whether for human agency or for change in the wider natural world. Some authors were critical of using sympathy to explain change. They call such principles “unintelligible” or assume they involve “mysterious” action at a distance. Others, including Margaret Cavendish, Anne Conway, and Gottfried Wilhelm Leibniz, appeal to sympathy to capture natural phenomena, or to supply a backbone to their metaphysics. Here I discuss (...) how concerns about sympathetic actions form at least a partial background for differing seventeenth-century conceptions of what it is to explain action. I argue that critics of sympathy generally insist on an “atomistic” approach to action explanation, which makes primitively relational phenomena come out as problematic. Proponents of sympathy, by contrast, allow for a more holistic approach to action explanation, which allows for such basic connections. Hence, divergent attitudes toward sympathetic action in part explain differences in approaches to explanation. I conclude by showing how some of these core concerns fade into the background when in the eighteenth-century sympathy gets psychologised and individualised. (shrink)

Previous work has shown that the Complex Conceptual Spaces − Single Observation Mathematical framework is a useful tool for event characterization. This mathematical framework is developed on the basis of Conceptual Spaces and uses integer linear programming to find the needed similarity values. The work of this paper is focused primarily on space event characterization. In particular, the focus is on the ranking of threats for malicious space events such as a kinetic kill. To make the Conceptual Spaces framework work, (...) the similarity values between the contents of observations on the one hand and the properties of the entities observed on the other needs to be found. This paper shows how to exploit Dempster-Shafer theory to implement a statistical approach for finding these similarities values. This approach will allow a user to identify the uncertainty involved in similarity value data, which can later be propagated through the developed mathematical model in order for the user to know the overall uncertainty in the observation-to-concept mappings needed for space event characterization. (shrink)

Part 1 of this exchange consists in a critique by Smith of Searle’s The Construction of Social Reality focusing on Searle’s use of the formula ‘X counts as Y in context C’. Smith argues that this formula works well for social objects such as dollar bills and presidents where the corresponding X terms (pieces of paper, human beings) are easy to identify. In cases such as debts and prices and money in a banks computers, however, the formula fails, (...) because these are cases of what he calls ‘free-standing Y terms’, since there is here no X which can count as the corresponding Y. In his response in Part 2, Searle argues that Smith’s critique rests on three misunderstandings: 1. in wrongly presupposing that Searle is trying to analyze the nature of what he calls “social objects”, rather than of social facts; 2. in thinking that the counts as formula is intended as a definition, rather than as a mere mnemonic; and 3. in neglecting the naturalism of Searle’s account. (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)

Common sense is on the one hand a certain set of processes of natural cognition – of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific (...) treatment of this world relate to traditional and contemporary metaphysics and formal ontology? Can we embrace a thesis of common-sense realism to the effect that the world of common sense exists uniquely? Or must we adopt instead a position of cultural relativism which would assign distinct worlds of common sense to each group and epoch? The present paper draws on recent work in computer science (especially in the fields of naive and qualitative physics), in perceptual and developmental psychology, and in cognitive anthropology, in order to consider in a new light these and related questions and to draw conclusions for the methodology and philosophical foundations of the cognitive sciences. (shrink)

The term ‘Continental philosophy’ designates not philosophy on the continent of Europe as a whole, but rather a selective slice of Franco-German philosophy. Through a critical analysis of the arguments advanced by Otto Neurath, the paper addresses the issue of why Austrian philosophers in particular are not counted in the pantheon of Continental philosophers. Austrian philosophy is marked by the predominance of philosophical analysis and of the philosophy of science. The paper concludes that it is not Austria which is the (...) special case when seen against the background of contemporary mainstream philosophy, but rather Germany and France. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

Common sense is on the one hand a certain set of processes of natural cognition – of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific (...) treatment of this world relate to traditional and contemporary metaphysics and formal ontology? Can we embrace a thesis of common-sense realism to the effect that the world of common sense exists uniquely? Or must we adopt instead a position of cultural relativism which would assign distinct worlds of common sense to each group and epoch? The present paper draws on recent work in computer science (especially in the fields of naive and qualitative physics), in perceptual and developmental psychology, and in cognitive anthropology, in order to consider in a new light these and related questions and to draw conclusions for the methodology and philosophical foundations of the cognitive sciences. (shrink)

La ricerca medica è afflitta da un problema di comunicazione. Comunità distinte di ricercatori si servono di terminologie diverse e spesso incompatibili per esprimere i risultati del loro lavoro, generando in questo modo problemi di integrazione tra database ogniqualvolta si presenti la necessità di inserire i dati medici nei computer. In un primo momento i problemi di integrazione tra database venivano risolti caso per caso, in seguito si è fatta strada l’idea di realizzare un’unica tassonomia di riferimento in cui tradurre, (...) una volta soltanto, tutti i vari sistemi di classificazione. Funzionando come una sorta di lingua franca, questa tassonomia di riferimento avrebbe automaticamente garantito ad ogni database calibrato su di essa la compatibilità con tutti gli altri. È curioso come gli informatici abbiano chiamato il sistema centrale di classificazione che stavano proponendo un’ontologia, riconoscendo così l’esistenza di più di un’affinità tra il lavoro di costruzione che un simile sistema comportava e la vecchia metafisica. Il presente articolo descrive un tentativo di sfruttare le risorse della filosofia per risolvere problemi che sorgono, in particolar modo, nel campo dell’integrazione delle terminologie mediche. Vengono delineati in particolare i contorni di un’iniziativa che è il frutto della collaborazione tra l’Istituto di Ontologia Formale e Informatica Medica e la società di software belga Language and Computing, iniziativa che prevede la messa alla prova di un’ontologia fondata su solidi principi filosofici nel contesto di potenti strumenti software per l’elaborazione di testo medico. (shrink)

The most obvious varieties of mental phenomena directed to non- existent objects occur in our experiences of works of art. The task of applying the Meinongian ontology of the non-existent to the working out of a theory of aesthetic phenomena was however carried out not by Meinong by his disciple Stephan Witasek in his Grundzüge der allgemeinen Ästhetik of 1904. Witasek shows in detail how our feelings undergo certain sorts of structural modifications when they are directed towards what does not (...) exist. He draws a distinction between genuine mental phenomena and what he calls `phantasy-material', asserting that `the job of the aesthetic object, whether it is a work of art or a product of nature, is to excite and support the actualisation of phantasy-material in the experiencing subject'. We might think of such phantasy-material as a matter of Ersatz-emotions or emotional `slop'. We could then see Witasek's aesthetics as an elaborate taxonomy of the various different sorts of Ersatz-emotions which the subject allows to be stimulated within himself in his intercourse with works of art, and see works of art themselves as machines for the production of ever more subtle varieties of such phantasy-material in the perceiving subject. (shrink)

When national borders in the modern sense first began to be established in early modern Europe, non-contiguous and perforated nations were a commonplace. According to the conception of the shapes of nations that is currently preferred, however, nations must conform to the topological model of circularity; their borders must guarantee contiguity and simple connectedness, and such borders must as far as possible conform to existing topographical features on the ground. The striving to conform to this model can be seen at (...) work today in Quebec and in Ireland, it underpins much of the rhetoric of the P.L.O., and was certainly to some degree involved as a motivating factor in much of the ethnic cleansing which took place in Bosnia in recent times. The question to be addressed in what follows is: to what extent could inter-group disputes be more peacefully resolved, and ethnic cleansing avoided, if political leaders, diplomats and others involved in the resolution of such disputes could be brought to accept weaker geometrical constraints on the shapes of nations? A number of associated questions then present themselves: What sorts of administrative and logistical problems have been encountered by existing non contiguous nations and by perforated nations, and by other nations deviating in different ways from the received geometrical ideal? To what degree is the desire for continuity and simple connectedness a rational desire, and to what degree does it rest on species of political rhetoric which might be countered by, for example, philosophical argument? These and a series of related questions will form the subject- matter of the present essay. (shrink)

Introduction to the special issue in Pragmatics & Cognition focused on creativity, cognition, and material culture. With contributions from Maurice Bloch, Chris Gosden, Tim Ingold, John Kirsh, Carl Knappett & Sander van der Leeuw, Lambros Malafouris, Frédéric Vallée-Tourangeau, Kevin Warwick, and Tom Wynn and Frederick L. Coolidge.

Presentiamo qui la traduzione di un lungo saggio sull’ontologia e i sistemi informativi. Abbiamo tradotto la parte più generale con le distinzioni base tra ontologia, metafisica e scienza. L’autore, fornendo un suo punto di vista peculiare sull’ontologia, descrive le diverse questioni e distinzioni connesse all’impresa ontologica, considerando sia il punto di vista dei filosofi che degli informatici.

Logique et existenceDeleuze à propos des « conditions du réel »Pour Deleuze, l’un des problèmes fondamentaux d’une théorie de la pensée est de savoir comment la pensée peut quitter la sphère du possible pour penser le réel, c’est-àdire pour penser l’existence elle-même. La position du réel semble être hors du concept. Des pré-kantiens comme Leibniz approchaient ce problème par le biais de la distinction entre vérités d’essence et vérités d’existence, alors que des post-kantiens comme Maimon l’approchaient par la distinction entre (...) les conditions de l’expérience possible et celles de l’expérience réelle. La logique classique définit la sphère du possible par trois principes logiques – l’identité, la non-contradiction et le tiers-exclu – et la présente étude examine les trois grandes trajectoires qui, dans cette histoire de la philosophie, ont tenté d’utiliser l’un de ces trois principes classiques pour pénétrer l’existence ellemême : 1) Leibniz (et les pré-kantiens) cherchait à étendre le principe de d’identité àl’existence entière ; 2) Hegel (et les post-kantiens) cherchait à étendre le principe de non-contradiction à la totalité de l’expérience ; et 3) le groupe des penseurs appelés de manière assez large « existentialistes » cherchait à étendre le principe du tiers-exclu à la totalité de l’existence. La conclusion examine les raisons pour lesquelles Deleuze a été fasciné par chacune de ces tentatives philosophiques pour « penser l’existence », tout en pensant néanmoins qu’elles ont toutes échoué ; et pourquoi aussi il a fini par développer sa propre réponse au problème en faisant appel à un principe de différence.Logica e EsistenzaLe ‘Condizioni del reale’ in DeleuzePer Deleuze, uno dei problemi fondamentali per una teoria del pensiero è: come può il pensiero abbandonare la sfera del possibile per pensare il reale, ossia, pensare l’esistenza stessa? La posizione del reale sembra essere fuori dal concetto. Prekantiani come Leibniz affrontano questo problema in termini di distinzione fra verità dell’essenza e verità dell’esistenza, mentre post-kantiani come Maimon affrontano il problema in termini di distinzione fra condizioni dell’esperienza possibile e condizioni dell’esperienza reale. La logica classica ha definito la sfera del possibile secondo tre principi logici – identità, non-contraddizione, terzo escluso – e questo saggio analizza tre grandi ‘parabole’ della storia della filosofia che hanno tentato di usare uno di questi tre principi della logica per penetrare l’esistenza stessa: (1) Leibniz (e i pre-kantiani) hanno tentato di estendere il principio di identità a tutta l’esistenza; (2) Hegel (ei post-kantiani) hanno tentato di estendere il principio di non-contraddizione a tutta l’esistenza; (3) il gruppo di pensatori (solo approssimativamente legati fra loro) chiamati “esistenzialisti” ha tentato di estendere il principio del terzo escluso all’esistenza. La conclusione analizza sia le ragioni per le quali Deleuze era affascinato da ciascuno di questi tentativi filosofici di “pensare l’esistenza” nonostante fosse convinto che essi avessero fallito, sia i motivi per cui egli in conclusione traccia la propria risposta al problema facendo appello al principio della differenza. (shrink)

Per Husserl, come per Bolzano, la logica e una dottrina della sdenza. Husserl prende pero piu sul serio l'idea che le teorie scientifiche siano costituite dagli atti mentali di soggetti conoscenti. Quella che segue e un' esposizione della concezione husserliana della logica e della scienza, fondata appunto sugli atti; essa approdera a una delineazione dell'idea husserliana di «ontologia formale».

Le présent article est une tentative nouvelle d’articuler le rôle d’une théorie des vérifacteurs. Nous soutenons que la théorie de la vérifaction constitue une pierre angulaire dans une bonne méthodologie en métaphysique, mais que l’amalgame entre la théorie de la vérifaction et la théorie de la vérité a été responsable de certains excès associés aux approches vérifactionnistes dans la littérature récente. Nous montrons que la théorie de la vérifaction conserve son attrait comme instrument d’investigation métaphysique, et ce, malgré notre accord (...) avec les doctrines déflationnistes telles que celles défendues par Ayer, Quine, Field et Horwich (ou, du moins, malgré notre neutralité à leur égard). Nous soutenons en outre que les intuitions sous-jacentes à la théorie de la vérifaction s’éclairent quand nous les dissocions d’une théorie de la vérité et, par-dessus tout, de la tentative de fournir une définition de la vérité. (shrink)

Radical democratic thinking is becoming intrigued by the material situatedness of its political agents and by the role of nonhuman participants in political interaction. At stake here is the displacement of narrow anthropocentrism that currently guides democratic theory and practice, and its repositioning into what we call ‘the nonhuman condition’. This Critical Exchange explores the nonhuman condition. It asks: What are the implications of decentering the human subject via a new materialist reading of radical democracy? Does this reading dilute political (...) agency? Or should this be seen, on the contrary, as an invitation for new voices and demands to enter into democratic assemblages? How might engagement with the more-than-human disrupt or extend theories of radical democracy? Hans Asenbaum and Amanda Machin discuss the human democratic subject both through radical democratic and new materialist lenses. They suggest that a new materialist decentred subject does not lose agency but further gains political responsibility in radical democracy. Jean-Paul Gagnon highlights the possibility of becoming through loss. In losing our anthropocentric arrogance—our understanding of being other and better than animal—we become more connected and discover our place in human-nonhuman assemblages. Melissa Orlie agrees that something can be gained through renouncing dominant human fantasies and presents a ‘radical democratic naturalism’. By renouncing land violence and acknowledging nature’s subjectivity, we can further nonexploitative radical democratic politics. This is where the notion of ‘tidalectic’ processes introduced by James L. Smith is helpful. Focusing on water and the Indigenous knowledges around rivers, he considers how democracy and community can be reimagined as plural, cyclical and attentive to the nonhuman with which the human is inevitably entangled. Diana Leong offers a different approach. Considering the nonhuman from the perspective of Black Studies demands an awareness to how blackness has long been constituted as non- or partially human. (shrink)

It is now generally recognized that figures such as Reid, Peirce, and Reinach formulated theories of speech acts avant la lettre of Austin and Searle, in Reid and Reinach’s cases under the heading ‘theory of social acts’. Here we address the question as to what conditions would have to be satisfied for such theories to count as ‘theories of speech acts’ in the now familiar sense.

Michael Slote’s Moral Sentimentalism is a wonderful model of a particular, under-appreciated philosophical method. It demonstrates that exciting, original work can be created by putting old ideas to new uses, proving once again that the classics of moral and political philosophy offer too rich an array of intellectual resources to leave to historians alone. Whenever one is reclaiming old ideas, however, the most important decision is which ideas to reclaim, and which to leave in the dustbin of history. Slote makes (...) use of many ideas drawn from history’s greatest moral sentimentalist, David Hume, but he rejects many others. The work of Hume’s closest friend and greatest sentimentalist ally, Adam Smith, is rejected without adequate explanation. Smith is mentioned, but quickly dismissed. Yet even though Smith makes little contribution to Slote’s own version of sentimentalism, I think he deserved greater discussion in this book. Smith and Slote address many of the same subjects, using the same basic sentimentalist approach, but they come to very different conclusions. It is thus possible to construct a fruitful debate between them—a debate in which, since he can no longer speak on his own behalf, I will be taking Smith’s side. (shrink)