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.

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 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)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

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

Élie HALÉVY (1870-1937), philosophe et historien des idées, fut professeur à l'École libre des sciences politiques, l'ancêtre de l'actuel Sciences Po. Comme son autre grand ouvrage, l'Histoire du peuple anglais au XIXe siècle, paru en six tomes de 1913 à 1932, les trois tomes de La formation du radicalisme philosophique, parus en 1901 pour les deux premiers et en 1904 pour le troisième, reflètent pour partie ses enseignements de l'Ecole libre consacrés à l'histoire britannique. Le premier tome, La jeunesse de (...) Bentham 1776-1789, étudie la doctrine utilitariste non seulement chez celui qu'on regarde comme son fondateur principal, Jeremy Bentham, mais aussi chez les nombreux auteurs qui, en Grande-Bretagne et sur le continent, en dessinèrent avant lui les contours. Le deuxième tome, L’évolution de la doctrine utilitaire de 1789 à 1815, montre comment l'utilitarisme revêtit la forme non seulement d'une école de pensée, mais aussi d'un mouvement pour la réforme économique, sociale et politique. Le rôle coordonnateur nouveau de James Mill, ainsi qu'une convergence de vues avec les économistes, qui poussaient dans le sens des réformes, marquèrent notamment cette évolution. Le troisième tome, Le radicalisme philosophique, continue d'étudier la transformation de l'école en mouvement après la fin des guerres napoléoniennes, lorsque celle-ci commence à engranger ses premiers grands succès réformistes. Bentham, James Mill et les autres penseurs utilitaires sont alors réunis sous l'appellation de philosophic radicals. Le terme temporel de l'ouvrage est le Reform Act de 1832, première étape vers la modernisation du système électoral, que la propagande de ce groupe ne contribua pas peu à faire aboutir. Quoique l'ouvrage d'Halévy vaille en premier lieu par l'immense savoir qu'il déploie, et le nombre et l'excellence des citations qu'il propose, il comporte aussi des thèses historiques et philosophiques originales. On peut citer parmi les premières la thèse, qui relie les trois tomes, voulant que l'utilitarisme britannique trouve sa forme achevée dans l'intervention sur la société, lorsqu'il se mue en radicalisme philosophique, et parmi les secondes, la thèse, énoncée au début du premier tome, voulant qu'il existe trois modèles dominants de jonction des intérêts individuels (la fusion sympathique, l'identification naturelle et l'identification artificielle). Une autre grande thèse, à la fois historique et philosophique, affirme en substance que l'économie politique classique serait un département spécialisé de la pensée utilitaire. La question de savoir jusqu'à quel point Smith, Ricardo et Malthus ont pu adhérer au "principe d'utilité" de Bentham est toujours débattue. En même temps que les élucidations apportées à ce principe, elle contribue à expliquer l'intérêt que les historiens de la pensée économique continuent de porter à l'ouvrage. L'auteur a participé à la réédition de La formation du radicalisme philosophique en 1995 par les Presses Universitaires de France (P.U.F.), suivant un projet collectif lancé par Monique Canto-Sperber. Dans le présent article, antérieur à cette réédition, l'auteur tentait de résumer brièvement un livre qui demeure irremplaçable en dépit d'une conception et d'un style quelque peu datés. (shrink)

If you utter sentence (1) ‘Obama was born in 1961’ now, you say something true about the past. Since the past will always be such that the year 1961 has the property of being a time in which Obama was born, it seems impossible that could ever be false in a future context of utterance. We shall consider the case of a sentence about the past exactly like (1), but which was true when uttered a few years ago and is (...) no longer true now. On this basis, we shall conclude that the past has changed. (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)

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 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)

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 collection brings together fourteen contributions by authors from around the globe. Each of the contributions engages with questions about how local and global bioethical issues are made to be comparable, in the hope of redressing basic needs and demands for justice. These works demonstrate the significant conceptual contributions that can be made through feminists' attention to debates in a range of interrelated fields, especially as they formulate appropriate responses to developments in medical technology, global economics, population shifts, and poverty.

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)

Known as the Darwin of the twenty-first century, the German biologist Ernst Walter Mayr (1904-2005) studied a great variety of subjects such as Ornithology, Genetics, Evolution, Classification, History, and Philosophy of Biology. This scientist was a giant of the previous century and an icon of Evolutionary Biology. He became famous for his Biological Species Concept and his conclusion that allopatry is the main cause for the origin of species. He provided a decisive contribution to the New Systematics and was the (...) pioneer of the punctuated equilibrium idea. Mayr was one of the main architects of the evolutionary synthesis as also of the Neo-Darwinian wave. Evaluated together, all of his works reveal several elements of his ambition – to organize a philosophical conception inherent for Biology. An assiduous defender of autonomous Biology, Mayr asserted that four sets of factors in Biology differ from those in the Exact Sciences: (I) refutation of essentialism, mechanism, vitalism, and teleology; (II) some physical principles cannot be applied to Biology; (III) absence of general laws in Biology; and (IV) basic principles of biology and their specific character cannot be applied to the inanimate world. The present study took as an axis a minor or even invisible theme from the Ernst Mayr literature and aims to analyze critically the theoretical and epistemological basis that subsidizes – or not– the affirmation that Biology is an autonomous Science. - O biólogo alemão Ernst Walter Mayr (1904-2005), conhecido como o Darwin do século XXI, trabalhou com uma grande variedade de temas: Ornitologia, Genética, Evolução, Classificação, História e Filosofia da Biologia. Esse cientista foi um dos gigantes do século XX e um ícone para a Biologia Evolutiva. Ficou famoso com o seu Conceito Biológico de Espécie e sua conclusão de que a alopatria era a principal causa da origem das espécies. Forneceu uma contribuição decisiva à Nova Sistemática, foi precursor da ideia de equilíbrio pontuado e um dos principais arquitetos da síntese evolutiva, bem como do movimento Neodarwinista. Quando avaliados em conjunto, seus trabalhos revelam os diversos elementos de sua ambição – organizar um corpo de concepções filosóficas próprias da Biologia. Defensor assíduo de uma Biologia autônoma, Mayr afirmou que há quatro conjuntos de fatores que diferenciam a Biologia do conjunto das Ciências Exatas: (I) refutação do essencialismo, do mecanicismo, do vitalismo e da teleologia; (II) convicção de que certos princípios da Física não podem ser aplicados à Biologia; (III) ausência de leis naturais universais em Biologia; e (IV) percepção do caráter único de certos princípios básicos da Biologia não aplicáveis ao mundo inanimado. O presente artigo tomou por eixo um tema aparentemente menor ou mesmo invisível na obra de Ernst Mayr e pretende realizar uma análise crítica acerca de suas bases teóricas e epistemológicas que subsidiaram – ou não – a afirmação da Biologia como uma Ciência autônoma. (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)

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 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)

This paper is founded on the assumption that Philippine Studies has five different discouses: 1) Philippine studies as a neutral discourse; 2) colonial Philippine studies as a discourse that is based on western power and reinforces such power; 3) generic postcolonial Philippine studies as a discourse that critiques western hegemony; 4) Pilipinolohiya as a specific postcolonial discourse that was inaugurated by Prospero Covar; and 5) pantayong pananaw as another specific postcolonial discourse that was inaugurated by Zeus Salazar. Malay Journal, on (...) the other hand, is a scholarly periodical intended for researchers in the field of Philippine studies who use the Filipino language. Currently, it is the most respected journal that is exclusively published in Filipino language, based on the fact that it is accredited by the Commission on Higher Education and listed in a number of international abstracting and indexing organizations. This paper intends to establish which among these five discourses of Philippine studies is the most dominant in as far as the articles of the said journal are concerned. In order to attain such goal, this paper analyzed 50% random sample of the articles that were published from 2011, when the journal had completed its shift towards Philippine studies, up to 2015, the present complete year of publication for the said journal. (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)

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)

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)

This paper is basically a presentation of the tenets of Pierre Bourdieu’s philosophy in a language and level that can be easily understood by Filipino students and scholars of philosophy, cultural studies and Philippine studies. The discussion of Bourdieu’s philosophy revolves around 1) his concepts of habitus, field and symbolic violence; 2) his critique of television; 3) his theory of capitals; 4) some implications of his theory of capitals; and 5) his being public intellectual. The ultimate aim of this paper (...) is to suggest some aspects and dimensions of Philippine society and culture that can be analyzed using some of bourdieu’s thoughts as interpretive frameworks, as well as to challenge the said Filipino students and scholars of philosophy, cultural studies and Philippine studies to creatively and effectively appropriate such theories for the enrichment of the theoretical corpus of Philippine studies. This paper is part of a series of similar works done by one of the co-authors that dealt with Adorno, Schleiermacher and Dilthey, Heidegger, Gadamer and Bultmann, and Lyotard. (shrink)

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

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)

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)

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)

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)

In this paper, we propose a new concept named the uniform single valued neutrosophic graph. An illustrative example and some properties are examined. Next, we develop an algorithmic approach for computing the complement of the single valued neutrosophic graph. A numerical example is demonstrated for computing the complement of single valued neutrosophic graphs and uniform single valued neutrosophic graph.

For much of the first fifty years of its existence, analytic philosophy shunned discussions of normativity and ethics. Ethical statements were considered as pseudo-propositions, or as expressions of pro- or con-attitudes of minor theoretical significance. Nowadays, in contrast, prominent analytic philosophers pay close attention to normative problems. Here we focus our attention on the work of Searle, at the same time drawing out an important connection between Searle’s work and that of two other seminal figures in this development: H.L.A. Hart (...) and John Rawls. We show that all three thinkers tend to assume that there is but one type of normativity within the realm of social institutions – roughly, the sort of normativity that is involved in following the results of chess – and that they thereby neglect features that are of crucial significance for an adequate understanding of social reality. (shrink)

As so often with his published texts, the experience of reading Nietzsche’s notebooks is at once mesmerising and infuriating. One is in the presence of a thinker who, on the one hand, meditates deeply on fundamental issues in philosophy and psychology but who, on the other, refuses to be pinned down. The fact that Nietzsche’s style is so elusive can account for the enormously disparate interpretations of his work and it is no surprise that his notebooks have been read in (...) the most extreme fashion. The notebooks have a chequered history having been variously touted as the crowning achievement of his philosophy, and as not repaying the effort of reading. (shrink)

Recreational Drugs European Network (ReDNet) project aims to use the Psychonaut Web Mapping Project database (Psychonaut Web Mapping Group, 2009) containing novel psychoactive compounds usually not mentioned in the scientific literature and thus unknown to clinicians as a unique source of information. The database will be used to develop an integrated ICT prevention approach targeted at vulnerable individuals and focused on novel synthetic and herbal compounds and combinations. Particular care will be taken in keeping the health professionals working directly with (...) young people showing problematic behaviors regularly updated in terms of novel compounds and combinations as well. A user-friendly project website will be developed aimed primarily at delivering the information/prevention approaches, but will also be a way of communicating with project partners and relevant stakeholders (e.g. thematic forum facilities, instant messages, blogs, video chat, wikiblog, newsletters distributed via mailing list). The website will support various ICT prevention tools, including an SMS alert service. Different areas and sections will be aimed specifically at the different target groups. -/- . (shrink)

In this аrtiсlе, thе аuthоr fосusеs оn еluсidаting sоmе philоsоphiсаl аspесts оf intеrсulturаl соmmuniсаtiоn in thе соntеxt оf glоbаlizаtiоn оn thе bаsis оf rесоgnizing thе соntributiоns аnd limitаtiоns оf Wittgеnstеin tо thе birth оf philоsоphy. сulturе study. Thоsе philоsоphiсаl issuеs аrе: thе similаrity in thinking аnd асting оf pеоplе асrоss сulturеs; divеrsity оf сulturеs, wоrldviеws аnd wаys оf lifе. Frоm thе Mаrxist pоint оf viеw, thе аuthоr pоintеd оut аnd сritiсizеd thе limitаtiоns оf Wittgеnstеin's philоsоphiсаl соnсеptiоn; аnd аt thе sаmе (...) timе оffеr аnd еxplаin sоlutiоns tо implеmеnt intеrсulturаl соmmuniсаtiоn in thе соntеxt оf сurrеnt glоbаlizаtiоn. (shrink)

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)

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)

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)

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 analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...) ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects). We describe the historical influence of this view, and also show how standard first-order predicate logic can be used for the logical formalization of a more adequate “six category ontology”, which recognizes, at the level of both particulars and universals, not only things or objects but also events and qualities. (shrink)

According to one large family of views, scientific explanations explain a phenomenon (such as an event or a regularity) by subsuming it under a general representation, model, prototype, or schema (see Bechtel, W., & Abrahamsen, A. (2005). Explanation: A mechanist alternative. Studies in History and Philosophy of Biological and Biomedical Sciences, 36(2), 421–441; Churchland, P. M. (1989). A neurocomputational perspective: The nature of mind and the structure of science. Cambridge: MIT Press; Darden (2006); Hempel, C. G. (1965). Aspects of scientific (...) explanation. In C. G. Hempel (Ed.), Aspects of scientific explanation (pp. 331–496). New York: Free Press; Kitcher (1989); Machamer, P., Darden, L., & Craver, C. F. (2000). Thinking about mechanisms. Philosophy of Science, 67(1), 1–25). My concern is with the minimal suggestion that an adequate philosophical theory of scientific explanation can limit its attention to the format or structure with which theories are represented. The representational subsumption view is a plausible hypothesis about the psychology of understanding. It is also a plausible claim about how scientists present their knowledge to the world. However, one cannot address the central questions for a philosophical theory of scientific explanation without turning one’s attention from the structure of representations to the basic commitments about the worldly structures that plausibly count as explanatory. A philosophical theory of scientific explanation should achieve two goals. The first is explanatory demarcation. It should show how explanation relates with other scientific achievements, such as control, description, measurement, prediction, and taxonomy. The second is explanatory normativity. It should say when putative explanations succeed and fail. One cannot achieve these goals without undertaking commitments about the kinds of ontic structures that plausibly count as explanatory. Representations convey explanatory information about a phenomenon when and only when they describe the ontic explanations for those phenomena. (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)

This interview, conducted over the span of several months, tracks the respective journeys of Constantin V. Boundas and Daniel W. Smith with the philosophy of Gilles Deleuze. Rather than “becoming Deleuzian,” which is neither desirable nor possible, these exchanges reflect an array of encounters with Deleuze. These include the initial discoveries of Deleuze’s writings by Boundas and Smith, in-person meetings between Boundas and Deleuze, and the wide-ranging and influential philosophical work on Deleuze’s concepts produced by both Boundas and (...) Smith. At stake in this discussion are key contributions by Deleuze to continental philosophy, including the distinction between the virtual and the actual and the very nature of a “concept.” Also at stake is the formative or pedagogical impact of a philosopher, like Deleuze, on those who find and fully engage with his texts, concepts, and project. Cette interview, menée sur plusieurs mois, suit les parcours respectifs de Constantin V. Boundas et Daniel W. Smith avec la philosophie de Gilles Deleuze. Au lieu de « devenir Deleuzien, » ce qui n’est ni souhaitable ni possible, ces échanges reflètent un éventail de rencontres avec Deleuze. Il s’agit notamment des premières découvertes des écrits de Deleuze par Boundas et Smith, des rencontres en personne entre Boundas et Deleuze, et du travail philosophique vaste et in????luent sur les concepts de Deleuze produit par Boundas et Smith. L’enjeu ici étant les contributions clés de Deleuze à la philosophie continentale, y compris la distinction entre le virtuel et l’actuel, et la nature même d’un « concept. » Mais il y a aussi l’impact formateur ou pédagogique d’un philosophe, comme Deleuze, sur ceux qui trouvent et s’engagent pleinement dans ses textes, ses concepts et ses projets. (shrink)

Equipped with the ultimate query answering system, computers would finally be in a position to address all our information needs in a natural way. In this paper, we describe how Language and Computing nv (L&C), a developer of ontology-based natural language understanding systems for the healthcare domain, is working towards the ultimate Question Answering (QA) System for healthcare workers. L&C’s company strategy in this area is to design in a step-by-step fashion the essential components of such a system, each component (...) being designed to solve some one part of the total problem and at the same time reflect well-defined needs on the prat of our customers. We compare our strategy with the research roadmap proposed by the Question Answering Committee of the National Institute of Standards and Technology (NIST), paying special attention to the role of ontology. (shrink)

D’un point de vue sociologique, l’architecture du droit global se caractérise par une prééminence des normes de « connectivité », qu’il convient de distinguer des normes de « possibilité » et des normes de « cohérence ». La centralité des normes de connectivité dans cette structure provient de la fonction même du droit global, qui vise à faciliter le transfert de composants sociaux condensés –_tels que le capital, les produits économiques, les doctrines religieuses ou les connaissances scientifiques_–, d’un environnement juridique (...) à un autre à l’échelle planétaire. Cela se vérifie aussi bien dans le cas du colonialisme et du droit colonial que dans celui, aujourd’hui, des chaînes de valeur globales et des droits de l’homme. Le droit colonial et le droit des droits humains peuvent tous deux être compris comme des moyens de remplir une même fonction constituante de stabilisation et de facilitation de la connectivité. Cette compréhension trouve un écho significatif dans le droit international privé, qui participe de la même fonction. (shrink)

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

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)