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 collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s LinKBase® (...) is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (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)

This paper seeks to clarify and defend the proposition that moral realism is best elaborated as a moral doctrine. I begin by upholding Ronald Dworkin’s anti-Archimedean critique of the error theory against some strictures by Michael Smith, and I then briefly suggest how a proponent of moral realism as a moral doctrine would respond to Smith’s defense of the Archimedeanism of expressivism. Thereafter, this paper moves to its chief endeavor. By differentiating clearly between expressivism and quasi-realism, the paper (...) highlights both their distinctness and their compatibility. In so doing, it underscores the affinities between Blackburnian quasi-realism and moral realism as a moral doctrine. Finally, this paper contends—in line with my earlier work on these matters—that moral realism as a moral doctrine points to the need for some reorienting of meta-ethical enquiries rather than for the abandoning of them. (shrink)

People maintain a positive identity in at least two ways: They evaluate themselves more favorably than other people, and they judge themselves to be better now than they were in the past. Both strategies rely on autobiographical memories. The authors investigate the role of autobiographical memories of lying and emotional harm in maintaining a positive identity. For memories of lying to or emotionally harming others, participants judge their own actions as less morally wrong and less negative than those in which (...) other people lied to or emotionally harmed them. Furthermore, people judge those actions that happened further in the past to be more morally wrong than those that happened more recently. Finally, for periods of the past when they believed that they were very different people than they are now, participants judge their actions to be more morally wrong and more negative than those actions from periods of their pasts when they believed that they were very similar to who they are now. The authors discuss these findings in relation to theories about the function of autobiographical memory and moral cognition in constructing and perceiving the self over time. (shrink)

People seem more divided than ever before over social and political issues, entrenched in their existing beliefs and unwilling to change them. Empirical research on mechanisms driving this resistance to belief change has focused on a limited set of well-known, charged, contentious issues and has not accounted for deliberation over reasons and arguments in belief formation prior to experimental sessions. With a large, heterogeneous sample (N = 3,001), we attempt to overcome these existing problems, and we investigate the causes and (...) consequences of resistance to belief change for five diverse and less contentious socio-political issues. After participants chose initially to support or oppose a given socio-political position, they were provided with reasons favoring their chosen position (affirming reasons), reasons favoring the other, unchosen position (conflicting reasons), or all reasons for both positions (reasons for both sides). Our results indicate that participants are more likely to stick with their initial decisions than to change them no matter which reasons are considered, and that this resistance to belief change is likely due to a motivated, biased evaluation of the reasons to support their initial beliefs (prior-belief bias). More specifically, they rated affirming reasons more favorably than conflicting reasons—even after accounting for reported prior knowledge about the issue, the novelty of the reasons presented, and the reported strategy used to make the initial decision. In many cases, participants who did not change their positions tended to become more confident in the superiority of their positions after considering many reasons for both sides. (shrink)

Having positive moral traits is central to one’s sense of self, and people generally are motivated to maintain a positive view of the self in the present. But it remains unclear how people foster a positive, morally good view of the self in the present. We suggest that recollecting and reflecting on moral and immoral actions from the personal past jointly help to construct a morally good view of the current self in complementary ways. More specifically, across four studies we (...) investigated the extent to which people believe they have changed over time after recollecting their own moral or immoral behaviors from the personal past. Our results indicate that recollecting past immoral actions is associated with stronger impressions of dissimilarity and change in the sense of self over time than recollecting past moral actions. These effects held for diverse domains of morality (i.e., honesty/dishonesty, helping/harming, fairness/unfairness, and loyalty/disloyalty), and they remained even after accounting for objective, calendar time. Further supporting a motivational explanation, these effects held when people recollected their own past actions but not when they recollected the actions of other people. (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)

Much of the discussion of the role of emerging technologies associated with AI, machine learning, digital simulacra, and relevant ethical considerations such as those discussed in the target article, take a relatively narrow and episodic view of a person’s healthcare needs. There is much speculation about diagnostic, treatment, and predictive applications but relatively little consideration of how such technologies might be used to address a person’s lived experience of illness and ongoing care needs. This is likely due to the greater (...) weight or priority given to acute care needs and the role of medical treatment in care provision, but it may also reflect the limitations of current technologies and our limited vision of their potential application. Such limitations are not surprising given that we are still grappling with the complexities and nuances of achieving the ethical and humanistic ideals of care, namely, care that addresses the hermeneutical, relational, contextual, temporal, and agential dimensions of a person’s health and wellbeing. (shrink)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

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

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)

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)

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.

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 chapter describes the attributionist approach to moral responsibility. Works by Pamela Hieronymi, T.M. Scanlon, Angela Smith, and Matthew Talbert are taken to representative of this approach. On the interpretation given here, attributionism is committed to the following: assessments of moral responsibility are, and ought to be, centrally concerned with the morally significant features of an agent’s orientation toward others that are attributable to her, and an agent is eligible for moral praise or blame solely on the basis (...) of these attributions. Attributionism is presented as rejecting the claim that agents are morally responsible only for what is under their voluntary control, as well as the claim that agents are responsible for wrongdoing only if they could have responded to the moral considerations that spoke against your behavior. These supposed conditions on moral responsibility are rejected for the same reason: agents may reveal features of their selves, in a way that is sufficient for moral responsibility, even in cases in which these conditions are not met. (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)

Glucagon-like peptide-1 (GLP-1) receptor agonists, such as semaglutide, and dual GLP-1 and glucose-dependent insulinotropic polypeptide (GIP) receptor agonists, such as tirzepatide, have been found to be effective for treating obesity and diabetes, significantly reducing weight and the risk or predicted risk of adverse cardiovascular events. There is a global shortage of these medications that could last several years and raises questions about how limited supplies should be allocated. We propose a fair-allocation framework that enables evaluation of the ethics of current (...) practices and could guide governments, professional societies, and physicians in allocation decisions. (shrink)

Broadening access to both computational and educational resources is crit- ical to diffusing machine learning (ML) innovation. However, today, most ML resources and experts are siloed in a few countries and organizations. In this article, we describe our pedagogical approach to increasing access to applied ML through a massive open online course (MOOC) on Tiny Machine Learning (TinyML). We suggest that TinyML, applied ML on resource-constrained embedded devices, is an attractive means to widen access because TinyML leverages low-cost and globally (...) accessible hardware and encourages the development of complete, self-contained applications, from data collection to deployment. To this end, a collaboration between academia and industry produced a four part MOOC that provides application-oriented instruction on how to develop solutions using TinyML. The series is openly available on the edX MOOC platform, has no prerequisites beyond basic programming, and is designed for global learners from a variety of backgrounds. It introduces real-world applications, ML algorithms, data-set engineering, and the ethi- cal considerations of these technologies through hands-on programming and deployment of TinyML applications in both the cloud and on their own microcontrollers. To facili- tate continued learning, community building, and collaboration beyond the courses, we launched a standalone website, a forum, a chat, and an optional course-project com- petition. We also open-sourced the course materials, hoping they will inspire the next generation of ML practitioners and educators and further broaden access to cutting-edge ML technologies. (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)

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)

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

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)

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 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)

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)

Imagine I hold up a Granny Smith apple for all to see. You would thereby gain justified beliefs that it was green, that it was apple, and that it is a Granny Smith apple. Under classical foundationalism, such simple visual beliefs are mediately justified on the basis of reasons concerning your experience. Under dogmatism, some or all of these beliefs are justified immediately by your experience and not by reasons you possess. This paper argues for what I call (...) the looks view of the justification of simple visual beliefs. According to the looks view, such beliefs are mediately justified on the basis of reasons concerning how the relevant things look. Unlike under classical foundationalism, under the looks view as I develop it, these reasons are public. They are public with respect to both their content and possession: with respect to content, they are not about ourselves and our experiences, and with respect to their possession, many people can have the very same looks-related reasons. (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)

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)

Assertion is governed by an epistemic norm requiring knowledge. This idea has been hotly debated in recent years, garnering attention in epistemology, philosophy of language, and linguistics. This chapter presents and extends the main arguments in favor of the knowledge norm, from faulty conjunctions, several conversational patterns, judgments of permission, excuse, and blame, and from showing how. (Paired with a chapter by Peter J. Graham and Nikolaj J. L. L. Pedersen, "Knowledge is Not Our Norm of Assertion.").

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)

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)

In un articolo comparso sul Wall Street Journal del 13 novembre 2oi:n viene descritto il modo in cui i computer potrebbero essere utilizzati al fine di allertare i responsabili della salute pubblica in relazione ad eventuali problemi provocati dal bioterrorismo. L'autore nota come gli attacchi biologici sarebbero probabilmente contraddistinti da picchi statistici negli acquisti senza ricetta medica di rimedi per specifici disturbi di tipo comune e come i dati che riguardano tali acquisti possano essere resi disponibili immediatamente grazie agli inventari (...) computerizzati dei rivenditori. (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)

In this essay, I evaluate four central metaethical readings of Spinoza’s moral philosophy in the literature: unqualified anti-realism, qualified anti-realism, qualified realism, and unqualified realism. More specifically, I discuss the metaethical readings of Charles Jarrett (unqualified anti-realism), Matthew Kisner (qualified anti-realism), Jon Miller (qualified realism), and Andrew Youpa (unqualified realism), each of which captures core aspects of this debate. My conclusions are that (1) Spinoza is neither an unqualified anti-realist nor an unqualified realist and (2) Spinoza’s ethical framework represents (...) a qualified synthesis of realist (naturalistic) and anti-realist (affective) features. (shrink)

La présente étude utilise les outils du domaine de la méréotopologie (la théorie des parts, ensembles et frontières) pour élaborer les implications de certaines analogies entre la 'psychologie écologique' de J.J.Gibson et la phénoménologie de Edmund Husserl. On présentera une théorie ontologique de frontières spatiales et des entités possédant une extension spatiale. S'en rapportant aux exemples de la sphère de géographie, on démontre qu'aussi bien les frontières que les entités à extension spatiale appartiennent à deux vastes catégories: des objets qui (...) existent indépendamment de nos actes cognitifs (par exemple: la planète Terre, sa surface extérieure); et des objets qui existent seulement grâce à ces actes (par exemple: l'équateur, la Mer du Nord). Le champ visuel, lui aussi, peut être conçu comme un exemple d'une entité à extension spatiale qui est dépendante dans le sens proposé ci-dessus. L'étude présente suggère une extension de cette analogie en postulant les entités qui, pour les vrais jugements, seraient ce que le champ visuel est pour les actes de perception visuelle. Le champ de jugement est défini plus précisément comme une entité étendue complexe, contenant toutes les entités essentielles pour la vérité d'un (vrai) jugement donné. Il est possible de démontrer que le travail des linguistes cognitifs tel Talmy ou Langacker, si l'on l'interprète convenablement, produit une explication détaillée des structures des champs de jugement correspondant aux phrases de sortes différentes. Un genre nouveau de définition de la vérité en tant que correspondance pour les expressions de la langue naturelle peut donc être formulé sur cette base. (shrink)

L'articolo usa la teoria delle parti, del tutto e dei contomi per elaborare alcune relazioni cruciali tra la «psicologia ecologica» di J.J. Gibson e la fenomenologia di Husserl. Presenta, inoltre, una teoria ontologica dei contomi spaziali e delle entita spazialmente estese, applicandola al cam po visivo, qui concepito come un' entita spazialmente estesa dipendente dal soggetto che percepisce. Su questa base e possibile formulare un nuovo tipo di definizione teoretico-correspondentista della verita per gli enunciati del linguaggio naturale.

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 is a short introduction to a book symposium on Paul Gowder's recent book, _The Rule of Law in thee Real World_ (Cambridge University Press, 2016). The book symposium will appear in the St. Luis University Law Journal, 62 St. Louis U. L.J., -- (2018), with commentaries on Gowder's book by colleen Murphy, Robin West, Chad Flanders, and Matthew Lister, along with replies by Paul Gowder.

How many championships have the Lakers won? Fourteen, if one counts those won in Minneapolis; nine, otherwise. Which is the correct answer? Is it even obvious that there is a correct answer? One is tempted to identify a team with its players. But teams, like ordinary objects, seem to survive gradual turnover of their parts. Suppose players from the Lakers are gradually replaced, one by one, over the years. We have the intuition that the team persists through this change, even (...) after none of the original players remain. Suppose too that these original players wind up playing for the Celtics. Lakers fans face an awkward question: for whom should they root? On the one hand, they have the team currently playing in L.A.—a team that has continued gradually through the years, who wear the same uniforms, but now can’t make the playoffs. On the other hand, there are the beloved Lakers starting five (responsible for all those championships) now playing together in the hated Boston garden—a team which looks (despite wearing those hated Celtics jerseys) and plays just like the Lakers of old. What’s a loyal fan to do? (shrink)

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)

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.

ABSTRACT: In his A Conceptual Investigation of Justice, Kyle Johannsen suggests a theory of disability that holds that to have a disability just is to be worse off, sometimes referred to as the ‘medical’ or ‘individual’ model of disability. I argue that Johannsen’s understanding of disability might force some of his key claims into an uncomfortable position. In particular, for his theory to avoid the thrust of Elizabeth Anderson’s criticisms of luck egalitarianism, the assumption of the medical model of disability (...) must be dropped, but this comes at the cost of his criticism of John Rawls’ difference principle. -/- RÉSUMÉ : Dans son livre, A Conceptual Investigation of Justice, Kyle Johannsen semble invoquer une théorie du handicap selon laquelle le fait d’avoir un handicap, c’est être pire qu’une autre personne, un modèle parfois appelé le modèle de handicap «médical» ou «individuel». Je soutiens que la compréhension de Johannsen en matière d’invalidité peut mettre sa theorie dans une position difficile. En particulier, pour que sa théorie évite les critiques d’Elizabeth Anderson sur l’égalitarisme de la chance, l’hypothèse du modèle médical du handicap doit être abandonnée. Cependant, cela se fait au détriment de la critique du principe de différence de John Rawls formulée par Johannsen. (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».