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 notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified (...) and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections. (shrink)

Two lines of evidence indicate that there exists a reciprocal inhibitory relationship between opposed brain networks. First, most attention-demanding cognitive tasks activate a stereotypical set of brain areas, known as the task-positive network and simultaneously deactivate a different set of brain regions, commonly referred to as the task negative or defaultmode network. Second, functional connectivity analyses show that these same opposed networks are anti-correlated in the resting state. Wehypothesize that these reciprocally inhibitory effects reflect two incompatible cognitive modes, each of (...) which may be directed towards understanding the external world. Thus, engaging onemode activates one set of regions and suppresses activity in the other.Wetest this hypothesis by identifying two types of problem-solving task which, on the basis of prior work, have been consistently associated with the task positive and task negative regions: tasks requiring social cognition, i.e., reasoning about the mental states of other persons, and tasks requiring physical cognition, i.e., reasoning about the causal/mechanical properties of inanimate objects. Social and mechanical reasoning tasks were presented to neurologically normal participants during fMRI. Each task type was presented using both text and video clips. Regardless of presentation modality, we observed clear evidence of reciprocal suppression: social tasks deactivated regions associated with mechanical reasoning and mechanical tasks deactivated regions associated with social reasoning. These findings are not explained by self-referential processes, task engagement, mental simulation,mental time travel or external vs. internal attention, all factors previously hypothesized to explain default mode network activity. Analyses of resting state data revealed a close match between the regions our tasks identified as reciprocally inhibitory and regions of maximal anti-correlation in the resting state. These results indicate the reciprocal inhibition is not attributable to constraints inherent in the tasks, but is neural in origin. Hence, there is a physiological constraint on our ability to simultaneously engage two distinct cognitive modes. Furtherwork is needed tomore precisely characterize these opposing cognitive domains. (shrink)

The last decade has witnessed the beginnings of a remarkable convergence of Husserlian phenonenology and analytic philosophy of language, and the present volumes provide original and important texts of the phenomenological philosophy of language. Powerfully influenced by the writings of the early Husserl, Reinach fashioned Husserl’s ideas into a rigorous analytical methodology of his own, which he applied in particular to problems in logic and the theory of knowledge, and to the philosophies of law and psychology. The central role of (...) the concept of state of affairs in Reinach’s philosophy will bring to mind immediately the formal ontology of Wittgenstein’s Tractatus. Reinach’s most significant contribution, however, is contained in his The a priori foundations of civil law (1913), above all in the detailed analysis of the a priori structure of the act of promising. This amounts to an elaborate phenomenological theory of speech acts which anticipates, and in some respects goes beyond, the later theories of Austin and Searle. The present edition is in two volumes. Volume 1, which includes a biographical and thematic introduction by the editors, contains critical editions of those pieces published by Reinach himself. Volume II is a collection of all those items in Reinach’s surviving Nachlass which are in publishable form, including a number of important pieces not hitherto obtainable on such themes as ethical predicates, speech acts (“soziale Akte”), perception and the theory of number, together with a comprehensive sketch of the problems in the theory of knowledge, logic and ethics. Appended to this is a text-critical apparatus which also contains extensive discussions of the origins and sources of the materials in question. (shrink)

Commentary about the role of AI in bioethics for the 10th anniversary issue of AJOB: Empirical Bioethics.

A diagnostic process is an investigative process that takes a clinical picture as input and outputs a diagnosis. We propose a method for distinguishing diagnoses that are warranted from those that are not, based on the cognitive processes of which they are the outputs. Processes designed and vetted to reliably produce correct diagnoses will output what we shall call ‘warranted diagnoses’. The latter are diagnoses that should be trusted even if they later turn out to have been wrong. Our work (...) is based on the recently developed Cognitive Process Ontology and further develops the Ontology of General Medical Science. It also has applications in fields such as intelligence, forensics, and predictive maintenance, all of which rely on vetted processes designed to secure the reliability of their outputs. (shrink)

This paper examines how professionals (N = 32) working on artificial intelligence (AI) view structural AI ethics challenges like injustices and inequalities beyond individual agents' direct intention and control. This paper answers the research question: What are professionals’ perceptions of the structural challenges of AI (in the agri-food sector)? This empirical paper shows that it is essential to broaden the scope of ethics of AI beyond micro- and meso-levels. While ethics guidelines and AI ethics often focus on the responsibility of (...) designers and the competencies and skills of designers to take this responsibility, our results show that many structural challenges are beyond their reach. This result means that while ethics guidelines and AI ethics frameworks are helpful, there is a risk that they overlook more complicated, nuanced, and intersected structural challenges. In addition, it highlights the need to include diverse stakeholders, such as quadruple helix (QH) participants, in discussions around AI ethics rather than solely focusing on the obligations of AI developers and companies. Overall, this paper demonstrates that addressing structural challenges in AI is challenging and requires an approach that considers four requirements: (1) multi-level, (2) multi-faceted, (3) interdisciplinary, and (4) polycentric governance. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data (...) relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. (shrink)

In this paper we propose an Ontology of Commercial Exchange (OCE) based on Basic Formal Ontology. OCE is designed for re-use in the Industrial Ontologies Foundry (IOF) and in other ontologies addressing different aspects of human social behavior involving purchasing, selling, marketing, and so forth. We first evaluate some of the design patterns used in the Financial Industry Business Ontology (FIBO) and Product Types Ontology (PTO). We then propose terms and definitions that we believe will improve the representation of contractual (...) obligations, sales processes, and their associated documents. A commercial exchange, for instance, involves mutual agreement to reciprocate actions, such as transferring money, performing a service, or transferring goods. (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)

What follows is a first step towards an ontology of conscious mental processes. We provide a theoretical foundation and characterization of conscious mental processes based on a realist theory of intentionality and using BFO as our top-level ontology. We distinguish three components of intentional mental process: character, directedness, and objective referent, and describe several features of the process character and directedness significant to defining and classifying mental processes. We arrive at the definition of representational mental process as a process that (...) is the bringing into being, sustaining, modifying, or terminating of a mental representation. We conclude by outlining some benefits and applications of this approach. (shrink)

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

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general, domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, which is intended to be the basis of a knowledge modelling language GOL (for: 'General Ontological Language'). It turns out that the upper- level ontology underlying standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. Set theory has considerable mathematical power and (...) great flexibility as a framework for modelling different sorts of structures. At the same time it has the disadvantage that sets are abstract entities (entities existing outside the realm of time, space and causality), and thus a set-theoretical framework should be supplemented by some other machinery if it is to support applications in the ripe, messy world of concrete objects. In the present paper we partition the entities of the real world into sets and urelements, and then we introduce several new ontological relations between these urelements. In contrast to standard modelling and representation formalisms, the concepts of GOL provide a machinery for representing and analysing such ontologically basic relations. (shrink)

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

We propose capability as a universal or type intermediate between function and disposition. A capability is, broadly speaking, a disposition that is of a type whose instances can be evaluated on the basis of how well they are realized. A function, on the view we are proposing, is a capability the possession of which is the rationale for the existence of its bearer. To say for example that a water pump has the function to pump water is to say that (...) the pump exists because something was needed that would pump water. A water pump may have many capabilities, including: to be weatherproof, to run without lubricant, to be transportable, and so forth. But its function is to pump water. We focus here on capabilities possessed by humans – such as piano playing or language using – and we explore the relation between capabilities of these sorts and structures in the brain. (shrink)

In this article, we develop a concept of stakeholder dialogue in responsible innovation (RI) processes. The problem with most concepts of communication is that they rely on ideals of openness, alignment and harmony, even while these ideals are rarely realized in practice. Based on the work of Burke, Habermas, Deetz and Levinas, we develop a concept of stakeholder dialogue that is able to deal with fundamentally different interests and value frames of actors involved in RI processes. We distinguish four main (...) characteristics of stakeholder dialogue. Dialogical responsiveness (1) enhances self-criticism, (2) is characterized by the constitution and the destruction of the self or identity of the actors involved, (3) consists only in the actual enactment of the dialogue and (4) is primarily responsive to the grand challenges of our time. Based on our findings, we provide a novel conceptualization of the central notion of responsiveness in the RI literature. (shrink)

Disputes over territory are a major contributing factor to the disruption of international relations. We believe that a cumulative, integrated, and continuously updated resource providing information about such disputes in an easily accessible form would be of benefit to intelligence analysts, military strategists, political scientists, and also to historians and others concerned with international disputes. We propose an ontology-based strategy for creating such a resource. The resource will contain information about territorial disputes, arguments for and against claims pertaining to sovereignty, (...) proffered evidence for such claims, political and military motives (overt or hidden), and associated conflicts. Our approach is designed to address several issues surrounding the representation of geopolitical conflict, including the tracking and individuation of disputes and the validation of disseminated information. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

Maintaining systems of military plans is critical for military effectiveness, but is also challenging. Plans will become obsolete as the world diverges from the assumptions on which they rest. If too many ad hoc changes are made to intermeshed plans, the ensemble may no longer lead to well-synchronized and coordinated operations, resulting in the system of plans becoming itself incoherent. We describe in what follows an Adaptive Planning process that we are developing on behalf of the Air Force Research Laboratory (...) (Rome) with the goal of addressing problems of these sorts through cyclical collaborative plan review and maintenance. The interactions of world state, blue force status and associated plans are too complex for manual adaptive processes, and computer-aided plan review and maintenance is thus indispensable. We argue that appropriate semantic technology can 1) provide richer representation of plan-related data and semantics, 2) allow for flexible, non-disruptive, agile, scalable, and coordinated changes in plans, and 3) support more intelligent analytical querying of plan-related data. (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)

In this article, we reflect on the conditions under which new technologies emerge in the Anthropocene and raise the question of how to conceptualize sustainable technologies therein. To this end, we explore an eco-centric approach to technology development, called biomimicry. We discuss opposing views on biomimetic technologies, ranging from a still anthropocentric orientation focusing on human management and control of Earth’s life-support systems, to a real eco-centric concept of nature, found in the responsive conativity of nature. This concept provides the (...) ontological and the epistemological condition for an eco-centric concept of biomimetic technologies in the Anthropocene. We distinguish five principles for this concept that can guide future technological developments. (shrink)

This volume brings together the advanced research results obtained by the European COST Action 2102: “Cross Modal Analysis of Verbal and Nonverbal Communication”. The research published in this book was discussed at the 3rd joint EUCOGII-COST 2102 International Training School entitled “Toward Autonomous, Adaptive, and Context-Aware Multimodal Interfaces: Theoretical and Practical Issues ” and held in Caserta, Italy, on March 15-19, 2010.

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

Traditionally, discussions of moral participation – and in particular moral agency – have focused on fully formed human actors. There has been some interest in the development of morality in humans, as well as interest in cultural differences when it comes to moral practices, commitments, and actions. However, until relatively recently, there has been little focus on the possibility that nonhuman animals have any role to play in morality, save being the objects of moral concern. Moreover, when nonhuman cases are (...) considered as evidence of moral agency or subjecthood, there has been an anthropocentric tendency to focus on those behaviors that inform our attributions of moral agency to humans. For example, some argue that the ability to evaluate the principles upon which a moral norm is grounded is required for full moral agency. Certainly, if a moral agent must understand what makes an action right or wrong, then most nonhuman animals would not qualify (and perhaps some humans too). However, if we are to understand the evolution of moral psychology and moral practice, we need to turn our attention to the foundations of full moral agency. We must first pay attention to the more broadly normative practices of other animals. Here, we begin that project by considering evidence that great apes and cetaceans participate in normative practices. (shrink)

This is the short version, in French translation by Anne Querrien, of the originally jointly authored paper: Müller, Vincent C., ‘Autonomous killer robots are probably good news’, in Ezio Di Nucci and Filippo Santoni de Sio, Drones and responsibility: Legal, philosophical and socio-technical perspectives on the use of remotely controlled weapons. - - - L’article qui suit présente un nouveau système d’armes fondé sur des robots qui risque d’être prochainement utilisé. À la différence des drones qui sont manoeuvrés à (...) distance mais comportent une part importante de discernement humain, il s’agit de machines programmées pour défendre, attaquer, ou tuer de manière autonome. Les auteurs, philosophes, préfèrent prévenir de leur prochaine diffusion et obtenir des Nations Unies leur régulation. Une campagne internationale propose plutôt leur interdiction. (shrink)

Artificial intelligence (AI) and robotics are digital technologies that will have significant impact on the development of humanity in the near future. They have raised fundamental questions about what we should do with these systems, what the systems themselves should do, what risks they involve, and how we can control these. - After the Introduction to the field (§1), the main themes (§2) of this article are: Ethical issues that arise with AI systems as objects, i.e., tools made and used (...) by humans. This includes issues of privacy (§2.1) and manipulation (§2.2), opacity (§2.3) and bias (§2.4), human-robot interaction (§2.5), employment (§2.6), and the effects of autonomy (§2.7). Then AI systems as subjects, i.e., ethics for the AI systems themselves in machine ethics (§2.8) and artificial moral agency (§2.9). Finally, the problem of a possible future AI superintelligence leading to a “singularity” (§2.10). We close with a remark on the vision of AI (§3). - For each section within these themes, we provide a general explanation of the ethical issues, outline existing positions and arguments, then analyse how these play out with current technologies and finally, what policy consequences may be drawn. (shrink)

in this article, we explore how responsible research and innovation (RRI) interacts with the current political context. We examine the (1) possible consequences for RRI and related agendas if values associated with ‘populist’ movements become more pervasive, (2) the role that a lack of RRI has potentially played in the development of this political context, and (3) how RRI as a concept, practice, and research agenda should respond. We argue that whilst RRI is threatened, it is now more important than (...) ever. We propose that RRI needs to go beyond being a method for facilitating societal input into research and innovation and for highlighting desired impacts. RRI needs to evolve to provide an effective conduit for criticisms and the input of critical thinking and reflexivity into science and innovation, including in terms of economic policy and politics. (shrink)

Report for "The Reasoner" on the conference "Philosophy and Theory of Artificial Intelligence", 3 & 4 October 2011, Thessaloniki, Anatolia College/ACT, http://www.pt-ai.org. --- Organization: Vincent C. Müller, Professor of Philosophy at ACT & James Martin Fellow, Oxford http://www.sophia.de --- Sponsors: EUCogII, Oxford-FutureTech, AAAI, ACM-SIGART, IACAP, ECCAI.

In this chapter, I philosophically reflect on the management of corporate responsibility in the case of innovation. I first set the scene by contrasting responsibility in corporate social responsibility and innovation ethics, and arguing that classical conceptualizations of backward and forward looking responsibility are inappropriate in the case of innovation. Next, I introduce the concept of responsible innovation as a lens to understand the management of corporate responsibility in the case of innovation and show that the notions of virtue ethics (...) and practical wisdom are inappropriate for understanding what is at stake in innovation ethics, because the notion of practical wisdom is at odds with the nature of innovation. I conclude this chapter by proposing a concept of action-based responsible management of corporate innovation, which will be framed in terms of innovation as ethos. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (shrink)

Management of information is facilitated by unambiguously tracking portions of reality over time. To track the portions of reality, a referent tracking system is used. The referent tracking system is able to communicate with other tracking systems and/or tradition information systems. Errors in the referent tracking system are detected and corrected to maintain actual representations of the portions of reality.

Despite the importance of human blood to clinical practice and research, hematology and blood transfusion data remain scattered throughout a range of disparate sources. This lack of systematization concerning the use and definition of terms poses problems for physicians and biomedical professionals. We are introducing here the Blood Ontology, an ongoing initiative designed to serve as a controlled vocabulary for use in organizing information about blood. The paper describes the scope of the Blood Ontology, its stage of development and some (...) of its anticipated uses. (shrink)

Human cognitive acts are directed towards entities of a wide range of different types. What follows is a new proposal for bringing order into this typological clutter. A categorial scheme for the objects of human cognition should be (1) critical and realistic. Cognitive subjects are liable to error, even to systematic error of the sort that is manifested by believers in the Pantheon of Olympian gods. Thus not all putative object-directed acts should be recognized as having objects of their own. (...) Broadly, the objects towards which human cognition is directed should be parts of reality in a sense that is at least consistent with the truths of natural science. But such a scheme should also be (2) comprehensive: it should do justice to each sort of object on its own terms, and not attempt to eliminate objects of one sort in favour of objects of other, more favoured sorts. Linguistic and other forms of idealism, as well as Meinongian theories, which assign to each and every referring expression or intentional act an object tailored to fit, yield categorial schemes which fail to satisfy (1). Physicalistic and other forms of reductionism yield categorial schemes which fail to satisfy (2). What follows is a categorial scheme that is both critically realistic and comprehensive. Thus it enjoys some of the benefits of linguistic idealism and physicalism, without (or so it is hoped) the corresponding disadvantages of each. (shrink)

This paper investigates the prospects of Rodney Brooks’ proposal for AI without representation. It turns out that the supposedly characteristic features of “new AI” (embodiment, situatedness, absence of reasoning, and absence of representation) are all present in conventional systems: “New AI” is just like old AI. Brooks proposal boils down to the architectural rejection of central control in intelligent agents—Which, however, turns out to be crucial. Some of more recent cognitive science suggests that we might do well to dispose of (...) the image of intelligent agents as central representation processors. If this paradigm shift is achieved, Brooks’ proposal for cognition without representation appears promising for full-blown intelligent agents—Though not for conscious agents. (shrink)

The paper presents a new method for generating typologies of formal-ontological relations. The guiding idea is that formal relations are those sorts of relations which hold between entities which are constituents of distinct ontologies. We provide examples of ontologies (in the spirit of Zemach’s classic “Four Ontologies” of 1970), and show how these can be used to give a rich typology of formal relations in a way which also throws light on the opposition between threeand four-dimensionalism.

Efficient markets are alienating if they inhibit us from recognizably caring about one another in our productive activities. I argue that efficient market behaviour is both exclusionary and fetishistic. As exclusionary, the efficient marketeer cannot manifest care alongside their market behaviour. As fetishistic, the efficient marketeer cannot manifest care in their market behaviour. The conjunction entails that efficient market behavior inhibits care. It doesn’t follow that efficient market behavior is vicious: individuals might justifiably commit to efficiency because doing so serves (...) the common good. But efficient market systems nevertheless have significant opportunity costs. The discussion yields a range of desiderata for non-alienated economic organization. (shrink)

Artificial intelligence (AI) is a digital technology that will be of major importance for the development of humanity in the near future. AI has raised fundamental questions about what we should do with such systems, what the systems themselves should do, what risks they involve and how we can control these. - After the background to the field (1), this article introduces the main debates (2), first on ethical issues that arise with AI systems as objects, i.e. tools made and (...) used by humans; here, the main sections are privacy (2.1), manipulation (2.2), opacity (2.3), bias (2.4), autonomy & responsibility (2.6) and the singularity (2.7). Then we look at AI systems as subjects, i.e. when ethics is for the AI systems themselves in machine ethics (2.8.) and artificial moral agency (2.9). Finally we look at future developments and the concept of AI (3). For each section within these themes, we provide a general explanation of the ethical issues, we outline existing positions and arguments, then we analyse how this plays out with current technologies and finally what policy conse-quences may be drawn. (shrink)

In this paper I want to propose an argument to support Jerry Fodor’s thesis (Fodor 1983) that input systems are modular and thus informationally encapsulated. The argument starts with the suggestion that there is a “grounding problem” in perception, i. e. that there is a problem in explaining how perception that can yield a visual experience is possible, how sensation can become meaningful perception of something for the subject. Given that visual experience is actually possible, this invites a transcendental argument (...) that explains the conditions of its possibility. I propose that one of these conditions is the existence of a visual module in Fodor’s sense that allows the step from sensation to object-identifying perception, thus enabling visual experience. It seems to follow that there is informationally encapsulated nonconceptual content in visual perception. (shrink)

This open access monograph offers a detailed study and a systematic defense of a key intuition we typically have, as human beings, with respect to the nature of time: the intuition that the future is open, whereas the past is fixed. For example, whereas it seems unsettled whether there will be a fourth world war, it is settled that there was a first world war. -/- The book contributes, in particular, three major and original insights. First, it provides a coherent, (...) non-metaphorical, and metaphysically illuminating elucidation of the intuition. Second, it determines which model of the temporal structure of the world is most appropriate to accommodate the intuition, and settles on a specific version of the Growing Block Theory of time (GBT). Third, it puts forward a naturalistic foundation for GBT, by exploiting recent results of our best physics (viz. General Relativity, Quantum Mechanics, and Quantum Gravity). Three main challenges are addressed: the dismissal of temporal asymmetries as non-fundamental phenomena only (e.g., thermodynamic or causal phenomena), the epistemic objection against GBT, and the apparent tension between GBT and relativistic physics. It is argued that the asymmetry between the open future and the fixed past must be grounded in the temporal structure of the world, and that this is neither precluded by our epistemic device, nor by the latest approaches to Quantum Gravity (​e.g., the Causal Set Theory). -/- Aiming at reconciling time as we find it in ordinary experience and time as physics describes it, this ​innovative book ​will raise the interest of both academic researchers and ​graduate students working on the philosophy of time. More generally, it ​presents contents of interest for all metaphysicians and non-dogmatic philosophers of physics. (shrink)

There is a basic distinction, in the realm of spatial boundaries, between bona fide boundaries on the one hand, and fiat boundaries on the other. The former are just the physical boundaries of old. The latter are exemplified especially by boundaries induced through human demarcation, for example in the geographic domain. The classical problems connected with the notions of adjacency, contact, separation and division can be resolved in an intuitive way by recognizing this two-sorted ontology of boundaries. Bona fide boundaries (...) yield a notion of contact that is effectively modeled by classical topology; the analogue of contact involving fiat boundaries calls, however, for a different account, based on the intuition that fiat boundaries do not support the open/closed distinction on which classical topology is based. In the presence of this two-sorted ontology it then transpires that mereotopology—topology erected on a mereological basis—is more than a trivial formal variant of classical point-set topology. (shrink)

There is, in some quarters, concern about high–level machine intelligence and superintelligent AI coming up in a few decades, bringing with it significant risks for humanity. In other quarters, these issues are ignored or considered science fiction. We wanted to clarify what the distribution of opinions actually is, what probability the best experts currently assign to high–level machine intelligence coming up within a particular time–frame, which risks they see with that development, and how fast they see these developing. We thus (...) designed a brief questionnaire and distributed it to four groups of experts in 2012/2013. The median estimate of respondents was for a one in two chance that high-level machine intelligence will be developed around 2040-2050, rising to a nine in ten chance by 2075. Experts expect that systems will move on to superintelligence in less than 30 years thereafter. They estimate the chance is about one in three that this development turns out to be ‘bad’ or ‘extremely bad’ for humanity. (shrink)

Autobiography of Barry Smith; emphasizes the role of Dummett and Husserl, Austrian philosophy and economics, and the Munich-Göttingen-Kraków school of realist phenomenology.

This review focuses on the Ogdoas scholastica by Jacob Lorhard, published in 1606. The importance of this document turns on the fact that it contains what is almost certainly the first published occurrence of the term “ontology.” The body of the work consists in a series of diagrams called “diagraphs.” Relevant features of this compendium of diagraphs are: 1. that it does not in fact contain the word “ontology,” and 2. that Lorhard himself was not responsible for its content.

Some authors have recently suggested that it is time to consider rights for robots. These suggestions are based on the claim that the question of robot rights should not depend on a standard set of conditions for ‘moral status’; but instead, the question is to be framed in a new way, by rejecting the is/ought distinction, making a relational turn, or assuming a methodological behaviourism. We try to clarify these suggestions and to show their highly problematic consequences. While we find (...) the suggestions ultimately unmotivated, the discussion shows that our epistemic condition with respect to the moral status of others does raise problems, and that the human tendency to empathise with things that do not have moral status should be taken seriously—we suggest that it produces a “derived moral status”. Finally, it turns out that there is typically no individual in real AI that could even be said to be the bearer of moral status. Overall, there is no reason to think that robot rights are an issue now. (shrink)