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

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

The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in publicly available databases. Such (...) annotation enables several objectives, including searching, browsing and cross-database data integration. A key benefit conferred by realismbased ontology is that suitably annotated research results are able to be aggregated and compared in a fashion that is based on the underlying reality that the science is studying. This has the potential of increasing the power of statistical analysis and meta-analysis in data-driven science. This aspect has been fruitfully exploited in the investigation of the functions of genes in molecular biology. Cognitive neuroscience uses functional neuroimaging to investigate the brain correlates of areas of mental functioning such as memory, planning and emotion. The use of functional neuroimaging to study affective phenomena such as the emotions is called ‘affective neuroscience’. BrainMap is the largest curated database of coordinates and metadata for studies in cognitive neuroscience, including affective neuroscience (Laird et al., 2005). BrainMap data is already classified and indexed using a terminology for classification, called the ‘Cognitive Paradigm Ontology’ (CogPO), that has been developed to facilitate searching and browsing. However, CogPO has been developed specifically for the BrainMap database, and the data are thus far not annotated to a realism-based ontology which would allow the discovery of interrelationships between research results across different databases on the basis of what the research is about. In this contribution, we describe ongoing work that aims to annotate affective neuroscience data, starting with the BrainMap database, using the Emotion Ontology. We describe our objectives and technical approach to the annotation, and mention some of the challenges. (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)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

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

History has left a territory composed of two municipalitics, whose shape is unique, belonging partly to the Netherlands and partly to Belgium. Earlier both parts belonged to the former Duchy of Brabant, a tenitory that is now split up into the Dutch province of Noord-Brabant (including Baarle-Nassau) and thc Belgian provinces of Antwerp (which includes Baarle-Hertog), Vlaams Brabant, Brussels, and Brabant-Wallon. People are quite comfortable with this situation, even though it raises many complicated and difficult problems that even the most (...) brilliant jurists are puzzled. Baarle-Hertog is called on older Belgian maps Barle-Duc (Hertog = Duke, fr: duc) and must not be confused with the prefectoral town of Bar-le-Duc, Meuse, France. (shrink)

It is plausible that there are epistemic reasons bearing on a distinctively epistemic standard of correctness for belief. It is also plausible that there are a range of practical reasons bearing on what to believe. These theses are often thought to be in tension with each other. Most significantly for our purposes, it is obscure how epistemic reasons and practical reasons might interact in the explanation of what one ought to believe. We draw an analogy with a similar distinction between (...) types of reasons for actions in the context of activities. The analogy motivates a two-level account of the structure of normativity that explains the interaction of correctness-based and other reasons. This account relies upon a distinction between normative reasons and authoritatively normative reasons. Only the latter play the reasons role in explaining what state one ought to be in. All and only practical reasons are authoritative reasons. Hence, in one important sense, all reasons for belief are practical reasons. But this account also preserves the autonomy and importance of epistemic reasons. Given the importance of having true beliefs about the world, our epistemic standard typically plays a key role in many cases in explaining what we ought to believe. In addition to reconciling (versions of) evidentialism and pragmatism, this two-level account has implications for a range of important debates in normative theory, including the interaction of right and wrong reasons for actions and other attitudes, the significance of reasons in understanding normativity and authoritative normativity, the distinction between ‘formal’ and ‘substantive’ normativity, and whether there is a unified source of authoritative normativity. (shrink)

Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied (...) to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters. (shrink)

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)

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.

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, (...) we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

This paper presents the main topics, arguments, and positions in the philosophy of AI at present (excluding ethics). Apart from the basic concepts of intelligence and computation, the main topics of ar-tificial cognition are perception, action, meaning, rational choice, free will, consciousness, and normativity. Through a better understanding of these topics, the philosophy of AI contributes to our understand-ing of the nature, prospects, and value of AI. Furthermore, these topics can be understood more deeply through the discussion of AI; so (...) we suggest that “AI Philosophy” provides a new method for philosophy. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of (...) making computers understand medical natural language. (shrink)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

Propomos uma tipologia dos artefatos de representação para as áreas de saúde e ciências biológicas, e a associação dessa tipologia com diferentes tipos de ontologia formal e lógica, chegando a conclusões quanto aos pontos fortes e limitações da ontologia de diferentes tipos de recursos lógicos, enquanto mantemos o foco na lógica descritiva. Consideramos quatro tipos de representação de área: (i) representação léxico-semântica, (ii) representação de tipos de entidades, (iii) representação de conhecimento prévio, e (iv) representação de indivíduos. Defendemos uma clara (...) distinção entre os quatro tipos de representação, de forma a oferecer uma base mais racional para o uso das ontologias e artefatos relacionados no avanço da integração de dados e interoperabilidade de sistemas de raciocínio associados. Destacamos que apenas uma pequena porção de fatos cientificamente relevantes em áreas como a biomedicina pode ser adequadamente representada por ontologias formais, quando estas últimas são concebidas como representações de tipos de entidades. Particularmente, a tentativa de codificar conhecimento padrão ou probabilístico pela utilização de ontologias assim concebidas é fadada à produção de modelos não intencionais e errôneos. (shrink)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

ABSTRACT We have previously argued that there are forms of greenhouse gas offsetting for which, when one emits and offsets, one imposes no risk. Orri Stefansson objects that our argument fails to distinguish properly between the people who stand to be harmed by one’s emissions and the people who stand to be benefited by one’s offsetting. We reply by emphasizing the difference between acting with a probability of making a difference to the distribution of harm and acting in a way (...) that worsen’s someone’s prospect. (shrink)

Various authors debate the question of whether neuroscience is relevant to criminal responsibility. However, a plethora of different techniques and technologies, each with their own abilities and drawbacks, lurks beneath the label “neuroscience”; and in criminal law responsibility is not a single, unitary and generic concept, but it is rather a syndrome of at least six different concepts. Consequently, there are at least six different responsibility questions that the criminal law asks—at least one for each responsibility concept—and, I will suggest, (...) a multitude of ways in which the techniques and technologies that comprise neuroscience might help us to address those diverse questions. In a way, on my account neuroscience is relevant to criminal responsibility in many ways, but I hesitate to state my position like this because doing so obscures two points which I would rather highlight: one, neither neuroscience nor criminal responsibility are as unified as that; and two, the criminal law asks many different responsibility questions and not just one generic question. (shrink)

The emphasis on evidence based medicine (EBM) has placed increased focus on finding timely answers to clinical questions in presence of patients. Using a combination of natural language processing for the generation of clinical excerpts and information theoretic distance based clustering, we evaluated multiple approaches for the efficient presentation of context-sensitive EBM excerpts.

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

Searle’s tool for understanding culture, law and society is the opposition between brute reality and institutional reality, or in other words between: observer-independent features of the world, such as force, mass and gravitational attraction, and observer-relative features of the world, such as money, property, marriage and government. The question posed here is: under which of these two headings do moral concepts fall? This is an important question because there are moral facts – for example pertaining to guilt and responsibility – (...) which hover uncomfortably close to the boundary between the observer-relative and the observer-independent. By means of a thought experiment involving an imagined Chinese society in which guilt is determined by the random throwing of sticks, I seek to show that moral concepts threaten the foundations of Searle’s philosophy of social reality. (shrink)

When a widely reused ontology appears in a new version which is not compatible with older versions, the ontologies reusing it need to be updated accordingly. Ontobull has been developed to automatically update ontologies with new term IRI(s) and associated metadata to take account of such version changes. To use the Ontobull web interface a user is required to (i) upload one or more ontology OWL source files; (ii) input an ontology term IRI mapping; and (where needed) (iii) provide update (...) settings for ontology headers and XML namespace IDs. Using this information, the backend Ontobull Java program automatically updates the OWL ontology files with desired term IRIs and ontology metadata. The Ontobull subprogram BFOConvert supports the conversion of an ontology that imports a previous version of BFO. A use case is provided to demonstrate the features of Ontobull and BFOConvert. (shrink)

An important part of the Unified Medical Language System (UMLS) is its Semantic Network, consisting of 134 Semantic Types connected to each other by edges formed by one or more of 54 distinct Relation Types. This Network is however for many purposes overcomplex, and various groups have thus made attempts at simplification. Here we take this work further by simplifying the relations which involve the three Semantic Types – Diagnostic Procedure, Laboratory Procedure and Therapeutic or Preventive Procedure. We define operators (...) which can be used to generate terms instantiating types from this selected set when applied to terms designating certain other Semantic Types, including almost all the terms specifying clinical tasks. Usage of such operators thus provides a useful and economical way of specifying clinical tasks. The operators allow us to define a mapping between those types within the UMLS which do not represent clinical tasks and those which do. This mapping then provides a basis for an ontology of clinical tasks that can be used in the formulation of computer-interpretable clinical guideline models. (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, and we outline an associated knowledge modelling language called GOL – for: General Ontological Language. It turns out that the upper-level ontology underlying well-known standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. In a set theory which allows Urelements, however, there (...) will be ontological relations between these Urelements which the set-theoretic machinery cannot capture. In contrast to standard modelling and representation formalisms, GOL provides a machinery for representing and analysing such ontologically basic relations. GOL is thus a genuine extension of KIF and of similar languages. In GOL entities are divided into sets and Urelements, the latter being divided in their turn into individuals and universals. Foremost among the individuals are things or substances, tropes or moments, and situoids: entities containing facts as components. (shrink)

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...) the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.

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)

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)

Long-standing neglect of the chemical senses in the philosophy of perception is due, mostly, to their being regarded as ‘lower’ senses. Smell, taste, and chemically irritated touch are thought to produce mere bodily sensations. However, empirically informed theories of perception can show how these senses lead to perception of objective properties, and why they cannot be treated as special cases of perception modelled on vision. The senses of taste, touch, and smell also combine to create unified perceptions of flavour. The (...) nature of these multimodal experiences and the character of our awareness of them puts pressure on the traditional idea that each episode of perception goes one or other of the five senses. Thus, the chemical senses, far from being peripheral to the concerns of the philosophy of perception, may hold important clues to the multisensory nature of perception in general. (shrink)

what is the ontology of planets?Our access point to this question is the ontology of planet Earth. Although the presence of life marks planet Earth as special among other planets, Earth shares a basic commonality with them – namely, its material existence. We take this commonality as a point of departure for our reflections on the ontology of both planet Earth and other planets. In this chapter, we ask for the ontology of this materiality of planets. We consult the ontology (...) of planet Earth as I developed it in an earlier contribution (Blok, 2019), explore the ontology of planets as absolute boundary of the natural habitats on Earth, and reflect on the opportunities and limitations such ontology provides for future human colonies on other planets. (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)

Ontology has been proposed as a solution to the 'Tower of Babel' problem that threatens the semantic interoperability of information systems constructed independently for the same domain. In information systems research and applications, ontologies are often implemented by formalizing the meanings of words from natural languages. However, words in different natural languages sometimes subdivide the same domain of reality in terms of different conceptual categories. If the words and their associated concepts in two natural languages, or even in two terminological (...) traditions within the same language, do not have common referents in the real world, an ontology based on word meanings will inherit the 'Tower of Babel' problem from the languages involved, rather than solve it. In this paper we present evidence from a preliminary comparison of landscape terms in English with those in the Yindjibarndi language of northwestern Australia demonstrating that this problem is not just hypothetical. Some possible solutions are suggested. (shrink)

In this article, we philosophically reflect on the nature of business management. We move beyond the political paradigm of the conceptualization of management in order to lay the ground for a philosophy of business management. First, we open-up the self-evident conceptualization of business management in contemporary management practices by comparing ancient and contemporary definitions of management. Second, we develop a framework with six dimensions of the nature of business management that can guide future philosophical and empirical work on the nature (...) of business management: management control, people management, asset management and entrepreneurial action, management as participation, management as responsive action and management as constituting meaning. (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)

When does a human being begin to exist? We argue that it is possible, through a combination of biological fact and philosophical analysis, to provide a definitive answer to this question. We lay down a set of conditions for being a human being, and we determine when, in the course of normal fetal development, these conditions are first satisfied. Issues dealt with along the way include: modes of substance-formation, twinning, the nature of the intra-uterine environment, and the nature of the (...) relation between fetus and mother (connection, parthood, dependence). (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)

Garrath Williams claims that truly responsible people must possess a “capacity … to respond [appropriately] to normative demands” (2008:462). However, there are people whom we would normally praise for their responsibility despite the fact that they do not yet possess such a capacity (e.g. consistently well-behaved young children), and others who have such capacity but who are still patently irresponsible (e.g. some badly-behaved adults). Thus, I argue that to qualify for the accolade “a responsible person” one need not possess such (...) a capacity, but only to be earnestly willing to do the right thing and to have a history that testifies to this willingness. Although we may have good reasons to prefer to have such a capacity ourselves, and to associate ourselves with others who have it, at a conceptual level I do not think that such considerations support the claim that having this capacity is a necessary condition of being a responsible person in the virtue sense. (shrink)

A collection of material on Husserl's Logical Investigations, and specifically on Husserl's formal theory of parts, wholes and dependence and its influence in ontology, logic and psychology. Includes translations of classic works by Adolf Reinach and Eugenie Ginsberg, as well as original contributions by Wolfgang Künne, Kevin Mulligan, Gilbert Null, Barry Smith, Peter M. Simons, Roger A. Simons and Dallas Willard. Documents work on Husserl's ontology arising out of early meetings of the Seminar for Austro-German Philosophy.

We take as our starting point a thesis to the effect that, at least for true judgments of many varieties, there are parts of reality which make such judgments are true. We argue that two distinct components are involved in this truthmaker relation. On the one hand is the relation of necessitation, which holds between an object x and a judgment p when the existence of x entails the truth of p. On the other hand is the dual notion of (...) projection, which holds between a judgment p and an object x when the truth of p entails the existence of x. A truthmaker for a judgment p is then a necessitator for p which satisfies the further constraint that it is part of p’s projection. We offer a formal theory of the truthmaker relation thus defined, exploiting ontological tools of basic mereology and the theory of dependence. We then apply the theory to a range of problems connected with generic expressions, ellipsis, vagueness, and indexical and perceptual judgments. (shrink)

We reflect on the nature of corporate codes of conduct is this article. Based on John Austin’s speech act theory, four characteristics of a performative concept of corporate codes will be introduced: 1) the existential self-performative of the firm identity, 2) which is demanded by and responsive to their stakeholders; 3) Because corporate codes are structurally threatened by the possibility of failure, 4) embracing the code not only consists in actual corporate responsible behaviour in light of the code, but in (...) the incessant recapturing of the code in the struggle of firms against the possible incongruence between their ethical principles and their actual responsible behaviour. A performative concept of corporate codes helps to bridge classical dichotomies like individualist versus collectivist approaches of moral agency and restrictive versus empowering ethics, and opens a new perspective on the interaction between individual ethical behaviour and the corporate institutionalisation of codes. (shrink)

The paper is an exercise in descriptive ontology, with specific applications to problems in the geographical sphere. It presents a general typology of spatial boundaries, based in particular on an opposition between bona fide or physical boundaries on the one hand, and fiat or human-demarcation-induced boundaries on the other. Cross-cutting this opposition are further oppositions in the realm of boundaries, for example between: crisp and indeterminate, complete and incomplete, enduring and transient, symmetrical and asymmetrical. The resulting typology generates a corresponding (...) categorization of the different sorts of objects which (complete) boundaries determine or demarcate. The theory is applied first of all in the areas of geography and of administrative and property law. Indications are then given as to how the typology may be applied also in other fields where physical and fiat boundaries are at work, including the field of cognitive linguistics and the related field of the ontology of truth. (shrink)

The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. (...) In what follows we show that the supervaluationist approach to singular reference, when wedded to the truthmaker idea, yields a framework of surprising power, which offers a uniform set of solutions to a range of problems regarding identity, reference and knowledge, problems which have hitherto been dealt with on an ad hoc basis. (shrink)