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)

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)

We propose a definition of capability as a class intermediate between function and disposition as the latter are defined in Basic Formal Ontology (BFO). A disposition inheres in a material entity and is realized in a certain kind of process. An example is the disposition of a glass to break when struck, which is realized when it shatters. A function is a disposition which is (simply put) 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. Capabilities are a special sort of disposition in that that, like functions, they can be evaluated on the basis of how well they are realized. They differ from functions in that their realizations are not the rationale – not the primary reason – for the existence of their bearers. Thus, a water pump may have many capabilities, including to be weatherproof, to run without lubricant, and so forth, but only one function. All functions are capabilities on the view we defend, but not all capabilities are functions. We develop a series of axioms to distinguish capabilities formally from both dispositions and functions and provide examples of the use of ‘capability’ in a variety of domains. (shrink)

Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...) consensus via a formal structured process by a panel of experts for revision of the RDC/TMD. Results: The recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for pain diagnoses and valid criteria for the most common pain-related TMDs and for one intra-articular disorder. The Axis II protocol retains selected RDC/TMD screening instruments augmented with new instruments to better assess the interactions between pain and psychosocial functioning. A comprehensive classification system is also presented. Conclusion: The recommended evidence-based DC/TMD protocol is appropriate for use in both the clinical and research settings. Simple Axis I and II screening tests augmented by validated Axis I and Axis II instruments allow for identification of simple to complex TMD patients. (shrink)

In “Toward an Ontology of Commercial Exchange” [11], we proposed human readable definitions for terms that are central to an ontology of commercial exchange. This paper furthers that project in two ways. First, the definitions have been modified to be compatible with the Common Core Ontologies (CCO). CCO is used in a wide variety of domains including the industrial and military domains. Having a commerce ontology compatible with CCO allows data about the exchange of goods relevant to those domains to (...) be tagged with compatible ontologies. Second, we propose preliminary formalizations of these definitions, with the aim of informing the creation of an ontology which can be used to assist in reasoning over businessrelated data. (shrink)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) testing, and (4) data (...) exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

We propose a domain-level ontology of plays for the facilitation of play-based collaborative autonomy among unmanned and manned-unmanned aircraft teams in the Army’s Unmanned Aircraft System (UAS) mission domain. We define a play as a type of plan that prescribes some pattern of intentional acts that are intended to reliably result in some goal in some competitive context, and which specifies one or more roles that are realized by those prescribed intentional acts. The ontology is well suited to be extended (...) to other types of military and nonmilitary unmanned vehicle operations. (shrink)

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (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)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

I argue that Smith proposed a new kind of imperialism, which we would describe as a species of ‘federalism,’ and that his plan influenced Bentham and Kant in their federal projects, although they seem to have been unaware of each other’s proposals. In what follows, I outline Smith’s position. I then describe Kant’s and Bentham’s debts to Smith in turn. This will also allow for greater clarity about the nature of early liberalism.

One of the deepest and longest-lasting debates in ethics concerns a version of the Euthyphro question: are choiceworthy things choiceworthy because agents have certain attitudes toward them or are they choiceworthy independent of any agents’ attitudes? Reasons internalists, such as Bernard Williams, Michael Smith, Mark Schroeder, Sharon Street, Kate Manne, Julia Markovits, and David Sobel answer in the first way. They think that all of an agent’s normative reasons for action are grounded in facts about that agent’s pro-attitudes (e.g., (...) her desires, valuing states, normative judgments). According to the most popular brand of internalism, idealizing internalism, an agent’s reasons are grounded, not in her actual pro-attitudes, but rather in what her pro-attitudes would be in suitably idealized conditions. Idealizing internalists presuppose that, for any agent with an irrational set of attitudes, there is one uniquely rational set that that agent would have if she were to undergo the relevant idealizing process. I argue that this assumption is false and that it raises two puzzles for idealizing internalism: one about the existence of practical reasons and another about their normative weight. I argue that idealizing internalists have an adequate solution to the first puzzle but not the second. Indeed, when they try to solve the second puzzle, they confront a dilemma. This second puzzle and the associated dilemma thus constitutes a powerful, but so far unnoticed, difficulty for idealizing internalism. (shrink)

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (shrink)

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

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)

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

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

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad scope. (...) We argue here, however, that its organization manifests certain structural problems, and we describe revisions which we believe are needed if the network is to be maximally successful in realizing its goals of supporting terminology integration. (shrink)

The dominant theory of judgment in 1870 was one or other variety of combination theory: the act of judgment is an act of combining concepts or ideas in the mind of the judging subject. In the decades to follow a succession of alternative theories arose to address defects in the combination theory, starting with Bolzano’s theory of propositions in themselves, Brentano’s theory of judgment as affirmation or denial of existence, theories distinguishing judgment act from judgment content advanced by Brentano’s students (...) Twardowski, Husserl and Meinong, and finally, Adolf Reinach’s addition of a linguistic dimension to the Brentano-Husserlian theory of judgment – an account of judgments as ways of doing things with words in what Reinach called ‘social acts’. (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)

Where humans can manipulate and integrate the information they receive in subtle and ever changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, chemistry, mathematics, (...) medicine and many other areas, and all of these dimensions, as well as fundamental philosophical issues, must be taken into account in the construction of a domain ontology. Here we describe the basic features of domain ontologies in the life sciences and show how they can be used. (shrink)

Individuals sometimes pass their duties on to collectives, which is one way in which collectives can come to have duties. The collective discharges its duties by acting through its members, which involves distributing duties back out to individuals. Individuals put duties in and get (transformed) duties out. In this paper we consider whether (and if so, to what extent) this general account can make sense of states' duties. Do some of the duties we typically take states to have come from (...) individuals having passed on certain individual duties? There are complications: states can discharge their duties by contracting fulfilment out to non-members; states seem able to dissolve the duties of non-members; and some of states' duties are not derived in this way. We demonstrate that these complicate, but do not undermine, the general account and its application to states. And the application has an interesting upshot: by asking which individuals robustly participate in this process of duty transfer-and-transformation with a given state, we can begin to get a grip on who counts as a member of that state. (shrink)

Objective: There are benefits and risks of giving patients more granular control of their personal health information in electronic health record (EHR) systems. When designing EHR systems and policies, informaticists and system developers must balance these benefits and risks. Ethical considerations should be an explicit part of this balancing. Our objective was to develop a structured ethics framework to accomplish this. -/- Methods: We reviewed existing literature on the ethical and policy issues, developed an ethics framework called a “Points to (...) Consider” (P2C) document, and convened a national expert panel to review and critique the P2C. -/- Results: We developed the P2C to aid informaticists designing an advanced query tool for an electronic health record (EHR) system in Indianapolis. The P2C consists of six questions (“Points”) that frame important ethical issues, apply accepted principles of bioethics and Fair Information Practices, comment on how questions might be answered, and address implications for patient care. -/- Discussion: The P2C is intended to clarify whatis at stake when designers try to accommodate potentially competing ethical commitments and logistical realities. The P2C was developed to guide informaticists who were designing a query tool in an existing EHR that would permit patient granular control. While consideration of ethical issues is coming to the forefront of medical informatics design and development practices, more reflection is needed to facilitate optimal collaboration between designers and ethicists. This report contributes to that discussion. (shrink)

Johannes Daubert he was an acknowledged leader, and in some respects the founder, of the early phenomenological movement, and was considered – as much by its members as by Husserl himself – the most brilliant member of the group. In Daubert’s unpublished writings we find a series of reflections on Lask, and on Neo-Kantianism, which form the subject-matter of this paper. They range over topics such as the ontology of the ‘Sachverhalt’ or state of affairs, truthvalues (Wahrheitswerte) and the value (...) of truth, negative judgments and the copula, and the relation between perception and judgment. (shrink)

The authors outline the way in which documents as social objects have evolved from their earliest forms to the electronic documents of the present day. They note that while certain features have remained consistent, processes regarding document authentication are seriously complicated by the easy reproducibility of digital entities. The authors argue that electronic documents also raise significant questions concerning the theory of ‘documentality’ advanced by Maurizio Ferraris, especially given the fact that interactive documents seem to blur the distinctions between the (...) static documents (or ‘inscriptions’) which form Ferraris’s starting point, and dynamic software processes. The authors argue further that the Ferraris view as applied to legal documents is flawed because of the fact that courts may treat contractual obligations as enduring even in spite of a complete absence of enduring inscriptions. Finally, the authors note that traces in brains, another important family of inscriptions (as Ferraris conceives them), differ significantly from genuinely documentary inscriptions by their lack of public inspectability. (shrink)

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

PREMISSA No século XIX, ocorreram transformações impulsionadas pela emergência de novas fontes energéticas (água e petróleo), por novos ramos industriais e pela alteração profunda nos processos produtivos, com a introdução de novas máquinas e equipamentos. Depois de 300 anos de exploração por parte das nações europeias, iniciou -se, principalmente nas colônias latino-americanas, um processo intenso de lutas pela independência. É no século XIX, já com a consolidação do sistema capitalista na Europa, que se encontra a herança intelectual mais próxima da (...) qual surgirá a Sociologia como ciência particular. No início desse século, as ideias do Conde de Saint-Simon (1760-1825), de Georg Wilhelm Friedrich Hegel (1770-1831), de David Ricardo (1772-1823) e de Charles Darwin (1809-1882), entre outros, foram o elo para que Alexis de Tocqueville (1805-1859), Auguste Comte (1798-1857), Karl Marx (1818 -1883) e Herbert Spencer (1820-1903), entre outros, desenvolvessem reflexões sobre a sociedade de seu tempo. Auguste Comte e Karl Marx foram os pensadores que lançaram as bases do pensamento sociológico e de duas grandes tradições – a positivista e a socialista – que muito influenciaram o desenvolvimento da Sociologia no Brasil. 1 AUGUSTE COMTE E A TRADIÇÃO POSITIVISTA Isidore Auguste Marie François Xavier Comte nasceu em Montpellier, na França, em 19 de janeiro de 1798. Com 16 anos de idade, ingressou na Escola Politécnica de Paris, fato que teria significativa influência na orientação posterior de seu pensamento. De 1817 a 1824, foi secretário do Conde de Saint-Simon. Comte declarou que, com Saint -Simon, aprendeu muitas coisas que jamais encontraria nos livros e que, no pouco tempo em que conviveu com o conde, fez mais progressos do que faria em muitos anos, se estivesse sozinho. Toda a obra de Comte está permeada pelos acontecimentos que ocorreram após a Revolução Francesa de 1789. Ele defendeu parte dos princípios revolucionários e criticou a restauração da monarquia, preocupando-se fundamentalmente em reorganizar a sociedade, que, no seu entender, estava em ebulição e mergulhada no caos. Para Comte, a desordem e a anarquia imperavam em virtude da confusão de princípios (metafísicos e teológicos), que não se adequavam à sociedade industrial em expansão. Era, portanto, necessário superar esse estado de coisas, usando a razão como fundamento da nova sociedade. Propôs, então, a mudança da sociedade por meio da reforma intelectual plena das pessoas. De acordo com o pensador, com a modificação do pensamento humano, por meio do método científico, que ele chamava de “filosofia positiva”, haveria uma reforma das instituições. Com a proposta do estudo da sociedade por meio da análise de seus processos e estruturas, e da reforma prática das instituições, Comte criou uma nova ciência, à qual deu o nome de “física social”, passando a chamá-la posteriormente de Sociologia. A Sociologia representava, para Comte, o coroamento da evolução do conhecimento, mediante o emprego de métodos utilizados por outras ciências, que buscavam conhecer os fenômenos constantes e repetitivos da natureza: a observação, a experimentação, a comparação e a classificação. De acordo com esse pensador, a Sociologia, como as ciências naturais, deve sempre procurar a reconciliação entre os aspectos estáticos e os dinâmicos do mundo natural ou, no caso da sociedade humana, entre a ordem e o progresso. O lema da “filosofia positiva” proposta por Comte era “conhecer para prever, prever para prover”, ou seja, o conhecimento é necessário para fazer previsões e também para solucionar possíveis problemas. A influência de Comte no desenvolvimento da Sociologia foi marcante, sobretudo, na escola francesa, evidenciando-se em Émile Durkheim e seus contemporâneos e seguidores. Seu pensamento esteve presente em muitas das tentativas de criar tipologias para explicar a sociedade. Suas principais obras são: Curso de filosofia positiva (1830-1842), Discurso sobre o espírito positivo (1848), Catecismo positivista (1852) e Sistema de política positiva (1854). Para concluirmos, Comte explanava que para a superação da anarquia reinante na nova sociedade industrial, a filosofia positivista defendia a subordinação do progresso à ordem. O mesmo era contra o retorno de Luís XVIII ao trono: em sua concepção, a sociedade industrial que emergia requeria um governo fundado na razão. 2 A TRADIÇÃO SOCIALISTA: KARL MARX E FRIEDRICH ENGELS Karl Heinrich Marx nasceu em Tréveris, na antiga Prússia, hoje Alemanha, em 1818 e, em 1830, ingressou no Liceu Friedrich Wilhelm, nessa mesma cidade. Anos depois, foi cursar Direito na Universidade de Bonn, transferindo-se para Berlim em seguida. Pouco a pouco, entretanto, seus interesses migraram para a Filosofia, área na qual defendeu, em 1841, a tese de doutorado A diferença da filosofia da natureza em Demócrito e Epicuro. Sua vida universitária foi marcada pelo debate político e intelectual influenciado pelo pensamento de Ludwig Feuerbach (1804-1872) e, principalmente, pelo de Georg Wilhelm Friedrich Hegel (1770- 1831). Friedrich Engels (1820-1895) nasceu em Barmen (Renânia), na antiga Prússia, hoje Alemanha, filho mais velho de um rico industrial do ramo têxtil. Terminou sua formação secundária em 1837 e a partir de então sua formação intelectual foi por conta própria (autodidata), com alguns cursos universitários esparsos e de curta duração. Desde cedo começou a trabalhar nas empresas de seu pai e foi nessa condição que se deslocou para Bremen por três anos e depois foi enviado pelos pais a Manchester, na Inglaterra, onde trabalhou nas fábricas da família. Engels ficou impressionado com a miséria na qual viviam os trabalhadores das fábricas inglesas. Os dois, Marx e Engels, se encontraram em 1842, quando Marx passou a escrever para A Gazeta Renana, jornal da província de Colônia, do qual Engels era colaborador e mais tarde editor-chefe. O jornal, que criticava o poder prussiano, foi fechado em 1843, e Marx se viu desempregado. Ao perder o emprego, mudou-se para Paris, na França. Ali escreveu, em 1844, os Manuscritos econômico-filosóficos (só publicados em 1932) e, junto com F. Engels, o livro A sagrada família. Por sua vez, F. Engels, em 1844, decidiu voltar para a Alemanha, onde publicou, em 1845, A situação da classe trabalhadora na Inglaterra. Entre 1845 e 1847, Marx exilou-se em Bruxelas, na Bélgica, onde escreveu A ideologia alemã (em parceria com Friedrich Engels) e Miséria da filosofia (1847), obra na qual criticou o filósofo Pierre-Joseph Proudhon (1809-1865). Em 1848, ainda na Bélgica, a parceria com Engels se solidificou ao escreverem juntos o livreto O Manifesto Comunista. Em 1848, Marx foi expulso da Bélgica e retornou a Colônia, na Alemanha (Prússia), sempre pensando na possibilidade de uma mudança estrutural em sua terra natal. Isso, entretanto, não aconteceu e Marx foi expulso da Alemanha em 1849, ano em que migrou para Londres, na Inglaterra, onde permaneceu até o fim da vida. Lá escreveu O 18 Brumário de Luís Bonaparte (1852), sua mais importante obra de reflexão sobre a vida política europeia do século XIX, desenvolveu pesquisas e concluiu seu maior trabalho: O capital: crítica da economia política. O primeiro volume dessa obra foi publicado em 1867; os outros três, em 1885, 1894 e 1905, após a morte de Marx, revisados por F. Engels. 2.1 O contexto histórico e a obra de Marx e Engels Para situar a obra de Marx e Engels, é necessário conhecer um pouco do que acontecia em meados do século XIX. Com as transformações que ocorriam no mundo ocidental, principalmente na esfera da produção industrial, houve um crescimento expressivo no número de trabalhadores industriais urbanos, com uma consequência evidente: precariedade da vida dos operários nas cidades. As condições de trabalho no interior das fábricas eram péssimas. Os empregados eram superexplorados, alimentavam-se mal e trabalhavam em ambientes insalubres. Para enfrentar essa situação e tentar modificá-la, os trabalhadores passaram a se organizar em associações e sindicatos e a promover movimentos de reivindicação. Desenvolveu-se, então, uma discussão das condições sociais, políticas e econômicas para se definirem as possibilidades de intervenção nessa realidade. Desde o início do século XIX, muitos pensadores discutiram essas questões, nas perspectivas socialista e anarquista. Na Inglaterra podem ser citados, entre outros: William Godwin (1756-1836), Thomas Spence (1750-1814), Thomas Paine (1737-1809), Robert Owen (1771-1858) e Thomas Hodgkin (1787-1866). Na França, destacaram-se Étienne Cabet (1788- 1856), Flora Tristan (1803-1844), Charles Fourier (1772-1837) e Pierre-Joseph Proudhon (1809-1865). Marx e Engels levaram em conta esses pensadores, debatendo com alguns contemporâneos e criticando-os. Além disso, incorporaram a tradição da economia clássica inglesa, presente principalmente nas obras de Adam Smith e de David Ricardo. Pode-se dizer, portanto, que Marx e Engels desenvolveram seu trabalho com base na análise crítica da economia política inglesa, do socialismo utópico francês e da filosofia alemã. Esses dois autores não buscavam definir uma ciência específica para estudar a sociedade (como a Sociologia, para Auguste Comte) ou situar seu trabalho em um campo científico particular. Em alguns escritos, Marx afirmou que a História seria a ciência que mais se aproximava de suas preocupações, por abarcar as múltiplas dimensões da sociedade, a qual deveria ser analisada na totalidade, não havendo uma separação rígida entre os aspectos sociais, econômicos, políticos, ideológicos, religiosos, culturais etc. O objetivo de Marx e Engels era estudar criticamente a sociedade capitalista com base em seus princípios constitutivos e em seu desenvolvimento, visando dotar a classe trabalhadora de uma análise política da sociedade de seu tempo. Assim, a tradição socialista nascida da luta dos trabalhadores, muitos anos antes e em situações diferentes, tem como expressão intelectual o pensamento de Karl Marx e Friedrich Engels. Para entender as concepções fundamentais de Marx e Engels é necessário fazer a conexão entre as lutas da classe trabalhadora, suas aspirações e as ideias revolucionárias que estavam presentes no século XIX na Europa. Para eles, o conhecimento científico da realidade só tem sentido quando visa à transformação dessa mesma realidade. A separação entre teoria e prática não é discutida, pois a “verdade histórica” não é algo abstrato e que se define teoricamente; sua verificação está na prática. Apesar de haver algumas diferenças em seus escritos, os elementos essenciais do pensamento de Marx e Engels podem ser assim sintetizados: • historicidade das ações humanas – crítica ao idealismo alemão; • divisão social do trabalho e o surgimento das classes sociais – a luta de classes; • o fetichismo da mercadoria e o processo de alienação; • crítica à economia política e ao capitalismo; • transformação social e revolução; • utopia – sociedade comunista. A obra desses dois autores é muito vasta e não ficou vinculada estritamente aos movimentos sociais dos trabalhadores. Pouco a pouco foi introduzida nas universidades como parte do estudo em diferentes áreas do conhecimento. Estudiosos de Filosofia, Sociologia, Ciência Política, Economia, História e Geografia, entre outras áreas, foram influenciados por ela. Na Sociologia, como afirma Irving M. Zeitlin, no livro Ideología y teoría sociológica, tanto Max Weber quanto Émile Durkheim fizeram, em suas obras, um debate com as ideias de Karl Marx. Pelas análises da sociedade capitalista de seu tempo e a repercussão que tiveram em todo o mundo, principalmente no século XX, nos movimentos sociais e nas universidades, Marx e Engels são considerados autores clássicos da Sociologia. No campo dessa disciplina, porém, o pensamento deles ficou um pouco restrito, pois perdeu aquela relação entre teoria e prática (práxis), ou seja, entre a análise crítica e a prática revolucionária. Essa relação esteve presente, por exemplo, na vida e na obra dos russos Vladimir Ilitch Ulianov, conhecido como Lênin (1870-1924), e Leon D. Bronstein, conhecido como Trotsky (1879-1940), da alemã Rosa Luxemburgo (1871-1919) e do italiano Antonio Gramsci (1891- 1937), que tiveram significativa influência no movimento operário do século XX. Com base no trabalho de Marx e Engels, muitos autores desenvolveram estudos acadêmicos em vários campos do conhecimento. Podemos citar, por exemplo, Georg Lukács (1885-1971), Theodor Adorno (1903-1969), Walter Benjamin (1892-1940), Henri Lefebvre (1901-1991), Lucien Goldmanm (1913 -1970), Louis Althusser (1918 -1990), Nikos Poulantzas (1936-1979), Edward P. Thompson (1924-1993) e Eric Hobsbawm (1917 -2012). O pensamento de Marx e Engels continua, assim, presente em todo o mundo, com múltiplas tendências e variações, sempre gerando controvérsias. REFERENCIAL TEÓRICO GEMKOW, H.; PSUA, I. M. L. Marx e Engels: Vida e Obra. São Paulo: Alfa e Ômega, 1984. 232 pp. GIANOTTI, J. A. Comte. São Paulo: Abril Cultural, 1978. 318 pp. (Col. Os Pensadores) KONDER, L. Marx: vida e obra. 7ª ed. São Paulo: Paz e Terra, 2007. 154 pp. (Col. Vida e Obra). (shrink)

The magisterial analyses of logic and meaning advanced in Husserl's Logical Investigations of 1900/01 have for a number of reasons been neglected by analytical philosophers in subsequent decades. This state of affairs has to do, in part, with the history of the editions and translations of Husserl's writings. Findlay's readable but imperfect translation appeared seventy years after the work itself was first published, and the editors and translators and expositors of Husserl's works have reflected the prevailing philosophical atmosphere on the (...) Continent by concentration their energies on Husserl's later writings. Now, however, over eighty years after the appearance of Husserl's one true masterpiece, a critical edition of the work is at last available in completed form. We here analyze the structure and content of this new edition, published as part of the Husserliana series by the Husserl Archive in Louvain. (shrink)

Changes in an upper level ontology have obvious conse-quences for the domain ontologies that use it at lower levels. It is therefore crucial to document the changes made between successive versions of ontologies of this kind. We describe and apply a method for tracking, explaining and measuring changes between successive versions of upper level ontologies such as the Basic Formal Ontology (BFO). The proposed change-tracking method extends earlier work on Realism-Based Ontology Versioning (RBOV) and Evolutionary Terminology Auditing (ETA). We describe (...) here the application of this evaluation method to changes between BFO 1.0, BFO 1.1, and BFO 2.0. We discuss the issues raised by this application and describe the extensions which we added to the original evaluation schema in order to account for changes in an ontology of this type. Our results show that BFO has undergone eight types of changes that can be systematically explained by the extended evaluation schema. Finally, we discuss problematic cases, possible pitfalls and certain limits of our study that we propose to address in future work. (shrink)

In this paper, we defend Socratic studies as a research programme against several recent attacks, including at least one recently published in Polis . Critics have argued that the study of Socrates, based upon evidence mostly or entirely derived from some set of Plato's dialogues, is founded upon faulty and indefensible historical or hermeneutical technique. We begin by identifying what we believe are the foundational principles of Socratic studies, as the field has been pursued in recent years, and we then (...) show how the research programme that derives from accepting these principles is not defeated by any of the most common recent criticisms of it. Specifically, we argue that challenges to sorting Plato's dialogues by date, more general challenges to historicist interpretations of Plato's dialogues, as well as recent literary criticisms of Socratic studies all fail to undermine the research programme. We conclude with some thoughts about how and why Socratic studies has proved itself a valuable and fruitful research programme. (shrink)

This essay is an introduction to a lecture course "Elements of Descriptive Psychology" delivered by Anton Marty in around 1903/04. Marty offered courses on descriptive psychology at regular intervals in the course of his career at the University of Prague. The content of these courses follows closely the ideas of Marty’s teacher Franz Brentano, though with some interesting divergences and extrapolations. The present work is a historical and systematic introduction to an extract from notes taken of Marty’s lecture, with some (...) discussion of the work of Dilthey on similar topics, and of Marty’s influence on Franz Kafka and on the Gestalt psychologist Max Wertheimer. (shrink)

Sleep has long been a topic of fascination for artists and scientists. Why do we sleep? What function does sleep serve? Why do we dream? What significance can we attach to our dreams? We spend so much of our lives sleeping, yet its precise function is unclear, in spite of our increasing understanding of the processes generating and maintaining sleep. We now know that sleep can be accompanied by periods of intense cerebral activity, yet only recently has experimental data started (...) to provide us with some insights into the type of processing taking place in the brain as we sleep. There is now strong evidence that sleep plays a crucial role in learning and in the consolidation of memories. Once the preserve of psychoanalysts, 'dreaming' is now a topic of increasing interest amongst scientists. With research into sleep growing, this volume is both timely and valuable in presenting a unique study of the relationship between sleep, learning, and memory. It brings together a team of international scientists researching sleep in both human and animal subjects. Aimed at researchers within the fields of neuroscience, cognitive neuroscience, psychiatry, and neurology, this book will be an important first step in developing a full scientific understanding of the most intriguing state of consciousness. (shrink)

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. The NCRO ontology is free and open to all users. (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)

Conscious states—state that there is something it is like to be in—seem both rich or full of detail and ineffable or hard to fully describe or recall. The problem of ineffability, in particular, is a longstanding issue in philosophy that partly motivates the explanatory gap: the belief that consciousness cannot be reduced to underlying physical processes. Here, we provide an information theoretic dynamical systems perspective on the richness and ineffability of consciousness. In our framework, the richness of conscious experience corresponds (...) to the amount of information in a conscious state and ineffability corresponds to the amount of information lost at different stages of processing. We describe how attractor dynamics in working memory would induce impoverished recollections of our original experiences, how the discrete symbolic nature of language is insufficient for describing the rich and high-dimensional structure of experiences, and how similarity in the cognitive function of two individuals relates to improved communicability of their experiences to each other. While our model may not settle all questions relating to the explanatory gap, it makes progress toward a fully physicalist explanation of the richness and ineffability of conscious experience—two important aspects that seem to be part of what makes qualitative character so puzzling. (shrink)

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

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)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

This review essay assesses Michael Jackson’s ongoing project of staging an encounter between anthropology and philosophy in two books: Lifeworlds (2013) and As Wide as the World Is Wise (2016). Considering his philosophical enrichment of ethnographic theory and method, this essay addresses foundational questions about the prospects and practices of interdisciplinary engagement. It also suggests future avenues for continued dialogue between philosophy and anthropology.

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

The common conception of justice as reciprocity seemingly is inapplicable to relations between non-overlapping generations. This is a challenge also to John Rawls’s theory of justice as fairness. This text responds to this by way of reinterpreting and developing Rawls’s theory. First, by examining the original position as a model, some revisions of it are shown to be wanting. Second, by drawing on the methodology of constructivism, an alternative solution is proposed: an amendment to the primary goods named ‘sustainability of (...) values’. This revised original position lends support to intergenerational justice as fairness. (shrink)

This article constructively retrieves St. Anselm of Canterbury’s theory of retributive justice and provides a defense of what can be called the retributive model of hell. In the first part of this article, we develop the place of retributive punishment in Anselm’s thinking and discuss how and when retributive punishment is a good thing. In the second part, we apply Anselm’s thinking on retributive justice to the problem of hell and provide a defense of how hell, defined as a state (...) of receiving retributive, damnatory, and irreversible punishment, is good. We then address a series of objections. Despite some criticism that both Anselm and the retributive model of hell receive in the contemporary literature, Anselm’s account of retributive justice can make unique and constructive contributions to the contemporary discussion of hell; by retrieving and applying Anselm’s thought to the problem of hell, we intend to kill two birds with one stone. (shrink)