The objective of this research programme is to contribute to the establishment of the emerging science of Formal Ontology in Information Systems via a collaborative project involving researchers from a range of disciplines including philosophy, logic, computer science, linguistics, and the medical sciences. The re­searchers will work together on the construction of a unified formal ontology, which means: a general framework for the construction of ontological theories in specific domains. The framework will be constructed using the axiomatic-deductive method of modern (...) formal ontology. It will be tested via a series of applications relating to on-going work in Leipzig on medical taxonomies and data dictionaries in the context of clinical trials. This will lead to the production of a domain-specific ontology which is designed to serve as a basis for applications in the medical field. (shrink)

An analysis of Cardinal Joseph Ratzinger's statements regarding relativism in his 2005 homily to the conclave meeting to elect the new pope in the context of the charge of "relativism" in 20th-century philosophy. Parts of this essay are adapted from Barbara Herrnstein Smith,"Pre-Post-Modern Relativism," in *Scandalous Knowledge: Science, Truth and the Human* (Edinburgh: Edinburgh University Press, 2005; Durham, NC: Duke University Press, 2006), 18 – 45.

Richard Rorty's rejection of prevailing interior-mirror understandings of the presumed relationship between “minds” and “nature,” along with his promotion of nonrepresentational accounts of knowledge, truth, and science, participates in a rich tradition of jointly pragmatist and constructivist views that spans the twentieth century. This contribution to the symposium “Whatever Happened to Richard Rorty?” considers Rorty's complex and ambivalent relation to that tradition, particularly to the work of his American pragmatist predecessors, William James and John Dewey, and to subsequent pragmatist-constructivist antirepresentationalism (...) in contemporary science and technology studies (STS) and “4E” (embodied, embedded, extended, enactive) cognitive theory. A final section on Nicholas Gaskill's contribution to the symposium questions his sense of Rorty's rhetorical recklessness and suggests that his worries over relativism, in Rorty's texts and more generally, are misplaced. (shrink)

Advocates of literary Darwinism, cognitive cultural studies, neuroaesthetics, digital humanities, and other such hybrid fields now seek explicitly to make the aims and methods of one or another humanities discipline approximate more closely the aims and methods of science, and at their most visionary, they urge as well the overall integration of the humanities and natural sciences. This essay indicates some major considerations—historical, conceptual, and pragmatic—that may be useful for assessing these efforts and predicting their future. Arguments promoting integration often (...) involve dubious teleological models of intellectual history and betray limited understandings of the distinctive epistemic orientations and cultural functions of the humanities vis-à-vis the sciences. Recurrent institutional difficulties encountered by scholars and/or scientists in hybrid fields reflect steep prestige differentials between the humanities and sciences, along with significant differences of training, experience, style, and temperament. Meanwhile, both the sciences and humanities are being shaken up by technological and related intellectual developments. Though worrisome, the new disciplinary configurations are thus likely to play out in surprising and, not inconceivably, positive ways. (shrink)

Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our experiments show geographic categories to be similar to their non-geographic counterparts in (...) the ways in which they generate instances of different relative frequencies at different levels. Other tests, however, provide preliminary evidence for the existence of important differences in subjects’ categorizations of geographic and non-geographic objects, and suggest further experimental work especially with regard to the role in cognitive categorization of different types of object-boundaries at different scales. (shrink)

Contemporary issues involving knowledge and science examined from a constructivist-pragmatist perspective often labeled "relativism." Individual chapters include a review of the difference between constructivist-pragmatist epistemology and "social constructivism;" an examination of recent writings by Bruno Latour; a critique of computational methods in literary studies; a skeptical look at current efforts to "integrate" the humanities and the natural sciences; and reflections on the social dynamics of belief in relation to denials of climate change and to hopes expressed by environmentalists.

I reply here to an article by philosopher Paul Boghossian in which my article "Cutting-Edge Equivocation: Conceptual Moves and Rhetorical Strategies in Contemporary Anti-Epistemology" (Smith, *SAQ* 2002) provides him with an occasion for a supposed exposure and refutation of the alleged illogic of the "unpalatable relativism" of what Boghossian, at some distance from his topic, (mis)understands as the "constructivism" of contemporary sociology of science.

A critical examination of the charge of self-refutation, particularly as leveled by orthodoxy-defending philosophers against those maintaining epistemologically unorthodox, especially relativistic or skeptical, views. Beginning with an analysis of its classic illustration in Plato’s *Theaetetus* as leveled against Protagoras’s “Man is the measure ...,” I consider various aspects of the charge, including logical, rhetorical, pedagogic, affective, and cognitive.

An examination of conceptually and rhetorically equivocating positions among academic philosophers and other theorists who are sympathetic to constructivist epistemological developments but unwilling to relinquish key aspects of traditional understandings of truth and knowledge and/or anxious to avoid charges of relativism. A major problem with the resulting hybrid formulations is that, seeking, as they often claim, to “steer a course between Scylla and Charybdis” and being composed of essentially incompatible elements, they can do little theoretical work. While the personal-intellectual and (...) professional-institutional pressures leading to such dubious navigations are substantial, so also, it is argued, are their intellectual costs. (shrink)

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

The essay considers two sets of interrelated difficulties that follow from our kinship to animals: those that arise chronically from our individual psychologically complex and often ambivalent relations to animals, and those that reflect the intellectually and ideologically criss-crossed connections among the various discourses currently concerned with those relations, including the movement for animal rights, ecological ethics, posthumanist theory, and such fields as primatology and evolutionary psychology. I begin with some general observations on classification and then turn to the increasingly (...) complex play of claims and counter-claims regarding the so-called species barrier. (shrink)

A critique of dubious contrasts between "science" and "religion" drawn on the basis of cognitive-evolutionary accounts of human psychology, e.g.,. the claim that religious concepts are “likely” and “natural” for the human mind whereas scientific thinking is “rare” and “unnatural.” Initially made by biologist Lewis Wolpert in *The Unnatural Nature of Science* (1993) and anthropologist Pascal Boyer in *Religion Explained: The Evolutionary Origins of Religious Thought* (2001), they are developed at length by philosopher R. N. McCauley in a*Why Religion is (...) Natural and Science is Not* (2011). These contrasts involve tendentiously narrow or broad definitions of the terms “science” and “religion” and the obliteration of the complex historical and intellectual relations between the ideas and practices currently identified by those terms. (shrink)

In this response to comments on my article, “The Chimera of Relativism,” in the same issue of *Common Knowledge* , by cognitive neuroscientist Andreas Roepstorff, classicist G. E. R. Lloyd, and anthropologist Martin Holbraad, I illustrate and reinforce Lloyd's cautions regarding the hazards of intercultural—here, Chinese-Western—comparisons in studies of culture and cognition. Examination of a foundational study in East-West cultural/cognitive differences cited by Roepstorff indicates extensive conceptual and methodological problems in that tradition of research. Although Holbraad champions a more radical (...) relativism than that offered in my work, the moves he urges have either been present in my work from the beginning or are both dubiously radical and otherwise undesirable. (shrink)

The Emergence of Relativism offers a range of perspectives on how “the problem of relativism” was framed in German intellectual discourses over the course of the long nineteenth century. The review suggests that the volume is at odds with itself in various ways and, both wittingly and unwittingly, illuminates some problems of philosophy, both across the period examined and in our own.

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

In lieu of an abstract, here is a brief excerpt of the content:Philosophy and Literature 25.2 (2001) 215-232 [Access article in PDF] Eighteenth-Century Print Culture and the "Truth" of Fictional Narrative Lisa Zunshine As a session entitled "Truth" at a recent Modern Language Association of America annual convention has demonstrated, the obsession with the epistemologies of truth is alive and well. Our "familiar ways of thinking and talking about truth," as one of the speakers, Barbara Herrnstein Smith, observed, (...) remain "theoretically elusive, discursively slippery, and hard or perhaps impossible to articulate clearly in relation to other current concepts and ideas" 1 --an irresistible invitation to further thinking and talking on the subject. My essay enters this conversation by attempting to contemplate truth not as a stable attribute but as a ongoing attribution, that is, not as an inherent property but rather as a dynamic process predicated upon functional idiosyncrasies of our evolved cognitive architecture. The broad question posed here is this: What if our never-ending quest for truth is itself cognitively constructed and the various forms that this quest takes manifest the (not necessarily harmonious) interaction between our evolved cognitive capacities and the ever-changing specifics of our cultural environment?Consider just one of the forms of such an interaction, namely, our age-long preoccupation with the "truth" of literary narrative. In many respects, this preoccupation is counterproductive: the most "fantastic" story contains a number of contingently useful "truths" about the world, whereas the most "factual" narrative manipulates facts by virtue of being a narrative or a subjective arrangementof information. Still, we persevere in wanting to put the label "fiction" or "nonfiction" onto any story that comes our way. As I will argue, the bookstore's organization of its sections satisfies this species of "cognitive" craving as well as [End Page 215] reinforces it, making it seem culturally inevitable. Viewed from this perspective, our culture appears to be a multifaceted feedback mechanism engaged in the process of satisfying, reinforcing, struggling with, and manipulating our cognitive predispositions.The cultural manipulation of our cognitive predispositions is the topic of the present essay, which discusses several examples of such manipulation that respond to our desire to assign a certain "truth-value" to a given narrative, i.e., to attach a label to it announcing its "factuality" or "fictionality." "Truth-value" is a loaded term, resisting definition, and liable to lead me into trouble. Imperfect as it is, however, I need it in order to shuffle between two scholarly discourses that do not (yet) have much vocabulary in common: literary criticism and cognitive science. The reason for turning to cognitive science in my discussion of literary narrative is that cognitive anthropologists and psychologists frequently engage the same problems that we do when we ask, What is "Fiction"? How is it different from "History"? How do we decide whether what we are reading is "true?" The key difference between the two approaches is, however, that whereas the literary critic focuses on specific texts produced and read in specific cultural circumstances, the cognitive anthropologist pays attention to the cross-cultural insistence with which people wish to and often claim to distinguish "truth" from "fiction" and inquires into the possible evolutionary history of the cognitive architecture implicated in our never-ending quest for "truth." The latter perspective can thus be useful for literary studies because, by suggesting that our evolved cognitive architecture often "encourages" us to construe the world as a negotiation of "truths" and "nontruths," this perspective begins to account--at least on some level--for the fact that people may approach a complex cultural artifact, such as a novel, with a "truth"/"non-truth" binary in mind that is ultimately not very productive. 2 Evolutionary psychologists and anthropologists frequently point to disjunctions between the tasks that our brain evolved to solve and the tasks that we have to deal with in the modern environment; our vexed insistence on determining the truth-value of the 500-page printed narrative--not an object one would come across in the Pleistocene--can be seen as yet another instance of such a disjunction.Thus, I suggest that, on the... (shrink)

Roland Greene and Stephen Cushman have revived the 1950s' edition of this book. & it is worth reading even by philosophers for in the final analysis, from Plato to Blanchot to Jean-Luc Marion are all poets. Where does poetry end and philosophy begin!!??

What are the prospects for a monistic view of biological individuality given the multiple epistemic roles the concept must satisfy? In this paper, I examine the epistemic adequacy of two recent accounts based on the capacity to undergo natural selection. One is from Ellen Clarke, and the other is by Peter Godfrey-Smith. Clarke’s position reflects a strong monism, in that she aims to characterize individuality in purely functional terms and refrains from privileging any specific material properties as important (...) in their own right. I argue that Clarke’s functionalism impairs the epistemic adequacy of her account compared to a middle-ground position taken by Godfrey-Smith. In comparing Clarke and Godfrey-Smith’s account, two pathways emerge to pluralism about biological individuality. The first develops from the contrast between functionalist and materialist approaches, and the second from an underlying temporal structure involved in using evolutionary processes to define individuality. (shrink)

Biologists, historians of biology, and philosophers of biology often ask what is it to be an individual, really. This book does not answer that question. Instead, it answers a much more interesting one: How do biologists individuate individuals? In answering that question, the authors explore why biologists individuate individuals, in what ways, and for what purposes. The cross-disciplinary, dialogical approach to answering metaphysical questions that is pursued in the volume may seem strange to metaphysicians who are not biologically focused, but (...) it is adroitly achieved by the editors. Scott Lidgard (a paleontologist and marine ecologist) and Lynn K. Nyhart (a historian of biology) orchestrate a dialogue among historians of biology, philosophers of biology, and practicing biologists over 10 chapters. These are followed by three reflective commentaries written to frame the different disciplinary perspectives and to highlight the historical, biological, and philosophical themes across the chapters. The result is a volume—in structure and in content—that has much to be generously commended. Biological individuality is a hotly discussed topic, but it is also part of a series of long-standing arguments within both the history and philosophy of biology (HPB) and metaphysics. Notable and fervent debates have centered on evolution and the units of selection, predominantly on Michael T. Ghiselin’s and David L. Hull’s notion of species as individuals, Peter Godfrey-Smith’s Darwinian individuals, and Ellen Clarke’s individuating mechanisms. Lately, it has encompassed non-Darwinian individuals, symbiotic associations like Thomas Pradeu’s immunological individuals, and John Dupré and Maureen A. O’Malley’s metabolic individuals.2 The present volume is curated in a way to introduce the reader to new research in HPB that articulates these debates as well as to introduce and engage in the study of further notions of biological individuality. But its aim is more than an introduction. As the subtitle suggests, it is also intended to give the reader insight into the working together of biologists, historians of biology, and philosophers of biology in figuring out how the notion of biological individuality is instantiated. As such, the problem-centered dialogue that results does more than talk through biological individuality. It shows how the different and often divergent goals of the authors’ disciplines shape not only how they think about individuality but how they communicate this thinking in reciprocal collaboration with others in different disciplines. … cont’d…. (shrink)

‘What is characteristic of every mental activity’, according to Brentano, is ‘the reference to something as an object. In this respect every mental activity seems to be something relational.’ But what sort of a relation, if any, is our cognitive access to the world? This question – which we shall call Brentano’s question – throws a new light on many of the traditional problems of epistemology. The paper defends a view of perceptual acts as real relations of a subject to (...) an object. To make this view coherent, a theory of different types of relations is developed, resting on ideas on formal ontology put forward by Husserl in his Logical Investigations and on the theory of relations sketched in Smith's "Acta cum fundamentis in re". The theory is applied to the notion of a Cambridge change, which proves to have an unforeseen relevance to our understanding of perception. (shrink)

The term ‘intelligence’ as used in this paper refers to items of knowledge collected for the sake of assessing and maintaining national security. The intelligence community (IC) of the United States (US) is a community of organizations that collaborate in collecting and processing intelligence for the US. The IC relies on human-machine-based analytic strategies that 1) access and integrate vast amounts of information from disparate sources, 2) continuously process this information, so that, 3) a maximally comprehensive understanding of world actors (...) and their behaviors can be developed and updated. Herein we describe an approach to utilizing outcomes-based learning (OBL) to support these efforts that is based on an ontology of the cognitive processes performed by intelligence analysts. Of particular importance to the Cognitive Process Ontology is the class Representation that is Warranted. Such a representation is descriptive in nature and deserving of trust in its veridicality. The latter is because a Representation that is Warranted is always produced by a process that was vetted (or successfully designed) to reliably produce veridical representations. As such, Representations that are Warranted are what in other contexts we might refer to as ‘items of knowledge’. (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)

This letter addresses the editorial decision to publish the article, “Research on group differences in intelligence: A defense of free inquiry” (Cofnas, 2020). Our letter points out several critical problems with Cofnas's article, which we believe should have either disqualified the manuscript upon submission or been addressed during the review process and resulted in substantial revisions.

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

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

Biological theory demands a clear organism concept, but at present biologists cannot agree on one. They know that counting particular units, and not counting others, allows them to generate explanatory and predictive descriptions of evolutionary processes. Yet they lack a unified theory telling them which units to count. In this paper, I offer a novel account of biological individuality, which reconciles conflicting definitions of ‘organism’ by interpreting them as describing alternative realisers of a common functional role, and then defines individual (...) organisms as essentially possessing some mechanisms that play this role. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

This document presents the Bonn PRINTEGER Consensus Statement: Working with Research Integrity—Guidance for research performing organisations. The aim of the statement is to complement existing instruments by focusing specifically on institutional responsibilities for strengthening integrity. It takes into account the daily challenges and organisational contexts of most researchers. The statement intends to make research integrity challenges recognisable from the work-floor perspective, providing concrete advice on organisational measures to strengthen integrity. The statement, which was concluded February 7th 2018, provides guidance on (...) the following key issues: § 1.Providing information about research integrity § 2.Providing education, training and mentoring § 3.Strengthening a research integrity culture § 4.Facilitating open dialogue § 5.Wise incentive management § 6.Implementing quality assurance procedures § 7.Improving the work environment and work satisfaction § 8.Increasing transparency of misconduct cases § 9.Opening up research § 10.Implementing safe and effective whistle-blowing channels § 11.Protecting the alleged perpetrators § 12.Establishing a research integrity committee and appointing an ombudsperson § 13.Making explicit the applicable standards for research integrity. (shrink)

The problem of plant individuality is something which has vexed botanists throughout the ages, with fashion swinging back and forth from treating plants as communities of individuals (Darwin 1800 ; Braun and Stone 1853 ; Münch 1938 ) to treating them as organisms in their own right, and although the latter view has dominated mainstream thought most recently (Harper 1977 ; Cook 1985 ; Ariew and Lewontin 2004 ), a lively debate conducted mostly in Scandinavian journals proves that the issues (...) are far from being resolved (Tuomi and Vuorisalo 1989b ; Fagerström 1992 ; Pan and Price 2001 ). In this paper I settle the matter once and for all, by showing which elements of each side are correct. (shrink)

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

This chapter develops the idea that the germ-soma split and the suppression of individual fitness differences within the corporate entity are not always essential steps in the evolution of corporate individuals. It illustrates some consequences for multilevel selection theory. It presents evidence that genetic heterogeneity may not always be a barrier to successful functioning as a higher-level individual. This chapter shows that levels-of-selection theorists are wrong to assume that the central problem in transitions is always that of minimizing within-group competition. (...) Evidence of intralevel conflict does not qualify as evidence against the existence of a higher level of selection. (shrink)

As health systems around the world turn towards highly distributed, specialized and cooperative structures to increase quality and safety of care as well as efficiency and efficacy of delivery processes, there is a growing need for supporting communication and collaboration of all parties involved with advanced ICT solutions. The Electronic Health Record (EHR) provides the information platform which is maturing towards the eHealth core application. To meet the requirements for sustainable, semantically interoperable, and trustworthy EHR solutions, different standards and different (...) national strategies have been established. The workshop summarizes the requirements for such advanced EHR systems and their underlying architecture, presents different strategies and solutions advocated by corresponding protagonists, discusses pros and cons as well as harmonization and migration strategies for those approaches. It particularly highlights a turn towards ontology-driven architectures. (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)

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)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

Manley and Wasserman (2008) have provided a convincing case against analyses of dispositions in terms of one conditional, and a very interesting positive proposal that links any disposition to a ‘suitable proportion’ of a particular set of precise conditionals. I focus on their positive proposal and ask just how precise those conditionals are to be. I argue that, contrary to what Manley and Wasserman imply in their paper, they must be maximally specific, describing in their antecedents complete centred worlds. This (...) suggests a natural semantics for dispositional expressions, which I briefly explore to argue that it lacks uniformity. I end by suggesting a variation on Manley and Wasserman's view which would preserve uniformity, though at the cost of some new puzzling questions. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...) the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (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)

In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular O/T as a (...) standard for data exchange purposes is often seen by the end-user as a function of the number of applications using that vocabulary (and, by extension, the size of the user base). Furthermore, the adoption of an O/T as an interoperability standard requires confidence in its stability and guaranteed continuity as a resource. (shrink)

Dispositions are modal properties. The standard conception of dispositions holds that each disposition is individuated by its stimulus condition(s) and its manifestation(s), and that their modality is best captured by some conditional construction that relates stimulus to manifestation as antecedent to consequent. I propose an alternative conception of dispositions: each disposition is individuated by its manifestation alone, and its modality is closest to that of possibility — a fragile vase, for instance, is one that can break easily. The view is (...) expounded in some detail and defended against the major objections. (shrink)

Abilities are in many ways central to what being an agent means, and they are appealed to in philosophical accounts of a great many different phenomena. It is often assumed that abilities are some kind of dispositional property, but it is rarely made explicit exactly which dispositional properties are our abilities. Two recent debates provide two different answers to that question: the new dispositionalism in the debate about free will, and virtue reliabilism in epistemology. This paper argues that both answers (...) fail as general accounts of abilities, and discusses the ramifications of this result. (shrink)

Buchanan and Powell hope to rescue optimism about moral perfectibility from the ’received view’ of human evolution, by tweaking our view of the innate character of morality. I argue that their intervention is hampered by an unnecessary commitment to nativism, by gender bias within the received view, and by liberal presuppositions.

I argue for the usefulness of the evolutionary kind of biological individual.