in Abortion and the Status of the Fetus, Volume XIII of the series, “Philosophy of Medicine,” eds. William B. Bondeson, H. Tristram Englehardt, Stuart Spicker, and Daniel H. Winship (Dordrecht, Holland/Boston, Massachusetts: D. Reidel, 1983), pp. 229-245.

Although the commentary on Aristotle’s problematic discussion of slavery is vast, his discussion of nobility receives little attention. The fragments of his dialogue On Noble Birth constitute his most extensive examination of nobility, and while their similarity to the παμβασιλεύς of the Politics has recently been recognized, their relevance to natural slavery has hitherto gone unnoticed. Yet by declaring that true nobles – particularly the god-like ἀρχηγός – preternaturally possess superhuman characteristics, Aristotle precludes their easy inclusion in the kind “human” (...) in a manner inversely mirroring the preternatural subhumanity of natural slaves. Building on recent scholarship which argues that Aristotle’s “defense” of natural slaves is better understood as an indictment, On Noble Birth becomes most coherent if read as a hypothetical investigation into what would be required for “nobility” to name something true rather than equivocal, with the conclusion that “true nobility” is an empty set. (shrink)

In celebration of Newton da Costa’s place in the history of paraconsistency, this paper considers the use and abuse of deliberate self-contradiction. Beginning with Parmenides, developed by Plato, and continued by Cicero, an ancient philosophical tradition used deliberately paraconsistent discourses to reveal the truth. In modern times, decisionism has used deliberate self-contradiction against Judeo-Christian revelation. • DOI:10.5007/1808-1711.2010v14n1p1.

This essay hypothesizes that the Universe contains a self-reproducing neural network of Black Holes with computational abilities—i.e., the Universe can “think”! It then rephrases the Final Anthropic Principle to state: “Intelligent information-processing must come into existence in each new Universe to assure the birth of intelligent successor universes”. Continued research into the theory of Early Universe and Black Hole information storage, processing and retrieval is recommended, as are observational searches for time-correlated electromagnetic and gravitational wave emission patterns from widely separated (...) Black Hole transient events indicative of the existence of a universal inter-Black Hole faster-than-light communications network. (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)

How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, Symbiosis and Individuality: Conceptual and Philosophical Issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of (...) incorporating into meetings experts from other disciplines, such as philosophy and history of science. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

While there has been significant discussion in the health sciences and ethics literatures about problems associated with publication practices (e.g., ghost- and gift-authorship, conflicts of interest), there has been relatively little practical guidance developed to help researchers determine how they should fairly allocate credit for multi-authored publications. Fair allocation of credit requires that participating authors be acknowledged for their contribution and responsibilities, but it is not obvious what contributions should warrant authorship, nor who should be responsible for the quality and (...) content of the scientific research findings presented in a publication. In this paper, we review arguments presented in the ethics and health science literatures, and the policies or guidelines proposed by learned societies and journals, in order to explore the link between author contribution and responsibility in multi-author multidisciplinary health science publications. We then critically examine the various procedures used in the field to help researchers fairly allocate authorship. (shrink)

We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping of intelligence data, and (...) describe how it can be applied in an agile fashion to new data resources in ways that address immediate needs of intelligence analysts. (shrink)

We describe on-going work on IAO-Intel, an information artifact ontology developed as part of a suite of ontologies designed to support the needs of the US Army intelligence community within the framework of the Distributed Common Ground System (DCGS-A). IAO-Intel provides a controlled, structured vocabulary for the consistent formulation of metadata about documents, images, emails and other carriers of information. It will provide a resource for uniform explication of the terms used in multiple existing military dictionaries, thesauri and metadata registries, (...) thereby enhancing the degree to which the content formulated with their aid will be available to computational reasoning. (shrink)

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of certain (...) organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

There is a common misconception across the lntelligence Community (IC) to the effect that information trapped within multiple heterogeneous data silos can be semantically integrated by the sorts of meaning-blind statistical methods employed in much of artificial intelligence (Al) and natural language processlng (NLP). This leads to the misconception that incoming data can be analysed coherently by relying exclusively on the use of statistical algorithms and thus without any shared framework for classifying what the data are about. Unfortunately, such approaches (...) do not yield sustainable results where we are dealing with widely distributed, highly heterogeneous and often changing bodies of data. We argue here that the needed integration requires the use of what we call an lntegrating Semantic Framework (ISF), which provldes a consistent set of categories and relationships that can be reused over and over again to tag successive bodies of data in ways which foster more coherent representation and reasoning. (shrink)

I suggest that the post-Hegelian tradition presents us with three contrasting normative models of work. According to the first model, the core norms of work are those of means-ends rationality. In this model, the modern world of work is constitutively a matter of deploying the most effective means to bring about given ends. The rational kernel of modern work, the core norm that has shaped its development, is on this view instrumental reason, and this very same normative core, in the (...) shape of advanced technology and more efficient, time-saving production, can help to liberate it. The second model, by contrast, takes the core norms of work to be internal to working activity. Rather than work gaining its normativity from something external to it, from ends to which the work is a contingent means, on this second view the core norms of work are expressions of values or meanings that are immanent to working practices themselves. The expressive model of work regards the actual world of work to be constituted historically by work-specific norms, norms which working subjects themselves have invoked and mobilised around in the course of their struggles for emancipation. According to the third model, the core norms of work have to do neither with instrumental rationality nor authentic self-expression. Rather they concern norms that relate either to individual achievement or contribution through work (in the form of esteem) or to the conditions that must in place for individuals to participate in the exchange of services by which market societies reproduce themselves (in the form of mutual respect). (shrink)

Research on research ethics—regarding both the governance and practice of the ethical review of human subjects research—has a tumultuous history in North America and Europe. Much of the academic literature focuses on issues to do with regulating the conduct and quality of ethics review of research protocols by ethics committees (research ethics boards (REBs) in Canada and institutional review boards (IRBs) in the United States). In addition, some of the literature attends to issues particular to the review of qualitative research, (...) and still other literature addresses the challenges posed by and the need for research on REBs/IRBs. It is this third group of literature within which our article is situated. (shrink)

I compare Bratman’s theory with Gilbert’s. I draw attention to their similarities, query Bratman’s claim that his theory is the more parsimonious, and point to one theoretical advantage of Gilbert’s theory.

I begin by picking up on Brandom’s suggestion that expressivism follows American pragmatism in seeking to advance the cause of the Enlightenment. This provides us with a first point of contrast with Taylor’s understanding of expressivism, since Taylor takes expressivism to be inseparably bound up with the Romantic critique of the Enlightenment and as fundamentally opposed to Enlightenment naturalism. I then distinguish two features of what we ordinarily mean by the term ‘expression’, one of which provides an intuitive basis for (...) understanding Brandom’s expressivist program, the other of which provides an interpretive key for understanding Taylor’s version of expressivism. After looking briefly at the main tenets of Taylor’s expressivism, I conclude by considering its relation to Romanticism on the one hand, and to Brandom’s expressivist renewal of the Enlightenment project on the other. (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)

An analysis of how the sphere of work can be considered to instantiate norms of recognition, even when those norms give rise to paradoxes and ideologies surrounding how work ought to be done and the goods at stake in it.

This paper examines the justice of unconditional basic income (UBI) through the lens of the Hegel-inspired recognition-theory of justice. As explained in the first part of the paper, this theory takes everyday social roles to be the primary subject-matter of the theory of justice, and it takes justice in these roles to be a matter of the kind of freedom that is available through their performance, namely ‘social’ freedom. The paper then identifies the key criteria of social freedom. The extent (...) to which the introduction of an UBI would meet these criteria is then examined, with a focus on the social role that stands to be most affected by an UBI, namely that of the worker-earner. It is argued that while an UBI is likely to be only partially effective as an instrument of specifically social freedom, its main justification lies not here, but in securing a basis for the subjective freedom that social freedom presupposes. (shrink)

Volume 19, Issue 9, September 2019, Page 64-66.

What is the fundamental purpose that justifies the existence of the modern university? The answer proposed in this essay is the promotion of social freedom. The essay begins by distinguishing social freedom from negative freedom and reflective freedom along the lines proposed by other theorists of social freedom, such as Frederick Neuhouser and Axel Honneth. After noting the need for a more developed account of the university than has so far been provided by these other theorists, the essay analyses the (...) various dimensions in which universities have, at their best, promoted social freedom. The essay then explains why it is through the promotion of social, as distinct from negative or reflective freedom, that universities fulfil their purpose. It concludes with some reflections on how this understanding of the purpose of the university fits an “immanent” model of social criticism. (shrink)

Although the contrast between ‘economy’ and culture’ that structures the Fraser-Honneth debate derives ultimately from Weber, it has a more proximate ancestry in Habermas’ work. I begin by glancing back at Habermas’ formulation, not just because its background role in shaping the current debate has not been properly acknowledged (though I believe that is the case), but because Fraser and Honneth’s original responses to it provide a nice segue into their current positions. After briefly reviewing what those responses were, I (...) then offer a critical analysis of the conceptions of economy and culture they now propose. (shrink)

A summary of the main features of a 'recognition-theoretic' research program in the social sciences and a brief account of how it promises to advance on rival research programs in the social sciences.

The goal of the Department of Defense Net-Centric Data Strategy is to improve data sharing throughout the DoD. Data sharing is a critical element of interoperability in the emerging system-of-systems. Achieving interoperability requires the elimination of two types of data heterogeneity: differences of syntax and differences of semantics. This paper builds a path toward semantic uniformity through application of a disciplined approach to ontology. An ontology is a consensus framework representing the types of entities within a given domain and the (...) relations between them. The construction of an ontology begins when a Community of Interest (COI) identifies its authoritative data sources (ADS), which are usually manifest in relevant doctrinal publications, glossaries, data dictionaries, and logical data models. The identified terms are then defined in relation to a common logical framework that has been designed to ensure interoperability with other ontologies created on the basis of the same strategy. As will be described, the Command and Control (C2) Ontology will include representations of a substantial number of entities within the Command and Control (C2) domain. If domain ontologies (e.g. Strike and Counterinsurgency) semantically align with the C2 Ontology, then a substantial barrier to systems interoperability is thereby crossed. (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)

What follows is a contribution to the horizontal integration of warfighter intelligence data as defined in Chairman of the Joint Chiefs of Staff Instruction J2 CJCSI 3340.02AL: -/- Horizontally integrating warfighter intelligence data improves the consumers’ production, analysis and dissemination capabilities. HI requires access (including discovery, search, retrieval, and display) to intelligence data among the warfighters and other producers and consumers via standardized services and architectures. These consumers include, but are not limited to, the combatant commands, Services, Defense agencies, and (...) the Intelligence Community. (shrink)

The essay reflects on Gadamer’s ambiguous legacy for the philosophy of work. On the one hand, there are times when Gadamer reproduces the problematic distinction between language and labor which short-circuits the very idea of a hermeneutics of work. This is particularly evident in Gadamer’s reflections on technique and craftsmanship in the central sections of Truth and Method, as well as in his descriptions of the “art” of dialogue and the tasks of hermeneutics that separate them emphatically them from the (...) sphere of “making.” I raise some questions about the adequacy of the distinction Gadamer draws between techne and phronesis that structures this account. I argue here that Gadamer’s characterization of the learning process involved in the mastery of a technique, as well as his conception of the instrumentality and monologicality of technical knowledge, is difficult to sustain, especially in view of recent research in the psychology and anthropology of work. I then go on to point out that elsewhere in his oeuvre Gadamer himself is critical of the conception of work that emerges through the lens of the techne / phronesis distinction. Indeed, on these occasions he hints at a conception of work that points beyond the Arendt / Habermas conception towards a critical hermeneutics of working life. This alternative approach to work is particularly apparent in Gadamer’s appropriation of Hegel’s dialectic, in his understanding of play, and in some of his later diagnostic reflections on the spirit of the age. In section four, I offer some suggestions for explaining how the tensions evident in Gadamer’s approach to work came about. Here I am interested in what prevented Gadamer from embracing whole-heartedly the project of a hermeneutics of work that he himself helped to lay the foundations for. I conclude with some brief remarks on why we should seek to build upon these foundations and renew the project of a critical hermeneutics of work today. (shrink)

Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in the (...) form of a list of terms and definitions designed to provide a consistent starting point for the representation of both disease and diagnosis in information systems in the future. (shrink)

We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices. If properly developed and extended, we believe the VSO (...) will find applications for the EMR, clinical informatics, and medical device communities. (shrink)

This chapter takes a critical look at universities from the perspective of the neopragmatist philosophy of education outlined by Richard Rorty. The chapter begins with a discussion of Rorty’s view of the ends that educational institutions properly serve in a liberal democracy. It then considers the kind of culture that Rorty takes to be conducive to those ends and the kind that is antithetical to them. Rorty sometimes characterizes the latter as a culture of ‘egotism’. After describing the main aspects (...) of such a culture, the chapter uses it as an interpretive key for understanding the ‘dark side’ of the contemporary university. Our thesis is that within a Rortyan, neo-pragmatist philosophy of higher education, the ends that universities are meant to serve in a liberal democracy are vulnerable to frustration and corruption by a culture of egotism. (shrink)

The current informal practice of pharmacometrics as a combination art and science makes it hard to appreciate the role that informatics can and should play in the future of the discipline and to comprehend the gaps that exist because of its absence. The development of pharmacometric informatics has important implications for expediting decision making and for improving the reliability of decisions made in model-based development. We argue that well-defined informatics for pharmacometrics can lead to much needed improvements in the efficiency, (...) effectiveness, and reliability of the pharmacometrics process. The purpose of this paper is to provide a description of the pervasive yet often poorly appreciated role of informatics in improving the process of data assembly, a critical task in the delivery of pharmacometric analysis results. First, we provide a brief description of the pharmacometric analysis process. Second, we describe the business processes required to create analysis-ready data sets for the pharmacometrician. Third, we describe selected informatic elements required to support the pharmacometrics and data assembly processes. Finally, we offer specific suggestions for performing a systematic analysis of existing challenges as an approach to defi ning the next generation of pharmacometric informatics. (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)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

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)

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)

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)

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework (...) for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

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

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

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.