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)

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)

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)

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)

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)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (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)

In the world according to Hume, people are complicated creatures, with convoluted, often contradictory characters. Consider, for example, Hume's controversial assessment of Charles I: "The character of this prince, as that of most men, if not of all men, was mixed .... To consider him in the most favourable light, it may be affirmed, that his dignity was free from pride, his humanity from weakness, his bravery from rashness, his temperance from austerity, his frugality from avarice .... To speak the (...) most harshly of him, we may affirm, that many of his good qualities were attended with some latent frailty, which, though seemingly inconsiderable, was able, when seconded by the extreme malevolence of his fortune, to disappoint them of all their influence: His beneficent disposition was clouded by a manner not very gracious; his virtue was tinctured with superstition; his good sense was disfigured by a deference to persons of a capacity inferior to his own; and his moderate temper exempted him not from hasty and precipitate resolutions." This sketch shows Charles in all his complexities, with his virtues, near virtues, and contradicting virtues. I have quoted it at length because it is hard to summarize without losing the subtleties that lie within it. Hume's moral theory is based fundamentally on judgments of character, 2 so those subtleties are important to his view. The character sketches that pervade the.. (shrink)

Public health is concerned with increasing the health of the community at whole. Insofar as health is a ‘good’ and the community constitutes a ‘public’, public health by definition promotes a ‘public good’. But ‘public good’ has a particular and much more narrow meaning in the economics literature, and some commentators have tried to limit the scope of public health to this more narrow meaning of a ‘public good’. While such a move makes the content of public health less controversial, (...) it also strips important goals from the realm of public health, goals that traditionally have been, and morally should be, a part of it. Instead, I will argue, while public health should be defined by public goods, it should be defined by a broader conception of public goods that I shall call ‘normative public goods’, goods that ought to be treated as if they were public goods in the more narrow sense. (shrink)

: The idea of enhancing our mental functions through medical means makes many people uncomfortable. People have a vague feeling that altering our brains tinkers with the core of our personalities and the core of ourselves. It changes who we are, and doing so seems wrong, even if the exact reasons for the unease are difficult to define. Many of the standard arguments against neuroenhancements—that they are unsafe, that they violate the distinction between therapy and enhancements, that they undermine equality, (...) and that they will be used coercively—fail to show why the use of any such technologies is wrong in principle. Two other objections—the arguments that such changes undermine our integrity and that they prevent us from living authentic lives—will condemn only a few of the uses that are proposed. The result is that very few uses of these drugs are morally suspect and that most uses are morally permissible. (shrink)

Tradução para o português do artigo "Berkeley and the pyrrhonism" publicado originalmente em The Review of Metaphysics 5 (1951); reimpresso em Burnyeat, Myles (org.) The Skeptical Tradition. University of California Press, 1983, p. 377-396 e em Richard A. Watson and James E. Force (Editors). The high road to Pyrrhonism, p. 297-318.

advanced directivesend-of-life decisionsharming the deadposthumous reproductiontransplant ethics.

After a long search, Jonathan has finally found someone willing to donate a kidney to him and thereby free him from dialysis. Meredith is Jonathan's second cousin, and she considers herself a generous person, so although she barely knows Jonathan, she is willing to help. However, as Meredith learns more about the donation process, she begins to ask questions about Jonathan: “Is he HIV positive? I heard he got it using drugs. Has he been in jail? He's already had one (...) live donor, so what happened to the first kidney? Did he forget to take his drugs or something?” The transplant center must, then, decide if Meredith is, in fact, entitled to answers to these kinds of questions. According to the Consensus Statement on the Live Organ Donor, “It is incumbent on the transplant center to provide full and accurate disclosure to potential donors of all pertinent information regarding risk and benefit to the donor and recipient.” But whether answers to the Meredith's questions count as “pertinent information regarding the risk and benefit” is the issue at hand. (shrink)

David Hume is an ardent supporter of the practice of religions toleration. For Hume, toleration forms part of the background that makes progress in philosophy possible, and it accounts for the superiority of philosophical thought in England in the eighteenth century. As he puts it in the introduction to the Treatise: “the improvements in reason and philosophy can only be owing to a land of toleration and of liberty” (T Intro.7; SBN xvii).1 Similarly, the narrator of part 11 of the (...) First Enquiry comments: -/- Our conversation began with my admiring the singular good fortune of philosophy, which, as it requires entire liberty above all other privileges, and chiefly flourishes from the free opposition of sentiments and argu­ mentation, received its first birth in an age and country of freedom and toleration. (EHU 11.2; SBN 132) -/- The toleration to which Hume refers is broader than religious toleration, but in the context of the eighteenth century, religious toleration is clearly the paradigm case. Indeed, religious toleration represents one of the key accomplishments of the culminating event of Hume’s History of England: the Glorious Revolution of 1688. -/- Yet even though religious toleration forms the background of philosophy in general—or perhaps just because it does so—Hume offers precious few arguments for it, and they are, for the most part, given implicitly rather than as formal argu­ ments. Nevertheless, we can distinguish three different, though interrelated, lines of support for toleration in Hume’s thought: (i) an argument based on a general skepticism; (ii) an argument based on a contempt for organized religion; and (iii) a pragmatic argument based on the need for peace and orderly government. From our point of view, what is striking about all of these argument is how un-Lockean they are: Hume does not rely on the idea of a fundamental conceptual separation of church and state, nor on a natural right to freedom of conscience that character­izes writers working in the Lockean tradition. However, of the arguments he gives, only the last, I will argue, has any hope to provide a useful case for toleration. (shrink)

Liberals often assume that once people see the costs of intolerance that they will come to embrace toleration and that once they can accept toleration as a modus vivendi, they will soon be able to see it as a good in its own right. But, I argue, that the logic that make in tolerance difficult to break also compel people to resist any attempts to make toleration more than a modus vivendi. True toleration will not be embraced unless the people (...) undergo a kind of conversion experience. (shrink)

According to a common judgement, a social planner should often use a lottery to decide which of two people should receive a good. This judgement undermines one of the best-known arguments for utilitarianism, due to John C. Harsanyi, and more generally undermines axiomatic arguments for utilitarianism and similar views. In this paper we ask which combinations of views about (a) the social planner’s attitude to risk and inequality, and (b) the subjects’ attitudes to risk are consistent with the aforementioned judgement. (...) We find that the class of combinations of views that can plausibly accommodate this judgement is quite limited. But one theory does better than others: the theory of chance-sensitive utility. (shrink)

Burke suggests that we should view society as a partnership between the past, the present, and the future. I defend this idea by outlining how we can understand the interests of the past and future people and the obligations that they have towards each other. I argue that we have forward-looking obligations to leave the world a decent place, and backward-looking obligations to respect the legacy of the past. The latter obligation requires an understanding of the role that traditions and (...) meta-traditions should (and should not) play in tying together societies—especially national societies—over time. (shrink)

It is proposed that our memory is made up of individual, unconnected Records, to each of which is attached a Heading. Retrieval of a Record can only be accomplished by addressing the attached Heading, the contents of which cannot itself be retrieved. Each Heading is made up of a mixture of content in more or less literal form and context, the latter including specification of environment and of internal states (e.g. drug states and mood). This view of memory allows an (...) easy account of a number of natural memory phenomena as well as a variety of laboratory findings such as the differences between recall and recognition. The theory further proposes that Headed Records can neither be deleted nor modified. Data apparently against such a hypothesis can be accounted for in terms of the retrieval process. (shrink)

Aims: Companies that should operate in competitive business environments must be able to sustain competitive responses over time. Making such responses, however, typically necessitates the firm's managerial capacity to constantly integrate its properties, ensuring that they are all matched with changing market needs. Based on the literature of Knowledge Management and Dynamic managerial capabilities, this paper contributes to our understanding by developing an Integrative Managerial Capabilities concept, which refers to “managers’ ability to orchestrate a firm resource base through the processes (...) of search, selection, configuration and deployment to achieve and sustain a firm competitive response”. Integration mechanisms are described which provide a key managerial capability. According to the literature on strategic management, limited past studies research has focused on facets of the firm's integrative capabilities. In the current literature, there is a notable lack of comprehensive insight into how companies actually orchestrate "integrate" resources and principal to achieve sustained success in complex environments. -/- Method/Approach: To answer the research questions, the study employed two data collection strategies: qualitative interviews; “semi-structured interviews”, and an openended survey, “online questionnaire”. -/- Findings: The relationship among managerial integrative capabilities and various levels of a firm's systemic structure, in particular, has never been clearly explained. The research concludes that the incorporation process is highly relevant to the case study examples, and that middle management can be seen to have a substantial effect on company change as a result of top and lower-level management integration. -/- Originality: this study argued that better and faster integration between the three main integrative mechanisms “search and selection, configuration and deployment” should itself be a potential source of sustained competitive respond; and that usually that integration will need to traverse “high, middle, and low managerial levels” of management structure. Implications: we recommend that future research into managerial integration processes, such as particular types of transition programs, be undertaken. (shrink)

Investigation of neural and cognitive processes underlying individual variation in moral preferences is underway, with notable similarities emerging between moral- and risk-based decision-making. Here we specifically assessed moral distributive justice preferences and non-moral financial gambling preferences in the same individuals, and report an association between these seemingly disparate forms of decision-making. Moreover, we find this association between distributive justice and risky decision-making exists primarily when the latter is assessed with the Iowa Gambling Task. These findings are consistent with neuroimaging studies (...) of brain function during moral and risky decision-making. This research also constitutes the first replication of a novel experimental measure of distributive justice decision-making, for which individual variation in performance was found. Further examination of decision-making processes across different contexts may lead to an improved understanding of the factors affecting moral behaviour. (shrink)

The desirability of what actually occurs is often influenced by what could have been. Preferences based on such value dependencies between actual and counterfactual outcomes generate a class of problems for orthodox decision theory, the best-known perhaps being the so-called Allais Paradox. In this paper we solve these problems by extending Richard Jeffrey's decision theory to counterfactual prospects, using a multidimensional possible-world semantics for conditionals, and showing that preferences that are sensitive to counterfactual considerations can still be desirability maximising. (...) We end the paper by investigating the conditions necessary and sufficient for a desirability function to be an expected utility. It turns out that the additional conditions imply highly implausible epistemic principles. (shrink)

According to the orthodox treatment of risk preferences in decision theory, they are to be explained in terms of the agent's desires about concrete outcomes. The orthodoxy has been criticised both for conflating two types of attitudes and for committing agents to attitudes that do not seem rationally required. To avoid these problems, it has been suggested that an agent's attitudes to risk should be captured by a risk function that is independent of her utility and probability functions. The main (...) problem with that approach is that it suggests that attitudes to risk are wholly distinct from people's (non-instrumental) desires. To overcome this problem, we develop a framework where an agent's utility function is defined over chance propositions (i.e., propositions describing objective probability distributions) as well as ordinary (non-chance) ones, and argue that one should explain different risk attitudes in terms of different forms of the utility function over such propositions. (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.

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)

Considerations of dynamic inconsistency have figured prominently in debates over the rationality of preferences that violate the separability conditions characteristic of expected utility theory. These debates have mostly focused on risk- and ambiguity averse preferences, but analogous considerations apply to preferences for fairness. We revisit these debates in the context of a specific hypothesis regarding the violations of separability by such preferences, namely that they are potentially both explained and rationalised by attitudes to the chances of goods that motivate a (...) preference for equality in the distribution of chances across people and possible events. Our main aim is to argue that, first, when these violations of static separability are motivated by such attitudes to chances, then they need not result in dynamically inconsistent behaviour. Second, and more generally, considerations of dynamic consistency do not, we argue, undermine the rationality of such attitudes towards the distribution of chances, despite the fact that such attitudes give rise to violations of the static separability assumptions of expected utility theory. (shrink)

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)

We present an ontology of pain and of other pain-related phenomena, building on the definition of pain provided by the International Association for the Study of Pain (IASP). Our strategy is to identify an evolutionarily basic canonical pain phenomenon, involving unpleasant sensory and emotional experience based causally in localized tissue damage that is concordant with that experience. We then show how different variant cases of this canonical pain phenomenon can be distinguished, including pain that is elevated relative to peripheral trauma, (...) pain that is caused neuropathically (thus with no necessary peripheral stimulus), and pain reports arising through deception either of self or of others. We describe how our approach can answer some of the objections raised against the IASP definition, and sketch how it can be used to support more sophisticated discrimination of different types of pain resulting in improved data analysis that can help in advancing pain research. (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.

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)

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)

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)

A letter to The Times of London, May 9, 1992 protesting the Cambridge University proposal to award an honorary degree to M. Jacques Derrida.

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

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.

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)

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)

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)

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.

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)

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)