In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within (...) the ACGT project thus far. (shrink)

The paper by Dupras and Bunnik is a useful addition to the literature on privacy in regards to datasets of human tissue/materials. In particular, the paper addresses import...

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user-friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage? Methods: Our focus here is on two different sets of answers to these questions that have been proposed, on the one hand in medicine, by the SNOMED CT community, (...) and on the other hand in biology, by the OBO Foundry. We address more specifically the issue as to how adherence to certain development principles can advance the usability and effectiveness of an ontology or terminology resource, for example by allowing more accurate maintenance, more reliable application, and more efficient interoperation with other ontologies and information resources. Results: SNOMED CT and the OBO Foundry differ considerably in their general approach.Nevertheless, a general trend towards more formal rigor and cross-domain interoperability can be seen in both and we argue that this trend should be accepted by all similar initiatives in the future. Conclusions: Future efforts in ontology development have to address the need for harmonization and integration of ontologies across disciplinary borders, and for this, coherent formalization of ontologies is a prerequisite. (shrink)

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...) paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

Ontologies are being ever more commonly used in biomedical informatics and we provide a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonised. We argue that one key foundation for both ontology evaluation and harmonisation is the adoption of a realist paradigm in (...) ontology development. For science-based ontologies of the sort which concern us in the eHealth arena, it is reality that provides the common benchmark against which ontologies can be evaluated and aligned within larger frameworks. Given the current multitude of ontologies in the biomedical domain the need for harmonisation is becoming ever more urgent. We describe one example of such harmonisation within the ACGT project, which draws on ontology-based computing as a basis for sharing clinical and laboratory data on cancer research. (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)

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)

Reuse of elements from existing ontologies in the construction of new ontologies is a foundational principle in ontological design. It offers the benefits, among others, of consistency and interoperability between such knowledge structures as well as sharing resources. Reuse is widely found within important collections of established ontologies, such as BioPortal and the OBO Foundry. However, reuse comes with its own potential problems involving ontological commitment, granularity, and ambiguity. Guidelines are proposed to aid ontology developers and curators in their prospective (...) reuse of content. These guidelines have been gleaned over years of practice in the ontology field. The guidelines are couched in experiential reports on designing and curating particular ontologies (e.g., EXACT and EXACT2) and using generally accepted approaches (e.g., MIREOT) in doing so. Various software tools to assist in ontology reuse are surveyed and discussed. (shrink)

Priority setting in health care is ubiquitous and health authorities are increasingly recognising the need for priority setting guidelines to ensure efficient, fair, and equitable resource allocation. While cost-effectiveness concerns seem to dominate many policies, the tension between utilitarian and deontological concerns is salient to many, and various severity criteria appear to fill this gap. Severity, then, must be subjected to rigorous ethical and philosophical analysis. Here we first give a brief history of the path to today’s severity criteria in (...) Norway and Sweden. The Scandinavian perspective on severity might be conducive to the international discussion, given its long-standing use as a priority setting criterion, despite having reached rather different conclusions so far. We then argue that severity can be viewed as a multidimensional concept, drawing on accounts of need, urgency, fairness, duty to save lives, and human dignity. Such concerns will often be relative to local mores, and the weighting placed on the various dimensions cannot be expected to be fixed. Thirdly, we present what we think are the most pertinent questions to answer about severity in order to facilitate decision making in the coming years of increased scarcity, and to further the understanding of underlying assumptions and values that go into these decisions. We conclude that severity is poorly understood, and that the topic needs substantial further inquiry; thus we hope this article may set a challenging and important research agenda. (shrink)

Mathias Frisch provides the first sustained philosophical discussion of conceptual problems in classical particle-field theories. Part of the book focuses on the problem of a satisfactory equation of motion for charged particles interacting with electromagnetic fields. As Frisch shows, the standard equation of motion results in a mathematically inconsistent theory, yet there is no fully consistent and conceptually unproblematic alternative theory. Frisch describes in detail how the search for a fundamental equation of motion is partly driven by pragmatic considerations (...) (like simplicity and mathematical tractability) that can override the aim for full consistency. The book also offers a comprehensive review and criticism of both the physical and philosophical literature on the temporal asymmetry exhibited by electromagnetic radiation fields, including Einstein's discussion of the asymmetry and Wheeler and Feynman's influential absorber theory of radiation. Frisch argues that attempts to derive the asymmetry from thermodynamic or cosmological considerations fail and proposes that we should understand the asymmetry as due to a fundamental causal constraint. The book's overarching philosophical thesis is that standard philosophical accounts that strictly identify scientific theories with a mathematical formalism and a mapping function specifying the theory's ontology are inadequate, since they permit neither inconsistent yet genuinely successful theories nor thick causal notions to be part of fundamental physics. (shrink)

Much has been written on the role of causal notions and causal reasoning in the so-called 'special sciences' and in common sense. But does causal reasoning also play a role in physics? Mathias Frisch argues that, contrary to what influential philosophical arguments purport to show, the answer is yes. Time-asymmetric causal structures are as integral a part of the representational toolkit of physics as a theory's dynamical equations. Frisch develops his argument partly through a critique of anti-causal arguments and (...) partly through a detailed examination of actual examples of causal notions in physics, including causal principles invoked in linear response theory and in representations of radiation phenomena. Offering a new perspective on the nature of scientific theories and causal reasoning, this book will be of interest to professional philosophers, graduate students, and anyone interested in the role of causal thinking in science. (shrink)

Poly(ADP‐ribosyl)ation is a post‐translational modification occurring in the nucleus. The most abundant and best‐characterized enzyme catalyzing this reaction, poly(ADP‐ribose) polymerase 1 (PARP1), participates in fundamental nuclear events. The enzyme functions as molecular “nick sensor”. It binds with high affinity to DNA single‐strand breaks resulting in the initiation of its catalytic activity. Activated PARP1 promotes base excision repair. In addition, PARP1 modifies several transcription factors and thereby precludes their binding to DNA. We propose that a major function of PARP1 includes the (...) silencing of transcription preventing expression of damaged genes. Concomitant stimulation of DNA repair suggests that PARP1 acts as a switch between transcription and DNA repair. Another PARP‐type enzyme, tankyrase, is involved in the regulation of telomere elongation. Tankyrase modifies a telomere‐associated protein and thereby prevents it masking telomeric repeats providing access of telomerase for telomere elongation. Therefore, poly(ADP‐ribosyl)ation reactions may act as molecular switches in DNA metabolism. BioEssays 23:543–548, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

Working in Z + KP, we give a new proof that the class of hereditarily finite sets cannot be proved to be a set in Zermelo set theory, extend the method to establish other failures of replacement, and exhibit a formula Φ(λ, a) such that for any sequence $\langle A_{\lambda} \mid \lambda \text{a limit ordinal} \rangle$ where for each $\lambda, A_{\lambda} \subseteq ^{\lambda}2$ , there is a supertransitive inner model of Zermelo containing all ordinals in which for every λ A (...) λ = {α ∣Φ(λ, a)}. (shrink)

Phillips argues that blindsight is due to response criterion artefacts under degraded conscious vision. His view provides alternative explanations for some studies, but may not work well when one considers several key findings in conjunction. Empirically, not all criterion effects are decidedly non-perceptual. Awareness is not completely abolished for some stimuli, in some patients. But in other cases, it was clearly impaired relative to the corresponding visual sensitivity. This relative dissociation is what makes blindsight so important and interesting.

This essay reconstructs the place of utopia in realist political theory, by examining the ways in which the literary genre of critical utopias can productively unsettle ongoing discussions about “how to do political theory.” I start by analyzing two prominent accounts of the relationship between realism and utopia: “real utopia” and “dystopic liberalism”. Elaborating on Raymond Geuss’s recent reflections, the essay then claims that an engagement with literature can shift the focus of these accounts. Utopian fiction, I maintain, is useful (...) for comprehending what is and for contemplating what might be. Ursula K. Le Guin’s novel The Dispossessed deploys this double function in an exemplary fashion: through her dynamic and open-ended portrayal of an Anarchist community, Le Guin succeeds in imagining a utopia that negates the status quo, without striving to construct a perfect society. The book’s radical, yet ambiguous, narrative hence reveals a strategy for locating utopia within realist political theory that moves beyond the positions dominating the current debate. Reading The Dispossessed ultimately demonstrates that realism without utopia is status quo–affirming, while utopia without realism is wishful thinking. (shrink)

Hintergrund: Biomedizinische Ontologien existieren unter anderem zur Integration von klinischen und experimentellen Daten. Um dies zu erreichen ist es erforderlich, dass die fraglichen Ontologien von einer großen Zahl von Benutzern zur Annotation von Daten verwendet werden. Wie können Ontologien das erforderliche Maß an Benutzerfreundlichkeit, Zuverlässigkeit, Kosteneffektivität und Domänenabdeckung erreichen, um weitreichende Akzeptanz herbeizuführen? -/- Material und Methoden: Wir konzentrieren uns auf zwei unterschiedliche Strategien, die zurzeit hierbei verfolgt werden. Eine davon wird von SNOMED CT im Bereich der Medizin vertreten, die (...) andere im Bereich der Biologie und Biomedizin von der OBO Foundry. Es soll aufgezeigt werden, wie die Verpflichtung zu speziellen Kriterien der Ontologieentwicklung die Nützlichkeit und Effektivität der Ontologien positiv beeinflusst, indem die Pflege der terminologischen Systeme und ihre Interoperabilität vereinfacht werden. -/- Ergebnisse: SNOMED CT und die OBO Foundry unterscheiden sich grundlegend in ihren Ansätzen und Zielen. Unabhängig davon kann jedoch ein allgemeiner Trend zur strengeren Formalisierung und Fokussierung auf Interoperabilität zwischen unterschiedlichen Domänen und ihren Repräsentationen beobachtet werden. (shrink)

The grounds of justice -- "Un pouvoir ordinaire": shared membership in a state as a ground of -- Justice -- Internationalism versus statism and globalism: contemporary debates -- What follows from our common humanity? : the institutional stance, human rights, and nonrelationism -- Hugo Grotius revisited : collective ownership of the Earth and global public reason -- "Our sole habitation" : a contemporary approach to collective ownership of the earth -- Toward a contingent derivation of human rights -- Proportionate use (...) : immigration and original ownership of the Earth -- "But the earth abideth for ever" : obligations to future generations -- Climate change and ownership of the atmosphere -- Human rights as membership rights in the global order -- Arguing for human rights : essential pharmaceuticals -- Arguing for human rights : labor rights as human rights -- Justice and trade -- The way we live now -- "Imagine there's no countries" : a reply to John Lennon -- Justice and accountability : the state -- Justice and accountability : the World Trade Organization. (shrink)

In Frisch 2004 and 2005 I showed that the standard ways of modeling particle-field interactions in classical electrodynamics, which exclude the interactions of a particle with its own field, results in a formal inconsistency, and I argued that attempts to include the self-field lead to numerous conceptual problems. In this paper I respond to criticism of my account in Belot 2007 and Muller 2007. I concede that this inconsistency in itself is less telling than I suggested earlier but argue that (...) existing solutions to the theory's foundational problems do not support the kind of traditional philosophical conception of scientific theorizing defended by Muller and Belot. *Received January 2007; revised October 2007. †To contact the author, please write to: Department of Philosophy, University of Maryland, Skinner Building, College Park, MD 20742; e-mail: [email protected]. (shrink)

Aratus has been notorious for his wordplay since the first decades of his reception. Hellenistic readers such as Callimachus, Leonidas, or ‘King Ptolemy’ seem to have picked up on the pun on the author's own name atPhaenomena2, as well as on the famous λεπτή acrostic atPhaen.783–6 that will be revisited here. Three carefully placed occurrences of the adjective have so far been uncovered in the passage, but for a full appreciation of its elegance we must note that Aratus has set (...) his readers up to notice a fourth. (shrink)

Working in Z + KP, we give a new proof that the class of hereditarily finite sets cannot be proved to be a set in Zermelo set theory, extend the method to establish other failures of replacement, and exhibit a formula $\Phi$ such that for any sequence $\langle A_{\lambda} \mid \lambda \text{a limit ordinal} \rangle$ where for each $\lambda, A_{\lambda} \subseteq ^{\lambda}2$, there is a supertransitive inner model of Zermelo containing all ordinals in which for every $\lambda A_{\lambda} = \{\alpha (...) \mid\Phi\}$. (shrink)

Though much attention has been paid to different principles of justice, far less has been done reflecting on what the larger concern behind the notion is. In this work, Mathias Risse proposes that the perennial quest for justice is about ensuring that each individual has an appropriate place in what our uniquely human capacities permit us to build, produce, and maintain, and is appropriately respected for the capacity to hold such a place to begin with. Risse begins by investigating (...) the role of political philosophers and exploring how to think about the global context where philosophical inquiry occurs. Next, he offers a quasi-historical narrative about how the notion of distributive justice identifies a genuinely human concern that arises independently of cultural context and has developed into the one we should adopt now. Finally, he investigates the core terms of this view, including stringency, moral value, ground and duties of justice. (shrink)

Vor dem Hintergrund der Debatte um nichtbegriffliche Vorstellungsinhalte sucht diese Arbeit ein adäquates Verständnis von Kants Lehre der Erkenntnisquellen, Sinnlichkeit und Verstand, und der Ungleichartigkeit der anschaulichen und begrifflichen Vorstellungsweise, speziell bezüglich der Transzendentalen Ästhetik, der Lehre der transzendentalen Synthesis der Einbildungskraft (Selbstaffektion) und der Theorie des transzendentalen Schematismus. -/- Engaging in the Kantian debate on the existence of non-conceptual content, this work attempts to provide an adequate understanding of Kant’s doctrine of the two sources of human knowledge, sensibility and (...) understanding, and of their heterogeneous ways of representing, through intuitions and concepts. It elaborates on a consistent reading of this dualism in relation to the Transcendental Aesthetic, the synthesis of imagination, and the schematism. (shrink)

We argue that the two temporal cognition systems are conceptually too confined to be helpful in understanding the evolution of temporal cognition. In fact, we doubt there are two systems. In relation to this, we question that the authors did not describe the results of our planning study on ravens correctly, as this is of consequence to their theory.

This article highlights the continuing relevance of a classic bioethical text, “Bioethics as a Discipline,” published by the Hastings Center’s cofounder Daniel Callahan in 1973. Connecting the text’s programmatic recommendations with later reflections and interventions Callahan wrote about the development of bioethics illuminates how the vision Callahan established and the reality this vision helped create were interrelated—just not in the way Callahan had hoped for. Although this portrait relies on an individual perception of the development of bioethics, it might nevertheless, (...) through its unique linkage of different bioethical temporalities, contribute to a broader reassessment of what bioethics became and why. (shrink)

Biographical note: Mathias Denecke is a PhD student at the University of Konstanz, Germany.Anne Ganzert is a PhD student at the University of Konstanz, Germany.Isabell Otto (PhD) is junior professor for Media Studies at the University of Konstanz, Germany.Robert Stock (MA) coordinates the research initiative ”Media and Participation“ at the University of Konstanz, Germany.

Speech planning is a sophisticated process. In dialog, it regularly starts in overlap with an incoming turn by a conversation partner. We show that planning spoken responses in overlap with incoming turns is associated with higher processing load than planning in silence. In a dialogic experiment, participants took turns with a confederate describing lists of objects. The confederate’s utterances (to which participants responded) were pre‐recorded and varied in whether they ended in a verb or an object noun and whether this (...) ending was predictable or not. We found that response planning in overlap with sentence‐final verbs evokes larger task‐evoked pupillary responses, while end predictability had no effect. This finding indicates that planning in overlap leads to higher processing load for next speakers in dialog and that next speakers do not proactively modulate the time course of their response planning based on their predictions of turn endings. The turn‐taking system exerts pressure on the language processing system by pushing speakers to plan in overlap despite the ensuing increase in processing load. (shrink)

David Albert and Barry Loewer have argued that the temporal asymmetry of our concept of causal influence or control is grounded in the statistical mechanical assumption of a low-entropy past. In this paper I critically examine Albert's and Loewer 's accounts.

The associative theory of creativity states that creativity is associated with differences in the structure of semantic memory, whereas the executive theory of creativity emphasises the role of top-down control for creative thought. For a powerful test of these accounts, individual semantic memory structure was modelled with a novel method based on semantic relatedness judgements and different criteria for network filtering were compared. The executive account was supported by a correlation between creative ability and broad retrieval ability. The associative account (...) was independently supported, when network filtering was based on a relatedness threshold, but not when it was based on a fixed edge number or on the analysis of weighted networks. In the former case, creative ability was associated with shorter average path lengths and higher clustering of the network, suggesting that the semantic networks of creative people show higher small-worldness. (shrink)

Bourbaki suggest that their definition of the number 1 runs to some tens of thousands of symbols. We show that that is a considerable under-estimate, the true number of symbols being that in the title, not counting 1 179 618 517 981 links between symbols that are needed to disambiguate the whole expression.

The practical goal of preventing premature death seems uncontroversial. But the term ‘premature death’ is vague with several, sometimes conflicting definitions. This ambiguity results in several conceptions with which not all will agree. Moreover, the normative rationale behind the goal of preventing premature deaths is masked by the operational definition of existing measures. In this article, we argue that ‘premature death’ should be recognized as a normative concept. We propose that normative theories should be used to justify measures of premature (...) death to provide them with normative validity and public legitimacy. (shrink)

As the record-breaking heat of 2016 continues into 2017, making it likely that 2017 will be the second hottest year on record just behind the El Niño year 2016, and as Arctic heat waves pushing the sea ice extent to record lows are mirrored by large scale sheets of meltwater and even rain in Antarctica—the Trump administration is taking dramatic steps to undo the Obama administration’s climate legacy.In its final years, the Obama administration pursued two principal strategies toward climate policy. (...) First, by signing the Paris Accord it committed the U.S. to contribute to global efforts to hold “the increase in the global average temperature to well below 2°C above pre-industrial levels and to pursue efforts to... (shrink)

von Lothar Brock Wer dieses Buch zur Hand nimmt, sollte sich einen Autor vorstellen, der einer Gruppe hartgesottener Geschäftsleute aus der Wüste von New Mexico morgens um sieben mit charmanter Leichtigkeit und spärlichen, aber Verbindung stiftenden Gesten einen Vortrag über die EU als einer vorgestellten Gemeinschaft hält und dafür überschwenglich gefeiert wird. Oder einen Theoretiker mit verblüffend praktischen Kenntnissen über Höhenmedizin und der unter bestimmten Umständen lebensrettenden Fähigkeit, panischen Berggefährten den Anblick der Tiefe erträglich zu machen. Oder den lead-Sänger einer (...) ziemlich professionellen Musikgruppe, die sich die öffentliche Pflege des Liedgutes der Rolling Stones zur Aufgabe gemacht hat und als Meister der Reproduktion die Bewunderer des Originals in Taumel versetzt - von Stockholm bis OfIenbach. Auf keinen Fall aber sollte man sich einen Autor vorstellen wie man ihn sich vorstellt, wenn man dieses Buch zur Hand nimmt. Oder doch? Doch! Es könnte ja sein, daß jemand dieses Buch nicht nur als lohnende Strapaze erlebt, sondern auch als Vergnügen, wenn er erst einmal über den Untertitel hinweggekommen ist. Zur Sache:,,Fallen der Welt-Ordnung" - die Fallen oder das Fallen? Das Thema verrät es nicht; denn zwischen Moderne und Postmoderne ist ein weites Feld, auf dem alles mögliche passieren kann. Worum also geht es? Mathias Albert versteht das Arbeitsgebiet der Internationalen Beziehungen (also der Lehre und Forschung über diesen Gegenstandsbereich) als jenen Teilbereich der Sozialwissenschaften, der sich mit der Weltordnung befaßt. (shrink)

In diesem Buch werden die zwei Grundsäulen der "Kritischen Patriarchatstheorie" - die Matriarchale Naturphilosophie und die Patriarchatskritische Geschichtsphilosophie - vorgestellt und im Rahmen einer kritischen Auseinandersetzung mit der Naturphilosophie Giordano Brunos sowie der Geschichtsphilosophie Martin Heideggers erläutert.