The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)
A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)
The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)
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)
Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological ontologies, including the Cell Ontology (CL), designed to provide a standardized representation of cell types for data annotation. Ontologies have been shown to have significant benefits for computational analyses of large data sets and for automated reasoning applications, leading to organized attempts to improve the structure and formal (...) rigor of ontologies to better support computation. 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 computation and for cross-species data integration. Results: To enhance the CL's utility for computational analyses, 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. We avoid multiple uses of is_a by linking DC-CL terms to terms in other ontologies via additional, formally defined relations such as has_function. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. Accordingly, we propose our method as a general strategy for the ontological representation of cells. DC-CL is available from http://www.obofoundry.org. (shrink)
To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.
The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)
In 'Literature Suspends Death: Sacrifice and Storytelling in Kierkegaard, Kafka and Blanchot' Chris Danta takes Genesis 22 as the starting point for an investigation of the role of literary imagination. His aim is to read the Genesis story from a literary-theoretical perspective in order to show how it can 'illuminate the secular situation of the literary writer.' To do this, Danta stages a fruitful confrontation between Søren Kierkegaard as defender of religion and inwardness and Franz Kafka and Maurice Blanchot (...) as defenders of literature. In this review, three important points in this confrontation are highlighted. 1. The problem of identification. 2. The moment of substitution. 3. The spectrality of the writer. (shrink)
Chris Dragos has recently presented two objections to criticisms I've published against Peter van Inwagen's No-Minimum argument. He also suggests that the best way to criticize the No-Minimum argument is via the concept of divine satisficing. In this article I argue that both of Dragos's objections fail, and I question whether satisficing is relevant to the viability of the No-Minimum argument.
The Philosopher Queen: Feminist Essays on War, Love, and Knowledge. By Chris Cuomo. Lanham, Md.: Rowman and Littlefield Publishers, Inc., 2003. The Philosopher Queen is a powerful illustration of what Cherríe Moraga calls a "theory in the flesh." That is, theorizing from a place where "physical realities of our lives—our skin color, the land or concrete we grow up on, our sexual longings—all fuse to create a politic [and, I would add, an ethics, spirituality, and epistemology] born out of (...) necessity" (Moraga 21). Cuomo's theory in the flesh combines standard philosophical essays with personal narratives and invites us to do philosophy from this joyful and witty place. Readers are invited to reframe and reexamine war, science, gender, sexuality, race, ecology, knowledge, and politics in a voice that is fearless, funny, faithful, and feminist—one that disrupts common understandings of how philosophy ought to be done. Instead philosophy should help us to "negotiate a wild, wicked world, and to provide some understanding of being and existence. The best philosophy aims to promote good and to produce knowledge, and therefore enable flourishing" (xi). Accepted philosophical approaches alone are inadequate. Life's challenges resist formulaic solutions. Knowledge is not always produced through neat deductions: truths are partial, power divides, stomachs growl, hearts are broken, and emotions influence... (shrink)
Why would anyone want there to be natural foundations for the social sciences? In a provocative essay exploring precisely that question, historian Chris Renwick uses an interwar debate featuring William Beveridge, Lancelot Hogben, and Friedrich Hayek to begin to imagine what might have been had such a program calling for biological knowledge to form the natural bases of the social sciences been realized at the London School of Economics. Yet perhaps Renwick grants too much attention to differences and “what-ifs” (...) and not enough to the historical question of “what happened” afterward. “Chickens and Eggs” offers an alternative view of this rather vexed question—one grounded in what happened, which suggests that Renwick’s concerns may be somewhat misplaced. (shrink)
Chris Frith's target chapters contain a wealth of interesting experiments and striking theoretical claims. In these comments I begin by drawing out some of the key themes in his discussion of action and the sense of agency. Frith's central claim about conscious action is that what we are primarily conscious of in acting is our own agency. I will review some of the experimental evidence that he interprets in support of this claim and then explore the following three questions (...) about the awareness of agency: Should we locate the phenomena that Frith describes as awareness of agency at the personal level or at the subpersonal level? If we are indeed operating at the personal level, then should we think about awareness of agency as something we experience, or as something that we believe? If awareness of agency is to be understood experientially, is there what some authors have called “a sense of agency“, where this is understood to be a distinctive type of experience that accompanies agentive behaviors but is absent in behaviors that are not under the control of the agent? In what follows I argue that awareness of agency should be located at the personal level, and that we should think of it as something we experience . But I will reject the claim that there is a distinctive sense of agency. (shrink)
Kant and Education brings together sixteen essays by an international group of scholars. The range of topics covered in the anthology is impressive. Kant's contribution to contemporary theories of education is central, as well as Kant's intellectual debt to Rousseau, the role of education in Kant's normative theories, and the impact of Kant's ideas on subsequent generations. Add to this the relative shortness of each essay (ten to fifteen pages), and one is left with an accessible introduction to a fascinating, (...) but often neglected, topic of Kant's ethical theory. The editors, Klas Roth and Chris W. Surprenant, have done an admirable job. (shrink)
I thought the paper by Kai-yee Wong and Chris Fraser was fascinating and insightful. Two things I especially appreciated are the clarity with which they summarize my views. I think they are quite fair and accurate. Second, I appreciate their suggestion that the way to deal with the practical problem of weakness of will has much to do with the role of the Background in shaping our actions. I think they are especially on the right track when they say (...) that the improvement of Background skills may actually narrow the range of real options for action, (p. 21) nonetheless, they do not decrease freedom. As they say, “It is a process of strengthening the self, and the agent is likely to experience the concomitant restriction of ‘live’ options not as a limitation but as strength of character.” (p. 21). That seems to me very much on the right track. What they are suggesting, and it is a powerful addition to my own writings, is that we should not just think of the Background as facilitating languages, games and social practices generally, but for morality as well (p. 23). (shrink)
El presente artículo explora la presencia de un principio dialógico en la configuración de las subjetividades que interactúan en Level Five de Chris Marker con el objetivo de matizar la metáfora crítica que califica de forma consistente el cine del director francés como ejemplo del autorretrato. Mediante el concepto bajtiniano de “devenir ideológico”, el texto presta especial atención a la creciente importancia que juegan las tecnologías de la comunicación en los procesos de reacentuación discursiva que determinan en último término (...) la construcción de subjetividades. La noción de “imagen-red” busca poner de relieve las formas en las que la imagen digital ha propiciado el desarrollo de un nuevo pasaje de la imagen hacia un régimen representativo dominado por las ideas de intercambio autoinscripción cuyos ecos Level Five explora mediante el análisis de aspectos que van desde la dicotomía entre historia y memoria al papel de la imagen documental en la construcción de la realidad. This article analyzes the presence of a dialogic principle in the way subjectivities are constructed within Chris Marker’s Level Five, with a view to critically counteract the notion of Marker’s films as forms of the self-portrait. Through the Bakhtinian concept of “ideological becoming”, special attention is paid to the role played by new technologies of information and communication in the processes of re- accentuation which determine how subjectivities evolve in the context of the film. The concept of an “image-network” attempts to highlight the development of a new passage of the image towards a mode of representation dominated by a principle of exchange, whose importance is echoed in the film through the analysis of issues ranging from the dichotomy between memory and history to the relevance of documentary image for reality construction. (shrink)
This is my response to the papers by Chris Pincock, Lisa Warenski and Jonathan Weinberg, which were presented at the Book Symposium on my Essays on A Priori Knowledge and Justification, American Philosophical Association Pacific Division Meetings, March 16–19, 2014.
Sciabarra replies to the seven respondents to his Fall 2002 essay on Rand, Rush, and progressive rock music. He defends the view that Rand's dialectical orientation underlies a fundamentally radical perspective. Rand shared with the counterculture—especially its libertarian progressive rock representatives—a repudiation of authoritarianism, while embracing the "unknown ideal" of capitalism. Her ability to trace the interrelationships among personal, cultural, and structural factors in social analysis and her repudiation of false alternatives is at the heart of that ideal vision, which (...) transcends left and right. (shrink)
The concept of archetypes has received a number of fundamentally different interpretations, and there are numerous additional philosophical concepts which can be characterized as modifications of those interpretations. Chris Nunn’s paper represents an approach to bringing a specific one among those concepts -- Richard Dawkins’ neo-Darwinistic conception of memes -- into contact with the notion of archetypes as it has been mainly popularized by Carl Gustav Jung. Nunn states rightly that Jung’s own understanding of and emphasis on archetypes changed (...) considerably during his lifetime. Therefore the difficulty is not only how to relate memes to archetypes, but also to distinguish that concept of archetypes to which memes relate from those to which they do not. (shrink)
Nurse Kaci Hickox is among the “Ebola Fighters” honored by Time magazine as its 2014 Person of the Year, having treated Ebola patients in Sierra Leone while volunteering with Médecins Sans Frontieres. When she returned to the United States in October 2014, she was quarantined in New Jersey for three days before returning home to Maine under the terms of a negotiated release. A year later, in October 2015, Hickox filed suit in federal court against Governor Chris Christie and (...) New Jersey health officials, claiming that the quarantine violated her civil rights. Her complaint asserts that New Jersey officials lacked the authority to quarantine her because she did not pose a significant risk of transmission. The lawsuit raises important questions about disease-transmission risk, the inability of science to rule out certain theoretical risks, and the state's power to quarantine. It also demonstrates that population health depends on respecting individual liberty and using the best available epidemiological data to set public health policy. (shrink)
We review Potts' influential book on the semantics of conventional implicature , offering an explication of his technical apparatus and drawing out the proposal's implications, focusing on the class of CIs he calls supplements. While we applaud many facets of this work, we argue that careful considerations of the pragmatics of CIs will be required in order to yield an empirically and explanatorily adequate account.
Ethics in Early China: An Anthology is a major contribution to the philosophical study of early Chinese ethics and comparative ethics by a collection of some of the most distinguished scholars in these fields. This anthology honors Professor Chad Hansen's many and important contributions to the study of Chinese philosophy, but the work is not a festschrift per se. Instead of discussing the honoree's oeuvre in a collection of essays, these new, innovative, and outstanding writings engage, bear upon, develop, and (...) contend with important themes in Hansen's work, including, for example, Hansen's provocative interpretations of the meanings of dao 道 and de 德 in early Chinese sources, his analysis of the action-guiding .. (shrink)