The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

This book addresses concerns about educational and moral standards in a world increasingly characterised by nihilism. On the one hand there is widespread anxiety that standards are falling; on the other, new machinery of accountability and inspection to show that they are not. The authors in this book state that we cannot avoid nihilism if we are simply _laissez-faire_ about values, neither can we reduce them to standards of performance, nor must we return to traditional values. They state that we (...) need to create a new set of values based on a critical assessment of contemporary practice in the light of a number of philosophical texts that address the question of nihilism, including the work of Nietzsche. (shrink)

In this important survey, an international group of leading philosophers chart the development of philosophy of education in the twentieth century and point to signficant questions for its future. Presents a definitive introduction to the core areas of philosophy of education. Contains 20 newly-commissioned articles, all of which are written by internationally distinguished scholars. Each chapter reviews a problem, examines the current state of the discipline with respect to the topic, and discusses possible futures of the field. Provides a solid (...) foundation for further study. (shrink)

In this important survey, an international group of leading philosophers chart the development of philosophy of education in the twentieth century and point to signficant questions for its future. Presents a definitive introduction to the core areas of philosophy of education. Contains 20 newly-commissioned articles, all of which are written by internationally distinguished scholars. Each chapter reviews a problem, examines the current state of the discipline with respect to the topic, and discusses possible futures of the field. Provides a solid (...) foundation for further study. (shrink)

This chapter contains sections titled: I II III.

ABSTRACTIn 1799 Dirk van Hogendorp published a Report on the Current Conditions of Dutch Possessions in the East Indies, a document that has garned comparisons to Adam Smith’s Wealth of Nations for its condemnation of the Dutch East India Company and for its insistence on the importance of property rights to economic growth. The text is also an anti-Chinese diatribe, castigating the supposedly inveterate avarice of Java’s Chinese minority. Hogendorp’s advocacy of colonial reform and sinophobia intertwine in his use (...) of the term ijver, then the standard Dutch translation of ‘emulation’, a keyword of eighteenth-century political economy. Read against the status of emulation in European thinking, Hogendorp’s employment of the ijver offers an opportunity to re-examine emulation’s fraught, ambivalent quality, which has been noted by scholars like Istvan Hont and Sophus Reinert concerned primarily with a division between benevolent domestic emulation and dangerous international emulation. The colonial sphere, neither wholly domestic nor wholly foreign, was a discursive site wherein the tensions of emulation were worked out in new ways. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...) large amounts of ncRNA biological and clinical data. (shrink)

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

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (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)

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

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

We report the identification of a recurrent, 520-kb 16p12.1 microdeletion associated with childhood developmental delay. The microdeletion was detected in 20 of 11,873 cases compared with 2 of 8,540 controls and replicated in a second series of 22 of 9,254 cases compared with 6 of 6,299 controls. Most deletions were inherited, with carrier parents likely to manifest neuropsychiatric phenotypes compared to non-carrier parents. Probands were more likely to carry an additional large copy-number variant when compared to matched controls. The clinical (...) features of individuals with two mutations were distinct from and/or more severe than those of individuals carrying only the co-occurring mutation. Our data support a two-hit model in which the 16p12.1 microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large deletions or duplications. Analysis of other microdeletions with variable expressivity indicates that this two-hit model might be more generally applicable to neuropsychiatric disease. © 2010 Nature America, Inc. All rights reserved. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

Today the ethical and normative concerns of everyday citizens are all too often sidelined from the study of political and social issues, driven out by an effort to create a more "scientific" study. This book offers a way for social scientists and political theorists to reintegrate the empirical and the normative, proposing a way out of the scientism that clouds our age. In Alasdair MacIntyre, Charles Taylor, and the Demise of Naturalism: Reunifying Political Theory and Social Science, Jason Blakely argues (...) that the resources for overcoming this divide are found in the respective intellectual developments of Charles Taylor and Alasdair MacIntyre. Blakely examines their often parallel intellectual journeys, which led them to critically engage the British New Left, analytic philosophy, phenomenology, continental hermeneutics, and modern social science. Although MacIntyre and Taylor are not sui generis, Blakely claims they each present a new, revived humanism, one that insists on the creative agency of the human person against reductive, instrumental, technocratic, and scientistic ways of thinking. The recovery of certain key themes in these philosophers' works generates a new political philosophy with which to face certain unprecedented problems of our age. Taylor's and MacIntyre's philosophies give social scientists working in all disciplines (from economics and sociology to political science and psychology) an alternative theoretical framework for conducting research. "This book does an excellent job in identifying a real problem in mainstream political theory--its overly normative character and its separation from social science. It contains many original contributions to the field. I particularly liked the way in which the problems of naturalism are presented as institutional, cultural, and political as well as philosophical. The historical background to these problems is also interesting and sheds fresh light on the issues." --Nicholas Smith, Macquarie University. (shrink)

A fresh look at the often-censured but imperfectly understood traditions of Utilitarianism and political economy in relation to Victorian literature and culture. Setting the writings of Bentham, Smith, Malthus, Mill, Dickens, Carlyle, Trollope, Eliot, Gaskell, and Tagore in historical context, Blake widens awareness of commonalities across the age.

Classical studies of the Idaian Daktyloi rely on evolutionary and survivalist models which assume prehistoric smiths as the locus of their meaning. More recent anthropologies of technology evaluate technological symbols for their integration of technology into the intellectual, ritual, historical and economic structures of the subject culture. A fragmenta incerta of Pherekydes affords a testing-ground for this approach to the Daktyloi. The investigation reveals adaptability and integration into Pythagorean tradition, magical practice, and Cretan history. This offers more cogent reasons for (...) the daimones’ longevity than previous models, and corrects the assumption that a fragmentary record reflects cultural insignificance.Les études classiques sur les Dactyles idéens se fondent sur des modèles évolutionnistes qui donnent sens à ces figures en les associant à des forgerons préhistoriques. Des approches anthropologiques récentes évaluent les symboles technologiques en fonction de l’intégration de la technologie qu’ils opèrent dans les structures intellectuelles, rituelles, historiques et économiques de la culture étudiée. Un fragment incertain de Phérécyde offre une possibilité de tester cette approche des Dactyles. L’étude révèle une adaptabilité et une intégration dans la tradition pythagoricienne, dans la pratique magique et l’histoire crétoise. Cela permet d’expliquer la longévité de ces daimones de manière plus convaincante que ne le faisaient les modèles précédents, et cela corrige l’affirmation qu’un témoignage fragmentaire n’a pas de signification culturelle. (shrink)

Paul Standish:Some people might expect us to start by explaining why we have written this chapter as a dialogue. Leaving aside the fact that Plato – to whom all philosophy, it has been said, is a series of footnotes – wrote in dialogue form, and never seems to have felt the need to tell us why, we might say that we have written it in this way because it is a dialogue. We push ideas to and fro, question each other, (...) disagree with each other, and so on.Reader:You say that it is a dialogue. Do you mean that this chapter is a transcription of an actual conversation between you?Richard Smith:There have been so many conversations among us that these pages are pretty well bound to be true to our spoken words at some time or another. And of course these conversations have involved Paul Smeyers too, and – for many years – Nigel Blake, whose presence can also be detected in these pages.Reader:So you are saying that there has been something essentially dialogic in your relationship with Paul Smeyers, and you felt that only a dialogue could do justice to that.Paul:Pretty much so. And while there is something worryingly self-confirming in justifying the dialogue form with a dialogic explanation, it would be odd to cast the justification in some other prose form, as if that were superior to dialogue in respect of clarity or persuasive power or in some other way.Richard:Then too dialogue is a fine medium for reminiscence, allowing for uncertainty, different perspectives, and debate rather than assuming that veridical record is what is at issue here.Paul:In any case, reminiscence is largely a way of revisiting philosophical projects and arguments from the past in order to subject their soundness to fresh critique.Reader:So, if I understand you, this dialogue is both true and fictive, and reminiscence looks forward, as much as back.Richard:Splendid. I only hope that what follows isn’t a disappointment to you. (shrink)

William Blake and Zadie Smith reached strikingly similar critical positions towards philosophical trends current in their respective eras. Both excoriate those who, for selfish ends, disparage beauty and in so doing sabotage justice, love, joy and genuine freedom. Smith’s On Beauty, like Blake’s America: A Prophecy and Visions of the Daughters of Albion, indicts the reprehensible intellectual discourses of the day that undermine human happiness and corrupt the social order. Whereas Blake critiqued the rights revolutions (...) set in motion by Thomas Paine, William Godwin, Mary Wollstonecraft and others from a more broadly moral and future-oriented angle than has generally been recognized (as Saree Makdisi has shown), Smith wittily dramatizes that same vision through a huge range of up-to-date ideological discourses and antagonisms–many of them descended from Paine et al.–to refurbish Blake’s particular brand of radical antinomianism and to celebrate much the same optimistic spirit that Blake invested in America and Visions. Indeed, Smith’s novel anticipates and critiques ab ovo the sweepingenthusiasms that are animating current uprisings worldwide. (shrink)

The foundation for a system of morals, this 1749 work is a landmark of moral and political thought. Its highly original theories of conscience, moral judgment, and virtue offer a reconstruction of the Enlightenment concept of social science, embracing both political economy and theories of law and government.

This volume puts together twelve new essays by scholars who have done groundbreaking work in epistemology over the past four decades. Unfortunately, the editor’s brief introduction offers only a sketchy presentation of the papers and their background. Given the variety and complexity of the issues tackled, one would have expected a more detailed account of the nature and developments of the epistemological theories and arguments put forward and discussed by the contributors. The absence of such an account is all the (...) more surprising considering that the editor does not himself contribute a paper to the volume. (shrink)

Over 5 million college students in the United States – nearly one-in-three students currently enrolled – are of immigrant origin, meaning they are either the children of immigrant parents or guardians and/or immigrants themselves. These students accounted for almost 60% of the growth in higher education enrolment in the 21st century. Nevertheless, there is very little research dedicated to this student population's specific experiences of postsecondary education, with similar absences discernible within the realms of higher education policy and practice. Although (...) college campuses are making important progress in building more inclusive spaces, conversations about climate and student care rarely account for the journeys of students of immigrant origin. Featuring 20 chapters written by more than 50 contributors, this book addresses this glaring omission. The authors examine how students of immigrant origin experience the road to, through, and beyond higher education, while, simultaneously, speaking to evidence-based implications for policy, research, and practice. (shrink)

This title presents a comprehensive guide to interpretative phenomenological analysis (IPA) which is an increasingly popular approach to qualitative inquiry taught to undergraduate and postgraduate students today.