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)

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.

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

The 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)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

This work has been selected by scholars as being culturally important and is part of the knowledge base of civilization as we know it. This work is in the public domain in the United States of America, and possibly other nations. Within the United States, you may freely copy and distribute this work, as no entity (individual or corporate) has a copyright on the body of the work. Scholars believe, and we concur, that this work is important enough to be (...) preserved, reproduced, and made generally available to the public. To ensure a quality reading experience, this work has been proofread and republished using a format that seamlessly blends the original graphical elements with text in an easy-to-read typeface. We appreciate your support of the preservation process, and thank you for being an important part of keeping this knowledge alive and relevant. (shrink)

This work has been selected by scholars as being culturally important and is part of the knowledge base of civilization as we know it. This work is in the public domain in the United States of America, and possibly other nations. Within the United States, you may freely copy and distribute this work, as no entity (individual or corporate) has a copyright on the body of the work. Scholars believe, and we concur, that this work is important enough to be (...) preserved, reproduced, and made generally available to the public. To ensure a quality reading experience, this work has been proofread and republished using a format that seamlessly blends the original graphical elements with text in an easy-to-read typeface. We appreciate your support of the preservation process, and thank you for being an important part of keeping this knowledge alive and relevant. (shrink)

Another title in the reissued Oxford Classic Texts in the Physical Sciences series, Jeffrey's Theory of Probability, first published in 1939, was the first to develop a fundamental theory of scientific inference based on the ideas of Bayesian statistics. His ideas were way ahead of their time and it is only in the past ten years that the subject of Bayes' factors has been significantly developed and extended. Until recently the two schools of statistics were distinctly different and set apart. (...) Recent work has changed all that and today's graduate students and researchers all require an understanding of Bayesian ideas. This book is their starting point. (shrink)

For many Christians, personal experiences of God provide an important ground or justification for accepting the truth of the gospel. But we are sometimes mistaken about our experiences, and followers of other religions also provide impressive testimonies to support their religious beliefs. This book explores from a philosophical and theological perspective the viability of divine encounters as support for belief in God, arguing that some religious experiences can be accepted as genuine experiences of God and can provide evidence for Christian (...) beliefs. (shrink)

BEGINNING with G. E. M. Anscombe's "Modern Moral Philosophy" in 1958, various critics--e.g., Frankena, Foot, MacIntyre, and Murdock--have, to one extent or another, expressed dissatisfaction with the condition of modern moral philosophy. Prior to this round of critiques, H. A. Prichard in 1912 asked the question "Is Moral Philosophy Based on a Mistake?" in an essay of that title in Mind. One finds precedent for these expressions of discontent with the ground rules of moral philosophy in both Aristotle and Kant, (...) two thinkers whose reformulations of the questions and procedures of ethics proved seminal for the discipline. Even neglecting other important developments in contemporary moral philosophy, the diversity and rigour of these critiques alone suggest that the prognosis for the discipline of ethics is quite favorable. Philosophy in at least one of its dimensions has recovered that self-reflective attentiveness that marks its most productive phases. So it is that several of these contemporary critiques raise the suspicion that what is wrong with moral philosophy is that it operates outside of a context in terms of which talk about moral laws or moral goods would be intelligible. Our contemporary situation can thus be contrasted with, for example, that of Aristotle for whom a discussion of "magnificence" was firmly rooted in an Athenian context in terms of which an argument over the merits of that particular virtue might be resolved. Alasdair MacIntyre's After Virtue brings this line of reflection into sharp new focus with a series of illuminating discussions concerning the role of the virtues both in the history of moral practices and in the logic of moral argument. In general, MacIntyre tries to show that "contemporary moral debate is interminable" ; that is, he tries to show why, given the nature of contemporary moral philosophy, there is "no rational way of securing moral agreement". Because I believe MacIntyre is successful in his demonstration, I shall, in this paper, take that demonstration for granted and try to construct a set of arguments designed to show how, in terms of a universally accessible paradigmatic character, we have at hand a way of avoiding the "interminable" regress of moral debate. Thus although my argument is derivative to MacIntyre's diagnosis and dependent, in part, upon his treatment of the concept of virtue, the proposal I develop here for the resolution of moral arguments is, sadly to say, somewhat at odds with his own. (shrink)

Thats logic. LEWIS CARROLL, Through the Looking Glass 1-1. The fundamental problem of this work is the question of the nature of scientific inference.

The essays in this volume apply philosophical analysis to address three kinds of questions: What are the implications of genetic science for our understanding of nature? What might it influence in our conception of human nature? What challenges does genetic science pose for specific issues of private conduct or public policy?

The following argument is presented and defended: We ought to aspire to become as good as we can be, and this requires that we do good deeds with not just any emotional attitude, but with joy (a lively, hopeful feeling), even in difficult circumstances. Theism (of the right sort) offers us the best prospects for achieving a fully joyful moral life. And so it is morally good for those of us who are not theists to undertake theism-to commit ourselves to (...) the religious project of coming to believe that God exists. (shrink)

During the 1992–1993 academic year, Harold Garfinkel offered a graduate seminar on Ethnomethodology in the Sociology Department at the University of California, Los Angeles. One topic that was given extensive coverage in the seminar has not been discussed at much length in Garfinkel’s published works to date: Aron Gurwitsch’s treatment of Gestalt theory, and particularly the themes of “phenomenal field” and “praxeological description”. The edited transcript of Garfinkel’s seminar shows why he recommended that “for the serious initiatives of ethnomethodological (...) investigations […] Gurwitsch is a theorist we can’t do without”. Garfinkel’s ethnomethodological “misreading” is not a mistaken reading, but is more a matter of taking Gurwitsch’s phenomenological demonstrations of Gestalt contextures in phenomenal fields and transposing them for making detailed, concrete observations and descriptions of organizationally achieved social phenomena. Where Gurwitsch addresses the organization of perception as an autochthonous achievement, inherent to the stream and field of individual consciousness, Garfinkel extends and elaborates this field into the social world of enacted practices. The April 1993 seminar also is rich with brief asides and digressions in which Garfinkel comments about his use of Alfred Schutz, his attitude toward publishing, his relationship with Erving Goffman, and many other matters. (shrink)

Editors’ AbstractDuring the 1992–1993 academic year, Harold Garfinkel (1917–2011) offered a graduate seminar on Ethnomethodology in the Sociology Department at the University of California, Los Angeles. One topic that was given extensive coverage in the seminar has not been discussed at much length in Garfinkel’s published works to date: Aron Gurwitsch’s treatment of Gestalt theory, and particularly the themes of “phenomenal field” and “praxeological description”. The edited transcript of Garfinkel’s seminar shows why he recommended that “for the serious initiatives (...) of ethnomethodological investigations […] Gurwitsch is a theorist we can’t do without”. Garfinkel’s ethnomethodological “misreading” is not a mistaken reading, but is more a matter of taking Gurwitsch’s phenomenological demonstrations of Gestalt contextures in phenomenal fields and transposing them for making detailed, concrete observations and descriptions of organizationally achieved social phenomena. Where Gurwitsch addresses the organization of perception as an autochthonous achievement, inherent to the stream and field of individual consciousness, Garfinkel extends and elaborates this field into the social world of enacted practices. The April 1993 seminar also is rich with brief asides and digressions in which Garfinkel comments about his use of Alfred Schutz, his attitude toward publishing, his relationship with Erving Goffman, and many other matters. (shrink)

In The Contemplative Foundations of Classical Daoism, Harold D. Roth explores the origins and nature of the Daoist tradition, arguing that its creators and innovators were not abstract philosophers but, rather, mystics engaged in self-exploration and self-cultivation, which in turn provided the insights embodied in such famed works as the Daodejing and Zhuangzi. In this compilation of essays and chapters representing nearly thirty years of scholarship, Roth examines the historical and intellectual origins of Daoism and demonstrates how this distinctive (...) philosophy emerged directly from practices that were essentially contemplative in nature. In the first part of the book, Roth applies text-critical methods to derive the hidden contemplative dimensions of classical Daoism. In the second part, he applies a "contemplative hermeneutic" to explore the relationship between contemplative practices and classical Daoist philosophy and, in so doing, brings early Daoist writings into conversation with contemporary contemplative studies. To this he adds an introduction in which he reflects on the arc and influence on the field of early Chinese thought of this rich vein of scholarship and an afterword in which he applies both interpretive methods to the vexing question of the authorship of the Inner Chapters of the Zhuangzi. The Contemplative Foundations of Classical Daoism brings to fruition the cumulative investigations and observations of a leading figure in the emerging field of contemplative studies as they pertain to a core component of early Chinese thought. (shrink)

As our scientific and technical abilities expand at breathtaking speeds, concern that modern genetics and bioengineering are leading us to a posthuman future is growing. Is Human Nature Obsolete? poses the overarching question of what it is to be human against the background of these current advances in biotechnology. Its perspective is philosophical and interdisciplinary rather than technical; the focus is on questions of fundamental ontological importance rather than the specifics of medical or scientific practice.The authors -- all distinguished scholars (...) in their fields -- take on questions about technology's goals and values that are often ignored or sidelined in the face of rapid scientific advances and the highly specialized nature of technical knowledge. The essays included represent a rich variety of thought, ranging from finely nuanced philosophical and theological arguments to historical studies and cultural commentaries. Several explore the historical background of today's biotechnology: Timothy Casey traces such developments as the emergence of cybernetic humanity from Cartesian dualism, and Diane Paul presents the history of "positive" versus coerced eugenics. Jean Bethke Elshtain discusses cloning as a "messianic project" to perfect the body and exclude natural diversity -- giving as an example the elimination of Down Syndrome as an acceptable human type -- while Harold Baillie calls for an examination of the metaphysical roots of personhood. Robert Proctor finds no evidence in paleontology for any "essence of humanity," and Tom Shannon argues against materialist reductionism. Addressing social concerns, Lisa Sowle Cahill finds the possibility of a political solution to the problems raised by genetic engineering in Catholic teachings on social justice, and Langdon Winner looks critically at the "scientific enthusiasts of a posthuman future." Taken as a whole, the book provides a humanistic overview of a subject too often considered only in its technological aspect. (shrink)

Revolutionizing received opinion of Taoism's origins in light of historic new discoveries, Harold D. Roth has uncovered China's oldest mystical text -- the original expression of Taoist philosophy -- and presents it here with a complete translation and commentary. Over the past twenty-five years, documents recovered from the tombs of China's ancient elite have sparked a revolution in scholarship about early Chinese thought, in particular the origins of Taoist philosophy and religion. In _Original Tao,_ Harold D. Roth exhumes (...) the seminal text of Taoism -- _Inward Training _ -- not from a tomb but from the pages of the _Kuan Tzu,_ a voluminous text on politics and economics in which this mystical tract had been "buried" for centuries. _Inward Training_ is composed of short poetic verses devoted to the practice of breath meditation, and to the insights about the nature of human beings and the form of the cosmos derived from this practice. In its poetic form and tone, the work closely resembles the _Tao-te Ching_; moreover, it clearly evokes Taoism's affinities to other mystical traditions, notably aspects of Hinduism and Buddhism. Roth argues that _Inward Training_ is the foundational text of early Taoism and traces the book to the mid-fourth century B.C.. These verses contain the oldest surviving expressions of a method for mystical "inner cultivation," which Roth identifies as the basis for all early Taoist texts, including the _Chuang Tzu_ and the world-renowned _Tao-te Ching._ With these historic discoveries, he reveals the possibility of a much deeper continuity between early "philosophical" Taoism and the later Taoist religion than scholars had previously suspected. _Original Tao_ contains an elegant and luminous complete translation of the original text. Roth's comprehensive analysis explains what _Inward Training_ meant to the people who wrote it, how this work came to be "entombed" within the _Kuan Tzu,_ and why the text was largely overlooked after the early Han period. (shrink)

Revolutionizing received opinion of Taoism's origins in light of historic new discoveries, Harold D. Roth has uncovered China's oldest mystical text--the original expression of Taoist philosophy--and presents it here with a complete translation and commentary. Over the past twenty-five years, documents recovered from the tombs of China's ancient elite have sparked a revolution in scholarship about early Chinese thought, in particular the origins of Taoist philosophy and religion. In _Original Tao,_ Harold D. Roth exhumes the seminal text of (...) Taoism--_Inward Training _--not from a tomb but from the pages of the _Kuan Tzu,_ a voluminous text on politics and economics in which this mystical tract had been "buried" for centuries. _Inward Training_ is composed of short poetic verses devoted to the practice of breath meditation, and to the insights about the nature of human beings and the form of the cosmos derived from this practice. In its poetic form and tone, the work closely resembles the _Tao-te Ching_; moreover, it clearly evokes Taoism's affinities to other mystical traditions, notably aspects of Hinduism and Buddhism. Roth argues that _Inward Training_ is the foundational text of early Taoism and traces the book to the mid-fourth century B.C.. These verses contain the oldest surviving expressions of a method for mystical "inner cultivation," which Roth identifies as the basis for all early Taoist texts, including the _Chuang Tzu_ and the world-renowned _Tao-te Ching._ With these historic discoveries, he reveals the possibility of a much deeper continuity between early "philosophical" Taoism and the later Taoist religion than scholars had previously suspected. _Original Tao_ contains an elegant and luminous complete translation of the original text. Roth's comprehensive analysis explains what _Inward Training_ meant to the people who wrote it, how this work came to be "entombed" within the _Kuan Tzu,_ and why the text was largely overlooked after the early Han period. (shrink)

A scientific theory is originally based on a particular set of observations. How can it be extended to apply outside this original range of cases? This question, which is fundamental to natural philosophy, is considered in detail in this book, which was originally published in 1931, and first published as this third edition in 1973. Sir Harold begins with the principle that 'it is possible to learn from experience and to make inferences from beyond the data directly known to (...) sensation'. He goes on to analyse this principle, discuss its status and investigate its logical consequences. The result is a book of importance to anyone interested in the foundations of modern scientific method. His thesis provides a consistent account of how the theories proposed by physicists have been derived from, and are supported by, experimental data. (shrink)