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.

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)

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) 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.

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) 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)

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)

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)

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)

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)

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) 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)

Many climate change ethicists argue wealthy nations have duties of justice to combat climate change. However, Posner and Weisbach disagree because there is a poor fit between the principles of justice and the problem of climate change. I argue in this paper that Posner and Weisbach’s argument relies on what Judith Shklar calls “the normal model of justice,” the view that injustice results when principles are violated. Applying Shklar’s critique of normal justice, I argue that Posner and Weisbach’s argument (...) limits injustice to include complaints that match rules and principles, shielding the unjust from responsibility and assuming falsely that judgments about injustice can be made from a singular perspective. Drawing on Shklar, this paper develops an account of climate change as a complement to mainstream climate ethicists. On this account, injustice results from indifference and the voices of those impacted by climate change and climate change policy have priority. (shrink)

Judith Jarvis Thomson; Killing, Letting Die, and The Trolley Problem, The Monist, Volume 59, Issue 2, 1 April 1976, Pages 204–217, https://doi.org/10.5840/monis.

A look at political ethics covers cruelty, hypocrisy, snobbery, betrayal and misanthropy, and is accompanied by a description of modern public opinion about ...

"The Blackwell Guide to Philosophy of Education" is state-of-the-art map to the field as well as a valuable reference book.

The text of each poem is given in letterpress on the page facing the beautiful color reproductions of the plate. The book is printed on vellum.

Logical pluralism is the view that there is more than one logic. Logical normativism is the view that logic is normative. These positions have often been assumed to go hand-in-hand, but we show that one can be a logical pluralist without being a logical normativist. We begin by arguing directly against logical normativism. Then we reformulate one popular version of pluralism—due to Beall and Restall—to avoid a normativist commitment. We give three non-normativist pluralist views, the most promising of which depends (...) not on logic’s normativity but on epistemic goals. (shrink)

An influential way of distinguishing inferential from non-inferential processes appeals to representational states: an agent infers a conclusion from some premises only if she represents those premises as supporting that conclusion. By contrast, when some premises merely cause an agent to believe the conclusion, there is no relevant representational state. While promising, the appeal to representational states invites a regress problem, first famously articulated by Lewis Carroll. This paper develops a novel account of inference that invokes representational states without succumbing (...) to regress. The key move is to reject the tempting idea that the relevant representational states are causally prior to inferences. I argue, instead, that an inference constitutes the relevant representational state. To infer is thus—in the very drawing of the conclusion—to represent the premises as supporting the conclusion, and thereby to commit to that support relation. (shrink)

The author considers the way in which psychic life is generated by the social operation of power, and how that social operation of power is concealed and fortified by the psyche that it produces. Power is no longer understood to be 'internalized' by an existing subject, but the subject is spawned as an ambivalent effect of power, one that is staged through the operation of conscience. To claim that power fabricates the psyche is also to claim that there is a (...) fictional and fabricated quality to the psyche. The figure of a psyche that 'turns against itself' is crucial to this study, and offers an alternative to describing power as 'internalized'. Although most readers of Foucault eschew psychoanalytic theory, and most thinkers of the psyche eschew Foucault, the author seeks to theorize this ambivalent relation between the social and the psychic as one of the most dynamic and difficult effects of power. (shrink)

Revisiting Edward Said's late proposals for a one-state solution, Butler has come to a startling suggestion: Jewish ethics not only demand a critique of Zionism, but must transcend its exclusive Jewishness in order to realize the ethical ...

Logical pluralism is the view that there is more than one correct logic. A key objection to logical pluralism is that it collapses into monism. The core of the Collapse Objection is that only the pluralist’s strongest logic does any genuine normative work; since a logic must do genuine normative work, this means that the pluralist is really a monist, who is committed to her strongest logic being the one true logic. This paper considers a neglected question in the collapse (...) debate: what is it for a logic to do genuine normative work? As well as having wider upshot for the connection between logic and normativity, grappling with this question provides a new response to the Collapse Objection on behalf of the pluralist. I suggest that we should allow logics to generate pro tanto reasons in a way that bears not just on combinations of attitudes but on how an agent’s attitudes are based on one another. This motivates adopting normative principles that allow the pluralist’s weaker logics to earn their normative keep. Rather than being ad hoc, these principles capture a sense in which good reasoning goes beyond the consistency of an agent’s attitudes. Good reasoning is also concerned with how an agent’s attitudes are based on one another. (shrink)

In The Realm of Rights Judith Thomson provides a full-scale, systematic theory of human and social rights, bringing out what in general makes an attribution of ...

This classic work by one of the most important philosophers and critics of our time charts the genesis and trajectory of the desiring subject from Hegel's formulation in Phenomenology of Spirit to its appropriation by Kojève, Hyppolite, Sartre, Lacan, Deleuze, and Foucault. Judith Butler plots the French reception of Hegel and the successive challenges waged against his metaphysics and view of the subject, all while revealing ambiguities within his position. The result is a sophisticated reconsideration of the post-Hegelian tradition (...) that has predominated in modern French thought, and her study remains a provocative and timely intervention in contemporary debates over the unconscious, the powers of subjection, and the subject. (shrink)

The celebrated author of _Gender Trouble_ here redefines Antigone's legacy, recovering her revolutionary significance and liberating it for a progressive feminism and sexual politics. Butler's new interpretation does nothing less than reconceptualize the incest taboo in relation to kinship -- and open up the concept of kinship to cultural change. Antigone, the renowned insurgent from Sophocles's _Oedipus,_ has long been a feminist icon of defiance. But what has remained unclear is whether she escapes from the forms of power that she (...) opposes. Antigone proves to be a more ambivalent figure for feminism than has been acknowledged, since the form of defiance she exemplifies also leads to her death. Butler argues that Antigone represents a form of feminist and sexual agency that is fraught with risk. Moreover, Antigone shows how the constraints of normative kinship unfairly decide what will and will not be a livable life. Butler explores the meaning of Antigone, wondering what forms of kinship might have allowed her to live. Along the way, she considers the works of such philosophers as Hegel, Lacan, and Irigaray. How, she asks, would psychoanalysis have been different if it had taken Antigone -- the "postoedipal" subject -- rather than Oedipus as its point of departure? If the incest taboo is reconceived so that it does not mandate heterosexuality as its solution, what forms of sexual alliance and new kinship might be acknowledged as a result? The book relates the courageous deeds of Antigone to the claims made by those whose relations are still not honored as those of proper kinship, showing how a culture of normative heterosexuality obstructs our capacity to see what sexual freedom and political agency could be. (shrink)

_The Power of Religion in the Public Sphere_ represents a rare opportunity to experience a diverse group of preeminent philosophers confronting one pervasive contemporary concern: what role does—or should—religion play in our public lives? Reflecting on her recent work concerning state violence in Israel-Palestine, Judith Butler explores the potential of religious perspectives for renewing cultural and political criticism, while Jürgen Habermas, best known for his seminal conception of the public sphere, thinks through the ambiguous legacy of the concept of (...) "the political" in contemporary theory. Charles Taylor argues for a radical redefinition of secularism, and Cornel West defends civil disobedience and emancipatory theology. Eduardo Mendieta and Jonathan VanAntwerpen detail the immense contribution of these philosophers to contemporary social and political theory, and an afterword by Craig Calhoun places these attempts to reconceive the significance of both religion and the secular in the context of contemporary national and international politics. (shrink)

Little work has been done to explore the moral foundations of the state’s right to territory.1 In modern times, the state has mostly been assumed to be a territorial unit, and no need was perceived to reflect on precisely what justifies its territorial jurisdiction. The state’s territoriality is related to another topic that has remained under-theorized: immigration. There is, moreover, an obvious relationship between these topics: the more powerful a state’s rights over its territory, the more powerful the right to (...) constrain access to that territory might become – or so, at any rate, we might suppose. Rights to territory and rights to immigration are usefully theorized together.2 Our starting point is a Lockean analysis of the moral foundations of territoriality offered by Simmons (2001). This is a natural starting point not only because Simmons is one of the very few contemporary writers who have taken up philosophical questions about territoriality in the first place, but also because Locke’s thought, as Simmons makes clear, actually allows for the development of a sophisticated account of territoriality. This makes Locke stand out simply because generally modern political.. (shrink)

In a series of memorable exchanges, three eminent theorists engage in a dialogue on central questions of contemporary philosophy and politics.

All justified beliefs ultimately rest on attitudes that are immediately justified. This book illuminates the nature of immediate justification and the states that provide it. Simply put, immediate justification arises from how things appear to us--from all and only our "seemings." The author defends each aspect of this "seemings foundationalism," including the assumption of foundationalism itself. Most notably, the author draws from common sense philosopher Thomas Reid to present new and improved arguments for phenomenal conservatism and gives the first systematic (...) argument that seemings alone are capable of immediately justifying. The discussion also delves deeply into the nature of seemings and how it is that their assertive phenomenal character makes them (and them alone) capable of immediately justifying. Along the way, the author makes novel contributions to perennial debates about justification such as: internalism versus externalism, deontologism and epistemic blame, epistemic circularity, and the common sense response to skepticism. Seemings and the Foundations of Justification will appeal to scholars and advanced students interested in epistemology, Thomas Reid, or the common sense tradition. (shrink)

To help professionals in all health care disciplines grapple with ethical issues, Ahronheim (medicine, New York Medical College), Moreno (biomedical ethics, U. of Virginia) and Zuckerman (Center for Ethics in Medicine, Beth Israel Medical Center) review the history and theory of clinical ethics and present 31 case studies analyzed from medical, ethical and legal perspectives. This second edition expands the original discussions of ethical dilemmas caused by advances in medical genetics, organ transplants, HIV medicine and other developments. The appendix includes (...) Internet references, suggested readings and other resources. (shrink)

This chapter contains sections titled: Deception and Dishonesty A Right to Know? Media Bias Is Neutrality a Virtue?

Doxastic involuntarists have paid insufficient attention to two debates in contemporary epistemology: the permissivism debate and the debate over norms of assertion and belief. In combination, these debates highlight a conception of belief on which, if you find yourself in what I will call an ‘equipollent case’ with respect to some proposition p, there will be no reason why you can’t believe p at will. While doxastic involuntarism is virtually epistemological orthodoxy, nothing in the entire stock of objections to belief (...) at will blocks this route to doxastic voluntarism. Against the backdrop of the permissivism debate and the literature on norms of belief and assertion, doxastic involuntarism emerges as an article of faith, not the obvious truth it’s usually purported to be. (shrink)

Does knowledge depend in any interesting way on our practical interests? This is the central question in the pragmatic encroachment debate. Pragmatists defend the affirmative answer to this question while purists defend the negative answer. The literature contains two kinds of arguments for pragmatism: principle-based arguments and case-based arguments. Principle-based arguments derive pragmatism from principles that connect knowledge to practical interests. Case-based arguments rely on intuitions about cases that differ with respect to practical interests. I argue that there are insurmountable (...) problems for both kinds of arguments, and that it is therefore unclear what motivates pragmatism. (shrink)

The celebrated author of _Gender Trouble_ here redefines Antigone's legacy, recovering her revolutionary significance and liberating it for a progressive feminism and sexual politics. Butler's new interpretation does nothing less than reconceptualize the incest taboo in relation to kinship -- and open up the concept of kinship to cultural change. Antigone, the renowned insurgent from Sophocles's _Oedipus,_ has long been a feminist icon of defiance. But what has remained unclear is whether she escapes from the forms of power that she (...) opposes. Antigone proves to be a more ambivalent figure for feminism than has been acknowledged, since the form of defiance she exemplifies also leads to her death. Butler argues that Antigone represents a form of feminist and sexual agency that is fraught with risk. Moreover, Antigone shows how the constraints of normative kinship unfairly decide what will and will not be a livable life. Butler explores the meaning of Antigone, wondering what forms of kinship might have allowed her to live. Along the way, she considers the works of such philosophers as Hegel, Lacan, and Irigaray. How, she asks, would psychoanalysis have been different if it had taken Antigone -- the "postoedipal" subject -- rather than Oedipus as its point of departure? If the incest taboo is reconceived so that it does not mandate heterosexuality as its solution, what forms of sexual alliance and new kinship might be acknowledged as a result? The book relates the courageous deeds of Antigone to the claims made by those whose relations are still not honored as those of proper kinship, showing how a culture of normative heterosexuality obstructs our capacity to see what sexual freedom and political agency could be. (shrink)