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)

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.

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)

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)

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.

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 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 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)

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)

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. (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)

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)

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

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 ...

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.

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)

In ____Bodies That Matter,__ Judith Butler further develops her distinctive theory of gender by examining the workings of power at the most "material" dimensions of sex and sexuality. Deepening the inquiries she began in _Gender_ _Trouble,_ Butler offers an original reformulation of the materiality of bodies, examining how the power of heterosexual hegemony forms the "matter" of bodies, sex, and gender. Butler argues that power operates to constrain "sex" from the start, delimiting what counts as a viable sex. She (...) offers a clarification of the notion of "performativity" introduced in _Gender Trouble_ and explores the meaning of a citational politics. The text includes readings of Plato, Irigaray, Lacan, and Freud on the formation of materiality and bodily boundaries; "Paris is Burning," Nella Larsen's "Passing," and short stories by Willa Cather; along with a reconsideration of "performativity" and politics in feminist, queer, and radical democratic theory. (shrink)

According to what I will call ‘the disanalogy thesis,’ beliefs differ from actions in at least the following important way: while cognitively healthy people often exhibit direct control over their actions, there is no possible scenario where a cognitively healthy person exhibits direct control over her beliefs. Recent arguments against the disanalogy thesis maintain that, if you find yourself in what I will call a ‘permissive situation’ with respect to p, then you can have direct control over whether you believe (...) p, and you can do so without manifesting any cognitive defect. These arguments focus primarily on the idea that we can have direct doxastic control in permissive situations, but they provide insufficient reason for thinking that permissive situations are actually possible, since they pay inadequate attention to the following worries: permissive situations seem inconsistent with the uniqueness thesis, permissive situations seem inconsistent with natural thoughts about epistemic akrasia, and vagueness threatens even if we push these worries aside. In this paper I argue that, on the understanding of permissive situations that is most useful for evaluating the disanalogy thesis, permissive situations clearly are possible. (shrink)

One of the most talked-about scholarly works of the past fifty years, Judith Butler’s _Gender Trouble_ is as celebrated as it is controversial. Arguing that traditional feminism is wrong to look to a natural, 'essential' notion of the female, or indeed of sex or gender, Butler starts by questioning the category 'woman' and continues in this vein with examinations of 'the masculine' and 'the feminine'. Best known however, but also most often misinterpreted, is Butler's concept of gender as a (...) reiterated social _performance _rather than the expression of a prior reality. Thrilling and provocative, few other academic works have roused passions to the same extent. (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)

One of the most talked-about scholarly works of the past fifty years, Judith Butler’s _Gender Trouble_ is as celebrated as it is controversial. Arguing that traditional feminism is wrong to look to a natural, 'essential' notion of the female, or indeed of sex or gender, Butler starts by questioning the category 'woman' and continues in this vein with examinations of 'the masculine' and 'the feminine'. Best known however, but also most often misinterpreted, is Butler's concept of gender as a (...) reiterated social _performance _rather than the expression of a prior reality. Thrilling and provocative, few other academic works have roused passions to the same extent. (shrink)

Purists think that changes in our practical interests can’t affect what we know unless those changes are truth-relevant with respect to the propositions in question. Impurists disagree. They think changes in our practical interests can affect what we know even if those changes aren’t truth-relevant with respect to the propositions in question. I argue that impurists are right, but for the wrong reasons, since they haven’t appreciated the best argument for their own view. Together with “Minimalism and the Limits of (...) Warranted Assertability Maneuvers,” “The Pragmatic Encroachment Debate,” and “Anti-Intellectualism” (below), this paper constitutes my attempt to refute the entire pragmatic encroachment debate. As I show in this paper, there is an argument for impurism sitting in plain sight that is considerably more plausible than any extant argument for pragmatism. (shrink)

Ever since feminist theory introduced the distinction between sex and gender, the question of what it means to be a woman has preoccupied feminist thought. In ____Gender__ ____Trouble ____ Judith Butler questions whether it is possible to "be" a woman at all or, for that matter, any gender.

Intellectualists disagree with anti-intellectualists about the relationship between knowledge and truth. According to intellectualists, this relationship is intimate. Knowledge entails true belief, and in fact everything required for knowledge is somehow relevant to the probability that the belief in question is true. According to anti-intellectualists, this relationship isn’t intimate. Or, at least, it’s not as intimate as intellectualists think. Factors that aren’t in any way relevant to the probability that a belief is true can make a difference to whether it (...) counts as knowledge. In this paper, I give a new argument for anti-intellectualism and draw out consequences of this argument for the pragmatic encroachment debate. The standard purist objection to pragmatism is that pragmatism entails anti-intellectualism. As I show, anti-intellectualism follows from premises that are plausible even if purism is true, so the standard purist objection to pragmatism fails. (shrink)

In ____Bodies That Matter,__ Judith Butler further develops her distinctive theory of gender by examining the workings of power at the most "material" dimensions of sex and sexuality. Deepening the inquiries she began in _Gender_ _Trouble,_ Butler offers an original reformulation of the materiality of bodies, examining how the power of heterosexual hegemony forms the "matter" of bodies, sex, and gender. Butler argues that power operates to constrain "sex" from the start, delimiting what counts as a viable sex. She (...) offers a clarification of the notion of "performativity" introduced in _Gender Trouble_ and explores the meaning of a citational politics. The text includes readings of Plato, Irigaray, Lacan, and Freud on the formation of materiality and bodily boundaries; "Paris is Burning," Nella Larsen's "Passing," and short stories by Willa Cather; along with a reconsideration of "performativity" and politics in feminist, queer, and radical democratic theory. (shrink)

Alvin Plantinga theorizes the existence of a sensus divinitatis – a special cognitive faulty or mechanism dedicated to the production and non-inferential justification of theistic belief. Following Chris Tucker, we offer an evidentialist-friendly model of the sensus divinitatis whereon it produces theistic seemings that non-inferentially justify theistic belief. We suggest that the sensus divinitatis produces these seemings by tacitly grasping support relations between the content of ordinary experiences (in conjunction with our background evidence) and propositions about God. Our model offers (...) advantages such as eliminating the need for a sui generis religious faculty, harmonizing the sensus divinitatis with prominent theories in the cognitive science of religion, and providing a superior account of natural revelation. (shrink)

In ____Bodies That Matter,__ Judith Butler further develops her distinctive theory of gender by examining the workings of power at the most "material" dimensions of sex and sexuality. Deepening the inquiries she began in _Gender_ _Trouble,_ Butler offers an original reformulation of the materiality of bodies, examining how the power of heterosexual hegemony forms the "matter" of bodies, sex, and gender. Butler argues that power operates to constrain "sex" from the start, delimiting what counts as a viable sex. She (...) offers a clarification of the notion of "performativity" introduced in _Gender Trouble_ and explores the meaning of a citational politics. The text includes readings of Plato, Irigaray, Lacan, and Freud on the formation of materiality and bodily boundaries; "Paris is Burning," Nella Larsen's "Passing," and short stories by Willa Cather; along with a reconsideration of "performativity" and politics in feminist, queer, and radical democratic theory. (shrink)

The epistemic value of seemings is increasingly debated. Such debates are hindered, however, by a lack of consensus about the nature of seemings. There are four prominent conceptions in the literature, and the plausibility of principles such as phenomenal conservatism, which assign a prominent epistemic role to seemings, varies greatly from one conception to another. It is therefore crucial that we identify the correct conception of seemings. I argue that seemings are best understood as sui generis mental states with propositional (...) content and a distinct phenomenal character. Rival conceptions are shown to succumb to numerous difficulties. (shrink)

Offers an outline for a new ethical practice - one responsive to the need for critical autonomy and grounded in a new sense of the human subject. The author demonstrates how difficult it is to give an account of oneself, and how this lack of self-transparency and narratibility is crucial to an ethical understanding of the human.

The cornerstone of contemporary nursing practice is the provision of individualised nursing care. Sustaining and nourishing the stream of research frameworks that inform individualised care are the findings from qualitative research. At the centre of much qualitative research practice, however, is an assumption that experiential understanding can be delivered through a thematisation of meaning which, it will be argued, can lead the researcher to make unsustainable assumptions about the relations of language and meaning‐making to experience. We will show that an (...) uncritical subscription to such assumptions can undermine the researcher's capacity to represent experience at the high level of abstraction consistent with experience itself and to thus inform genuinely individualised care. Instead, using qualia as a touchstone for the possibilities of understanding and representing experience, we trace the ‘designative’ and ‘expressive’ distinction to language in order to raise critical questions concerning both these assumptions and common practices within qualitative research. Following the ‘expressive’ account of language, we foreground in particular the hermeneutic work of Gadamer through which we explore the possibilities for a qualitative research approach that would better seek the mot juste of individual experience and illuminate qualia in order to better inform genuinely individualised care. (shrink)

The book constitutes a reconsideration of her earlier view on gender performativity from Gender Trouble. In this work, the critique of gender norms is clearly situated within the framework of human persistence and survival.

Early moderns such as Locke and Descartes thought we could guarantee the justification of our beliefs, even in worlds most hostile to their truth, if only we form those beliefs with sufficient care. That is, they thought it possible for us to be impeccable with respect to justification. This principle has traditionally been used to argue for internalism. By placing all of the normatively relevant conditions in our minds, we ensure reflective access to what those norms require of us and (...) so sustain the possibility of impeccability (unlike externalism). However, recent challenges to transparency leave this reasoning vulnerable. In response, I show how impeccability can be sustained without requiring transparency. The account only works if we define internal states as those directly accessible to our rational belief forming systems. I argue that this sort of causal internalism, while somewhat revisionary, preserves traditional motivations for internalism while avoiding problems faced by other varieties. The result is a renewed argument for internalism that simultaneously moves us away from access internalism and towards a species of mentalism. (shrink)

The epistemic value of seemings is increasingly debated. Such debates are hindered, however, by a lack of consensus about the nature of seemings. There are four prominent conceptions in the literature, and the plausibility of principles such as phenomenal conservatism, which assign a prominent epistemic role to seemings, varies greatly from one conception to another. It is therefore crucial that we identify the correct conception of seemings. I argue that seemings are best understood as sui generis mental states with propositional (...) content and a distinct phenomenal character. Rival conceptions are shown to succumb to numerous difficulties. (shrink)

With the same intellectual courage with which she addressed issues of gender, Judith Butler turns her attention to speech and conduct in contemporary political life, looking at several efforts to target speech as conduct that has become subject to political debate and regulation. Reviewing hate speech regulations, anti-pornography arguments, and recent controversies about gay self-declaration in the military, Judith Butler asks whether and how language acts in each of these cultural sites.

In a landmark text, ‘The Theological Turn of French Phenomenology’, Dominique Janicaud posits a boundary that sharply divides the legitimate phenomenological tradition from a problematic variant seen to be fundamentally compromised by theology. This article develops an immanent critique of Janicaud’s position. It demonstrates that his boundary relies on the mature work of Maurice Merleau-Ponty as a constitutive exemplar of the tradition, that this work is centrally concerned with beauty, and that its notion of beauty is irreducibly theological. Merleau-Ponty himself (...) will thus be shown to enact his own version of the theological turn. I shall consequently propose a reconstrual of the boundary of phenomenology. My argument relies fundamentally on Merleau-Ponty’s essay, ‘Eye and Mind’, and includes a critical restatement of Galen Johnson’s reading of this text. In addition to its direct relevance to phenomenology, this article bears upon broader concerns, including the relationships between theory, the body, aesthetics, and the post-secular. (shrink)