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)

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)

This important handbook provides a comprehensive, authoritative review of achievement motivation and establishes the concept of competence as an organizing ...

Disasters overwhelm resources and threaten the safety and functioning of communities. Mental health and community needs after catastrophic disasters can be substantial, however the effects of traumatic events are not exclusively bad with many people showing individual resilience and some reporting growth. Sustaining the social fabric of the community and facilitating recovery following disaster depends on leadership=s knowledge of a community=s resilience and vulnerabilities as well as an understanding of the distress, disorder, and health risk behavioral responses. A coordinated systems (...) approach across medical care, public health, and emergency response system is necessary to meet the mental health care needs of a disaster region. (shrink)

Randomised controlled trials (RCTs) are often seen as the 'gold standard' of evaluative research. However, whilst randomisation will ensure comparable groups, trials are still vulnerable to a range of biases that can undermine their internal validity. In this paper we describe a number of common threats to the internal validity of RCTs and methods of countering them. We highlight a number of examples from randomised trials in education and health care where problems of execution and analysis of the RCT has (...) undermined their internal validity. However, awareness of these potential biases can lead to careful planning to avoid or reduce their occurrence. If good quality randomised trials are to inform policy and practice in education then rigorous trials need to be designed that are the least susceptible to threats to their validity. (shrink)

Recent neuroscience research makes it clear that human biology is cultural biology - we develop and live our lives in socially constructed worlds that vary widely in their structure values, and institutions. This integrative volume brings together interdisciplinary perspectives from the human, social, and biological sciences to explore culture, mind, and brain interactions and their impact on personal and societal issues. Contributors provide a fresh look at emerging concepts, models, and applications of the co-constitution of culture, mind, and brain. Chapters (...) survey the latest theoretical and methodological insights alongside the challenges in this area, and describe how these new ideas are being applied in the sciences, humanities, arts, mental health, and everyday life. Readers will gain new appreciation of the ways in which our unique biology and cultural diversity shape behavior and experience, and our ongoing adaptation to a constantly changing world. (shrink)

The existential analysis -- The death of dasein -- The timeliness of dasein -- The derivation of time -- The time of being.

In this paper, we extend Michel Foucault’s final works on the ‘care of the self’ to an empirical examination of research practice in community-based research (CBR). We use Foucault’s ‘morality of behaviors’ to analyze interview data from a national sample of Canadian CBR practitioners working with communities affected by HIV. Despite claims in the literature that ethics review is overly burdensome for non-traditional forms of research, our findings suggest that many researchers using CBR have an ambivalent but ultimately productive relationship (...) with institutional research ethics review requirements. They understand and use prescribed codes, but adapt them in practice to account for the needs of participating community members, members of their research teams and the larger communities with whom they work. Complying with ethics protocols was seen as only the beginning, a minimum standard; our research suggests that the real ethical work happens in the field, where CBR practitioners encounter community members in diverse public roles and must forge ethical consensus across communities. CBR represents an ethical terrain in which practitioners challenge themselves to work differently, and as a result they care for themselves—and others—in ways that often resist the propensity for domination through public health research.‘…there are different ways to “conduct oneself” morally, different ways for the acting individual to operate, not just as an agent, but as an ethical subject of action.’ (Foucault, 1985: 26). (shrink)

New Tenth Anniversary edition of this classic text with a new preface by the author, compares myths about meat-eating with myths about manliness, and seeks to ...

In this paper, we extend Michel Foucault’s final works on the ‘care of the self’ to an empirical examination of research practice in community-based research (CBR). We use Foucault’s ‘morality of behaviors’ to analyze interview data from a national sample of Canadian CBR practitioners working with communities affected by HIV. Despite claims in the literature that ethics review is overly burdensome for non-traditional forms of research, our findings suggest that many researchers using CBR have an ambivalent but ultimately productive relationship (...) with institutional research ethics review requirements. They understand and use prescribed codes, but adapt them in practice to account for the needs of participating community members, members of their research teams and the larger communities with whom they work. Complying with ethics protocols was seen as only the beginning, a minimum standard; our research suggests that the real ethical work happens in the field, where CBR practitioners encounter community members in diverse public roles and must forge ethical consensus across communities. CBR represents an ethical terrain in which practitioners challenge themselves to work differently, and as a result they care for themselves—and others—in ways that often resist the propensity for domination through public health research.‘…there are different ways to “conduct oneself” morally, different ways for the acting individual to operate, not just as an agent, but as an ethical subject of action.’ (Foucault, 1985: 26). (shrink)

Deeply rooted structures of racism, ableism, misogyny, ageism, and transphobia hurt great numbers of people, exposing them to intolerance, economic exclusion, and physical harm around the globe. Billions of land animals suffer and die annually in concentrated feeding operations and slaughterhouses. Our planet and all who live here are in perilous straights as the climate changes. In the face of such grievous problems, people who want to find positive ways to respond often grapple with difficult questions about how to make (...) a difference. Effective Altruism has arisen as an attempt to help answer these questions, encouraging people to give as much money as they can in the most effective ways to address human and animal suffering. But the Effective Altruists’ answers support some of the very social structures that cause suffering, undermining its efforts to “do the most good.” The Good It Promises, The Harm It Does is the first book-length critique of Effective Altruism. It brings together a diverse group of activists and scholars to explore Effective Altruism’s failure to meaningfully address forms of human and animal suffering. (shrink)

In just a few years, the book became an underground classic. Neither Man Nor Beast takes Adams' thought one step further.

The Carol J. Adams Reader gathers together Adams's foundational and recent articles in the fields of critical studies, animal studies, media studies, vegan studies, ecofeminism and feminism, as well as relevant interviews and conversations in which Adams identifies key concepts and new developments in her decades-long work. This volume, a companion to The Sexual Politics of Meat (Bloomsbury Revelations), offers insight into a variety of urgent issues for our contemporary world: Why do batterers harm animals? What is the relationship (...) between genocide and attitudes toward other animals? How do activism and theory feed each other? How do race, gender, and species categories interact in strengthening oppressive attitudes? In clear language, Adams identifies the often hidden aspects of cultural presumptions. The essays and conversations found here capture the decades-long energy and vision that continue to shape new ways of thinking about and responding to oppression. (shrink)

In this essay, I will argue that contemporary ecofeminist discourse, while potentially adequate to deal with the issue of animals, is now inadequate because it fails to give consistent conceptual place to the domination of animals as a significant aspect of the domination of nature. I will examine six answers ecofeminists could give for not including animals explicitly in ecofeminist analyses and show how a persistent patriarchal ideology regarding animals as instruments has kept the experience of animals from being fully (...) incorporated within ecofeminism. (shrink)

In this essay, I will argue that contemporary ecofeminist discourse, while potentially adequate to deal with the issue of animals, is now inadequate because it fails to give consistent conceptual place to the domination of animals as a significant aspect of the domination of nature. I will examine six answers ecofeminists could give for not including animals explicitly in ecofeminist analyses and show how a persistent patriarchal ideology regarding animals as instruments has kept the experience of animals from being fully (...) incorporated within ecofeminism.2. (shrink)

Research on bias in peer review examines scholarly communication and funding processes to assess the epistemic and social legitimacy of the mechanisms by which knowledge communities vet and self-regulate their work. Despite vocal concerns, a closer look at the empirical and methodological limitations of research on bias raises questions about the existence and extent of many hypothesized forms of bias. In addition, the notion of bias is predicated on an implicit ideal that, once articulated, raises questions about the normative implications (...) of research on bias in peer review. This review provides a brief description of the function, history, and scope of peer review; articulates and critiques the conception of bias unifying research on bias in peer review; characterizes and examines the empirical, methodological, and normative claims of bias in peer review research; and assesses possible alternatives to the status quo. We close by identifying ways to expand conceptions and studies of bias to countenance the complexity of social interactions among actors involved directly and indirectly in peer review. (shrink)

In this essay, I connect the sexual victimization of women, children, and pet animals with the violence manifest in a patriarchal culture. After discussing these connections, I demonstrate the importance of taking seriously these connections because of their implications for conceptual analysis, epistemology, and political, environmental, and applied philosophy. My goal is to broaden our understanding of issues relevant to creating peace and to provide some suggestions about what must be included in any adequate feminist peace politics.

To arrive at their final evaluation of a manuscript or grant proposal, reviewers must convert a submission’s strengths and weaknesses for heterogeneous peer review criteria into a single metric of quality or merit. I identify this process of commensuration as the locus for a new kind of peer review bias. Commensuration bias illuminates how the systematic prioritization of some peer review criteria over others permits and facilitates problematic patterns of publication and funding in science. Commensuration bias also foregrounds a range (...) of structural strategies for realigning peer review practices and institutions with the aims of science. (shrink)

An empirically sensitive formulation of the norms of transformative criticism must recognize that even public and shared standards of evaluation can be implemented in ways that unintentionally perpetuate and reproduce forms of social bias that are epistemically detrimental. Helen Longino’s theory can explain and redress such social bias by treating peer evaluations as hypotheses based on data and by requiring a kind of perspectival diversity that bears, not on the content of the community’s knowledge claims, but on the beliefs and (...) norms of the culture of the knowledge community itself. To illustrate how socializing cognition can bias evaluations, we focus on peer-review practices, with some discussion of peer-review practices in philosophy. Data include responses to surveys by editors from general philosophy journals, as well as analyses of reviews and editorial decisions for the 2007 Cognitive Science Society Conference. (shrink)

Sister Species: Women, Animals, and Social Justice addresses interconnections between speciesism, sexism, racism, and homophobia, clarifying why social justice activists in the twenty-first century must challenge intersecting forms of oppression. This anthology presents bold and gripping--sometimes horrifying--personal narratives from fourteen activists who have personally explored links of oppression between humans and animals, including such exploitative enterprises as cockfighting, factory farming, vivisection, and the bushmeat trade. Sister Species asks readers to rethink how they view "others," how they affect animals with their (...) daily choices, and how they might bring change for all who are abused. These essays remind readers that women have always been important to social justice and animal advocacy, and they urge each of us to recognize the links that continue to bind all oppressed individuals. The astonishing honesty of these contributors demonstrates with painful clarity why every woman should be an animal activist and why every animal activist should be a feminist. Contributors are Carol J. Adams, Tara Sophia Bahna-James, Karen Davis, Elizabeth Jane Farians, Hope Ferdowsian, Linda Fisher, Twyla François, Christine Garcia, A. Breeze Harper, Sangamithra Iyer, Pattrice Jones, Lisa Kemmerer, Allison Lance, Ingrid Newkirk, Lauren Ornelas, and Miyun Park. (shrink)

Psychometrically oriented researchers construe low inter-rater reliability measures for expert peer reviewers as damning for the practice of peer review. I argue that this perspective overlooks different forms of normatively appropriate disagreement among reviewers. Of special interest are Kuhnian questions about the extent to which variance in reviewer ratings can be accounted for by normatively appropriate disagreements about how to interpret and apply evaluative criteria within disciplines during times of normal science. Until these empirical-cum-philosophical analyses are done, it will remain (...) unclear the extent to which low inter-rater reliability measures represent reasonable disagreement rather than arbitrary differences between reviewers. (shrink)

Scholars belong to multiple communities of credit simultaneously. When these communities disagree about a scholarly achievement’s credit assignment, this raises a puzzle for decision and game theor...

Under the traditional system of peer-reviewed publication, the degree of prestige conferred to authors by successful publication is tied to the degree of the intellectual rigor of its peer review process: ambitious scientists do well professionally by doing well epistemically. As a result, we should expect journal editors, in their dual role as epistemic evaluators and prestige-allocators, to have the power to motivate improved author behavior through the tightening of publication requirements. Contrary to this expectation, I will argue that the (...) publication bias literature in academic medicine demonstrates that editor interventions have had limited effectiveness in improving the health of the publication and trial registration record, suggesting that much stronger interventions are needed. (shrink)

One of the central features of Western existence is the objectification and use of other beings in creating the subjectification of human beings. My argument is for a Christian veganism that rejects the dependence of the subject on the object status of other beings. The roadblocks to recognizing the necessity for Christian veganism I call the pedagogy of the oppressor. I propose that one way to change the subject-object relationship is a poetics of Christian engagement. Christian veganism may seem a (...) radical position theoretically and pragmatically, but I will offer suggestions for expanding Christian engagement with other animals and for the food and environmental justice movements of which veganism is a part. (shrink)

On the surface, developing a social psychology of science seems compelling as a way to understand how individual social cognition – in aggregate – contributes towards individual and group behavior within scientific communities (Kitcher, 2002). However, in cases where the functional input-output profile of psychological processes cannot be mapped directly onto the observed behavior of working scientists, it becomes clear that the relationship between psychological claims and normative philosophy of science should be refined. For example, a robust body of social (...) psychological research demonstrates implicit gender bias in the evaluation of others (e.g., Steinpreis, Anders, & Ritzke, 1999). Many expected implicit bias to be a major cause of women’s underrepresentation in math intensive fields of science; however, quantitative sociological research of hiring and manuscript and grant evaluation has discovered no gender disparity in outcomes (Ceci & Williams, 2011). Why might this be so? This paper will discuss methodological challenges that go beyond classic problems of external validity in extrapolating psychological effects and explanations to scientific communities. These problems include more complex external validity issues raised by the introduction of multi-process models of cognition (e.g., implicit versus explicit social cognition) as well as the reflexive role that folk and experimental theories of social psychology play in guiding the behavior of scientists at the individual and community level. (shrink)

There is an increasing push by journals to ensure that data and products related to published papers are shared as part of a cultural move to promote transparency, reproducibility, and trust in the scientific literature. Yet few journals commit to evaluating their effectiveness in implementing reporting standards aimed at meeting those goals (1, 2). Similarly, though the vast majority of journals endorse peer review as an approach to ensure trust in the literature, few make their peer review data available to (...) evaluate effectiveness toward achieving concrete measures of quality, including consistency and completeness in meeting reporting standards. Remedying these apparent disconnects is critical for closing the gap between guidance recommendations and actual reporting behavior. We see this as a collective action problem requiring leadership and investment by publishers, who can be incentivized through mechanisms that allow them to manage reputational risk and through continued innovation in journal assessment. (shrink)