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

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

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 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.

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)

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)

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)

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; 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)

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)

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) 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 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)

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)

Using selections from writers like Margaret Atwood, Octavia Butler, Marion Zimmer Bradley, Karen Joy Fowler, Ursula K. Le Guin, James Tiptree jr., and many others, this collection shows how the imagined worlds of science fiction create hold experiments for testing feminist hypotheses and for interpreting philosophical questions about humanity, gender, equality and more. Four main themes: Part 1, 'Human nature and reality', concentrates on whether there is an intrinsic difference between males and females. Part 2, 'Dystopias: the worst of all (...) possible worlds', portrays misogynistic societies uncomfortably familiar to the early 21st-century reader. Part 3, 'Separatist utopias: worlds of difference', assembles stories that scrutinize both the virtues and vices of separatism. In Part 4, 'Androgynous utopias: worlds of equality', the authors create worlds that anticipate the consequences, good and bad, of perfect sexual equality in education, intelligence, capability, and reproduction. (shrink)

Last year the editors of Signs: Journal of Women in Culture and Society invited feminists worldwide to comment on the millennial transition. Representing a disciplinary and generational range of writers, the resulting collection is at turns inspiring, troubling, provocative, despairing, celebratory. Some of the essays give voice to anxieties, others are more hopeful some reflect back, others look forward. Many of these fifty-plus short essays speak to themes of gender, nationality, global independence, transnational corporate domination, racial and ethnic identities, and (...) complex intersections among these systems. Readers will find eye-opening writing that is thoughtful, committed, and passionate about feminist futures. (shrink)

The author draws on the policy analysis literature to delineate the linkage between conceptualization of risk and the formulation and proposed solution of risk-related policy problems. Two concepts of risk are identified: a concept of risk as a physically given attribute of hazardous technologies and a concept of risk as a socially constructed attribute. The argument is advanced that the social construction of risk provides a firm, theoretical basis for the design of policy. The discussion links the perception, manage ment, (...) and communication of risk to the more fundamental issue of the nature and role of science and technology. (shrink)

Two decades of research on euthanasia in the Netherlands have resulted into clear insights in the frequency and characteristics of euthanasia and other medical end-of-life decisions in the Netherlands. These empirical studies have contributed to the quality of the public debate, and to the regulating and public control of euthanasia and physician-assisted suicide. No slippery slope seems to have occurred. Physicians seem to adhere to the criteria for due care in the large majority of cases. Further, it has been shown (...) that the majority of physicians think that the euthanasia Act has improved their legal certainty and contributes to the carefulness of life-terminating acts. In 2005, eighty percent of the euthanasia cases were reported to the review committees. Thus, the transparency envisaged by the Act still does not extend to all cases. Unreported cases almost all involve the use of opioids, and are not considered to be euthanasia by physicians. More education and debate is needed to disentangle in these situations which acts should be regarded as euthanasia and which should not. Medical end-of-life decision-making is a crucial part of end-of-life care. It should therefore be given continuous attention in health care policy and medical training. Systematic periodic research is crucial for enhancing our understanding of end-of-life care in modern medicine, in which the pursuit of a good quality of dying is nowadays widely recognized as an important goal, in addition to the traditional goals such as curing diseases and prolonging life. (shrink)

Background Studies describing physicians’ experiences with sedation at the end of life are indispensible for informed palliative care practice, but they are scarce. We describe the accounts of physicians from the USA and the Netherlands, two countries with different regulations on end-of-life decisions regarding their use of sedation.Methods Qualitative face-to-face interviews were held in 2007–2008 with 36 physicians , including primary care physicians and specialists. We applied purposive sampling and conducted constant comparative analyses.Results In both countries, the use of sedation (...) was described in diverse terms, especially in the USA, and was often experienced as emotionally challenging. Respondents stated different and sometimes multiple intentions for their use of sedation. Besides alleviating severe suffering, most Dutch respondents justified its use by stating that it does not hasten death, while most American respondents indicated that it might hasten death but that this was justifiable as long as that was not their primary intention. While many Dutch respondents indicated that they initiated open discussions about sedation proactively to inform patients about their options and to allow planning, the accounts of American respondents showed fewer and less-open discussions, mostly late in the dying process and with the patient's relatives.Conclusions The justification for sedation and the openness with which it is discussed were found to differ in the accounts of respondents from the USA and the Netherlands. Further clarification of practices and research into the effect and effectiveness of the use of sedation is recommended to enhance informed reflection and policy making. (shrink)

Moral theory -- Abortion -- Genetic engineering, cloning, and stem cell research -- Euthanasia and assisted suicide -- The death penalty -- Drug and alcohol use -- Sexual intimacy and marriage -- Feminism, motherhood, and the workplace -- Freedom of speech -- Racial discrimination and global justice.

In lieu of an abstract, here is a brief excerpt of the content:The Understanding and Experience of Compassion:Aquinas and the Dalai LamaJudith BaradHis Holiness the fourteenth Dalai Lama writes that the essence of Mahayana Buddhism is compassion.1 Although most people recognize compassion as one of the most admirable virtues, it is not easy to find discussions of it by Christian theologians. Instead, Christian theologians tend to discuss charity, a virtue infused by God into a person. Some of these theologians, such (...) as Cardinal Henri de Lubac,2 insist that Christian charity and Buddhist compassion are very different from each other. Are they correct? A good source to investigate this claim is in Aquinas's Summa Theologica, which contains a very developed discussion of charity. If we look at Aquinas's text and compare it to what the current Dalai Lama writes about compassion, we will recognize that they are discussing the same virtue. Moreover, by combining the insights from East and West, as expressed by the thoughts of the current Dalai Lama and St. Thomas Aquinas, we can achieve a better grasp of compassion so that we can more easily practice it in our daily lives. Though remarkably similar, the two accounts offer differing perspectives, which can be incorporated for mutual enrichment.Much of Aquinas's philosophy of compassion derives from his Christian beliefs, just as much of the Dalai Lama's teachings on compassion are based on Tibetan Buddhism. This explains some of the differences in their accounts. Unlike Christians, Buddhists neither believe in a personal God nor in a soul. Yet despite their theological differences, Aquinas and the Dalai Lama generally share a very similar view of compassion. In fact, one could well imagine Aquinas agreeing with the Dalai Lama who, after acknowledging his religious influence, writes that his goal is "to appeal for an approach to ethics based on universal rather than religious principles."3 It is appropriate, therefore, to begin by considering the similarities in their accounts of compassion, starting with their definitions of compassion. [End Page 11]DefinitionsEtymologically, the word "compassion"—compassio—comes from two Latin words: com means "with" and pati means "suffer." Literally, then, "compassion" means "to suffer with." Aquinas discusses compassion as an interior effect of charity, a theological virtue. It is interior because compassion is felt within the person who has charity. The cause of compassion, charity, Aquinas describes as the friendship between God's children and God Himself. Although Aquinas wrote prolifically on the subject of charity, someone could overlook his writing on compassion because he discusses it under the term "mercy." Diana Fritz Cates, for instance, who draws on an Aristotelian-Thomistic ethical framework to develop a theory of compassion, observes, "Aristotle and Thomas have little to say about compassion: hence, it will not be helpful to begin with their accounts."4 However, Aquinas uses the word misericordia (mercy) as a synonym of compassio (compassion). The synonymous relationship between compassion and mercy is also recognized by the Dalai Lama, who affirms, "Mercy and compassion are the same."5Aquinas defines mercy as "heartfelt sympathy for another's distress, impelling us to succor him if we can." If we experience this heartfelt sympathy, we're not discouraged if the person we try to help doesn't respond. Explicitly connecting mercy and compassion, Aquinas add that mercy, misericordia, gets its name "from denoting a person's compassionate heart (miserum cor) for another's unhappiness."6 The concept of "another's unhappiness" is important to his discussion. A necessary condition of being happy, in Aquinas's view, is that an individual must obtain what he or she wishes. Conversely, someone is unhappy when he suffers what he doesn't wish to suffer. Aquinas maintains that the suffering produced by one's frustrated desire for what he or she perceives as good is a sufficient condition for evoking mercy. In regard to the merciful response, it shouldn't matter what the suffering person perceives as good. So long as the person is suffering what he doesn't wish to suffer, this person should be treated mercifully. Suppose a teenager suffers from being unpopular with his peers. Although the compassionate person may not value popularity, she should extend compassion to the... (shrink)

MACDONNELL JA. Nursing Inquiry 2011; 18: 313–324 Gender, sexuality and the participatory dimensions of a comparative life history policy studyIn this paper, I explore how a critical feminist lens was a crucial element in creating a participatory policy study which used a qualitative design and comparative life history methodology. This study focused on Canadian nurses’ political practice related to advocacy for lesbian health. Findings show that the combination of the gender lens and life history approach offers potential to create knowledge (...) in ways aligned with health‐promoting and emancipatory outcomes. However, the nature of participation and interaction by researcher and participants is contexualized and contested given complex dynamics of power that shape all aspects of this doctoral study process. The critical feminist lens with its focus on reflexivity informed the content and process of knowledge production in this study and shaped key turning points: the ways in which this policy study was conceptualized, the choice of comparative life history methodology, ethical considerations, data collection and analysis and representation of findings. Life history is unlikely to be the methodology that first comes to mind when undertaking a policy study. Its historical roots are associated with biographical, oral history and narrative approaches, which typically aim to elicit understanding of lived experience. Yet, it was this very aspect, this focus on lived experience, which rendered life history methodology fitting as I contemplated how to examine the relationship between nurses and policy. I was interested in understanding nurses’ political practice, how policy influenced nurses’ capacity to advocate in their everyday lives, as well as nurses’ impacts on policy processes and their larger social worlds. (shrink)

The Proceedings of the National Summit on Legal Preparedness for Obesity Prevention and Control is based on a two-part conceptual framework composed of public health and legal perspectives. The public health perspective comprises the six target areas and intervention settings that are the focus of the obesity prevention and control efforts of the Centers for Disease Control and Prevention.This paper presents the legal perspective. Legal preparedness in public health is the underpinning of the framework for the four “assessment” papers and (...) the four “action” papers that are integral to the application of public health law to any particular health issue. In addition, this paper gives real-world grounding to the legal framework through examples that illustrate the four core elements of legal preparedness in public health that are at work in obesity prevention and control. (shrink)

The Proceedings of the National Summit on Legal Preparedness for Obesity Prevention and Control is based on a two-part conceptual framework composed of public health and legal perspectives. The public health perspective comprises the six target areas and intervention settings that are the focus of the obesity prevention and control efforts of the Centers for Disease Control and Prevention.This paper presents the legal perspective. Legal preparedness in public health is the underpinning of the framework for the four “assessment” papers and (...) the four “action” papers that are integral to the application of public health law to any particular health issue. In addition, this paper gives real-world grounding to the legal framework through examples that illustrate the four core elements of legal preparedness in public health that are at work in obesity prevention and control. (shrink)

In a previous paper, I argued that expert nursing intuition is a form of what James J. Gibson termed ‘direct perception’ and, as such, is information‐based and can be accepted as part of nursing science. In this paper, I explore the philosophical basis for these claims. I begin by describing analogous problems in philosophy and psychology related to how we know the world. After describing the various solutions proposed and the problems they engender, I summarize Gibson’s theoretical solution together with (...) some of the supporting empirical evidence, but emphasizing the ecological realism on which it relies. I then use these insights to reconsider nursing intuition and the implications for its further exploration. (shrink)

Race, Crime, and the Law. Randall Kennedy. New York: Vintage Books/Random House, 1997, xiv + 539 pp.

To learn more about Rowman & Littlefield titles please visit us at www.rowmanlittlefield.com.

Previous research suggests that individuals diagnosed with morbid jealousy have jealousy mechanisms that are activated at lower thresholds than individuals with normal jealousy, but that these mechanisms produce behavior that is similar to individuals with normal jealousy. We extended previous research documenting these similarities by investigating sex differences in partner-directed violence committed by individuals diagnosed with morbid jealousy. The results support some of our predictions. For example, a greater percentage of men than women diagnosed with morbid jealousy used physical violence, (...) attempted to kill, and actually killed their partners, and used their hands rather than an object to kill their partners. These results replicate results generated for individuals with normal jealousy. Discussion addresses implications of the current research and highlights directions for future research on the psychology of morbid jealousy. (shrink)

After identifying similarities in the paradigmatic problems of biorobotics and ecological psychology, we suggest a way to compare the performance of robots with that of their biological targets. The crucial comparison is between the intentional dynamics of the robot and those of the targeted animal, a measure that depends critically on recognizing and describing the underlying affordance-effectivity match of the target system.

Aristotle wrote that "the ultimate purpose in studying ethics is not as it is in other inquiries, the attainment of theoretical knowledge; we are not conducting this inquiry in order to know what virtue is, but in order to become good, else there would be no advantage in studying it." Ethics for Life is a multicultural and interdisciplinary introductory ethics textbook that provides students with an ethics curriculum that has been shown to significantly improve students' ability to make real-life moral (...) decisions. (shrink)