The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (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)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

A single mother is a person who is accountable for raising their children alone because they do not have a husband or live-in partner. Single mothers claim to have no co-parenting relationships at all, comparing single parents to those who are married, cohabiting, or without children, single parents experience the worst work-life balance. A single parent may feel overwhelmed by the demands of juggling child care, a career, paying bills, and maintaining household responsibilities. Single-parent households frequently deal with several extra (...) obligations and possible complications that other families would not. The study also emphasizes the difficulties and coping mechanisms faced by contractual single parents as well as their lived experiences. The study's findings, which were based on an Interpretative Phenomenological Analysis, were as follows: (1) Work-life balance can be difficult for single parents. They struggle to keep their jobs while taking care of their family because they are the only ones in charge of the children. (2) Single contractual mothers face particular difficulties due to a lack of resources for basic expenses. (3) Contractual single women lean on their kids, the good people in their lives, and their faith in God to get through problems. (shrink)

What enables individually simple insects like ants to act with such precision and purpose as a group? How do trillions of individual neurons produce something as extraordinarily complex as consciousness? What is it that guides self-organizing structures like the immune system, the World Wide Web, the global economy, and the human genome? These are just a few of the fascinating and elusive questions that the science of complexity seeks to answer. In this remarkably accessible and companionable book, leading complex systems (...) scientist Melanie Mitchell provides an intimate, detailed tour of the sciences of complexity, a broad set of efforts that seek to explain how large-scale complex, organized, and adaptive behavior can emerge from simple interactions among myriad individuals. Comprehending such systems requires a wholly new approach, one that goes beyond traditional scientific reductionism and that re-maps long-standing disciplinary boundaries. Based on her work at the Santa Fe Institute and drawing on its interdisciplinary strategies, Mitchell brings clarity to the workings of complexity across a broad range of biological, technological, and social phenomena, seeking out the general principles or laws that apply to all of them. She explores as well the relationship between complexity and evolution, artificial intelligence, computation, genetics, information processing, and many other fields. Richly illustrated and vividly written, Complexity : A Guided Tour offers a comprehensive and eminently comprehensible overview of the ideas underlying complex systems science, the current research at the forefront of this field, and the prospects for the field's contribution to solving some of the most important scientific questions of our time. (shrink)

This article offers an argument of genocide denial as an injustice perpetrated not only against direct victims and survivors of genocide, but also against future members of the victim group. In particular, I argue that in cases of persistent and systematic denial, i.e. denialism, it perpetrates an epistemic injustice against them: testimonial oppression. First, I offer an account of testimonial oppression and introduce Kristie Dotson’s notion of testimonial smothering as one form of testimonial oppression, a mechanism of coerced silencing particularly (...) pertinent to genocide denialism. Secondly, I turn to the epistemology of genocide denialism and, using the example of Turkey’s denialism of the Armenian genocide, show how it presents what Linda Martín Alcoff calls a substantive practice of ignorance. Thirdly, I apply these considerations to individual practices of genocide denial and analyse the particular characteristics of testimony on genocide, the speaker vulnerabilities involved and the conditions under which hearers will reliably fail to meet the dependencies of a speaker testifying to genocide. Finally, I explore the harms that testimonial oppression perpetrates on members of the victim group, insofar as it systematically deprives them of epistemic recognition. (shrink)

Genocide remembrance is a complex epistemological/ethical achievement, whereby survivors and descendants give meaning to the past in the quest for both personal-historical and social-historical truth. This paper offers an argument of epistemic injustice specifically as it occurs in relation to practices of (individual and collective) genocide remembrance. In particular, I argue that under conditions of genocide denialism, understood as collective genocide misremembrance and memory distortion, genocide survivors and descendants are confronted with hermeneutical oppression. Drawing on Sue Campbell’s relational, reconstructive account (...) of remembering, I argue that genocide denialism involves disrespectful challenges to memory, which systematically misrecognize rememberers. Adopting the case of Turkey’s denialism of the Armenian genocide, I discuss two interrelated mechanisms through which this can happen: i) through the systematic portrayal of survivors and descendants as vicious rememberers, and ii) through distortions of the very concept of ‘genocide’. Based on this, I show how hermeneutical and testimonial injustice are crucially interrelated when it comes to “contested” memories of historical injustice and the biographical testimony it gives rise to. (shrink)

Developmental perspectives on prejudice provide a fundamental and important key to the puzzle for determining how to address prejudice. Research with historically disadvantaged and advantaged groups in childhood and adolescence reveals the complexity of social cognitive and moral judgments about prejudice, discrimination, bias, and exclusion. Children are aware of status and hierarchies, and often reject the status quo. Intervention, to be effective, must happen early in development, before prejudice and stereotypes are deeply entrenched.

La pandemia del coronavirus llegó intempestivamente y el afán de compartir esta experiencia, unió a escritores a través de diversas plataformas. Ya existía interés en conformar un grupo de minificcionistas antes de la pandemia y este pareció el momento propicio. Cada integrante trajo a otros, hasta conformar un grupo de 19 escritores de Argentina, Bolivia, Colombia, Chile, Ecuador, España, Guatemala, Honduras, Marruecos, México, Nicaragua, Panamá, Perú y Venezuela.

As we become more aware of the potential causes and consequences of climate change we are left wondering: who is responsible? Climate change has the potential to harm large portions of the global population and, arguably, is already doing so. Further, climate change is argued to be human-caused. If this is true, then it seems to be the case that we can analyze climate change in terms of responsibility. I argue that we can approach environmental harms, such as climate change, (...) through a theory of collective responsibility. I propose an account of reductive collective responsibility that can apply to the unstructured collective causing climate change and determine what we are each individually morally responsible for. To avoid the critiques of reductive collective responsibility for large unstructured harms, I propose we separate the determination of membership and eligibility for responsibility from the attribution of responsibility. Through this method, I can speak to the individual responsibility of each member who contributes to climate change without holding them responsible for that which is outside their control. (shrink)

In _Jain Approaches to Plurality_ Melanie Barbato offers a new perspective on the Jain teaching of plurality and how it allowed Jains to engage with other discourses from Indian inter-school philosophy to global interreligious dialogue.

This paper examines six cross-sector partnerships in South Africa and Zambia. These partnerships were part of a research study undertaken between 2003 and 2005 and were selected because of their potential to contribute to poverty reduction in their respective countries. This paper examines the context in which the partnerships were established, their governance and accountability mechanisms and the engagement and participation of the partners and the intended beneficiaries in the partnerships. We argue that a partnership approach which has proven successful (...) in one context can be used as a valuable learning resource. However, a partnership's work, which includes all aspects of the partnership and its activities, cannot necessarily be transferred directly to another partnership without a thorough and locally informed analysis of the context in which it is implemented. In addition, we suggest that it is difficult to assess whether the good intentions behind partnerships were translated into real benefits for target groups as effective monitoring and evaluation procedures were not in place in the partnerships studied. Similarly, the absence of regularised governance and accountability systems in partnerships made it difficult to support partner and beneficiary participation and engagement. We conclude that there is a need to move beyond a 'one-size-fits-all' approach to partnerships and that partnership replication should focus more strongly on the transfer of learning about partnership processes instead of simply copying partnership activities. Moreover, the development of stronger mechanisms for assessing and ensuring accountability towards both partners and intended beneficiaries is required if partnerships are to meet their intended objectives. (shrink)

This text collects Melaine Klein's writings from 1946 until her death in 1960, including two papers published posthumously. This was her last major work which introduces her theory of primary envy.

In this article I am concerned with how relatively privileged people who wish to act in anti-oppressive ways respond to their own ignorance in ways that fall short of what is necessary for building coalitions against oppression. I consider María Lugones's sense of “world”-travel and José Medina's notion of epistemic friction-seeking as strategies for combating privileged ignorance, and assess how well they fare when put into practice by those suffering from privileged ignorance. Drawing on the resources of tourism studies, I (...) critique the political and material context that can turn these attempts to “world”-travel or seek epistemic friction into a morally and epistemically problematic epistemic tourism. Centrally, I argue that trying to learn what it's like to experience oppression is not an effective method of counteracting privileged ignorance, since the epistemic vices and cognitive distortions that created the ignorance in the first place continue to influence knowledge-creation even after they are acknowledged. Rather than attempting to understand “what it's like” to experience oppression, privileged progressives should undertake to learn about the provenance and purpose of their ignorance and the structures of oppression that facilitate and are facilitated by that ignorance. (shrink)

This article was developed as part of the forthcoming special issue on "Reparations" for the Journal of Social Philosophy and was accepted (with minor revisions) by the guest editors Christina Nick and Susan Stark in November 2021. The special issue article is available online open access for early view. -/- Abstract: The United Nations Commission on Human Rights acknowledges the Right to Know as part of state obligations to combat impunity and thereby protect and promote human rights in the aftermath (...) of “serious crimes under international law”. In light of such an institutionally acknowledged epistemic right of victims, this paper explores the normative foundations of the idea of epistemic reparation in the aftermath of genocide. I argue that such epistemic reparation requires not only fulfilment of the informational needs of victims, survivors and descendants, including access to knowledge about the violations. By taking into account epistemic injuries, which are part and parcel of genocide, it ought to also re-establish victims’ epistemic standing. This is because genocide is enabled, justified and even prescribed through a genocidal epistemology involving the propagation of falsehoods and misinformation about social reality as well as abuses of epistemic authority and epistemic authoritarianism. Hence, epistemic reparation ought to correct the dysfunctional epistemic practices that underlie and sustain a genocidal epistemology. It thereby provides victims, survivors and descendants with epistemic recognition that has been systematically withdrawn from them, making epistemic reparation a crucial element of restorative justice. (shrink)

The Dreaming Mind provides an insightful, interdisciplinary approach to the study of dreaming, exploring its nature and examining some of the implications of dream states for theories of consciousness, cognition and the self. Offering an integrative approach into our understanding of dreams and the mind, it is essential reading for students and researchers of consciousness, dreams, philosophy and cognitive sciences, as well as anyone who is curious about dreaming.

Diese Studie analysiert die Konzepte «Wissenskulturen» und «Experimentalkulturen», um sich dem Problem der Repräsentation mittels einer Mehrfaktoren-Analyse zu nähern.

Seit ihrer Begründung im 18. Jahrhundert war die Ästhetik auch ein Korrektiv der Logik, indem sie die Sinnlichkeit des Menschen - Wahrnehmungen, Gefühle, Erinnerungen sowie deren Ausdruck in Kunst, Literatur und Wissenschaft - in den Blick genommen hat. In diesem Band wird die Vielfalt ästhetischer Perspektiven dokumentiert: Als Gesellschaftskritik und Erkenntnistheorie, als Lehre vom Schönen und Theorie der Kunst ist die Ästhetik nicht wegzudenken, wenn man den Menschen in seiner kulturellen Existenz begreifen möchte.

Integrative and naturalistic philosophy of mind can both learn from and contribute to the contemporary cognitive sciences of dreaming. Two related phenomena concerning self-representation in dreams demonstrate the need to bring disparate fields together. In most dreams, the protagonist or dream self who experiences and actively participates in dream events is or represents the dreamer: but in an intriguing minority of cases, self-representation in dreams is displaced, disrupted, or even absent. Working from dream reports in established databanks, we examine two (...) key forms of polymorphism of self-representation: dreams in which I take an external visuospatial perspective on myself, and those in which I take someone else's perspective on events. In remembering my past experiences or imagining future or possible experiences when awake, I sometimes see myself from an external or 'observer' perspective. By relating the issue of perspective in dreams to established research traditions in the study of memory and imagery, and noting the flexibility of perspective in dreams, we identify new lines of enquiry. In other dreams, the dreamer does not appear to figure at all, and the first person perspective on dream events is occupied by someone else, some other person or character. We call these puzzling cases 'vicarious dreams' and assess some potential ways to make sense of them. Questions about self-representation and perspectives in dreams are intriguing in their own right and pose empirical and conceptual problems about the nature of self-representation with implications beyond the case of dreaming. (shrink)

This is the introduction to the special issue "Themes from Testimonial Injustice and Trust" for the International Journal of Philosophical Studies.

As earlier research on Korsakoff syndrome, a frequent neurological complication of alcohol-dependence, mainly focused on cognition, affective impairments have been little investigated despite their crucial impact in AD. This article proposes new research avenues on this topic by combining two theoretical frameworks: dual-process models, positing that addictions are due to an imbalance between underactivated reflective system and overactivated affective-automatic one; continuity theory, postulating a gradual worsening of cognitive impairments from AD to KS. We suggest that this joint perspective may renew (...) the current knowledge by clarifying the affective-automatic deficits in KS and their interactions with reflective impairments, but also by offering a direct exploration of the continuity between AD and KS regarding reflective and affective-automatic abilities. (shrink)

How does the body influence the way we see the world? _Imagination, Illness and Injury_ examines the psychological factors behind perceptual limitations and distortions and links a broad range of somatic manifestations with their resolution. Melanie Starr Costello applies Jungian theory to a variety of cases, attributing psychosomatic phenomena to cognitive processes that are common to us all. She analyses the role of illness in several life narratives, and interprets the appearance of somatic phenomena during important phases of analytic treatment. (...) Together these case narratives present a significant challenge to established views of psychosomatics. Subjects covered include: archetypal constrictions of identity somatic elements of perception the psyche-soma split. _Imagination, Illness and Injury _brings a fresh perspective to the understanding and treatment of the psychotherapy client as a psycho-somatic unity. Jungian analysts, psychoanalysts, and psychotherapists will greatly benefit from the clinical applications of archetypal theory presented here. (shrink)

In this introduction to the special issue ‘Epistemic Injustice and Collective Wrongdoing,’ we show how the eight contributions examine the collective dimensions of epistemic injustice. First, we contextualize the articles within theories of epistemic injustice. Second, we provide an overview of the eight articles by highlighting three central topics addressed by them: i) the effects of epistemic injustice and collective wrongdoing, ii) the underlying epistemic structures in collective wrongdoing, unjust relations and unjust societies, and iii) the remedies and strategies of (...) resistance to epistemic injustice. We close by pointing to connections and issues that may motivate further research. (shrink)

Given the profound influence of social media and emerging evidence of its effects on human behavior and health, bioethicists have an important role to play in the development of professional standards of conduct for health professionals using social media and in the design of online systems themselves. In short, social media is a bioethics issue that has serious implications for medical practice, research, and public health. Here, we inventory several ethical issues across four areas at the intersection of social media (...) and health: the impact of social networking sites on the doctor‐patient relationship, the development of e‐health platforms to deliver care, the use of online data and algorithms to inform health research, and the broader public health consequences of widespread social media use. In doing so, we review discussions of these topics and emphasize the need for bioethics to focus more deeply on the ways online technology platforms are designed and implemented. We argue that bioethicists should turn their attention to the ways in which consumer engagement, bias, and profit maximization shape online content and, consequently, human behavior and health. We also offer a set of recommendations and suggest future directions for addressing ethical challenges in these domains. (shrink)

ABSTRACTEmployees who possess cross-cultural capabilities are increasingly sought after due to unparalleled numbers of cross-cultural interactions. Previous research has primarily focused on the bright side of these capabilities, including important individual and work outcomes. In contrast, the purpose of this study is to demonstrate that the cross-cultural capability of cultural intelligence can lead to both positive and negative outcomes. Applying the general theory of confluence, we propose that expatriates high in CQ excel in customer relationship performance, while simultaneously behaving opportunistically. (...) We also suggest that ethical relativism moderates these relationships. Using mixed methods, four separate studies generally support our predictions while also deepening our understanding of various forms of opportunism and the mechanism behind two seemingly opposing effects. Conceptual and managerial implications of CQ for opportunism, customer relationship performance, and ethics are discussed. (shrink)

In this essay we argue that there is a contradiction lurking at the heart of Bernard Suits's seminal book on the philosophy of games, The Grasshopper, which has oddly gone unnoticed for 43 years. Suits argues that games need inefficiency and defines inefficiency such that it wouldn't exist in Utopia. This trivially entails that there could be no games in Utopia, yet the whole normative point of The Grasshopper is that games would be the only worthwhileactivity in Utopia. We then (...) diagnose Suits's error and suggest some ways forward. (shrink)

Understanding transitional justice and dealing with the past as elements of intergenerational justice puts our focus on the establishment of sustainable, peaceful, social relationships among groups or members thereof within an intergenerational polity or society after violent conflicts, such as genocide or other crimes against humanity. However, what if this process is undermined by institutionally supported denialism? This paper addresses the question of the normative importance of genocide recognition negatively, by examining the way in which subsequent genocide denialism might be (...) considered as a perpetuation of injustice against genocide survivors and their descendants. I will argue that genocide denialism can be considered as a continuation of genocidal violence in epistemic form, that is, an epistemic injustice, whereby members of the victim group are negatively discriminated against with regard to their credibility and intelligibility. Institutional genocide denialism, then, does not just prevent societies from dealing with their genocidal past, but in the first instance constitutes renewed humiliation and violation of the epistemic authority of genocide survivors and their descendants, thus becoming an instance of intergenerational injustice. (shrink)

A discussion of ethical decision-making literature is overdue. In this article, we summarize the current literature of ethical decision-making models used in mental health professions. Of 1,520 articles published between 2001 and 2020 that met initial search criteria, 38 articles were included. We report on the status of empirical evidence for the use of these models along with comparisons, limitations, and considerations. Ethical decision-making models were synthesized into eight core procedural components and presented based on the composition of steps present (...) in each model. This taxonomy provides practitioners, trainers, students, and supervisors relevant information regarding ethical decision-making models. (shrink)

Our eyes, bodies, and perspectives are constantly shifting as we observe the world. Despite this, we are very good at distinguishing between self-caused visual changes and changes in the environment: the world appears mostly stable despite our visual field moving around. This, it seems, also occurs when we are dreaming. As we visually investigate the dream environment, we track moving objects with our dream eyes, examine objects, and shift focus. These movements, research suggests, are reflected in the rapid movements or (...) saccades of our sleeping eyes. Do we really see the dream world in the same way that we see the real world? If we do, how could dreaming, usually assumed to be mind-generated hallucinations, replicate such an experience? This problem would be deflated if dreams are not hallucinations at all, but rather imagination, illusion or simply unrealistic. I argue that imagination and illusion views do not satisfactorily explain away the problem of vision and action in sleep. The imagination model is not a complete description of dreaming that is consistent with empirical research, and it is unlikely that the visual dream world is an illusion. Given that the dreaming visual experience is most likely active, hallucinatory, and at times a realistic world simulation, there are important implications for our understanding of visual perception and its relationship to movement. Evidence suggests that our dream eyes investigate the dream world as our waking eyes investigate the waking world. If changes to the unconsciously generated dream environment are perceived as external and unintentional while dream body movements are perceived as self-generated and intentional, current theory of visual perception may have to be expanded to account for how the dreaming mind generates a stable world in which we track and visually explore mind-generated objects. (shrink)