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)

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) 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)

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 current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (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)

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)

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)

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.

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)

By questions of “canon,” we mean questions of what is fictionally true of some character, story, or world. What is canon is treated as authoritative or official, usually by creators and fans alike. But disputes about canon have arisen as storytellers and publishers have sought to capitalize on the popularity of their characters, churning out more and more stories to meet public demand, and at the same time engaging with growing fan bases. As audiences have become more involved, and as (...) fictional worlds have become messier, the authoritative nature of canon—and who authorizes it—has begun to erode. In this paper, we characterize canon as an article in the evolving relation between authors and audiences. More specifically, we characterize canon as an intangible good, subject to a form of cultural negotiation, resting on a power relation between producers and consumers of fictions. In Part I, we consider the author’s evolving role, and the rights of the creator to a story, character, or world. In Part II, we discuss the emerging activities of fans, particularly as they weigh on issues of canon. In Part III, we discuss canon as being subject to cultural negotiation, highlighting the importance of power dynamics in this negotiation. (shrink)

The book moves from descriptive through to more interpretative phenomenological methods to enable the reader to learn to use the main approaches to ...

An objection to shifty epistemologies such as subject-sensitive invariantism is that it predicts that agents are susceptible to guaranteed losses. Bob Beddor (Analysis, 81, 193–198, 2021) argues that these guaranteed losses are not a symptom of irrationality, on the grounds that forgetful agents are susceptible to guaranteed losses without being irrational. I agree that forgetful agents are susceptible to guaranteed losses without being irrational– but when we investigate why, the analogy with shifty epistemology breaks down. I argue that agents with (...) shifty epistemologies are susceptible to guaranteed losses in a way which is a symptom of irrationality. Along the way I make a suggestion about what it takes for an agent to be coherent over time. I close by offering a taxonomy of shifty epistemologies. (shrink)

Much ink has been spilled in philosophy over the question of whether morality is an objective or subjective matter. In the world of The Good Place, the answer to the moral question seems fairly firmly determined: right and wrong are objective matters, and there is a fact about whether our actions are good or bad. The ancient Greek philosopher Pythagoras believed that beauty was a quantifiable principle of nature, and that we could find the source of beauty in the harmony, (...) order, and regularity of beautiful things. In some ways, The Good Place appears to treat aesthetic goodness and badness as if they were objective matters. The Good Place is a sort of extended version of Jean‐Paul Sartre's (1905–1980) existentialist play No Exit. In The Good Place, hell is other people's tastes. (shrink)

This chapter contains sections titled: Introduction A Pre‐Emptive Strike How Comics Mean The Unified Comic Conclusion Notes References.

How do we access the authentic self in order to live fulfilling, meaningful lives? In straightforward terms, The Heart of the Matter: Gifts in Strange Wrapping Paper explains a simple but extraordinarily powerful technique called the See, Feel, Hear Challenge that enables people to easily gain entry into the storehouse of their subconscious core beliefs. In the process, it cracks the coded messages that those beliefs release in the form of disease, suffering, addictions, unhappy relationships, and victimized circumstances. Based in (...) the latest findings in neuroscience and neurocardiology, this book guides readers to an uncomplicated understanding of the astounding power of our emotions and how life automatically delivers experiences that trigger negative reactions that subconsciously impact us. These emotions form the foundation of core beliefs that create unhealthy attitudes and dis-ease patterns that keep us from experiencing the authentic, satisfying lives we desire. Using clear examples and true stories from clients, Dr. Weissman’s latest work demonstrates how we can release these stored emotions and their wisdom via the See, Feel, Hear Challenge. It then explains how to use this simple method to evoke feelings that positively impact the quantum field, remolding our bodies, minds, and everyday lives into purposeful expressions of inner joy and radiant well-being. Whether you’re dealing with addictions, dysfunctional relationships, or illness, or are focused on becoming an Olympic champion, The Heart of the Matter gives you a potent tool for positive change and transformation that you can use for the rest of your life. (shrink)

If an agent believes that the probability of E being true is 1/2, should she accept a bet on E at even odds or better? Yes, but only given certain conditions. This paper is about what those conditions are. In particular, we think that there is a condition that has been overlooked so far in the literature. We discovered it in response to a paper by Hitchcock (2004) in which he argues for the 1/3 answer to the Sleeping Beauty problem. (...) Hitchcock argues that this credence follows from calculating her fair betting odds, plus the assumption that Sleeping Beauty’s credences should track her fair betting odds. We will show that this last assumption is false. Sleeping Beauty’s credences should not follow her fair betting odds due to a peculiar feature of her epistemic situation. (shrink)

Whilst continuing racism is often invoked as evidence of the urgent need for Philosophy for Children, there is little in the current literature that addresses the topic. Drawing on Critical Race Theory and the related field of Critical Whiteness Studies , I argue that racism is deeply ingrained culturally in society, and best understood in the context of ‘Whiteness’. Following a CRT-informed analysis of two picturebooks that have been recommended as starting points for philosophical enquiry into multiculturalism, racism and diversity (...) – ‘Elmer’ and ‘Tusk Tusk’ by David McKee, I argue that whilst the use of stories with animals is commonly regarded as offering children the comfort of distance from emotionally challenging topics, this has the effect of separating racism from its temporal and spatial realities, which limits rather than enhances opportunities for engaging philosophically with it. I argue in favour of the practice of ‘reading against the text’ and consider the epistemological and practical obstacles to this practice drawing on my own experiences discussing race with P4C practitioners in the UK. I attempt to illustrate how the selection of recommended materials, combined with commonly held principles of P4C, make for a climate where a philosophical engagement with race and racism that considers the discourse of ‘Whiteness’ is highly unlikely to occur. This leads me to posit the idea of The Gated Community of Enquiry. (shrink)

In this title the author explores the time-tested practice and philosophy using modern examples from more than a decade of experience with this ancient practice. He brings the principles of yoga into focus and makes them user-friendly for yogis living in the post modern era.

Interpreting the world through a social lens is a central characteristic of human cognition. Humans ascribe intentions to the behaviors of other individuals and groups. Humans also make inferences about others’ emotional and mental states. This capacity for social attribution underlies many of the concepts at the core of legal and political systems. The developing scientific understanding of the neural mechanisms used in social attribution may alter many earlier suppositions. However, just as often, these new methods will lead back to (...) old conundrums. Cognitive neuroscience will not dispel the hard problems of social judgment. (shrink)

Did you know that insects could be tried for criminal acts in pre-industrial Europe, that the dead could be executed, that statues could be subjected to public humiliation, or that it was widely accepted that corpses could return to life? What made reasonable, educated men and women behave in ways that seem utterly nonsensical to us today? Strange Histories presents for the first time a serious account of some of the most extraordinary occurrences of European history. Throughout the ages, people (...) have held ideas and events have taken place which have baffled later societies. Religious disbelievers were thought deserving of death, insects were occasionally excommunicated, studying the biology of angels was a legitimate activity, and the pursuit of personal happiness was considered rather misguided as a life strategy. Using case studies from the Middle Ages and the early modern period with some from the more recent past, this book provides fascinating insights into the world-view through the ages, and shows how such goings-on fitted in quite naturally with the "common sense" of the time. Explanations of these phenomena, riveting and ultimately rational, encourage further reflection on what really shapes our beliefs. In the light of history, can we be sure of the validity of our own ideas? How many of our own beliefs might no longer "make sense" a few centuries from now? (shrink)

In this paper I argue that whether or not a computer can be built that passes the Turing test is a central question in the philosophy of mind. Then I show that the possibility of building such a computer depends on open questions in the philosophy of computer science: the physical Church-Turing thesis and the extended Church-Turing thesis. I use the link between the issues identified in philosophy of mind and philosophy of computer science to respond to a prominent argument (...) against the possibility of building a machine that passes the Turing test. Finally, I respond to objections against the proposed link between questions in the philosophy of mind and philosophy of computer science. (shrink)

The essay reflects on how Hans-Georg Gadamer and Karl Barth view interpretation of the Christian Bible. It proceeds in three main sections. The first contends that Gadamer secularizes Christian theology, and that this has drawbacks for the sort of reading his hermeneutic can give to Christian Scripture. The second part turns to Barth, arguing that the whole structure of his approach to the Bible factors in theological commitment, with benefits for the readings he can deliver. The final part makes a (...) case that contemporary reflection on interpretation can nonetheless glean important insights from Gadamer, especially regarding the readerly reception of texts, because his perspective has a certain sort of richness that Barth’s cannot match. The overall suggestion emerging from the interrogation of these two thinkers is that phenomenology and theology might learn from one another, that they each contribute something valuable to discussions of biblical interpretation. (shrink)

This book shows that cyberculture has been a long time coming.In Prefiguring Cyberculture, media critics and theorists, philosophers, and historians of science ...

In this paper, I argue that the notion of ‘reasonableness’ that is, for many, at the heart of the Philosophy for Children approach particularly and education for democratic citizenship more broadly, is constituted within the epistemology of ‘white ignorance’ and operates in such a way that it is unlikely to transgress the boundaries of white ignorance so as to view it from without. Drawing on scholarship in critical legal studies and social epistemology, I highlight how notions of reasonableness often include (...) consensus, ‘racialised common sense’ and the ‘typical’ view. In addition the promotion of particular dispositions on the grounds of ‘reasonableness’ both promotes stability and limits how one may think otherwise. Thus, P4C practices that fail to historicise, examine and challenge prevailing notions of reasonableness establish an epistemically ‘gated’ community of inquiry. (shrink)

Using files declassified and released to Great Britain's National Archives, this article shows how Britain's domestic spy agency, MI5, recruited Louis de Wohl (1903-61), a flashy Hungarian astrologer and Christian writer to create horoscopes for Adolf Hitler during World War II. De Wohl was a controversial figure. His origin story does not check out. His MI5 handlers found him showy. And recent journalists dismiss him as a ‘persuasive fake’. Yet his pre-war fictions were adapted for cinema, his later theological novels (...) remain bestsellers, and his personal story deserves greater attention if we are to better understand Christian historical fiction's popularity. (shrink)

Psychology has benefited from an enormous wealth of knowledge about processes of cognition in relation to how the brain organizes information. Within the categorization literature, this behavior is often explained through theories of memory construction called exemplar theory and prototype theory which are typically based on similarity or rule functions as explanations of how categories emerge. Although these theories work well at modeling highly controlled stimuli in laboratory settings, they often perform less well outside of these settings, such as explaining (...) the emergence of background knowledge processes. In order to explain background knowledge, we present a non-similarity-based post-Skinnerian theory of human language called Relational Frame Theory which is rooted in a philosophical world view called functional contextualism. This theory offers a very different interpretation of how categories emerge through the functions of behavior and through contextual cues, which may be of some benefit to existing categorization theories. Specifically, RFT may be able to offer a novel explanation of how background knowledge arises, and we provide some mathematical considerations in order to identify a formal model. Finally, we discuss much of this work within the broader context of general semantic knowledge and artificial intelligence research. (shrink)

I argue that Diogenes and early Cynicism can be understood in an explicitly social and political context, where Cynic praxis, performative public action, can be seen to make visible oppositions inherent to the polity. In doing so, Diogenes’ praxis should be understood as a form of immanent critique, one that demonstrates, for example, that nature and custom are interrelated oppositions in the polis. Cynicism here is understood as a form of immanent critique because Diogenes challenges the social norms of the (...) polis without endorsing external universal standards or predetermined models, but from illuminating dynamics from within the polis and polity. (shrink)

Daniel Bensaïd’s theoretical and political framework deserves to be habitually known in the English-speaking world. His philosophical work has a universal dimension, but because it was also the product of particular political upsurges and downturns, it is necessary to understand these particular political moments to thoroughly understand the universal scope and significance of his work. This paper will look at these political developments and pay particular attention to the crisis of the workers’ movement, strategy and Marxism.