Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...) large amounts of ncRNA biological and clinical data. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

I intend to dismantle a piece of historiographic mythology created by self-styled ‘Revisionists’ (Hill, Alvey, Oslington, etc.). According to the myth, Adam Smith endorsed several of the traditional proofs of God’s existence; he believed that the order existing in the world is a morally good order implemented by Divine Providence; he believed that evil in the world is part of an all-encompassing Divine Plan; and that the ‘invisible hand’ is the hand of the Christian God who leads the rich (...) to employ their wealth for the greater benefit of the greatest number. -/- I argue instead that there is a remarkable analogy between Smith’s and Kant’s theory of religion. Smith’s philosophy is a third way between Rationalism and Phyrronism, arguing that doctrines confirmed by reason in every field, from natural science to theology, are nothing more than combinations of ideas agreeable to the imagination; if we try, on the basis of both Smithian texts and their context and co-text, to reconstruct his lectures on natural theology, all kind of evidence converge in indicating that he reduced proofs of God´s existence to ‘inventions of the imagination’ and argued that philosophical theism is not different in status from primitive belief in invisible beings, or that it is as unwarranted as any system is, and besides that it generates a moral conundrum; he argued also that teleological explanations are no more and no less imaginary than those based on efficient causes, that the teleological order we may imagine in the world is not too bad from a ‘consequentialist’ point of view, and yet it is far below any moral standard; I argued that this is by no means a proof of Smith’s ‘irreligion’ and also that no convincing proof of any turn from religion to irreligion on his part has been provided so far, and finally that the two viable options he left open were either dismal unbelief or Theism on a moral basis. -/- I defend this third way by proving that what Smith’s lost lectures on natural religion said can be reconstruct with some plausibility and what they did not say with absolute certainty; I argue that he developed a sharp criticism of natural theology, that he argued that at the root of religion there are a number of principles of the mind that make religious belief a ‘natural belief’; I do so by reconstructing, first, the context of the missing lectures (sect. 2); then the contents of their first part, considering the proofs of God’s existence and his attributes (sects 3-4); the ‘principles of the mind’ lying at the root of polytheism (sect. 5), of philosophical monotheism (par. 6), and of pure and rational religion (par.7); I contend, then, that his vindication of toleration is consistent with ‘pure and rational religion’ (par. 8) and that attempts to prove a phantom conversion to ‘natural religion’ or ‘irreligion’ result from misreading (par.9). -/- My conclusions are: i) Adam Smith claimed that any natural theology is impossible; ii) There is in fact some kind of order in the world, and it proves useful to a point in allowing for humankind’s survival, but it doesn’t meet any minimal moral criterion; iii) the world is not teleologically ordered; we may indeed imagine such order for mental economy, but the world abounds in misery and depravity; iv) consequences of human wickedness and insanity do, happily enough, deviate from intended outcomes; we may feign invisible mechanisms at work behind, but to mistake them for a hidden mechanism is as childish as the primitive’s belief in ‘invisible beings’. v) there are indeed themes from theological doctrines in Smithian economic theory, but they not the kind of rational theology ‘discovered’ by the ‘New View’; they are instead Augustinian and Jansenist themes. vi) Smith’s theological doctrines did – as suggested by Waterman – have a bearing on his economic theory not by ‘doctrinal dependence’ but – as suggested by Harrison – in the more modest role of source of blueprints for economic explanation. (shrink)

Population obesity and associated morbidities pose significant public health and economic burdens in the United Kingdom, United States, and globally. As a response, public health initiatives often seek to change individuals’ unhealthy behavior, with the dual aims of improving their health and conserving health care resources. One such initiative—taxes on sugar‐sweetened beverages (SSB)—has sparked considerable ethical debate. Prominent in the debate are arguments seeking to demonstrate the supposed impermissibility of SSB taxes and similar policies on the grounds that they interfere (...) with individuals’ freedom and autonomy. Commentators have often assumed that a policy intended to restrict or change private individuals’ consumption behavior will necessarily curtail freedom and, as a corollary, will undermine individuals’ autonomy with respect to their consumption choices. Yet this assumption involves a conceptual mistake. To address the misunderstanding, it’s necessary to attend to the differences between negative liberty, freedom of options, and autonomy. Ultimately, concerns about negative liberty, freedom, and autonomy do not provide strong grounds for opposing SSB taxes. (shrink)

Jeremy Waldron argues that claims to reparation for historic injustices can be superseded by the demands of justice in the present. For example, justified Maori claims to reparation resulting from the wrongful appropriation of their land by European settlers may be superseded by the claim to a just distribution of resources possessed by the world’s existing inhabitants. However, if we distinguish between reparative and restitutive claims, we see that while claims to restitution may be superseded by changes in circumstance, this (...) does not entail that claims to reparation are. In contrast, claims to reparation are robust to changes in circumstance. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

In her recent paper ‘The Epistemology of Propaganda’ Rachel McKinnon discusses what she refers to as ‘TERF propaganda’. We take issue with three points in her paper. The first is her rejection of the claim that ‘TERF’ is a misogynistic slur. The second is the examples she presents as commitments of so-called ‘TERFs’, in order to establish that radical (and gender critical) feminists rely on a flawed ideology. The third is her claim that standpoint epistemology can be used to establish (...) that such feminists are wrong to worry about a threat of male violence in relation to trans women. In Section 1 we argue that ‘TERF’ is not a merely descriptive term; that to the extent that McKinnon offers considerations in support of the claim that ‘TERF’ is not a slur, these considerations fail; and that ‘TERF’ is a slur according to several prominent accounts in the contemporary literature. In Section 2, we argue that McKinnon misrepresents the position of gender critical feminists, and in doing so fails to establish the claim that the ideology behind these positions is flawed. In Section 3 we argue that McKinnon’s criticism of Stanley fails, and one implication of this is that those she characterizes as ‘positively privileged’ cannot rely on the standpoint-relative knowledge of those she characterizes as ‘negatively privileged’. We also emphasize in this section McKinnon’s failure to understand and account for multiple axes of oppression, of which the cis/trans axis is only one. (shrink)

Feminist standpoint theory is a variety of feminist epistemology that has been active since the 1980s. Its two central tenets are (1) that knowledge is necessarily situated within a socio-political context, and (2) that certain socio-political positions or standpoints are epistemically privileged when it comes to “reveal[ing] the truth of social reality” (Hekman 1997). Over the course of its history, standpoint theory has encountered a number of problems which have revealed divisions among its supporters over certain fundamental philosophical commitments. In (...) this paper, I sketch out a phenomenological account of perception that can begin to address these problems, drawn largely from Maurice Merleau-Ponty’s Phenomenology of Perception. There are two major issues that I believe a Merleau-Pontyan view of perception can help alleviate. One is that there has never been a thorough articulation of a theory of perception underlying standpoint theory’s central claims. This is surprising, since arguments in favor of standpoint theory often emphasize that occupying a certain standpoint enables one to see the world differently (see Hartsock 1983, among others). The other problem is the complex tension between standpoint theory’s two central theses. Positing that knowledge is necessarily situated seems to make it difficult to account for one single reality about which some particular group could be epistemically privileged (Hekman 1997). Merleau-Ponty can help us resolve these issues by providing an account of perspectival perception wherein a multiplicity of different perceptual standpoints all nonetheless put us in touch with a single "external" world. Merleau-Ponty’s account also explains how it could be that some standpoints are better than others when it comes to accessing certain features of this world. For Merleau-Ponty, it is not a problem if each perspective is incomplete, partial, or even apparently conflicting with other perspectives. The proliferation of standpoints need not lead us into an unacceptably relativistic framework, as long as we are able to conceive of each of these standpoints as giving whoever occupies it access to some particular aspect of a singular, real, shared world. (shrink)

This paper presents a moral argument in support of the view that the mind is a nonphysical object. It is intuitively obvious that we, the bearers of conscious experiences, have an inherent value that is not reducible to the value of our conscious experiences. It remains intuitively obvious that we have inherent value even when we represent ourselves to have no physical bodies whatsoever. Given certain assumptions about morality and moral intuitions, this implies that the bearers of conscious experiences—the objects (...) possessing inherent value—are not physical objects. This moral evidence is corroborated by introspective evidence. (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

Definitions vary according to context of use and target audience. They must be made relevant for each context to fulfill their cognitive and linguistic goals. This involves adapting their logical structure, type of content, and form to each context of use. We examine from these perspectives the case of definitions in ontologies.

Ex Machina is a 2014 science-fiction film written and directed by Alex Garland, centered around the creation of a human-like artificial intelligence (AI) named Ava. The plot focuses on testing Ava for consciousness by offering a unique reinterpretation of the Turing Test. The film offers an excellent thought experiment demonstrating the consequences of various approaches to a potentially conscious AI. In this paper, I will argue that intelligence testing has significant epistemological shortcomings that necessitate an ethical approach not reliant on (...) ontological commitments. As such, we should be prepared to treat AI as though it is a living being that is deserving of corresponding moral obligations. For a sufficiently human-like AI, such as Ava, I will argue that socio-relational ethics is the best starting point in order to nurture the machine towards ethical proclivities, as evident by the consequences of the characters’ behavior throughout the film. I conclude that intelligence testing is an insufficient determinant of machine ethics, that the project of machine ethics should focus as much on how we treat AI as how AI treats us, and that from a consequentialist perspective it is better to treat machines ethically before they gain consciousness rather than after. (shrink)

Benatar’s central argument for antinatalism develops an asymmetry between the pain and pleasure in a potential life. I am going to present an alternative route to the antinatalist conclusion. I argue that duties require victims and that as a result there is no duty to create the pleasures contained within a prospective life but a duty not to create any of its sufferings. My argument can supplement Benatar’s, but it also enjoys some advantages: it achieves a better fit with our (...) intuitions; it does not require us to acknowledge that life is a harm, or that a world devoid of life is a good thing; and it is easy to see why it does not have any pro-mortalist implications. (shrink)

This paper argues for the value of the ‘strange’ as a hermeneutical tool to open fresh perspectives on an issue of widespread human concern, specifically how to deal with and relate to the dead. Traditional Chinese folk religion and the animistic ghost culture found within it is introduced and the role of gods, ancestors, and ghosts explained. The view that death is not the end of life but the transition to a new relationship with the living raises questions about our (...) potential obligations to the dead. It also has implications for our thinking about intergenerational justice and the role of our memory of the past in shaping our present and future experience. (shrink)

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (shrink)

Might fiction films have cognitive value, and if so, how might such value interact with films’ artistic and aesthetic values? Philosophical consideration of this question tends to consist in either ceteris paribus extensions of claims relating to prose fiction and literature; meta-philosophical inquiries into the capacity of films to be or do philosophy; or generalised investigations into the cognitive value of any, and thereby all, artworks. I first establish that fiction films can be works of art, then address this lacuna (...) and identify three hitherto unrecognised values relevant to the issue of learning from fiction films. These values are (i) a film’s stance-based cinematic value, which is neither an artistic nor an aesthetic value, but which pertains to the integration of a film’s content, its form, and its themes and/or theses; (ii) a film’s dramatic value, which recognises the use of dramatic argumentation to enable us to make sense of agents’ intentional actions; and (iii) a film’s humanistic value which acknowledges a film’s power to provide illuminating insights into the human condition. In tandem with a series of sceptical arguments that question the very notion of cognitive value, I demonstrate how stance-based cinematic value, dramatic value, and humanistic value can provide fresh ways with which to understand and appreciate that we learn from films, what we learn from films, and how we learn from films. Grouping these values together under the rubric of cinematic humanism offers new resources for a paradigm shift capable of staying true to the spirit that informs both sides of the cognitivist/non-cognitivist debate whilst cutting through the Gordian knot it has become. (shrink)

A Cinematic Humanist approach to film is committed inter alia to the following tenet: Some fiction films illuminate the human condition thereby enriching our understanding of ourselves, each other and our world. As such, Cinematic Humanism might reasonably be regarded as an example of what one might call ‘Cinematic Cognitivism’. This assumption would, however, be mistaken. For Cinematic Humanism is an alternative, indeed a corrective, to Cinematic Cognitivism. Motivating the need for such a corrective is a genuine scepticism about the (...) very notion of the cognitive. Using historical reconstruction, I reveal how ‘cognitive’ has become a multiply ambiguous, theory-laden term in the wake of, indeed as a consequence of, Noam Chomsky’s original stipulative definition. This generates a constitutive problem for cognitivism as both a research programme and a set of claims, and as such poses a trilemma for philosophers of film, art and beyond. I propose a Cinematic Humanist solution to the problematic commitments of cognitive film theorising and, in so doing, gesture towards a methodology I am calling ‘philosophy of film without theory’. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

This paper focuses on the process of self-transformation through which a person comes to embody the ideal of her religion’s vision of the divine, as far as that ideal is expressible in a human life. The paper is concerned with the self as the subject of religious commitments, traits, religious aspirations and religiously inspired ideals. The self-transformative journey that people are invited to undertake poses a number of philosophical and practical difficulties; the paper explores some of these difficulties, concentrating on (...) those that arise in connection with the notion of potential future selves. This paper suggests that imaginative reflection upon exemplary individuals provides one way through these difficulties, for these individuals can show us what it looks like when someone achieves, or draws close to, the ideal. (shrink)

This is a revised version of the introductory essay in C. Eschenbach, C. Habel and B. Smith (eds.), Topological Foundations of Cognitive Science, Hamburg: Graduiertenkolleg Kognitionswissenschaft, 1994, the text of a talk delivered at the First International Summer Institute in Cognitive Science in Buffalo in July 1994.

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (shrink)

Ontologies formally represent reality in a way that limits ambiguity and facilitates automated reasoning and data fusion, but is often daunting to the non-technical user. Thus, many researchers have endeavored to hide the formal syntax and semantics of ontologies behind the constructs of Controlled Natural Languages (CNLs), which retain the formal properties of ontologies while simultaneously presenting that information in a comprehensible natural language format. In this paper, we build upon previous work in this field by evaluating prospects of implementing (...) International Technology Alliance Controlled English (ITACE) as a middleware for ontology editing. We also discuss at length a prototype of a natural language conversational interface application designed to facilitate ontology editing via the formulation of CNL constructs. (shrink)

Referent Tracking (RT) advocates the use of instance unique identifiers to refer to the entities comprising the subject matter of patient health records. RT promises many benefits to those who use health record data to improve patient care. To further the adoption of the paradigm we provide an illustration of how data from an EHR application needs to be decomposed in order to make it accord with the tenets of RT. We describe the ontological principles on which this decomposition is (...) based in order to allow integration efforts to be applied in similar ways to other EHR applications. We find that an ordinary statement from an EHR contains a surprising amount of “hidden” data that are only revealed by its decomposition according to these principles. (shrink)

The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical presentation (...) including signs and symptoms. (shrink)

By definition, pain is a sensory and emotional experience that is felt in a particular part of the body. The precise relationship between somatic events at the site where pain is experienced, and central processing giving rise to the mental experience of pain remains the subject of debate, but there is little disagreement in scholarly circles that both aspects of pain are critical to its experience. Recent experimental work, however, suggests a public view that is at odds with this conceptualisation. (...) By demonstrating that the public does not necessarily endorse central tenets of the “mental” view of pain (subjectivity, privacy, and incorrigibility), experimental philosophers have argued that the public holds a more “body-centric” view than most clinicians and scholars. Such a discrepancy would have important implications for how the public interacts with pain science and clinical care. In response, we tested the hypothesis that the public is capable of a more “mind-centric” view of pain. Using a series of vignettes, we demonstrate that in situations which highlight mental aspects of pain the public can, and does, recognize pain as a mental phenomenon. We also demonstrate that the public view is subject to context effects, by showing that the public’s view is modified when situations emphasizing mental and somatic aspects of pain are presented together. (shrink)

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s LinKBase® (...) is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (shrink)

This paper will set out in plain language the basic ontology of “Deleuze’s Spinoza”; it will then critically examine whether such a Spinoza has, or indeed could have, ever truly existed. In this, it will be shown that Deleuze’s reading of Spinoza involves the imposition of three interlocking, formal principles. These are (1) Necessitarianism, (2) Immanence, and (3) Univocity. The uncovering of Deleuze’s use of these three principles, how they relate to one another, and what they jointly imply in terms (...) of ontology, will occupy Part 1 of this paper. The critique of these principles from a Spinozist perspective, i.e. that their use by Deleuze is incompatible with Spinoza’s own metaphysics, will occupy Part 2 of this paper. (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)

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within (...) the ACGT project thus far. (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)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, (...) we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist and (b) (...) they do this in terms of the types and type-level relationships described in these ontologies. While much attention has been devoted to (1), work on (2), which is the topic of this paper, is comparatively rare. Using Referent Tracking as basis, we describe a technical data wrangling strategy which consists in creating for each dataset a template that, when applied to each particular record in the dataset, leads to the generation of a collection of Referent Tracking Tuples (RTT) built out of unique identifiers for the entities described by means of the data items in the record. The proposed strategy is based on (i) the distinction between data and what data are about, and (ii) the explicit descriptions of portions of reality which RTTs provide and which range not only over the particulars described by data items in a dataset, but also over these data items themselves. This last feature allows us to describe particulars that are only implicitly referred to by the dataset; to provide information about correspondences between data items in a dataset; and to assert which data items are unjustifiably or redundantly present in or absent from the dataset. The approach has been tested on a dataset collected from patients seeking treatment for orofacial pain at two German universities and made available for the NIDCR-funded OPMQoL project. (shrink)

Gilles Deleuze was one of the most influential philosophers of the twentieth-century, and Smith is widely recognized to be one of his most penetrating interpreters, as well as an important philosophical voice in his own right. Combining his most important pieces over the last fifteen years along with two new essays, this book is Smith 's definitive treatise on Deleuze. The essays are divided into four sections, which cover Deleuze's use of the history of philosophy, an overview of (...) his philosophical system, an analysis of several Deleuzian concepts, as well as an assessment of his position within contemporary philosophy. (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.

This book explores a question central to philosophy--namely, what does it take for a belief to be justified or rational? According to a widespread view, whether one has justification for believing a proposition is determined by how probable that proposition is, given one's evidence. In this book this view is rejected and replaced with another: in order for one to have justification for believing a proposition, one's evidence must normically support it--roughly, one's evidence must make the falsity of that proposition (...) abnormal in the sense of calling for special, independent explanation. This conception of justification bears upon a range of topics in epistemology and beyond. Ultimately, this way of looking at justification guides us to a new, unfamiliar picture of how we should respond to our evidence and manage our own fallibility. This picture is developed here. (shrink)

Propomos uma tipologia dos artefatos de representação para as áreas de saúde e ciências biológicas, e a associação dessa tipologia com diferentes tipos de ontologia formal e lógica, chegando a conclusões quanto aos pontos fortes e limitações da ontologia de diferentes tipos de recursos lógicos, enquanto mantemos o foco na lógica descritiva. Consideramos quatro tipos de representação de área: (i) representação léxico-semântica, (ii) representação de tipos de entidades, (iii) representação de conhecimento prévio, e (iv) representação de indivíduos. Defendemos uma clara (...) distinção entre os quatro tipos de representação, de forma a oferecer uma base mais racional para o uso das ontologias e artefatos relacionados no avanço da integração de dados e interoperabilidade de sistemas de raciocínio associados. Destacamos que apenas uma pequena porção de fatos cientificamente relevantes em áreas como a biomedicina pode ser adequadamente representada por ontologias formais, quando estas últimas são concebidas como representações de tipos de entidades. Particularmente, a tentativa de codificar conhecimento padrão ou probabilístico pela utilização de ontologias assim concebidas é fadada à produção de modelos não intencionais e errôneos. (shrink)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

In the graphical representation of ontologies, it is customary to use graph theory as the representational background. We claim here that the standard graph-based approach has a number of limitations. We focus here on a problem in the graph-based representation of ontologies in complex domains such as biomedical, engineering and manufacturing: lack of mereotopological representation. Based on such limitation, we proposed a diagrammatic way to represent an entity’s structure and various forms of mereotopological relationships between the entities.

The emphasis on evidence based medicine (EBM) has placed increased focus on finding timely answers to clinical questions in presence of patients. Using a combination of natural language processing for the generation of clinical excerpts and information theoretic distance based clustering, we evaluated multiple approaches for the efficient presentation of context-sensitive EBM excerpts.

In the visual representation of ontologies, in particular of part-whole relationships, it is customary to use graph theory as the representational background. We claim here that the standard graph-based approach has a number of limitations, and we propose instead a new representation of part-whole structures for ontologies, and describe the results of experiments designed to show the effectiveness of this new proposal especially as concerns reduction of visual complexity. The proposal is developed to serve visualization of ontologies conformant to the (...) Basic Formal Ontology. But it can be used also for more general applications, particularly in the biomedical domain. (shrink)

In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular O/T as a (...) standard for data exchange purposes is often seen by the end-user as a function of the number of applications using that vocabulary (and, by extension, the size of the user base). Furthermore, the adoption of an O/T as an interoperability standard requires confidence in its stability and guaranteed continuity as a resource. (shrink)

Electronic health records (EHRs) serve as repositories of documented data collected in a health care encounter. An EHR records information about who receives, who provides the health care and about the place where the encounter happens. We also observe additional elements relating to social relations in which the healthcare consumer is involved. To provide a consensus representation of common data and to enhance interoperability between different EHR repositories we have created a solution grounded in formal ontology. Here, we present how (...) an ontology for the obstetric and neonatal domain deals with these general elements documented in health care encounters. Our goal is to promote the interoperability of information among EHRs created in different specialties. To develop our ontology, we used two main approaches: one based on ontological realism, the other based on the principles of the OBO Foundry, including reuse of reference ontologies. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

In a recent paper in this journal Duncan Pritchard responds to an objection to the modal account of risk pressed by Ebert, Smith and Durbach ( 2020 ). In this paper, I expand upon the objection and argue that it still stands. I go on to consider a more general question raised by this exchange – whether risk is ‘objective’, or whether it is something that varies from one perspective to another.