This paper first argues that we can bring out a tension between the following three popular doctrines: (i) the canonical reduction of metaphysical modality to essence, due to Fine, (ii) contingentism, which says that possibly something could have failed to be something, and (iii) the doctrine that metaphysical modality obeys the modal logic S5. After presenting two such arguments (one from the theorems of S4 and another from the theorems of B), I turn to exploring various conclusions we might draw (...) in light of these results, and argue that none comes cost free. In the course of laying out possible responses to my arguments, we'll have a chance to evaluate various doctrines about the interplay between contingency and essence, as well as develop some alternative reductions of metaphysical modality to essence. I don't decisively come down in favor of one response over the others, though I say some things that point towards the conclusion that essence has no role to play in reducing metaphysical modality. (shrink)

The consensus among spacetime substantivalists is to respond to Leibniz's classic shift arguments, and their contemporary incarnation in the form of the hole argument, by pruning the allegedly problematic metaphysical possibilities that generate these arguments. Some substantivalists do so by directly appealing to a modal doctrine akin to anti-haecceitism. Other substantivalists do so by appealing to an underlying hyperintensional doctrine that implies some such modal doctrine. My first aim in this paper is to pose a challenge for all extant forms (...) of this consensus position. My second aim is to show what form substantivalism must take in order to uphold the consensus while addressing this challenge. The result is a novel "plenitudinous" substantivalist view, which predicts that certain modal facts about spacetime are vague or indeterminate. I then argue against this view on independent grounds, concluding that substantivalists should reject the consensus position. The paper also discusses the way forward for substantivalists in light of this conclusion. (shrink)

Formal criteria of theoretical equivalence are mathematical mappings between specific sorts of mathematical objects, notably including those objects used in mathematical physics. Proponents of formal criteria claim that results involving these criteria have implications that extend beyond pure mathematics. For instance, they claim that formal criteria bear on the project of using our best mathematical physics as a guide to what the world is like, and also have deflationary implications for various debates in the metaphysics of physics. In this paper, (...) I investigate whether there is a defensible view according to which formal criteria have significant non-mathematical implications, of these sorts or any other, reaching a chiefly negative verdict. Along the way, I discuss various foundational issues concerning how we use mathematical objects to describe the world when doing physics, and how this practice should inform metaphysics. I diagnose the prominence of formal criteria as stemming from contentious views on these foundational issues, and endeavor to motivate some alternative views in their stead. (shrink)

The hole argument purports to show that all spacetime theories of a certain form are indeterministic, including the General Theory of Relativity. The argument has given rise to an industry of searching for a metaphysics of spacetime that delivers the right modal implications to rescue determinism. In this paper, I first argue that certain prominent extant replies to the hole argument—namely, those that appeal to an essentialist doctrine about spacetime—fail to deliver the requisite modal implications. As part of my argument, (...) I show that threats to determinism of the sort brought out by the hole argument are more general than has heretofore been recognized. I then use these results to propose a novel essentialist doctrine about spacetime that successfully rescues determinism, what I call sufficiency metric essentialism. However, I go on to argue that once we realize what an essentialist doctrine about spacetime must look like in order to address the hole argument, we should reject all such doctrines, because they can't fulfill their ambition of improving on standard modal replies to the argument. I close by suggesting some lessons for future work on spacetime and the metaphysics of physics more broadly, and also drawing some general morals for contemporary metaphysics, in particular about (i) whether essence can be used to articulate a precise structuralist doctrine, and (ii) the relationship between essence and modality. (shrink)

Environmental ethicists have not reached a consensus about whether or not individuals who contribute to climate change have a moral obligation to reduce their personal greenhouse gas emissions. In this paper, I side with those who think that such individuals do have such an obligation by appealing to the concept of integrity. I argue that adopting a political commitment to work toward a collective solution to climate change—a commitment we all ought to share—requires also adopting a personal commitment to reduce (...) one’s emissions. On these grounds, individuals who contribute to climate change have a prima facie moral duty to lower their personal greenhouse gas emissions. After presenting this argument and supporting each of its premises, I defend it from two major lines of objection: skepticism about integrity’s status as a virtue and concerns that the resulting moral duty would be too demanding to be morally required. I then consider the role that an appeal to integrity could play in galvanizing the American public to take personal and political action regarding climate change. (shrink)

Supererogatory acts, those which are praiseworthy but not obligatory, have become a significant topic in contemporary moral philosophy, primarily because morally supererogatory acts have proven difficult to reconcile with other important aspects of normative ethics. However, despite the similarities between ethics and epistemology, epistemic supererogation has received very little attention. In this paper, I aim to further the discussion of supererogation by arguing for the existence of epistemically supererogatory acts and considering the potential implications of their existence. First, I offer (...) a brief account of moral supererogation and how morally supererogatory acts generate a strong intuition that a similar phenomenon should exist in epistemology. Afterward, I argue for the existence of epistemically supererogatory acts by examining five cases where an epistemic activity appears to be epistemically supererogatory. Epistemic supererogation appears to provide the best explanation for our considered judgments about the individuals’ behavior in these different cases. Finally, I consider how epistemic supererogation might impact the contemporary study of epistemology, particularly with regard to how we appraise certain epistemic duties. (shrink)

Background independence begins life as an informal property that a physical theory might have, often glossed as 'doesn't posit a fixed spacetime background'. Interest in trying to offer a precise account of background independence has been sparked by the pronouncements of several theorists working on quantum gravity that background independence embodies in some sense an essential discovery of the General Theory of Relativity, and a feature we should strive to carry forward to future physical theories. This paper has two goals. (...) The first is to investigate what a world must be like in order to be truly described by a background independent theory given extant accounts of background independence. The second is to argue that there are no non-empirical reasons to be more confident in theories that satisfy extant accounts of background independence than in theories that don't. The paper concludes by drawing a general moral about a way in which focussing primarily on mathematical formulations of our physical theories can adversely affect debates in the metaphysics of physics. (shrink)

This paper will explore an epistemic aspect of hope, namely hope’s relationship to knowledge. It has been taken for granted that people do not hope for things to occur that they know will occur. I will be giving an argument that hope and knowledge are compatible, and I will defend that argument against one primary objection. More specifically, I will argue that there are instances when an agent knows that p and still hopes that p.

This paper addresses the plausibility of practical apatheism: an attitude of apathy or indifference about philosophical questions pertaining to God’s existence grounded in the belief that they lack practical significance. Since apatheism is rarely discussed, we begin by clarifying the position and explaining how it differs from some of the other positions one may take with regard to the existence of God. Afterward, we examine six distinct objections to practical apatheism. Each of these objections posits a different reason for thinking (...) that belief in God is practically significant. Five of these objections prove unsuccessful. The sixth, which appeals to the practical significance of belief in God with respect to our fates in the afterlife, is more promising but nonetheless encounters significant obstacles. Since the success of this objection is controversial, whether we have good grounds to reject practical apatheism should be similarly controversial, and the view should be given further examination. (shrink)

Primary objective: This study represents the first large-scale research on high school philosophy in a public education curriculum in North America. Our objective was to identify the impacts of high school philosophy, as well as the challenges of teaching it in its current format in Ontario high schools. Research design: The qualitative research design captured the perspectives of students and teachers with respect to philosophy at the high school level. All data collection was structured around central questions to provide insight (...) into the dynamics of their shared process of teaching/learning. Methods and procedures: We conducted semi-structured with interviews philosophy teachers (n = 9), classroom observations (n = 142), and student focus groups at 16 diverse high schools. Transcripts were coded according to themes. Results: Our findings reflect the complicated nature of philosophy as a discipline characterized by abstract thinking. Participants found it mind-opening, yet challenging, providing educational opportunities that are largely absent in conventional schooling. They saw multiple connections between philosophy and other subjects, but also appreciated its distinctive benefits. Teachers relied primarily on textbooks and contemporary media to deliver the curriculum. We found that a teacher’s background in philosophy may influence what is taught in philosophy courses and how, especially given the flexibility of the provincial curriculum. Conclusions: The findings suggest that philosophy is a unique, beneficial subject that teachers enjoy teaching and students greatly value, characterizing it as both difficult and rewarding. Our study revealed that considerable differences exist in how philosophy is taught and learned around the province. The flexibility of the provincial curriculum appears to be an invitation for creative and responsive teaching; however, philosophy teachers’ weak preparation can, by their own admission, be a hindrance to effective curriculum delivery. Studying philosophy enhances students’ thinking about other academic areas of study and in some cases opens them up to new ways of thinking. (shrink)

In Animal Ethics in Context, Clare Palmer tries to harmonise two competing approaches to animal ethics. One focuses on the morally relevant capacities that animals possess. The other is the Laissez-Faire Intuition (LFI): the claim that we have duties to assist domesticated animals but should (at least generally) leave wild animals alone. In this paper, I critique the arguments that Palmer offers in favour of the No-Contact LFI - the view that we have (prima facie) duties not to harm wild (...) animals but no duties to assist them. I argue that Palmer's endorsement of the No-Contact LFI is unwarranted. Her arguments actually provide strong reasons to endorse what I call the Gradient View - a position that posits weak presumptive duties to assist wild animals that become stronger as our relations with the animals grow stronger. (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)

Volume 25, Issue 4, December 2019, Page 293-294.

The Asymmetry in procreative ethics consists of two claims. The first is that it is morally wrong to bring into existence a child who will have an abjectly miserable life; the second is that it is permissible not to bring into existence a child who will enjoy a very happy life. In this paper, I distinguish between two variations of the Asymmetry. The first is the Abstract Asymmetry, the idealized variation of the Asymmetry that many philosophers have been trying to (...) solve. The second is the Real-World Asymmetry, a non-idealized variation that applies explicitly to cases of ordinary human reproduction. I argue that the Real-World Asymmetry can be defended by properly acknowledging the general wrongness of causing someone else to suffer, the limits of what morality can reasonably demand of us, and the significance of respecting women’s autonomy. I then argue that the Abstract Asymmetry is indefensible. (shrink)

Bergson identifies multiple forms of memory throughout his work. In Matter and Memory, Bergson considers memory from the perspectives of both psychology and metaphysics, and he describes what we might refer to as contraction memory, perception memory, habit memory, recollection memory, and pure memory. Further, in subsequent works, Bergson discusses at least two additional forms of memory – namely, a memory of the present and a non-intellectual memory of the will. However, it is often not clear how these different forms (...) of memory relate to one another. With the aim of providing an overview of Bergson's philosophy of memory that can also serve as a point of entry to his philosophy as a whole, this article explores the different senses and forms of memory that Bergson describes, paying special attention to how they are distinct from one another and how they are unified. It is my intention to show that, although these various senses and forms of memory are different from one another , they are also continuous and unified insofar as they are equivalent to different tones of one's mental life and to different tensions of one duration. (shrink)

Although better known for his phenomenology of perception and the perceived world, Merleau-Ponty’s writings also contain the outlines of a rich and unique account of the imagination and the imaginary. In this paper, I explicate the phenomenology of the image that Merleau-Ponty develops throughout his work. I show how Merleau-Ponty develops this account of the image in critical response to Sartre and in a way that follows from his own descriptions of what painters do when they paint and of what (...) we experience when we look at their paintings. The investigation of the particular mode of being of images leads to a consideration of the body and Merleau-Ponty’s later ontology. (shrink)

Editorial for issue with articles on tranhumanism, principlism, total body transplants and inter-uterine surgery for myelomeningocele.

Volume 25, Issue 2, June 2019, Page 101-102.

Volume 25, Issue 1, March 2019, Page 1-2.

In 2017, The New Bioethics published its first special-themed issue on the topic of personalized medicine. It proved highly popular, especially Gyawali and Sullivan’s paper ‘Economics of Can...

‘There is a tide in the affairs of men.Which, taken at the flood, leads on to fortune;’Those who edit academic journals rarely seek fortune in finan...

The central aim of this paper is to use a particular view about how the laws of nature govern the evolution of our universe in order to develop and evaluate the two main competing options in the metaphysics of persistence, namely endurantism and perdurantism. We begin by motivating the view that our laws of nature dictate not only qualitative facts about the future, but also which objects will instantiate which qualitative properties. We then show that both traditional doctrines in the (...) metaphysics of persistence must take on surprising further commitments in order to vindicate our universe being law-governed in this strong sense. For example, we argue that endurantists should adopt a particular version of monism, and that perdurantists should adopt a qualitativist doctrine that dispenses with all individuals at the fundamental level. (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)

Editorial on papers relating to among other infanticide and intersex.

A review of the range of articles in the summer issue of The New Bioethics.

Counterfactuals are context-sensitive. However, we argue that various debates and doctrines in metaphysics and the philosophy of science are premised on ignoring the full extent of counterfactual context-sensitivity. Our focus is on the prominent "miracle" versus "no-miracle" debate about counterfactuals under the assumption that our laws of nature are deterministic. But we also discuss doctrines that employ counterfactuals in theories of rational decision, as well as doctrines that explain what it is to be a law of nature in terms of (...) counterfactuals. We conclude by drawing some morals about the use of counterfactuals in philosophical theorizing more generally. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (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)

Most of our best scientific descriptions of the world employ rates of change of some continuous quantity with respect to some other continuous quantity. For instance, in classical physics we arrive at a particle’s velocity by taking the time-derivative of its position, and we arrive at a particle’s acceleration by taking the time-derivative of its velocity. Because rates of change are defined in terms of other continuous quantities, most think that facts about some rate of change obtain in virtue of (...) facts about those other continuous quantities. For example, on this view facts about a particle’s velocity at a time obtain in virtue of facts about how that particle’s position is changing at that time. In this paper we raise a puzzle for this orthodox reductionist account of rate of change quantities and evaluate some possible replies. We don’t decisively come down in favour of one reply over the others, though we say some things to support taking our puzzle to cast doubt on the standard view that spacetime is continuous. (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)

Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied (...) to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters. (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.

Discussion of moral responsibility has traditionally centred around actions and the possibility of alternative actions. In this short paper I take a different approach and focus on choices rather than actions. I argue that a person is morally responsible directly for their choices and only indirectly for resulting actions. This subtle shift helps to clarify many issues such as moral luck, thwarted choice and coercion.

In this essay I try to link Derek Hook’s interpretation of Žižek’s reading of Lacan of racial resentment as a kind of jouissance or enjoyment to what Christian Fuchs terms an ideology of hate. In my view, slurs are instances of subordinating speech partially to dehumanize targets but primarily function to signal and deploy ideology. The enjoyment racists derive from using a slurring term from a key feature of the offensiveness of a slurring term. My objective is two-fold. I intend (...) to (1) outline and argue for the enjoyment account of subordinating speech as an improvement upon prohibitionist accounts of slurring terms offensive content and (2) illustrate how slurs function in a libidinal system to reproduce and reinforce ideology. An enjoyment account of subordinating speech depends upon an interpretation of Lacanian concept of jouissance and symptom, supplemented by Hook’s libidinal object. (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)

An orthodox view in marketing ethics is that it is morally impermissible to market goods to specially vulnerable populations in ways that take advantage of their vulnerabilities. In his signature article “Marketing and the Vulnerable,” Brenkert (Bus Ethics Q Ruffin Ser 1:7–20, 1998) provided the first substantive defense of this position, one which has become a well-established view in marketing ethics. In what follows, we throw new light on marketing to the vulnerable by critically evaluating key components of Brenkert’s general (...) arguments. Specifically, we contend that Brenkert has failed to offer us any persuasive reasons to think that it is immoral to market to the vulnerable in ways that take advantage of their vulnerability. Although Brenkert does highlight the fact that the specially vulnerable are at greater risk of being harmed by already immoral marketing practices (e.g., deception, manipulation), he fails to establish that the specially vulnerable are a unique moral category of market clients or that there are special moral standards that apply to them. Moreover, even if Brenkert’s position were theoretically defensible, the practical implications of his position are far less tenable than he suggests. If our criticisms are sound, then Brenkert and others who endorse his position are seriously mistaken regarding how one can permissibly market products to vulnerable populations, and, in addition, they have improperly categorized certain morally permissible marketing practices as being immoral. (shrink)

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)

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)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of (...) making computers understand medical natural language. (shrink)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

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)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

The 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)