In classically based modal logic, there are three common conceptions of necessity, the universal conception, the equivalence relation conception, and the axiomatic conception. They provide distinct presentations of the modal logic S5, all of which coincide in the basic modal language. We explore these different conceptions in the context of the relevant logic R, demonstrating where they come apart. This reveals that there are many options for being an S5-ish extension of R. It further reveals a divide between the universal (...) conception of necessity on the one hand, and the axiomatic conception on the other: The latter is consistent with motivations for relevant logics while the former is not. For the committed relevant logician, necessity cannot be the truth in all possible worlds. (shrink)

Few debates in environmental philosophy have been more heated than the one over the nature of wilderness. And yet, when one surveys the present scene, one finds that a variety of different conceptions of wilderness are still quite popular – some more so in certain professions than others. In this paper, I look at three popular conceptions of wilderness with an eye toward sussing out the good and the bad them. I look at what I call (1) the folk view (...) of wilderness, (2) Leopold’s conception of wilderness, and (3) the legal conception of wilderness (as found in the Wilderness Act of 1964). In the final part of the paper, I sketch out a sort of spectrum account of wilderness, one that I argue allows us to capture more cases of wilderness and might serve as a useful tool in future conservation efforts. (shrink)

Environmental philosophy plays an important role, directly and indirectly, in many parts of society, including land and wildlife management (Leopold, 1949; Minteer, 2015), political activism (Abbey, 1968; Malm, 2020),and technological research and development (Baum & Owe, 2022; Donhauser et al., 2021). Environmental philosophy uncovers the ethical relationships existing between humans and the living and non-living world. It reveals the nuances of our scientific ecological concepts. And it tries to tell us how we might act – individually or collectively – to (...) better achieve our environmental goals. The aim of this special issue is to explore the limits and ever-expanding outer edges of this increasingly important area of philosophical thought. (shrink)

There appears to be few, if any, limits on what sorts of logical connectives can be added to a given logic. One source of potential limitations is the motivating ideology associated with a logic. While extraneous to the logic, the motivating ideology is often important for the development of formal and philosophical work on that logic, as is the case with intuitionistic logic. One family of logics for which the philosophical ideology is important is the family of relevant logics. In (...) this paper, I explore the limits of what a relevant connective is, showing how some basic criteria motivated by the ideology of relevant logicians provide robust limits on potential connectives. These criteria provide some plausible necessary conditions on being a relevant connective. (shrink)

In this article, we present a definition of a hyperintensionality appropriate to relevant logics. We then show that relevant logics are hyperintensional in this sense, drawing consequences for other non-classical logics, including HYPE and some substructural logics. We further prove results concerning extensionality in relevant logics. We close by discussing related concepts for classifying formula contexts and potential applications of these results.

In this paper, I motivate the addition of an actuality operator to relevant logics. Straightforward ways of doing this are in tension with standard motivations for relevant logics, but I show how to add the operator in a way that permits one to maintain the intuitions behind relevant logics. I close by exploring some of the philosophical consequences of the addition.

The operational semantics of Urquhart is a deep and important part of the development of relevant logics. In this paper, I present an overview of work on Urquhart’s operational semantics. I then present the basics of collection frames. Finally, I show how one kind of collection frame, namely, functional set frames, is equivalent to Urquhart’s semilattice semantics.

Various theorists have endorsed the “communication argument”: communicative capacities are necessary for morally responsible agency because blame aims at a distinctive kind of moral communication. I contend that existing versions of the argument, including those defended by Gary Watson and Coleen Macnamara, face a pluralist challenge: they do not seem to sit well with the plausible view that blame has multiple aims. I then examine three possible rejoinders to the challenge, suggesting that a context-specific, function-based approach constitutes the most promising (...) modification of the communication argument. (shrink)

Relevant logics are a family of non-classical logics characterized by the behavior of their implication connectives. Unlike some other non-classical logics, such as intuitionistic logic, there are multiple philosophical views motivating relevant logics. Further, different views seem to motivate different logics. In this article, we survey five major views motivating the adoption of relevant logics: Use Criterion, sufficiency, meaning containment, theory construction, and truthmaking. We highlight the philosophical differences as well as the different logics they support. We end with some (...) questions for future research. (shrink)

It is widely agreed that reactive attitudes play a central role in our practices concerned with holding people responsible. However, it remains controversial which emotional attitudes count as reactive attitudes such that they are eligible for this central role. Specifically, though theorists near universally agree that guilt is a reactive attitude, they are much more hesitant on whether to also include shame. This paper presents novel arguments for the view that shame is a reactive attitude. The arguments also support the (...) view that shame is a reactive attitude in the sense that concerns moral accountability. The discussion thereby challenges both the view that shame is not a reactive attitude at all, suggested by philosophers such as R. Jay Wallace and Stephen Darwall, and the view that shame is a reactive attitude but does not concern moral accountability, recently defended by Andreas Carlsson and Douglas Portmore. (shrink)

An important question for proponents of non-contractive approaches to paradox is why contraction fails. Zardini offers an answer, namely that paradoxical sentences exhibit a kind of instability. I elaborate this idea using revision theory, and I argue that while instability does motivate failures of contraction, it equally motivates failure of many principles that non-contractive theorists want to maintain.

An explicit formal-ontological representation of entities existing at multiple levels of granularity is an urgent requirement for biomedical information processing. We discuss some fundamental principles which can form a basis for such a representation. We also comment on some of the implicit treatments of granularity in currently available ontologies and terminologies (GO, FMA, SNOMED CT).

We present a new frame semantics for positive relevant and substructural propositional logics. This frame semantics is both a generalisation of Routley–Meyer ternary frames and a simplification of them. The key innovation of this semantics is the use of a single accessibility relation to relate collections of points to points. Different logics are modeled by varying the kinds of collections used: they can be sets, multisets, lists or trees. We show that collection frames on trees are sound and complete for (...) the basic positive distributive substructural logic $\mathsf {B}^+$, that collection frames on multisets are sound and complete for $\mathsf {RW}^+$ (the relevant logic $\mathsf {R}^+$, without contraction, or equivalently, positive multiplicative and additive linear logic with distribution for the additive connectives), and that collection frames on sets are sound for the positive relevant logic $\mathsf {R}^+$. The completeness of set frames for $\mathsf {R}^+$ is, currently, an open question. (shrink)

In Saving Truth from Paradox, Hartry Field presents and defends a theory of truth with a new conditional. In this paper, I present two criticisms of this theory, one concerning its assessments of validity and one concerning its treatment of truth-preservation claims. One way of adjusting the theory adequately responds to the truth-preservation criticism, at the cost of making the validity criticism worse. I show that in a restricted setting, Field has a way to respond to the validity criticism. I (...) close with some general considerations on the use of revision-theoretic methods in theories of truth. (shrink)

This article examines how facial recognition technology reshapes the philosophical debate over the ethics of video surveillance. When video surveillance is augmented with facial recognition, the data collected is no longer anonymous, and the data can be aggregated to produce detailed psychological profiles. I argue that – as this non-anonymous data of people’s mundane activities is collected – unjust risks of harm are imposed upon individuals. In addition, this technology can be used to catalogue all who publicly participate in political, (...) religious, and socially stigmatised activities, and I argue that this would undermine central interests of liberal democracies. I examine the degree to which the interests of individuals and the societal interests of liberal democracies to maintain people’s obscurity while in public coincide with privacy interests, as popularly understood, and conclude that there is a practical need to articulate a novel right to obscurity to protect the interests of liberal democratic societies. (shrink)

The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to an example drawn from the (...) context of the pathophysiology of hypertension. This exercise is designed to demonstrate how, by taking ontological principles into account we can create more realistic biomedical ontologies which will also bring advantages in terms of efficiency and robustness of associated software applications. (shrink)

A common refrain in and outside academia is that prominent sports figures ought to engage more in the public discourse about political issues. This idea parallels the idea that athletes ought to be role models in general. This paper first examines and critiques the “athlete as role model” argument and then applies this critique to the “athlete as political activist” argument. Appealing to the empirical political psychological literature, the paper sketches an argument that athlete activism might actually do more harm (...) than good. (shrink)

In this paper, I examine the ethics of nonviolent protest when a violent response is either foreseen or intended. One central concern is whether protesters, who foresee a violent response but persist, are provoking the violence and whether they are culpable for any eventual harms. A second concern is whether it is permissible to publicize the violent response for political advantage. I begin by distinguishing between two senses of the term provoke: a normative sense where a provocateur knowingly imposes an (...) unjustified risk of a violent response, and a descriptive sense where the respondent feels provoked. I argue that, when the risk of a violent response is justified, the protesters are not provocateurs but akin to nonculpable, entrapping agents who create an opportunity for the regime to respond with disproportionate violence. The regime’s response can disclose its brutality or criminality and this can be fairly publicized for political advantage. When nonviolent protesters create an unjustified risk of violence either because the injustice they oppose is insufficient to justify the risk of a violent response or because the risked harms are disproportionate with the likely political advantages derived from the protest, they are partially culpable provocateurs. However, I argue these partially culpable provocateurs can still permissibly publicize the disproportionate violence of the regime so as to shape public opinion. (shrink)

When asked which of our concepts are normative concepts, metaethicists would be quick to list such concepts as GOOD, OUGHT, and REASON. When asked why such concepts belong on the list, metaethicists would be much slower to respond. Matti Eklund is a notable exception. In his recent book, Choosing Normative Concepts, Eklund argues by elimination for “the Normative Role view” that normative concepts are normative in virtue of having a “normative role” or being “used normatively”. One view that Eklund aims (...) to eliminate is “the Metaphysical view” that normative concepts are normative in virtue of referring to normative properties. In addition to arguing that Eklund’s objection looks doubtful by its own lights, we argue that there are several plausible versions of the Metaphysical view that Eklund doesn’t eliminate, defending various claims about normative concepts and their relationships to deliberation, competence, reference, and possession along the way. (shrink)

In this article, I analyze how the Harry Potter novels bring to awareness two fundamental aspects of the human condition: the importance of one’s choices and the inevitability of one’s mortality. These are highlighted through the contrast of the characters of Harry Potter and Lord Voldemort.

The theory of granular partitions (TGP) is a new approach to the understanding of ontologies and other classificatory systems. The paper explores the use of this new theory in the treatment of task-based clinical guidelines as a means for better understanding the relations between different clinical tasks, both within the framework of a single guideline and between related guidelines. We used as our starting point a DAML+OIL-based ontology for the WHO guideline for hypertension management, comparing this with related guidelines and (...) attempting to show that TGP provides a flexible and highly expressive basis for the manipulation of ontologies of a sort which might be useful in providing more adequate Computer Interpretable Guideline Models (CIGMs) in the future. (shrink)

Can reasoning improve moral judgments and lead to moral progress? Pessimistic answers to this question are often based on caricatures of reasoning, weak scientific evidence, and flawed interpretations of solid evidence. In support of optimism, we discuss three forms of moral reasoning (principle reasoning, consistency reasoning, and social proof) that can spur progressive changes in attitudes and behavior on a variety of issues, such as charitable giving, gay rights, and meat consumption. We conclude that moral reasoning, particularly when embedded in (...) social networks with mutual trust and respect, is integral to moral progress. (shrink)

Arguments attempting to debunk moral beliefs, by showing they are unjustified, have tended to be global, targeting all moral beliefs or a large set of them. Popular debunking arguments point to various factors purportedly influencing moral beliefs, from evolutionary pressures, to automatic and emotionally-driven processes, to framing effects. We show that these sweeping arguments face a debunker’s dilemma: either the relevant factor is not a main basis for belief or it does not render the relevant beliefs unjustified. Empirical debunking arguments (...) in ethics can avoid this predicament, but only if they are refocused on highly selective classes of moral belief. Experimental data can combine with familiar consistency reasoning to reveal that like cases are not being treated alike. Selective debunking arguments are unlikely to yield sweeping sceptical conclusions, but they can lead to rational moral change. (shrink)

The present investigation was undertaken to investigate the acute toxicity of cadmium, a heavy metal widely detected in the aquatic environment due to natural effects and anthropogenic activities, in freshwater teleost, Channa punctata (Bloch). The experiments for the bioassay were performed in semi-static test condition according to the standard guidelines. The behavioural changes in the fish were observed for all tested concentrations of the metal. The data obtained for bioassay were analyzed for median lethal concentrations (LC ) of the metal (...) by SPSS computer software. The LC 50 50 values, estimated by SPSS, with 95% confidence level were found to be:20.589 (18.326-23.221), 17.133 (14.840- 19.734), 11.815 (9.696 – 13.850) mg/L and 9.908 (7.635-12381) mg/L for cadmium chloride at 24, 48, 72 and 96 h exposure, respectively. (shrink)

We argue that distinct conditionals—conditionals that are governed by different logics—are needed to formalize the rules of Truth Introduction and Truth Elimination. We show that revision theory, when enriched with the new conditionals, yields an attractive theory of truth. We go on to compare this theory with one recently proposed by Hartry Field.

that can serve as a foundation for more refined ontologies in the field of proteomics. Standard data sources classify proteins in terms of just one or two specific aspects. Thus SCOP (Structural Classification of Proteins) is described as classifying proteins on the basis of structural features; SWISSPROT annotates proteins on the basis of their structure and of parameters like post-translational modifications. Such data sources are connected to each other by pairwise term-to-term mappings. However, there are obstacles which stand in the (...) way of combining them together to form a robust meta-classification of the needed sort. We discuss some formal ontological principles which should be taken into account within the existing datasources in order to make such a metaclassification possible, taking into account also the Gene Ontology (GO) and its application to the annotation of proteins. (shrink)

We provide a methodology for the creation of ontological partitions in biomedicine and we test the methodology via an application to the phenomenon of blood pressure. An ontology of blood pressure must do justice to the complex networks of intersecting pathways in the organism by which blood pressure is regulated. To this end it must deal not only with the anatomical structures and physiological processes involved in such regulation but also with the relations between these at different levels of granularity. (...) For this purpose our ontology offers a variety of distinct partitions � of substances, processes and functions � and integrates these together within a single framework via transitive networks of part-whole and dependence relations among the entities in each of these categories. The paper concludes with a comparison of this methodology with the approaches of GOTM, KEGG, DIP and BIND and provides an outline of how the methodology is currently being applied in the field of biomedical database integration. (shrink)

The International Classification of Functioning, Disability and Health provides a classification of human bodily functions, which, while exhibiting non-conformance to many formal ontological principles, provides an insight into which basic functions such a classification should include. Its evaluation is an important first step towards such an adequate ontology of this domain. Presented at the 13th Annual North American WHO Collaborating Center Conference on the ICF, 2007.

There are a number of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications represent classes of entities which exist at various anatomical levels of granularity. We argue that in order to apply such representations to the Electronic Health Records one needs sound ontologies which take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal theory for addressing these issues in a (...) way that the ontologies can be used to support inferences relating to entities which exist at different anatomical levels of granularity. Our case study is the colon carcinoma, one of the most common carcinomas prevalent within the European population. (shrink)

An important part of the Unified Medical Language System (UMLS) is its Semantic Network, consisting of 134 Semantic Types connected to each other by edges formed by one or more of 54 distinct Relation Types. This Network is however for many purposes overcomplex, and various groups have thus made attempts at simplification. Here we take this work further by simplifying the relations which involve the three Semantic Types – Diagnostic Procedure, Laboratory Procedure and Therapeutic or Preventive Procedure. We define operators (...) which can be used to generate terms instantiating types from this selected set when applied to terms designating certain other Semantic Types, including almost all the terms specifying clinical tasks. Usage of such operators thus provides a useful and economical way of specifying clinical tasks. The operators allow us to define a mapping between those types within the UMLS which do not represent clinical tasks and those which do. This mapping then provides a basis for an ontology of clinical tasks that can be used in the formulation of computer-interpretable clinical guideline models. (shrink)

Outcomes research in healthcare has been a topic much addressed in recent years. Efforts in this direction have been supplemented by work in the areas of guidelines for clinical practice and computer-interpretable workflow and careflow models.In what follows we present the outlines of a framework for understanding the relations between organizations, guidelines, individual patients and patient-related functions. The derived framework provides a means to extract the knowledge contained in the guideline text at different granularities, in ways that can help us (...) to assign tasks within the healthcare organization and to assess clinical performance in realizing the guideline. It does this in a way that preserves the flexibility of the organization in the adoption of the guidelines. (shrink)

In one of his earliest dialogues, the Soliloquia, Augustine identifies the liberal arts (disciplinae) with truth (veritas), and employs this somewhat puzzling identification as a premise in his infamous proof of the immortality of the soul (Sol. 2.24). In this paper, I examine Augustine’s argument for this peculiar identification. Augustine maintains both (1) that the constituent propositions of the liberal arts are true, and (2) that the liberal art of dialectic (disciplina disputandi) is the “truth through which all disciplines are (...) true” (Sol. 2.21). I argue that Augustine identifies the liberal arts with truth because (1) the constituent propositions of the liberal arts are learned, and (2) dialectic’s structure is essential to the liberal arts. I further suggest that the subject matter of each liberal art reflects a distinct segment of intelligible reality, that is, the realm of the intelligible Forms. (shrink)

The Internet of Things (IoT) wireless LAN in healthcare has moved away from traditional methods that include hospital visits and continuous monitoring. The Internet of Things allows the use of certain means, including the detection, processing and transmission of physical and biomedical parameters. With powerful algorithms and intelligent systems, it will be available to provide unprecedented levels of critical data for real-time life that are collected and analyzed to guide people in research, management and emergency care. This chapter provides a (...) quick overview of IoT features and how they relate to wireless discovery and technology to deploy the medical applications you need. In the world, the revolution in any industry is to connect your products and devices to the Internet and make them independent and remotely connected, so that anyone can use and view them from anywhere and anytime. The Internet of Things provides us with a home automation system that uses smart devices to overcome this obstacle, allowing us to easily manage our appliances. A smart city is a vision to integrate a variety of information and communication solutions for residents with essential services, such as smart parking on all streets. The main motivation for using the Internet for parking objects is simply collecting data to get free parking. The IoT-based RTSSPS architecture is divided into three parts: a WSN-based smart street parking module, an IoT-based smart street parking module, and an IoT-based smart street parking module. IoT-based cloud with street parking algorithm, rating and future directions. (shrink)

A Better Ape covers the evolution of morality from the birth of our ape family through the evolution of human species and all the way up to the development of modern societies. In this summary, we highlight several main elements of this account: the co-evolution of morality with intelligence and complex sociality; the role of social institutions and religious morality in the cultural evolution of behaviorally modern humans in prehistory; the increasing complexity of the moral mind through biological evolution in (...) apes, gene-culture co-evolution in various human species, cultural evolution in Homo sapiens, and rational-cultural evolution in recent centuries; and, finally, a cultural evolutionary model of progressive and regressive moral change on which a key factor driving moral progress is social and democratic integration. (shrink)

How can we make moral progress on factory farming? Part of the answer lies in human moral psychology. Meat consumption remains high, despite increased awareness of its negative impact on animal welfare. Weakness of will is part of the explanation: acceptance of the ethical arguments doesn’t always motivate changes in dietary habits. However, we draw on scientific evidence to argue that many consumers aren’t fully convinced that they morally ought to reduce their meat consumption. We then identify two key psychological (...) mechanisms—motivated reasoning and social proof—that lead people to resist the ethical reasons. Finally, we show how to harness these psychological mechanisms to encourage reductions in meat consumption. A central lesson for moral progress generally is that durable social change requires socially-embedded reasoning. (shrink)

This chapter discusses contemporary scientific research on the role of reason and emotion in moral judgment. The literature suggests that moral judgment is influenced by both reasoning and emotion separately, but there is also emerging evidence of the interaction between the two. While there are clear implications for the rationalism-sentimentalism debate, we conclude that important questions remain open about how central emotion is to moral judgment. We also suggest ways in which moral philosophy is not only guided by empirical research (...) but continues to guide it. (shrink)

This paper has two aims. First, it sets out an interpretation of the relevant logic E of relevant entailment based on the theory of situated inference. Second, it uses this interpretation, together with Anderson and Belnap’s natural deduc- tion system for E, to generalise E to a range of other systems of strict relevant implication. Routley–Meyer ternary relation semantics for these systems are produced and completeness theorems are proven. -/- .

The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of (...) entities which are fundamental to an ontology of colon carcinoma. We here describe the problems we uncovered concerning classification, synonymy, relations and definitions, and we draw conclusions for the work needed to establish the NCIT as a reference ontology for the cancer domain in the future. (shrink)

Quality assurance in large terminologies is a difficult issue. We present two algorithms that can help terminology developers and users to identify potential mistakes. We demon­strate the methodology by outlining the different types of mistakes that are found when the algorithms are applied to SNOMED-CT. On the basis of the results, we argue that both formal logical and linguistic tools should be used in the development and quality-assurance process of large terminologies.

1. Over the last 50 years or so, and especially over the last few decades, the U.S. and many other societies have undergone a large, rapid, and broad decline in anti-gay attitudes. The magnitude, s...

Formalisms such as description logics (DL) are sometimes expected to help terminologies ensure compliance with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) complies with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of SNOMED CT classes with respect to these principles. Our major results are: 31% of (...) the classes have a single child; 27% have multiple parents; 51% do not exhibit any differentiae between the description of the parent and that of the child. The applications of this study to quality assurance for ontologies are discussed and suggestions are made for dealing with multiple inheritance. (shrink)

In this paper current author proposes a need for studying intricate differences between psychological aspects, factors, cognitions, affect, behaviour and related dynamics. It can be promoted as a separate branch within the domain of Psychology as Intricacy Psychology. Case history taking for the new Intervention Meditation of current author is proposed in line with capturing such intricacies of the client. The current also proposes to study the intricacies belonging to ‘Self’ as an important factor within his new Intervention Meditation approach. (...) View of Self in line with current author’s new Intervention Meditation is also outlined. This paper is at the initial stage of the series of papers planned to develop his new Intervention Meditation approach which is entirely different from all other meditations in vogue. (shrink)

This paper defends “Animal Universalism,” the thesis that all sentient non-human animals will be brought into Heaven and remain there for eternity. It assumes that God exists and is all-powerful, perfectly loving, and perfectly just. From these background theses, the authors argue that Animal Universalism follows. If God is perfectly loving, then God is concerned about the well-being of non-human animals, and God chooses to maximize the well-being of each individual animal when doing so does not harm other individual creatures (...) or violate creaturely freedom. If God is perfectly just, then God does not arbitrarily discriminate against non-human animals by offering humans an opportunity to enter Heaven but not offering the same to each animal. Each of these conclusions implies Animal Universalism. (shrink)

One of the disadvantages of the point estimate in survey sampling is that it fluctuates from sample to sample due to sampling error, as the estimator only provides a point value for the parameter under discussion. The neutrosophic approach, pioneered by Florentin Smarandache, is an excellent tool for estimating the parameters under consideration in sampling theory since it yields interval estimates in which the parameter lies with a very high probability. As a result, the neutrosophic technique, which is a generalization (...) of classical approach, is used to deal with ambiguous, indeterminate, and uncertain data. In this investigation, we suggest a new general family of ratio and exponential ratio type estimators for the elevated estimation of neutrosophic population mean of the primary variable utilizing known neutrosophic auxiliary parameters. For the first degree approximation, the bias and Mean Squared Error (MSE) of the suggested estimators are computed. The neutrosophic optimum values of the characterizing constants are determined, as well as the minimum value of the neutrosophic MSE of the suggested estimator is obtained for these optimum values of the characterizing scalars. Because the minimum MSE of the classical estimators of population mean lies inside the estimated interval of the neutrosophic estimators, the neutrosophic estimators are better than the equivalent classical estimators. The empirical investigation, which used both real and simulated data sets, backs up the theoretical findings. For practical utility in various areas of applications, the estimator with the lowest MSE or highest Percentage Relative Efficiency (PRE) is recommended. (shrink)

Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of of effort has been invested in the development of various tools which automate the representation and execution of the recommendations contained within such guidelines and protocols by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based on standard terminology systems like UMLS, form one of the core components of such a model. We have created DAML+OIL-based CTOs for the tasks mentioned in the (...) WHO guideline for hypertension management, drawing comparisons also with other related guidelines. The advantages of CTOs include: contextualization of ontologies, providing ontologies tailored to specific aspects of the phenomena of interest, dividing the complexity involved in creating ontologies into different levels, providing a methodology by means of which the task recommendations contained within guidelines can be integrated into the clinical practices of a health care set-up. (shrink)

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies (...) in anatomy, physiology and pathology. (shrink)

The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We use statistical methods and (...) formal ontological principles as a first step towards finding answers to this question. (shrink)

Recent work on the quality assurance of the Gene Ontology (GO, Gene Ontology Consortium 2004) from the perspective of both linguistic and ontological organization has made it clear that GO lacks the kind of formalism needed to support logic-based reasoning. At the same time it is no less clear that GO has proven itself to be an excellent terminological resource that can serve to combine together a variety of biomedical database and information systems. Given the strengths of GO, it is (...) worth investigating whether, by overcoming some of its weaknesses from the point of view of formal-ontological principles, we might not be able to enhance a version of GO which can come even closer to serving the needs of the various communities of biomedical researchers and practitioners. It is accepted that clinical and bioinformatics need to find common ground if the results of data-intensive biomedical research are to be harvested to the full. It is also widely accepted that no single method will be sufficient to create the needed common framework. We believe that the principles-based approach to life-science data integration and knowledge representation must be one of the methods applied. Indeed in dealing with the ontological representation of carcinomas, and specifically of colon carcinomas, we have established that, had GO (and related biomedical ontologies) followed some of the basic formal-ontological principles we have identified (Smith et al. 2004, Ceusters et al. 2004), then the effort required to navigate successfully between clinical and bioinformatics systems would have been reduced. We point here to the sources of ontologically-related errors in GO, and also provide arguments as to why and how such errors need to be resolved. (shrink)

It is widely understood that protein functions can be exhaustively described in terms of no single parameter, whether this be amino acid sequence or the three-dimensional structure of the underlying protein molecule. This means that a number of different attributes must be used to create an ontology of protein functions. Certainly much of the required information is already stored in databases such as Swiss-Prot, Protein Data Bank, SCOP and MIPS. But the latter have been developed for different purposes and the (...) separate data-structures which they employ are not conducive to the needed data integration. When we attempt to classify the entities in the domain of proteins, we find ourselves faced with a number of cross-cutting principles of classification. Our question here is: how can we bring together these separate taxonomies in order to describe protein functions? Our proposed answer is: via a careful top-level ontological analysis of the relevant principles of classification, combined with a new framework for the simultaneous manipulation of classifications constructed for different purposes. (shrink)