The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of data. To provide effective solutions computers need to integrate data deriving from myriad heterogeneous sources by bringing the data together within a single framework. The meeting brought together leaders in the field of what are called "top-level ontologies" to address this issue, and to establish strategies among leaders in (...) the field of biomedical ontology for the creation of interoperable biomedical ontologies which will serve the goal of useful data integration. (shrink)

In 2005, IOS Press published the first issue of applied Ontology. At the time, we argued that, at the core of the journal, there was “a desire to understand the nature of reality and how people construe their world”. We declared that ontology was both “fundamental to human thought” and “to translating our thoughts into computational artifacts” (Guarino & Musen,2005). With an editorial board of distinguished scholars representing the fields of computer science, informatics, information science, philosophy, linguistics, psychology, and (...) social science, we had the firm belief that applied Ontologywould fulfill an important academic niche, becoming an essential forum for discussion on topics such as ontological analysis, conceptual modeling, and the role of domain models in building and managing information systems. The facts now show that we were correct. (shrink)

In a world that is overflowing with journals and other outlets for scientific publication, the appearance of any new periodical requires some justification. There are already more journals than we can read and more conferences than we can attend. In the case of applied Ontology, we believe that the creation of anew journal not only is completely justifiable, it is downright exciting. For too long, workers in computer science have assumed that content comes for free. “Theory” in computer science has (...) always meant the theory of processes and of computation. We measure the complexity of computer programs in terms of how long it takes machines to execute them, not in terms of how long it takes people to understand and to represent the data on which those programs might operate. We typically describe computer code in terms of algorithms that operate on formal parameters, often without pausing to discuss where the data that might satisfy those parameters come from. This journal was founded on the premise that workers in computer science, informatics, and information science are overdue in paying as much attention to contents as they do to algorithms. (shrink)

Each annual Ontology Summit initiative makes a statement appropriate to each Summit’s theme as part of our general advocacy designed to bring ontology science and engineering into the mainstream. The theme this year is "Towards an Open Ontology Repository". This communiqué represents the joint position of those who were engaged in the year's summit discourse on an Open Ontology Repository (OOR) and of those who endorse below. In this discussion, we have agreed that an "ontology repository is a facility where (...) ontologies and related information artifacts can be stored, retrieved and managed." -/- We believe in the promise of semantic technologies based on logic, databases and the Semantic Web, a Web of exposed data and of interpretations of that data (i.e., of semantics), using common standards. Such technologies enable distinguishable, computable, reusable, and sharable meaning of Web and other artifacts, including data, documents, and services. We also believe that making that vision a reality requires additional supporting resources and these resources should be open, extensible, and provide common services over the ontologies. (shrink)

Semantic interoperability requires the use of standards, not only for Electronic Health Record (EHR) data to be transferred and structurally mapped into a receiving repository, but also for the clinical content of the EHR to be interpreted in conformity with the original meanings intended by its authors. Accurate and complete clinical documentation, faithful to the patient’s situation, and interoperability between systems, require widespread and dependable access to published and maintained collections of coherent and quality-assured semantic resources, including models such as (...) archetypes and templates that would (1) provide clinical context, (2) be mapped to interoperability standards for EHR data, (3) be linked to well specified, multi-lingual terminology value sets, and (4) be derived from high quality ontologies. Wide-scale engagement with professional bodies, globally, is needed to develop these clinical information standards. (shrink)

This is a short editorial to introduce the double issue of Applied Ontology that celebrates the journal's tenth anniversary. At a time when information technology of all kinds depends on the use of explicit ontologies, our journal addresses the modeling issues that underlie the next generation of computational systems. As the editors of Applied Ontology, we are excited by how far we have come in the past decade and by the opportunities that await our research community.

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)

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 National Cancer Institute's (NCI) Thesaurus is a biomedical reference ontology. The NCI Thesaurus is represented using description logic, more specifically Ontylog, a description logic implemen...

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

There are three major weaknesses with Glenberg 's theory. The first is that his theory makes assumptions about internal representations that cannot be adequately tested. The second is that he tries to accommodate data from three disparate domains: mental models, linguistics, and memory. The third is that he makes light of advances in cognitive neuroscience.

Causation is one of philosophy's most venerable and thoroughly-analyzed concepts. However, the study of how ordinary people make causal judgments is a much more recent addition to the philosophical arsenal. One of the most prominent views of causal explanation, especially in the realm of harmful or potentially harmful behavior, is that unusual or counternormative events are accorded privileged status in ordinary causal explanations. This is a fundamental assumption in psychological theories of counterfactual reasoning, and has been transported to philosophy by (...) Hitchcock and Knobe (2009). A different view--the basis of the culpable control model of blame (CCM)--is that primary causal status is accorded to behaviors that arouse negative evaluative reactions, including behaviors that stem from nefarious motives, negligence or recklessness, a faulty character, or behaviors that lead to harmful or potentially harmful consequences. This paper describes four empirical studies that show consistent support for the CCM. (shrink)

A while ago I pulled the short straw, and became chair of my department. One nice part of the job is to praise people I work with, which I can do sincerely because they are very praiseworthy. I also have to read a lot of praise by others; the familiar things—project evaluations, letters of recommendation, promotion dossiers, and so on and so forth. As a result, I have learnt to attend to praise a little more closely.

This article considers two important problems for the idea that what we ought to do is determined by the balance of competing reasons. The problems are distinct, but the object of the article is to explore how they admit of a single solution. It is a consequence of this solution that objective reasons—facts that count in favor—are in an important sense less objective than they have consistently been assumed to be. This raises but does not answer the question as to (...) what evidence we ever had that reasons are as objective as has been assumed. (shrink)

Colors are sensible qualities. They are qualities that objects are perceived to have. Thus, when Norm, a normal perceiver, perceives a blue bead, the bead is perceived have a certain quality, perceived blueness. `Quality', here, is no mere synonym for property; rather, a quality is a kind of property a qualitative, as opposed to quan• titative, property. (The quantitative is a way of contrasting with the qualitative perhaps not the only way.).

I know that I could have been where you are right now and that you could have been where I am right now, but that neither of us could have been turnips or natural numbers. This knowledge of metaphysical modality stands in need of explanation. I will offer an account based on our knowledge of the natures, or essencess, of things. I will argue that essences need not be viewed as metaphysically bizarre entities; that we can conceptualise and refer to (...) essences; and that we can gain knowledge of them. We can know about which properties are, and which properties are not, essential to a given entity. This knowledge of essence offers a route to knowledge of the ways those entities must be or could be. (shrink)

Preregistration has been proposed as a useful method for making a publicly verifiable distinction between confirmatory hypothesis tests, which involve planned tests of ante hoc hypotheses, and exploratory hypothesis tests, which involve unplanned tests of post hoc hypotheses. This distinction is thought to be important because it has been proposed that confirmatory hypothesis tests provide more compelling results (less uncertain, less tentative, less open to bias) than exploratory hypothesis tests. In this article, we challenge this proposition and argue that there (...) are several advantages of exploratory hypothesis tests that can make their results more compelling than those of confirmatory hypothesis tests. We also consider some potential disadvantages of exploratory hypothesis tests and conclude that their advantages can outweigh the disadvantages. We conclude that exploratory hypothesis tests avoid researcher commitment and researcher prophecy biases, reduce the probability of data fraud, are more appropriate in the context of unplanned deviations, facilitate inference to the best explanation, and allow peer reviewers to make additional contributions at the data analysis stage. In contrast, confirmatory hypothesis tests may lead to an inappropriate level of confidence in research conclusions, less appropriate analyses in the context of unplanned deviations, and greater bias and errors in theoretical inferences. (shrink)

Moral philosophers, legal theorists, and psychologists who study moral judgment are remarkably agreed in prescribing how to blame people. A blameworthy act occurs when an actor intentionally, negligently or recklessly causes foreseen, or foreseeable, harmful consequences without any compelling mitigating or extenuating circumstances. This simple formulation conveniently forestalls intricacies about how to construe concepts such as will, causation, foresight, and mitigation, but putting that aside for the moment, it seems fair to say that blame “professionals” share compatible conceptions of how (...) to make fair and rational blame ascriptions. Blame “amateurs,” on the other hand, sometimes stretch these rational prescriptions for blame beyond the breaking point. Numerous psychological studies on blame and responsibility, as well as the perplexing outcomes of high-profile criminal and civil trials, demonstrate that everyday blamers are capable of violating virtually every rational prescription that moral philosophers, legal scholars, and rational decision theorists hold dear. (shrink)

According to a standard account of patient decision-making capacity, patients can provide ethically valid consent or refusal only if they are able to understand and appreciate their medical c...

Presentism is the view, roughly speaking, that only presently existing things exist. Though presentism offers many attractive solutions to problems in metaphysics, philosophy of language, and philosophy of mind, it faces threats from two main sources: McTaggart and the special theory of relativity. This paper explores the prospects for fitting presentism together with the special theory. Two models are proposed, one which fits presentism into a relativistic setting (the cone model) and one which fits the special theory into a presentistic (...) setting (the surface model). It is concluded that there is no good reason arising from the special theory of relativity for rejecting presentism. Presentism is tenable here and preferable elsewhere. (shrink)

What is the function of concepts pertaining to meaning in socio-linguistic practice? In this study, the authors argue that we can approach a satisfactory answer by displacing the standard picture of meaning talk as a sort of description with a picture that takes seriously the similarity between meaning talk and various types of normative injunction. In their discussion of this approach, they investigate the more general question of the nature of the normative, as well as a range of important topics (...) specific to the philosophy of language. (shrink)

Scientists often adjust their significance threshold during null hypothesis significance testing in order to take into account multiple testing and multiple comparisons. This alpha adjustment has become particularly relevant in the context of the replication crisis in science. The present article considers the conditions in which this alpha adjustment is appropriate and the conditions in which it is inappropriate. A distinction is drawn between three types of multiple testing: disjunction testing, conjunction testing, and individual testing. It is argued that alpha (...) adjustment is only appropriate in the case of disjunction testing, in which at least one test result must be significant in order to reject the associated joint null hypothesis. Alpha adjustment is inappropriate in the case of conjunction testing, in which all relevant results must be significant in order to reject the joint null hypothesis. Alpha adjustment is also inappropriate in the case of individual testing, in which each individual result must be significant in order to reject each associated individual null hypothesis. The conditions under which each of these three types of multiple testing is warranted are examined. It is concluded that researchers should not automatically assume that alpha adjustment is necessary during multiple testing. Illustrations are provided in relation to joint studywise hypotheses and joint multiway ANOVAwise hypotheses. (shrink)

In philosophy of logic and elsewhere, it is generally thought that similar problems should be solved by similar means. This advice is sometimes elevated to the status of a principle: the principle of uniform solution. In this paper I will explore the question of what counts as a similar problem and consider reasons for subscribing to the principle of uniform solution.

It seems to be a widely shared view that any defensible desire-fulfillment theory of welfare must be framed not in terms of what an agent, in fact, desires but rather in terms of what an agent would desire under hypothetical conditions that include improved information. Unfortunately, though, such accounts are subject to serious criticisms. In this paper I show that in the face of these criticisms the best response is to jettison any appeal to idealized information conditions: the considerations put (...) forward in support of the appeal to what would be desired in hypothetical circumstances of improved information do not, in fact, give adequate reason to make that appeal. (shrink)

I discuss three ways of responding to the logical omniscience problems faced by traditional ‘possible worlds’ epistemic logics. Two of these responses were put forward by Hintikka and the third by Cresswell; all three have been influential in the literature on epistemic logic. I show that both of Hintikka's responses fail and present some problems for Cresswell’s. Although Cresswell's approach can be amended to avoid certain unpalatable consequences, the resulting formal framework collapses to a sentential model of knowledge, which defenders (...) of the ‘possible worlds’ approach are frequently critical of. (shrink)

Fisher criticised the Neyman-Pearson approach to hypothesis testing by arguing that it relies on the assumption of “repeated sampling from the same population.” The present article considers the responses to this criticism provided by Pearson and Neyman. Pearson interpreted alpha levels in relation to imaginary replications of the original test. This interpretation is appropriate when test users are sure that their replications will be equivalent to one another. However, by definition, scientific researchers do not possess sufficient knowledge about the relevant (...) and irrelevant aspects of their tests and populations to be sure that their replications will be equivalent to one another. Pearson also interpreted the alpha level as a personal rule that guides researchers’ behavior during hypothesis testing. However, this interpretation fails to acknowledge that the same researcher may use different alpha levels in different testing situations. Addressing this problem, Neyman proposed that the average alpha level adopted by a particular researcher can be viewed as an indicator of that researcher’s typical Type I error rate. Researchers’ average alpha levels may be informative from a metascientific perspective. However, they are not useful from a scientific perspective. Scientists are more concerned with the error rates of specific tests of specific hypotheses, rather than the error rates of their colleagues. It is concluded that neither Neyman nor Pearson adequately rebutted Fisher’s “repeated sampling” criticism. Fisher’s significance testing approach is briefly considered as an alternative to the Neyman-Pearson approach. (shrink)

ABSTRACTWhile extant replies to Jonathan Schaffer’s putative counterexamples to the transitivity of grounding have made significant strides against the charge of transitivity failure, the replies pay insufficient attention to the common structure of the counterexamples, overlooking a deeper structural feature that contributes to their prima facie plausibility. Putative counterexamples to the transitivity of grounding, I argue, trade on the distinction between what I call ‘rigid’ and ‘non-rigid’ grounding, and confusion over how rigid and non-rigid grounding react when combined pumps the (...) intuition that the counterexamples’ chained conclusions are false. The rigid/non-rigid grounding distinction also reveals plausible weakening inference rules that have been overlooked in treatments of the logic of grounding. (shrink)

Philosophy of ecology has been slow to become established as an area of philosophical interest, but it is now receiving considerable attention. This area holds great promise for the advancement of both ecology and the philosophy of science. Insights from the philosophy of science can advance ecology in a number of ways. For example, philosophy can assist with the development of improved models of ecological hypothesis testing and theory choice. Philosophy can also help ecologists understand the role and limitations of (...) mathematical models in ecology. On the other side, philosophy of science will be advanced by having ecological case studies as part of the stock of examples. Ecological case studies can shed light on old philosophical topics as well as raise novel issues for the philosophy of science. For example, understanding theoretical terms such as “biodiversity” is important for scientific reasons, but such terms also carry political importance. Formulating appropriate definitions for such terms is thus not a purely scientific matter, and this may prompt a reevaluation of philosophical accounts of defining theoretical terms. We consider some of the topics currently receiving attention in the philosophy of ecology and other topics in need of attention. Our aim is to prompt further exchange between ecology and philosophy of science and to help set the agenda for future work in the philosophy of ecology. The topics covered include: the role of mathematical models, environmental problem formulation, biodiversity, and environmental ethics. (shrink)

As machines take over more tasks previously done by humans, artistic creation is also considered as a candidate to be automated. But, can machines create art? This paper offers a conceptual framework for a philosophical discussion of this question regarding the status of machine art and machine creativity. It breaks the main question down in three sub-questions, and then analyses each question in order to arrive at more precise problems with regard to machine art and machine creativity: What is art (...) creation? What do we mean by art? And, what do we mean by machines create art? This then provides criteria we can use to discuss the main question in relation to particular cases. In the course of the analysis, the paper engages with theory in aesthetics, refers to literature on computational creativity, and contributes to the philosophy of technology and philosophical anthropology by reflecting on the role of technology in art creation. It is shown that the distinctions between process versus outcome criteria and subjective versus objective criteria of creativity are unstable. It is also argued that we should consider non-human forms of creativity, and not only cases where either humans or machines create art but also collaborations between humans and machines, which makes us reflect on human-technology relations. Finally, the paper questions the very approach that seeks criteria and suggests that the artistic status of machines may be shown and revealed in the human/non-human encounter before any theorizing or agreement takes place; an experience which then is presupposed when we theorize. This hints at a more general model of what happens in artistic perception and engagement as a hybrid human-technological and emergent or even poetic process, a model which leaves more room for letting ourselves be surprised by creativity—human and perhaps non-human. (shrink)

Substantial facts are not well-understood entities. Many philosophers object to their existence on this basis. Yet facts, if they can be understood, promise to do a lot of philosophical work: they can be used to construct theories of property possession and truthmaking, for example. Here, I give a formal theory of facts, including negative and logically complex facts. I provide a theory of reduction similar to that of the typed λ -calculus and use it to provide identity conditions for facts. (...) This theory validates truthmaker maximalism : it provides truthmakers for all truths. I then show how the usual truth-in-a-model relation can be replaced by two relations: one between models and facts, saying that a given fact obtains relative to the model, and the other between facts and propositions: the truthmaking relation. (shrink)

One important objection to virtue ethical theories is that they apparently must account for the wrongness of a wrong action in terms of a lack of virtue (or presence of vice) in the agent, and not in terms of the effects of the action on its victim. We take such effects to ground deontic constraints on how we may act, and virtue theory appears unable to account for such constraints. I claim, however, that eudaimonist virtue theory can account for wrongness (...) in just this way. I draw on recent work by Stephen Darwall on the “second-person standpoint,” in which we see others as independent sources of claims on us —as sources of “deontic constraints.” We have reason to occupy that standpoint as a matter of virtue, and thus virtuous agents should and will have reasons to respect deontic constraints. I argue for this claim as an element of a plausible eudaimonist virtue theory, and rebut objections that the view misunderstands the nature of or reasons for respecting such constraints. (shrink)

In industries populated by small and medium enterprises, managers' good intentions frequently incur barriers to superior environmental performance (Tilley, Bus Strategy Environ 8:238-248, 1999). During the period when the U.S. wine industry was beginning to promote voluntary adoption of sound environmental practices, we examined managers' attitudes, norms, and perceptions of stakeholder pressures to assess their intentions to implement environmental management programs (EMP). We found that managers within the simple structures of these small and medium firms are responsive to attitudes, norms, (...) and pressures from internal stakeholders and that voluntarily established EMP increased the success of firms' implementation of energy conservation and recycling practices. Applications of our findings to future research on small and medium enterprises as well as direct practical applications of our results are discussed. (shrink)

It seems true to say that Sherlock Holmes is a detective, despite there being no Sherlock Holmes. When asked to explain this fact, philosophers of language often opt for some version of Lewis’s view that sentences like ‘Sherlock Holmes is a detective’ may be taken as abbreviations for sentences prefixed with ‘In the Sherlock Holmes stories …’. I present two problems for this view. First, I provide reason to deny that these sentences are abbreviations. In short, these sentences have aesthetic (...) properties that we should not expect of abbreviations. Second, I argue that the apparent truth of these sentences would not be explained even if they were abbreviations. An alternative is presented that avoids these problems. Following Walton, talk about fiction is viewed as a game of make-believe; following Lewis, interpretations of fiction are modelled using possible worlds. (shrink)

In this paper, I explore the role for anticipated regret in major life decision-making, focusing on how it is employed by realistic decision-makers in a variety of realistic cases. I argue that the most obvious answers to how regret might matter in decision do not make these cases intelligible, but that we can make them intelligible through consideration of the significance of narrative in our own self-understanding.

Jago uses a Fitch-style argument in an attempt to demonstrate that every truth has a truthmaker. But Trueman shows that there is a parallel argument, this time to the conclusion that no truth has a truthmaker. Since we cannot accept both, we must ditch at least one Fitch. But which? Keywords: Truth, truthmaking, truthmaker maximalism, Fitch paradox, Robert Trueman.