Ludger Jansen

Ontology engineering is mainly done by domain experts who are specialists in their domain but have, if at all, limited knowledge in logics, computer science, or analytic philosophy. The literature on formal ontologies and biomedical ontologies is neither suited nor intended to serve as an educational resource that would help domain experts to become good ontologists. Existing educational resources focus rather on ontology tools and languages than on good practice. The purpose of the GoodOD guideline is to pave the road for domain experts who want (or need) to become ontology engineers. It pursues the openly pragmatic approach that ontology engineers only need to know ontology theory to the extent which supports the (measurable) outcome of their work. The GoodOD Guideline builds upon given philosophical and methodological principles as well as preexisting tools and resources. In particular (pragmatic) scientific realism, first order logics and its subset OWL-DL (description logics), set theory, an upper-level ontology with high-level categories and a canonic set of relations, constraints which limit the freedom of choice when building coordinate expressions, the ontology editor Protégé 4, a complete DL reasoner, such as HermIT, ontology design patterns, and naming conventions. Given these precepts the guideline contains all the knowledge to be acquired by a user to be able to solve ontology engineering problems in a foreseeable and non-arbitrary way. The didactic concept is to convey the skills not only by theory but also by practical examples.

Ontologies aim to represent what is general, by means of universal statements. In contrast, dispositional predications capture knowledge about what is likely to happen if a certain set of circumstances obtain, which is crucial in investigative research such as in drug discovery and systems biology, where entities which are constitutionally dissimilar can nevertheless have similar behavior in a biological context. While such dispositional properties are increasingly included in biomedical ontologies, the circumstances under which the dispositions are realized are seldom explicitly modeled, and doing so is problematic due to the necessary restriction to binary relations in OWL ontologies. In this paper we address this shortcoming, focusing on the bioactivity of small molecules at varying levels of concentration within a living organism as our problem domain, although our approach is generalizable to other problems. We discuss the ontological nature and representation of dispositions and their realization; consider the nature of concentrations and their representation; and finally we detail an approach to linking dispositions to the conditions for their realization which regards conditions as triggers for the process in which the disposition is realized.

While genomic and proteomic information describe the overall cellular machinery available to an organism, the metabolic profile of an individual at a given time provides a canvas as to the current physiological state. Concentration levels of relevant metabolites vary under different conditions, in particular, in the presence or absence of different disorders. Metabolite concentrations thus mediate an important link between chemistry and biology, contributing to a systems-wide understanding of biological processes and pathways. However, there are a number of challenges in the ontological representation of such information. Firstly, concentration information is numeric and ranges over continuous values, while ontologies consist of discrete classes. Secondly, ontologies usually model only what is certain, and their logical formalisms are adapted to reasoning from certain axioms to logical deductions, however, the link between chemicals and diseases via concentration levels, like many threshold phenomena, is both uncertain and vague. In this paper we evaluate the representation of this knowledge using a combination of concrete domains and probabilistic reasoning. We parse concentration values from HMDB and create an ontology able to distinguish normal from abnormal concentrations and able to evaluate a probabilistic risk category for the presence of an associated disorder.

: Background: In responsible research and innovation (RRI), innovation is seen as a way in which humankind finds solutions for societal issues. However, studies on commercial innovation show that firms respond in a different manner and at a different speed to the same societal issue. This study investigates what role organizational motives play in the product innovation processes of firms when aiming for socially responsible outcomes. Methods: This multiple-case study investigates the motives of food firms for healthier product innovation by interviewing firms about the organizational motives behind product reformulation and innovation. Results: This study highlights the importance of having both instrumental and moral motives in the innovation process when aiming for socially responsible outcomes, and how both these motives interact and contribute to responsible innovation in industry. Furthermore, the study results question the nature of relational motives as a separate category from the other two categories of motives, as suggested by corporate social responsibility (CSR) scholars. Conclusions: If commercial innovation needs to contribute to solutions for societal issues, the importance of moral motives has to be stressed without annihilating the instrumental objectives of firms. Both motives contribute to the success factors of responsible product innovation in industry.

In order to strengthen RI in the private sector, it is imperative to understand how companies organise this process, where it takes place, and what considerations and motivations are central in the innovation process. In this chapter, the questions of whether and where normative considerations play a role in the innovation process, and whether dimensions of RI are present in the innovation process, are addressed. In order answer these research questions, a theoretical framework is developed based on Jones’s theory of ethical decision making and Cooper’s stagegate model of innovation management. In order to answer the research questions, a specific case of innovations that contribute to public health is explored, namely, that of food companies that participate in a Front-of-Pack logo for healthier food. As the use of healthy food logos does not necessarily have a positive impact on sales and profits, it is expected that in the decision-making process, as part of their innovation process, companies make several trade-offs between economic, technical and moral factors. As the social-ethical values at stake in corporate innovation processes have remained to a large extent unexplored in research on innovation management, the aim of this chapter is to identify the motivations and barriers for companies embracing and continuing a FoP logo for healthier food, and to assess whether ethical considerations play a role in this innovation process. From the findings in this research, it will become clear that although the studied companies participated in a programme for healthy food and thus are responsive to the needs of society, and although the companies feel responsible for public health, ethical considerations do not play a central role in the operational innovation process. Instead, technical and economic considerations seem to prevail in the operational innovation process. Furthermore, none of the procedural dimensions of RI seems to be present at this level in the innovation trajectory. It is argued that this may be an indication that the ethical decision-making process for RI is not located at the level of the operational innovation process itself, but is something that might be located on a higher strategic level in the company. It is at this level that the moral decision is taken to adopt the FoP logo and to engage in the RI process. The findings cast a new light on the discourse on RI in general, and in the private sector in particular.

Traditionally, nature has often been thought to be structured by essential forms providing the generic features of natural things and thus the foundations for scientific explanations. In contrast, human history and the social domain have been thought to be the realm of ever-changing appearances, where contingency prevails. The paper argues that the existence of essential forms is compatible with the contingent, mind-dependent and historical character of the social world, and that essential forms can also be found in the social domain. Two categories of entities are discussed that suggest themselves to be identified as social forms, namely social kinds and social identities. To this end, it is shown that standard arguments for the existence of essential forms also apply to the social domain, and objections to the existence of social forms are rebutted. Particular attention is paid to the explanatory appeal of social forms. The paper concludes by suggesting that, far from being oppressive, essential social forms are presupposed by liberating social practices.

It is often claimed that the intentions of physicians are multiple, ambiguous, and uncertain—at least with respect to end-of-life care. This claim provides support for the conclusion that the principle of double effect is of little or no value as a guide to end-of-life pain management. This paper critically discusses this claim. It argues that proponents of the claim fail to distinguish two different senses of “intention,” and that, as a result, they are led to exaggerate the extent to which clinical intentions in end-of-life contexts are ambiguous and uncertain. It argues further that physicians, like others who make life and death decisions, have a duty to get clear on what their intentions are. Finally, it argues that even if the principle of double effect should be rejected, clinical intentions remain ethically significant because they condition the meaning of extraordinary clinical interventions, such as that of palliative sedation

In recent years, many states in the United States have passed legislation requiring laboratories to report the names of patients with low CD4 cell counts to their state Departments of Health. This name reporting is an integral part of the growing number of “HIV Reporting and Partner Notification Laws” which have emerged in response to recently revised guidelines suggested by the National Centers for Disease Control (CDC). Name reporting for patients with low CD4 cell counts allows for a more accurate tracking of the natural history of HIV disease. However, given that this test is now considered to be an “indicator” of HIV, should it be subject to the same strict consent required for HIV testing? While the CDC has recommended that each state develop its own consent requirements for CD4 cell testing, most states have continued to rely on the presumed consent standards for CD4 cell testing that were in place before the passage of name reporting statutes. This allows physicians who treat patients who refuse HIV testing to order a CD4 cell blood analysis to gather information that is indicative of their patient’s HIV status. This paper examines the ethical and legal issues associated with the practice of “conscientious subversion” as it arises when clinicians use CD4 cell counts as a surrogate for HIV testing

Researchers and ethicists have long been concerned about the expectations for direct medical benefit expressed by participants in early phase clinical trials. Early work on the issue considered the possibility that participants misunderstand the purpose of clinical research or that they are misinformed about the prospects for medical benefit from these trials. Recently, however, attention has turned to the possibility that research participants are simply expressing optimism or hope about their participation in these trials. The ethical significance of this therapeutic optimism remains unclear. This paper argues that there are two distinct phenomena that can be associated with the term ‘therapeutic optimism’—one is ethically benign and the other is potentially worrisome. Distinguishing these two phenomena is crucial for understanding the nature and ethical significance of therapeutic optimism. The failure to draw a distinction between these phenomena also helps to explain why different writers on the topic often speak past one another

In an era of rapidly rising health care costs, physicians and policymakers are searching for new and effective ways to contain health care spending without sacrificing the quality of services provided. These proposals are increasingly articulated in terms of an ethical duty of stewardship. The duty of stewardship in medicine, however, is not at present well understood, and it is frequently conflated with other duties. This article presents a critical analysis of the notion of stewardship, which shows that it has an important and distinctive place in medical ethics. It claims that stewardship in medicine concerns the responsible use of a society’s medical resources and it discusses the extent to which medical professionals are the proper stewards of these resources. The article argues that the duty of stewardship is best understood as a duty that applies in a space between the obligations of health care providers to provide beneficent care to their patients on the one hand and the obligations of citizens to bring about and support a just health care system on the other. Seen with clear eyes, stewardship in medicine is neither a consequence of beneficent medical care nor a substitute for justice

Much work in social ontology analyzes how social entities are based on collective intentionality. A neglected perspective is, however, the distinction between those social entities that are explicitly established (often called formal institutions, like marriages), those that are established but not explicitly (informal institutions, like friendships), and those that are not established at all (social macro entities, like episodes of inflation). To shed more light on this trichotomy, a collection of examples taken from the works of John Searle will be discussed, comprising money, marriages, friendship, cocktail parties, natural language, and episodes of inflation. The chapter argues that explicit establishment confers certain typical characteristics on formal institutions that informal institutions lack, thus explaining the typical differences between marriages and friendship. The focus on explicit establishment further develops Khalidi’s classification of social kinds, and it contributes to Epstein’s quest for grounds and anchors of social entities. It can thus contribute to overcoming the narrow focus on collective intentionality.

Sparrows fly because they are birds. This mushroom is poisonous because it is an Amanita muscaria. Pointing out the kind to which things belong explains many of their properties. Jonathan Lowe’s four-category ontology and his account of laws of nature provide a framework to account for the explanatory appeal of referring to kind membership. For Lowe, “Electron has Unit-negative charge” is a typical example for a law of nature: a kind universal characterized by a property universal. We present both Lowe’s original account of laws of nature and later developments, and show how Lowe’s account can help to solve notorious problems of other accounts, namely, the regularity view and the Armstrong-Dretske-Tooley view. We argue that there are two challenges that Lowe’s view cannot master. First, Lowe conflates generics and dispositions, which is a considerable problem for Lowe, because his account of dispositional predication and his account of laws of nature are intimately connected. Second, there is the identification problem of fully specifying and identifying the formal ontological relation of characterization between kind universals and property universals. In order to solve these problems, we develop an account of formal causation inspired by Aristotle’s theory of explanation in his Posterior Analytics. Though very close to Lowe’s own account, our neo-Aristotelian account avoids Lowe’s confusion regarding dispositions, avoids overdetermination through several similar laws of nature, and provides an answer to the identification problem: The characterization of a kind universal by a property universal constitutes the relation of formal causation. By virtue of this relation, the kind Amanita muscaria is the formal cause of this mushroom having the attribute of being poisonous.

With substance dualism and the existence of God, Swinburne (2004, The Existence of God, Oxford University Press, Oxford) and Moreland (2010, Consciousness and the Existence of God, Routledge, New York) have argued for a very powerful explanatory mechanism that can readily explain several philosophical problems related to consciousness. However, their positions come with presuppositions and ontological commitments which many are not prepared to share. The aim of this paper is to improve on the Swinburne-Moreland argument from consciousness by developing an argument for the existence of God from consciousness without being committed to substance dualism. The argument proceeds by suggesting a solution to the exceptional-point-of-view problem, i.e., the question how it can be explained that there is a conscious being lucky enough to experience the point of view of a relatively tiny brain amidst a giant universe that is indifferent about which physical entities it brings about according to the laws of physics.