In the debate about semantic context dependence, various truth-conditional frameworks have been proposed. Indexicalism, associated with e.g. Jason Stanley, accounts for contextual effects on truth conditions in terms of a rich covert syntax. Truth-conditional pragmatics, associated with e.g. François Recanati, does not locate the mechanisms for context dependence in the syntactic structure but provides a more complex semantics. In this dissertation, the hypothesis that indexicalism and truth-conditional pragmatics are empirically equivalent is explored. The conclusion that the hypothesis is correct emerges, (...) when claims and accounts in the debate are made formally precise, within the framework of model-theoretic semantics. -/- . (shrink)

We propose a new account of collective moral obligation. We argue that several agents have a moral obligation together only if they each have (i) a context-specific capacity to view their situation from the group’s perspective, and (ii) at least a general capacity to deliberate about what they ought to do together. Such an obligation is irreducibly collective, in that it does not imply that the individuals have any obligations to contribute to what is required of the group. We highlight (...) various distinctive features of our account. One such feature is that moral obligations are always relative to an agential perspective. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

The counterfactual comparative account of harm has counterintuitive implications in cases involving overdetermination and preemption. A popular strategy for dealing with these problems appeals to plural harm—several events being jointly harmful. Björn Petersson criticizes this strategy on the grounds that it conflicts with a strong intuition that helps to motivate the counterfactual comparative account, namely, that harming someone essentially involves making a difference for the worse for her. In this paper, I argue that Petersson’s argument is unconvincing.

This paper argues that there is reason to distinguish between moral responsibility and blameworthiness and, in particular, that we can acknowledge that a person is responsible for the negative outcomes of their behavior without this necessarily informing our judgments about the person’s blameworthiness. This general theme is elaborated in the context of a discussion of some of Björn Petersson’s work on collective moral responsibility.

In this essay, I argue that the objections that have been raised against the view that equality is intrinsically valuable also provide objections to the view that all practical reasons can be explained in terms of value. Plausible egalitarian principles entail that under certain conditions people have claims to an equal share. These claims entail reasons to distribute goods equally that cannot be explained by value if equality has no intrinsic value.

In this paper I articulate and respond to Kent Hurtig's objection to the fitting attitude account of value (FA). According to the objection, when a good or bad state of affairs is indexed to the actual world, but is such that the actual world does not contain anyone for whom it is fitting to (dis)favor it, it cannot be fitting for anyone in a non-actual world to (dis)favor it. So there are good or bad states of affairs that it is (...) not fitting for anyone to (dis)favor. First I comment on a solution proposed by Toni Rønnow-Rasmussen. Then I argue that if, due to their location in modal space, the relevant states of affairs cannot even be evaluated as good or bad (and a fortiori favored or disfavored) by readers, then such cases are dialectically powerless against FA; if, on the other hand, they can be evaluated as good or bad—despite their location in modal space—then they can also be favored or disfavored, and it will be fitting for us (if for no one else) to favor or disfavor them, thus defusing the challenge. (shrink)

Invasive alien species are frequently discussed in academic literature by practitioners, government agencies, and popular media, but what does it mean for a species to be alien and why it this seen as a bad thing? To answer these questions, I have analysed texts about invasive alien species in academic journals and in communication from government agencies. The almost totally unanimous answer to the first question was that a species is alien if and only if it is introduced to an (...) area outside its natural range by humans. I found three primary answers to the second question, namely that (1) alien species are more probable to behave invasively or that it is impossible to know for sure if an alien species will behave invasively, (2) being alien is bad in itself or at least that alien species have a lower value than native species and native environments, and (3) being moved by humans is unnatural and being unnatural has negative value. All three answers probably contribute to why being alien is considered a negative property in species but none of them seem like a satisfying answer to why being alien should be seen as a bad thing in a species. (shrink)

This paper argues against the correctness of the more popular -first views (fittingness first, reasons first, and value first). The aim of this paper is to argue that there are at least two categories of normative properties that are basic and that one of those categories is value. Although the emphasis of this paper is on reductionist -first accounts, most of the arguments work equally well against weaker views that are only committed to different categories of normative properties' being linked (...) by a necessary bi-conditional. -/- . (shrink)

The literature on the problem of evil does not draw enough upon the relevant debates in (meta)ethics, and ethical theorists (broadly understood) can engage with the problem of evil as a way of inquiry in their field. I review how the problem of evil is essentially formed based on (evaluative and deontic) ethical judgments, and how responses to it, either theistic or atheistic, are mainly based on the relevant ethical judgments. Meanwhile, though contemporary debates in metaphysics and epistemology have influenced (...) the literature on the problem of evil, the same does not hold true for ethics. This suggests that there are ways to engage with the problem of evil as doing axiology or ethical theory more generally, which may be fruitful regardless of their being theodicy. I end by briefly discussing an example focused on the idea of moral progress. (shrink)

The paper is structured as follows. §1 lays out the worry that the FA analysis fosters a revisionary understanding of emotional values. §2 introduces the distinction between enablers and favourers and how it is pressed into service by Toni to reply to this worry. While I agree that the reply is attractive, since casting emotions in the role of enablers chimes well with how we pre-theoretically understand the relations between emotions and values, I observe that doing so requires that we (...) tackle two connected issues. First, how do emotions function as value enablers? Second, is the resulting picture compatible with the FA analysis? The rest of the discussion is structured around these issues. §3 looks at the role of emotions within the FA analysis so as to specify the kind of enabling role they can play. On this backdrop, I explore in §4 a contrast between how belief relates to truth and how emotions relate to values, a contrast which helps uncover what we are after. A first reaction to this contrast, according to which emotions are value enablers by allowing us to access values, which differ from truth, is examined in §5. I argue that this idea cannot do justice to the key insight of the FA analysis. §6 defends an alternative idea, according to which emotions are enablers in virtue of their attitudinal shapes. (shrink)