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 10th International Conference on Biomedical Ontology (ICBO 2019), was held at the Jacobs School of Medicine and Biomedical Sciences of the University at Buffalo, in Buffalo, NY, USA. It was the 10-year anniversary of the ICBO series, and the return of the conference to Buffalo after the first two ICBO conferences were held in Buffalo in 2009 and 2011. ICBO 2019 was well attended, with 115 registered attendees and additional walk-ins from the local academic community. The program included excellent (...) keynote talks by Barry Smith, “International Standard Ontology,” and Bjoern Peters, “Putting principles into practice: OBO ontologies and applications in immunology,” as well as 23 oral presentations, 26 posters, and one software presentation. There were 53 papers and abstracts submitted for peer-review to ICBO 2019. Each submission was reviewed by three members chosen from the Program Committee. Of these submissions, 43 were accepted for this volume: 19 full papers, 23 poster abstracts, and 1 software demonstration extended abstract. We thank our program committee for their thoughtful reviews. There were also three workshops and four tutorials (listed below) held in conjunction with the main ICBO 2019 meeting. (shrink)

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

The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical (...) presentation including signs and symptoms. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

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)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Can there be grounding without necessitation? Can a fact obtain wholly in virtue of metaphysically more fundamental facts, even though there are possible worlds at which the latter facts obtain but not the former? It is an orthodoxy in recent literature about the nature of grounding, and in first-order philosophical disputes about what grounds what, that the answer is no. I will argue that the correct answer is yes. I present two novel arguments against grounding necessitarianism, and show that grounding (...) contingentism is fully compatible with the various explanatory roles that grounding is widely thought to play. (shrink)

Whether or not quantum physics can account for molecular structure is a matter of considerable controversy. Three of the problems raised in this regard are the problems of molecular structure. We argue that these problems are just special cases of the measurement problem of quantum mechanics: insofar as the measurement problem is solved, the problems of molecular structure are resolved as well. In addition, we explore one consequence of our argument: that claims about the reduction or emergence of molecular structure (...) cannot be settled independently of the choice of a particular resolution to the measurement problem. Specifically, we consider how three standard putative solutions to the measurement problem inform our under- standing of a molecule in isolation, as well as of chemistry’s relation to quantum physics. (shrink)

This is an expanded and thoroughly revised edition of the widely adopted introduction to the philosophical foundations of the human sciences. Ranging from cultural anthropology to mathematical economics, Alexander Rosenberg leads the reader through behaviorism, naturalism, interpretativism about human action, and macrosocial scientific perspectives, illuminating the motivation and strategy of each.Rewritten throughout to increase accessibility, this new edition retains the remarkable achievement of revealing the social sciences’ enduring relation to the fundamental problems of philosophy. It includes new discussions of (...) positivism, European philosophy of history, causation, statistical laws, quantitative models, and postempiricist social science, along with a completely updated literature guide that keys chapters to widely anthologized papers. (shrink)

While it might seem prima facie plausible that divine foreknowledge is all that is needed for prophecy, this seems incorrect. To issue a prophecy, God hasto know not just how someone will act, but how someone would act were the prophecy issued. This makes some think that Middle Knowledge is required.I argue that Thomas Flint’s two Middle Knowledge based accounts of prophecy are unsatisfactory, but one of them can be repaired. However the resources needed for repair also yield a sketch (...) of a foreknowledge-only account of prophecy. (shrink)

Argues that Nietzsche tried to create a specific literary character in his writings and discusses the paradoxes of his work.

Researchers are often faced with attempting to estimate a correlation based on the aggregation of sample rs either from several samples or from repeated measures within a single sample. The usual approach is either to average the observed correlations or to average the Fisher’s z- transformed rs and to back-transform the average z value. This note describes a minimum-variance unbiased estimator for the situation that is superior to either approach and is also simple to compute.

For a novice this book is a mathematically-oriented introduction to modal logic, the discipline within mathematical logic studying mathematical models of reasoning which involve various kinds of modal operators. It starts with very fundamental concepts and gradually proceeds to the front line of current research, introducing in full details the modern semantic and algebraic apparatus and covering practically all classical results in the field. It contains both numerous exercises and open problems, and presupposes only minimal knowledge in mathematics. A specialist (...) can use the book as a source of references. Results and methods of many directions in propositional modal logic, from completeness and duality to algorithmic problems, are collected and systematically presented in one volume. (shrink)

Discussion of the relevance of grounding to substantiveness, theory-choice, and “location problems” in metaphysics.

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework (...) for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (shrink)

Some combinations of attitudes--of beliefs, credences, intentions, preferences, hopes, fears, and so on--do not fit together right: they are incoherent. A natural idea is that there are requirements of "structural rationality" that forbid us from being in these incoherent states. Yet a number of surprisingly difficult challenges arise for this idea. These challenges have recently led many philosophers to attempt to minimize or eliminate structural rationality, arguing that it is just a "shadow" of "substantive rationality"--that is, correctly responding to one's (...) reasons. -/- In *Fitting Things Together*, Alex Worsnip pushes back against this trend--defending the view that structural rationality is a genuine kind of rationality, distinct from and irreducible to substantive rationality, and tackling the most important challenges for this view. In so doing, he gives an original positive theory of the nature of coherence and structural rationality that explains how the diverse range of instances of incoherence can be unified under a general account, and how facts about coherence are normatively significant. He also shows how a failure to focus on coherence requirements as a distinctive phenomenon and distinguish them adequately from requirements of substantive rationality has led to confusion and mistakes in several substantive debates in epistemology and ethics. -/- Taken as a whole, Fitting Things Together provides the first sustained defense of the view that structural rationality is a genuine, autonomous, unified, and normatively significant phenomenon. (shrink)

Professional philosophers and advanced students working in metaphysics and the philosophy of science will find this book both provocative and stimulating.

A counterpossible is a counterfactual with an impossible antecedent. Counterpossibles present a puzzle for standard theories of counterfactuals, which predict that all counterpossibles are semantically vacuous. Moreover, counterpossibles play an important role in many debates within metaphysics and epistemology, including debates over grounding, causation, modality, mathematics, science, and even God. In this article, we will explore various positions on counterpossibles as well as their potential philosophical consequences.

The present study investigated whether individual differences between psychologists in thinking styles are associated with accuracy in diagnostic classification. We asked novice and experienced clinicians to classify two clinical cases of clients with two co-occurring psychological disorders. No significant difference in diagnostic accuracy was found between the two groups, but when combining the data from novices and experienced psychologists accuracy was found to be negatively associated with certain decision making strategies and with a higher self-assessed ability and preference for a (...) rational thinking style. Our results underscore the idea that it might be fruitful to look for explanations of differences in the accuracy of diagnostic judgments in individual differences between psychologists (such as in thinking styles or decision making strategies used), rather than in experience level. (shrink)

Otto Neurath’s empiricist methodology of economics and his contributions to politi- cal economy have gained increasing attention in recent years. We connect this research with contemporary debates regarding the epistemological status of thought experiments by reconstructing Neurath’s utopias as linchpins of thought experiments. In our three reconstructed examples of different uses of utopias/dystopias in thought experiments we employ a reformulation of Häggqvist’s model for thought experiments and we argue that: (1) Our reformulation of Häggqvist’s model more adequately complies with many (...) uses of thought experiments, especially with the open-ended discussions of utopias and dys- topias in thought experiments. (2) As a strict logical empiricist, Neurath is committed to a strictly empiricist account of thought experiments. John Norton’s empiricist argument view can indeed account for the justifications of empirical beliefs and genuine discoveries targeted by scientific utopianism in three distinct (yet connected) ways, all of which Neur- ath already contemplated: (2.I) Dealing with utopias and thought experiments on a regular basis increases creativity and inventiveness. (2.II) Particular ways of presenting knowl- edge facilitate scientific discovery and social progress. (2.III) The use of utopias in thought experiments can prompt conceptual change and allow access to new phenomena. We con- clude by highlighting that, even though thought experiments support a positive attitude for exploring new social possibilities, Neurath points out that active decisions are unavoidable. The exploration of alternatives and the awareness of a need for decisions in policy discus- sion avert a technocratic outlook in social science. (shrink)

This study examines how institutional logics interplay in a cross-sector social partnership that manages refugee integration in a rural district in Germany. In an inductive 15-month case study that drew on interviews and observations, we observe the dynamic materialization of institutional logics in day-to-day practices and an increasing contradiction and even rivalry between community- and market-based institutional logics over time. As a result, we delineate a model explaining the interplay of institutional logics along two dimensions: the dominance of one salient (...) logic and whether conflicts arise among logics. Our analysis also addresses the unifying properties of community as an institutional logic, especially in the context of urgency conditions. In addition, we show the influence of exogenous events and their media coverage on the interplay and conflicts of institutional logics. By unfolding the complexity of refugee integration—one of the global grand challenges of the present—we deepen the current understanding of the specific challenges addressed by cross-sector social partnerships. (shrink)

In this paper, I explore a fundamental but under-appreciated distinction between two ways of understanding the desire-satisfaction theory of well-being. According to proactive desire satisfactionism, a person is benefited by the acquisition of new satisfied desires. According to reactive desire satisfactionism, a person can be benefited only by the satisfaction of their existing desires. I first offer an overview of this distinction. I then canvass several ways of developing a general formulation of desire satisfactionism that would capture the reactive view, (...) and argue that all come with significant costs. (shrink)

Recent metaphysics has turned its focus to two notions that are—as well as having a common Aristotelian pedigree—widely thought to be intimately related: grounding and essence. Yet how, exactly, the two are related remains opaque. We develop a unified and uniform account of grounding and essence, one which understands them both in terms of a generalized notion of identity examined in recent work by Fabrice Correia, Cian Dorr, Agustín Rayo, and others. We argue that the account comports with antecedently plausible (...) principles governing grounding, essence, and identity taken individually, and illuminates how the three interact. We also argue that the account compares favorably to an alternative unification of grounding and essence recently proposed by Kit Fine. (shrink)

A collection of essays by Alexander Rosenberg, the distinguished philosopher of science. The essays cover three broad areas related to Darwinian thought and naturalism: the first deals with the solution of philosophical problems such as reductionism, the second with the development of social theories, and the third with the intersection of evolutionary biology with economics, political philosophy, and public policy. Specific papers deal with naturalistic epistemology, the limits of reductionism, the biological justification of ethics, the so-called 'trolley problem' in (...) moral philosophy, the political philosophy of biological endowments, and the Human Genome Project and its implications for policy. Rosenberg's important writings on a variety of issues are here organized into a coherent philosophical framework which promises to be a significant and controversial contribution to scholarship in many areas. (shrink)

This book provides an accessible, critical introduction to the three main approaches that dominated work in the philosophy of mathematics during the twentieth century: logicism, intuitionism and formalism.

Managers tasked with organizational change often face irreconcilable demands on how to enact justice—situations we call _justice conundrums_. Drawing on interviews held with managers before and after a planned large-scale change, we identify specific conundrums and illustrate how managers grapple with these through three prototypical paths. Among our participants, the paths increasingly diverged over time, culminating in distinct career decisions. Based on our findings, we develop an integrative process model that illustrates how managers grapple with justice conundrums. Our contributions are (...) threefold. First, we elucidate three types of justice conundrums that managers may encounter when enacting justice in the context of planned organizational change (the justice intention-action gap, competing justice expectations, and the justice of care vs. managerial-strategic justice) and show how managers handle them differently. Second, drawing on the motivated cognition and moral disengagement literature, we illustrate how cognitive mechanisms coalesce to allow managers to soothe their moral (self-) concerns when grappling with these conundrums. Third, we show how motivated justice intentions ensuing from specific justice motives, moral emotions, and circles of moral regard predict the types of justice conundrums managers face and the paths they take to grapple with them. (shrink)

The first part of this paper argues that if Craver’s ([2007a], [2007b]) popular mutual manipulability account (MM) of mechanistic constitution is embedded within Woodward’s ([2003]) interventionist theory of causation--for which it is explicitly designed--it either undermines the mechanistic research paradigm by entailing that there do not exist relationships of constitutive relevance or it gives rise to the unwanted consequence that constitution is a form of causation. The second part shows how Woodward’s theory can be adapted in such a way that (...) (MM) neither undermines the mechanistic paradigm nor reduces constitution to causation. However, it turns out that this modified theoretical embedding of (MM) makes it impossible to produce empirical evidence for constitutive relations. The paper ends by suggesting an additional criterion, the fat-handedness criterion, which, when combined with (MM), generates indirect empirical evidence for constitutive relevance. (shrink)

Could it be true that even though we as a group ought to do something, you as an individual ought not to do your part? And under what conditions, in particular, could this happen? In this article, I discuss how a certain kind of case, introduced by David Copp, illustrates the possibility that you ought not to do your part even when you would be playing a crucial causal role in the group action. This is because you may have special (...) agent-relative reasons against participating that are not shared by the group as a whole. I defend the claim that these are indeed cases in which you ought not to do your part in what the group ought to do. I then argue that we can expect these cases to produce a troubling kind of rational conflict. (shrink)

Elselijn Kingma argues that, in cases of mammalian placental pregnancy, the foster (roughly, the post-implantation embryo/foetus) is part of the gravida (the pregnant organism). But she does not consider the possibility of proper overlap. I show that this generates a number of serious problems for her argument and trace the oversight to a quite general issue within the literature on biological individuality. Doing so provides an opportunity to pull apart and clarify the relations between some importantly distinct questions concerning organismality (...) and organismic parthood, and to identify the implications that this has for those who want to draw on this literature when making metaphysical or mereological arguments. (shrink)

Pattern-based reasons are reasons for action deriving not from the features of our own actions, but from the features of the larger patterns of action in which we might be participating. These reasons might relate to the patterns of action that will actually be carried out, or they might relate to merely hypothetical patterns. In past work, I have argued that accepting merely hypothetical pattern-based reasons, together with a plausible account of how to weigh these reasons, can lead to disastrous (...) consequences. However, in this article, I argue that this problem is not limited to hypothetical pattern-based reasons: it turns out that there are analogous issues for reasons deriving from actual patterns. I then suggest that we can avoid this problem by adopting a different account of the weight of pattern-based reasons. (shrink)

ABSTRACTThe political is changing its shape. Ideologies are no longer stable, but instead build hybrid combinations. Populism is getting popular. In addition, there are new forms of political exper...