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)

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)

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)

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)

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)

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)

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 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.

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)

This volume discusses the origin and structure of the universe in mystical Islam (Sufism) and Islam's civilizational predecessors with special reference to parallel realms of existence and their interaction. Contributors address Sufi ideas about the fate of human beings in this and future life under three rubrics: (1) cosmogony and eschatology ("where do we come from?" and "where do we go?"); (2) conceptualizations of the world of the here-and-now ("where are we now?"); and (3) visualizations of realms of existence, their (...) hierarchy and mutual relationships ("where are we in relation to other times and places?"). Contributors are Christian Lange, Alexander Knysh, Noah Gardiner, Stephen Hirtenstein, Saeko Yazaki, Jean-Jacques Thibon, Leah Kinberg, Sara Sviri, Munjed M. Murad, Simon O'Meara, Pierre Lory, Mathieu Terrier, Michael Ebstein, Binyamin Abrahamov and Frederick Colby. (shrink)

The notion of biopolitical sovereignty and the theory of the state of exception are perspectives derived from Carl Schmitt’s thought and Michel Foucault’s writings that have been popularized by critical political theorists like Giorgio Agamben and Michael Hardt and Antonio Negri of late. This article argues that these perspectives are not sufficient analytical points of departure for a critique of the contemporary politics of terror, violence and war marked by a growing global exploitation of bodies, tightened management of life, and (...) endless and unpredictable abusive force. To better capture the singularity of our present condition of violence, war and terror, a supplementation of Schmitt’s and Foucault’s approaches by way of Hannah Arendt’s language of political action and agonistic engagement is useful. By bringing Arendt’s language of political agony to bear on contemporary biopolitical debates and discourses, we wish to revisit common practices of war and terror as matters of ‘agonal sovereignty’. ‘Agonal sovereignty’ allows us to peer into the ‘abyss of total violence’ that manifests itself after sovereign decisionism and biopolitical modalities of power have taken over the everyday conduct of political affairs. (shrink)

The author demonstrates that researchers in quantum physics and inflationary cosmology have in practice loosened the rigorous traditional principles of scientific methodology . He formulates some principles of the new methodology.

An overview of the concept of Strong Emergence, and a summary of the papers within the special issue.

Contends that psychologists can contribute to the debate on the nature of science. The author suggests that the work of individual scientists can best be understood as a joint product of intellectual background and willingness to adopt a position with respect to important elements of that context.

This paper reconsiders the event in International Relations (IR) through the writings of Hannah Arendt. The event has for too long been neglected in IR; international events are overwhelmingly conceived as mere happenings that have meaning only within the process and temporal structure of the theory from which they are understood, and as holding no or only limited meaning in and of themselves. In her work on political theory and her reflections on totalitarianism, however, Arendt elaborates a rich view of (...) the event and its relationship to history, one that offers an alternative way of thinking about international relations. Arendt urges us to remain open to the possibility, however difficult, of conceiving of the event as meaningful outside of the processes within which our established mode of thoughts would have us subsume it. This requires on the part of the historian a commitment to judgement, to a recognition of the importance of imagination and impartiality that gives meaning to the event for others. In explicating Arendt's complex notion of the genuine political event, the paper aims not merely to demonstrate the intrinsic interest of this conception of the event to her thought, but to add to the small but growing number of works in IR that have found fruitful new avenues of thought in Arendt's various writings, and also to recent discussions on the proper relationship between history and IR theory. (shrink)

This paper proceeds from the assumption that the spiritual beliefs of native people of northern Kamchatka (Koryaks, Chukchis, Evens) are not false consciousness, nor "really" about something else. I situate beliefs about vampiric shamans in the larger cultural context of the spiritual world, the human soul, and the afterlife. After this description of d iscourse about shamans, the second half of the paper demonstrates how the way people talk about the spiritual world is interconnected with their social reality.

A summary of the papers within the Philosophica special issue on Strong Emergence.

This short paper explores how issues concerning the metaphysics of powers/dispositions might bear on the view that formative influence in education involves instilling appropriate dispositions.

This paper examines the prevalent assumption that when people interact online via proxies—avatars—they encounter each other. Through an exploration of the ontology of users and their avatars we argue that, contrary to the trend within current discussions of interaction online, this cannot be unproblematically assumed. If users could be considered in some sense identical to their avatars, then it would be clear how an encounter with an avatar could ground an encounter with another user. We therefore engage in a systematic (...) investigation of several conceptions of identity, concluding that in none of these senses can users and avatars be identified. We go on to explore how current accounts of identity-as-selfhood online might resolve this problem by appealing to narrativity or authorship, ultimately concluding that as these accounts stand they are unable to provide grounds for the claim that users encounter each other online and so supplementary work is required. (shrink)

Physicalism can be roughly characterised as the view that everything is physical, or that everything that is fundamental is physical, or that any non-physical entity—property, substance, fact, event, kind and what have you—is both dependent upon and fully determined by physical entities. Perhaps the greatest challenge facing physicalism is to explain how conscious experience can be accounted for within the physicalist framework. Given these rough characterisations of physicalism, before setting out to address the problem posed by consciousness, there is some (...) prior conceptual work that must be done. In order for debates concerning the nature of consciousness and the ontology of mind and body to proceed in good order, something needs to be said about what it is for an entity to be a specifically physical entity. This paper offers reasons to think that, (i) at least given certain common metaphysical assumptions, discussions of what it is to be physical in general ought to be primarily concerned with what it is to be a physical property and that (ii) two popular approaches to characterising the physical - the Via Negativa and Object Physicalist approaches - face a serious problem. (shrink)

An Islamic coffin discovered in the church of Maria Spilaiotissa near the old Seljuk capital of Konya in central Anatolia bears the following Greek inscription: “Here lies the descendant of men born in the purple, Michael Amiraslan, the grandson of the great-grandson of the blessed emperor born in the purple, Kyr John Komnenos Maurozomes, the son of the humble John Komnenos.”.

Growing evidence suggests the presence of a female leadership advantage (FLA), such that women leaders tend to be associated with more effective outcomes in uncertain conditions. However, mechanisms linking women's leadership to effective outcomes are less well understood. We integrate FLA insights with ethics of care philosophical framework to conceptualize how women leaders achieve effective outcomes in the context of the urban revitalization crisis in the United States. We propose and empirically test the mediating role of ethics of care leadership (...) in the relationship between women mayors and economic health of their cities. We used data from the Urban Institute that includes 272 United States cities and measures of variables in our conceptual model at five points in time spanning 36 years (_n_ = 1185 city-year observations). We capture ethics of care leadership focused on racial inclusion with an index measure of a city’s racial spatial segregation, homeownership gap, poverty gap, and education gap, and we capture economic health with an index measure of a city’s employment growth, unemployment rate, housing vacancy rate, and median family income. We found that female-led cities were associated with better economic health, and this association was mediated by female-led cities’ association with greater racial inclusion. Ethics of care leadership appears to be one pathway through which a FLA manifests itself in the context of the urban revitalization crisis. This underscores the importance of city leadership that balances social and economic prerogatives. Implications are discussed. (shrink)