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)

Embedding ethics modules within computer science courses has become a popular response to the growing recognition that CS programs need to better equip their students to navigate the ethical dimensions of computing technologies like AI, machine learning, and big data analytics. However, the popularity of this approach has outpaced the evidence of its positive outcomes. To help close that gap, this empirical study reports positive results from Northeastern’s program that embeds values analysis modules into CS courses. The resulting data suggest (...) that such modules have a positive effect on students’ moral attitudes and that students leave the modules believing they are more prepared to navigate the ethical dimensions they’ll likely face in their eventual careers. Importantly, these gains were accomplished at an institution without a philosophy doctoral program, suggesting this strategy can be effectively employed by a wider range of institutions than many have thought. (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)

This dissertation re-examines the principal philosophical thrusts of the German Enlightenment period, from the perspective of their totalizing-mythological function, and investigates how this function is criticized by the non-totalizing function of myth found within the primary mythical images in the work of Goethe, Nietzsche, Rilke, and Walter Benjamin. ;Utilizing the revolutionary book by Hans Blumenberg on the function of myth in German Idealism and Romanticism, I instigate a discourse between Blumenberg's totalizing work on myth and the negative-dialectical work on myth (...) as proposed by Theodor Adorno. I locate the German origins of this negative-dialectical myth-making in the work of Goethe, specifically his non-totalizing image, Wilhelm Meister. I locate the development of this use of myth in Nietzsche's Zarathustra, and, finally, trace a similar function at work in Rilke's Malte and Walter Benjamin's historical materialist. ;Contrary to Habermas, who argues that Nietzsche opened up two roads to postmodernity, one leading to the "ontologization of aesthetics" and the other to the "totalizing critique" of reason , I put forth the argument that the Nietzschean "two roads" metaphor is useful but needs to be re-shaped, configuring one road toward the mythological history and historical mythology of Rilke and Walter Benjamin, and another road the Theodor Adorno's "thorough critique" of reason. ;The need to revise Habermas's "two roads to post-modernity" theory mythographically, rests on the primary investigation of this dissertation: to trace by de-scription the practical incarnation of the word on German soil . I define this process of "practical incarnation" as that word which subversively desires to de-scribe and trans-figure the neurotic -psychotic structure that has defined the parameters of Western discourse, at least since neo-Platonic Christianity influenced cultural codifications of the West. Finally, I maintain that the primary image of criticism which emerges from the dialectical work of the writers herein, is the image of man-child, a classless, non-totalizing image implicit in Goethe's Wilhelm Meister, and developed in the Kind-Mensch constellation in the work of Nietzsche, Rilke, and Walter Benjamin. (shrink)

Lauritz Munch and Björn Lundgren have recently replied to a paper published by us in this journal. In our original paper, we defended a novel version of the so-called ‘control theory’ of the moral right to privacy. We argued that control theorists should define ‘control’ as what we coined ‘Negative Control’. Munch and Lundgren have recently provided a range of interesting and challenging objections to our view. Independently of each other, they give almost identical counterexamples to our (...) definition of Negative Control. In this comment, we show that while the counterexamples are genuine counterexamples, they do not force us to abandon the idea of Negative Control. Furthermore, we reply to two additional objections raised by Lundgren. One of these replies involves giving a new account of what the relation is between the concept of privacy and the right to privacy. (shrink)