Journal of Philosophy of Education, EarlyView.

For researchers who study technology designs, the application and execution of so-called design-oriented research projects are a common way of funding their research. Against this background, we propose a new methodical approach with which VSD can easily be implemented in such projects and which we call “value declaration”. We share our experience with this method which we gained in two design-oriented research projects.

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)

Carol Gilligan has delineated two ethics, the ethic of rights and the ethic of care. In this article I argue that the two ethics are part of one overall system, the ethic of care functioning as a necessary base for the ethic of rights. I also argue that the system is seriously flawed. Because women are held accountable to both ethics and because the two ethics frequently conflict, women recurrently find themselves in a moral double bind.

Carol Gilligan has delineated two ethics, the ethic of rights and the ethic of care. In this article I argue that the two ethics are part of one overall system, the ethic of care functioning as a necessary base for the ethic of rights. 1 also argue that the system is seriously flawed. Because women are held accountable to both ethics and because the two ethics frequently conflict, women recurrently find themselves in a moral double bind.

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)

BackgroundAustralian health and medical research funders support substantial research efforts, and incentives within grant funding schemes influence researcher behaviour. We aimed to determine to what extent Australian health and medical funders incentivise responsible research practices.MethodsWe conducted an audit of instructions from research grant and fellowship schemes. Eight national research grants and fellowships were purposively sampled to select schemes that awarded the largest amount of funds. The funding scheme instructions were assessed against 9 criteria to determine to what extent they incentivised (...) these responsible research and reporting practices: publicly register study protocols before starting data collection, register analysis protocols before starting data analysis, make study data openly available, make analysis code openly available, make research materials openly available, discourage use of publication metrics, conduct quality research, collaborate with a statistician, and adhere to other responsible research practices. Each criterion was answered using one of the following responses: “Instructed”, “Encouraged”, or “No mention”.ResultsAcross the 8 schemes from 5 funders, applicants were instructed or encouraged to address a median of 4 of the 9 criteria. Three criteria received no mention in any scheme. Importantly, most incentives did not seem strong as applicants were only instructed to register study protocols, discourage use of publication metrics and conduct quality research. Other criteria were encouraged but were not required.ConclusionsFunders could strengthen the incentives for responsible research practices by requiring grant and fellowship applicants to implement these practices in their proposals. Administering institutions could be required to implement these practices to be eligible for funding. Strongly rewarding researchers for implementing robust research practices could lead to sustained improvements in the quality of health and medical research. (shrink)

Distractibility is one of the key features of attention deficit hyperactivity disorder and has been associated with alterations in the neural orienting and alerting networks. Task-irrelevant stimuli are thus expected to have detrimental effects on the performance of patients with ADHD. However, task-irrelevant presentation of novel sounds seems to have the opposite effect and improve subsequent attentional performance particularly in patients with ADHD. Here, we aimed to understand the neural modulations of the attention networks underlying these improvements. Fifty boys participated (...) in a functional magnetic resonance imaging study in which unique or repeatedly presented sounds were placed before a visual flanker task in 2/3 of the trials. We found that presenting any sound improved task performance in all participants, but the underlying neural mechanisms differed for the type of sound. Familiar sounds led to a stronger increase in activity in the left posterior insula in patients with ADHD compared to typically developing peers. Novel sounds led to activations of the fronto-temporoparietal ventral attention network, likewise in ADHD and TD. These changes in signaling by novelty in the right inferior frontal gyrus were directly related to improved response speed showing that neural orienting network activity following novel sounds facilitated subsequent attentional performance. This mechanism of behavioral enhancement by short distractions could potentially be useful for cognitive trainings or homework situations. (shrink)