Analysis of biomedical data with multilevel glyphs

BACKGROUND: This paper presents multilevel data glyphs optimized for the interactive knowledge discovery and visualization of large biomedical data sets. Data glyphs are three- dimensional objects defined by multiple levels of geometric descriptions (levels of detail) combined with a mapping of data attributes to graphical elements and methods, which specify their spatial position. METHODS: In the data mapping phase, which is done by a biomedical expert, meta information about the data attributes (scale, number of distinct values) are compared with the visual capabilities of the graphical elements in order to give a feedback to the user about the correctness of the variable mapping. The spatial arrangement of glyphs is done in a dimetric view, which leads to high data density, a simplified 3D navigation and avoids perspective distortion. RESULTS: We show the usage of data glyphs in the disease analyser a visual analytics application for personalized medicine and provide an outlook to a biomedical web visualization scenario. CONCLUSIONS: Data glyphs can be successfully applied in the disease analyser for the analysis of big medical data sets. Especially the automatic validation of the data mapping, selection of subgroups within histograms and the visual comparison of the value distributions were seen by experts as an important functionality

BBMRI-ERIC's contributions to research and knowledge exchange on COVID-19

During the COVID-19 pandemic, the European biobanking infrastructure is in a unique position to preserve valuable biological material complemented with detailed data for future research purposes. Biobanks can be either integrated into healthcare, where preservation of the biological material is a fork in clinical routine diagnostics and medical treatment processes or they can also host prospective cohorts or material related to clinical trials. The paper discussed objectives of BBMRI-ERIC, the European research infrastructure established to facilitate access to quality-defined biological materials and data for research purposes, with respect to the COVID-19 crisis: (a) to collect information on available European as well as non-European COVID-19-relevant biobanking resources in BBMRI-ERIC Directory and to facilitate access to these via BBMRI-ERIC Negotiator platform; (b) to help harmonizing guidelines on how data and biological material is to be collected to maximize utility for future research, including large-scale data processing in artificial intelligence, by participating in activities such as COVID-19 Host Genetics Initiative; (c) to minimize risks for all involved parties dealing with (potentially) infectious material by developing recommendations and guidelines; (d) to provide a European-wide platform of exchange in relation to ethical, legal, and societal issues (ELSI) specific to the collection of biological material and data during the COVID-19 pandemic

BBMRI-ERIC Negotiator:Implementing Efficient Access to Biobanks

Various biological resources, such as biobanks and disease-specific registries, have become indispensable resources to better understand the epidemiology and biological mechanisms of disease and are fundamental for advancing medical research. Nevertheless, biobanks and similar resources still face significant challenges to become more findable and accessible by users on both national and global scales. One of the main challenges for users is to find relevant resources using cataloging and search services such as the BBMRI-ERIC Directory, operated by European Research Infrastructure on Biobanking and Biomolecular Resources (BBMRI-ERIC), as these often do not contain the information needed by the researchers to decide if the resource has relevant material/data; these resources are only weakly characterized. Hence, the researcher is typically left with too many resources to explore and investigate. In addition, resources often have complex procedures for accessing holdings, particularly for depletable biological materials. This article focuses on designing a system for effective negotiation of access to holdings, in which a researcher can approach many resources simultaneously, while giving each resource team the ability to implement their own mechanisms to check if the material/data are available and to decide if access should be provided. The BBMRI-ERIC has developed and implemented an access and negotiation tool called the BBMRI-ERIC Negotiator. The Negotiator enables access negotiation to more than 600 biobanks from the BBMRI-ERIC Directory and other discovery services such as GBA/BBMRI-ERIC Locator or RD-Connect Finder. This article summarizes the principles that guided the design of the tool, the terminology used and underlying data model, request workflows, authentication and authorization mechanism(s), and the mechanisms and monitoring processes to stimulate the desired behavior of the resources: to effectively deliver access to biological material and data