Eos and OMOCL: Towards a seamless integration of openEHR records into the OMOP Common Data Model.

BACKGROUND: The reuse of data from electronic health records (EHRs) for research purposes promises to improve the data foundation for clinical trials and may even support to enable them. Nevertheless, EHRs are characterized by both, heterogeneous structure and semantics. To standardize this data for research, the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) standard has recently seen an increase in use. However, the conversion of these EHRs into the OMOP CDM requires complex and resource intensive Extract Transform and Load (ETL) processes. This hampers the reuse of clinical data for research. To solve the issues of heterogeneity of EHRs and the lack of semantic precision on the care site, the openEHR standard has recently seen wider adoption. A standardized process to integrate openEHR records into the CDM potentially lowers the barriers of making EHRs accessible for research. Yet, a comprehensive approach about the integration of openEHR records into the OMOP CDM has not yet been made. METHODS: We analyzed both standards and compared their models to identify possible mappings. Based on this, we defined the necessary processes to transform openEHR records into CDM tables. We also discuss the limitation of openEHR with its unspecific demographics model and propose two possible solutions. RESULTS: We developed the OMOP Conversion Language (OMOCL) which enabled us to define a declarative openEHR archetype-to-CDM mapping language. Using OMOCL, it was possible to define a set of mappings. As a proof-of-concept, we implemented the Eos tool, which uses the OMOCL-files to successfully automatize the ETL from real-world and sample EHRs into the OMOP CDM. DISCUSSION: Both Eos and OMOCL provide a way to define generic mappings for an integration of openEHR records into OMOP. Thus, it represents a significant step towards achieving interoperability between the clinical and the research data domains. However, the transformation of openEHR data into the less expressive OMOP CDM leads to a loss of semantics.

A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects.

Sustainable noncommercial bioinformatics infrastructures are a prerequisite to use and take advantage of the potential of big data analysis for research and economy. Consequently, funders, universities and institutes as well as users ask for a transparent value model for the tools and services offered. In this article, a generally applicable lightweight method is described by which bioinformatics infrastructure projects can estimate the value of tools and services offered without determining exactly the total costs of ownership. Five representative scenarios for value estimation from a rough estimation to a detailed breakdown of costs are presented. To account for the diversity in bioinformatics applications and services, the notion of service-specific 'service provision units' is introduced together with the factors influencing them and the main underlying assumptions for these 'value influencing factors'. Special attention is given on how to handle personnel costs and indirect costs such as electricity. Four examples are presented for the calculation of the value of tools and services provided by the German Network for Bioinformatics Infrastructure (de.NBI): one for tool usage, one for (Web-based) database analyses, one for consulting services and one for bioinformatics training events. Finally, from the discussed values, the costs of direct funding and the costs of payment of services by funded projects are calculated and compared.

A Scholarly Knowledge Graph-Powered Dashboard: Implementation and User Evaluation.

Scholarly knowledge graphs provide researchers with a novel modality of information retrieval, and their wider use in academia is beneficial for the digitalization of published works and the development of scholarly communication. To increase the acceptance of scholarly knowledge graphs, we present a dashboard, which visualizes the research contributions on an educational science topic in the frame of the Open Research Knowledge Graph (ORKG). As dashboards are created at the intersection of computer science, graphic design, and human-technology interaction, we used these three perspectives to develop a multi-relational visualization tool aimed at improving the user experience. According to preliminary results of the user evaluation survey, the dashboard was perceived as more appealing than the baseline ORKG-powered interface. Our findings can be used for the development of scholarly knowledge graph-powered dashboards in different domains, thus facilitating acceptance of these novel instruments by research communities and increasing versatility in scholarly communication.

A star-shaped heteronuclear Cr(III)Mn(II)3 species and its precise electronic and magnetic structure: spin frustration studied by X-ray spectroscopic, magnetic, and theoretical methods.

Molecular magnets incorporate transition-metal ions with organic groups providing a bridge to mediate magnetic exchange interactions between the ions. Among them are star-shaped molecules in which antiferromagnetic couplings between the central and peripheral atoms are predominantly present. Those configurations lead to an appreciable spin moment in the nonfrustrated ground state. In spite of its topologically simple magnetic structure, the [Cr(III)Mn(II)(3) (PyA)(6)Cl(3)] (CrMn(3)) molecule, in which PyA represents the monoanion of syn-pyridine-2-aldoxime, exhibits nontrivial magnetic properties, which emerge from the combined action of single-ion anisotropy and frustration. In the present work, we elucidate the underlying electronic and magnetic properties of the heteronuclear, spin-frustrated CrMn(3) molecule by applying X-ray magnetic circular dichroism (XMCD), as well as magnetization measurements in high magnetic fields, density functional theory, and ligand-field multiplet calculations. Quantum-model calculations based on a Heisenberg Hamiltonian augmented with local anisotropic terms enable us not only to improve the accuracy of the exchange interactions but also to determine the dominant local anisotropies. A discussion of the various spin Hamiltonian parameters not only leads to a validation of our element selective transition metal L edge XMCD spin moments at a magnetic field of 5 T and a temperature of 5 K but also allows us to monitor an interesting effect of anisotropy and frustration of the manganese and chromium ions.

de.NBI Cloud federation through ELIXIR AAI.

The academic de.NBI Cloud offers compute resources for life science research in Germany.  At the beginning of 2017, de.NBI Cloud started to implement a federated cloud consisting of five compute centers, with the aim of acting as one resource to their users. A federated cloud introduces multiple challenges, such as a central access and project management point, a unified account across all cloud sites and an interchangeable project setup across the federation. In order to implement the federation concept, de.NBI Cloud integrated with the ELIXIR authentication and authorization infrastructure system (ELIXIR AAI) and in particular Perun, the identity and access management system of ELIXIR. The integration solves the mentioned challenges and represents a backbone, connecting five compute centers which are based on OpenStack and a web portal for accessing the federation.This article explains the steps taken and software components implemented for setting up a federated cloud based on the collaboration between de.NBI Cloud and ELIXIR AAI. Furthermore, the setup and components that are described are generic and can therefore be used for other upcoming or existing federated OpenStack clouds in Europe.

OTP: An automatized system for managing and processing NGS data.

The One Touch Pipeline (OTP) is an automation platform managing Next-Generation Sequencing (NGS) data and calling bioinformatic pipelines for processing these data. OTP handles the complete digital process from import of raw sequence data via alignment of sequencing reads to identify genomic events in an automated and scalable way. Three major goals are pursued: firstly, reduction of human resources required for data management by introducing automated processes. Secondly, reduction of time until the sequences can be analyzed by bioinformatic experts, by executing all operations more reliably and quickly. Thirdly, storing all information in one system with secure web access and search capabilities. From software architecture perspective, OTP is both information center and workflow management system. As a workflow management system, OTP call several NGS pipelines that can easily be adapted and extended according to new requirements. As an information center, it comprises a database for metadata information as well as a structured file system. Based on complete and consistent information, data management and bioinformatic pipelines within OTP are executed automatically with all steps book-kept in a database.

Electronic structure and soft-X-ray-induced photoreduction studies of iron-based magnetic polyoxometalates of type {(M)M5}12Fe(III)30 (M = Mo(VI), W(VI)).

Giant Keplerate-type molecules with a {Mo72Fe30} core show a number of very interesting properties, making them particularly promising for various applications. So far, only limited data on the electronic structure of these molecules from X-ray spectra and electronic structure calculations have been available. Here we present a combined electronic and magnetic structure study of three Keplerate-type nanospheres--two with a {Mo72Fe30} core and one with a {W72Fe30} core by means of X-ray absorption spectroscopy, X-ray magnetic circular dichroism (XMCD), SQUID magnetometry, and complementary theoretical approaches. Furthermore, we present detailed studies of the Fe(3+)-to-Fe(2+) photoreduction process, which is induced under soft X-ray radiation in these molecules. We observe that the photoreduction rate greatly depends on the ligand structure surrounding the Fe ions, with negatively charged ligands leading to a dramatically reduced photoreduction rate. This opens the possibility of tailoring such polyoxometalates by X-ray spectroscopic studies and also for potential applications in the field of X-ray induced photochemistry.

Backbone rigidity and static presentation of guanidinium groups increases cellular uptake of arginine-rich cell-penetrating peptides.

In addition to endocytosis-mediated cellular uptake, hydrophilic cell-penetrating peptides are able to traverse biological membranes in a non-endocytic mode termed transduction, resulting in immediate bioavailability. Here we analysed structural requirements for the non-endocytic uptake mode of arginine-rich cell-penetrating peptides, by a combination of live-cell microscopy, molecular dynamics simulations and analytical ultracentrifugation. We demonstrate that the transduction efficiency of arginine-rich peptides increases with higher peptide structural rigidity. Consequently, cyclic arginine-rich cell-penetrating peptides showed enhanced cellular uptake kinetics relative to their linear and more flexible counterpart. We propose that guanidinium groups are forced into maximally distant positions by cyclization. This orientation increases membrane contacts leading to enhanced cell penetration.

Star-shaped molecule of MnII4O6 core with an St=10 high-spin state. A theoretical and experimental study with XPS, XMCD, and other magnetic methods.

We report a comprehensive study of the electronic and magnetic properties of a star-shaped molecule comprising a MnII4O6 core. One feature of this compound is weak magnetic coupling constants compared to other similar polyoxo compounds. This leads to complicated low-lying magnetic states in which the ground state is not well separated from the upper-lying states, yielding a high-spin molecule with a giant magnetic moment of up to 20 microB/formula unit. We apply X-ray diffraction and magnetometry as well as other X-ray spectroscopic techniques, namely, X-ray photoelectron spectroscopy, X-ray magnetic circular dichroism, and X-ray emission spectroscopy. We compare our experimental results with ab initio electronic band structure calculations as well as the localized electronic structure around the Mn2+ ions with charge-transfer multiplet calculations.