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115 Publications visible to you, out of a total of 115
BioHackEU24 report: Creating user benefit from ARC-ISA RO-Crate machine-actionability & Increasing FAIRness of digital agrosystem resources by extending Bioschemas

Abstract (Expand)

As part of the BioHackathon Europe 2024, we here report on the progress that both project 19 and project 24 have made during the event. For the purpose of this report we will present the abstract of … abstract of both projects and then dive deeper on what work was done during the BioHackathon.

Authors: Sebastian Beier, Daniel Arend, Daniel Bauer, Marco Brandizi, Dominik Brilhaus, Eli Chadwick, Vera Clemens, Michael Robin Crusoe, Manuel Feser, Jonas Grieb, Xiaoming Hu, Abigail Miller, Timo Mühlhaus, Stuart Owen, Maja Rey, Gabriel Schneider, Julian Schneider, Kevin Schneider, Heinrich Lukas Weil, Florian Wetzels

Date Published: 2nd Feb 2025

Publication Type: Tech report

NFDI4Health Local Data Hubs Implementing a Tailored Metadata Schema for Health Data

Abstract (Expand)

Introduction: NFDI4Health is a consortium funded by the German Research Foundation to make structured health data findable and accessible internationally according to the FAIR principles. Its goal is …s. Its goal is bringing data users and Data Holding Organizations (DHOs) together. It mainly considers DHOs conducting epidemiological and public health studies or clinical trials. Methods: Local data hubs (LDH) are provided for such DHOs to connect decentralized local research data management within their organizations with the option of publishing shareable metadata via centralized NFDI4Health services such as the German central Health Study Hub. The LDH platform is based on FAIRDOM SEEK and provides a complete and flexible, locally controlled data and information management platform for health research data. A tailored NFDI4Health metadata schema for studies and their corresponding resources has been developed which is fully supported by the LDH software, e.g. for metadata transfer to other NFDI4Health services. Results: The SEEK platform has been technically enhanced to support extended metadata structures tailored to the needs of the user communities in addition to the existing metadata structuring of SEEK. Conclusion: With the LDH and the MDS, the NFDI4Health provides all DHOs with a standardized and free and open source research data management platform for the FAIR exchange of structured health data.

Authors: Xiaoming Hu, Haitham Abaza, Rene Hänsel, Masoud Abedi, Martin Golebiewski, Wolfgang Müller, Frank Meineke

Date Published: 30th Aug 2024

Publication Type: InProceedings

Using Health IT Standards to Facilitate Metadata Exchange Between Research Data Management Systems

Abstract (Expand)

The National Research Data Infrastructure for Personal Health Data (NFDI4Health) uses Local Data Hubs (LDHs) to manage locally research studies, documents and sensitive personal data to support controlled …ort controlled data sharing. While research data management (RDM) systems facilitate the storage and preparation of data and metadata as well as organizational access, they often lack support for interoperability standards of the application domain. To support the exchange with external registries of research studies, we chose 17 attributes to characterize the most relevant aspects of clinical trials (in the following named “metadata profile”). We implemented the metadata profile in the RDM system FAIRDOM SEEK using core attributes and SEEK’s extended metadata feature and created a mapping conforming to the Health Level 7 Fast Healthcare Interoperability Resources (FHIR) standard version R4. Finally, we implemented a prototype application interface for exports in FHIR-JSON format. We plan to extend the interface to serve central registries and support specific FHIR Implementation Guides from various use cases.

Authors: Matthias Löbe, Xiaoming Hu, Sophie A.I. Klopfenstein

Date Published: 22nd Aug 2024

Publication Type: Journal

Towards an Interoperability Landscape for a National Research Data Infrastructure for Personal Health Data.

Abstract (Expand)

The German initiative "National Research Data Infrastructure for Personal Health Data" (NFDI4Health) focuses on research data management in health research. It aims to foster and develop … harmonized informatics standards for public health, epidemiological studies, and clinical trials, facilitating access to relevant data and metadata standards. This publication lists syntactic and semantic data standards of potential use for NFDI4Health and beyond, based on interdisciplinary meetings and workshops, mappings of study questionnaires and the NFDI4Health metadata schema, and literature search. Included are 7 syntactic, 32 semantic and 9 combined syntactic and semantic standards. In addition, 101 ISO Standards from ISO/TC 215 Health Informatics and ISO/TC 276 Biotechnology could be identified as being potentially relevant. The work emphasizes the utilization of standards for epidemiological and health research data ensuring interoperability as well as the compatibility to NFDI4Health, its use cases, and to (inter-)national efforts within these sectors. The goal is to foster collaborative and inter-sectoral work in health research and initiate a debate around the potential of using common standards.

Authors: C. N. Vorisek, S. A. I. Klopfenstein, M. Lobe, C. O. Schmidt, P. J. Mayer, M. Golebiewski, S. Thun

Date Published: 13th Jul 2024

Publication Type: Journal

Making Epidemiological and Clinical Studies FAIR Using the Example of COVID-19

Abstract (Expand)

Abstract FAIRification of personal health data is of utmost importance to improve health research and political as well as medical decision-making, which ultimately contributes to a better health of …utes to a better health of the general population. Despite the many advances in information technology, several obstacles such as interoperability problems remain and relevant research on the health topic of interest is likely to be missed out due to time-consuming search and access processes. A recent example is the COVID-19 pandemic, where a better understanding of the virus’ transmission dynamics as well as preventive and therapeutic options would have improved public health and medical decision-making. Consequently, the NFDI4Health Task Force COVID-19 was established to foster the FAIRification of German COVID-19 studies. This paper describes the various steps that have been taken to create low barrier workflows for scientists in finding and accessing German COVID-19 research. It provides an overview on the building blocks for FAIR health research within the Task Force COVID-19 and how this initial work was subsequently expanded by the German consortium National Research Data Infrastructure for Personal Health Data (NFDI4Health) to cover a wider range of studies and research areas in epidemiological, public health and clinical research. Lessons learned from the Task Force helped to improve the respective tasks of NFDI4Health.

Authors: Iris Pigeot, Wolfgang Ahrens, Johannes Darms, Juliane Fluck, Martin Golebiewski, Horst K. Hahn, Xiaoming Hu, Timm Intemann, Elisa Kasbohm, Toralf Kirsten, Sebastian Klammt, Sophie Anne Ines Klopfenstein, Bianca Lassen-Schmidt, Manuela Peters, Ulrich Sax, Dagmar Waltemath, Carsten Oliver Schmidt

Date Published: 1st Jul 2024

Publication Type: Journal

Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024.

Abstract

Not specified

Authors: M. Golebiewski, G. Bader, P. Gleeson, T. E. Gorochowski, S. M. Keating, M. Konig, C. J. Myers, D. P. Nickerson, B. Sommer, D. Waltemath, F. Schreiber

Date Published: 1st Mar 2024

Publication Type: Journal

Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.

Abstract (Expand)

INTRODUCTION: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing … SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. METHODS: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors. RESULTS: Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19. DISCUSSION: The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.

Authors: A. Niarakis, M. Ostaszewski, A. Mazein, I. Kuperstein, M. Kutmon, M. E. Gillespie, A. Funahashi, M. L. Acencio, A. Hemedan, M. Aichem, K. Klein, T. Czauderna, F. Burtscher, T. G. Yamada, Y. Hiki, N. F. Hiroi, F. Hu, N. Pham, F. Ehrhart, E. L. Willighagen, A. Valdeolivas, A. Dugourd, F. Messina, M. Esteban-Medina, M. Pena-Chilet, K. Rian, S. Soliman, S. S. Aghamiri, B. L. Puniya, A. Naldi, T. Helikar, V. Singh, M. F. Fernandez, V. Bermudez, E. Tsirvouli, A. Montagud, V. Noel, M. Ponce-de-Leon, D. Maier, A. Bauch, B. M. Gyori, J. A. Bachman, A. Luna, J. Pinero, L. I. Furlong, I. Balaur, A. Rougny, Y. Jarosz, R. W. Overall, R. Phair, L. Perfetto, L. Matthews, D. A. B. Rex, M. Orlic-Milacic, L. C. M. Gomez, B. De Meulder, J. M. Ravel, B. Jassal, V. Satagopam, G. Wu, M. Golebiewski, P. Gawron, L. Calzone, J. S. Beckmann, C. T. Evelo, P. D'Eustachio, F. Schreiber, J. Saez-Rodriguez, J. Dopazo, M. Kuiper, A. Valencia, O. Wolkenhauer, H. Kitano, E. Barillot, C. Auffray, R. Balling, R. Schneider

Date Published: 29th Feb 2024

Publication Type: Journal

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