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104 Publications visible to you, out of a total of 104
NFDI4Health Local Data Hubs for Finding and Accessing Health Data

Abstract (Expand)

To support federated data structuring and sharing for sensitive health data from clinical trial, epidemiological and public health studies in the context of the German National Research Data Infrastructure … for Personal Health Data (NFDI4Health), we have developed Local Data Hubs (LDHs) based on the FAIRDOM-SEEK platform. Those LDHs connect to the German Central Health Study Hub (CSH) to make the health data searchable and findable. This decentralised approach supports researchers to make health studies with their data FAIR (Findable, Accessible, Interoperable and Reusable), and at the same time fully preserves data protection for sensitive data.

Authors: Frank Meineke, Martin Golebiewski, Xiaoming Hu, Toralf Kirsten, Matthias Löbe, Sebastian Klammt, Ulrich Sax, Wolfgang Müller

Date Published: 7th Sep 2023

Publication Type: Proceedings

Provenance Core Data Set: A Minimal Information Model for Data Provenance in Biomedical Research

Abstract (Expand)

The exchange, dissemination, and reuse of biological specimens and data have become essentialfor life sciences research. This requires standards that enable cross-organizational documentation, traceability, … and tracking of data and its corresponding metadata. Thus, data provenance, or the lineage of data, is an important aspect of data management in any information system integrating data from different sources [1]. It provides crucial information about the origin, transformation, and accountability of data, which is essential for ensuring trustworthiness, transparency, and quality of healthcare data [2]. For biological material and derived data, a novel ISO standard was recently introduced that specifies a general concept for a provenance information model for biological material and data and requirements for provenance data interoperability and serialization [3,4]. However, a specific standard for health data provenance is currently missing. In recent years, there has been a growing need for developing a minimal core data set for representing provenance information in health information systems. This paper presents a Provenance Core Data Set (PCDS), a generalized data model that aims to provide a set of attributes for describing data provenance in health information systems and beyond. 

Authors: Ulrich Sax, Christian Henke, Christian Dräger, Theresa Bender, Alessandra Kuntz, Martin Golebiewski, Hannes Ulrich, Mattias Löbe

Date Published: 7th Sep 2023

Publication Type: Journal

Metadata schema of the NFDI4Health and the NFDI4Health Task Force COVID-19 (V3_2)

Abstract (Expand)

The Metadata Schema of the NFDI4Health and the NFDI4Health Task Force COVID-19 (Metadata Schema) contains a list of properties that describe a resource to be registered in the German Central Health … Study Hub. Currently, two main types of resources are distinguished: a) study descriptions (i.e., metadata set describing a study) and b) study documents. However, due to the generic character of the Metadata Schema, other types of resources may also be described and registered. The metadata properties are divided into mandatory and recommended ones. Along with bibliographic information such as title and description of the resource, the related persons and organizations contributing to the development of the resource can also be specified. The results of studies published in journal articles or other text publications can be linked too. For studies, information about study design and accessibility of the collected data should be additionally provided. The Metadata Schema consists mainly of properties adapted from established standards and models such as DataCite Metadata Schema 4.4, data models of the ClinicalTrials.gov, German Clinical Trials Register, International Clinical Trials Registry, HL7® FHIR, MIABIS, Maelstrom Research cataloguing toolkit and DDI Controlled Vocabularies. This is an updated version V3_2 of the Metadata Schema, which improves the modules of the previous version via refined description texts and added, deleted, moved, or renamed items. Additional use case-specific requirements, particularly for the chronic diseases and record linkage modules, have also been considered in this new version along with updating the list of sources. The undertaken changes are described within the document.

Authors: Haitham Abaza, A. Shutsko, Martin Golebiewski, Sophie Klopfenstein, Carsten Oliver Schmidt, Carina Vorisek, NFDI4Health Task Force COVID-19, NFDI4Health, C. Brünings-Kuppe, V. Clemens, J. Darms, S. Hanß, T. Intemann, F. Jannasch, E. Kasbohm, Birte Lindstädt, Matthias Löbe, E. Orban, I. Perrar, M. Peters, U. Sax, M. Schulze, C. Schupp, F. Schwarz, C. Schwedhelm, S. Strathmann, Dagmar Waltemath, H. Wünsche, A. Zeleke

Date Published: 14th Aug 2023

Publication Type: Misc

First Draft of the VHT Roadmap

Abstract (Expand)

The VHT Roadmap is due – in its final version – by the end of the EDITH Coordination and Support Action (i.e., September 2024). The present document is the first draft of the Roadmap, This preliminary …y version of the Roadmap was planned in EDITH’s Grant Agreement as an initial contribution to the internal decision-making process of the European Commission. It has the declared purpose of allowing the Commission to start specifying already at an early stage by what steps the goal of pursuing the development of a VHT-based healthcare will be likely to trigger an effective engagement of Europe’s researchers, clinicians, industries, and regulators. This interim version is therefore meant to highlight what is currently the envisioned structure of what will be in a year time the final roadmap and its main contents, leaving open the possibility that these contents can still be subject to both substantial and formal changes, in response to suggestions coming from both the European Commission and from different sectors of the broadening community of practice that the EDITH CSA is addressing. In consideration of these double-edge purposes, this preliminary draft aims to capture the main concepts and the overall approach of the VHT Roadmap, while also identifying relevant challenges (from the perspective of research, infrastructure, and other specific aspects) that need to be addressed in the remaining year of the EDITH CSA (and beyond) and which will require further analysis, with the support of the whole VHT Community. For the technology, standards, regulatory, and legal aspects, the draft provides an overview of the state of the art and an analysis of VHT-specific needs, without determining as yet any conclusive choice. Given the evolving nature of this document, the submitted text will again be made publicly available for further comments and feedback, in view of possibly including valuable inputs in a next version. For general discussions, we encourage everyone to use the slack channel on the In silico World Community of Practice (ISW_CoP: https://insilico.world/community/join-the-community-of-practice-channels/). Critical remarks are welcome, as well as additional contributions, but also comments highlighting what sections are particularly appreciated will definitely help. if you would like to stay updated on EDITH's progress, you can enter your details via the contact form on the website: https://www.edith-csa.eu/contact/

Author: Gerhard Mayer, Martin Golebiewski

Date Published: 31st Jul 2023

Publication Type: Misc

ISO/TS 9491-1:2023 Biotechnology — Predictive computational models in personalized medicine research — Part 1: Constructing, verifying and validating models

Abstract (Expand)

This document defines challenges and requirements for predictive computational models constructed for research purposes in personalized medicine. It specifies recommendations and requirements for the … setup, formatting, validation, simulation, storing and sharing of such models, as well as their application in clinical trials and other research areas. It summarizes specific challenges regarding data input, as well as verifying and validating of such models that can be considered as best practices for modelling in research and development in the field of personalized medicine. This document also specifies recommendations and requirements for data used to construct or needed for validating models, including rules and requirements for formatting, description, annotation, interoperability, integration, accessing, as well as recording and documenting the provenance of such data. This document does not provide specific rules or requirements for the use of computational models in the clinical routine, or for diagnostic or therapeutic purposes.

Authors: Marc Kirschner, Martin Golebiewski, Heike Moser, EU-STANDS4PM consortium, ISO/TC 276/WG 5

Date Published: 8th Jun 2023

Publication Type: Manual

BioModelsML: Building a FAIR and reproducible collection of machine learning models in life sciences and medicine for easy reuse

Abstract (Expand)

Abstract Machine learning (ML) models are widely used in life sciences and medicine; however, they are scattered across various platforms and there are several challenges that hinder their accessibility, …r their accessibility, reproducibility and reuse. In this manuscript, we present the formalisation and pilot implementation of community protocol to enable FAIReR (Findable, Accessible, Interoperable, Reusable, and Reproducible) sharing of ML models. The protocol consists of eight steps, including sharing model training code, dataset information, reproduced figures, model evaluation metrics, trained models, Dockerfiles, model metadata, and FAIR dissemination. Applying these measures we aim to build and share a comprehensive public collection of FAIR ML models in the BioModels repository through incentivized community curation. In a pilot implementation, we curated diverse ML models to demonstrate the feasibility of our approach and we discussed the current challenges. Building a FAIReR collection of ML models will directly enhance the reproducibility and reusability of ML models, minimising the effort needed to reimplement models, maximising the impact on the application and significantly accelerating the advancement in the field of life science and medicine.

Authors: Divyang Deep Tiwari, Nils Hoffmann, Kieran Didi, Sumukh Deshpande, Sucheta Ghosh, Tung V. N. Nguyen, Karthik Raman, Henning Hermjakob, Rahuman Sheriff

Date Published: 23rd May 2023

Publication Type: Misc

Metadata schema of the NFDI4Health and the NFDI4Health Task Force COVID-19 (V3_1)

Abstract (Expand)

The Metadata Schema of the NFDI4Health and the NFDI4Health Task Force COVID-19 (Metadata Schema) contains a list of properties that describe a resource to be registered in the German Central Health … Study Hub. Currently, two main types of resources are distinguished: a) study descriptions (i.e., metadata set describing a study) and b) study documents. However, due to the generic character of the Metadata Schema, other types of resources may also be described and registered. The metadata properties are divided into mandatory and recommended ones. Along with bibliographic information such as title and description of the resource, the related persons and organizations contributing to the development of the resource can also be specified. The results of studies published in journal articles or other text publications can be linked too. For studies, information about study design and accessibility of the collected data should be additionally provided. The Metadata Schema consists mainly of properties adapted from established standards and models such as DataCite Metadata Schema 4.4, data models of the ClinicalTrials.gov, German Clinical Trials Register, International Clinical Trials Registry, HL7® FHIR, MIABIS, Maelstrom Research cataloguing toolkit and DDI Controlled Vocabularies. This is an updated version V3_1 of the Metadata Schema, which introduces two new resource types, namely registries and secondary data sources. Accordingly, the metadata set describing studies, which was part of the core module in previous versions, has been split into a separate module and adapted to also apply to registries and secondary data sources. An additional use case-specific module has also been added, including metadata specific to record linkage. The undertaken changes are described within the document.

Authors: Haitham Abaza, A. Shutsko, M. Golebiewski, Sophie Klopfenstein, C. O. Schmidt, Carina Vorisek, NFDI4Health Task Force COVID-19, NFDI4Health, C. Brünings-Kuppe, V. Clemens, J. Darms, S. Hanß, T. Intemann, F. Jannasch, E. Kasbohm, B. Lindstadt, M. Lobe, E. Orban, I. Perrar, M. Peters, U. Sax, M. Schulze, C. Schupp, F. Schwarz, C. Schwedhelm, S. Strathmann, D. Waltemath, H. Wünsche, A. A. Zeleke

Date Published: 10th May 2023

Publication Type: Misc

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