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107 Publications visible to you, out of a total of 107
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

Toward a common standard for data and specimen provenance in life sciences

Abstract (Expand)

Open and practical exchange, dissemination, and reuse of specimens and data have become a fundamental requirement for life sciences research. The quality of the data obtained and thus the findings and … knowledge derived is thus significantly influenced by the quality of the samples, the experimental methods, and the data analysis. Therefore, a comprehensive and precise documentation of the pre-analytical conditions, the analytical procedures, and the data processing are essential to be able to assess the validity of the research results. With the increasing importance of the exchange, reuse, and sharing of data and samples, procedures are required that enable cross-organizational documentation, traceability, and non-repudiation. At present, this information on the provenance of samples and data is mostly either sparse, incomplete, or incoherent. Since there is no uniform framework, this information is usually only provided within the organization and not interoperably. At the same time, the collection and sharing of biological and environmental specimens increasingly require definition and documentation of benefit sharing and compliance to regulatory requirements rather than consideration of pure scientific needs. In this publication, we present an ongoing standardization effort to provide trustworthy machine-actionable documentation of the data lineage and specimens. We would like to invite experts from the biotechnology and biomedical fields to further contribute to the standard.

Authors: Rudolf Wittner, Petr Holub, Cecilia Mascia, Francesca Frexia, Heimo Müller, Markus Plass, Clare Allocca, Fay Betsou, Tony Burdett, Ibon Cancio, Adriane Chapman, Martin Chapman, Mélanie Courtot, Vasa Curcin, Johann Eder, Mark Elliot, Katrina Exter, Carole Goble, Martin Golebiewski, Bron Kisler, Andreas Kremer, Simone Leo, Sheng Lin‐Gibson, Anna Marsano, Marco Mattavelli, Josh Moore, Hiroki Nakae, Isabelle Perseil, Ayat Salman, James Sluka, Stian Soiland‐Reyes, Caterina Strambio‐De‐Castillia, Michael Sussman, Jason R. Swedlow, Kurt Zatloukal, Jörg Geiger

Date Published: 18th Apr 2023

Publication Type: Journal

Improved insights into the SABIO-RK database via visualization.

Abstract (Expand)

SABIO-RK is a database for biochemical reactions and their kinetics. Data in SABIO-RK are inherently multidimensional and complex. The complex relationships between the data are often difficult to … follow or even not represented when using standard tabular views. With an increasing number of data points the mismatch between tables and insights becomes more obvious, and getting an overview of the data becomes harder. Such complex data benefit from being presented using specially adapted visual tools. Visualization is a natural and user-friendly way to quickly get an overview of the data and to detect clusters and outliers. Here, we describe the implementation of a variety of visualization concepts into a common interface within the SABIO-RK biochemical reaction kinetics database. For that purpose, we use a heat map, parallel coordinates and scatter plots to allow the interactive visual exploration of general entry-based information of biochemical reactions and specific kinetic parameter values. Database URL https://sabiork.h-its.org/.

Authors: D. Dudas, U. Wittig, M. Rey, A. Weidemann, W. Muller

Date Published: 31st Mar 2023

Publication Type: Journal

Vision for the Virtual Human Twin and Roadmap Outline

Abstract (Expand)

The present document is the first written presentation of the Virtual Human Twin (VHT) vision as it has been prepared by the EDITH consortium and discussed with select representatives of the wider … ecosystem. After a brief statement on the genesis of the vision, the document is composed of two main parts: the outline of the VHT roadmap and the elaboration of the vision for the integrated Virtual Human Twin.

Author: Gerhard Mayer, Martin Golebiewski

Date Published: 31st Mar 2023

Publication Type: Misc

Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022.

Abstract (Expand)

This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2022 special issue presents three updates to … the standards: CellML 2.0.1, SBML Level 3 Package: Spatial Processes, Version 1, Release 1, and Synthetic Biology Open Language (SBOL) Version 3.1.0. This document can also be used to identify the latest specifications for all COMBINE standards. In addition, this editorial provides a brief overview of the COMBINE 2022 meeting in Berlin.

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

Date Published: 1st Mar 2023

Publication Type: Journal

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