EU-wide mapping report on good practice examples for integrating phenotype and large scale data
Scientific Databases and Visualisation

Abstract (Expand)

The report focusses on national and EU-case studies (good practice examples) for integrating patient derived data, such as phenotype and large scale data, for in silico modelling in personalized medicine. …Not specified

Authors: Martin Golebiewski, Marc Kirschner, Sylvia Krobitsch, EU-STANDS4PM consortium

Date Published: 15th Dec 2022

Publication Type: Tech report

Data Formats for Systems Biology and Quantitative Modeling
Scientific Databases and Visualisation

Abstract (Expand)

Data standards support the reliable exchange of information, the interoperability of tools, and the reproducibility of scientific results. In systems biology standards are agreed ways of structuring, … describing, and associating models and data, as well as their respective parts, graphical visualization, and information about applied experimental or computational methods. Such standards also assist with describing how constituent parts interact together, or are linked, and how they are embedded in their environmental and experimental context. Here the focus will be on standards for formatting models and their content, and on metadata checklists and ontologies that support modeling.

Author: Martin Golebiewski

Date Published: 2019

Publication Type: Journal

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)
Scientific Databases and Visualisation

Abstract (Expand)

This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together … researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.

Authors: Dagmar Waltemath, Martin Golebiewski, Michael L Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M Keating, Matthias König, Olga Krebs, Rahuman S Malik-Sheriff, David Nickerson, Ernst Oberortner, Herbert M Sauro, Falk Schreiber, Lucian Smith, Melanie I Stefan, Ulrike Wittig, Chris J Myers

Date Published: 24th Aug 2020

Publication Type: Journal

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

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

White Paper: Towards in silico approaches for personalised medicine – Recommendations for verifying and validating predictive computational models in EU collaborative research
Scientific Databases and Visualisation

Abstract (Expand)

Harmonization of data integration is the key to standardization efforts in personalised medicine, which would also facilitate cross-European studies. Standardization of the models themselves is less … essential within a research context, where new models are created and tested in line with research progress, harmonization and/or standardization of input data is both feasible and necessary. We argue that model validation should receive more attention, and other measures should be implemented such that validation of models within personalised medicine becomes easier, also across borders. While this is an evident necessity within the context of models implemented as medical devices or decision tools, which are regulated by the European Medicines Agency and national competent authorities, we argue that model validation should be a higher priority at research level also, facilitating assessment by peers and by medical doctors – who themselves should receive better training in assessment of research using in silico models. This will also ease the implementation of translational research results in the clinic. Acceptance by doctors and the relevant medical specialties is a key hurdle for in silico models in personalised medicine. Any medical product - device, algorithm or drug - has to prove itself safe and effective to be licensed for use by regulators; however, it has also to be accepted by medical experts as being a good choice, and be recommended within clinical specialties. EU-STANDS4PM joined forces to examine to what extent existing standards or standards under development for both format and semantics can be used to link clinical and health as well as research data to computational models relevant for personalised medicine. As all requirements should be equally understood and fulfilled by users it is important to define them uniformly in an international context. To achieve this the conclusion of our work shall be also discussed in international standardization and technical committees, especially in the case of standards that are still being drawn up, and new standardization projects shall be initiated where necessary. We present a White Paper featuring recommendations for standardization of data integration as well as recommendations for standardization of model validation within a collaborative research context, such that health-related data can be optimally used for translational research and personalised medicine across Europe. As such the White Paper showcases the approach that takes big data in health through harmonized data integration to the most relevant predictive computational models for personalised medicine. As they are refined and validated these models can provide guidance not just how to use data, but also how to best cope with disease and preserve wellbeing in the daily lives of patients.

Authors: Kirstine Belling, Marina Caldara, Catherine Bjerre Collin, Tom Gebhardt, Martin Golebiewski, Tugce Karaderi, Faiz M. Khan, Marc Kirschner, Sylvia Krobitsch, Lars Küpfer, Heike Moser, Flora Musuamba Tschinanu, Mariam Nassar, Tito Poli, Philip Rosenstiel, Dagmar Waltemath, Olaf Wolkehnauer, EU-STANDS4PM consortium

Date Published: 7th Feb 2022

Publication Type: Misc

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

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

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

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

Computational Models for Clinical Applications in Personalized Medicine-Guidelines and Recommendations for Data Integration and Model Validation.
Scientific Databases and Visualisation

Abstract (Expand)

The future development of personalized medicine depends on a vast exchange of data from different sources, as well as harmonized integrative analysis of large-scale clinical health and sample data. … Computational-modelling approaches play a key role in the analysis of the underlying molecular processes and pathways that characterize human biology, but they also lead to a more profound understanding of the mechanisms and factors that drive diseases; hence, they allow personalized treatment strategies that are guided by central clinical questions. However, despite the growing popularity of computational-modelling approaches in different stakeholder communities, there are still many hurdles to overcome for their clinical routine implementation in the future. Especially the integration of heterogeneous data from multiple sources and types are challenging tasks that require clear guidelines that also have to comply with high ethical and legal standards. Here, we discuss the most relevant computational models for personalized medicine in detail that can be considered as best-practice guidelines for application in clinical care. We define specific challenges and provide applicable guidelines and recommendations for study design, data acquisition, and operation as well as for model validation and clinical translation and other research areas.

Authors: C. B. Collin, T. Gebhardt, M. Golebiewski, T. Karaderi, M. Hillemanns, F. M. Khan, A. Salehzadeh-Yazdi, M. Kirschner, S. Krobitsch, C. o. n. s. o. r. t. i. u. m. Eu-Stands Pm, L. Kuepfer

Date Published: 26th Jan 2022

Publication Type: Journal

Specifications of standards in systems and synthetic biology: status and developments in 2020
Scientific Databases and Visualisation

Abstract (Expand)

This special issue of the Journal of Integrative Bioinformatics presents papers related to the 10th COMBINE meeting together with the annual update of COMBINE standards in systems and synthetic biology. …Not specified

Authors: Falk Schreiber, Björn Sommer, Tobias Czauderna, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath

Date Published: 29th Jun 2020

Publication Type: Journal

Towards standardization guidelines for in silico approaches in personalized medicine
Scientific Databases and Visualisation

Abstract (Expand)

Despite the ever-progressing technological advances in producing data in health and clinical research, the generation of new knowledge for medical benefits through advanced analytics still lags behind … its full potential. Reasons for this obstacle are the inherent heterogeneity of data sources and the lack of broadly accepted standards. Further hurdles are associated with legal and ethical issues surrounding the use of personal/patient data across disciplines and borders. Consequently, there is a need for broadly applicable standards compliant with legal and ethical regulations that allow interpretation of heterogeneous health data through in silico methodologies to advance personalized medicine. To tackle these standardization challenges, the Horizon2020 Coordinating and Support Action EU-STANDS4PM initiated an EU-wide mapping process to evaluate strategies for data integration and data-driven in silico modelling approaches to develop standards, recommendations and guidelines for personalized medicine. A first step towards this goal is a broad stakeholder consultation process initiated by an EU-STANDS4PM workshop at the annual COMBINE meeting (COMBINE 2019 workshop report in same issue). This forum analysed the status quo of data and model standards and reflected on possibilities as well as challenges for cross-domain data integration to facilitate in silico modelling approaches for personalized medicine.

Authors: Søren Brunak, Catherine Bjerre Collin, Katharina Eva Ó Cathaoir, Martin Golebiewski, Marc Kirschner, Ingrid Kockum, Heike Moser, Dagmar Waltemath

Date Published: 24th Jul 2020

Publication Type: Journal

Challenges for an enzymatic reaction kinetics database.
Scientific Databases and Visualisation

Abstract (Expand)

The scientific literature contains a tremendous amount of kinetic data describing the dynamic behaviour of biochemical reactions over time. These data are needed for computational modelling to create … models of biochemical reaction networks and to obtain a better understanding of the processes in living cells. To extract the knowledge from the literature, biocurators are required to understand a paper and interpret the data. For modellers, as well as experimentalists, this process is very time consuming because the information is distributed across the publication and, in most cases, is insufficiently structured and often described without standard terminology. In recent years, biological databases for different data types have been developed. The advantages of these databases lie in their unified structure, searchability and the potential for augmented analysis by software, which supports the modelling process. We have developed the SABIO-RK database for biochemical reaction kinetics. In the present review, we describe the challenges for database developers and curators, beginning with an analysis of relevant publications up to the export of database information in a standardized format. The aim of the present review is to draw the experimentalist's attention to the problem (from a data integration point of view) of incompletely and imprecisely written publications. We describe how to lower the barrier to curators and improve this situation. At the same time, we are aware that curating experimental data takes time. There is a community concerned with making the task of publishing data with the proper structure and annotation to ontologies much easier. In this respect, we highlight some useful initiatives and tools.

Authors: U. Wittig, M. Rey, R. Kania, M. Bittkowski, L. Shi, M. Golebiewski, A. Weidemann, W. Muller, I. Rojas

Date Published: 30th Oct 2013

Publication Type: Journal

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