195 results on '"Golebiewski, Martin"'
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2. Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024
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Golebiewski Martin, Bader Gary, Gleeson Padraig, Gorochowski Thomas E., Keating Sarah M., König Matthias, Myers Chris J., Nickerson David P., Sommer Björn, Waltemath Dagmar, and Schreiber Falk
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Biotechnology ,TP248.13-248.65 - Published
- 2024
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3. SBML Level 3: an extensible format for the exchange and reuse of biological models
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Keating, Sarah M, Waltemath, Dagmar, König, Matthias, Zhang, Fengkai, Dräger, Andreas, Chaouiya, Claudine, Bergmann, Frank T, Finney, Andrew, Gillespie, Colin S, Helikar, Tomáš, Hoops, Stefan, Malik‐Sheriff, Rahuman S, Moodie, Stuart L, Moraru, Ion I, Myers, Chris J, Naldi, Aurélien, Olivier, Brett G, Sahle, Sven, Schaff, James C, Smith, Lucian P, Swat, Maciej J, Thieffry, Denis, Watanabe, Leandro, Wilkinson, Darren J, Blinov, Michael L, Begley, Kimberly, Faeder, James R, Gómez, Harold F, Hamm, Thomas M, Inagaki, Yuichiro, Liebermeister, Wolfram, Lister, Allyson L, Lucio, Daniel, Mjolsness, Eric, Proctor, Carole J, Raman, Karthik, Rodriguez, Nicolas, Shaffer, Clifford A, Shapiro, Bruce E, Stelling, Joerg, Swainston, Neil, Tanimura, Naoki, Wagner, John, Meier‐Schellersheim, Martin, Sauro, Herbert M, Palsson, Bernhard, Bolouri, Hamid, Kitano, Hiroaki, Funahashi, Akira, Hermjakob, Henning, Doyle, John C, Hucka, Michael, Adams, Richard R, Allen, Nicholas A, Angermann, Bastian R, Antoniotti, Marco, Bader, Gary D, Červený, Jan, Courtot, Mélanie, Cox, Chris D, Pezze, Piero Dalle, Demir, Emek, Denney, William S, Dharuri, Harish, Dorier, Julien, Drasdo, Dirk, Ebrahim, Ali, Eichner, Johannes, Elf, Johan, Endler, Lukas, Evelo, Chris T, Flamm, Christoph, Fleming, Ronan MT, Fröhlich, Martina, Glont, Mihai, Gonçalves, Emanuel, Golebiewski, Martin, Grabski, Hovakim, Gutteridge, Alex, Hachmeister, Damon, Harris, Leonard A, Heavner, Benjamin D, Henkel, Ron, Hlavacek, William S, Hu, Bin, Hyduke, Daniel R, de Jong, Hidde, Juty, Nick, Karp, Peter D, Karr, Jonathan R, Kell, Douglas B, Keller, Roland, Kiselev, Ilya, Klamt, Steffen, Klipp, Edda, Knüpfer, Christian, Kolpakov, Fedor, Krause, Falko, Kutmon, Martina, and Laibe, Camille
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Bioengineering ,Networking and Information Technology R&D (NITRD) ,Animals ,Humans ,Logistic Models ,Models ,Biological ,Software ,Systems Biology ,computational modeling ,file format ,interoperability ,reproducibility ,systems biology ,SBML Level 3 Community members ,Biochemistry and Cell Biology ,Other Biological Sciences ,Bioinformatics - Abstract
Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.
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- 2020
4. Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022
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König Matthias, Gleeson Padraig, Golebiewski Martin, Gorochowski Thomas E., Hucka Michael, Keating Sarah M., Myers Chris J., Nickerson David P., Sommer Björn, Waltemath Dagmar, and Schreiber Falk
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Biotechnology ,TP248.13-248.65 - Abstract
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.
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- 2023
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5. Towards an Interoperability Landscape for a National Research Data Infrastructure for Personal Health Data.
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Vorisek, Carina Nina, Klopfenstein, Sophie Anne Inès, Löbe, Matthias, Schmidt, Carsten Oliver, Mayer, Paula Josephine, Golebiewski, Martin, and Thun, Sylvia
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PUBLIC health infrastructure ,PERSONALLY identifiable information ,MEDICAL informatics ,DATA management ,ADULT education workshops - Abstract
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. [ABSTRACT FROM AUTHOR]
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- 2024
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6. The AIMe registry for artificial intelligence in biomedical research
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Matschinske, Julian, Alcaraz, Nicolas, Benis, Arriel, Golebiewski, Martin, Grimm, Dominik G., Heumos, Lukas, Kacprowski, Tim, Lazareva, Olga, List, Markus, Louadi, Zakaria, Pauling, Josch K., Pfeifer, Nico, Röttger, Richard, Schwämmle, Veit, Sturm, Gregor, Traverso, Alberto, Van Steen, Kristel, de Freitas, Martiela Vaz, Villalba Silva, Gerda Cristal, Wee, Leonard, Wenke, Nina K., Zanin, Massimiliano, Zolotareva, Olga, Baumbach, Jan, and Blumenthal, David B.
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- 2021
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7. Specifications of standards in systems and synthetic biology: status and developments in 2021
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Schreiber Falk, Gleeson Padraig, Golebiewski Martin, Gorochowski Thomas E., Hucka Michael, Keating Sarah M., König Matthias, Myers Chris J., Nickerson David P., Sommer Björn, and Waltemath Dagmar
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Biotechnology ,TP248.13-248.65 - Abstract
This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2021 special issue presents four updates of standards: Synthetic Biology Open Language Visual Version 2.3, Synthetic Biology Open Language Visual Version 3.0, Simulation Experiment Description Markup Language Level 1 Version 4, and OMEX Metadata specification Version 1.2. This document can also be consulted to identify the latest specifications of all COMBINE standards.
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- 2021
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8. One file to share them all: Using the COMBINE Archive and the OMEX format to share all information about a modeling project
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Bergmann, Frank T., Adams, Richard, Moodie, Stuart, Cooper, Jonathan, Glont, Mihai, Golebiewski, Martin, Hucka, Michael, Laibe, Camille, Miller, Andrew K., Nickerson, David P., Olivier, Brett G., Rodriguez, Nicolas, Sauro, Herbert M., Scharm, Martin, Soiland-Reyes, Stian, Waltemath, Dagmar, Yvon, Florent, and Novère, Nicolas Le
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Computer Science - Digital Libraries ,Quantitative Biology - Molecular Networks - Abstract
Background: With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result. Results: We describe the Open Modeling EXchange format (OMEX). Together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive, a single file that supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. Several tools that support the COMBINE Archive are available, either as independent libraries or embedded in modeling software. Conclusions: The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails. We anticipate that the COMBINE Archive will become a significant help for modellers, as the domain moves to larger, more complex experiments such as multi-scale models of organs, digital organisms, and bioengineering., Comment: 3 figures, 1 table
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- 2014
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9. Towards standardization guidelines for in silico approaches in personalized medicine
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Brunak Søren, Bjerre Collin Catherine, Eva Ó Cathaoir Katharina, Golebiewski Martin, Kirschner Marc, Kockum Ingrid, Moser Heike, and Waltemath Dagmar
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data integration ,in silico modelling ,personalized medicine ,reproducibility ,standards ,Biotechnology ,TP248.13-248.65 - Abstract
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.
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- 2020
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10. The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)
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Waltemath Dagmar, Golebiewski Martin, Blinov Michael L, Gleeson Padraig, Hermjakob Henning, Hucka Michael, Inau Esther Thea, Keating Sarah M, König Matthias, Krebs Olga, Malik-Sheriff Rahuman S, Nickerson David, Oberortner Ernst, Sauro Herbert M, Schreiber Falk, Smith Lucian, Stefan Melanie I, Wittig Ulrike, and Myers Chris J
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combine ,community building ,meeting report ,standardization ,Biotechnology ,TP248.13-248.65 - Abstract
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.
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- 2020
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11. Specifications of standards in systems and synthetic biology: status and developments in 2020
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Schreiber Falk, Sommer Björn, Czauderna Tobias, Golebiewski Martin, Gorochowski Thomas E., Hucka Michael, Keating Sarah M., König Matthias, Myers Chris, Nickerson David, and Waltemath Dagmar
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ontologies ,standards ,systems biology ,synthetic biology ,Biotechnology ,TP248.13-248.65 - Abstract
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.
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- 2020
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12. Large-scale generation of computational models from biochemical pathway maps
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Büchel, Finja, Rodriguez, Nicolas, Swainston, Neil, Wrzodek, Clemens, Czauderna, Tobias, Keller, Roland, Mittag, Florian, Schubert, Michael, Glont, Mihai, Golebiewski, Martin, van Iersel, Martijn, Keating, Sarah, Rall, Matthias, Wybrow, Michael, Hermjakob, Henning, Hucka, Michael, Kell, Douglas B., Müller, Wolfgang, Mendes, Pedro, Zell, Andreas, Chaouiya, Claudine, Saez-Rodriguez, Julio, Schreiber, Falk, Laibe, Camille, Dräger, Andreas, and Novère, Nicolas Le
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Quantitative Biology - Molecular Networks - Abstract
Background: Systems biology projects and omics technologies have led to a growing number of biochemical pathway reconstructions. However, mathematical models are still most often created de novo, based on reading the literature and processing pathway data manually. Results: To increase the efficiency with which such models can be created, we automatically generated mathematical models from pathway representations using a suite of freely available software. We produced models that combine data from KEGG PATHWAY, BioCarta, MetaCyc and SABIO-RK; According to the source data, three types of models are provided: kinetic, logical and constraint-based. All models are encoded using SBML Core and Qual packages, and available through BioModels Database. Each model contains the list of participants, the interactions, and the relevant mathematical constructs, but, in most cases, no meaningful parameter values. Most models are also available as easy to understand graphical SBGN maps. Conclusions: to date, the project has resulted in more than 140000 models freely available. We believe this resource can tremendously accelerate the development of mathematical models by providing initial starting points ready for parametrization., Comment: 29 pages, 8 figures
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- 2013
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13. Toward a common standard for data and specimen provenance in life sciences.
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Wittner, Rudolf, Holub, Petr, Mascia, Cecilia, Frexia, Francesca, Müller, Heimo, Plass, Markus, Allocca, Clare, Betsou, Fay, Burdett, Tony, Cancio, Ibon, Chapman, Adriane, Chapman, Martin, Courtot, Mélanie, Curcin, Vasa, Eder, Johann, Elliot, Mark, Exter, Katrina, Goble, Carole, Golebiewski, Martin, and Kisler, Bron
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LIFE sciences ,BIOLOGICAL specimens ,REGULATORY compliance ,ELECTRONIC data processing ,INFORMATION sharing - Abstract
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. [ABSTRACT FROM AUTHOR]
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- 2024
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14. Data Publication for Personalised Health Data
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Fluck, Juliane, primary, Golebiewski, Martin, additional, and Darms, Johannes, additional
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- 2023
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15. NFDI4Health Local Data Hubs for Finding and Accessing Health Data
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Meineke, Frank, primary, Golebiewski, Martin, additional, Hu, Xiaoming, additional, Kirsten, Toralf, additional, Löbe, Matthias, additional, Klammt, Sebastian, additional, Sax, Ulrich, additional, and Müller, Wolfgang, additional
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- 2023
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16. Provenance Core Data Set
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Sax, Ulrich, primary, Henke, Christian, additional, Dräger, Christian, additional, Bender, Theresa, additional, Kuntz, Alessandra, additional, Golebiewski, Martin, additional, Ulrich, Hannes, additional, and Löbe, Mattias, additional
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- 2023
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17. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019
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Schreiber Falk, Sommer Björn, Bader Gary D., Gleeson Padraig, Golebiewski Martin, Hucka Michael, Keating Sarah M., König Matthias, Myers Chris, Nickerson David, and Waltemath Dagmar
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Biotechnology ,TP248.13-248.65 - Abstract
This special issue of the Journal of Integrative Bioinformatics presents an overview of COMBINE standards and their latest specifications. The standards cover representation formats for computational modeling in synthetic and systems biology and include BioPAX, CellML, NeuroML, SBML, SBGN, SBOL and SED-ML. The articles in this issue contain updated specifications of SBGN Process Description Level 1 Version 2, SBML Level 3 Core Version 2 Release 2, SBOL Version 2.3.0, and SBOL Visual Version 2.1.
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- 2019
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18. Path2Models: large-scale generation of computational models from biochemical pathway maps
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Büchel, Finja, Rodriguez, Nicolas, Swainston, Neil, Wrzodek, Clemens, Czauderna, Tobias, Keller, Roland, Mittag, Florian, Schubert, Michael, Glont, Mihai, Golebiewski, Martin, van Iersel, Martijn, Keating, Sarah, Rall, Matthias, Wybrow, Michael, Hermjakob, Henning, Hucka, Michael, Kell, Douglas B, Müller, Wolfgang, Mendes, Pedro, Zell, Andreas, Chaouiya, Claudine, Saez-Rodriguez, Julio, Schreiber, Falk, Laibe, Camille, Dräger, Andreas, and Le Novère, Nicolas
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Abstract Background Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data. Results To increase the efficiency of model creation, the Path2Models project has automatically generated mathematical models from pathway representations using a suite of freely available software. Data sources include KEGG, BioCarta, MetaCyc and SABIO-RK. Depending on the source data, three types of models are provided: kinetic, logical and constraint-based. Models from over 2 600 organisms are encoded consistently in SBML, and are made freely available through BioModels Database at http://www.ebi.ac.uk/biomodels-main/path2models. Each model contains the list of participants, their interactions, the relevant mathematical constructs, and initial parameter values. Most models are also available as easy-to-understand graphical SBGN maps. Conclusions To date, the project has resulted in more than 140 000 freely available models. Such a resource can tremendously accelerate the development of mathematical models by providing initial starting models for simulation and analysis, which can be subsequently curated and further parameterized.
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- 2013
19. Toward a common standard for data and specimen provenance in life sciences
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Wittner, Rudolf, primary, Holub, Petr, additional, Mascia, Cecilia, additional, Frexia, Francesca, additional, Müller, Heimo, additional, Plass, Markus, additional, Allocca, Clare, additional, Betsou, Fay, additional, Burdett, Tony, additional, Cancio, Ibon, additional, Chapman, Adriane, additional, Chapman, Martin, additional, Courtot, Mélanie, additional, Curcin, Vasa, additional, Eder, Johann, additional, Elliot, Mark, additional, Exter, Katrina, additional, Goble, Carole, additional, Golebiewski, Martin, additional, Kisler, Bron, additional, Kremer, Andreas, additional, Leo, Simone, additional, Lin‐Gibson, Sheng, additional, Marsano, Anna, additional, Mattavelli, Marco, additional, Moore, Josh, additional, Nakae, Hiroki, additional, Perseil, Isabelle, additional, Salman, Ayat, additional, Sluka, James, additional, Soiland‐Reyes, Stian, additional, Strambio‐De‐Castillia, Caterina, additional, Sussman, Michael, additional, Swedlow, Jason R., additional, Zatloukal, Kurt, additional, and Geiger, Jörg, additional
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- 2023
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20. Data Formats for Systems Biology and Quantitative Modeling
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Golebiewski, Martin, primary
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- 2019
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21. Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices
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Stanford, Natalie J., primary, Scharm, Martin, additional, Dobson, Paul D., additional, Golebiewski, Martin, additional, Hucka, Michael, additional, Kothamachu, Varun B., additional, Nickerson, David, additional, Owen, Stuart, additional, Pahle, Jürgen, additional, Wittig, Ulrike, additional, Waltemath, Dagmar, additional, Goble, Carole, additional, Mendes, Pedro, additional, and Snoep, Jacky, additional
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- 2019
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22. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017
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Schreiber Falk, Bader Gary D., Gleeson Padraig, Golebiewski Martin, Hucka Michael, Keating Sarah M., Novère Nicolas Le, Myers Chris, Nickerson David, Sommer Björn, and Waltemath Dagmar
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combine ,systems biology ,synthetic biology ,standards ,Biotechnology ,TP248.13-248.65 - Abstract
Standards are essential to the advancement of Systems and Synthetic Biology. COMBINE provides a formal body and a centralised platform to help develop and disseminate relevant standards and related resources. The regular special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards by providing unified, easily citable access. This paper provides an overview of existing COMBINE standards and presents developments of the last year.
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- 2018
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23. A Semantic Representation of the NFDI4Health Metadata Schema Utilizing the CEDAR Workbench - Poster
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Löbe, Matthias, Shutsko, Aliaksandra, Schmidt, Carsten, Darms, Johannes, Klopfenstein, Sophie, Vorisek, Carina, Hu, Xioaming, Golebiewski, Martin, and Fluck, Juliane
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Metadata Schema ,CEDAR ,BioPortal ,Dublin Core ,RDF ,Clinical Trial Registries ,DataCite ,DCAT - Abstract
Rich metadata is required for a comprehensive description of research assets. We developed a metadata schema for clinical and epidemiological research studies based on existing generic and domain-specific metadata vocabularies. It forms the basis for various search and data management services. Interoperability remains a challenge, as various health research standards are to be supported in the medium term. At the same time, embedding our infrastructure in national and international initiatives requires the use of overarching syntactic and semantic standards and vocabularies. In this paper we present a prototypical implementation in CEDAR Workbench. This not only provides a graphical web interface for collaboration and a possibility for form-based data entry for testing purposes. CEDAR also enables the use of standard vocabularies, annotation of concepts with medical terminologies, and a serialization in an RDF-JSON format.
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- 2023
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24. Metadata schema of the NFDI4Health and the NFDI4Health Task Force COVID-19 (V3_1)
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NFDI4Health Task Force COVID-19, Abaza, Haitham, Klopfenstein, Sophie Anne Ines, Golebiewski, Martin, NFDI4Health, Schmidt, Carsten Oliver, Shutsko, Aliaksandra, Vorisek, Carina Nina, and Darms, Johannes
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Metadata ,Clinical trials ,FAIR principles ,Metadata model ,Epidemiology ,COVID-19 ,Public Health ,Standard - Published
- 2023
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25. Bringing Communities Together: Mapping the Investigation-Study-Assay-Model (ISA) to Fast Healthcare Interoperability Resources (FHIR).
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KLOPFENSTEIN, Sophie A. I., SASS, Julian, VORISEK, Carina N., JORCZIK, Felix, SCHMIDT, Carsten Oliver, LÖBE, Matthias, GOLEBIEWSKI, Martin, ABAZA, Haitham, and THUN, Sylvia
- Abstract
Adhering to FAIR principles (findability, accessibility, interoperability, reusability) ensures sustainability and reliable exchange of data and metadata. Research communities need common infrastructures and information models to collect, store, manage and work with data and metadata. The German initiative NFDI4Health created a metadata schema and an infrastructure integrating existing platforms based on different information models and standards. To ensure system compatibility and enhance data integration possibilities, we mapped the Investigation-Study-Assay (ISA) model to Fast Healthcare Interoperability Resources (FHIR). We present the mapping in FHIR logical models, a resulting FHIR resources' network and challenges that we encountered. Challenges mainly related to ISA's genericness, and to different structures and datatypes used in ISA and FHIR. Mapping ISA to FHIR is feasible but requires further analyses of example data and adaptations to better specify target FHIR elements, and enable possible automatized conversions from ISA to FHIR. [ABSTRACT FROM AUTHOR]
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- 2023
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26. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016
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Schreiber Falk, Bader Gary D., Gleeson Padraig, Golebiewski Martin, Hucka Michael, Novère Nicolas Le, Myers Chris, Nickerson David, Sommer Björn, and Waltemath Dagmar
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Biotechnology ,TP248.13-248.65 - Abstract
Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards, as well as to provide centralised and easily citable access to them.
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- 2016
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27. Systems Biology in ELIXIR: modelling in the spotlight
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Martins dos Santos, Vitor, primary, Anton, Mihail, additional, Szomolay, Barbara, additional, Ostaszewski, Marek, additional, Arts, Ilja, additional, Benfeitas, Rui, additional, Dominguez Del Angel, Victoria, additional, Ferk, Polonca, additional, Fey, Dirk, additional, Goble, Carole, additional, Golebiewski, Martin, additional, Gruden, Kristina, additional, Heil, Katharina F., additional, Hermjakob, Henning, additional, Kahlem, Pascal, additional, Klapa, Maria I., additional, Koehorst, Jasper, additional, Kolodkin, Alexey, additional, Kutmon, Martina, additional, Leskošek, Brane, additional, Moretti, Sébastien, additional, Müller, Wolfgang, additional, Pagni, Marco, additional, Rezen, Tadeja, additional, Rocha, Miguel, additional, Rozman, Damjana, additional, Šafránek, David, additional, Sheriff, Rahuman S. Malik, additional, Suarez Diez, Maria, additional, Van Steen, Kristel, additional, Westerhoff, Hans V, additional, Wittig, Ulrike, additional, Wolstencroft, Katherine, additional, Zupanic, Anze, additional, Evelo, Chris T., additional, and Hancock, John M., additional
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- 2022
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28. SABIO-RK, von Daten in der Publikation zur Suchlösung für Spezialisten
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Müller, Wolfgang, Bittkowski, Meik, Golebiewski, Martin, Kania, Renate, Rey, Maja, Weidemann, Andreas, and Wittig, Ulrike
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- 2017
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29. A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms
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Niarakis, Anna, Ostaszewski, Marek, Mazein, Alexander, Kuperstein, Inna, Kutmon, Martina, Gillespie, Marc, Funahashi, Akira, Acencio, Marcio, Hemedan, Ahmed, Aichem, Michael, Klein, Karsten, Czauderna, Tobias, Burtscher, Felicia, Yamada, Takahiro, Hiki, Yusuke, Hiroi, Noriko, Hu, Finterly, Pham, Nhung, Ehrhart, Friederike, Willighagen, Egon, Valdeolivas, Alberto, Dugourd, Aurelien, Messina, Francesco, Esteban-Medina, Marina, Pena-Chilet, Maria, Rian, Kinza, Soliman, Sylvain, Aghamiri, Sara, Puniya, Bhanwar, Naldi, Aurelien, Helikar, Tomas, Singh, Vidisha, Farinas Fernandez, Marco, Bermudez, Viviam, Tsirvouli, Eirini, Montagud, Arnau, Noel, Vincent, Ponce de Leon, Miguel, Maier, Dieter, Bauch, Angela, Gyori, Benjamin, Bachman, John, Luna, Agustin, Pinero, Janet, Furlong, Laura, Balaur, Irina, Rougny, Adrien, Jarosz, Yohan, Overall, Rupert, Phair, Robert, Perfetto, Livia, Matthews, Lisa, Rex, Devasahayam, Orlic-Milacic, Marija, Monraz Gomez, Luis, de Meulder, Bertrand, Ravel, Jean, Jassal, Bijay, Satagopam, Venkata, Wu, Guanming, Golebiewski, Martin, Gawron, Piotr, Calzone, Laurence, Beckmann, Jacques, Evelo, Chris, d'Eustachio, Peter, Schreiber, Falk, Saez-Rodriguez, Julio, Dopazo, Joaquin, Kuiper, Martin, Valencia, Alfonso, Wolkenhauer, Olaf, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, Computational systems biology and optimization (Lifeware), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Laboratoire de recherche européen pour la polyarthrite rhumatoïde (GenHotel), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay, University of Luxembourg [Luxembourg], Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris sciences et lettres (PSL), Maastricht Centre for Systems Biology [Maastricht] (MaCSBio), Maastricht University [Maastricht], Ontario Institute for Cancer Research [Canada] (OICR), Ontario Institute for Cancer Research, Keio University, Luxembourg Centre For Systems Biomedicine (LCSB), University of Konstanz, Hochschule Mittweida - University of Applied Sciences, Kanagawa Institute of Technology, Heidelberg University Hospital [Heidelberg], National Institute for Infectious Diseases 'Lazzaro Spallanzani', Hospital Universitario Virgen del Rocío [Sevilla], Biomedicine Institute of Sevilla [Seville, Spain], University of Nebraska–Lincoln, University of Nebraska System, Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Harvard Medical School [Boston] (HMS), Universitat Pompeu Fabra [Barcelona] (UPF), National Institute of Advanced Industrial Science and Technology (AIST), Humboldt University Of Berlin, Integrative Bioinformatics Inc [Mountain View], Department of Informatics and System Sciences (Sapienza University of Rome), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), New York University Langone Medical Center (NYU Langone Medical Center), NYU System (NYU), Yenepoya University, Janet Piñero, Laura I. Furlong: IMI2-JU grants, resources which are composed of financial contributions from the European Union’s Horizon 2020 Research and Innovation Programme and EFPIA [GA: 777365 eTRANSAFE], and the EU H2020 Programme [GA:964537 RISKHUNT3R], Project 001-P-001647—Valorisation of EGA for Industry and Society funded by the European Regional Development Fund (ERDF) and Generalitat de Catalunya, and Institute of Health Carlos III (project IMPaCT-Data, exp. IMP/00019), co-funded by the European Union, European Regional Development Fund (ERDF, 'A way to make Europe').
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SARS-CoV-2 ,disease maps ,systems biology ,dynamic models ,systems medicine ,large-scale community effort ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,mechanistic models - Abstract
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. Community-driven and highly interdisciplinary, the project is collaborative and supports community standards, open access, and the FAIR data principles. The coordination of community work allowed for an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework links key molecules highlighted from broad omics data analysis and computational modeling to dysregulated pathways in a cell-, tissue- or patient-specific manner. We also employ text mining and AI-assisted analysis to identify potential drugs and drug targets and use topological analysis to reveal interesting structural features of the map. The proposed framework is versatile and expandable, offering a significant upgrade in the arsenal used to understand virus-host interactions and other complex pathologies.
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- 2022
30. Systems Biology in ELIXIR: modelling in the spotlight:[version 1; peer review: 1 approved, 2 approved with reservations]
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Martins dos Santos, Vitor, Anton, Mihail, Szomolay, Barbara, Ostaszewski, Marek, Arts, Ilja, Benfeitas, Rui, Dominguez del Angel, Victoria, Ferk, Polonca, Fey, Dirk, Goble, Carole, Golebiewski, Martin, Gruden, Kristina, Heil, Katharina F., Hermjakob, Henning, Kahlem, Pascal, Klapa, Maria I., Koehorst, Jasper, Kolodkin, Alexey, Kutmon, Martina, Leskošek, Brane, Moretti, Sébastien, Müller, Wolfgang, Pagni, Marco, Rezen, Tadeja, Rocha, Miguel, Rozman, Damjana, Šafránek, David, Sheriff, Rahuman S. Malik, Suarez diez, Maria, Van steen, Kristel, Westerhoff, Hans V, Wittig, Ulrike, Wolstencroft, Katherine, Zupanic, Anze, Evelo, Chris T., and Hancock, John M.
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Network Biology ,Biological data ,ELIXIR Communities ,Biomolecular Models ,Systems Biology ,Systems Medicine ,FAIR ,Biotechnology - Abstract
In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR’s future support of advanced biological applications and personalised medicine.By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology.A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives.
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- 2022
31. Data extraction for the reaction kinetics database SABIO-RK
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Wittig, Ulrike, Kania, Renate, Bittkowski, Meik, Wetsch, Elina, Shi, Lei, Jong, Lenneke, Golebiewski, Martin, Rey, Maja, Weidemann, Andreas, Rojas, Isabel, and Müller, Wolfgang
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- 2014
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32. Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)
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Waltemath, Dagmar, Bergmann, Frank T., Chaouiya, Claudine, Czauderna, Tobias, Gleeson, Padraig, Goble, Carole, Golebiewski, Martin, Hucka, Michael, Juty, Nick, Krebs, Olga, Le Novère, Nicolas, Mi, Huaiyu, Moraru, Ion I., Myers, Chris J., Nickerson, David, Olivier, Brett G., Rodriguez, Nicolas, Schreiber, Falk, Smith, Lucian, Zhang, Fengkai, and Bonnet, Eric
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- 2018
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33. SABIO-RK: Integration and Curation of Reaction Kinetics Data
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Wittig, Ulrike, Golebiewski, Martin, Kania, Renate, Krebs, Olga, Mir, Saqib, Weidemann, Andreas, Anstein, Stefanie, Saric, Jasmin, Rojas, Isabel, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Leser, Ulf, editor, Naumann, Felix, editor, and Eckman, Barbara, editor
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- 2006
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34. Specifications of Standards in Systems and Synthetic Biology
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Schreiber Falk, Bader Gary D., Golebiewski Martin, Hucka Michael, Kormeier Benjamin, Le Novère Nicolas, Myers Chris, Nickerson David, Sommer Björn, Waltemath Dagmar, and Weise Stephan
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Biotechnology ,TP248.13-248.65 - Abstract
Standards shape our everyday life. From nuts and bolts to electronic devices and technological processes, standardised products and processes are all around us. Standards have technological and economic benefits, such as making information exchange, production, and services more efficient. However, novel, innovative areas often either lack proper standards, or documents about standards in these areas are not available from a centralised platform or formal body (such as the International Standardisation Organisation).
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- 2015
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35. Metadata schema of the NFDI4Health and the NFDI4Health Task Force COVID-19 (V3_0)
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NFDI4Health Task Force COVID-19, Abaza, Haitham, Klopfenstein, Sophie Anne Ines, Golebiewski, Martin, NFDI4Health, Schmidt, Carsten Oliver, Shutsko, Aliaksandra, Vorisek, Carina Nina, and Darms, Johannes
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Metadata ,Clinical trials ,FAIR principles ,Metadata model ,Epidemiology ,COVID-19 ,Public Health ,Standard - Published
- 2022
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36. NFDI4Health Task Force COVID-19 Metadata schema V2_0
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Klopfenstein, Sophie Anne Ines, Golebiewski, Martin, Schmidt, Carsten Oliver, Shutsko, Aliaksandra, Vorisek, Carina Nina, and Darms, Johannes
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- 2022
- Full Text
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37. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)
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Waltemath, Dagmar, Bergmann, Frank T., Chaouiya, Claudine, Czauderna, Tobias, Gleeson, Padraig, Goble, Carole, Golebiewski, Martin, Hucka, Michael, Juty, Nick, Krebs, Olga, Le Novère, Nicolas, Mi, Huaiyu, Moraru, Ion I., Myers, Chris J., Nickerson, David, Olivier, Brett G., Rodriguez, Nicolas, Schreiber, Falk, Smith, Lucian, Zhang, Fengkai, and Bonnet, Eric
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- 2014
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38. Ten Simple Rules for FAIR Sharing of Experimental and Clinical Data with the Modeling Community
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König, Matthias, primary, Grzegorzewski, Jan, additional, Golebiewski, Martin, additional, Hermjakob, Henning, additional, Hucka, Mike, additional, Olivier, Brett, additional, Keating, Sarah, additional, Nickerson, David, additional, Schreiber, Falk, additional, Sheriff, Rahuman, additional, and Waltemath, Dagmar, additional
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- 2021
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39. How to Make Health Data 'FAIR' - Requirements for Biomedical Research Data Infrastructures
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Golebiewski, Martin, Löbe, Matthias, Löhnhardt, Benjamin, and Kusch, Harald
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NFDI ,ddc: 610 ,Medicine and health ,standards ,interoperability ,data management ,infrastructures ,FAIR - Abstract
This workshop will be organized by the GMDS project group "FAIR Data Infrastructures for Biomedical Informatic” ([link:https://www.gmds.de/de/aktivitaeten/medizinische-informatik/projektgruppenseiten/faire-dateninfrastrukturen-fuer-die-biomedizinische-informatik/*https://www.gmds.de/de/aktivitaeten/medizinische-informatik/projektgruppenseiten/faire-dateninfrastrukturen-fuer-die-biomedizinische-informatik/]). [for full text, please go to the a.m. URL]
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- 2021
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40. NFDI4Health – Nationale Forschungsdateninfrastruktur für personenbezogene Gesundheitsdaten
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Fluck, Juliane, Lindstädt, Birte, Ahrens, Wolfgang, Beyan, Oya, Buchner, Benedikt, Darms, Johannes, Depping, Ralf, Dierkes, Jens, Neuhausen, Hubertus, Müller, Wolfgang, Zeeb, Hajo, Golebiewski, Martin, Löffler, Markus, Löbe, Matthias, Meineke, Franke, Klammt, Sebastian, Brosteanu, Oana, Fröhlich, Holger, Hahn, Horst, Schulze, Matthias, Pischon, Tobias, Nöthlings, Ute, Sax, Ulrich, Kusch, Harald, Grabenhenrich, Linnus, Schmidt, Carsten Oliver, Waltemath, Dagmar, Semler, Sebastian, Gehrke, Juliane, Kirsten, Toralf, Praßer, Fabian, Thun, Sylvia, Wieler, Lothar, and Pigeot, Iris
- Abstract
doch erfüllen Studienprotokolle, eingesetzte Erhebungsinstrumente und erhobene Daten die Anforderungen der FAIR-Prinzipien nicht in ausreichendem Maße. NFDI4Health wird daher eine Struktur schaffen, die eine zentrale Suche nach existierenden, dezentral verwalteten Datenkörpern und zugehörigen Dokumenten sowie einen FAIRen Zugang zu diesen erleichtert. Dazu werden die Auffindbarkeit und der Zugang zu strukturierten Gesundheitsdaten aus Registern, administrativen Gesundheitsdatenbanken, klinischen und epidemiologischen sowie Public Health-Studien verbessert und die Qualität und Harmonisierung der zugrundeliegenden Daten optimiert.Eine weitere Herausforderung entsteht durch die Verwendung personenbezogener Gesundheitsdaten. Diese sind hoch sensibel, so dass ihre Nutzung restriktive Datenschutzbestimmungen und informierte Einwilligungserklärungen der Studienteilnehmenden erfordert, was jedoch ihre Wiederverwendbarkeit einschränkt. NFDI4Health zielt daher darauf ab, den Austausch und die Verknüpfung von personenbezogenen Gesundheitsdaten sowie verteilte Datenanalysen unter Einhaltung datenschutzrechtlicher und ethischer Bestimmungen zu erleichtern. Um dies möglichst effizient zu erreichen, wird NFDI4Health die Entwicklung neuer, maschinenprozessierbarer Zustimmungsmöglichkeiten sowie innovativer Datenzugriffsservices auf Grundlage der FAIR-Prinzipien vorantreiben und die Interoperabilität von IT-Lösungen für Metadatenrepositorien stärken. Komplementiert wird dies durch die Entwicklung entsprechender Angebote für Training und Ausbildung, um der Herausforderung der Umsetzung der Lösungen in den Universitäten und Forschungseinrichtungen zu begegnen. Schließlich wird durch die gemeinsame Arbeit in der NFDI4Health die Kooperation zwischen klinischer und epidemiologischer/Public Health-Forschung gestärkt.
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- 2021
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41. SABIO-RK: A data warehouse for biochemical reactions and their kinetics
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Krebs Olga, Golebiewski Martin, Kania Renate, Mir Saqib, Saric Jasmin, Weidemann Andreas, Wittig Ulrike, and Rojas Isabel
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Biotechnology ,TP248.13-248.65 - Abstract
Systems biology is an emerging field that aims at obtaining a system-level understanding of biological processes. The modelling and simulation of networks of biochemical reactions have great and promising application potential but require reliable kinetic data. In order to support the systems biology community with such data we have developed SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics), a curated database with information about biochemical reactions and their kinetic properties, which allows researchers to obtain and compare kinetic data and to integrate them into models of biochemical networks. SABIO-RK is freely available for academic use at http://sabio.villa-bosch.de/SABIORK/.
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- 2007
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42. Ten Simple Rules for Sharing Experimental and Clinical Data with the Modeling Community
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König, Matthias, primary, Grzegorzewski, Jan, additional, Golebiewski, Martin, additional, Hermjakob, Henning, additional, Hucka, Mike, additional, Olivier, Brett, additional, Keating, Sarah, additional, Nickerson, David, additional, Schreiber, Falk, additional, Sheriff, Rahuman, additional, and Waltemath, Dagmar, additional
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- 2021
- Full Text
- View/download PDF
43. Workshop FAIR Data Infrastructures for Biomedical Communities
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Golebiewski, Martin, Löhnhardt, Benjamin, Kusch, Harald, and Löbe, Matthias
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ddc: 610 ,research infrastructure ,data management ,610 Medical sciences ,Medicine ,FAIR - Abstract
Workshop Organizers: Martin Golebiewski (HITS Heidelberg), Benjamin Löhnhardt (Universitätsmedizin Göttingen), Harald Kusch (Universitätsmedizin Göttingen), Matthias Löbe (IMISE, Universität Leipzig) This workshop is organized by the GMDS project group “FAIRe[for full text, please go to the a.m. URL], 65th Annual Meeting of the German Association for Medical Informatics, Biometry and Epidemiology (GMDS), Meeting of the Central European Network (CEN: German Region, Austro-Swiss Region and Polish Region) of the International Biometric Society (IBS)
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- 2021
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44. Computational Models for Clinical Applications in Personalized Medicine—Guidelines and Recommendations for Data Integration and Model Validation
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Collin, Catherine Bjerre, Gebhardt, Tom, Golebiewski, Martin, Karaderi, Tugce, Hillemanns, Maximilian, Khan, Faiz Muhammad, Salehzadeh-Yazdi, Ali, Kirschner, Marc, Krobitsch, Sylvia, EU-STANDS4PM Consortium, and Kuepfer, Lars
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Clinical translation ,Model validation ,Computational models ,Medicine (miscellaneous) ,Data integration ,Ethical and legal requirements ,Personalized medicine ,Guidelines and recommendations - Abstract
Journal of Personalized Medicine 12(2), 166 (2022). doi:10.3390/jpm12020166 special issue: "Special Issue "Systems Medicine and Bioinformatics" / Special Issue Editors: Dr. Ali Salehzadeh-Yazdi, Guest Editor; Dr. Mohieddin Jafari, Guest Editor", Published by MDPI, Basel
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- 2022
45. Challenges for an enzymatic reaction kinetics database
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Wittig, Ulrike, Rey, Maja, Kania, Renate, Bittkowski, Meik, Shi, Lei, Golebiewski, Martin, Weidemann, Andreas, Müller, Wolfgang, and Rojas, Isabel
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- 2014
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46. SABIO-RK—database for biochemical reaction kinetics
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Wittig, Ulrike, Kania, Renate, Golebiewski, Martin, Rey, Maja, Shi, Lei, Jong, Lenneke, Algaa, Enkhjargal, Weidemann, Andreas, Sauer-Danzwith, Heidrun, Mir, Saqib, Krebs, Olga, Bittkowski, Meik, Wetsch, Elina, Rojas, Isabel, and Müller, Wolfgang
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- 2012
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47. Enzyme kinetics informatics: from instrument to browser
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Swainston, Neil, Golebiewski, Martin, Messiha, Hanan L., Malys, Naglis, Kania, Renate, Kengne, Sylvestre, Krebs, Olga, Mir, Saqib, Sauer-Danzwith, Heidrun, Smallbone, Kieran, Weidemann, Andreas, Wittig, Ulrike, Kell, Douglas B., Mendes, Pedro, Müller, Wolfgang, Paton, Norman W., and Rojas, Isabel
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- 2010
- Full Text
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48. SBML2LATEX: Conversion of SBML files into human-readable reports
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Dräger, Andreas, Planatscher, Hannes, Motsou Wouamba, Dieudonné, Schröder, Adrian, Hucka, Michael, Endler, Lukas, Golebiewski, Martin, Müller, Wolfgang, and Zell, Andreas
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- 2009
49. Improving the FAIRness of Health Studies in Germany: The German Central Health Study Hub COVID-19.
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DARMS, Johannes, HENKE, Jörg, Xioaming HU, SCHMIDT, Carsten Oliver, GOLEBIEWSKI, Martin, and FLUCK, Juliane
- Abstract
The German Central Health Study Hub COVID-19 is an online service that offers bundled access to COVID-19 related studies conducted in Germany. It combines metadata and other information of epidemiologic, public health and clinical studies into a single data repository for FAIR data access. In addition to study characteristics the system also allows easy access to study documents, as well as instruments for data collection. Study metadata and survey instruments are decomposed into individual data items and semantically enriched to ease the findability. Data from existing clinical trial registries (DRKS, clinicaltrails.gov and WHO ICTRP) are merged with epidemiological and public health studies manually collected and entered. More than 850 studies are listed as of September 2021. [ABSTRACT FROM AUTHOR]
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- 2021
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50. FAIRe Dateninfrastrukturen für biomedizinische Fachcommunities
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Löhnhardt, Benjamin, Kusch, Harald, Löbe, Matthias, and Golebiewski, Martin
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ddc: 610 ,610 Medical sciences ,Medicine ,FAIR data management - Abstract
Dieser Workshop wird von der Anfang 2019 eingerichteten GMDS-Projektgruppe „FAIRe Daten-Infrastrukturen für die Biomedizinische Informatik“ organisiert. Ziel dieser Projektgruppe soll sein, die Aktivitäten in den verschiedensten Projekten sowie an den unterschiedlichen deutschen[zum vollständigen Text gelangen Sie über die oben angegebene URL], 64. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e.V. (GMDS)
- Published
- 2019
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