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1. The challenges of research data management in cardiovascular science: a DGK and DZHK position paper—executive summary

Author

Steffens, Sabine, Schröder, Katrin, Krüger, Martina, Maack, Christoph, Streckfuss-Bömeke, Katrin, Backs, Johannes, Backofen, Rolf, Baeßler, Bettina, Devaux, Yvan, Gilsbach, Ralf, Heijman, Jordi, Knaus, Jochen, Kramann, Rafael, Linz, Dominik, Lister, Allyson L., Maatz, Henrike, Maegdefessel, Lars, Mayr, Manuel, Meder, Benjamin, Nussbeck, Sara Y., Rog-Zielinska, Eva A., Schulz, Marcel H., Sickmann, Albert, Yigit, Gökhan, and Kohl, Peter

Published
2024
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2. SBML Level 3: an extensible format for the exchange and reuse of biological models.

Author

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, and SBML Level 3 Community members

Subjects
SBML Level 3 Community members, Animals, Humans, Logistic Models, Systems Biology, Models, Biological, Software, computational modeling, file format, interoperability, reproducibility, systems biology, Bioengineering, Networking and Information Technology R&D, Bioinformatics, Biochemistry and Cell Biology, Other Biological Sciences
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.

Published
2020

3. The challenges of research data management in cardiovascular science:a DGK and DZHK position paper—executive summary

Author

Steffens, Sabine, Schröder, Katrin, Krüger, Martina, Maack, Christoph, Streckfuss-Bömeke, Katrin, Backs, Johannes, Backofen, Rolf, Baeßler, Bettina, Devaux, Yvan, Gilsbach, Ralf, Heijman, Jordi, Knaus, Jochen, Kramann, Rafael, Linz, Dominik, Lister, Allyson L., Maatz, Henrike, Maegdefessel, Lars, Mayr, Manuel, Meder, Benjamin, Nussbeck, Sara Y., Rog-Zielinska, Eva A., Schulz, Marcel H., Sickmann, Albert, Yigit, Gökhan, Kohl, Peter, Steffens, Sabine, Schröder, Katrin, Krüger, Martina, Maack, Christoph, Streckfuss-Bömeke, Katrin, Backs, Johannes, Backofen, Rolf, Baeßler, Bettina, Devaux, Yvan, Gilsbach, Ralf, Heijman, Jordi, Knaus, Jochen, Kramann, Rafael, Linz, Dominik, Lister, Allyson L., Maatz, Henrike, Maegdefessel, Lars, Mayr, Manuel, Meder, Benjamin, Nussbeck, Sara Y., Rog-Zielinska, Eva A., Schulz, Marcel H., Sickmann, Albert, Yigit, Gökhan, and Kohl, Peter

Abstract

The sharing and documentation of cardiovascular research data are essential for efficient use and reuse of data, thereby aiding scientific transparency, accelerating the progress of cardiovascular research and healthcare, and contributing to the reproducibility of research results. However, challenges remain. This position paper, written on behalf of and approved by the German Cardiac Society and German Centre for Cardiovascular Research, summarizes our current understanding of the challenges in cardiovascular research data management (RDM). These challenges include lack of time, awareness, incentives, and funding for implementing effective RDM; lack of standardization in RDM processes; a need to better identify meaningful and actionable data among the increasing volume and complexity of data being acquired; and a lack of understanding of the legal aspects of data sharing. While several tools exist to increase the degree to which data are findable, accessible, interoperable, and reusable (FAIR), more work is needed to lower the threshold for effective RDM not just in cardiovascular research but in all biomedical research, with data sharing and reuse being factored in at every stage of the scientific process. A culture of open science with FAIR research data should be fostered through education and training of early-career and established research professionals. Ultimately, FAIR RDM requires permanent, long-term effort at all levels. If outcomes can be shown to be superior and to promote better (and better value) science, modern RDM will make a positive difference to cardiovascular science and practice. The full position paper is available in the supplementary materials.

Published
2024

4. “Be sustainable”: EOSC‐Life recommendations for implementation of FAIR principles in life science data handling

Author

David, Romain, primary, Rybina, Arina, additional, Burel, Jean‐Marie, additional, Heriche, Jean‐Karim, additional, Audergon, Pauline, additional, Boiten, Jan‐Willem, additional, Coppens, Frederik, additional, Crockett, Sara, additional, Exter, Katrina, additional, Fahrner, Sven, additional, Fratelli, Maddalena, additional, Goble, Carole, additional, Gormanns, Philipp, additional, Grantner, Tobias, additional, Grüning, Björn, additional, Gurwitz, Kim Tamara, additional, Hancock, John M, additional, Harmse, Henriette, additional, Holub, Petr, additional, Juty, Nick, additional, Karnbach, Geoffrey, additional, Karoune, Emma, additional, Keppler, Antje, additional, Klemeier, Jessica, additional, Lancelotti, Carla, additional, Legras, Jean‐Luc, additional, Lister, Allyson L, additional, Longo, Dario Livio, additional, Ludwig, Rebecca, additional, Madon, Bénédicte, additional, Massimi, Marzia, additional, Matser, Vera, additional, Matteoni, Rafaele, additional, Mayrhofer, Michaela Th, additional, Ohmann, Christian, additional, Panagiotopoulou, Maria, additional, Parkinson, Helen, additional, Perseil, Isabelle, additional, Pfander, Claudia, additional, Pieruschka, Roland, additional, Raess, Michael, additional, Rauber, Andreas, additional, Richard, Audrey S, additional, Romano, Paolo, additional, Rosato, Antonio, additional, Sánchez‐Pla, Alex, additional, Sansone, Susanna‐Assunta, additional, Sarkans, Ugis, additional, Serrano‐Solano, Beatriz, additional, Tang, Jing, additional, Tanoli, Ziaurrehman, additional, Tedds, Jonathan, additional, Wagener, Harald, additional, Weise, Martin, additional, Westerhoff, Hans V, additional, Wittner, Rudolf, additional, Ewbank, Jonathan, additional, Blomberg, Niklas, additional, and Gribbon, Philip, additional

Published
2023
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5. The challenges of research data management in cardiovascular science: a DGK and DZHK position paper—executive summary

Author

Steffens, Sabine, primary, Schröder, Katrin, additional, Krüger, Martina, additional, Maack, Christoph, additional, Streckfuss-Bömeke, Katrin, additional, Backs, Johannes, additional, Backofen, Rolf, additional, Baeßler, Bettina, additional, Devaux, Yvan, additional, Gilsbach, Ralf, additional, Heijman, Jordi, additional, Knaus, Jochen, additional, Kramann, Rafael, additional, Linz, Dominik, additional, Lister, Allyson L., additional, Maatz, Henrike, additional, Maegdefessel, Lars, additional, Mayr, Manuel, additional, Meder, Benjamin, additional, Nussbeck, Sara Y., additional, Rog-Zielinska, Eva A., additional, Schulz, Marcel H., additional, Sickmann, Albert, additional, Yigit, Gökhan, additional, and Kohl, Peter, additional

Published
2023
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6. Umbrella Data Management Plans to Integrate FAIR Data: Lessons From the ISIDORe and BY-COVID Consortia for Pandemic Preparedness

Author

David, Romain, primary, Richard, Audrey S., additional, Connellan, Claire, additional, Lauer, Katharina B., additional, Chiusano, Maria Luisa, additional, Goble, Carole, additional, Houde, Martin, additional, Kemmer, Isabel, additional, Keppler, Antje, additional, Lieutaud, Philippe, additional, Ohmann, Christian, additional, Panagiotopoulou, Maria, additional, Khan, Sara Raza, additional, Rybina, Arina, additional, Soiland-Reyes, Stian, additional, Wit, Charlotte, additional, Wittner, Rudolf, additional, Buono, Rafael Andrade, additional, Marsh, Sarah Arnaud, additional, Audergon, Pauline, additional, Bonfils, Dylan, additional, Carazo, Jose-Maria, additional, Charrel, Remi, additional, Coppens, Frederik, additional, Fecke, Wolfgang, additional, Filippone, Claudia, additional, Alvarez, Eva Garcia, additional, Gul, Sheraz, additional, Hermjakob, Henning, additional, Herzog, Katja, additional, Holub, Petr, additional, Kozera, Lukasz, additional, Lister, Allyson L., additional, López-Coronado, José, additional, Madon, Bénédicte, additional, Majcen, Kurt, additional, Martin, William, additional, Müller, Wolfgang, additional, Papadopoulou, Elli, additional, Prat, Christine M.A., additional, Romano, Paolo, additional, Sansone, Susanna-Assunta, additional, Saunders, Gary, additional, Blomberg, Niklas, additional, and Ewbank, Jonathan, additional

Published
2023
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7. PREreview of 'A maturity model for catalogues of semantic artefacts'

Author

Lister, Allyson L.

Abstract

This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/7937430. Thank you for this work. However, it is important to note that not all resources in the comparison table are the same type: some are ontology look-up services / repositories (e.g., AgroPortal, OLS), others are wider registries of standards/databases/policies (e.g., FAIRsharing), including -- but not limited to -- ontologies. As such, their scope and functionalities are inevitably different. This means that, for resources like FAIRsharing, many of the dimensions (e.g. machine-readability and human readability) are implemented, but relevant to what is in scope for the resource. We suggest that this distinction is make clear. More specifically for FAIRsharing, the following dimension features should be enabled in addition to those already selected (unless I am misunderstanding your definitions, in which case please get in touch if you have any questions): custom vs standard vocabulary: we have a custom vocabulary for describing all FAIRsharing records, however this draws from a set of standard vocabularies. How can this be best represented? curation by owner (our maintainers *are* the owners of the resource) human readable machine readable metadata by editor governance rules governance description community suggestion transparency versioning Finally, as a generic comment, the 'fully' vs 'customised' oss doesn't take into account if the system runs on partially (but not completely) open-source software. Thank you. Best wishes, Allyson Lister, FAIRsharing Content and Community Coordinator (contact@fairsharing.org) Competing interests The author declares that they have no competing interests.

Published
2023
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8. Umbrella Data Management Plans to integrate FAIR data : lessons from the ISIDORe and BY-COVID consortia for pandemic preparedness

Author

David, Romain, Richard, Audrey S., Connellan, Claire, Lauer, Katharina B., Chiusano, Maria Luisa, Goble, Carole, Houde, Martin, Kemmer, Isabel, Keppler, Antje, Lieutaud, Philippe, Ohmann, Christian, Panagiotopoulou, Maria, Raza Khan, Sara, Rybina, Arina, Soiland-Reyes, Stian, Wit, Charlotte, Wittner, Rudolf, Andrade Buono, Rafael, Marsh, Sarah Arnaud, Audergon, Pauline, Bonfils, Dylan, Carazo, Jose-Maria, Charrel, Remi, Coppens, Frederik, Fecke, Wolfgang, Filippone, Claudia, Garcia Alvarez, Eva, Gul, Sheraz, Hermjakob, Henning, Herzog, Katja, Holub, Petr, Kozera, Lukasz, Lister, Allyson L., López-Coronado, José, Madon, Bénédicte, Majcen, Kurt, Martin, William, Müller, Wolfgang, Papadopoulou, Elli, Prat, Christine M.A., Romano, Paolo, Sansone, Susanna-Assunta, Saunders, Gary, Blomberg, Niklas, and Ewbank, Jonathan

Subjects
Data Management Plan, DMP, Research Data Management, RDM, data management quality, research data, pandemic, outbreak, data services harmonisation, data reuse, FAIR principles, data stewards
Abstract

The Horizon Europe project ISIDORe is dedicated to pandemic preparedness and responsiveness research. It brings together 17 Research Infrastructures (RIs) and networks to provide a broad range of services to infectious disease researchers. An efficient and structured treatment of data is central to ISIDORe’s aim to furnish seamless access to its multidisciplinary catalogue of services, and to ensure that users’ results are treated FAIRly. ISIDORe therefore requires a data management plan (DMP) covering both access management and research outputs, applicable over a broad range of disciplines, and compatible with the constraints and existing practices of its diverse partners. We undertook an iterative, step-by-step, process to build a community-approved living document, identifying good practices and processes, on the basis of use cases, presented as proof of concepts. International fora such as the RDA and EOSC, and primarily the BY-COVID project, furnished registries, tools and online data platforms, as well as standards, and the support of data scientists. Together, these elements provide a path for building an umbrella, FAIR-compliant DMP, aligned as fully as possible with FAIR principles, which could also be applied as a framework for data management harmonisation in other large-scale, challenge-driven projects. Finally, we discuss how data management and reuse can be further improved through the writing of realistic DMPs using 'DMP profiles' and, in the future, the contribution of an inter RIs data steward network, to produce a Community of Practice that could be integrated into planned trans-RI competence centres., Preprint added on zenodo with the autorisation of DSJ Editor

Published
2023
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9. EOSC-Life EOSC FAIR services deployment for open calls

Author

Parkinson, Helen, Gribbon, Philip, Sarkans, Ugis, Witt, Gesa, Zaliani, Andrea, Kohler, Manfred, Swedlow, Jason, Burel, Jean-Marie, Swertz, Morris, van Enckevort, Esther, Holub, Petr, Massimi, Marzia, Matteoni, Rafaele, Maier, Holger, Hinttala, Reetta, Heikkinen, Anne, Gormanns, Philipp, Vasseur, Laurent, Leblanc, Sophie, Herault, Yann, Kontoyiannis, Dimitris, Chandras, Christina, Panou, Dimitra, López Coronado, José Miguel, Aznar Novella, Rosa, Robert, Vincent, Hadj Amor, Ammar Ben, Casaregola, Serge, Legras, Jean-Luc, Mistou, Michel-Yves, Romano, Paolo, Perseil, Isabelle, David, Romain, Pieruschka, Roland, Exter, Katrina, Portier, Marc, Decruw, Cedric, Canham, Steve, Ohmann, Christian, Goryanin, Sergey, Del Cano, Laura, Fratelli, Maddalena, Goble, Carole, Owen, Stuart, Soiland- Reyes, Stian, Juty, Nick, Harmse, Henriette, Longo, Dario, Sansone, Susanna, Lister, Allyson L., McQuilton, Peter, Tursthon, Milo, Granell, Ramon, Mirian, Hossein, Roos, Marco, and Bonino, Luiz

Subjects
FAIR data, Life science research infrastructures, FAIR services
Abstract

This deliverable summarises the work of WP1 to deliver Findable, Accessible, Interoperable and Re-usable (FAIR) services in the context of EOSC-Life’s funding calls, using these to improve FAIR services, service uptake and to inform sustainable development and future use. We describe service delivery and development around the FAIR principles and present the funded projects which have driven our implementation of FAIR Services. We address sustainability and describe the processes used to engage the EOSC-Life funded projects, as well as future work.

Published
2022
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10. EOSC-Life -D1.3 EOSC-Life EOSC FAIR services deployment for open calls

Author

Parkinson, Helen, Gribbon, Philip, Sarkans, Ugis, Witt, Gesa, Zaliani, Andrea, Kohler, Manfred, Swedlow, Jason, Burel, Jean-Marie, Swertz, Morris, van Enckevort, Esther, Holub, Petr, Massimi, Marzia, Matteoni, Rafaele, Maier, Holger, Hinttala, Reetta, Heikkinen, Anne, Gormanns, Philipp, Vasseur, Laurent, Leblanc, Sophie, Herault, Yann, Kontoyiannis, Dimitris, Chandras, Christina, Panou, Dimitra, López-Coronado, José-Miguel, Aznar-Novella, Rosa, Robert, Vincent, Hadj-Amor, Ammar-Ben, Casaregola, Serge, Legras, Jean-Luc, Mistou, Michel-Yves, Romano, Paolo, Perseil, Isabelle, David, Romain, Pieruschka, Roland, Exter, Katrina, Portier, Marc, Decruw, Cedric, Canham, Steve, Ohmann, Christian, Goryanin, Sergey, Del-Cano, Laura, Fratelli, Maddalena, Goble, Carole, Owen, Stuart, Soiland-Reyes, Stian, Juty, Nick, Harmse, Henriette, Longo, Dario, Sansone, Susanna, Lister, Allyson-L., Mcquilton, Peter, Tursthon, Milo, Granell, Ramon, Mirian, Hossein, Roos, Marco, Bonino, Luiz, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), European Molecular Biology Laboratory [Hinxton], Centre for Gene Regulation and Expression, School of Life Sciences Dundee, University of Dundee, Division of Computational Biology, Erasmus University Medical Center [Rotterdam] (Erasmus MC), University Medical Center Groningen [Groningen] (UMCG), European research infrastructure for biobanking (BBMRI-ERIC), Consiglio Nazionale delle Ricerche [Bologna] (CNR), University of South Australia [Adelaide], MRC Harwell Institute [UK], INFRAFRONTIER GmbH [Neuherberg], Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), IRCCS Ospedale Policlinico San Martino [Genoa, Italy], INSERM-TRANSFERT [Paris] (IT), Institut National de la Santé et de la Recherche Médicale (INSERM), European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), IBG-2: Plant Sciences, Flanders Marine Institute (VLIZ), European Clinical Research Infrastructures Network [Dusseldorf] (ECRIN), IRCCS - Istituto di Ricerche Farmacologiche 'Mario Negri' [Milan, Italy], The University of Manchester, University of Oxford, Fraunhofer-Institut für Offene Kommunikationssysteme (FOKUS Fraunhofer), EMBL, CSIC, VU, BBMRI, KNAW, UVEG, USMI, IMG, UNIMAN, LUMC, EATRIS, UNIMIB, EBI, ECRIN, EMBRC, EMPHASIS (FZJ), ERINHA, INFRAFRONTIER, INRAE, UNIVDUN, HMGU, CERBM, BSCRC, UOULU, CRRMMP, and European Project: 824087,EOSC-Life

Subjects
Life science, FAIR data, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], research infrastructures, FAIR services
Abstract

This deliverable summarises the work of WP1 to deliver Findable, Accessible, Interoperable and Re-usable (FAIR) services in the context of EOSC-Life’s funding calls, using these to improve FAIR services, service uptake and to inform sustainable development and future use. We describe service delivery and development around the FAIR principles and present the funded projects which have driven our implementation of FAIR Services. We address sustainability and describe the processes used to engage the EOSC-Life funded projects, as well as future work.

Published
2022

11. FAIRsharing: promoting the value of standards and repositories for scholarly communication

Author

Lister, Allyson L.

Subjects
FAIR data, Databases, Data standards, FAIRsharing, Data policies, Resource discovery
Abstract

FAIRsharing is an informative and educational resource on interlinked standards, repositories and policies, three key elements of the FAIR ecosystem. FAIRsharing promotes the existence and value of these resources to aid data sharing and consequently strengthen scholarly communication. FAIRsharing aims to foster a culture change within the research community such that use of databases and standards for FAIRer data is pervasive and seamless. This is achieved by guiding consumers to discover, select and use these resources with confidence. FAIRsharing is adopted by funders, publishers and communities across all disciplines.

Published
2021
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12. Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models

Author

Lister Allyson L., Pocock Matthew, and Wipat Anil

Subjects
Biotechnology, TP248.13-248.65
Abstract

The creation of quantitative, simulatable, Systems Biology Markup Language (SBML) models that accurately simulate the system under study is a time-intensive manual process that requires careful checking. Currently, the rules and constraints of model creation, curation, and annotation are distributed over at least three separate documents: the SBML schema document (XSD), the Systems Biology Ontology (SBO), and the “Structures and Facilities for Model Definition” document. The latter document contains the richest set of constraints on models, and yet it is not amenable to computational processing. We have developed a Web Ontology Language (OWL) knowledge base that integrates these three structure documents, and that contains a representative sample of the information contained within them. This Model Format OWL (MFO) performs both structural and constraint integration and can be reasoned over and validated. SBML Models are represented as individuals of OWL classes, resulting in a single computationally amenable resource for model checking. Knowledge that was only accessible to humans is now explicitly and directly available for computational approaches. The integration of all structural knowledge for SBML models into a single resource creates a new style of model development and checking.

Published
2007
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13. Annotation of SBML models through rule-based semantic integration

Author

Lister Allyson L, Lord Phillip, Pocock Matthew, and Wipat Anil

Subjects
Computer applications to medicine. Medical informatics, R858-859.7
Abstract

Abstract Background The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort. Results Here we present rule-based mediation, a method of semantic data integration applied to systems biology model annotation. The heterogeneous data sources are first syntactically converted into ontologies, which are then aligned to a small domain ontology by applying a rule base. We demonstrate proof-of-principle of this application of rule-based mediation using off-the-shelf semantic web technology through two use cases for SBML model annotation. Existing tools and technology provide a framework around which the system is built, reducing development time and increasing usability. Conclusions Integrating resources in this way accommodates multiple formats with different semantics, and provides richly-modelled biological knowledge suitable for annotation of SBML models. This initial work establishes the feasibility of rule-based mediation as part of an automated SBML model annotation system. Availability Detailed information on the project files as well as further information on and comparisons with similar projects is available from the project page at http://cisban-silico.cs.ncl.ac.uk/RBM/.

Published
2010
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16. Helping the consumers and producers of standards, repositories and policies to enable fair data

Author

McQuilton, Peter, Batista, Dominique, Beyan, Oya, Granell, Ramon, Coles, Simon, Izzo, Massimiliano, Lister, Allyson L., Pergl, Robert, Rocca-Serra, Philippe, Schaap, Ben, Shanahan, Hugh, Thurston, Milo, Sansone, Susanna Assunta, McQuilton, Peter, Batista, Dominique, Beyan, Oya, Granell, Ramon, Coles, Simon, Izzo, Massimiliano, Lister, Allyson L., Pergl, Robert, Rocca-Serra, Philippe, Schaap, Ben, Shanahan, Hugh, Thurston, Milo, and Sansone, Susanna Assunta

Abstract

Thousands of community-developed (meta)data guidelines, models, ontologies, schemas and formats have been created and implemented by several thousand data repositories and knowledge-bases, across all disciplines. These resources are necessary to meet government, funder and publisher expectations of greater transparency and access to and preservation of data related to research publications. This obligates researchers to ensure their data is FAIR, share their data using the appropriate standards, store their data in sustainable and community-adopted repositories, and to conform to funder and publisher data policies. FAIR data sharing also plays a key role in enabling researchers to evaluate, re-analyse and reproduce each other’s work. We can map the landscape of relationships between community-adopted standards and repositories, and the journal publisher and funder data policies that recommend their use. In this paper, we show how the work of the GO-FAIR FAIR Standards, Repositories and Policies (StRePo) Implementation Network serves as a central integration and cross-fertilisation point for the reuse of FAIR standards, repositories and data policies in general. Pivotal to this effort, the FAIRsharing, an endorsed flagship resource of the Research Data Alliance that maps the landscape of relationships between community-adopted standards and repositories, and the journal publisher and funder data policies that recommend their use. Lastly, we highlight a number of activities around FAIR tools, services and educational efforts to raise awareness and encourage participation.

Published
2020

17. SBML Level 3: an extensible format for the exchange and reuse of biological models

Author

Computer Science, Keating, Sarah M., Waltemath, Dagmar, Koenig, Matthias, Zhang, Fengkai, Draeger, Andreas, Chaouiya, Claudine, Bergmann, Frank T., Finney, Andrew, Gillespie, Colin S., Helikar, Tomas, Hoops, Stefan, Malik-Sheriff, Rahuman S., Moodie, Stuart L., Moraru, Ion I., Myers, Chris J., Naldi, Aurelien, 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., Gomez, 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, Computer Science, Keating, Sarah M., Waltemath, Dagmar, Koenig, Matthias, Zhang, Fengkai, Draeger, Andreas, Chaouiya, Claudine, Bergmann, Frank T., Finney, Andrew, Gillespie, Colin S., Helikar, Tomas, Hoops, Stefan, Malik-Sheriff, Rahuman S., Moodie, Stuart L., Moraru, Ion I., Myers, Chris J., Naldi, Aurelien, 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., Gomez, 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., and Hucka, Michael

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 developedSBMLLevel 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 ofSBMLand 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 howSBMLLevel 3 provides the foundation needed to support this evolution.

Published
2020

18. Helping the Consumers and Producers of Standards, Repositories and Policies to Enable FAIR Data

Author

McQuilton, Peter, primary, Batista, Dominique, additional, Beyan, Oya, additional, Granell, Ramon, additional, Coles, Simon, additional, Izzo, Massimiliano, additional, Lister, Allyson L., additional, Pergl, Robert, additional, Rocca-Serra, Philippe, additional, Schaap, Ben, additional, Shanahan, Hugh, additional, Thurston, Milo, additional, and Sansone, Susanna-Assunta, additional

Published
2020
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20. The BioSharing Registry: mapping the landscape of standards and databases resources in the life sciences

Author

McQuilton, Peter, Gonzalez-Beltran, Alejandra, Lister, Allyson L., Maguire, Eamonn, Rocca-Serra, Philippe, Thurston, Milo, Ball, Michael, Bloom, Theodora, Boyd, Jennifer, Edmunds, Scott, Ganley, Emma, Grethe, Jeffrey, Haendel, Melissa, Hodson, Simon, Jimenez, Rafael, Amye Kenall, Khodiyar, Varsha, Lemberger, Thomas, Lawrence, Rebecca, Lin, Jennifer, Naughton, Linda, Shell, Joseph, Tedds, Jonathan, Tenenbaum, Jessica, Vision, Todd, Witt, Michael, and Susanna-Assunta Sansone

Abstract

BioSharing (http://www.biosharing.org) is a curated, web-based, searchable portal of three linked registries of content standards, databases and data policies in the life sciences, broadly encompassing the biological, natural and biomedical sciences. Our records are informative and discoverable, maximizing standards adoption and (re)use (e.g. in data policies), and allowing the monitoring of their maturity and evolution (Tenenbaum, Sansone, Haendel; Am Med Inform Assoc, 2014). With over 1,300 records, BioSharing content can be searched using simple or advanced searches, filtered via a filtering matrix, or grouped via the ‘Collection’ feature, according to field of interest or focus. Examples are the NPG Scientific Data and BioMedCentral Collections, collating and linking the recommended standards and repositories from their Data Policy for author. Similarly other publishers, projects and organizations are creating Collections by selecting and filtering standards and databases relevant to their work, such as the BD2K bioCADDIE project. As a community effort, BioSharing offers users the ability to ‘claim’ records, allowing their update. Each claimant also has a user profile that can be linked to their resources, publications and ORCID ID, thus providing visibility for them as an individual.Launched in 2011 as an extension and evolution of the MIBBI portal (founded by the same Operational Team, led by Sansone), BioSharing is working with a growing number of journals and other registries; it is also part of ELIXIR-UK Node and contributing to the NIH BD2K CEDAR. Driven by an international Advisory Board (co-chaired by Tenenbaum, Haendel) the BioSharing userbase has grown by 40% over the last year, thanks to successful engagement with researchers, publishers, librarians, developers and other stakeholders via several routes, including a joint RDA/Force11 working group (co-chaired by Lawrence and Hodson) and a collaboration with the International Biocuration Society.

Published
2015
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21. The Ontology for Biomedical Investigations

Author

Bandrowski, Anita, primary, Brinkman, Ryan, additional, Brochhausen, Mathias, additional, Brush, Matthew H., additional, Bug, Bill, additional, Chibucos, Marcus C., additional, Clancy, Kevin, additional, Courtot, Mélanie, additional, Derom, Dirk, additional, Dumontier, Michel, additional, Fan, Liju, additional, Fostel, Jennifer, additional, Fragoso, Gilberto, additional, Gibson, Frank, additional, Gonzalez-Beltran, Alejandra, additional, Haendel, Melissa A., additional, He, Yongqun, additional, Heiskanen, Mervi, additional, Hernandez-Boussard, Tina, additional, Jensen, Mark, additional, Lin, Yu, additional, Lister, Allyson L., additional, Lord, Phillip, additional, Malone, James, additional, Manduchi, Elisabetta, additional, McGee, Monnie, additional, Morrison, Norman, additional, Overton, James A., additional, Parkinson, Helen, additional, Peters, Bjoern, additional, Rocca-Serra, Philippe, additional, Ruttenberg, Alan, additional, Sansone, Susanna-Assunta, additional, Scheuermann, Richard H., additional, Schober, Daniel, additional, Smith, Barry, additional, Soldatova, Larisa N., additional, Stoeckert, Christian J., additional, Taylor, Chris F., additional, Torniai, Carlo, additional, Turner, Jessica A., additional, Vita, Randi, additional, Whetzel, Patricia L., additional, and Zheng, Jie, additional

Published
2016
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22. Live Coverage of Intelligent Systems for Molecular Biology

Author

Lister, Allyson L., Datta, Ruchira S., Hofmann, Oliver, Krause, Roland, Kuhn, Michael, Roth, Bettina, Schneider, Reinhard, and Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center]

Subjects
Biochemistry, biophysics & molecular biology [F05] [Life sciences], Biochimie, biophysique & biologie moléculaire [F05] [Sciences du vivant]
Published
2010

24. Live Coverage of Scientific Conferences Using Web Technologies

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Lister, Allyson L., Datta, Ruchira S., Hofmann, Oliver, Krause, Roland, Kuhn, Michael, Roth, Bettina, Schneider, Reinhard, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Lister, Allyson L., Datta, Ruchira S., Hofmann, Oliver, Krause, Roland, Kuhn, Michael, Roth, Bettina, and Schneider, Reinhard

Published
2010
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25. Live Coverage of Intelligent Systems for Molecular Biology

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Lister, Allyson L., Datta, Ruchira S., Hofmann, Oliver, Krause, Roland, Kuhn, Michael, Roth, Bettina, Schneider, Reinhard, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Lister, Allyson L., Datta, Ruchira S., Hofmann, Oliver, Krause, Roland, Kuhn, Michael, Roth, Bettina, and Schneider, Reinhard

Published
2010
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26. The minimum information about a genome sequence (MIGS) specification.

Author

Field, Dawn, Garrity, George, Gray, Tanya, Morrison, Norman, Selengut, Jeremy, Sterk, Peter, Tatusova, Tatiana, Thomson, Nicholas, Allen, Michael J, Angiuoli, Samuel V, Ashburner, Michael, Axelrod, Nelson, Baldauf, Sandra, Ballard, Stuart, Boore, Jeffrey, Cochrane, Guy, Cole, James, Dawyndt, Peter, De Vos, Paul, DePamphilis, Claude, Edwards, Robert, Faruque, Nadeem, Feldman, Robert, Gilbert, Jack, Gilna, Paul, Glöckner, Frank Oliver, Goldstein, Philip, Guralnick, Robert, Haft, Dan, Hancock, David, Hermjakob, Henning, Hertz-Fowler, Christiane, Hugenholtz, Phil, Joint, Ian, Kagan, Leonid, Kane, Matthew, Kennedy, Jessie, Kowalchuk, George, Kottmann, Renzo, Kolker, Eugene, Kravitz, Saul, Kyrpides, Nikos, Leebens-Mack, Jim, Lewis, Suzanna E, Li, Kelvin, Lister, Allyson L, Lord, Phillip, Maltsev, Natalia, Markowitz, Victor, Martiny, Jennifer, Methe, Barbara, Mizrachi, Ilene, Moxon, Richard, Nelson, Karen, Parkhill, Julian, Proctor, Lita, White, Owen, Sansone, Susanna-Assunta, Spiers, Andrew, Stevens, Robert, Swift, Paul, Taylor, Chris, Tateno, Yoshio, Tett, Adrian, Turner, Sarah, Ussery, David, Vaughan, Bob, Ward, Naomi, Whetzel, Trish, San Gil, Ingio, Wilson, Gareth, Wipat, Anil, Field, Dawn, Garrity, George, Gray, Tanya, Morrison, Norman, Selengut, Jeremy, Sterk, Peter, Tatusova, Tatiana, Thomson, Nicholas, Allen, Michael J, Angiuoli, Samuel V, Ashburner, Michael, Axelrod, Nelson, Baldauf, Sandra, Ballard, Stuart, Boore, Jeffrey, Cochrane, Guy, Cole, James, Dawyndt, Peter, De Vos, Paul, DePamphilis, Claude, Edwards, Robert, Faruque, Nadeem, Feldman, Robert, Gilbert, Jack, Gilna, Paul, Glöckner, Frank Oliver, Goldstein, Philip, Guralnick, Robert, Haft, Dan, Hancock, David, Hermjakob, Henning, Hertz-Fowler, Christiane, Hugenholtz, Phil, Joint, Ian, Kagan, Leonid, Kane, Matthew, Kennedy, Jessie, Kowalchuk, George, Kottmann, Renzo, Kolker, Eugene, Kravitz, Saul, Kyrpides, Nikos, Leebens-Mack, Jim, Lewis, Suzanna E, Li, Kelvin, Lister, Allyson L, Lord, Phillip, Maltsev, Natalia, Markowitz, Victor, Martiny, Jennifer, Methe, Barbara, Mizrachi, Ilene, Moxon, Richard, Nelson, Karen, Parkhill, Julian, Proctor, Lita, White, Owen, Sansone, Susanna-Assunta, Spiers, Andrew, Stevens, Robert, Swift, Paul, Taylor, Chris, Tateno, Yoshio, Tett, Adrian, Turner, Sarah, Ussery, David, Vaughan, Bob, Ward, Naomi, Whetzel, Trish, San Gil, Ingio, Wilson, Gareth, and Wipat, Anil

Abstract

With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.

Published
2008
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27. Meeting report: the fourth Genomics Standards Consortium Workshop

Author

Field, Dawn, Glockner, Frank Oliver, Garrity, George M., Gray, Tanya, Sterk, Peter, Cochrane, Guy, Vaughan, Robert, Kolker, Eugene, Kottmann, Renzo, Kyrpides, Nikos, Angiuoli, Sam, Dawyndt, Peter, Guralnick, Robert, Goldstein, Philip, Hall, Neil, Hirschman, Lynette, Kravitz, Saul, Lister, Allyson L., Markowitz, Victor, Thomson, Nick, Whetzel, Trish, Field, Dawn, Glockner, Frank Oliver, Garrity, George M., Gray, Tanya, Sterk, Peter, Cochrane, Guy, Vaughan, Robert, Kolker, Eugene, Kottmann, Renzo, Kyrpides, Nikos, Angiuoli, Sam, Dawyndt, Peter, Guralnick, Robert, Goldstein, Philip, Hall, Neil, Hirschman, Lynette, Kravitz, Saul, Lister, Allyson L., Markowitz, Victor, Thomson, Nick, and Whetzel, Trish

Abstract

This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection IV” workshop held June 6–8, 2007, at the National Institute for Environmental eScience (NIEeS), Cambridge, United Kingdom. This fourth workshop of the Genomic Standards Consortium (GSC) was a mix of short presentations, strategy discussions, and technical sessions. Speakers provided progress reports on the development of the “Minimum Information about a Genome Sequence” (MIGS) specification and the closely integrated “Minimum Information about a Metagenome Sequence” (MIMS) specification. The key outcome of the workshop was consensus on the next version of the MIGS/MIMS specification (v1.2). This drove further definition and restructuring of the MIGS/MIMS XML schema (syntax). With respect to semantics, a term vetting group was established to ensure that terms are properly defined and submitted to the appropriate ontology projects. Perhaps the single most important outcome of the workshop was a proposal to move beyond the concept of “minimum” to create a far richer XML schema that would define a “Genomic Contextual Data Markup Language” (GCDML) suitable for wider semantic integration across databases. GCDML will contain not only curated information (e.g., compliant with MIGS/MIMS), but also be extended to include a variety of data processing and calculations. Further information about the Genomic Standards Consortium and its range of activities can be found at http://gensc.org

Published
2008

31. Modeling and Managing Experimental Data Using FuGE

Author

Jones, Andrew R., primary, Lister, Allyson L., additional, Hermida, Leandro, additional, Wilkinson, Peter, additional, Eisenacher, Martin, additional, Belhajjame, Khalid, additional, Gibson, Frank, additional, Lord, Phil, additional, Pocock, Matthew, additional, Rosenfelder, Heiko, additional, Santoyo-Lopez, Javier, additional, Wipat, Anil, additional, and Paton, Norman W., additional

Published
2009
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32. Meeting Report: The Fourth Genomic Standards Consortium (GSC) Workshop

Author

Field, Dawn, primary, Glöckner, Frank Oliver, additional, Garrity, George M., additional, Gray, Tanya, additional, Sterk, Peter, additional, Cochrane, Guy, additional, Vaughan, Robert, additional, Kolker, Eugene, additional, Kottmann, Renzo, additional, Kyrpides, Nikos, additional, Angiuoli, Sam, additional, Dawyndt, Peter, additional, Guralnick, Robert, additional, Goldstein, Philip, additional, Hall, Neil, additional, Hirschman, Lynette, additional, Kravitz, Saul, additional, Lister, Allyson L., additional, Markowitz, Victor, additional, Thomson, Nick, additional, and Whetzel, Trish, additional

Published
2008
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33. The minimum information about a genome sequence (MIGS) specification

Author

Field, Dawn, primary, Garrity, George, additional, Gray, Tanya, additional, Morrison, Norman, additional, Selengut, Jeremy, additional, Sterk, Peter, additional, Tatusova, Tatiana, additional, Thomson, Nicholas, additional, Allen, Michael J, additional, Angiuoli, Samuel V, additional, Ashburner, Michael, additional, Axelrod, Nelson, additional, Baldauf, Sandra, additional, Ballard, Stuart, additional, Boore, Jeffrey, additional, Cochrane, Guy, additional, Cole, James, additional, Dawyndt, Peter, additional, De Vos, Paul, additional, dePamphilis, Claude, additional, Edwards, Robert, additional, Faruque, Nadeem, additional, Feldman, Robert, additional, Gilbert, Jack, additional, Gilna, Paul, additional, Glöckner, Frank Oliver, additional, Goldstein, Philip, additional, Guralnick, Robert, additional, Haft, Dan, additional, Hancock, David, additional, Hermjakob, Henning, additional, Hertz-Fowler, Christiane, additional, Hugenholtz, Phil, additional, Joint, Ian, additional, Kagan, Leonid, additional, Kane, Matthew, additional, Kennedy, Jessie, additional, Kowalchuk, George, additional, Kottmann, Renzo, additional, Kolker, Eugene, additional, Kravitz, Saul, additional, Kyrpides, Nikos, additional, Leebens-Mack, Jim, additional, Lewis, Suzanna E, additional, Li, Kelvin, additional, Lister, Allyson L, additional, Lord, Phillip, additional, Maltsev, Natalia, additional, Markowitz, Victor, additional, Martiny, Jennifer, additional, Methe, Barbara, additional, Mizrachi, Ilene, additional, Moxon, Richard, additional, Nelson, Karen, additional, Parkhill, Julian, additional, Proctor, Lita, additional, White, Owen, additional, Sansone, Susanna-Assunta, additional, Spiers, Andrew, additional, Stevens, Robert, additional, Swift, Paul, additional, Taylor, Chris, additional, Tateno, Yoshio, additional, Tett, Adrian, additional, Turner, Sarah, additional, Ussery, David, additional, Vaughan, Bob, additional, Ward, Naomi, additional, Whetzel, Trish, additional, San Gil, Ingio, additional, Wilson, Gareth, additional, and Wipat, Anil, additional

Published
2008
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34. eGenomics: Cataloguing Our Complete Genome Collection III

Author

Field, Dawn, primary, Garrity, George, additional, Gray, Tanya, additional, Selengut, Jeremy, additional, Sterk, Peter, additional, Thomson, Nick, additional, Tatusova, Tatiana, additional, Cochrane, Guy, additional, Glöckner, Frank Oliver, additional, Kottmann, Renzo, additional, Lister, Allyson L., additional, Tateno, Yoshio, additional, and Vaughan, Robert, additional

Published
2007
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36. Managing experimental data using FuGE.

Author

Jones AR and Lister AL

Subjects
Computational Biology methods, Genomics methods, Genomics standards, Proteomics methods, Proteomics standards, Workflow, Computational Biology standards, Database Management Systems standards, Databases, Genetic standards, Software standards
Abstract

Data management and sharing in omics science is highly challenging due to the constant evolution of experimental techniques, the range of instrument types and software used for analysis, and the high volumes of data produced. The Functional Genomics Experiment (FuGE) Model was created to provide a model for capturing descriptions of sample processing, experimental protocols and multidimensional data for any kind of omics experiment. FuGE has two modes of action: (a) as a storage architecture for experimental workflows and (b) as a framework for building new technology-specific data standards.FuGE is an object model that is converted into an XML implementation for data exchange. Software toolkits have been developed for data handling and for bridging between XML data files and relational database implementations. FuGE has been adopted by the Proteomics Standards Initiative (PSI, http://www.psidev.info ) for building several new data formats, and it is being used in a variety of other experimental contexts, thus allowing data to be integrated across a range of experimental types to support Systems Biology approaches. This chapter provides a practical guide for laboratories or groups wishing to manage their data, and for developers wishing to create new data formats using FuGE.

Published
2010
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37. Modeling and managing experimental data using FuGE.

Author

Jones AR, Lister AL, Hermida L, Wilkinson P, Eisenacher M, Belhajjame K, Gibson F, Lord P, Pocock M, Rosenfelder H, Santoyo-Lopez J, Wipat A, and Paton NW

Subjects
Computer Simulation, Flow Cytometry instrumentation, Flow Cytometry methods, Reproducibility of Results, Software, User-Computer Interface, Computational Biology methods, Genomics methods, Models, Theoretical
Abstract

The Functional Genomics Experiment data model (FuGE) has been developed to increase the consistency and efficiency of experimental data modeling in the life sciences, and it has been adopted by a number of high-profile standardization organizations. FuGE can be used: (1) directly, whereby generic modeling constructs are used to represent concepts from specific experimental activities; or (2) as a framework within which method-specific models can be developed. FuGE is both rich and flexible, providing a considerable number of modeling constructs, which can be used in a range of different ways. However, such richness and flexibility also mean that modelers and application developers have choices to make when applying FuGE in a given context. This paper captures emerging best practice in the use of FuGE in the light of the experience of several groups by: (1) proposing guidelines for the use and extension of the FuGE data model; (2) presenting design patterns that reflect recurring requirements in experimental data modeling; and (3) describing a community software tool kit (STK) that supports application development using FuGE. We anticipate that these guidelines will encourage consistent usage of FuGE, and as such, will contribute to the development of convergent data standards in omics research.

Published
2009
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38. Meeting report: the fourth Genomic Standards Consortium (GSC) workshop.

Author

Field D, Glöckner FO, Garrity GM, Gray T, Sterk P, Cochrane G, Vaughan R, Kolker E, Kottmann R, Kyrpides N, Angiuoli S, Dawyndt P, Guralnick R, Goldstein P, Hall N, Hirschman L, Kravitz S, Lister AL, Markowitz V, Thomson N, and Whetzel T

Subjects
Education, Programming Languages, Reference Standards, Databases, Genetic, Genomics
Abstract

This meeting report summarizes the proceedings of the "eGenomics: Cataloguing our Complete Genome Collection IV" workshop held June 6-8, 2007, at the National Institute for Environmental eScience (NIEeS), Cambridge, United Kingdom. This fourth workshop of the Genomic Standards Consortium (GSC) was a mix of short presentations, strategy discussions, and technical sessions. Speakers provided progress reports on the development of the "Minimum Information about a Genome Sequence" (MIGS) specification and the closely integrated "Minimum Information about a Metagenome Sequence" (MIMS) specification. The key outcome of the workshop was consensus on the next version of the MIGS/MIMS specification (v1.2). This drove further definition and restructuring of the MIGS/MIMS XML schema (syntax). With respect to semantics, a term vetting group was established to ensure that terms are properly defined and submitted to the appropriate ontology projects. Perhaps the single most important outcome of the workshop was a proposal to move beyond the concept of "minimum" to create a far richer XML schema that would define a "Genomic Contextual Data Markup Language" (GCDML) suitable for wider semantic integration across databases. GCDML will contain not only curated information (e.g., compliant with MIGS/MIMS), but also be extended to include a variety of data processing and calculations. Further information about the Genomic Standards Consortium and its range of activities can be found at http://gensc.org.

Published
2008
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