133 results on '"Lister, Allyson"'
Search Results
2. The FAIR Cookbook - the essential resource for and by FAIR doers
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Rocca-Serra, Philippe, Gu, Wei, Ioannidis, Vassilios, Abbassi-Daloii, Tooba, Capella-Gutierrez, Salvador, Chandramouliswaran, Ishwar, Splendiani, Andrea, Burdett, Tony, Giessmann, Robert T., Henderson, David, Batista, Dominique, Emam, Ibrahim, Gadiya, Yojana, Giovanni, Lucas, Willighagen, Egon, Evelo, Chris, Gray, Alasdair J. G., Gribbon, Philip, Juty, Nick, Welter, Danielle, Quast, Karsten, Peeters, Paul, Plasterer, Tom, Wood, Colin, van der Horst, Eelke, Reilly, Dorothy, van Vlijmen, Herman, Scollen, Serena, Lister, Allyson, Thurston, Milo, Granell, Ramon, and Sansone, Susanna-Assunta
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- 2023
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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, and SBML Level 3 Community members
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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.
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- 2020
4. The challenges of research data management in cardiovascular science:a DGK and DZHK position paper—executive summary
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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
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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.
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- 2024
5. “Be sustainable”: EOSC‐Life recommendations for implementation of FAIR principles in life science data handling
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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
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- 2023
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6. The challenges of research data management in cardiovascular science: a DGK and DZHK position paper—executive summary
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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
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- 2023
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7. Umbrella Data Management Plans to Integrate FAIR Data: Lessons From the ISIDORe and BY-COVID Consortia for Pandemic Preparedness
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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
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- 2023
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8. Enhancing systems biology models through semantic data integration
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Lister, Allyson Lurena
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570.11 - Abstract
Studying and modelling biology at a systems level requires a large amount of data of different experimental types. Historically, each of these types is stored in its own distinct format, with its own internal structure for holding the data produced by those experiments. While the use of community data standards can reduce the need for specialised, independent formats by providing a common syntax, standards uptake is not universal and a single standard cannot yet describe all biological data. In the work described in this thesis, a variety of integrative methods have been developed to reuse and restructure already extant systems biology data. SyMBA is a simple Web interface which stores experimental metadata in a published, common format. The creation of accurate quantitative SBML models is a time-intensive manual process. Modellers need to understand both the systems they are modelling and the intricacies of the SBML format. However, the amount of relevant data for even a relatively small and well-scoped model can be overwhelming. Saint is a Web application which accesses a number of external Web services and which provides suggested annotation for SBML and CellML models. MFO was developed to formalise all of the knowledge within the multiple SBML specification documents in a manner which is both human and computationally accessible. Rule-based mediation, a form of semantic data integration, is a useful way of reusing and re-purposing heterogeneous datasets which cannot, or are not, structured according to a common standard. This method of ontology-based integration is generic and can be used in any context, but has been implemented specifically to integrate systems biology data and to enrich systems biology models through the creation of new biological annotations. The work described in this thesis is one step towards the formalisation of biological knowledge useful to systems biology. Experimental metadata has been transformed into common structures, a Web application has been created for the retrieval of data appropriate to the annotation of systems biology models and multiple data models have been formalised and made accessible to semantic integration techniques.
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- 2012
9. PREreview of 'A maturity model for catalogues of semantic artefacts'
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Lister, Allyson L.
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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.
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- 2023
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10. Umbrella Data Management Plans to integrate FAIR data : lessons from the ISIDORe and BY-COVID consortia for pandemic preparedness
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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
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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
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- 2023
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11. FAIRsharing Community Curation: Mapping the Social Sciences Resource Landscape
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Lister, Allyson
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FAIRsharing is an informative and educational resource on interlinked standards, databases and policies, three key elements of the FAIR ecosystem. FAIRsharing is adopted by funders, publishers and communities across all research disciplines. It promotes the existence and value of these resources to aid data discovery, interoperability and sharing across all of our stakeholder groups. Enabling FAIR data is a key role within FAIRsharing, and we work with a variety of stakeholders (funders, researchers, research support such as librarians and data stewards, publishers, and resource developers) throughout the data management lifecycle to achieve this goal. Here we will discuss how FAIRsharing can be searched and updated by our user community, and how the social sciences in particular can make the best use out of it as part of a broader data management infrastructure. We also will discuss the benefits of both in-house curation and community-driven curation provided by our stakeholder groups. Finally, we will show you how to take part and contribute to the development of the description of databases and standards within FAIRsharing through our Community Curation Programme (https://fairsharing.org/community_curation). 
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- 2022
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12. Journal and Data Archive Collaboration Forum [online event]
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Alvanides, Serafeim, Kleiner, Brian, Doorn, Peter, Fisher, Ruth, Glavica, Marijana, Lister, Allyson, Bosma, Ulbe, Peer, Limor, and Štebe, Janez
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Data journal ,FAIRsharing ,CESSDA ,Curration ,Data repository ,Open research ,Reproducibility - Abstract
The availability of research data underlying articles published in journals is becoming a common practice in scientific communication. The European Commission and other funders of scientific research have set high expectations for scientists towards openness and availability of scientific work and results. Scientific publishers, through journals and scholarly publications are the main point of realising open science in practice. This event was part of the continuous Journals Outreach initiative (https://www.cessda.eu/Training/Journals-outreach), bringing together CESSDA service providers (SPs) with Social Science & Humanities Journals. Its target audiences were publishers, editors, researchers, and CESSDA Service providers.The event was also an opportunity for publishers/journals to highlight new initiatives in research data services linked to scientific publications. Programme 14:00-14:20 Activities of the CESSDA Journals Outreach group; Profiles of CESSDA Service Providers related to accepting data linked to journals / Serafeim Alvanides Moderator: Brian Kleiner 14:20-14:40 Data showcases: the data journal in a multimodal world / Peter Doorn, Leen Breure 14:40-15:00 An Introduction to Open Research Europe, focusing on Humanities and Social Sciences (HSS) / Ruth Fisher 15:00-15:10 Break Moderator: Marijana Glavica 15:10-15:30 FAIRsharing: An ecosystem of research standards and databases for enabling FAIR data / Allyson Lister 15:30-15:50 The Research Data Journal: objectives and processes / Ulbe Bosma 15:50-16:10 The CURE (Curation for Reproducibility) Consortium / Limor Peer Moderator: Janez Štebe 16:10-16:30 General discussion
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- 2022
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13. BY-COVID D3.2: Implementation of cloud-based, high performance, scalable indexing system
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Hermjakob, Henning, Kleemola, Mari, Moilanen, Katja, Tuominen, Markus, Sansone, Susanna-Assunta, Lister, Allyson, David, Romain, Panagiotopoulou, Maria, Ohmann, Christian, Belien, Jeroen, Lischke, Julia, Juty, Nick, Soiland-Reyes, Stian, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Tampere University of Technology [Tampere] (TUT), Finnish Social Science Data Archive, Consortium of European Social Science Data Archives (CESSDA ERIC), University of Oxford, European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), European Clinical Research Infrastructures Network [Dusseldorf] (ECRIN), ELIXIR Hub [Cambridge], University of Manchester [Manchester], University of Amsterdam [Amsterdam] (UvA), ELIXIR-Hub, EMBL-EBI, CESSDA/TAU-FSD, ERINHA, UOXF, ECRIN, ELIXIR-NL/VUmc, ELIXIR-NL, Lygature, and European Project: 101046203,BY-COVID
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BY-COVID ,portal ,training ,tools ,[INFO.INFO-OH]Computer Science [cs]/Other [cs.OH] ,workflows ,Scalable indexing system ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,Covid-19 ,COVID-19 Data Portal ,documentation ,Covid-19 portal ,COVID - Abstract
BY-COVID Work Package 3 is focused on services for the discovery and integration of COVID-19 data by delivering a flexible, tiered metadata discovery system across different domains, metadata standards, and maturity/robustness levels of data sources. This will enable the linking of FAIR data and metadata on SARS-CoV-2 and COVID-19, on other related viruses and diseases, and on socio-economic consequences, across research fields, from omics, clinical, and epidemiological research, to social sciences and humanities. Building on the metadata format developed in D3.1, in a series of work package meetings and a workshop, with participation from all other work packages, we have developed tools (example Validator), workflows (Semi-automated transfer of resource metadata from FAIRsharing to Covid-19 portal), and documentation and training (Training: Discoverability hackathon) to support the efficient integration of additional resources from a broad range of domains into the COVID-19 Data Portal as well as improved the end user facing COVID-19 Data Portal itself (Global search). This work establishes the basis for the further development of the COVID-19 Data Portal metadata discovery, and provides a path for integration of metadata from multi-domain partners in BY-COVID, as well as our ISIDORe sibling project, and other relevant external resources. To ensure smooth integration of partner provided metadata, we anticipate re-running our “Discoverability hackathon” in the future and will continue to evolve our metadata format and presentation of the COVID-19 Data Portal. We anticipate significant development and metadata modelling work for the use-case driven support of complex data sources in close collaboration with WPs 2, 4 and 5. 
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- 2022
14. EOSC-Life FAIRsharing webpage
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Sansone, Susanna-Assunta, Lister, Allyson, Thurston, Milo, Mirian, Hossein, Rocca-Serra, Philippe, Batista, Dominique, Granell, Ramon, and Gailani, Prakhyat
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FAIR data resources ,Life science research infrastructures ,FAIR standards ,FAIRsharing collection - Abstract
FAIRsharinghas been selected by WP1 as the project’s registry of data resources and standards that are part of and used by research infrastructures in EOSC-Life. This deliverable summarises the work of WP6 to deliver a FAIRsharing Collection of these data resources (and associated standards) to ensure these resources are Findable (e.g. discoverable and citable via a DOI), Accessible (e.g. access methods to their data is clearly described), Interoperable (e.g. standards implemented are declared) and Re-usable (e.g. terms of use of the data are made explicit to users). This work is described in detail in D1.2and D1.3, and the EOSC-Life FAIRsharing Collection of 133 records (as of Aug 2022) is publicly available. As this is a live view of the EOSCLife resource ecosystem, a variety of stages of the resource life cycle are displayed. Indevelopment, Ready and Deprecated resources are marked as such allowing users to assess their relevance. In Jan 2022 a newly improved FAIRsharing backend and frontend was also released by the UOXF partner, who also runs and curates the registry. This new version is set to improve the discoverability of and the relationships among the resources, and also offers new RI-centric pages (e.g. ELIXIRand MIRRI). These pages enable attribution at the level of the RIs and the responsible individuals themselves. Each RI page in FAIRsharing showcases its associated repositories, standards and collections and identifies and attributes (via ORCID) related users. The records in the EOSC-Life FAIRsharing Collection are a part of the wider FAIRsharing registry, which is computationally accessible to a wide variety of third-party tools, and which is interoperable with pan-EOSC activities via the FAIRsharing collaboration with OpenAIRE.
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- 2022
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15. BY-COVID - D3.1 - Metadata standards. Documentation on metadata standards for inclusion of resources in data portal
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Hermjakob, Henning, Kleemola, Mari, Moilanen, Katja, Sansone, Susanna-Assunta, Lister, Allyson, David, Romain, Panagiotopoulou, Maria, Ohmann, Christian, Belien, Jeroen, Lischke, Julia, Juty, Nick, and Soiland-Reyes, Stian
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Metadata, standards, resources, bioinformatics, genomics, EU-funded - Abstract
BY-COVID Work Package 3 is focused on services for the discovery and integration of COVID-19 data by delivering a flexible, tiered metadata discovery system across different domains, metadata standards, and maturity/robustness levels of data sources. This will enable the linking of FAIR data and metadata on SARS-CoV-2 and COVID-19, on other related viruses and diseases, and on socio-economic consequences, across research fields, from omics, clinical, and epidemiological research, to social sciences and humanities. In a series of work package meetings and a workshop, with participation from all other work packages, we have surveyed community metadata standards used by (potential) BY-COVID-19 portal resources (4.1), defined a flexible, three-tiered approach to metadata indexing in the COVID-19 portal (section 4.2), derived common metadata attributes for record level discovery (4.3) and established a workflow with FAIRsharing for resource level metadata capture and exchange (4.4). This work establishes the basis for the further development of the COVID-19 Portal metadata discovery and provides a path for integration of metadata from multi-domain partners in BY-COVID, as well as our ISIDORe sibling project, and relevant external resources. To ensure smooth integration of partner-provided metadata, we will run a technical workshop open to all partners, discussing workflows, metadata attributes and formats, and support tools., Contributor: Morris Swertz (UMCG/BBMRI)
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- 2022
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16. NFDI4Ing CC-41 Community Meeting 2022: Stand und Ausblick des FDMs in Maschinenbau und Produktionstechnik
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Hamann, Tobias, Moser, Mario, Schmitt, Robert, Richter, Manuela, Mozgova, Iryna, Pelz, Peter, Grischka, Petri, Kim, Soo-Yon, Schönau, Sabine, Hausen, Daniela, Bronger, Torsten, Weisweiler, Nina, Schabinger, Rouven, Strecker, Dorothea, Ulrich, Robert, Gläser, Dennis, Flemisch, Bernd, Arndt, Susanne, Schimmler, Sonja, Stotzka, Rainer, Engel, Felix, Heinrichs, Benedikt, Lang, Ilona, Farhang Ghahfarokhi, Anahita, Lister, Allyson, Logan, Kevin, Leštáková, Michaela, Heine, Ina, Stäcker, Thomas, Politze, Marius, and Mies, Robert
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Archivierung ,Metadata ,FDM ,Ontology ,Production engineering ,Research Data Management ,Ontologie ,FOS: Mechanical engineering ,Forschungsdatenmanagement ,Electronic Laboratory Notebook ,Gute wissenschaftliche Praxis ,Datenorganisation ,Mechanical engineering ,NFDI ,Ingenieurwissenschaften ,Engineering ,Maschinenbau ,Metadaten ,RDM ,NFDI4ING ,Produktionstechnik - Abstract
DasNFDI4Ing CC-41 Community Meeting 2022 des Maschinenbaus und der Produktionstechnik fand am 03. März 2022 statt. The NFDI4Ing CC-41 Community Meeting 2022 of Mechanical and Production Engineering took place on 03 March 2022. Die Autorinnen und Autoren möchten sich bei Bund, Ländern und bei der Gemeinsamen Wissenschaftskonferenz (GWK) für die Förderung und Unterstützung im Rahmen des Konsortiums NFDI4Ing bedanken. Gefördert durch die Deutsche Forschungsgemeinschaft (DFG) - Projektnummer 442146713. The authors would like to thank the Federal Government and the Heads of Government of the Länder, as well as the Joint Science Conference (GWK), for their funding and support within the framework of the NFDI4Ing consortium. Funded by the German Research Foundation (DFG) - project number 442146713. Sofern im jeweiligen Dokument nicht anders angegeben, stehen die Dateien unter der CC-BY 4.0 Lizenz. Bitte beachten Sie die Lizenzkommentare in den jeweiligen Slide Decks. If not stated otherwise within the respective document, the files go by CC-BY 4.0 license. Please refer to the license comments in the resprective slide decks.
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- 2022
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17. EOSC-Life EOSC FAIR services deployment for open calls
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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.
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- 2022
18. EOSC-Life -D1.3 EOSC-Life EOSC FAIR services deployment for open calls
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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
19. ELIXIR Report of the 19th Plenary of the RDA, June 2022
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Nyberg Åkerström, Wolmar, Lieby, Paulette, Suchánek, Marek, Farrell, Gavin, Lister, Allyson, Psomopoulos, Fotis, Nyberg Åkerström, Wolmar, Lieby, Paulette, Suchánek, Marek, Farrell, Gavin, Lister, Allyson, and Psomopoulos, Fotis
- Abstract
This report document has been prepared by ELIXIR’s RDA Activities Focus Group to showcase the synergies and activities of the Research Data Alliance (RDA) which may be useful for ELIXIR members operating in the life sciences domain. The RDA was launched as a community-driven initiative in 2013 with the goal of building the social and technical infrastructure to enable open sharing and re-use of data. The ELIXIR RDA Activities Focus Group has prepared eighteen reports of RDA Plenary events to date containing overviews of highlighted RDA recommendations and outputs. This report contains highlights from various sessions of the RDA 19th Plenary which took place as a hybrid event in South Korea, 20-23 June, 2022.
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- 2022
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20. FAIRsharing: promoting the value of standards and repositories for scholarly communication
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Lister, Allyson L.
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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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21. FAIR in practice: FAIRsharing and the FAIR Cookbook
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Lister, Allyson
- Subjects
FAIR principles ,FAIRness ,Assessment ,FAIR in practice - Abstract
FAIR principles provide a unique framework for creating a machine actionable data management environment supporting Open Science and Open data but also data and information exchange within organizations such as industries. In this session, we aim at discussing the theory and practice of implementing FAIR Principles for applied science and industrial research. The workshop is a meeting point for OntoCommons (www.ontocommons.eu), an EU Horizon 2020 project that aims to improve the state of the art in ontology data documentation in science and industry, and several key initiatives focusing on FAIR (such as GOFAIR, FAIRsFAIR, FairSharing) and the Open Science community. Through this workshop we aim at gathering inputs and suggestions for implementing FAIR and Open Science/Data from the Open Science community. We will briefly introduce key general projects and initiatives related to FAIR, the ongoing work in OntoCommons and discuss how OntoCommons can leverage their work to support a better integration of FAIR principles into current and forthcoming industrial demonstrators including Open Science demonstrators.
- Published
- 2021
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22. Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models
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Lister Allyson L., Pocock Matthew, and Wipat Anil
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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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23. Helping the consumers and producers of standards, repositories and policies to enable fair data
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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
24. SBML Level 3: an extensible format for the exchange and reuse of biological models
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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.
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- 2020
25. Annotation of SBML models through rule-based semantic integration
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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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26. Managing Experimental Data Using FuGE
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Jones, Andrew R., primary and Lister, Allyson L., additional
- Published
- 2009
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27. Helping the Consumers and Producers of Standards, Repositories and Policies to Enable FAIR Data
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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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- View/download PDF
28. Saint: a lightweight integration environment for model annotation
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Lister, Allyson L., Pocock, Matthew, Taschuk, Morgan, and Wipat, Anil
- Published
- 2009
29. FAIRsharing - Describing and Connecting Standards, Databases and Policies Across Disciplines
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McQuilton, Peter, Rocca-Serra, Philippe, Gonzalez-Beltran, Alejandra, Thurston, Milo, Izzo, Massimiliano, Lister, Allyson, Dauga, Delphine, Adekale, Melanie, and Sansone, Susanna-Assunta
- Abstract
International workshop on sharing, citation and publication of scientific data across disciplines: Session 2: Database, Data System - Network & AdministrationTue. 5 Dec./Lecture Room (4F, NIPR)
- Published
- 2017
30. SBML Level 3 Package Proposal: Annotation
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Hucka, Michael, Laibe, Camille, Juty, Nick, Liebermeister, Wolfram, Keating, Sarah, Lloyd, Catherine, Knuepfer, Christian, Misirli, Goksel, Schulz, Marvin, Waltemath, Dagmar, Taschuk, Morgan, Swainston, Neil, Le Novère, Nicolas, Lister, Allyson, Bergmann, Frank, Henkel, Ron, Krause, Falko, and Hoops, Stefan
- Published
- 2011
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31. MIREOT: the Minimum Information to Reference an External Ontology Term
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Ruttenberg, Alan, Courtot, Melanie, Gibson, Frank, Lister, Allyson, Malone, James, Schober, Daniel, and Brinkman, Ryan
- Published
- 2009
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32. MIREOT: the Minimum Information to Reference an External Ontology Term
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Courtot, Mélanie, Gibson, Frank, Lister, Allyson, Malone, James, Schober, Daniel, Brinkman, Ryan, and Ruttenberg, Alan
- Published
- 2009
- Full Text
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33. Annotation of SBML Models Through Rule-Based Semantic Integration
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Lister, Allyson, Lord, Phillip, Pocock, Matthew, and Wipat, Anil
- Published
- 2009
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34. BioSharing poster - ISB 2016
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Sansone, Susanna-Assunta, McQuilton, Peter, Gonzalez-Beltran, Alejandra, Izzo, Massimiliano, Lister, Allyson, Maguire, Eamonn, Rocca-Serra, Philippe, and Thurston, Milo
- Abstract
A curated, searchable portal of inter-related data standards, databases, and policies in the life, environmental and biomedical sciences: https://biosharing.org
- Published
- 2016
- Full Text
- View/download PDF
35. BioSharing poster - April 2016 (focus on standards)
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Sansone, Susanna-Assunta, McQuilton, Peter, Gonzalez-Beltran, Alejandra, Izzo, Massimiliano, L. Lister, Allyson, Maguire, Eamonn, Rocca-Serra, Philippe, and Thurston, Milo
- Abstract
A curated, searchable portal of inter-related data standards, databases, and policies in the life, environmental and biomedical scienceshttps://biosharing.org
- Published
- 2016
- Full Text
- View/download PDF
36. BioSharing poster - April 2016 (focus on databases)
- Author
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Sansone, Susanna-Assunta, McQuilton, Peter, Gonzalez-Beltran, Alejandra, Izzo, Massimiliano, Lister, Allyson, Maguire, Eamonn, Rocca-Serra, Philippe, and Thurston, Milo
- Abstract
A curated, searchable portal of inter-related data standards, databases, and policies in the life, environmental and biomedical sciences: https://biosharing.org
- Published
- 2016
- Full Text
- View/download PDF
37. BioSharing: Harnessing Metadata Standards for the Data Commons
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Sansone, Susanna-Assunta, primary, Gonzalez-Beltran, Alejandra, additional, Rocca-Serra, Philippe, additional, McQuilton, Peter, additional, Izzo, Massimiliano, additional, Lister, Allyson, additional, and Thurston, Milo, additional
- Published
- 2017
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38. The BioSharing Registry: mapping the landscape of standards and databases resources in the life sciences
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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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39. FAIRsharing as a community approach to standards, repositories and policies.
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Sansone, Susanna-Assunta, McQuilton, Peter, Rocca-Serra, Philippe, Gonzalez-Beltran, Alejandra, Izzo, Massimiliano, Lister, Allyson L., and Thurston, Milo
- Published
- 2019
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40. The Ontology for Biomedical Investigations
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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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41. BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences
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McQuilton, Peter, primary, Gonzalez-Beltran, Alejandra, additional, Rocca-Serra, Philippe, additional, Thurston, Milo, additional, Lister, Allyson, additional, Maguire, Eamonn, additional, and Sansone, Susanna-Assunta, additional
- Published
- 2016
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42. Data Resource Profile: Accessible Resource for Integrated Epigenomic Studies (ARIES)
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Relton, Caroline L, primary, Gaunt, Tom, additional, McArdle, Wendy, additional, Ho, Karen, additional, Duggirala, Aparna, additional, Shihab, Hashem, additional, Woodward, Geoff, additional, Lyttleton, Oliver, additional, Evans, David M, additional, Reik, Wolf, additional, Paul, Yu-Lee, additional, Ficz, Gabriella, additional, Ozanne, Susan E, additional, Wipat, Anil, additional, Flanagan, Keith, additional, Lister, Allyson, additional, Heijmans, Bastiaan T, additional, Ring, Susan M, additional, and Davey Smith, George, additional
- Published
- 2015
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43. Live Coverage of Intelligent Systems for Molecular Biology
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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
44. The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation
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Malone, James, primary, Brown, Andy, additional, Lister, Allyson L, additional, Ison, Jon, additional, Hull, Duncan, additional, Parkinson, Helen, additional, and Stevens, Robert, additional
- Published
- 2014
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45. Live Coverage of Scientific Conferences Using Web Technologies
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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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- View/download PDF
46. Live Coverage of Intelligent Systems for Molecular Biology
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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
- Full Text
- View/download PDF
47. The minimum information about a genome sequence (MIGS) specification.
- Author
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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
- Full Text
- View/download PDF
48. Meeting report: the fourth Genomics Standards Consortium Workshop
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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
49. The first RSBI (ISA-TAB) workshop: 'can a simple format work for complex studies?'
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Sansone, Susanna-Assunta, Rocca-Serra, Philippe, Brandizi, Marco, Brazma, Alvis, Field, Dawn, Fostel, Jennifer, Garrow, Andrew G., Gilbert, Jack, Goodsaid, Federico, Hardy, Nigel, Jones, Phil, Lister, Allyson, Miller, Michael, Morrison, Norman, Rayner, Tim, Skylar, Natalia, Taylor, Chris, Tong, Weida, Warner, Guy, Wiemann, Stefan, Sansone, Susanna-Assunta, Rocca-Serra, Philippe, Brandizi, Marco, Brazma, Alvis, Field, Dawn, Fostel, Jennifer, Garrow, Andrew G., Gilbert, Jack, Goodsaid, Federico, Hardy, Nigel, Jones, Phil, Lister, Allyson, Miller, Michael, Morrison, Norman, Rayner, Tim, Skylar, Natalia, Taylor, Chris, Tong, Weida, Warner, Guy, and Wiemann, Stefan
- Abstract
This article summarizes the motivation for, and the proceedings of, the first ISA-TAB workshop held December 6–8, 2007, at the EBI, Cambridge, UK. This exploratory workshop, organized by members of the Microarray Gene Expression Data (MGED) Society's Reporting Structure for Biological Investigations (RSBI) working group, brought together a group of developers of a range of collaborative systems to discuss the use of a common format to address the pressing need of reporting and communicating data and metadata from biological, biomedical, and environmental studies employing combinations of genomics, transcriptomics, proteomics, and metabolomics technologies along with more conventional methodologies. The expertise of the participants comprised database development, data management, and hands-on experience in the development of data communication standards. The workshop's outcomes are set to help formalize the proposed Investigation, Study, Assay (ISA)-TAB tab-delimited format for representing and communicating experimental metadata. This article is part of the special issue of OMICS on the activities of the Genomics Standards Consortium (GSC).
- Published
- 2008
50. Quantitative Fitness Analysis Shows That NMD Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects
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Addinall, Stephen Gregory, primary, Holstein, Eva-Maria, additional, Lawless, Conor, additional, Yu, Min, additional, Chapman, Kaye, additional, Banks, A. Peter, additional, Ngo, Hien-Ping, additional, Maringele, Laura, additional, Taschuk, Morgan, additional, Young, Alexander, additional, Ciesiolka, Adam, additional, Lister, Allyson Lurena, additional, Wipat, Anil, additional, Wilkinson, Darren James, additional, and Lydall, David, additional
- Published
- 2011
- Full Text
- View/download PDF
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