Toward interoperable bioscience data

Sansone, Susanna-Assunta, Rocca-Serra, Philippe, Field, Dawn, Maguire, Eamonn, Taylor, Chris, Hofmann, Oliver, Fang, Hong, Neumann, Steffen +42 more·2012·Nature Genetics

Cited by (512)

Items 101–200 of 512

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  2. Responsible sharing of biomedical data and biospecimens via the “Automatable Discovery and Access Matrix” (ADA-M)
    Jessica Woolley, Emily Kirby, Josh Leslie, Francis Jeanson, Moran N. Cabili, Gregory T. Rushton, James G. Hazard, Vagelis Ladas, Colin Veal, Spencer Gibson et al. · 2018 · npj Genomic Medicine
  3. Mass spectrometry‐based forest tree metabolomics
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  6. Minimum information for dielectric measurements of biological tissues (MINDER): A framework for repeatable and reusable data
    Emily Porter, Alessandra La Gioia, Saqib Salahuddin, Stefan Decker, Atif Shahzad, Adnan Elahi, Martin O’Halloran, Oya Beyan · 2017 · International Journal of RF and Microwave Computer-Aided Engineering
  7. From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics
    Alejandra N Gonzalez-Beltran, Peter Li, Jun Zhao, María Susana Ávila-García, Marco Roos, Mark Thompson, Eelke van der Horst, Rajaram Kaliyaperumal, Ruibang Luo, TL Lee et al. · 2015 · PLoS ONE
  8. Operational Considerations regarding On-Demand Air Mobility: A Literature Review and Research Challenges
    Xiaoqian Sun, Sebastian Wandelt, Michael Husemann, Eike Stumpf · 2021 · Journal of Advanced Transportation
  9. Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking
    Salvador Capella-Gutiérrez, Diana de la Iglesia, Juergen Haas, Anália Maria Garcia Lourenço, José M. Fernández, Dmitry Repchevsky, Christophe Dessimoz, Torsten F. Schwede, Cédric Notredame, Josep Lluis Gelpí et al. · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  10. The road towards data integration in human genomics: players, steps and interactions
    Anna Bernasconi, Arif Canakoglu, Marco Masseroli, Stefano Ceri · 2020 · Briefings in Bioinformatics
  11. Your Spreadsheets Can Be FAIR: A Tool and FAIRification Workflow for the eNanoMapper Database
    Nikolay T. Kochev, Nina Jeliazkova, Vesselina Paskaleva, Gergana Tancheva, Luchesar Iliev, Peter J. Ritchie, Vedrin Jeliazkov · 2020 · Nanomaterials
  12. LabTrove: A Lightweight, Web Based, Laboratory “Blog” as a Route towards a Marked Up Record of Work in a Bioscience Research Laboratory
    Andrew J. Milsted, Jennifer R. Hale, Jeremy Graham Frey, Cameron Neylon · 2013 · PLoS ONE
  13. Health inequity in genomic personalized medicine in underrepresented populations: a look at the current evidence
    Sherouk M. Tawfik, Aliaa A Elhosseiny, Aya A. Galal, Martina B. William, Esraa M Qansuwa, Rana M. Elbaz, Mohamed Salama · 2023 · Functional & Integrative Genomics
  14. Connecting high‐throughput biodiversity inventories: Opportunities for a site‐based genomic framework for global integration and synthesis
    Paula Arribas, Carmelo Andújar, Martin I. Bidartondo, Kristine Bohmann, Éric Coissac, Simon Creer, Jeremy R deWaard, Vasco Elbrecht, Gentile Francesco Ficetola, Marta Goberna et al. · 2021 · Molecular Ecology
  15. Data management strategies for multinational large-scale systems biology projects
    W. Wruck, M. Peuker, C. Regenbrecht · 2012 · Briefings Bioinform.
  16. Perspectives on Big Data applications of health information
    Isaac Cano, Ákos Tényi, Emili Vela, Felip Miralles, Josep Roca · 2017 · Current Opinion in Systems Biology
  17. Generation and Profiling of 2,135 Human ESC Lines for the Systematic Analyses of Cell States Perturbed by Inducing Single Transcription Factors
    Yuhki Nakatake, Shigeru B. H. Ko, Alexei A. Sharov, Shunichi Wakabayashi, Miyako Murakami, Miki Sakota, Nana Chikazawa-Nohtomi, Chiaki Ookura, Saeko Sato, Noriko Ito et al. · 2020 · Cell Reports
  18. COPO: a metadata platform for brokering FAIR data in the life sciences
    Felix Shaw, Anthony Etuk, Alice Minotto, Alejandra N Gonzalez-Beltran, David Johnson, Philippe Rocca‐Serra, Marie‐Angélique Laporte, Elizabeth Arnaud, Medha Devare, Paul Julian Kersey et al. · 2020 · F1000Research
  19. A multi-omics digital research object for the genetics of sleep regulation
    Maxime Jan, Nastassia Gobet, Shanaz Diessler, Paul Franken, Ioannis Xénarios · 2019 · Scientific Data
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    Reza M. Salek, Kenneth Haug, Christoph Steinbeck · 2013 · GigaScience
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    Yi Chen, Fons J. Verbeek, Katherine Wolstencroft · 2021 · BMC Bioinformatics
  22. MetaDB a Data Processing Workflow in Untargeted MS-Based Metabolomics Experiments
    Pietro Franceschi, Roman Mylonas, Nir Shahaf, Matthias Scholz, Panagiotis Arapitsas, Domenico Masuero, Georg Weingart, Silvia Carlin, Urška Vrhovšek, Fulvio Mattivi et al. · 2014 · Frontiers in Bioengineering and Biotechnology
  23. An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology
    Richard Marchese Robinson, M Cronin, Andrea-Nicole Richarz, Robert Ralló · 2015 · Beilstein Journal of Nanotechnology
  24. Preparing Laboratory and Real-World EEG Data for Large-Scale Analysis: A Containerized Approach
    Nima Bigdely-Shamlo, Scott Makeig, Kay A. Robbins · 2016 · Frontiers in Neuroinformatics
  25. Unipept Desktop: A Faster, More Powerful Metaproteomics Results Analysis Tool
    Pieter Verschaffelt, Tim Van Den Bossche, Lennart Martens, Peter Dawyndt, Bart Mesuere · 2021 · Journal of Proteome Research
  26. Regional synapse gain and loss accompany memory formation in larval zebrafish
    William P. Dempsey, Zhuowei Du, Anna Nadtochiy, Colton D. Smith, Karl Czajkowski, Andrey Andreev, Drew N. Robson, Jennifer Li, Serina S. Applebaum, Thai V. Truong et al. · 2022 · Proceedings of the National Academy of Sciences
  27. An International Framework for Data Sharing: Moving Forward with the Global Alliance for Genomics and Health
    Vasiliki Nataly Rahimzadeh, Stephanie O. M. Dyke, Bartha Maria Knoppers · 2016 · Biopreservation and Biobanking
  28. Biomedical Image Processing with Containers and Deep Learning: An Automated Analysis Pipeline
    Germán González, Conor L. Evans · 2019 · BioEssays
  29. ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies
    Emmanuel Ruhamyankaka, B. Brunk, G. Dorsey, O. Harb, Danica A Helb, John Judkins, J. Kissinger, B. Lindsay, D. Roos, E. J. San et al. · 2019 · Gates Open Research
  30. From data to knowledge – big data needs stewardship, a plant phenomics perspective
    Daniel Arend, Dennis Psaroudakis, Junaid Altaf Memon, Elena Rey Mazón, Danuta Schüler, Jędrzej Szymański, Uwe Scholz, Astrid Junker, Matthias Lange · 2022 · The Plant Journal
  31. Towards Responsible Plant Data Linkage: Data Challenges for Agricultural Research and Development
    Hugh F. Williamson, Sabina Leonelli · 2022 · Springer eBooks
  32. A call for an international network of genomic observatories (GOs)
    Neil Davies, Chris Meyer, Jack A. Gilbert, Linda Amaral‐Zettler, John Deck, Mesude Bicak, Philippe Rocca‐Serra, Susanna‐Assunta Sansone, Kathy Willis, Dawn Field · 2012 · GigaScience
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    Dimitris Zeginis, Ali Hasnain, Νικόλαος Λούτας, Helena Deus, Ronan Fox, Konstantinos A. Tarabanis · 2014 · Semantic Web
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    Shannan J. Ho Sui, Kimberly Begley, Dorothy Silver Reilly, Brad Chapman, Ray McGovern, Philippe Rocca‐Serra, Eamonn Maguire, Gabriel M. Altschuler, Terah A.A. Hansen, Ramakrishna R. Sompallae et al. · 2011 · Nucleic Acids Research
  35. Using imputation to provide harmonized longitudinal measures of cognition across AIBL and ADNI
    Rosita Shishegar, Timothy Cox, David A. Rolls, Pierrick Bourgeat, Vincent Doré, Fiona Lamb, Joanne Robertson, Simon Matthew Laws, Tenielle Porter, Jürgen Fripp et al. · 2021 · Scientific Reports
  36. Gabi wheat a panel of European elite lines as central stock for wheat genetic research
    Abhishek Gogna, Albert Wilhelm Schulthess, Marion S. Röder, Martin W. Ganal, Jochen Christoph Reif · 2022 · Scientific Data
  37. The Complex Permittivity of Biological Tissues: A Practical Measurement Guideline
    Lourdes Farrugia, Emily Porter, Raquel C. Conceição, Simona Di Meo, Daniela M. Godinho, Julian Bonello, Mykolas Ragulskis, Ilja Ocket, Laura Farina, Marta Cavagnaro et al. · 2024 · IEEE Access
  38. Interoperable and scalable data analysis with microservices: applications in metabolomics
    Payam Emami Khoonsari, Pablo A Moreno, Sven Bergmann, Joachim Burman, Marco Capuccini, Matteo Carone, Marta Cascante, Pedro de Atauri, Carles Foguet, Alejandra N Gonzalez-Beltran et al. · 2019 · Bioinformatics
  39. Why Open Drug Discovery Needs Four Simple Rules for Licensing Data and Models
    Antony John Williams, JOHN T. WILBANKS, Sean Ekins · 2012 · PLoS Computational Biology
  40. Biomedical research in a Digital Health Framework
    Isaac Cano, Magí Lluch-Ariet, David Gómez-Cabrero, Dieter Maier, Susana Graciela Kalko, Marta Cascante, Jesper N. Tegner, Felip Miralles, Diego Herrera, Josep Roca · 2014 · Journal of Translational Medicine
  41. Proteomic Contributions to Medicinal Plant Research: From Plant Metabolism to Pharmacological Action
    Akiko Hashiguchi, Jingkui Tian, Setsuko Komatsu · 2017 · Proteomes
  42. Making Big Data Useful for Health Care: A Summary of the Inaugural MIT Critical Data Conference
    Omar Badawi, Thomas J. Brennan, Leo Anthony Celi, Mengling Feng, Marzyeh Ghassemi, Andrea Ippolito, Alistair E. W. Johnson, Roger G. Mark, Louis Mayaud, George B Moody et al. · 2014 · DSpace@MIT (Massachusetts Institute of Technology)
  43. Community standards for open cell migration data
    Alejandra N Gonzalez-Beltran, Paola Masuzzo, Christophe Ampè, Gert‐Jan Bakker, Sébastien Besson, Robert H. Eibl, Peter Friedl, Matthias Gunzer, Mark Kittisopikul, Sylvia E. Le Dévédec et al. · 2020 · GigaScience
  44. Overview of Antifungal Drugs against Paracoccidioidomycosis: How Do We Start, Where Are We, and Where Are We Going?
    Lívia do Carmo Silva, Amanda Alves de Oliveira, Dienny Rodrigues de Souza, Katheryne Lohany Barros Barbosa, Kleber Santiago Freitas e Silva, Marcos Antonio Batista de Carvalho Júnior, Olivia Basso Rocha, Raisa Melo Lima, Thaynara Gonzaga Santos, Célia Maria de Almeida Soares et al. · 2020 · Journal of Fungi
  45. Investigation-Study-Assay, a toolkit for standardizing data capture and sharing
    Philippe Rocca‐Serra, Eamonn Maguire, Chris F. Taylor, Dawn Field, Timo Wittenberger, Annapaola Santarsiero, Alejandra N Gonzalez-Beltran, Susanna‐Assunta Sansone · 2012 · Elsevier eBooks
  46. GigaDB: promoting data dissemination and reproducibility
    Tam P. Sneddon, Xiao Si Zhe, Scott Edmunds, Peter Li, Laurie Goodman, Chris Hunter · 2014 · Database
  47. Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases
    Gerhard Mayer, Wolfgang Müller, Karin Schork, Julian Uszkoreit, Andreas Weidemann, Ulrike Wittig, Maja Rey, Christian Quast, Janine Felden, Frank Oliver Glöckner et al. · 2021 · Briefings in Bioinformatics
  48. Cardiovascular RNA markers and artificial intelligence may improve COVID-19 outcome: a position paper from the EU-CardioRNA COST Action CA17129
    Lina Badimón, Emma Louise Robinson, Amela Jusić, Irina Carpusca, León J. De Windt, Costanza Emanueli, Péter Ferdinandy, Wei Gu, Mariann Gyöngyösi, Matthias Hackl et al. · 2021 · Cardiovascular Research
  49. Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure
    Lela Lackey, Aaztli R. Coria, Chanin Tolson Woods, Evonne McArthur, Alain Laederach · 2018 · RNA
  50. Social networks, web-based tools and diseases: implications for biomedical research
    Fabrício Falconi Costa · 2012 · Drug Discovery Today
  51. Investing in Food Safety for Developing Countries: Opportunities and Challenges in Applying Whole-Genome Sequencing for Food Safety Management
    I. Apruzzese, Eunyeong Song, Ernest Bonah, Vernadette S. Sanidad, Pimlapas Leekitcharoenphon, Julius John Medardus, Nagmeldin Abdalla, Hedayat Hosseini, Masami T. Takeuchi · 2019 · Foodborne Pathogens and Disease
  52. Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies
    Yu-Ning Huang, Viorel Munteanu, Michael I. Love, Cynthia Ronkowski, Dhrithi Deshpande, Annie Wong‐Beringer, Russell B Corbett-Detig, Mihai Dimian, Jason H. Moore, Lana X. Garmire et al. · 2025 · Cell Genomics
  53. Visual Compression of Workflow Visualizations with Automated Detection of Macro Motifs
    Eamonn Maguire, Philippe Rocca‐Serra, Susanna‐Assunta Sansone, Jim Davies, Chén Mĭn · 2013 · IEEE Transactions on Visualization and Computer Graphics
  54. cBiT: A transcriptomics database for innovative biomaterial engineering
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  56. Experiences with DERIVA: An Asset Management Platform for Accelerating eScience
    Alejandro Bugacov, Karl Czajkowski, Carl Kesselman, Anoop Kumar, Robert E. Schuler, Hongsuda Tangmunarunkit · 2017 · IEEE International Conference on eScience
  57. Toward a data infrastructure for the Plant Cell Atlas
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  58. The future of metabolomics in ELIXIR
    Merlijn van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Domínguez Del Angel, Warwick B. Dunn, Timothy M. D. Ebbels, Franck Giacomoni, Alejandra N Gonzalez-Beltran, Thomas Hankemeier et al. · 2017 · F1000Research
  59. Cancer Biology, Toxicology and Alternative Methods Development Go Hand‐in‐Hand
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  60. An open data ecosystem for cell migration research
    Paola Masuzzo, Lennart Martens · 2014 · Trends in Cell Biology
  61. Concealment and discovery: The role of information security in biomedical data re-use
    Niccolò Tempini, Sabina Leonelli · 2018 · Social Studies of Science
  62. Multilingual translation for zero-shot biomedical classification using BioTranslator
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  63. A template wizard for the cocreation of machine-readable data-reporting to harmonize the evaluation of (nano)materials
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  64. Computational annotation of plant metabolomics profiles via a novel network-assisted approach
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  68. Data management and data enrichment for systems biology projects.
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  70. FAIR digital objects in environmental and life sciences should comprise workflow operation design data and method information for repeatability of study setups and reproducibility of results
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  74. Unbalanced historical phenotypic data from seed regeneration of a barley ex situ collection
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