Twelve quick tips for deploying a Beacon.

Authors: Lauren A Fromont, Mauricio Moldes, Michael Baudis, Anthony J Brookes, Arcadi Navarro, Jordi Rambla

Source: PLoS Computational Biology, Vol 20, Iss 3, p e1011817 (2024)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/b026c29be1854967a5611f46ceef516c

Data infrastructures for AI in medical imaging: a report on the experiences of five EU projects

Authors: Haridimos Kondylakis, Varvara Kalokyri, Stelios Sfakianakis, Kostas Marias, Manolis Tsiknakis, Ana Jimenez-Pastor, Eduardo Camacho-Ramos, Ignacio Blanquer, J. Damian Segrelles, Sergio López-Huguet, Caroline Barelle, Magdalena Kogut-Czarkowska, Gianna Tsakou, Nikolaos Siopis, Zisis Sakellariou, Paschalis Bizopoulos, Vicky Drossou, Antonios Lalas, Konstantinos Votis, Pedro Mallol, Luis Marti-Bonmati, Leonor Cerdá Alberich, Karine Seymour, Samuel Boucher, Esther Ciarrocchi, Lauren Fromont, Jordi Rambla, Alexander Harms, Andrea Gutierrez, Martijn P. A. Starmans, Fred Prior, Josep Ll. Gelpi, Karim Lekadir

Source: European Radiology Experimental, Vol 7, Iss 1, Pp 1-13 (2023)

Subject Terms: Artificial intelligence, Data anonymization, Data management, Diagnostic imaging, Neoplasms, Medical physics. Medical radiology. Nuclear medicine, R895-920

File Description: electronic resource

Relation: https://doaj.org/toc/2509-9280

Access URL: https://doaj.org/article/a9710911be714bd29067ed9733586a3c

Phenopacket-tools: Building and validating GA4GH Phenopackets.

Authors: Daniel Danis, Julius O B Jacobsen, Alex H Wagner, Tudor Groza, Martha A Beckwith, Lauren Rekerle, Leigh C Carmody, Justin Reese, Harshad Hegde, Markus S Ladewig, Berthold Seitz, Monica Munoz-Torres, Nomi L Harris, Jordi Rambla, Michael Baudis, Christopher J Mungall, Melissa A Haendel, Peter N Robinson

Source: PLoS ONE, Vol 18, Iss 5, p e0285433 (2023)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/82b7a50d7c6748b381f7924aa14f9c23

The Data Use Ontology to streamline responsible access to human biomedical datasets

Authors: Jonathan Lawson, Moran N. Cabili, Giselle Kerry, Tiffany Boughtwood, Adrian Thorogood, Pinar Alper, Sarion R. Bowers, Rebecca R. Boyles, Anthony J. Brookes, Matthew Brush, Tony Burdett, Hayley Clissold, Stacey Donnelly, Stephanie O.M. Dyke, Mallory A. Freeberg, Melissa A. Haendel, Chihiro Hata, Petr Holub, Francis Jeanson, Aina Jene, Minae Kawashima, Shuichi Kawashima, Melissa Konopko, Irene Kyomugisha, Haoyuan Li, Mikael Linden, Laura Lyman Rodriguez, Mizuki Morita, Nicola Mulder, Jean Muller, Satoshi Nagaie, Jamal Nasir, Soichi Ogishima, Vivian Ota Wang, Laura D. Paglione, Ravi N. Pandya, Helen Parkinson, Anthony A. Philippakis, Fabian Prasser, Jordi Rambla, Kathy Reinold, Gregory A. Rushton, Andrea Saltzman, Gary Saunders, Heidi J. Sofia, John D. Spalding, Morris A. Swertz, Ilia Tulchinsky, Esther J. van Enckevort, Susheel Varma, Craig Voisin, Natsuko Yamamoto, Chisato Yamasaki, Lyndon Zass, Jaime M. Guidry Auvil, Tommi H. Nyrönen, Mélanie Courtot

Source: Cell Genomics, Vol 1, Iss 2, Pp 100028- (2021)

Subject Terms: data access, consent, FAIR, ontology, GA4GH, standard, Genetics, QH426-470, Internal medicine, RC31-1245

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666979X21000355; https://doaj.org/toc/2666-979X

Access URL: https://doaj.org/article/f8726db3840b428bad60870042b49eab

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Authors: Heidi L. Rehm, Angela J.H. Page, Lindsay Smith, Jeremy B. Adams, Gil Alterovitz, Lawrence J. Babb, Maxmillian P. Barkley, Michael Baudis, Michael J.S. Beauvais, Tim Beck, Jacques S. Beckmann, Sergi Beltran, David Bernick, Alexander Bernier, James K. Bonfield, Tiffany F. Boughtwood, Guillaume Bourque, Sarion R. Bowers, Anthony J. Brookes, Michael Brudno, Matthew H. Brush, David Bujold, Tony Burdett, Orion J. Buske, Moran N. Cabili, Daniel L. Cameron, Robert J. Carroll, Esmeralda Casas-Silva, Debyani Chakravarty, Bimal P. Chaudhari, Shu Hui Chen, J. Michael Cherry, Justina Chung, Melissa Cline, Hayley L. Clissold, Robert M. Cook-Deegan, Mélanie Courtot, Fiona Cunningham, Miro Cupak, Robert M. Davies, Danielle Denisko, Megan J. Doerr, Lena I. Dolman, Edward S. Dove, L. Jonathan Dursi, Stephanie O.M. Dyke, James A. Eddy, Karen Eilbeck, Kyle P. Ellrott, Susan Fairley, Khalid A. Fakhro, Helen V. Firth, Michael S. Fitzsimons, Marc Fiume, Paul Flicek, Ian M. Fore, Mallory A. Freeberg, Robert R. Freimuth, Lauren A. Fromont, Jonathan Fuerth, Clara L. Gaff, Weiniu Gan, Elena M. Ghanaim, David Glazer, Robert C. Green, Malachi Griffith, Obi L. Griffith, Robert L. Grossman, Tudor Groza, Jaime M. Guidry Auvil, Roderic Guigó, Dipayan Gupta, Melissa A. Haendel, Ada Hamosh, David P. Hansen, Reece K. Hart, Dean Mitchell Hartley, David Haussler, Rachele M. Hendricks-Sturrup, Calvin W.L. Ho, Ashley E. Hobb, Michael M. Hoffman, Oliver M. Hofmann, Petr Holub, Jacob Shujui Hsu, Jean-Pierre Hubaux, Sarah E. Hunt, Ammar Husami, Julius O. Jacobsen, Saumya S. Jamuar, Elizabeth L. Janes, Francis Jeanson, Aina Jené, Amber L. Johns, Yann Joly, Steven J.M. Jones, Alexander Kanitz, Kazuto Kato, Thomas M. Keane, Kristina Kekesi-Lafrance, Jerome Kelleher, Giselle Kerry, Seik-Soon Khor, Bartha M. Knoppers, Melissa A. Konopko, Kenjiro Kosaki, Martin Kuba, Jonathan Lawson, Rasko Leinonen, Stephanie Li, Michael F. Lin, Mikael Linden, Xianglin Liu, Isuru Udara Liyanage, Javier Lopez, Anneke M. Lucassen, Michael Lukowski, Alice L. Mann, John Marshall, Michele Mattioni, Alejandro Metke-Jimenez, Anna Middleton, Richard J. Milne, Fruzsina Molnár-Gábor, Nicola Mulder, Monica C. Munoz-Torres, Rishi Nag, Hidewaki Nakagawa, Jamal Nasir, Arcadi Navarro, Tristan H. Nelson, Ania Niewielska, Amy Nisselle, Jeffrey Niu, Tommi H. Nyrönen, Brian D. O’Connor, Sabine Oesterle, Soichi Ogishima, Vivian Ota Wang, Laura A.D. Paglione, Emilio Palumbo, Helen E. Parkinson, Anthony A. Philippakis, Angel D. Pizarro, Andreas Prlic, Jordi Rambla, Augusto Rendon, Renee A. Rider, Peter N. Robinson, Kurt W. Rodarmer, Laura Lyman Rodriguez, Alan F. Rubin, Manuel Rueda, Gregory A. Rushton, Rosalyn S. Ryan, Gary I. Saunders, Helen Schuilenburg, Torsten Schwede, Serena Scollen, Alexander Senf, Nathan C. Sheffield, Neerjah Skantharajah, Albert V. Smith, Heidi J. Sofia, Dylan Spalding, Amanda B. Spurdle, Zornitza Stark, Lincoln D. Stein, Makoto Suematsu, Patrick Tan, Jonathan A. Tedds, Alastair A. Thomson, Adrian Thorogood, Timothy L. Tickle, Katsushi Tokunaga, Juha Törnroos, David Torrents, Sean Upchurch, Alfonso Valencia, Roman Valls Guimera, Jessica Vamathevan, Susheel Varma, Danya F. Vears, Coby Viner, Craig Voisin, Alex H. Wagner, Susan E. Wallace, Brian P. Walsh, Marc S. Williams, Eva C. Winkler, Barbara J. Wold, Grant M. Wood, J. Patrick Woolley, Chisato Yamasaki, Andrew D. Yates, Christina K. Yung, Lyndon J. Zass, Ksenia Zaytseva, Junjun Zhang, Peter Goodhand, Kathryn North, Ewan Birney

Source: Cell Genomics, Vol 1, Iss 2, Pp 100029- (2021)

Subject Terms: data sharing, data access, precision medicine, learning health system, genomics, standards, Genetics, QH426-470, Internal medicine, RC31-1245

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666979X21000367; https://doaj.org/toc/2666-979X

Access URL: https://doaj.org/article/8843ca96b8394774b7bfa2e49aa0584a

International federation of genomic medicine databases using GA4GH standards

Authors: Adrian Thorogood, Heidi L. Rehm, Peter Goodhand, Angela J.H. Page, Yann Joly, Michael Baudis, Jordi Rambla, Arcadi Navarro, Tommi H. Nyronen, Mikael Linden, Edward S. Dove, Marc Fiume, Michael Brudno, Melissa S. Cline, Ewan Birney

Source: Cell Genomics, Vol 1, Iss 2, Pp 100032- (2021)

Subject Terms: data sharing, federation, genomics, standards, networks, data security, Genetics, QH426-470, Internal medicine, RC31-1245

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666979X21000392; https://doaj.org/toc/2666-979X

Access URL: https://doaj.org/article/987b2c84029b42118da264cdf8f943f0

iASiS: Towards Heterogeneous Big Data Analysis for Personalized Medicine

Authors: Krithara, Anastasia, Aisopos, Fotis, Rentoumi, Vassiliki, Nentidis, Anastasios, Bougatiotis, Konstantinos, Vidal, Maria-Esther, Menasalvas, Ernestina, Rodriguez-Gonzalez, Alejandro, Samaras, Eleftherios G., Garrard, Peter, Torrente, Maria, Pulla, Mariano Provencio, Dimakopoulos, Nikos, Mauricio, Rui, De Argila, Jordi Rambla, Tartaglia, Gian Gaetano, Paliouras, George

Source: 2019 IEEE 32nd International Symposium on Computer-Based Medical Systems (CBMS), Cordoba, Spain, 2019, pp. 106-111

Subject Terms: Computer Science - Artificial Intelligence, Computer Science - Databases

Access URL: http://arxiv.org/abs/2407.06748

Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data [version 1; referees: 2 approved]

Authors: Chao Zhang, Jochem Bijlard, Christine Staiger, Serena Scollen, David van Enckevort, Youri Hoogstrate, Alexander Senf, Saskia Hiltemann, Susanna Repo, Wibo Pipping, Mariska Bierkens, Stefan Payralbe, Bas Stringer, Jaap Heringa, Andrew Stubbs, Luiz Olavo Bonino Da Silva Santos, Jeroen Belien, Ward Weistra, Rita Azevedo, Kees van Bochove, Gerrit Meijer, Jan-Willem Boiten, Jordi Rambla, Remond Fijneman, J. Dylan Spalding, Sanne Abeln

Source: F1000Research, Vol 6 (2017)

Subject Terms: Bioinformatics, Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/6-1488/v1; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/8068df77a81040238f5683ddfcc9daad

Integration of EGA secure data access into Galaxy [version 1; referees: 2 approved]

Authors: Youri Hoogstrate, Chao Zhang, Alexander Senf, Jochem Bijlard, Saskia Hiltemann, David van Enckevort, Susanna Repo, Jaap Heringa, Guido Jenster, Remond J.A. Fijneman, Jan-Willem Boiten, Gerrit A. Meijer, Andrew Stubbs, Jordi Rambla, Dylan Spalding, Sanne Abeln

Source: F1000Research, Vol 5 (2016)

Subject Terms: Bioinformatics, Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/5-2841/v1; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/2f45112fd2b54b64862983518402ef2d

Consent Codes: Upholding Standard Data Use Conditions.

Authors: Stephanie O M Dyke, Anthony A Philippakis, Jordi Rambla De Argila, Dina N Paltoo, Erin S Luetkemeier, Bartha M Knoppers, Anthony J Brookes, J Dylan Spalding, Mark Thompson, Marco Roos, Kym M Boycott, Michael Brudno, Matthew Hurles, Heidi L Rehm, Andreas Matern, Marc Fiume, Stephen T Sherry

Source: PLoS Genetics, Vol 12, Iss 1, p e1005772 (2016)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1005772&type=printable; https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/dba8b7865e8c40ae9da832cc978bc9f9

Accelerating FaST-LMM for Epistasis Tests
Algorithms and architectures for parallel processing (International Conference)

Authors: Martínez, Héctor, Barrachina, Sergio, Castillo, Maribel, Quintana-Ortí, Enrique S., De Argila, Jordi Rambla, Farré, Xavier, Navarro, Arcadi

Source: Lecture notes in computer science. 10393:548-557

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCCN602748350&indx=1&recIds=ETOCCN602748350

Consent Codes: Maintaining Consent in an Ever-expanding Open Science Ecosystem.

Authors: Dyke, Stephanie O. M., Connor, Kathleen, Nembaware, Victoria, Munung, Nchangwi S., Reinold, Kathy, Kerry, Giselle, Mbiyavanga, Mamana, Zass, Lyndon, Moldes, Mauricio, Das, Samir, Davis, John M., De Argila, Jordi Rambla, Spalding, J. Dylan, Evans, Alan C., Mulder, Nicola, Karamchandani, Jason

Source: NeuroInformatics; Jan2023, Vol. 21 Issue 1, p89-100, 12p

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Ready-to-use public infrastructure for global SARS-CoV-2 monitoring.

Authors: Maier, Wolfgang, Bray, Simon, van den Beek, Marius, Bouvier, Dave, Coraor, Nathan, Miladi, Milad, Singh, Babita, De Argila, Jordi Rambla, Baker, Dannon, Roach, Nathan, Gladman, Simon, Coppens, Frederik, Martin, Darren P., Lonie, Andrew, Grüning, Björn, Kosakovsky Pond, Sergei L., Nekrutenko, Anton

Source: Nature Biotechnology; Oct2021, Vol. 39 Issue 10, p1178-1179, 2p