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

Autor: Zhang, C, Bijlard, J, Staiger, C., Scollen, S., van Enckevort, D., Hoogstrate, Youri, Senf, Alexander, Hiltemann, Saskia, Repo, Susanna, Pipping, W, Bierkens, M., Payralbe, S, Stringer, B, Heringa, J, Stubbs, Andrew, Bonino Da Silva Santos, LO, Belien, J.A.M., Weistra, W, Azevedo, R.V.D.M., van Bochove, K, Meijer, G., Boiten, Jan-Willem, Rambla, Jordi, Fijneman, R.J., Spalding, JD, Abeln, S

Publikováno v: F1000Research, 6(1488). F1000 Research Ltd.
Zhang, C, Bijlard, J, Staiger, C, Scollen, S, van Enckevort, D, Hoogstrate, Y, Senf, A, Hiltemann, S, Repo, S, Pipping, W, Bierkens, M, Payralbe, S, Stringer, B, Heringa, J, Stubbs, A, Bonino Da Silva Santos, LO, Belien, J A M, Weistra, W, Azevedo, R V D M, van Bochove, K, Meijer, G, Boiten, J-W, Rambla, J, Fijneman, R J, Spalding, JD & Abeln, S 2017, ' Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data [version 1; referees: awaiting peer review] ', F1000Research, vol. 6, no. 1488 . https://doi.org/10.12688/f1000research.12168.1

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::3a24b87aae0a42f0a79c2c7fcd9e6d48
https://research.vu.nl/en/publications/8391f741-2881-4a6e-a6a7-6cbcf6b3f5b9

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

Autor: Dyke SOM; McGill Centre for Integrative Neuroscience, Department of Neurology & Neurosurgery, Faculty of Medicine and Health Sciences, Montreal Neurological Institute, McGill University, Montreal, QC, Canada. dykesom@gmail.com., Connor K; Health Level 7 (HL7) & Veterans Health Administration, Washington, D.C, USA., Nembaware V; Computational Biology Division, IDM, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.; Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa., Munung NS; Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa., Reinold K; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Kerry G; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK., Mbiyavanga M; Computational Biology Division, IDM, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa., Zass L; Computational Biology Division, IDM, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa., Moldes M; Centre for Genomic Regulation, Barcelona, Spain.; Universitat Pompeu Fabra, Barcelona, Spain., Das S; McGill Centre for Integrative Neuroscience, Department of Neurology & Neurosurgery, Faculty of Medicine and Health Sciences, Montreal Neurological Institute, McGill University, Montreal, QC, Canada., Davis JM; Health Level 7 (HL7) & Veterans Health Administration, Washington, D.C, USA., De Argila JR; Centre for Genomic Regulation, Barcelona, Spain.; Universitat Pompeu Fabra, Barcelona, Spain., Spalding JD; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK., Evans AC; McGill Centre for Integrative Neuroscience, Department of Neurology & Neurosurgery, Faculty of Medicine and Health Sciences, Montreal Neurological Institute, McGill University, Montreal, QC, Canada., Mulder N; Computational Biology Division, IDM, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa., Karamchandani J; Department of Pathology, Faculty of Medicine and Health Sciences, McGill University Health Centre & Montreal Neurological Institute, McGill University, Montreal, QC, Canada.

Publikováno v: Neuroinformatics [Neuroinformatics] 2023 Jan; Vol. 21 (1), pp. 89-100. Date of Electronic Publication: 2022 Dec 15.

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

Autor: Lawson J; Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA., Cabili MN; Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA., Kerry G; European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, UK., Boughtwood T; Australian Genomics, Murdoch Children's Research Institute, Parkville, VIC, Australia., Thorogood A; Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, QC, Canada.; ELIXIR-Luxembourg, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Alper P; ELIXIR-Luxembourg, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Bowers SR; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK., Boyles RR; RTI International, Research Triangle Park, NC, USA., Brookes AJ; University of Leicester, Leicester, UK., Brush M; University of Colorado Anschutz Medical Campus, Aurora, CO, USA., Burdett T; European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, UK., Clissold H; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK., Donnelly S; Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA., Dyke SOM; McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, Department of Neurology & Neurosurgery, Faculty of Medicine, McGill University, Montreal, QC, Canada., Freeberg MA; European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, UK., Haendel MA; University of Colorado Anschutz Medical Campus, Aurora, CO, USA., Hata C; Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan., Holub P; BBMRI-ERIC, AT and Masaryk University, Brno, Czech Republic., Jeanson F; University Health Network, Toronto, ON, Canada., Jene A; Centre de Regulació Genòmica (CRG), Barcelona, Spain., Kawashima M; National Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan., Kawashima S; Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa, Japan., Konopko M; ELIXIR Hub, Wellcome Genome Campus, Hinxton, UK., Kyomugisha I; Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa., Li H; Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada., Linden M; ELIXIR-Finland, CSC - IT Center for Science Ltd, Espoo, Finland., Rodriguez LL; Patient-Centered Outcomes Research Institute, Washington, DC, USA., Morita M; Okayama University, Okayama, Japan., Mulder N; Computational Biology Division, IDM, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa., Muller J; Laboratoire de Génétique Médicale, Institut de Génétique Médicale d'Alsace, INSERM U1112, Université; de Strasbourg, Strasbourg, France.; Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France., Nagaie S; Tohoku Medical Megabank Organization (ToMMo), Tohoku University, Sendai, Japan., Nasir J; Department of Life Sciences, University of Northampton, Northampton, UK., Ogishima S; Tohoku Medical Megabank Organization (ToMMo), Tohoku University, Sendai, Japan., Ota Wang V; Office of Data Sharing, National Cancer Institute, NIH, Rockville, MD, USA., Paglione LD; Spherical Cow Group, Rego Park, NY 11374, USA., Pandya RN; Microsoft Research, Redmond, WA 98052, USA., Parkinson H; European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, UK., Philippakis AA; Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA., Prasser F; Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany., Rambla J; Centre de Regulació Genòmica (CRG), Barcelona, Spain., Reinold K; Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA., Rushton GA; Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA., Saltzman A; Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA., Saunders G; ELIXIR Hub, Wellcome Genome Campus, Hinxton, UK., Sofia HJ; National Human Genome Research Institute, NIH, Bethesda, MD, USA., Spalding JD; European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, UK., Swertz MA; Genomics Coordination Center, Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands., Tulchinsky I; Google Cloud, Kitchener, ON N2H 5G5, Canada., van Enckevort EJ; Genomics Coordination Center, Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands., Varma S; Health Data Research UK, Gibbs Building, 215 Euston Road, London NW1 2BE, UK., Voisin C; Google Cloud, Kitchener, ON N2H 5G5, Canada., Yamamoto N; Osaka University, Osaka, Japan., Yamasaki C; Osaka University, Osaka, Japan., Zass L; Computational Biology Division, IDM, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa., Guidry Auvil JM; Office of Data Sharing, National Cancer Institute, NIH, Rockville, MD, USA., Nyrönen TH; ELIXIR-Finland, CSC - IT Center for Science Ltd, Espoo, Finland., Courtot M; European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.

Publikováno v: Cell genomics [Cell Genom] 2021 Nov 10; Vol. 1 (2), pp. None. Date of Electronic Publication: 2021 Nov 10.

Publisher Correction: Federated discovery and sharing of genomic data using Beacons.

Autor: Fiume M; DNAstack, Toronto, Ontario, Canada. marc@dnastack.com., Cupak M; DNAstack, Toronto, Ontario, Canada., Keenan S; Global Alliance for Genomics and Health, Toronto, Ontario, Canada.; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK., Rambla J; Centre de Regulació Genòmica, Barcelona, Spain., de la Torre S; Centre de Regulació Genòmica, Barcelona, Spain., Dyke SOM; Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, Quebec, Canada., Brookes AJ; Department of Genetics, University of Leicester, Leicester, UK., Carey K; Genecloud, Sunnyvale, CA, USA., Lloyd D; ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK., Goodhand P; Global Alliance for Genomics and Health, Toronto, Ontario, Canada.; Ontario Institute for Cancer Research, Toronto, Ontario, Canada., Haeussler M; Genomics Institute, University of California at Santa Cruz, Santa Cruz, CA, USA., Baudis M; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland., Stockinger H; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland., Dolman L; Global Alliance for Genomics and Health, Toronto, Ontario, Canada.; Ontario Institute for Cancer Research, Toronto, Ontario, Canada., Lappalainen I; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.; CSC - IT Center for Science Ltd, Espoo, Finland., Törnroos J; CSC - IT Center for Science Ltd, Espoo, Finland., Linden M; CSC - IT Center for Science Ltd, Espoo, Finland., Spalding JD; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK., Ur-Rehman S; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK., Page A; Global Alliance for Genomics and Health, Toronto, Ontario, Canada.; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Flicek P; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK., Sherry S; National Center for Biotechnology Information, US National Library of Medicine, Bethesda, MD, USA., Haussler D; Genomics Institute, University of California at Santa Cruz, Santa Cruz, CA, USA., Varma S; ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK., Saunders G; ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK., Scollen S; ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK.

Publikováno v: Nature biotechnology [Nat Biotechnol] 2019 Apr; Vol. 37 (4), pp. 480.

Registered access: authorizing data access.

Autor: Dyke SOM; Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, QC, Canada. stephanie.dyke@mcgill.ca.; Montreal Neurological Institute, Faculty of Medicine, McGill University, Montreal, QC, Canada. stephanie.dyke@mcgill.ca., Linden M; CSC - IT Center for Science, Espoo, Finland.; ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK., Lappalainen I; CSC - IT Center for Science, Espoo, Finland.; ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK.; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK., De Argila JR; Centre for Genomic Regulation, Barcelona, Spain.; Universitat Pompeu Fabra, Barcelona, Spain., Carey K, Lloyd D; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.; The Global Alliance for Genomics and Health, MaRS Centre, West Tower, 661 University Avenue, Suite 510, Toronto, M5G 0A3, ON, Canada., Spalding JD; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK., Cabili MN; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Kerry G; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK., Foreman J; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK., Cutts T; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK., Shabani M; Center for Biomedical Ethics and Law, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium., Rodriguez LL; National Human Genome Research Institute, NIH, Bethesda, MD, USA., Haeussler M; Genomics Institute, University of California at Santa Cruz, Santa Cruz, CA, USA., Walsh B; OHSU, Portland, OR, USA., Jiang X; Department of Biomedical Informatics, UC San Diego, La Jolla, CA, USA., Wang S; Department of Biomedical Informatics, UC San Diego, La Jolla, CA, USA., Perrett D; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK., Boughtwood T; Australian Genomics Health Alliance, 50 Flemington Road, Parkville, VIC, 3052, Australia., Matern A; Bioreference Laboratories, Inc., Elmwood Park, NJ, USA., Brookes AJ; Department of Genetics and Genome Biology, University of Leicester, Leicester, UK., Cupak M; DNAstack, Toronto, ON, Canada., Fiume M; DNAstack, Toronto, ON, Canada., Pandya R; Microsoft, Redmond, WA, USA., Tulchinsky I; Google, Mountain View, CA, USA., Scollen S; ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK., Törnroos J; CSC - IT Center for Science, Espoo, Finland., Das S; McGill Centre for Integrative Neurosciences, Montreal Neurological Institute, McGill University, Montreal, QC, Canada., Evans AC; McGill Centre for Integrative Neurosciences, Montreal Neurological Institute, McGill University, Montreal, QC, Canada., Malin BA; Vanderbilt University Medical Center, Nashville, TN, USA., Beck S; UCL Cancer Institute, University College London, London, UK., Brenner SE; Department of Plant & Microbial Biology, University of California, Berkeley, CA, USA., Nyrönen T; CSC - IT Center for Science, Espoo, Finland.; ELIXIR Compute Platform, ELIXIR, Wellcome Genome Campus, Hinxton, Cambridge, UK., Blomberg N; ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK., Firth HV; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK., Hurles M; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK., Philippakis AA; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Rätsch G; Department of Computer Science, Biomedical Informatics, ETH Zurich, Zurich, Switzerland., Brudno M; Department of Computer Science, University of Toronto, Toronto, ON, Canada.; Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON, Canada., Boycott KM; Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada., Rehm HL; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Pathology, Brigham & Women's Hospital & Harvard Medical School, Boston, MA, USA., Baudis M; University of Zurich & Swiss Institute of Bioinformatics, Zurich, Switzerland., Sherry ST; National Centre for Biotechnology Information, US National Library of Medicine, Bethesda, MD, USA., Kato K; Department of Biomedical Ethics and Public Policy, Graduate School of Medicine, Osaka University, Osaka, Japan., Knoppers BM; Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, QC, Canada., Baker D; Martin, Blanck & Associates, Alexandria, VA, USA., Flicek P; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.

Publikováno v: European journal of human genetics : EJHG [Eur J Hum Genet] 2018 Dec; Vol. 26 (12), pp. 1721-1731. Date of Electronic Publication: 2018 Aug 02.