Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data

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 (+14 others)
2017 F1000Research  
The availability of high-throughput molecular profiling techniques has provided more accurate and informative data for regular clinical studies. Nevertheless, complex computational workflows are required to interpret these data. PubMed Abstract | Publisher Full Text | Free Full Text 2. Woolf SH: The meaning of translational research and why it matters. JAMA. 2008; 299(2): 211-213. PubMed Abstract | Publisher Full Text 3. Schuster SC: Next-generation sequencing transforms today's biology. Nat
more » ... hods. 2008; 5(1): 16-18. PubMed Abstract | Publisher Full Text 4. Lee H, Gurtowski J, Yoo S, et al.: Third-generation sequencing and the future of genomics. bioRxiv. 2016. Publisher Full Text 5. Hunt DF, Yates JR 3rd, Shabanowitz J, et al.: Protein sequencing by tandem mass spectrometry. Proc Natl Acad Sci U S A. 1986; 83(17): 6233-6237. PubMed Abstract | Publisher Full Text | Free Full Text 6. Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A. 2001; 98(9): 5116-5121. PubMed Abstract | Publisher Full Text | Free Full Text 7. da Silva RF, Filgueira R, Pietri I, et al.: A characterization of workflow management systems for extreme-scale applications. Future Gener Comput Syst. 2017; 75: 228-238. Publisher Full Text 8. van Nimwegen KJ, van Soest RA, Veltman JA, et al.: Is the $1000 genome as near as we think? a cost analysis of Next-Generation sequencing. Clin Chem. 2016; 62(11): 1458-1464. PubMed Abstract | Publisher Full Text 9. Griffith M, Spies NC, Krysiak K, et al.: CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nat Genet. 2017; 49(2): 170-174. PubMed Abstract | Publisher Full Text | Free Full Text 10. Scheufele E, Aronzon D, Coopersmith R, et al.: tranSMART: An open source knowledge management and high content data analytics platform. AMIA Jt Summits Transl Sci Proc. 2014; 2014: 96-101. PubMed Abstract | Free Full Text 11. Cerami E, Gao J, Dogrusoz U, et al.: The cbio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012; 2(5): 401-404. PubMed Abstract | Publisher Full Text | Free Full Text 12. Grossman RL, Heath AP, Ferretti V, et al.: Toward a shared vision for cancer genomic data. N Engl J Med. 2016; 375(12): 1109-1112. PubMed Abstract | Publisher Full Text 13. Kasprzyk A: BioMart: driving a paradigm change in biological data management. Database (Oxford). 2011; bar049. PubMed Abstract | Publisher Full Text | Free Full Text 14. Bourne PE, Bonazzi V, Dunn M, et al.: The NIH big data to knowledge (BD2K) initiative. J Am Med Inform Assoc. 2015; 22(6): 1114. PubMed Abstract | Publisher Full Text | Free Full Text 15. Margolis R, Derr L, Dunn M, et al.: The national institutes of health's big data to knowledge (BD2K) initiative: capitalizing on biomedical big data. J Am Med Inform Assoc. 2014; 21(6): 957-958. PubMed Abstract | Publisher Full Text | Free Full Text 16. Wilkinson MD, Dumontier M, Aalbersberg IJ, et al.: The FAIR guiding principles for scientific data management and stewardship. Sci Data. 2016; 3: 160018. PubMed Abstract | Publisher Full Text | Free Full Text 17. Wells TN, Willis P, Burrows JN, et al.: Open data in drug discovery and development: lessons from malaria. Nat Rev Drug Discov. 2016; 15(10): 661-662. PubMed Abstract | Publisher Full Text 18. Levin N, Leonelli S, Weckowska D, et al.: How do scientists define openness? exploring the relationship between open science policies and research practice. Bull Sci Technol Soc. 2016; 36(2): 128-141. PubMed Abstract | Publisher Full Text | Free Full Text 19. McKiernan EC, Bourne PE, Brown CT, et al.: How open science helps researchers succeed. eLife. 2016; 5: pii: e16800. PubMed Abstract | Publisher Full Text | Free Full Text 20. Crosswell LC, Thornton JM: ELIXIR: a distributed infrastructure for european biological data. Trends Biotechnol. 2012; 30(5): 241-242. PubMed Abstract | Publisher Full Text 21. Lappalainen I, Almeida-King J, Kumanduri V, et al.: The european genomephenome archive of human data consented for biomedical research. Nat Genet. 2015; 47(7): 692-695. PubMed Abstract | Publisher Full Text | Free Full Text 22. Herzinger S, Gu W, Satagopam V, et al.: SmartR: An open-source platform for interactive visual analytics for translational research data. Bioinformatics. 2017; 33(14): 2229-2231. PubMed Abstract | Publisher Full Text
doi:10.12688/f1000research.12168.1 pmid:29123641 pmcid:PMC5657030 fatcat:pmccjyaoffbmfd4rdcreqnx7je