Biobanks-A source of large biological data sets: Open problems and future challenges

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 8401, Issue , 2014, Pages 317-330

  Huppertz, Berthold ^a   Holzinger, Andreas ^a  

^a MEDICAL UNIVERSITY OF GRAZ   (Austria)

Author keywords

Big data; Biobank; Biological data; Personalized medicine

Indexed keywords

BIG DATA; BODY FLUIDS; DATA FUSION; DATA MINING; OPEN DATA; SECURITY OF DATA;

BIOBANK; BIOLOGICAL DATA; BIOLOGICAL SAMPLES; HETEROGENEOUS DATA; KNOWLEDGE DISCOVERY AND DATA MININGS; PERSONALIZED MEDICINES; SAFETY AND SECURITIES; SCIENTIFIC RESEARCHES;

DATA INTEGRATION;

EID: 84927645895     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-662-43968-5_18     Document Type: Article

References (46)

1. Holzinger, A.: On Knowledge Discovery and Interactive Intelligent Visualization of Biomedical Data-Challenges in Human-Computer Interaction & Biomedical Informatics. In: DATA 2012, pp. 9-20. INSTICC (2012)
2. Howe, D., Costanzo, M., Fey, P., Gojobori, T., Hannick, L., Hide, W., Hill, D.P., Kania, R., Schaeffer, M., St Pierre, S., Twigger, S., White, O., Rhee, S.Y.: Big data: The future of biocuration. Nature 455(7209), 47-50 (2008)
3. Holzinger, A.: Biomedical Informatics: Computational Sciences meets Life Sciences. BoD, Norderstedt (2012)
4. Holzinger, A.: Biomedical Informatics: Discovering Knowledge in Big Data. Springer, New York (2014)
5. Fan, W.: Querying big social data. In: Gottlob, G., Grasso, G., Olteanu, D., Schallhart, C. (eds.) BNCOD 2013. LNCS, vol. 7968, pp. 14-28. Springer, Heidelberg (2013)
6. Hood, L., Friend, S.H.: Predictive, personalized, preventive, participatory (P4) cancer medicine. Nature Reviews Clinical Oncology 8(3), 184-187 (2011)
7. Emmert-Streib, F., de Matos Simoes, R., Glazko, G., McDade, S., Haibe-Kains, B., Holzinger, A., Dehmer, M., Campbell, F.: Functional and genetic analysis of the colon cancer network. BMC Bioinformatics 15(suppl. 6), S6 (2014)
8. Pennisi, E.: Human genome 10th anniversary. Will computers crash genomics? Science 331, 666-668 (2011)
9. Boguski, M.S., McIntosh, M.W.: Biomedical informatics for proteomics. Nature 422(6928), 233-237 (2003)
10. Tomita, M., Kami, K.: Systems Biology, Metabolomics, and Cancer Metabolism. Science 336(6084), 990-991 (2012)
11. Wenk, M.R.: The emerging field of lipidomics. Nature Reviews Drug Discovery 4(7), 594-610 (2005)
12. Wang, Z., Gerstein, M., Snyder, M.: RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10(1), 57-63 (2009)
13. Egger, G., Liang, G.N., Aparicio, A., Jones, P.A.: Epigenetics in human disease and prospects for epigenetic therapy. Nature 429(6990), 457-463 (2004)
14. Egert, M., de Graaf, A.A., Smidt, H., de Vos, W.M., Venema, K.: Beyond diversity: functional microbiomics of the human colon. Trends in Microbiology 14(2), 86-91 (2006)
15. Winter, G., Kromer, J.O.: Fluxomics-connecting ’omics analysis and phenotypes. Environmental Microbiology 15(7), 1901-1916 (2013)
16. Houle, D., Govindaraju, D.R., Omholt, S.: Phenomics: the next challenge. Nature Reviews Genetics 11(12), 855-866 (2010)
17. Sawyers, C.L.: The cancer biomarker problem. Nature 452(7187), 548-552 (2008)
18. Simeon-Dubach, D., Perren, A.: Better provenance for biobank samples. Nature 475(7357), 454-455 (2011)
19. Loft, S., Poulsen, H.E.: Cancer risk and oxidative DNA damage in man. Journal of Molecular Medicine 74(6), 297-312 (1996)
20. Hewitt, R., Watson, P.: Defining Biobank. Biopreservation and Biobanking 11(5), 309-315 (2013)
21. Shaw, D.M., Elger, B.S., Colledge, F.: What is a biobank? Differing definitions among biobank stakeholders. Clinical Genetics 85(3), 223-227 (2014)
22. Olson, J.E., Ryu, E., Johnson, K.J., Koenig, B.A., Maschke, K.J., Morrisette, J.A., Liebow, M., Takahashi, P.Y., Fredericksen, Z.S., Sharma, R.G., Anderson, K.S., Hathcock, M.A., Carnahan, J.A., Pathak, J., Lindor, N.M., Beebe, T.J., Thibodeau, S.N., Cerhan, J.R.: The Mayo Clinic Biobank: A Building Block for Individualized Medicine. Mayo Clinic Proceedings 88(9), 952-962 (2013)
23. Akervall, J., Pruetz, B.L., Geddes, T.J., Larson, D., Felten, D.J., Wilson, G.D.: Beaumont Health System BioBank: A Multidisciplinary Biorepository and Translational Research Facility. Biopreservation and Biobanking 11(4), 221-228 (2013)
24. Riegman, P.H.J., Morente, M.M., Betsou, F., de Blasio, P., Geary, P.: Biobanking for better healthcare. Molecular Oncology 2(3), 213-222 (2008)
25. Kang, B., Park, J., Cho, S., Lee, M., Kim, N., Min, H., Lee, S., Park, O., Han, B.: Current Status, Challenges, Policies, and Bioethics of Biobanks. Genomics & Informatics 11(4), 211-217 (2013)
26. Roden, D.M., Pulley, J.M., Basford, M.A., Bernard, G.R., Clayton, E.W., Balser, J.R., Masys, D.R.: Development of a Large-Scale De-Identified DNA Biobank to Enable Personalized Medicine. Clin. Pharmacol. Ther. 84(3), 362-369 (2008)
27. Kim, H., Yi, B.K., Kim, I.K., Kwak, Y.S.: Integrating Clinical Information in National Biobank of Korea. Journal of Medical Systems 35(4), 647-656 (2011)
28. Norling, M., Kihara, A., Kemp, S.: Web-Based Biobank System Infrastructure Monitoring Using Python, Perl, and PHP. Biopreservation and Biobanking 11(6), 355-358 (2013)
29. Holzinger, A., Geierhofer, R., Modritscher, F., Tatzl, R.: Semantic Information in Medical Information Systems: Utilization of Text Mining Techniques to Analyze Medical Diagnoses. J. Univers. Comput. Sci. 14(22), 3781-3795 (2008)
30. Woodbridge, M., Fagiolo, G., O’Regan, D.P.: MRIdb: Medical Image Management for Biobank Research. J. Digit. Imaging 26(5), 886-890 (2013)
31. Scudellari, M.: Biobank managers bemoan underuse of collected samples. Nature Medicine 19(3), 253-253 (2013)
32. Wolf, S.M.: Return of results in genomic biobank research: ethics matters. Genetics in Medicine 15(2), 157-159 (2013)
33. Sandor, J., Bard, P., Tamburrini, C., Tannsjo, T.: The case of biobank with the law: between a legal and scientific fiction. Journal of Medical Ethics 38(6), 347-350 (2012)
34. Puchois, P.: Finding ways to improve the use of biobanks. Nat. Med. 19(7), 814-815 (2013)
35. Paradiso, A., Hansson, M.: Finding ways to improve the use of biobanks. Nat. Med. 19(7), 815-815 (2013)
36. Marko-Varga, G., Vegvari, A., Welinder, C., Lindberg, H., Rezeli, M., Edula, G., Svensson, K.J., Belting, M., Laurell, T., Fehniger, T.E.: Standardization and Utilization of Biobank Resources in Clinical Protein Science with Examples of Emerging Applications. Journal of Proteome Research 11(11), 5124-5134 (2012)
37. LaBaer, J.: Improving International Research with Clinical Specimens: 5 Achievable Objectives. Journal of Proteome Research 11(12), 5592-5601 (2012)
38. Norlin, L., Fransson, M.N., Eriksson, M., Merino-Martinez, R., Anderberg, M., Kurtovic, S., Litton, J.E.: A Minimum Data Set for Sharing Biobank Samples, Information, and Data: MIABIS. Biopreservation and Biobanking 10(4), 343-348 (2012)
39. Norstedt, I.: Horizon 2020: European perspectives in healthcare sciences and implementation. EPMA Journal 5(suppl. 1), A1 (2014)
40. Kieseberg, P., Hobel, H., Schrittwieser, S., Weippl, E., Holzinger, A.: Protecting Anonymity in the Data-Driven Medical Sciences. In: Holzinger, A., Jurisica, I. (eds.) Knowledge Discovery and Data Mining. LNCS, vol. 8401, pp. 303-318. Springer, Heidelberg (2014)
41. Holzinger, A., Stocker, C., Ofner, B., Prohaska, G., Brabenetz, A., Hofmann-Wellenhof, R.: Combining HCI, Natural Language Processing, and Knowledge Discovery-Potential of IBM Content Analytics as an assistive technology in the biomedical field. In: Holzinger, A., Pasi, G. (eds.) HCI-KDD 2013. LNCS, vol. 7947, pp. 13-24. Springer, Heidelberg (2013)
42. Holzinger, A., Dehmer, M., Jurisica, I.: Knowledge Discovery and Interactive Data Mining in Bioinformatics-State-of-the-Art, Future challenges and Research Directions. BMC Bioinformatics 15(suppl. 6) (I1) (2014)
43. Holzinger, A., Jurisica, I.: Knowledge Discovery and Data Mining in Biomedical Informatics: The future is in Integrative, Interactive Machine Learning Solutions. In: Holzinger, A., Jurisica, I. (eds.) Knowledge Discovery and Data Mining. LNCS, vol. 8401, pp. 1-18. Springer, Berlin (2014)
44. Shneiderman, B.: The Big Picture for Big Data: Visualization. Science 343(6172), 730-730 (2014)
45. Jeanquartier, F., Holzinger, A.: On Visual Analytics and Evaluation In Cell Physiology: A Case Study. In: Cuzzocrea, A., Kittl, C., Simos, D.E., Weippl, E., Xu, L. (eds.) CD-ARES 2013. LNCS, vol. 8127, pp. 495-502. Springer, Heidelberg (2013)
46. hci4all.at, http://www.hci4all.at/expert-network-hci-kdd/