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Title: Data publication with the structural biology data grid supports live analysis

Abstract

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. In conclusion, it is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.

Authors:
 [1];  [1];  [1];  [1];  [1];  [2];  [3];  [1];  [4];  [4];  [4];  [5];  [6];  [1];  [5];  [7];  [8];  [9];  [10];  [11] more »;  [12];  [13];  [14];  [15];  [16];  [17];  [18];  [19];  [12];  [20];  [21];  [22];  [23];  [24];  [25];  [1];  [26];  [27];  [15];  [1];  [28];  [29];  [30];  [8];  [8];  [31];  [32];  [33];  [34];  [35];  [36];  [8];  [37];  [5];  [18];  [38];  [39];  [38];  [9];  [40];  [8];  [41];  [42];  [43];  [44];  [45];  [46];  [47];  [24];  [1] « less
  1. Harvard Medical School, Boston, MA (United States)
  2. Institut Pasteur de Montevideo, Montevideo (Uruguay)
  3. Chinese Academy of Sciences (CAS), Shanghai (China). Shanghai Institutes for Biological Sciences
  4. Cornell Univ., Ithaca, NY (United States). NE-CAT and Department of Chemistry and Chemical Biology
  5. Yale Univ. School of Medicine, New Haven, CT (United States)
  6. Yale Univ., New Haven, CT (United States)
  7. Univ. of Utrecht (Netherlands)
  8. Univ. of Texas Southwestern Medical Center, Dallas, TX (United States)
  9. Washington Univ. School of Medicine, St. Louis, MO (United States)
  10. Univ. of Zurich (Switzerland)
  11. Academia Sinica, Taipei (Taiwan)
  12. Vanderbilt Univ., Nashville, TN (United States)
  13. Ludwig Institute for Cancer Research, La Jolla, CA (United States); Univ. of California, San Diego, CA (United States)
  14. SUNY Upstate Medical University, Syracuse, NY (United States)
  15. Univ. of Chicago, IL (United States)
  16. Dana-Farber Cancer Institute, Boston, MA (United States)
  17. Saint Louis Univ. School of Medicine, St. Louis, MO (United States)
  18. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
  19. Harvard Medical School, Boston, MA (United States); Dana-Farber Cancer Institute, Boston, MA (United States)
  20. Columbia Univ., New York, NY (United States)
  21. National Heart, Lung and Blood Institute (NIH), Bethesda, MD (United States)
  22. Cornell Univ., Ithaca, NY (United States)
  23. Stanford Univ. School of Medicine, Stanford, CA (United States)
  24. Harvard Univ., Cambridge, MA (United States)
  25. Chinese Academy of Sciences, Wuhan (China)
  26. Tufts Univ. School of Medicine, Boston, MA (United States)
  27. Queen's Univ., Kingston, ON (Canada)
  28. La Trobe Univ., Melbourne (Australia)
  29. Geisel School of Medicine at Dartmouth, Hanover, NH (United States)
  30. Univ. of Cambridge (United Kingdom)
  31. Univ. of Toronto, ON (Canada); Ontario Cancer Institute/University Health Network, Toronto, ON (Canada)
  32. Universidade do Porto, Porto (Portugal)
  33. Univ. Grenoble Alpes/CNRS/CEA, Grenoble (France)
  34. Univ. of Maryland, Baltimore, MD (United States)
  35. Howard Hughes Medical Institute and Harvard Medical School, Boston, MA (United States)
  36. National Institute of Neurological Disorders and Stroke, Bethesda, MA (United States); National Heart, Lung and Blood Institute, Bethesda, MA (United States)
  37. Univ. of Texas Medical Branch, Galveston, TX (United States)
  38. Rice Univ., Houston, TX (United States)
  39. Cornell Univ., Ithaca, NY (United States). College of Veterinary Medicine
  40. Univ. of Kentucky, Lexington, KY (United States)
  41. Harvard Medical School, Boston, MA (United States); Boston Children's Hospital, Boston, MA (United States)
  42. Argonne National Lab. (ANL), Argonne, IL (United States)
  43. Univ. of California, San Francisco, CA (United States)
  44. Uppsala Univ. (Sweden). Dept. of Cell and Molecular Biology, Lab. of Molecular Biophysics; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). NERC
  45. Howard Hughes Medical Institute, Ashburn, VA (United States)
  46. Boston Children's Hospital, Boston, MA (United States); Harvard Medical School, Boston, MA (United States)
  47. Univ. of Konstanz, Konstanz (Germany)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Institutes of Health (NIH); National Science Foundation (NSF)
OSTI Identifier:
1241078
Alternate Identifier(s):
OSTI ID: 1392999; OSTI ID: 1414751
Grant/Contract Number:  
AC02-06CH11357; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 7; Journal Issue: 03, 2016; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Meyer, Peter A., Socias, Stephanie, Key, Jason, Ransey, Elizabeth, Tjon, Emily C., Buschiazzo, Alejandro, Lei, Ming, Botka, Chris, Withrow, James, Neau, David, Rajashankar, Kanagalaghatta, Anderson, Karen S., Baxter, Richard H., Blacklow, Stephen C., Boggon, Titus J., Bonvin, Alexandre M. J. J., Borek, Dominika, Brett, Tom J., Caflisch, Amedeo, Chang, Chung-I, Chazin, Walter J., Corbett, Kevin D., Cosgrove, Michael S., Crosson, Sean, Dhe-Paganon, Sirano, Di Cera, Enrico, Drennan, Catherine L., Eck, Michael J., Eichman, Brandt F., Fan, Qing R., Ferré-D'Amaré, Adrian R., Christopher Fromme, J., Garcia, K. Christopher, Gaudet, Rachelle, Gong, Peng, Harrison, Stephen C., Heldwein, Ekaterina E., Jia, Zongchao, Keenan, Robert J., Kruse, Andrew C., Kvansakul, Marc, McLellan, Jason S., Modis, Yorgo, Nam, Yunsun, Otwinowski, Zbyszek, Pai, Emil F., Pereira, Pedro Jose Barbosa, Petosa, Carlo, Raman, C. S., Rapoport, Tom A., Roll-Mecak, Antonina, Rosen, Michael K., Rudenko, Gabby, Schlessinger, Joseph, Schwartz, Thomas U., Shamoo, Yousif, Sondermann, Holger, Tao, Yizhi J., Tolia, Niraj H., Tsodikov, Oleg V., Westover, Kenneth D., Wu, Hao, Foster, Ian, Fraser, James S., Maia, Filipe R. N. C., Gonen, Tamir, Kirchhausen, Tom, Diederichs, Kay, Crosas, Mercè, and Sliz, Piotr. Data publication with the structural biology data grid supports live analysis. United States: N. p., 2016. Web. doi:10.1038/ncomms10882.
Meyer, Peter A., Socias, Stephanie, Key, Jason, Ransey, Elizabeth, Tjon, Emily C., Buschiazzo, Alejandro, Lei, Ming, Botka, Chris, Withrow, James, Neau, David, Rajashankar, Kanagalaghatta, Anderson, Karen S., Baxter, Richard H., Blacklow, Stephen C., Boggon, Titus J., Bonvin, Alexandre M. J. J., Borek, Dominika, Brett, Tom J., Caflisch, Amedeo, Chang, Chung-I, Chazin, Walter J., Corbett, Kevin D., Cosgrove, Michael S., Crosson, Sean, Dhe-Paganon, Sirano, Di Cera, Enrico, Drennan, Catherine L., Eck, Michael J., Eichman, Brandt F., Fan, Qing R., Ferré-D'Amaré, Adrian R., Christopher Fromme, J., Garcia, K. Christopher, Gaudet, Rachelle, Gong, Peng, Harrison, Stephen C., Heldwein, Ekaterina E., Jia, Zongchao, Keenan, Robert J., Kruse, Andrew C., Kvansakul, Marc, McLellan, Jason S., Modis, Yorgo, Nam, Yunsun, Otwinowski, Zbyszek, Pai, Emil F., Pereira, Pedro Jose Barbosa, Petosa, Carlo, Raman, C. S., Rapoport, Tom A., Roll-Mecak, Antonina, Rosen, Michael K., Rudenko, Gabby, Schlessinger, Joseph, Schwartz, Thomas U., Shamoo, Yousif, Sondermann, Holger, Tao, Yizhi J., Tolia, Niraj H., Tsodikov, Oleg V., Westover, Kenneth D., Wu, Hao, Foster, Ian, Fraser, James S., Maia, Filipe R. N. C., Gonen, Tamir, Kirchhausen, Tom, Diederichs, Kay, Crosas, Mercè, & Sliz, Piotr. Data publication with the structural biology data grid supports live analysis. United States. doi:10.1038/ncomms10882.
Meyer, Peter A., Socias, Stephanie, Key, Jason, Ransey, Elizabeth, Tjon, Emily C., Buschiazzo, Alejandro, Lei, Ming, Botka, Chris, Withrow, James, Neau, David, Rajashankar, Kanagalaghatta, Anderson, Karen S., Baxter, Richard H., Blacklow, Stephen C., Boggon, Titus J., Bonvin, Alexandre M. J. J., Borek, Dominika, Brett, Tom J., Caflisch, Amedeo, Chang, Chung-I, Chazin, Walter J., Corbett, Kevin D., Cosgrove, Michael S., Crosson, Sean, Dhe-Paganon, Sirano, Di Cera, Enrico, Drennan, Catherine L., Eck, Michael J., Eichman, Brandt F., Fan, Qing R., Ferré-D'Amaré, Adrian R., Christopher Fromme, J., Garcia, K. Christopher, Gaudet, Rachelle, Gong, Peng, Harrison, Stephen C., Heldwein, Ekaterina E., Jia, Zongchao, Keenan, Robert J., Kruse, Andrew C., Kvansakul, Marc, McLellan, Jason S., Modis, Yorgo, Nam, Yunsun, Otwinowski, Zbyszek, Pai, Emil F., Pereira, Pedro Jose Barbosa, Petosa, Carlo, Raman, C. S., Rapoport, Tom A., Roll-Mecak, Antonina, Rosen, Michael K., Rudenko, Gabby, Schlessinger, Joseph, Schwartz, Thomas U., Shamoo, Yousif, Sondermann, Holger, Tao, Yizhi J., Tolia, Niraj H., Tsodikov, Oleg V., Westover, Kenneth D., Wu, Hao, Foster, Ian, Fraser, James S., Maia, Filipe R. N. C., Gonen, Tamir, Kirchhausen, Tom, Diederichs, Kay, Crosas, Mercè, and Sliz, Piotr. Mon . "Data publication with the structural biology data grid supports live analysis". United States. doi:10.1038/ncomms10882. https://www.osti.gov/servlets/purl/1241078.
@article{osti_1241078,
title = {Data publication with the structural biology data grid supports live analysis},
author = {Meyer, Peter A. and Socias, Stephanie and Key, Jason and Ransey, Elizabeth and Tjon, Emily C. and Buschiazzo, Alejandro and Lei, Ming and Botka, Chris and Withrow, James and Neau, David and Rajashankar, Kanagalaghatta and Anderson, Karen S. and Baxter, Richard H. and Blacklow, Stephen C. and Boggon, Titus J. and Bonvin, Alexandre M. J. J. and Borek, Dominika and Brett, Tom J. and Caflisch, Amedeo and Chang, Chung-I and Chazin, Walter J. and Corbett, Kevin D. and Cosgrove, Michael S. and Crosson, Sean and Dhe-Paganon, Sirano and Di Cera, Enrico and Drennan, Catherine L. and Eck, Michael J. and Eichman, Brandt F. and Fan, Qing R. and Ferré-D'Amaré, Adrian R. and Christopher Fromme, J. and Garcia, K. Christopher and Gaudet, Rachelle and Gong, Peng and Harrison, Stephen C. and Heldwein, Ekaterina E. and Jia, Zongchao and Keenan, Robert J. and Kruse, Andrew C. and Kvansakul, Marc and McLellan, Jason S. and Modis, Yorgo and Nam, Yunsun and Otwinowski, Zbyszek and Pai, Emil F. and Pereira, Pedro Jose Barbosa and Petosa, Carlo and Raman, C. S. and Rapoport, Tom A. and Roll-Mecak, Antonina and Rosen, Michael K. and Rudenko, Gabby and Schlessinger, Joseph and Schwartz, Thomas U. and Shamoo, Yousif and Sondermann, Holger and Tao, Yizhi J. and Tolia, Niraj H. and Tsodikov, Oleg V. and Westover, Kenneth D. and Wu, Hao and Foster, Ian and Fraser, James S. and Maia, Filipe R. N. C. and Gonen, Tamir and Kirchhausen, Tom and Diederichs, Kay and Crosas, Mercè and Sliz, Piotr},
abstractNote = {Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. In conclusion, it is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.},
doi = {10.1038/ncomms10882},
journal = {Nature Communications},
number = 03, 2016,
volume = 7,
place = {United States},
year = {2016},
month = {3}
}

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