Data publication with the structural biology data grid supports live analysis

Peter A. Meyer, Stephanie Socias, Jason Key, Elizabeth Ransey, Emily C. Tjon, Alejandro Buschiazzo, Ming Lei, Chris Botka, James Withrow, David Neau, Kanagalaghatta Rajashankar, Karen S. Anderson, Richard H. Baxter, Stephen C. Blacklow, Titus J. Boggon, Alexandre M J J Bonvin, Dominika Borek, Tom J. Brett, Amedeo Caflisch, Chung I. Chang & 50 others Walter J. Chazin, Kevin D. Corbett, Michael S. Cosgrove, Sean Crosson, Sirano Dhe-Paganon, Enrico Di Cera, Catherine L. Drennan, Michael J. Eck, Brandt F. Eichman, Qing R. Fan, Adrian R. Ferré-D'Amaré, J. Christopher Fromme, K. Christopher Garcia, Rachelle Gaudet, Peng Gong, Stephen C. Harrison, Ekaterina E. Heldwein, Zongchao Jia, Robert J. Keenan, Andrew C. Kruse, Marc Kvansakul, Jason S. McLellan, Yorgo Modis, Yunsun Nam, Zbyszek Otwinowski, Emil F. Pai, Pedro José Barbosa Pereira, Carlo Petosa, C. S. Raman, Tom A. Rapoport, Antonina Roll-Mecak, Michael K. Rosen, Gabrielle Rudenko, Joseph Schlessinger, Thomas U. Schwartz, Yousif Shamoo, Holger Sondermann, Yizhi J. Tao, Niraj H. Tolia, Oleg V. Tsodikov, Kenneth D. Westover, Hao Wu, Ian Foster, James S. Fraser, Filipe R N C Maia, Tamir Gonen, Tom Kirchhausen, Kay Diederichs, Mercé Crosas, Piotr Sliz

Research output: Contribution to journalArticle

53 Citations (Scopus)

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. 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.

Original languageEnglish (US)
Article number10882
JournalNature Communications
Volume7
DOIs
StatePublished - Mar 7 2016

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biology
Publications
grids
biomedical data
Diffraction
Statistics
diffraction
X ray diffraction
Processing
statistics
Systems Biology
X-Ray Diffraction
shift
Reproduction
Research Personnel
Datasets
x rays

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Chemistry(all)
  • Physics and Astronomy(all)

Cite this

Meyer, P. A., Socias, S., Key, J., Ransey, E., Tjon, E. C., Buschiazzo, A., ... Sliz, P. (2016). Data publication with the structural biology data grid supports live analysis. Nature Communications, 7, [10882]. https://doi.org/10.1038/ncomms10882

Data publication with the structural biology data grid supports live analysis. / 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.; Fromme, J. Christopher; 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 José Barbosa; Petosa, Carlo; Raman, C. S.; Rapoport, Tom A.; Roll-Mecak, Antonina; Rosen, Michael K.; Rudenko, Gabrielle; 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, Mercé; Sliz, Piotr.

In: Nature Communications, Vol. 7, 10882, 07.03.2016.

Research output: Contribution to journalArticle

Meyer, PA, Socias, S, Key, J, Ransey, E, Tjon, EC, Buschiazzo, A, Lei, M, Botka, C, Withrow, J, Neau, D, Rajashankar, K, Anderson, KS, Baxter, RH, Blacklow, SC, Boggon, TJ, Bonvin, AMJJ, Borek, D, Brett, TJ, Caflisch, A, Chang, CI, Chazin, WJ, Corbett, KD, Cosgrove, MS, Crosson, S, Dhe-Paganon, S, Di Cera, E, Drennan, CL, Eck, MJ, Eichman, BF, Fan, QR, Ferré-D'Amaré, AR, Fromme, JC, Garcia, KC, Gaudet, R, Gong, P, Harrison, SC, Heldwein, EE, Jia, Z, Keenan, RJ, Kruse, AC, Kvansakul, M, McLellan, JS, Modis, Y, Nam, Y, Otwinowski, Z, Pai, EF, Pereira, PJB, Petosa, C, Raman, CS, Rapoport, TA, Roll-Mecak, A, Rosen, MK, Rudenko, G, Schlessinger, J, Schwartz, TU, Shamoo, Y, Sondermann, H, Tao, YJ, Tolia, NH, Tsodikov, OV, Westover, KD, Wu, H, Foster, I, Fraser, JS, Maia, FRNC, Gonen, T, Kirchhausen, T, Diederichs, K, Crosas, M & Sliz, P 2016, 'Data publication with the structural biology data grid supports live analysis', Nature Communications, vol. 7, 10882. https://doi.org/10.1038/ncomms10882
Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A et al. Data publication with the structural biology data grid supports live analysis. Nature Communications. 2016 Mar 7;7. 10882. https://doi.org/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. ; Fromme, J. Christopher ; 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 José Barbosa ; Petosa, Carlo ; Raman, C. S. ; Rapoport, Tom A. ; Roll-Mecak, Antonina ; Rosen, Michael K. ; Rudenko, Gabrielle ; 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, Mercé ; Sliz, Piotr. / Data publication with the structural biology data grid supports live analysis. In: Nature Communications. 2016 ; Vol. 7.
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