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; 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; Gabby 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

doi:10.1038/ncomms10882

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

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, Gabby 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 journal › Article › peer-review

111 Scopus citations

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 language	English
Article number	10882
Journal	Nature Communications
Volume	7
DOIs	https://doi.org/10.1038/ncomms10882
State	Published - Mar 7 2016

Bibliographical note

Funding Information:
Development of the Structural Biology Data Grid is funded by The Leona M. and Harry B. Helmsley Charitable Trust 2016PG-BRI002 to PS and MC. Development of citation workflows is supported NSF 1448069 (to PS). DAA is being developed as a pilot project of the National Data Service, with additional funds to support storage and technology development, including NIH P41 GM103403 (NE-CAT) and 1S10RR028832 (HMS) and DOE DE-AC02-06CH11357; NIH 1U54EB020406-01, Big Data for Discovery Science Center; and NIST 60NANB15D077 (Globus Project). AB acknowledges Ariel Chaparro for assistance with the DAA setup (Inst Pasteur Montevideo). Collections of pilot data sets were supported by various grants (see Supplementary Table 1).

Funding

Development of the Structural Biology Data Grid is funded by The Leona M. and Harry B. Helmsley Charitable Trust 2016PG-BRI002 to PS and MC. Development of citation workflows is supported NSF 1448069 (to PS). DAA is being developed as a pilot project of the National Data Service, with additional funds to support storage and technology development, including NIH P41 GM103403 (NE-CAT) and 1S10RR028832 (HMS) and DOE DE-AC02-06CH11357; NIH 1U54EB020406-01, Big Data for Discovery Science Center; and NIST 60NANB15D077 (Globus Project). AB acknowledges Ariel Chaparro for assistance with the DAA setup (Inst Pasteur Montevideo). Collections of pilot data sets were supported by various grants (see Supplementary Table 1).

Funders	Funder number
Leona M. and Harry B. Helmsley Charitable Trust
NIH Office of the Director	DP2OD001996
National Institute of General Medical Sciences DP2GM119177 Sophie Dumont National Institute of General Medical Sciences	R01GM114358, R01GM110352, R01GM112973, R01GM049551, R01GM053163, R01GM117299, R01GM069857, R01GM087353, R01GM086487, R01GM088454, T32GM008320, R01GM117080, R01GM065484, R21GM110580, P41GM103485, R01GM104141, P41GM103403
National Heart, Lung, and Blood Institute (NHLBI)	R01HL119813, U54HL112303, ZIAHL006102
Institute of Neurological Disorders and Stroke National Advisory Neurological Disorders and Stroke Council	R01NS085078, ZIANS003122
European Commission	291602
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung	149897
National Institute of Allergy and Infectious F32-AI286447 Cydney N. Johnson Diseases National Institute of Allergy and Infectious R01AI168214 Jason W. Rosch Diseases National Institute of Allergy and Infectious P30 Cydney N. Johnson Diseases National Institute of Allergy and Infectious R00-AI166116 Christopher D. Radka Diseases National Institute of Allergy and Infectious T32-AI106700 Cydney N. Johnson Diseases National Institute of Allergy and Infectious R01AI192221 Jason W. Rosch Diseases National Inst...	R21AI065886, R43AI112124, U19AI107792, R01AI045937
National Institute of Mental Health, National Institutes of Health	R01MH077303
National Science Foundation Arctic Social Science Program	1517695, 1448069
National Center for Research Resources	S10RR028832
National Childhood Cancer Registry – National Cancer Institute	R01CA140522, R01CA163647
Horizon 2020 Framework Programme	675858
National Institute of Biomedical Imaging and Bioengineering	U54EB020406

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General
General Physics and Astronomy

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10.1038/ncomms10882

Cite this

Meyer, P. A., Socias, S., Key, J., Ransey, E., Tjon, E. C., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D., Rajashankar, K., Anderson, K. S., Baxter, R. H., Blacklow, S. C., Boggon, T. J., Bonvin, A. M. J. J., Borek, D., Brett, T. J., Caflisch, A., ... Sliz, P. (2016). Data publication with the structural biology data grid supports live analysis. Nature Communications, 7, Article 10882. https://doi.org/10.1038/ncomms10882

@article{1999371a664c46878caf240be9df7005,

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. 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.",

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

note = "Funding Information: Development of the Structural Biology Data Grid is funded by The Leona M. and Harry B. Helmsley Charitable Trust 2016PG-BRI002 to PS and MC. Development of citation workflows is supported NSF 1448069 (to PS). DAA is being developed as a pilot project of the National Data Service, with additional funds to support storage and technology development, including NIH P41 GM103403 (NE-CAT) and 1S10RR028832 (HMS) and DOE DE-AC02-06CH11357; NIH 1U54EB020406-01, Big Data for Discovery Science Center; and NIST 60NANB15D077 (Globus Project). AB acknowledges Ariel Chaparro for assistance with the DAA setup (Inst Pasteur Montevideo). Collections of pilot data sets were supported by various grants (see Supplementary Table 1).",

year = "2016",

month = mar,

day = "7",

doi = "10.1038/ncomms10882",

language = "English",

volume = "7",

}

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

TY - JOUR

T1 - Data publication with the structural biology data grid supports live analysis

AU - Meyer, Peter A.

AU - Socias, Stephanie

AU - Key, Jason

AU - Ransey, Elizabeth

AU - Tjon, Emily C.

AU - Buschiazzo, Alejandro

AU - Lei, Ming

AU - Botka, Chris

AU - Withrow, James

AU - Neau, David

AU - Rajashankar, Kanagalaghatta

AU - Anderson, Karen S.

AU - Baxter, Richard H.

AU - Blacklow, Stephen C.

AU - Boggon, Titus J.

AU - Bonvin, Alexandre M.J.J.

AU - Borek, Dominika

AU - Brett, Tom J.

AU - Caflisch, Amedeo

AU - Chang, Chung I.

AU - Chazin, Walter J.

AU - Corbett, Kevin D.

AU - Cosgrove, Michael S.

AU - Crosson, Sean

AU - Dhe-Paganon, Sirano

AU - Di Cera, Enrico

AU - Drennan, Catherine L.

AU - Eck, Michael J.

AU - Eichman, Brandt F.

AU - Fan, Qing R.

AU - Ferré-D'Amaré, Adrian R.

AU - Fromme, J. Christopher

AU - Garcia, K. Christopher

AU - Gaudet, Rachelle

AU - Gong, Peng

AU - Harrison, Stephen C.

AU - Heldwein, Ekaterina E.

AU - Jia, Zongchao

AU - Keenan, Robert J.

AU - Kruse, Andrew C.

AU - Kvansakul, Marc

AU - McLellan, Jason S.

AU - Modis, Yorgo

AU - Nam, Yunsun

AU - Otwinowski, Zbyszek

AU - Pai, Emil F.

AU - Pereira, Pedro José Barbosa

AU - Petosa, Carlo

AU - Raman, C. S.

AU - Rapoport, Tom A.

AU - Roll-Mecak, Antonina

AU - Rosen, Michael K.

AU - Rudenko, Gabby

AU - Schlessinger, Joseph

AU - Schwartz, Thomas U.

AU - Shamoo, Yousif

AU - Sondermann, Holger

AU - Tao, Yizhi J.

AU - Tolia, Niraj H.

AU - Tsodikov, Oleg V.

AU - Westover, Kenneth D.

AU - Wu, Hao

AU - Foster, Ian

AU - Fraser, James S.

AU - Maia, Filipe R.N.C.

AU - Gonen, Tamir

AU - Kirchhausen, Tom

AU - Diederichs, Kay

AU - Crosas, Mercé

AU - Sliz, Piotr

N1 - Funding Information: Development of the Structural Biology Data Grid is funded by The Leona M. and Harry B. Helmsley Charitable Trust 2016PG-BRI002 to PS and MC. Development of citation workflows is supported NSF 1448069 (to PS). DAA is being developed as a pilot project of the National Data Service, with additional funds to support storage and technology development, including NIH P41 GM103403 (NE-CAT) and 1S10RR028832 (HMS) and DOE DE-AC02-06CH11357; NIH 1U54EB020406-01, Big Data for Discovery Science Center; and NIST 60NANB15D077 (Globus Project). AB acknowledges Ariel Chaparro for assistance with the DAA setup (Inst Pasteur Montevideo). Collections of pilot data sets were supported by various grants (see Supplementary Table 1).

PY - 2016/3/7

Y1 - 2016/3/7

N2 - 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.

AB - 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.

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UR - https://www.scopus.com/pages/publications/84960381776#tab=citedBy

U2 - 10.1038/ncomms10882

DO - 10.1038/ncomms10882

M3 - Article

C2 - 26947396

AN - SCOPUS:84960381776

SN - 2041-1723

VL - 7

JO - Nature Communications

JF - Nature Communications

M1 - 10882

ER -

Data publication with the structural biology data grid supports live analysis

Abstract

Bibliographical note

Funding

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