Advertisement

VASEM: visual analytics system for electron microscopy data bank

  • Jun Liu
  • Yang Gao
  • Guihua Shan
  • Xuebin ChiEmail author
Regular Paper
  • 6 Downloads

Abstract

Electron Microscopy Data Bank (EMDB) provides biological researchers with a platform for uploading and downloading data obtained mainly by electron microscopy. With the continuous expansion of the total amount of data stored in EMDB in recent years, its influence has also been continuously improved. In order to make it easier for domain scientists to make better use of these data, we analyzed the EMDB meta-information structure and developed a visual analytics system, called VASEM, to provide convenient data exploration, searching, and analysis tools. Domain scientists can use our system to interactively filter massive EMDB data into relatively small subset for analysis and obtain subset depiction from visualization results. A modified parallel coordinates plot suitable for large-scale multi-dimensional ranking data visualization is also proposed for EM data subset depiction tasks. We present two usage scenarios to describe how the proposed system achieves the design goals.

Graphic abstract

Keywords

Search visualization Visual analytics Parallel coordinates Electron microscopy metadata 

Notes

Acknowledgements

This work was supported in part by a grant from National Key R&D Program of China (2017YFB0203504), the 13th 5-year Informatization Plan of Chinese Academy of Sciences, Grant No. XXH13504 and Key Research Program of Frontier Sciences, CAS, Grant No. QYZDB-SSW-SMC004-02.

References

  1. Beck F, Koch S, Weiskopf D (2016) Visual analysis and dissemination of scientific literature collections with SurVis. IEEE Trans Vis Comput Graph 22(1):180–189CrossRefGoogle Scholar
  2. Collins C, Viegas FB, Wattenberg M (2009) Parallel tag clouds to explore and analyze faceted text corpora. In: IEEE symposium on visual analytics science and technology, pp 91–98Google Scholar
  3. Dasgupta A, Kosara R (2010) Pargnostics: screen-space metrics for parallel coordinates. IEEE Trans Vis Comput Graph 16(6):1017–1026CrossRefGoogle Scholar
  4. Dörk M, Carpendale MST, Collins C, Williamson C (2008) VisGets: coordinated visualizations for web-based information exploration and discovery. IEEE Trans Vis Comput Graph 14(6):1205–1212CrossRefGoogle Scholar
  5. Esquivel-Rodríguez J, Xiong Y, Han X, Guang S, Christoffer C, Kihara D (2015) Navigating 3D electron microscopy maps with EM-SURFER. BMC Bioinformatics 16(1):181CrossRefGoogle Scholar
  6. Gratzl S, Lex A, Gehlenborg N, Pfister H, Streit M (2013) LineUp: visual analysis of multi-attribute rankings. IEEE Trans Vis Comput Graph 19(12):2277–2286CrossRefGoogle Scholar
  7. Heinrich J, Weiskopf D (2009) Continuous parallel coordinates. IEEE Trans Vis Comput Graph 15(6):1531–1538CrossRefGoogle Scholar
  8. Inselberg A (1985) The plane with parallel coordinates. Vis Comput 1(2):69–91MathSciNetCrossRefzbMATHGoogle Scholar
  9. Inselberg A, Dimsdale B (1990) Parallel coordinates: a tool for visualizing multi-dimensional geometry. Proc First IEEE Conf Vis Vis 90:361–378CrossRefGoogle Scholar
  10. Kinjo AR et al (2012) Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Res 40(Database):D453–D460CrossRefGoogle Scholar
  11. Kinjo AR et al (2017) Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. Nucleic Acids Res 45(Database):D282–D288CrossRefGoogle Scholar
  12. Kosara R, Bendix F, Hauser H (2006) Parallel sets: interactive exploration and visual analysis of categorical data. IEEE Trans Vis Comput Graph 12(4):558–568CrossRefGoogle Scholar
  13. Lagerstedt I et al (2013) Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB. J Struct Biol 184(2):173–181CrossRefGoogle Scholar
  14. Lawson CL, Patwardhan A, Baker ML et al (2016) EMDataBank unified data resource for 3DEM. Nucleic Acids Res 44(D1):D396–D403CrossRefGoogle Scholar
  15. Lekschas F, Gehlenborg N (2018) SATORI: a system for ontology-guided visual exploration of biomedical data repositories. Bioinformatics 34(7):1200–1207CrossRefGoogle Scholar
  16. Li D, Mei H, Shen Y, Su S, Zhang W, Wang J, Chen W (2018) ECharts: a declarative framework for rapid construction of web-based visualization. Vis Inform 2(2):136–146CrossRefGoogle Scholar
  17. Perin C, Boy J, Vernier F (2016) Using gap charts to visualize the temporal evolution of ranks and scores. IEEE Comput Graph Appl 36(5):38–49CrossRefGoogle Scholar
  18. Pirolli P, Stuart C (2005) The sensemaking process and leverage points for analyst technology as identified through cognitive task analysis. In: Proceedings of international conference on intelligence analysisGoogle Scholar
  19. Reiterer H, Tullius G, Mann TM (2005) INSYDER: a content-based visual-information-seeking system for the Web. Int J Digit Libr 5(1):25–41CrossRefGoogle Scholar
  20. Riehmann P, Hanfler M, Froehlich B (2005) Interactive sankey diagrams. In: IEEE symposium on information visualizationGoogle Scholar
  21. Salavert-Torres José, José IudinA, Lagerstedt I et al (2016) Web-based volume slicer for 3D electron-microscopy data from EMDB. J Struct Biol 194(2):164–170CrossRefGoogle Scholar
  22. Shi C, Cui W, Liu S, Xu P, Chen W, Qu H (2012) RankExplorer: visualization of ranking changes in large time series data. IEEE Trans Vis Comput Graph 18(12):2669–2678CrossRefGoogle Scholar
  23. Shneiderman B (1994) Dynamic queries for visual information seeking. IEEE Softw 11(6):70–77CrossRefGoogle Scholar
  24. Shneiderman B (1996) The eyes have it: a task by data type taxonomy for information visualizations. In: Proceedings visual languages. IEEE CS Press, pp 336–343Google Scholar
  25. Tufte ER (2006) Beautiful evidence, vol 1. Graphics Press, CheshireGoogle Scholar
  26. Velankar SS, Best C, Beuth B et al (2010) PDBe: protein data bank in Europe. Nucleic Acids Res 38(Database issue):308–317CrossRefGoogle Scholar
  27. Wang J, Liu X, Shen H-W, Lin G (2017) Multi-resolution climate ensemble parameter analysis with nested parallel coordinates plots. IEEE Trans Vis Comput Graph 23(1):81–90CrossRefGoogle Scholar
  28. Xia J, Hou Y, Chen YV, Qian ZC, Ebert DS, Chen W (2017) Visualizing rank time series of wikipedia top-viewed pages. IEEE Comput Graph Appl 37(2):42–53CrossRefGoogle Scholar
  29. Yang J, Peng W, Ward MO, Rundensteiner EA (2003) Interactive hierarchical dimension ordering, spacing and filtering for exploration of high dimensional datasets. In: Computer Science Faculty publications, pp 105–112Google Scholar
  30. Young JY et al (2017) OneDep: unified wwPDB system for deposition, biocuration, and validation of macromolecular structures in the PDB archive. Structure 25(3):536–545CrossRefGoogle Scholar

Copyright information

© The Visualization Society of Japan 2019

Authors and Affiliations

  1. 1.Computer Network and Information CenterChinese Academy of SciencesBeijingChina
  2. 2.University of Chinese Academy of SciencesBeijingChina

Personalised recommendations