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
Similar content being viewed by others
References
Beck F, Koch S, Weiskopf D (2016) Visual analysis and dissemination of scientific literature collections with SurVis. IEEE Trans Vis Comput Graph 22(1):180–189
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 91–98
Dasgupta A, Kosara R (2010) Pargnostics: screen-space metrics for parallel coordinates. IEEE Trans Vis Comput Graph 16(6):1017–1026
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):1205–1212
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):181
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):2277–2286
Heinrich J, Weiskopf D (2009) Continuous parallel coordinates. IEEE Trans Vis Comput Graph 15(6):1531–1538
Inselberg A (1985) The plane with parallel coordinates. Vis Comput 1(2):69–91
Inselberg A, Dimsdale B (1990) Parallel coordinates: a tool for visualizing multi-dimensional geometry. Proc First IEEE Conf Vis Vis 90:361–378
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–D460
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–D288
Kosara R, Bendix F, Hauser H (2006) Parallel sets: interactive exploration and visual analysis of categorical data. IEEE Trans Vis Comput Graph 12(4):558–568
Lagerstedt I et al (2013) Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB. J Struct Biol 184(2):173–181
Lawson CL, Patwardhan A, Baker ML et al (2016) EMDataBank unified data resource for 3DEM. Nucleic Acids Res 44(D1):D396–D403
Lekschas F, Gehlenborg N (2018) SATORI: a system for ontology-guided visual exploration of biomedical data repositories. Bioinformatics 34(7):1200–1207
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):136–146
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):38–49
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 analysis
Reiterer H, Tullius G, Mann TM (2005) INSYDER: a content-based visual-information-seeking system for the Web. Int J Digit Libr 5(1):25–41
Riehmann P, Hanfler M, Froehlich B (2005) Interactive sankey diagrams. In: IEEE symposium on information visualization
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):164–170
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):2669–2678
Shneiderman B (1994) Dynamic queries for visual information seeking. IEEE Softw 11(6):70–77
Shneiderman B (1996) The eyes have it: a task by data type taxonomy for information visualizations. In: Proceedings visual languages. IEEE CS Press, pp 336–343
Tufte ER (2006) Beautiful evidence, vol 1. Graphics Press, Cheshire
Velankar SS, Best C, Beuth B et al (2010) PDBe: protein data bank in Europe. Nucleic Acids Res 38(Database issue):308–317
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):81–90
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):42–53
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 105–112
Young JY et al (2017) OneDep: unified wwPDB system for deposition, biocuration, and validation of macromolecular structures in the PDB archive. Structure 25(3):536–545
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.
Author information
Authors and Affiliations
Corresponding author
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Liu, J., Gao, Y., Shan, G. et al. VASEM: visual analytics system for electron microscopy data bank. J Vis 22, 1145–1159 (2019). https://doi.org/10.1007/s12650-019-00597-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12650-019-00597-y