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VASEM: visual analytics system for electron microscopy data bank

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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.

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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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Heinrich J, Weiskopf D (2009) Continuous parallel coordinates. IEEE Trans Vis Comput Graph 15(6):1531–1538

    Article  Google Scholar 

  • Inselberg A (1985) The plane with parallel coordinates. Vis Comput 1(2):69–91

    Article  MathSciNet  Google Scholar 

  • Inselberg A, Dimsdale B (1990) Parallel coordinates: a tool for visualizing multi-dimensional geometry. Proc First IEEE Conf Vis Vis 90:361–378

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Lawson CL, Patwardhan A, Baker ML et al (2016) EMDataBank unified data resource for 3DEM. Nucleic Acids Res 44(D1):D396–D403

    Article  Google Scholar 

  • Lekschas F, Gehlenborg N (2018) SATORI: a system for ontology-guided visual exploration of biomedical data repositories. Bioinformatics 34(7):1200–1207

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Shneiderman B (1994) Dynamic queries for visual information seeking. IEEE Softw 11(6):70–77

    Article  Google Scholar 

  • 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

    Google Scholar 

  • Velankar SS, Best C, Beuth B et al (2010) PDBe: protein data bank in Europe. Nucleic Acids Res 38(Database issue):308–317

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

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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.

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Authors and Affiliations

  1. Computer Network and Information Center, Chinese Academy of Sciences, Beijing, China

    Jun Liu, Yang Gao, Guihua Shan & Xuebin Chi

  2. University of Chinese Academy of Sciences, Beijing, China

    Jun Liu & Xuebin Chi

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  1. Jun Liu
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  2. Yang Gao
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  3. Guihua Shan
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  4. Xuebin Chi
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Correspondence to Xuebin Chi.

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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

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