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bioRxiv · 10.64898/2025.12.03.691848

Chart Builder: An Interactive Tool for User Driven Data Visualization in the Electron Microscopy Data Bank

Fonseca, N.·Duraisamy, A. K.·Wang, Z.·Somasundharam, S.·Tayebinia, M.·Oliveira, L.·Ma, M.·Turner, J.·Patwardhan, A.·Kleywegt, G. J.·Hartley, M.·Morris, K. L.
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Abstract

The cryogenic sample-electron microscopy (cryoEM) field has generated significant amounts of 3D Electron Microscopy (3DEM) volumetric data and associated metadata, now comprehensively archived in the Electron Microscopy Data Bank (EMDB - www.emdatabank.org) and the Electron Microscopy Public Image Archive (EMPIAR - www.empiar.org). Harnessing the full potential of these resources requires robust, flexible, and publicly accessible tools for data exploration, analysis and retrieval. Here, we present Chart Builder, an interactive web-based platform that enables researchers to create customizable, publication-quality visualizations directly from archival metadata, validation assessments, and cross-reference annotations. Chart Builder integrates the same query-driven and flexible Solr search system as EMDB search, into a user interface with tools to assist users to filter, group, and compare data without programming expertise. It supports multiple chart types (including line, bar, area, scatter (2D and 3D), histogram, bubble, pie, geographic and Venn diagrams) with customizable axes, data series, and statistical operators. Users can apply global filters, define temporal, categorical, or custom query-based axes, and explore multi-dimensional relationships interactively. Chart data-points are linked to their underlying datasets, such that visualisation interaction opens entry-level or archive-level search results for inspection and datasets from charts may be exported in several ways. Findability, accessibility, interoperability and reusability of data are facilitated by these direct access and export mechanisms, including HTML embedding, persistent URL sharing and chart/data download options. By combining interactivity and ease of use with up-to-date access to the EMDB and EMPIAR archive metadata, both computational and experimental communities may explore and visualize current metadata and export to formats for further analysis or as publication-ready figures. Chart Builder promotes community-driven data analysis and empowers users to evaluate trends in the biological 3DEM field. Chart Builder is freely accessible and fully integrated into the EMDB website at https://www.ebi.ac.uk/emdb/statistics/builder/.

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Fonseca, N., Duraisamy, A. K., Wang, Z., Somasundharam, S., Tayebinia, M., Oliveira, L., Ma, M., Turner, J., Patwardhan, A., Kleywegt, G. J., Hartley, M., Morris, K. L.. 2025-12-06. Chart Builder: An Interactive Tool for User Driven Data Visualization in the Electron Microscopy Data Bank. https://doi.org/10.64898/2025.12.03.691848

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