TECHNOLOGY AND CODE article
Front. Bioinform.
Sec. Data Visualization
This article is part of the Research Topic15th International Meeting on Visualizing Biological Data (VIZBI 2025)View all 4 articles
Chart Builder: An Interactive Tool for User Driven Data Visualization in the Electron Microscopy Data Bank
Provisionally accepted
Neli José Da Fonseca Júnior
Amudha Kumari DuraisamyZhe WangSriram SomasundharamMinoosadat TayebiniaLucas C. de OliveiraMiao Ma
Jack Turner
Ardan PatwardhanGerard J. Kleywegt
Matthew Hartley
Kyle L Morris*- European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
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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/.
Keywords: cryoEM (cryo-electron microscopy), data repository, data visualization, FAIR (findable accessible interoperable andreusable) principles, graph
Received: 08 Dec 2025; Accepted: 28 Jan 2026.
Copyright: © 2026 Da Fonseca Júnior, Duraisamy, Wang, Somasundharam, Tayebinia, de Oliveira, Ma, Turner, Patwardhan, Kleywegt, Hartley and Morris. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Kyle L Morris
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