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Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank
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DOI：10.3389/fbinf.2026.1763403.png)
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Abstract
En 中文
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:
data visualization
data repository
graph
cryoEM (cryo-electron microscopy)
FAIR (findable accessible interoperable andreusable) principles
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