Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank

Area of Science:

• Structural Biology
• Biophysics
• Data Science

Background:

• The fields of cryogenic sample-electron microscopy (cryoEM) and 3D Electron Microscopy (3DEM) generate vast amounts of data archived in EMDB and EMPIAR.
• Effective data exploration, analysis, and retrieval tools are crucial for maximizing the utility of these archives.

Purpose of the Study:

• To introduce Chart Builder, an interactive, web-based platform for visualizing cryoEM and 3DEM metadata.
• To provide researchers with a user-friendly tool for creating customizable, publication-quality visualizations from archival data.

Main Methods:

• Chart Builder utilizes a Solr search system for flexible data querying, similar to EMDB search.
• The platform supports various chart types (e.g., scatter, bar, line, Venn diagrams) with customizable axes and statistical operators.
• Interactive filtering, grouping, and comparison of data are enabled without requiring programming expertise.

Main Results:

• Researchers can create diverse, publication-quality visualizations directly from EMDB and EMPIAR metadata.
• Data points in visualizations are linked to underlying datasets, facilitating direct access and inspection.
• Export options include HTML embedding, persistent URLs, and data downloads, enhancing data sharing and reusability.

Conclusions:

• Chart Builder empowers both computational and experimental researchers to explore and visualize 3DEM metadata interactively.
• The platform promotes community-driven data analysis and aids in identifying trends within the biological 3DEM field.
• Freely accessible and integrated into the EMDB website, Chart Builder enhances data findability, accessibility, interoperability, and reusability (FAIR principles).