The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Chart Builder: An Interactive Tool for User Driven Data Visualization in the Electron Microscopy Data Bank
Open accessPreprint — published as 10.3389/fbinf.2026.1763403 · Paper page
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/ .
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Flagged first, then by citations
Research works printed but not linked: 36
- 10.1107/s2059798318009324 · DOI
- 10.1093/genetics/iyad031 · DOI
- 10.1093/nar/gkz1064 · DOI
- 10.1016/j.ultramic.2013.06.004 · DOI
- 2025, EMICSS: Added-value annotations for EMDB entries, Bioinformatics Advances, 5, vbaf203
- 2012, ORCID: a system to uniquely identify researchers, Learned publishing, 25, 259, 10.1087/20120404 · DOI
- 10.1093/nar/gkv1031 · DOI · Paper page
- 10.1093/nar/gkac1062 · DOI
- 10.1038/s41586-024-07215-4 · DOI · Paper page
- 10.1016/j.jsb.2017.05.007 · DOI
- 10.1093/NAR/GKAA1047 · DOI
- 10.1016/j.jsb.2013.09.021 · DOI
- 2021, Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge, Nature methods, 18, 156, 10.1038/s41592-020-01051-w · DOI
- 2019, Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix, Biological Crystallography, 75, 861
- 2024, Data-driven regularization lowers the size barrier of cryo-EM structure determination, Nature Methods, 21, 1216, 10.1038/s41592-024-02304-8 · DOI
- 10.1093/nar/gkad976 · DOI
- 10.1126/science.1251652 · DOI · Paper page
- 10.1093/nar/gku975 · DOI
- 10.1093/NAR/GKAA913 · DOI · Paper page
- 10.7554/eLife.25835 · DOI
- 10.1093/NAR/GKAC993 · DOI
- 10.1093/nar/gkab988 · DOI · Paper page
- 2020, Measurement of atom resolvability in cryo-EM maps with Q-scores, Nature methods, 17, 328, 10.1038/s41592-020-0731-1 · DOI
- 10.1093/nar/gkad1085 · DOI
- 10.1093/nar/gkab314 · DOI · Paper page
- 10.1093/nar/gkaa1079 · DOI · Paper page
- 10.1016/S0968-0004(02)02176-X · DOI
- 10.1093/nar/gkae1010 · DOI · Paper page
- 10.1093/NAR/GKAB1061 · DOI · Paper page
- 10.1093/nar/gkv1047 · DOI
- 2022, Validation analysis of EMDB entries, Biological Crystallography, 78, 542
- 10.1016/j.jmb.2022.167599 · DOI
- 10.1093/nar/gkad1019 · DOI
- 10.1093/nar/gky949 · DOI · Paper page
- 10.1016/j.str.2017.01.004 · DOI
- 10.1093/nar/gkad1004 · DOI
Metadata
- Authors
- Fonseca, N., Duraisamy, A. K., Wang, Z., Somasundharam, S., Tayebinia, M., de Oliveira, L. C., Ma, M., Turner, J., Patwardhan, A., Kleywegt, G. J., Hartley, M., & Morris, K. L.
- Affiliations
- European Bioinformatics Institute (GB)
- Corresponding author
- Morris, Kyle L.
- ORCID
- Venue
- Frontiers in Bioinformatics
- Publisher
- openRxiv
- Published
- 2025-12-06
- Volume
- 6
- Pages
- 1763403-1763403
- ISSN
- 2673-7647 (ISSN-L)
- PMC
- PMC13002805
- OpenAlex
- W7134047437
- Cited by
- 0
- References
- 1
- FWCI
- 0.00
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Bioinformatics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Wellcome Trust (212977/Z/18/Z)
- European Bioinformatics Institute
- European Molecular Biology Laboratory
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Physical Sciences › Computer Science › Computer Graphics and Computer-Aided Design › Data Visualization and Analytics
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Keywords
- EMPIAR, 3D electron microscopy, data visualization, interactive web tool, data archiving, publication-quality figures, data reusability, data interoperability
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
