{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T09:31:18Z","timestamp":1772789478453,"version":"3.50.1"},"reference-count":43,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T00:00:00Z","timestamp":1772755200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100012116","name":"European Bioinformatics Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012116","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["212977\/Z\/18\/Z"],"award-info":[{"award-number":["212977\/Z\/18\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p>\n                    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 -\n                    <jats:ext-link>www.emdatabank.org<\/jats:ext-link>\n                    ) and the Electron Microscopy Public Image Archive (EMPIAR -\n                    <jats:ext-link>www.empiar.org<\/jats:ext-link>\n                    ). 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\n                    <jats:ext-link>https:\/\/www.ebi.ac.uk\/emdb\/statistics\/builder\/<\/jats:ext-link>\n                    .\n                  <\/jats:p>","DOI":"10.3389\/fbinf.2026.1763403","type":"journal-article","created":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T06:43:43Z","timestamp":1772779423000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank"],"prefix":"10.3389","volume":"6","author":[{"given":"Neli","family":"Fonseca","sequence":"first","affiliation":[{"name":"Electron Microscopy Data Bank (EMDB), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)","place":["Cambridgeshire, United Kingdom"]}]},{"given":"Amudha Kumari","family":"Duraisamy","sequence":"additional","affiliation":[{"name":"Electron Microscopy Data Bank (EMDB), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)","place":["Cambridgeshire, United Kingdom"]}]},{"given":"Zhe","family":"Wang","sequence":"additional","affiliation":[{"name":"Electron Microscopy Data Bank (EMDB), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)","place":["Cambridgeshire, United Kingdom"]}]},{"given":"Sriram","family":"Somasundharam","sequence":"additional","affiliation":[{"name":"Electron Microscopy Public Image Archive (EMPIAR), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)","place":["Cambridgeshire, United Kingdom"]}]},{"given":"Minoosadat","family":"Tayebinia","sequence":"additional","affiliation":[{"name":"Electron Microscopy Data Bank (EMDB), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)","place":["Cambridgeshire, United Kingdom"]}]},{"given":"Lucas C.","family":"de Oliveira","sequence":"additional","affiliation":[{"name":"Electron Microscopy Data Bank (EMDB), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)","place":["Cambridgeshire, United Kingdom"]}]},{"given":"Miao","family":"Ma","sequence":"additional","affiliation":[{"name":"Electron Microscopy Data Bank (EMDB), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)","place":["Cambridgeshire, United Kingdom"]}]},{"given":"Jack","family":"Turner","sequence":"additional","affiliation":[{"name":"Electron Microscopy Data Bank (EMDB), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)","place":["Cambridgeshire, United Kingdom"]}]},{"given":"Ardan","family":"Patwardhan","sequence":"additional","affiliation":[{"name":"Cellular Structure and 3D Bioimaging (CS3DB), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)","place":["Cambridgeshire, United Kingdom"]}]},{"given":"Gerard J.","family":"Kleywegt","sequence":"additional","affiliation":[{"name":"Cellular Structure and 3D Bioimaging (CS3DB), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)","place":["Cambridgeshire, United Kingdom"]}]},{"given":"Matthew","family":"Hartley","sequence":"additional","affiliation":[{"name":"Electron Microscopy Public Image Archive (EMPIAR), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)","place":["Cambridgeshire, United Kingdom"]}]},{"given":"Kyle L.","family":"Morris","sequence":"additional","affiliation":[{"name":"Electron Microscopy Data Bank (EMDB), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)","place":["Cambridgeshire, United Kingdom"]}]}],"member":"1965","published-online":{"date-parts":[[2026,3,6]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1107\/s2059798318009324","article-title":"New tools for the analysis and validation of cryo-EM maps and atomic models","volume":"74","author":"Afonine","year":"2018","journal-title":"Acta Crystallogr. D. Struct. Biol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"iyad031","DOI":"10.1093\/genetics\/iyad031","article-title":"The gene ontology knowledgebase in 2023","volume":"224","author":"Aleksander","year":"2023","journal-title":"Genetics"},{"key":"B3","doi-asserted-by":"publisher","first-page":"D376","DOI":"10.1093\/nar\/gkz1064","article-title":"The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures","volume":"48","author":"Andreeva","year":"2020","journal-title":"Nucleic Acids Research"},{"key":"B4","unstructured":"Apache solr\n          \n          \n          2025"},{"key":"B5","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1016\/j.ultramic.2013.06.004","article-title":"High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy","volume":"135","author":"Chen","year":"2013","journal-title":"Ultramicroscopy"},{"key":"B6","unstructured":"Django: the web framework for perfectionists with deadlines\n          \n          \n          2025"},{"key":"B7","doi-asserted-by":"publisher","first-page":"vbaf203","DOI":"10.1093\/bioadv\/vbaf203","article-title":"EMICSS: added-value annotations for EMDB entries","volume":"5","author":"Duraisamy","year":"2025","journal-title":"Bioinforma. Adv."},{"key":"B8","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1087\/20120404","article-title":"ORCID: a system to uniquely identify researchers","volume":"25","author":"Haak","year":"2012","journal-title":"Learn. Publishing"},{"key":"B9","doi-asserted-by":"publisher","first-page":"D1214","DOI":"10.1093\/nar\/gkv1031","article-title":"ChEBI in 2016: improved services and an expanding collection of metabolites","volume":"44","author":"Hastings","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"B10","unstructured":"Highcharts: interactive JavaScript charts\n          \n          \n          2025"},{"key":"B11","doi-asserted-by":"publisher","first-page":"D1503","DOI":"10.1093\/nar\/gkac1062","article-title":"EMPIAR: the electron microscopy public image archive","volume":"51","author":"Iudin","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B12","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1038\/s41586-024-07215-4","article-title":"Automated model building and protein identification in cryo-EM maps","volume":"628","author":"Jamali","year":"2024","journal-title":"Nature"},{"key":"B13","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1016\/j.jsb.2017.05.007","article-title":"Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy","volume":"199","author":"Joseph","year":"2017","journal-title":"J. Structural Biology"},{"key":"B14","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"B15","doi-asserted-by":"publisher","first-page":"D192","DOI":"10.1093\/nar\/gkaa1047","article-title":"Rfam 14: expanded coverage of metagenomic, viral and microRNA families","volume":"49","author":"Kalvari","year":"2021","journal-title":"Nucleic Acids Research"},{"key":"B16","doi-asserted-by":"publisher","first-page":"1216","DOI":"10.1038\/s41592-024-02304-8","article-title":"Data-driven regularization lowers the size barrier of cryo-EM structure determination","volume":"21","author":"Kimanius","year":"2024","journal-title":"Nat. Methods"},{"key":"B17","doi-asserted-by":"publisher","first-page":"D1265","DOI":"10.1093\/nar\/gkad976","article-title":"DrugBank 6.0: the DrugBank knowledgebase for 2024","volume":"52","author":"Knox","year":"2024","journal-title":"Nucleic Acids Research"},{"key":"B18","doi-asserted-by":"crossref","first-page":"1443","DOI":"10.1126\/science.1251652","article-title":"The resolution revolution","volume":"343","author":"K\u00fchlbrandt","year":"2014","journal-title":"Science"},{"key":"B19","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1016\/j.jsb.2013.09.021","article-title":"Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB","volume":"184","author":"Lagerstedt","year":"2013","journal-title":"J. Structural Biology"},{"key":"B20","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1038\/s41592-020-01051-w","article-title":"Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge","volume":"18","author":"Lawson","year":"2021","journal-title":"Nat. Methods"},{"key":"B21","doi-asserted-by":"publisher","first-page":"861","DOI":"10.1107\/S2059798319011471","article-title":"Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix","volume":"75","author":"Liebschner","year":"2019","journal-title":"Biol. Crystallogr."},{"key":"B22","doi-asserted-by":"publisher","first-page":"D479","DOI":"10.1093\/nar\/gku975","article-title":"The complex portal-an encyclopaedia of macromolecular complexes","volume":"43","author":"Meldal","year":"2015","journal-title":"Nucleic Acids Research"},{"key":"B23","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: the protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Research"},{"key":"B24","doi-asserted-by":"publisher","first-page":"e25835","DOI":"10.7554\/eLife.25835","article-title":"Building bridges between cellular and molecular structural biology","volume":"6","author":"Patwardhan","year":"2017","journal-title":"Elife"},{"key":"B25","doi-asserted-by":"publisher","first-page":"D418","DOI":"10.1093\/nar\/gkac993","article-title":"InterPro in 2022","volume":"51","author":"Paysan-Lafosse","year":"2023","journal-title":"Nucleic Acids Research"},{"key":"B26","doi-asserted-by":"publisher","first-page":"D534","DOI":"10.1093\/nar\/gkab988","article-title":"PDBe-KB: collaboratively defining the biological context of structural data","volume":"50","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"B27","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1038\/s41592-020-0731-1","article-title":"Measurement of atom resolvability in cryo-EM maps with Q-scores","volume":"17","author":"Pintilie","year":"2020","journal-title":"Nat. Methods"},{"key":"B28","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nmeth.4169","article-title":"cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination","volume":"14","author":"Punjani","year":"2017","journal-title":"Nat. Methods"},{"key":"B29","article-title":"Research Organization registry","year":"2024","journal-title":"Res. Organ. Registry"},{"key":"B30","doi-asserted-by":"publisher","first-page":"D1668","DOI":"10.1093\/nar\/gkad1085","article-title":"Europe PMC in 2023","volume":"52","author":"Rosonovski","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"B31","doi-asserted-by":"publisher","first-page":"W431","DOI":"10.1093\/nar\/gkab314","article-title":"Mol Viewer: modern web app for 3D visualization and analysis of large biomolecular structures","volume":"49","author":"Sehnal","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"B32","doi-asserted-by":"publisher","first-page":"D266","DOI":"10.1093\/nar\/gkaa1079","article-title":"CATH: increased structural coverage of functional space","volume":"49","author":"Sillitoe","year":"2021","journal-title":"Nucleic Acids Research"},{"key":"B33","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1016\/s0968-0004(02)02176-x","article-title":"New electron microscopy database and deposition system","volume":"27","author":"Tagari","year":"2002","journal-title":"Trends Biochemical Sciences"},{"key":"B34","doi-asserted-by":"publisher","first-page":"D609","DOI":"10.1093\/nar\/gkae1010","article-title":"UniProt: the universal protein knowledgebase in 2025","volume":"53","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"B35","doi-asserted-by":"publisher","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"Varadi","year":"2022","journal-title":"Nucleic Acids Research"},{"key":"B36","doi-asserted-by":"publisher","first-page":"D385","DOI":"10.1093\/nar\/gkv1047","article-title":"PDBe: improved accessibility of macromolecular structure data from PDB and EMDB","volume":"44","author":"Velankar","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"B37","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1107\/S205979832200328X","article-title":"Validation analysis of EMDB entries","volume":"78","author":"Wang","year":"2022","journal-title":"Biol. Crystallogr."},{"key":"B38","doi-asserted-by":"publisher","first-page":"167599","DOI":"10.1016\/j.jmb.2022.167599","article-title":"PDBx\/mmCIF ecosystem: foundational semantic tools for structural biology","volume":"434","author":"Westbrook","year":"2022","journal-title":"J. Molecular Biology"},{"key":"B39","doi-asserted-by":"publisher","first-page":"D520","DOI":"10.1093\/nar\/gky949","article-title":"Protein Data Bank: the single global archive for 3D macromolecular structure data, Nucleic Acids Research","volume":"47","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B40","first-page":"D456","volume-title":"EMDB\u2014The electron microscopy data bank,","year":"2024"},{"key":"B41","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1016\/j.str.2017.01.004","article-title":"OneDep: unified wwPDB system for deposition, biocuration, and validation of macromolecular structures in the PDB archive","volume":"25","author":"Young","year":"2017","journal-title":"Structure"},{"key":"B42","doi-asserted-by":"publisher","first-page":"D1180","DOI":"10.1093\/nar\/gkad1004","article-title":"The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods","volume":"52","author":"Zdrazil","year":"2024","journal-title":"Nucleic Acids Research"},{"key":"B43","doi-asserted-by":"publisher","first-page":"e42166","DOI":"10.7554\/eLife.42166","article-title":"New tools for automated high-resolution cryo-EM structure determination in RELION-3","volume":"7","author":"Zivanov","year":"2018","journal-title":"Elife. Nov."}],"container-title":["Frontiers in Bioinformatics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fbinf.2026.1763403\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T06:43:48Z","timestamp":1772779428000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fbinf.2026.1763403\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,6]]},"references-count":43,"alternative-id":["10.3389\/fbinf.2026.1763403"],"URL":"https:\/\/doi.org\/10.3389\/fbinf.2026.1763403","relation":{},"ISSN":["2673-7647"],"issn-type":[{"value":"2673-7647","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,6]]},"article-number":"1763403"}}