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

doi:10.3389/fbinf.2026.1763403

2026-03-06

Neli Fonseca

Amudha Kumari Duraisamy

Zhe Wang

Sriram Somasundharam

Minoosadat Tayebinia

Lucas Carrijo de Oliveira

DOI：10.3389/fbinf.2026.1763403

原文链接

查看原文

摘要

En 中文

低温样本电子显微镜（cryoEM）领域已经产生了大量的三维电子显微镜（3DEM）体数据及相关的元数据；这些数据现已全面存档于电子显微镜数据库（EMDB - www.emdatabank.org）和电子显微镜公共图像档案库（EMPIAR - www.empiar.org）。要充分利用这些资源，需要稳健、灵活且公开可用的工具来进行数据探索、分析和检索。在此，我们介绍Chart Builder，这是一个交互式网络平台，允许研究人员直接从存档元数据、验证评估和交叉引用注释中创建可定制、具备出版质量的可视化图表。Chart Builder集成了与EMDB搜索相同的基于查询驱动且灵活的Solr搜索系统，并将其整合到一个具有辅助用户筛选、分组和比较数据工具的用户界面中，无需编程专业知识。它支持多种图表类型（包括线图、条形图、面积图、散点图（2D和3D）、直方图、气泡图、饼图、地理图和维恩图），并支持可定制的坐标轴、数据序列和统计运算符。用户可以应用全局筛选器，定义时间、类别或基于自定义查询的坐标轴，并交互式地探索多维关系。图表数据点与其基础数据集相关联，因此可视化交互可以打开入门级或存档级的搜索结果以供检查，并且可以从图表中通过多种方式导出数据集。通过这些直接访问和导出机制，包括HTML嵌入、持久URL共享和图表/数据下载选项，数据的可发现性、可访问性、互操作性和可重用性得到促进。通过结合交互性和易用性，以及及时访问EMDB和EMPIAR存档元数据，计算和实验社区可以探索和可视化当前元数据，并将其导出为用于进一步分析或作为出版级图形的格式。Chart Builder促进社区驱动的数据分析，并使用户能够评估生物3DEM领域的趋势。Chart Builder免费访问，并完全集成在EMDB网站（https://www.ebi.ac.uk/emdb/statistics/builder/）中。

Keyword:

data visualization

data repository

graph

cryoEM (cryo-electron microscopy)

FAIR (findable accessible interoperable andreusable) principles

AI总结

对已上传原文的论文进行重点信息的提取，主要内容包括：简要概述、研究摘要、背景介绍、关键亮点、图文解析、展望与总结。

期刊

Frontiers in Bioinformatics

IF:

3.9

论文数:

448

被引数:

1.0K

机构

emdb

学者数:

论文数: 1

被引数: 0

EMPIAR

学者数:

论文数: 1

被引数: 0

csdb

学者数:

论文数: 1

被引数: 0

查看更多机构

引用论文

Data-driven regularization lowers the size barrier of cryo-EM structure determination

NATURE METHODS

IF32.1

2024-06-11

OAAI

Kimanius, Dari; Jamali, Kiarash; Wilkinson, Max E.; Lovestam, Sofia; Velazhahan, Vaithish; Nakane, Takanori; Scheres, Sjors H. W.

Rfam 14: expanded coverage of metagenomic, viral and microRNA families

NUCLEIC ACIDS RESEARCH

IF13.1

2020-11-19

519

OAAI

Kalvari, Ioanna; Nawrocki, Eric P.; Ontiveros-Palacios, Nancy; Argasinska, Joanna; Lamkiewicz, Kevin; Marz, Manja; Griffiths-Jones, Sam; Toffano-Nioche, Claire; Gautheret, Daniel; Weinberg, Zasha; Rivas, Elena; Eddy, Sean R.; Finn, Robert D.; Bateman, Alex; Petrov, Anton, I

EMICSS: added-value annotations for EMDB entries EMICSS：为EMDB条目添加增值注释

Bioinformatics Advances

IF0

2024-12-26

PREAI

Duraisamy,Amudha Kumari; Fonseca,Neli; Kleywegt,Gerard J; Patwardhan,Ardan; Morris,Kyle L

New tools for the analysis and validation of cryo-EM maps and atomic models 用于分析和验证cryo-em图和原子模型的新工具

Acta Crystallographica Section D Structural Biology

IF0

2018-09-03

OAAI

Pavel V. Afonine; Bruno P. Klaholz; Nigel W. Moriarty; Billy K. Poon; Oleg V. Sobolev; Thomas C. Terwilliger; Paul D. Adams; Alexandre Urzhumtsev

UniProt: the Universal Protein Knowledgebase in 2025 UniProt: 通用蛋白质知识库2025年

Nucleic Acids Research

IF0

2024-11-18

OAAI

Alex Bateman; Maria-Jesus Martin; Sandra Orchard; Michele Magrane; Aduragbemi Adesina; Shadab Ahmad; Emily H Bowler-Barnett; Hema Bye-A-Jee; David Carpentier; Paul Denny; Jun Fan; Penelope Garmiri; Leonardo Jose da Costa Gonzales; Abdulrahman Hussein; Alexandr Ignatchenko; Giuseppe Insana; Rizwan Ishtiaq; Vishal Joshi; Dushyanth Jyothi; Swaathi Kandasaamy; Antonia Lock; Aurelien Luciani; Jie Luo; Yvonne Lussi; Juan Sebastian Martinez Marin; Pedro Raposo; Daniel L Rice; Rafael Santos; Elena Speretta; James Stephenson; Prabhat Totoo; Nidhi Tyagi; Nadya Urakova; Preethi Vasudev; Kate Warner; Supun Wijerathne; Conny Wing-Heng Yu; Rossana Zaru; Alan J Bridge; Lucila Aimo; Ghislaine Argoud-Puy; Andrea H Auchincloss; Kristian B Axelsen; Parit Bansal; Delphine Baratin; Teresa M Batista Neto; Marie-Claude Blatter; Jerven T Bolleman; Emmanuel Boutet; Lionel Breuza; Blanca Cabrera Gil; Cristina Casals-Casas; Kamal Chikh Echioukh; Elisabeth Coudert; Beatrice Cuche; Edouard de Castro; Anne Estreicher; Maria L Famiglietti; Marc Feuermann; Elisabeth Gasteiger; Pascale Gaudet; Sebastien Gehant; Vivienne Gerritsen; Arnaud Gos; Nadine Gruaz; Chantal Hulo; Nevila Hyka-Nouspikel; Florence Jungo; Arnaud Kerhornou; Philippe Le Mercier; Damien Lieberherr; Patrick Masson; Anne Morgat; Salvo Paesano; Ivo Pedruzzi; Sandrine Pilbout; Lucille Pourcel; Sylvain Poux; Monica Pozzato; Manuela Pruess; Nicole Redaschi; Catherine Rivoire; Christian J A Sigrist; Karin Sonesson; Shyamala Sundaram; Anastasia Sveshnikova; Cathy H Wu; Cecilia N Arighi; Chuming Chen; Yongxing Chen; Hongzhan Huang; Kati Laiho; Minna Lehvaslaiho; Peter McGarvey; Darren A Natale; Karen Ross; C R Vinayaka; Yuqi Wang; Jian Zhang

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures Mol * Viewer: 用于3D可视化和分析大型生物分子结构的现代web应用程序

NUCLEIC ACIDS RESEARCH

IF13.1

2021-05-06

587

OAAI

Sehnal, David; Bittrich, Sebastian; Deshpande, Mandar; Svobodova, Radka; Berka, Karel; Bazgier, Vaclav; Velankar, Sameer; Burley, Stephen K.; Koca, Jaroslav; Rose, Alexander S.

InterPro in 2022 InterPro 2022年

NUCLEIC ACIDS RESEARCH

IF13.1

2022-11-09

1.1K

OAAI

Paysan-Lafosse, Typhaine; Blum, Matthias; Chuguransky, Sara; Grego, Tiago; Pinto, Beatriz Lazaro; Salazar, Gustavo A.; Bileschi, Maxwell L.; Bork, Peer; Bridge, Alan; Colwell, Lucy; Gough, Julian; Haft, Daniel H.; Letunic, Ivica; Marchler-Bauer, Aron; Mi, Huaiyu; Natale, Darren A.; Orengo, Christine A.; Pandurangan, Arun P.; Rivoire, Catherine; Sigrist, Christian J. A.; Sillitoe, Ian; Thanki, Narmada; Thomas, Paul D.; Tosatto, Silvio C. E.; Wu, Cathy H.; Bateman, Alex

DrugBank 6.0: the DrugBank Knowledgebase for 2024 DrugBank 6.0: 2024的DrugBank知识库

NUCLEIC ACIDS RESEARCH

IF13.1

2023-11-11

157

OAAI

Knox, Craig; Wilson, Mike; Klinger, Christen M.; Franklin, Mark; Oler, Eponine; Wilson, Alex; Pon, Allison; Cox, Jordan; Chin, Na Eun (Lucy); Strawbridge, Seth A.; Garcia-Patino, Marysol; Kruger, Ray; Sivakumaran, Aadhavya; Sanford, Selena; Doshi, Rahil; Khetarpal, Nitya; Fatokun, Omolola; Doucet, Daphnee; Zubkowski, Ashley; Rayat, Dorsa Yahya; Jackson, Hayley; Harford, Karxena; Anjum, Afia; Zakir, Mahi; Wang, Fei; Tian, Siyang; Lee, Brian; Liigand, Jaanus; Peters, Harrison; Wang, Ruo Qi (Rachel); Nguyen, Tue; So, Denise; Sharp, Matthew; da Silva, Rodolfo; Gabriel, Cyrella; Scantlebury, Joshua; Jasinski, Marissa; Ackerman, David; Jewison, Timothy; Sajed, Tanvir; Gautam, Vasuk; Wishart, David S.

The complex portal - an encyclopaedia of macromolecular complexes

NUCLEIC ACIDS RESEARCH

IF13.1

2014-10-13

OAAI

Meldal, Birgit H. M.; Forner-Martinez, Oscar; Costanzo, Maria C.; Dana, Jose; Demeter, Janos; Dumousseau, Marine; Dwight, Selina S.; Gaulton, Anna; Licata, Luana; Melidoni, Anna N.; Ricard-Blum, Sylvie; Roechert, Bernd; Skyzypek, Marek S.; Tiwari, Manu; Velankar, Sameer; Wong, Edith D.; Hermjakob, Henning; Orchard, Sandra

Cutting edge:: Building bridges between cellular and molecular structural biology

ELIFE

IF0

2017-07-06

OAAI

Patwardhan, Ardan; Brandt, Robert; Butcher, Sarah J.; Collinson, Lucy; Gault, David; Grunewald, Kay; Hecksel, Corey; Huiskonen, Juha T.; Iudin, Andrii; Jones, Martin L.; Korir, Paul K.; Koster, Abraham J.; Lagerstedt, Ingvar; Lawson, Catherine L.; Mastronarde, David; McCormick, Matthew; Parkinson, Helen; Rosenthal, Peter B.; Saalfeld, Stephan; Saibil, Helen R.; Sarntivijai, Sirarat; Valero, Irene Solanes; Subramaniam, Sriram; Swedlow, Jason R.; Tudose, Ilinca; Winn, Martyn; Kleywegt, Gerard J.

查看更多内容