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In developing this portal, we worked closely with the developers and supporters of EMPIAR (https://empiar.org), a public archive for electron microscopy images at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI)4,5. EMPIAR already provides annotated cryoET data, but without a standardized format; developed and adopted annotations are in a wide variety of formats with varying forms and completeness of metadata.

在开发这个门户时，我们与EMPIAR的开发人员和支持者密切合作(https://empiar.org)，欧洲分子生物学实验室欧洲生物信息学研究所（EMBL-EBI）4,5的电子显微镜图像公共档案。EMPIAR已经提供了带注释的cryoET数据，但没有标准化的格式；开发和采用的注释格式多种多样，元数据的形式和完整性各不相同。

This lack of uniformity makes it challenging for someone without deep domain expertise to easily make use of the annotations to develop new algorithms to replace manual labeling and speed the scientific process. Following discussions at a recent joint EBI/CZ Imaging Institute workshop (April 2024), a working group will be established to suggest and recommend formatting and metadata standards for cryoET, with the goal of delivering recommendations to the scientific and instrumentation communities, software developers and archives.The cryoET Data Portal currently provides over 15,000 tomograms, along with partial annotations, from ~300 datasets representing ~40 species, contributed by the groups of Julia Mahamid, Jürgen Plitzko, David Agard, John Briggs, Abhay Kotecha, Ben Engel, Danielle Grotjahn, Grant Jensen (data from the former Electron Tomography Database6), Ellen Zhong and Tristan Bepler.

这种缺乏统一性使得没有深层领域专业知识的人很难轻松地利用注释来开发新算法来取代手动标记并加快科学过程。在最近的EBI/CZ成像研究所联合研讨会（2024年4月）上进行讨论后，将成立一个工作组，为cryoET提出格式和元数据标准的建议和建议，目标是向科学和仪器界、软件开发人员和档案馆提供建议。cryoET数据门户目前提供了超过15000张断层图，以及来自约300个代表约40个物种的数据集的部分注释，这些数据集由Julia Mahamid，Jürgen Plitzko，David Agard，John Briggs，Abhay Kotecha，Ben Engel，Danielle Grotjahn，Grant Jensen（来自前电子断层扫描数据库6的数据），Ellen Zhong和Tristan Bepler小组贡献。

All data, including annotations, are published with a CC0 license, meaning they are available in the public domain for other researchers to freely download, share and use for their work..

所有数据，包括注释，都是通过CC0许可证发布的，这意味着其他研究人员可以在公共领域免费下载，共享和使用它们的工作。。

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Access Nature and 54 other Nature Portfolio journalsGet Nature+, our best-value online-access subscription24,99 € / 30 dayscancel any timeLearn moreSubscription info for Chinese customersWe have a dedicated website for our Chinese customers. Please go to naturechina.com to subscribe to this journal.Go to naturechina.comBuy this articlePurchase on SpringerLinkInstant access to full article PDFBuy nowPrices may be subject to local taxes which are calculated during checkout.

Access Nature和54篇其他Nature Portfolio journalsGet Nature+，我们最有价值的在线订阅24,99欧元/30天，随时为中国客户获取更多订阅信息我们为中国客户提供了一个专门的网站。请访问naturechina.com订阅本期刊。访问naturechina.comBuy本文在Springerlink上购买即时访问完整文章PDFBuy Now价格可能需要缴纳结帐时计算的地方税。

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Fig. 1: cryoET Data Portal web interface.

图1:cryoET数据门户网站界面。

Data availability

数据可用性

No new data were collected as part of this study, but all data stored on the portal are accessible under CC0 (public domain) license at https://cryoetdataportal.czscience.com/.

作为这项研究的一部分，没有收集到新的数据，但门户网站上存储的所有数据都可以通过CC0（公共领域）许可证访问https://cryoetdataportal.czscience.com/.

Code availability

代码可用性

The source code11 for the cryoET data portal web front end and GraphQL API is made available under the open source MIT license and available online at https://github.com/chanzuckerberg/cryoet-data-portal. The source code11 for data ingestion, standardization and the cryoET data portal back-end infrastructure is made available under the open source MIT license and available online at https://github.com/chanzuckerberg/cryoet-data-portal-backend.

cryoET数据门户网站前端和GraphQL API的源代码11已获得麻省理工学院的开源许可，可在https://github.com/chanzuckerberg/cryoet-data-portal.数据摄取、标准化和cryoET数据门户后端基础设施的源代码11是根据麻省理工学院的开源许可证提供的，可在https://github.com/chanzuckerberg/cryoet-data-portal-backend.

The source code11 for the cryoET data portal napari plug-in is available under the open source MIT license and available online at https://github.com/chanzuckerberg/napari-cryoet-data-portal..

cryoET数据门户napari插件的源代码11可在麻省理工学院的开源许可下获得，并可在https://github.com/chanzuckerberg/napari-cryoet-data-portal..

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We thank N. Sofroniew for initial consulting, D. Li and A. Burt for input on the data schema and conventions, C. Chui for help regarding napari integration and I. Riezler, L. Duran and S. Yammine for comments on the manuscript. CZ Imaging Institute is made possible with support from the Chan Zuckerberg Initiative (CZII-2023–327779).Author informationAuthor notesThese authors contributed equally: Utz Ermel, Anchi Cheng.Authors and AffiliationsChan Zuckerberg Institute for Advanced Biological Imaging (CZ Imaging Institute), Redwood City, CA, USAUtz Ermel, Anchi Cheng & Bridget CarragherChan Zuckerberg Initiative (CZI), Redwood City, CA, USAJun Xi Ni, Jessica Gadling, Manasa Venkatakrishnan, Kira Evans, Jeremy Asuncion, Andrew Sweet, Janeece Pourroy, Zun Shi Wang, Kandarp Khandwala, Benjamin Nelson, Dannielle McCarthy, Eric M.

我们感谢N.Sofroniew的初步咨询，D.Li和A.Burt对数据模式和约定的投入，C.Chui对napari集成的帮助以及I.Riezler，L.Duran和S.Yammine对手稿的评论。在Chan Zuckerberg倡议（CZII-2023–327779）的支持下，CZ成像研究所成为可能。作者信息作者注意到这些作者做出了同样的贡献：Utz Ermel，Anchi Cheng。作者和附属机构加利福尼亚州红木市桑扎克伯格高级生物成像研究所（CZ成像研究所），USAUtz Ermel，Anchi Cheng＆Bridget CarragherChan Zuckerberg Initiative（CZI），加利福尼亚州红木市，USAJun Xi Ni，杰西卡·加德林，马纳萨·文卡塔克里希南，基拉·埃文斯，杰里米·亚松森，安德鲁·斯威特，珍妮卡·波里，Zun Shi Wang，坎达普·坎德瓦拉，本杰明·尼尔森，丹妮尔·麦卡锡，埃里克·M。

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PubMed Google ScholarContributionsB.C. and A.C. conceptualized the project. B.C., A.C. and U.H.E. supervised design and development. J.P. and Z.S.W. carried out web front end design. K.E. and J.A. implemented the web front end. J.G. and M.V. implemented the data portal back end, with contributions from U.H.E.

PubMed谷歌学术贡献b。C、 A.C.对该项目进行了概念化。B、 C.，A.C.和U.H.E.监督设计和开发。J、 P.和Z.S.W.进行了web前端设计。K、 E.和J.A.实现了web前端。J、 G.和M.V.在U.H.E.的贡献下实施了数据门户后端。

and A.C. A.S. developed the napari-plugin. D.M. provided documentation. U.H.E. and A.C. performed data curation and validation. J.X.N., E.M.W. and R.A. provided project management support. K.K. carried out user experience research. B.N. performed web analytics. A.C., B.C. and U.H.E. wrote the manuscript.

A.C.A.S.开发了napari插件。D、 M.提供的文件。U、 H.E.和A.C.进行了数据管理和验证。J、 X.N.，E.M.W.和R.A.提供了项目管理支持。K、 K.进行了用户体验研究。B、 N.进行网络分析。A、 C.，B.C.和U.H.E.撰写了手稿。

U.H.E. prepared figures. E.M.W., D.M., J.X.N. and K.K. edited the manuscript.Corresponding authorCorrespondence to.

U、 H.E.准备好的数字。E、 M.W.，D.M.，J.X.N.和K.K.编辑了手稿。对应作者对应。

Bridget Carragher.Ethics declarations

布里奇特·卡拉格。道德宣言

Competing interests

相互竞争的利益

The authors declare no competing interests.

作者声明没有利益冲突。

Peer review

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Peer review information

同行评审信息

Nature Methods thanks Benjamin Barad and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

《自然方法》感谢本杰明·巴拉德（Benjamin Barad）和另一位匿名审稿人对这项工作的同行评审做出的贡献。

Rights and permissionsReprints and permissionsAbout this articleCite this articleErmel, U., Cheng, A., Ni, J.X. et al. A data portal for providing standardized annotations for cryo-electron tomography.

权利和许可打印和许可本文引用本文Ermel，U.，Cheng，A.，Ni，J.X。等人。一个为低温电子断层扫描提供标准化注释的数据门户。

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