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A data portal for providing standardized annotations for cryo-electron tomography

Nature Methods volume 21, pages 2200–2202 (2024)Cite this article

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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. 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. 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.

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Fig. 1: cryoET Data Portal web interface.

Data availability

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/.

Code availability

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. 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.

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Acknowledgements

We thank the Chan Zuckerberg Initiative Central Tech and Chan Zuckerberg Biohub Network IT teams for technical support. We thank D. Agard, B. Barad, F. Bec, J. Briggs, Z. Chen, J. Ding, B. Engel, R. Feathers, S. Goetz, D. Grotjahn, G. Hart, G. Jensen, M. Kaplan, Z. Ke, S. Khavnekar, A. Kotecha, J. Liu, J. Mahamid, M. Medina, J. Plitzko, R. Righetto, K. Sochacki, M. Swulius, L. Xue, H. Yu, and E. Zhong for generously providing the first datasets available on the cryoET Data Portal. 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).

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  1. These authors contributed equally: Utz Ermel, Anchi Cheng.

Authors and Affiliations

  1. Chan Zuckerberg Institute for Advanced Biological Imaging (CZ Imaging Institute), Redwood City, CA, USA

    Utz Ermel, Anchi Cheng & Bridget Carragher

  2. Chan Zuckerberg Initiative (CZI), Redwood City, CA, USA

    Jun 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. Wang & Richa Agarwal

Authors
  1. Utz Ermel
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  16. Bridget Carragher
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Contributions

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

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Correspondence to Bridget Carragher.

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

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Ermel, U., Cheng, A., Ni, J.X. et al. A data portal for providing standardized annotations for cryo-electron tomography. Nat Methods 21, 2200–2202 (2024). https://doi.org/10.1038/s41592-024-02477-2

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