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. 2019 Apr 15;14(4):e0215531.
doi: 10.1371/journal.pone.0215531. eCollection 2019.

ETDB-Caltech: A blockchain-based distributed public database for electron tomography

Davi R Ortega  1 , Catherine M Oikonomou  1 , H Jane Ding  1 , Prudence Rees-Lee  1 ; Alexandria; Grant J Jensen  1   2
Affiliations

ETDB-Caltech: A blockchain-based distributed public database for electron tomography

Davi R Ortega et al. PLoS One. .

Abstract

Three-dimensional electron microscopy techniques like electron tomography provide valuable insights into cellular structures, and present significant challenges for data storage and dissemination. Here we explored a novel method to publicly release more than 11,000 such datasets, more than 30 TB in total, collected by our group. Our method, based on a peer-to-peer file sharing network built around a blockchain ledger, offers a distributed solution to data storage. In addition, we offer a user-friendly browser-based interface, https://etdb.caltech.edu, for anyone interested to explore and download our data. We discuss the relative advantages and disadvantages of this system and provide tools for other groups to mine our data and/or use the same approach to share their own imaging datasets.

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Conflict of interest statement

Alexandria and its contributors hold various cryptocurrency tokens, including FLO. DRO and Alexandria contributed to FLO blockchain development.

Figures

Fig 1
Fig 1. Information flow in the ETDB-Caltech file-sharing network.
Datasets hosted from a local server are distributed to IPFS, a network of seeding nodes that includes the local server. The associated metadata and locations of the files are recorded in the FLO blockchain using the OIP specification. Users can query this ledger to locate and retrieve desired files from the IPFS.
Fig 2
Fig 2. Sample entry page in the browser-based ETDB-Caltech interface.
A sample electron cryotomography dataset from a Vibrio cholerae cell is shown. An embedded video of the reconstruction appears at left and plays automatically. The metadata is shown at right. Files associated with the dataset are listed at the bottom of the page, where they can be downloaded individually.
Fig 3
Fig 3. Featured Tomograms page of the ETDB-Caltech interface.
Targeting students and others unfamiliar with ET data, the page highlights cellular features of bacteria and archaea visible by cryo-ET. Selecting a category takes the user to a page with a brief description of the structure and a few datasets containing examples.
See this image and copyright information in PMC

References

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