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Zenodo Community Setup

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This guide covers setting up the TSL Structures community on Zenodo and adding datasets to it. Community setup is typically a one-time task, but this reference documents the process.

Overview

Zenodo communities provide a curated collection where users can discover all TSL structure datasets in one place. The tslstructures R package queries this community via list_datasets().

User runs list_datasets()
        ↓
Queries Zenodo API: /communities/tsl-structures/records
        ↓
Returns all datasets in the community

Creating the Community (One-Time)

Note: This only needs to be done once per Zenodo environment (sandbox and production are separate).

Sandbox (Testing)

  1. Go to https://sandbox.zenodo.org and log in (create account if needed - separate from production)
  2. Navigate to Communities → New Community (or go directly to https://sandbox.zenodo.org/communities/new)
  3. Fill in the form:
Field Value
Identifier tsl-structures (must match R package default)
Title TSL Structure Datasets
Description Protein structure prediction datasets from The Sainsbury Laboratory. Distributed in TSP (TSL Structure Package) format for use with the tslstructures R package.
  1. Click Create

Production

Same steps at https://zenodo.org. Use identical identifier (tsl-structures) so the R package works without configuration.

Adding a Dataset to the Community

After uploading a dataset to Zenodo, submit it to the community for inclusion.

Method 1: From Record Page (Existing Records)

  1. Go to your record page (e.g., https://sandbox.zenodo.org/records/415123)
  2. Click the cog-wheel icon (⚙️) near the top of the page
  3. Select "Submit to community" from the dropdown
  4. Search for tsl-structures and click "Select"
  5. Optionally add a message to curators
  6. Click "Submit to community"

If you're the community owner, the submission auto-approves. Otherwise, a curator must approve it.

Method 2: During Upload (New Records)

When creating a new upload on Zenodo:

  1. In the upload form, find the Community section
  2. Click "Select a community"
  3. Search for tsl-structures and select it
  4. Complete the upload and publish

The record will be submitted to the community upon publication.

Approving Submissions (For Curators)

If you're a community curator/owner:

  1. Go to your community page (e.g., https://sandbox.zenodo.org/communities/tsl-structures)
  2. Click "Requests" or "Review submissions"
  3. Review pending submissions
  4. Click "Accept" to add the record to the community

Verifying the Setup

Test that discovery works in R:

library(tslstructures)

# List datasets in sandbox community
list_datasets(sandbox = TRUE)
#> # A tibble: 1 x 6
#>   record_id title                   doi                   version created description
#>   <chr>     <chr>                   <chr>                 <chr>   <chr>   <chr>
#> 1 415123    TSL Test Structure Da…
 10.5072/zenodo.415123 1.0.0   2024-…  Test dataset...

# Get details on a specific dataset
dataset_info(415123, sandbox = TRUE)

Troubleshooting

"Community not found" message

list_datasets(sandbox = TRUE)
#> ! Community 'tsl-structures' not found

The community hasn't been created yet, or the identifier doesn't match. Create the community with identifier tsl-structures.

Dataset not appearing in list

  • Check the submission was approved (see curator requests)
  • Verify you submitted to the correct community
  • Try refresh = TRUE: list_datasets(sandbox = TRUE, refresh = TRUE)

Sandbox vs Production confusion

Sandbox (https://sandbox.zenodo.org) and production (https://zenodo.org) are completely separate: - Separate user accounts - Separate communities - Separate records - Sandbox DOIs use prefix 10.5072, production uses 10.5281