This is a demo instance. You can upload any data you like, including test data to try things out. You can find test data to upload in the example data repository. This instance should not be used for analysis.

Restricted Data Terms of Use

Note

This summary is provided as a general guideline to the Restricted Data Terms of Use, but only the full terms are used to interpret, enforce, and arbitrate. For the full terms, and guidance, see the Data Use Terms document.

Summary

Restricted Data on Pathoplexus is subject to specific use conditions for a limited time period, up to one year after submission. Afterwards the data automatically becomes Open Data. In the following, we state the main Data Use terms for Restricted Data as a summary.

Key Points

  1. Availability & Usage: Restricted Data is freely accessible to all users, but with restrictions on how it can be used.
  2. Duration: Data can be restricted for up to 1 year after submission, as set by the submitter.
  3. Onward Submission: Restricted data is made available on INSDC after the restricted period ends.
  4. Attribution: Data must be attributed according to the requirements detailed below.

Usage Requirements

Unpublished and Un-Preprinted Work

  • Restricted data can be used for unpublished work (e.g., graphical representations, blog posts, reports).
  • Data submitters must be acknowledged by providing accession numbers or using a SeqSet when using restricted data.
  • Work must link back to Pathoplexus for original data and submitters.
  • The institution and leading author(s) need to be credited if all sequences are from one institution.

Publications and Preprints

  • Use of restricted data often requires explicit permission from the Submitting Group.
  • Users must create a SeqSet, generate a DOI, and cite it in the manuscript.
  • Users need to specify the division of sequences into “Focal Set” and “Background Set” (see below, and full terms for details).

Focal Set Use

  • Sequences are part of the focal set if they are key to the analysis being performed: without these sequences the analysis would not be possible
  • Usage requires either:
    1. Including one or more Submitters as an author on the manuscript, or
    2. Obtaining explicit written permission (“Authorship Waiver”) from the Submitting Group.

Background Set Use

  • Sequences are part of the background set if they could be replaced with other sequences with the same analysis outcome
  • The Background set may be used without authorship or waiver, but careful consideration is required to determine if the sequences are background sequences.
  • Users must create a SeqSet, generate a DOI, and cite it in the manuscript.

Third Party Data Sharing

When sharing Restricted Data from Pathoplexus onward:

  • Clearly communicate the Data Use Terms.
  • Keep the Data Use Terms columns intact in the metadata.
  • If displayed publicly, include a direct link to the original sequence page on Pathoplexus.
  • If re-sharing Pathoplexus data as part of a database with many users, access restrictions may not be imposed

Using All Data

To study general viral properties or patterns, such as mutation frequencies, across broad regions or globally, it is sometimes permissible to use all sequences for a pathogen as a “Background Set”.

  • The dataset must contain contributions from many submitting groups
  • Users must create a SeqSet containing all the data, generate a DOI, and cite it in the manuscript.

If only a few submitters have generated sequences for a pathogen, it’s unethical to use all sequences from that pathogen without contacting and involving those submitters.

Ethical Considerations

  • Avoid “scooping” others’ work.
  • Consider involving authors from regions where data originates.
  • Ensure fair representation and genuine collaboration efforts.