Restricted Data Terms of Use

Summary

Restricted-Use 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-Use Data as a summary.

Key Points

1. Availability & Usage: Restricted-Use Data is available to all users, on condition of acceptance of the Data Use Terms. By accessing the data in any form, users agree to these terms, which restrict how the data can be used.
2. Duration: Data can be restricted for up to 1 year after submission, as set by the submitter.
3. Onward Submission: When the restricted period ends, the data becomes Open Data and is released on INSDC.
4. Attribution: Data must be attributed according to the requirements detailed below.

Usage Requirements

Unpublished and Un-Preprinted Work

(full terms)

• Restricted-Use Data can be used for unpublished and un-preprinted work (e.g., graphical representations, blog posts, social media, public health and governmental reports, web programs and applications). For web programs and applications, see also Third Party Data Sharing below.
• Data submitters must be acknowledged by providing a list of the accession numbers used or using a SeqSet. If more than 5 sequences are used, creating a SeqSet is highly recommended.
• Work must link back to Pathoplexus for original data and submitters.
• If all sequences are from one institution, the institution and leading author(s) should be credited explicitly.

Publications and Preprints

(full terms)

• Users must divide the sequences they use into a “Focal Set” and a “Background Set” (see below).
• Restricted-Use Data in a Focal Set always requires the consent of the Submitting Group. Restricted-Use Data in a Background Set does not, but its classification as background must be carefully justified (see below and full terms for details).
• Users must create a SeqSet, generate a DOI, and cite it in the References section of the manuscript.

Focal Set Use

• Sequences are part of the Focal Set if they are key to the analysis and its conclusions: they could not be removed, or replaced with a randomly selected similar set, without significantly changing the results. This should be interpreted broadly.
• Sequences are part of the Focal Set if any of the following apply (full terms):
  • Removing them would make the analysis impossible or the result completely different.
  • Replacing them with sequences from another country or time period would make the analysis impossible or completely different.
  • The accessions or sequence names are mentioned explicitly in the manuscript.
  • They are from a specific geographic area that the analysis focuses on (e.g., where a new variant originated or where a mutation of interest is present).
• If Restricted-Use Data is part of the Focal Set, all three of the following are required:
  1. Consent of the Submitting Group, as indicated by either:
     • Inclusion of one or more Submitters as authors on the manuscript, as the result of an agreed collaboration, or
     • Obtaining explicit written permission (“Authorship Waiver”) from the Submitting Group, included with the manuscript as a supplemental document.
  2. A SeqSet containing all Focal Set data from Pathoplexus, with a DOI cited as a reference in the manuscript.
  3. The following statement in the Acknowledgement section of the manuscript: “We confirm that we have adhered to the Data Use Terms of Pathoplexus.”

Background Set Use

• Sequences may be part of the Background Set only if all of the following are true:
  • They could be replaced with other, randomly selected sequences from the entire dataset and the analysis would still be meaningful, with the same result.
  • If sequences from multiple countries or regions are used, any one country or region could be removed without affecting the main results. Any country or region for which this is not true belongs in the Focal Set.
• 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 containing all Background Set data from Pathoplexus, generate a DOI, and cite it in the References section of the manuscript.

If unsure whether data should be in the Focal or Background Set, treat it as part of the Focal Set.

Third Party Data Sharing

(full terms)

When sharing Restricted-Use Data from Pathoplexus onward:

• Clearly communicate the Data Use Terms.
• Keep the Data Use Terms columns (dataUseTerms, dataUseTermsRestrictedUntil and dataUseTermsUrl) intact in the metadata.
• If displayed on a website or in another database, each sequence must have a direct link to the original sequence page on Pathoplexus and display the Pathoplexus accession.
• If re-sharing Pathoplexus data as part of a database with many users, access restrictions may not be imposed

Using All Data

(full terms)

To study overarching sequence properties, such as mutation frequencies, globally or across continents, it is sometimes permissible to use all sequences for a pathogen as a “Background Set”.

• The dataset must contain contributions from a large number of submitting groups.
• The analysis must address only global or international trends, with no specific focus on a country or region (especially one where a virus, variant, strain or clade originated, or where a mutation of interest is only found).
• 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.

During an outbreak, key data may come from a small number of submitting groups and still be Restricted-Use. Such data should be treated as part of the Focal Set, not as background.

Ethical Considerations

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