Terms of use

Phage Annotation Server is a free academic service. By submitting a sequence you agree to the terms below. In short: it is built for research use, you are responsible for complying with the licences of the underlying databases, results are kept for 30 days, and nothing here is validated for clinical use.

1. Intended use

This service is provided for academic and research use. That is what it is designed, resourced and supported for.

We do not impose a blanket ban on commercial use -- but several of the reference databases behind these results are separately licensed, and some of them do restrict commercial use. It is your responsibility to hold whatever licences your intended use requires, directly from those providers. See section 2.

In other words: we are not the licensor of that data and cannot grant you rights to it. If you are unsure whether your use is covered, check with the upstream providers before relying on the results.

2. Third-party tools and databases

This service does not perform annotation of its own. It runs pharokka, phold and phynteny, which in turn draw on a number of separately-licensed reference databases and models. Those licences are set by their own maintainers, not by us, and your use of the results is subject to them.

Two in particular are not fully open source and carry restrictions on commercial use:

• CARD -- the Comprehensive Antibiotic Resistance Database. Antimicrobial-resistance hits in your results derive from CARD. CARD licence terms
• VFDB -- the Virulence Factor Database. Virulence-factor hits in your results derive from VFDB. VFDB terms of use

We deliberately link to those terms rather than paraphrase them: the licence text of record is the maintainers', and it can change. If you intend to use these results commercially, read those terms and obtain the necessary licence directly from the provider. Holding it is what makes such use permissible -- it is your responsibility, not ours, and running a job here does not grant you any right to the underlying data.

If you would rather avoid the restricted databases altogether, note that the antimicrobial-resistance and virulence-factor steps are optional: switching on --skip_extra_annotations under Advanced options produces results without the CARD and VFDB searches.

A full component-by-component list of the tools, databases and models used, with their licences, is on the licences page.

3. How long results are kept

Job inputs and outputs are retained for 30 days from submission, then permanently deleted. This applies to our backups too -- a backup copy is deleted when the job it belongs to expires, so the retention window is a real deletion deadline and not just a display setting.

Download anything you want to keep before then. Your job link will stop working once the job expires, and we cannot recover it afterwards.

Backups exist to protect against hardware failure, not to extend retention. We make no guarantee that a given result will still be retrievable -- treat this service as a compute tool, not as storage of record.

4. What we store

• Your sequence. It is rewritten into a canonical form before any processing touches it; your original contig names are kept only in a small mapping file so they can be displayed back to you.
• Your IP address, for abuse prevention (rate limiting) and internal, non-public usage statistics. It is never published or shared, and is deleted with the job.
• Your email address, only if you choose to supply one, and only to send you your results link. It is never used for anything else and is deleted with the job.

Uploaded sequence data is processed on shared research infrastructure. If your sequences are confidential or subject to a data-sharing agreement that forbids this, run the tools locally instead -- they are all freely installable, and the citations page links to each project.

5. No warranty, and not for clinical use

This service is provided as is, without warranty of any kind. It is a best-effort academic service with no uptime guarantee, and it may be changed, interrupted or withdrawn at any time.

Annotations are predictions. In particular, antimicrobial-resistance and virulence-factor hits are research indicators only. They are not validated for, and must not be used for, clinical, diagnostic, therapeutic or public-health decision-making.

6. Fair use

Submissions are rate-limited per IP address, and inputs are capped by size and contig count. Please don't attempt to circumvent those limits. If you have a genuine need for bulk annotation, install the tools locally -- that will be faster for you and kinder to everyone else sharing this server.

7. Citation

If this service contributed to published work, please cite the underlying tools -- they are the science, this is just a convenient way to run them. See the citations page.

8. Contact

Questions, bug reports and takedown requests: George Bouras, (email address).