Hello, we are currently in the situation that qzv artifacts are not recogniszed as ‘typical’ formats for supplementary information in microbiologiocal (!) journals. We had already a discussion in this forum last jear, which is closed. Minimum information needed for publication
Some usggestions in that post do not work (a rename to zip does not allow to view the package anymore by view.qiime2.org) or time-consuming; the DOI to a repository would be acceptable.
However, I would prefer to get visualizations accepted as suppl. files, I’m wondering whether you can provide some ‘official’ statement that we can forward to editorial offices to convince them that qzv and qza files are valuable supplementary electronic files in microbiological publications? Or have you ever contacted journals like ‘Applied Microbiology and Biotechnology’?
This is actually something we could fix really easily… My only fear is that q2view will get a surge of normal zip files, but the right answer there is to improve the error messages probably so we don’t get (too many) questions about that.
That would be ideal, but I’m not sure how we would go about doing that @gregcaporaso any thoughts?
For the QIIME 2 paper (just accepted at Nature Biotechnology ) we put all of our relevant .qzv files in one supplementary .zip file. Readers can download and extract that, and then view the contained visualizations at view.qiime2.org. I’d recommend doing that for now (even if you just put one .qzv in the zip). You could describe that as Supplementary QIIME 2 Results, or something along those lines.
@ebolyen and I just chatted in person about allowing .zip files to be viewed at view.qiime2.org (e.g., if you just change the extension from .qzv to .zip). We may end up doing this or something similar (e.g., if you provide a .zip of .qzv files, it will prompt you about which one should be viewed) in the near future, but it’s not something that we could commit to on a timeframe that will work for your paper.
If you wanted to share the QIIME 2 pre-print with the journal to try to use that to convince them to accept .qza or .qzv files as supplements, you could try that. The Online Methods talks a bit about what those files are and why they exist. In my opinion it’s probably a reach right now though. I think any personal statement that I provided about it might be viewed as a little biased…