This is just a quick guide explaining how to move your references from Paperpile to Zotero. They’re both great reference managers with different pros and cons (which I’ll leave for another blog post).
This guide will show you how to move your PDFs, with their annotations, as well as your folders and tags.
Organize your Paperpile files. In Paperpile, click on the gear icon in the upper right and then click Settings. Select Storage & Sync and then click Configure under Google Drive. Speciy that the files should be organized by Author and toggle on the three options below. Click Apply changes, wait a bit, and then check on Google Drive that your files are now organized by author. (I found that skipping this step resulted in missing PDFs in Zotero. I’m not totally sure why, but I think this was because I had previously organized my files by my folder structure, and each file could exist in multiple locations.)
Download your Paperpile files. Download the folder in Google Drive that contains all of your papers.
Download your Paperpile metadata. In Paperpile, click on the gear icon in the upper right and then click Settings. Select Export and then click Export to RIS. Save this file at the same level as the folder you downloaded above (not inside that folder but at the same level). Your file structure should look something like this:
My Paperpile Papers
/ Paperpile - Apr 10 RIS Export.ris
/ All Papers
/ A
/ B
/ C
/ ...
In Zotero, select My Library at the top of your folder structure on the left. Then from the top menu, click File and then Import. Toggle A file… and then select the RIS file you saved above. In the following options screen, toggle on the first two options (Place imported collections… and Copy files to…).
That’s it! It will take a little while to import if you have a large library, but you should soon see your formatted references along with PDF icons indicating that the PDF was identified and linked.
In the end, folders are saved as tags for me, which I don’t really mind. But it would be nice if the Paperpile folders appeared as Zotero folders, so tips are welcome.
One unanswered question is how to do all of this without creating any “automatic tags” in Zotero. I don’t know the story behind these tags, but they definitely come from Zotero, not from Paperpile, and I can’t imagine they’re useful for anyone. Isn’t the whole point of tags their customization? Frustratingly, I can’t find a way to prevent the creation of these automatic tags in the hundreds (even when I’ve deselected them in Zotero’s preferences), and there’s no way to bulk delete them once they exist. If anyone knows of a solution, I’d love to hear.
April 11, 2023