Can folder hierarchy on harddrive mimic Zotero folder hierarchy?

Hi there,

I recently decided to give Zotero a try after being pressured into finally getting a citation manager (Zotero seemed to tick the most boxes and have the most active development).

I do have a major concern so far though. I've noticed that Zotero just randomly saves PDFs into folders with gibberish names.

I currently organize all research folders on my computer based on things like subject.

I've changed my destination folder for Zotero to my OneDrive so at least everything is being backed up, but I'm still concerned that if I ever stop using Zotero, or if Zotero ever stops being supported, that all of my research will suddenly become a mess.

Is there some way to get Zotero to organize folders on my harddrive to mimic the folder structure within Zotero? And if Zotero can't do that, is there another citation manager that can?
  • Why would you need or want such a folder hierarchy? You can more easily search and retrieve the PDFs through the Zotero user interface.
  • You can use the Zotfile plugin to mimic your Zotero hierarchy, though I personally also recommend just allowing Zotero to Manage your file location and using Zotero to search and navigate.
  • edited February 15, 2019
    @StefanK1 I recently switched to Zotero from Mendeley, and initially I shared the same concerns as you. Below are my opinions regarding to your question.

    Decide if you want to want to store PDFs as "link to files" or "stored copy of files". With "link to files", you can manually organize PDFs on your PC, however, you will NOT be able to take advantage of native sync feature. With "stored copy", you can take advantage of syncing.

    If decide to go with "link to files", you can still take advantage of non-native syncing by configuring the "Linked attachment base directory". This directory (folder) will contain all your linked PDFs and will sync through third party services such as Dropbox, OneDrive, etc...

    If you are worried that in future you will stop using Zotero, or Zotero stops being supported, you can use the "zotero-file-hierarchy" translator which will export all files organized into folders which mimic the hierarchical structure of your Zotero library. Thanks to this translator, I also decided to stop organizing my PDFs manually and allow Zotero to handle it internally. If I ever want to recreate the files/folder hierarchical structure, I can use the zotero-file-hierarchy translator.
  • I've changed my destination folder for Zotero to my OneDrive so at least everything is being backed up
    Also, careful with that -- the Zotero data directory shouldn't sit on OneDrive (if you end up using ZotFile, you can specify a target custom folder on OneDrive, though).

    If you have a strong preference for having the local folder hierarchy, by all means use ZotFile to achieve that. Many people do. But if long-term sustainability (an absolutely valid concern) is the main motivation, I wouldn't.
    1. There are multiple ways to get your data and files, including collection structure out of Zotero: via Zotero RDF, reading directly from the Zotero sqlite database (the way Mendeley does), or via the Zotero API (which several tools also already use for this purpose).
    2. If Zotero goes away, your collection/folder structure is going to be a minor concern compared to the notes and citation metadata you have collected over years. You'll want to look for a way to get those back, and having a folder hierarchy isn't going to help you. You'll want to rely on some form of export in that case anyway.
  • @01baftb Thank you so much for the detailed reply. This is exactly what I was looking for!

    @adamsmith I'll keep that in my mind. Thanks.
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