Multiple Research Areas: File Directory Organization

Hello, all -

Any advice on how best to organize the local file attachments directory (or directories) for multiple research areas? For example, I have Library folders on the hard drive within folders of different research areas (disciplines); within these are topical folders, as well as specific author folders. Within the author folders, I typically have at least 2 folders, named "1" (for primary literature) and "2" (for secondary literature).

So there is a folder within my Philosophy folder as such:
Philosophy: Library: Aristotle: 1
Philosophy: Library: Kant: Critique of Pure Reason: 1
etc.

And a folder within my Music folder as such:
Music: Library: Theory
Music Library: Genres
etc.

And so on.

I would prefer to continue using local folder organization, and started out using absolute paths, but now thought to switch to relative paths, which requires specifying a base folder in Zotero. However, it seems Zotero only allows a single base folder path. I wish to keep the research libraries of different research areas separated.

So now I am thinking to create an over-arching LIBRARY folder, which contains:
Library - Philosophy
Library - Music
Library - Psychology
etc.

Then I would set Zotero's base folder to the over-arching LIBRARY folder.

This is not ideal, as I preferred to keep each Library within the larger research area folder, but it seems it should work.

A few questions…
1. How many hierarchical levels within the base directory can Zotero handle?
2. Is there a better way to organize Zotero use, and the local file system, for multiple research areas?

(Nota Bene: I do not wish to use Zotero's internal file system, as I cannot easily navigate in that to find files manually in the Finder)

Thank you for any advice from the gurus herein.
  • 1. There's no theoretical limit except path length on some Windows system.
    2. If you want to use links to files, no (FWIW, and I know you say you don't want to, but you do ask for advice: the vast majority of power users relies on Zotero's file organization for good reasons. It's easier to setup, maintain, and provides more functionality)
  • Dear Mr. Smith,
    Thank you for the impossibly fast response!
    Glad to know. Is there a FAQ/summary of the detailed pros (and cons) of using the internal database?

    An additional concern I have is that if I ever move from Zotero to some other manager (deities forbid, but stranger things have happened), how would I transfer over from Zotero's, how do you say, idiosyncratic internal folder and file structure? (Perhaps this is covered in the aforewished FAQ/summary).
  • Is there a FAQ/summary of the detailed pros (and cons) of using the internal database?
    Not that I'm aware of, but here are the key advantages imo:
    1. File management: When you delete an item in Zotero, attached files stored in Zoter will be deleted from the file system. That's not the case for linked files.
    2. Easier import: ZotFile helps you with keeping your linked files organized in a pretty automated way, but it still requires some maintenance, e.g. when you drag a PDF into Zotero and have it recognize metadata, ZotFile doesn't move it automatically
    3. Working with groups: Groups require stored attachments, so moving items with local links into groups doesn't work, making collaboration harder
    4. API support: Stored files are accessible via API (both when you sync them with Zotero file storage and when you do so via webDAV) allowing third party integration, including mobile apps.
    An additional concern I have is that if I ever move from Zotero to some other manager (deities forbid, but stranger things have happened), how would I transfer over from Zotero's, how do you say, idiosyncratic internal folder and file structure? (Perhaps this is covered in the aforewished FAQ/summary).
    The ability to get your data out is a crucial concern which all of us here take very seriously, but if anything, storing your files in Zotero makes this easier: There are three ways to migrate from Zotero to a different tool:
    1. The tool reads straight from the sqlite database (like Mendeley does). In that case, the location of files doesn't matter
    2. The tool uses the Zotero API, in which case, as per 4. above, storing files in Zotero makes this easier
    3. You export from Zotero in a standard format and import in the other tool. For all exports with files, Zotero includes attachments in a folder with relative links in the export file (RIS, BibTeX, Endnote XML, etc.). Again, the file location doesn't matter in this case.
  • Thank you for the explanation of the benefits of the internal database. I will consider those carefully as I go forward.

    Meanwhile, is there a way to change the behavior of Zotero when dragging PDFs into its interface, such that this creates a link to the file, rather than copying it into Zotero's database? I could not find a preference for this behavior, but perhaps I've missed it.
  • edited April 5, 2019
    There's a modifier key you press while dragging to link instead of store. It depends on the operating system. It's ctrl+shift+drag on Windows.
  • P.S. Since there is no real hierarchy limit, I tested organizing multiple libraries by my preferred method (LIBRARY folders within subject area subfolders), and it seems to work. I set Zotero's base directory to my general documents directory, which contains documents on every topic of interest, whether or not these relate to Zotero, organized by category. It's the LIBRARY subfolders in some of these folders which Zotero would need to access for PDFs and such.

    So I have my general documents directory called "ZM" (my initials, of course), inside my Home folder on the Mac. ZM includes folders like:
    - Philosophy
    - Art
    - Music
    - Literature
    - etc.

    The ones with libraries of texts will include a LIBRARY subfolder.

    Typical Zotero Paths then will be, for example:
    : Philosophy: LIBRARY: Kant: 1: Critique of Pure Reason: Critique of Pure Reason (XXX translation).pdf

    This seems to work fine. So it does not seem to matter that the "base directory" includes lots of other kinds of documents and info which are irrelevant to Zotero. I suppose that should have been obvious, but I wanted to test it. All seems to work fine.

    The internal hieararchy within the base directory is really very flexible....but then once chosen, it's a commitment, since changing any paths (including folder names) will break the Zotero links to the attachments contained therein.

    Hopefully that makes sense, and may be of use to some others facing the same questions of how to organize information. Think it through carefully once, and then stay with what you decide...
  • Thank you for the modifier-key answer! Sorry that I missed that in the docs. Found it here now:
    "By default, files dragged into Zotero are added as copies of the original files. To instead add links to the original files, hold down Ctrl+Shift (Windows/Linux) or Cmd+Option (Mac) while dropping."

    That makes life much easier. Still, if I may voice a feature request (is there a proper place to put those, hopefully not in the trash?), it would be nice to have the default behavior settable via preference. Meanwhile the modifier key combination is simple enough; just have to inscribe it on my faulty memory.
  • Ah, now I remember that keyboard shortcut, which never worked properly on my system. Trying it now in a very different version of the OS (High Sierra), and the problem recurs. No matter how I handle the Command-Option-Drag, Zotero copies the file into its internal database, instead of creating a link.

    I found the old thread on this issue, and will post there...will try to create a viddy of the problem:

    https://forums.zotero.org/discussion/34571/batch-add-pdfs-as-links-to-files/p1
  • edited April 5, 2019
    I posted the video of the problem in that thread.
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