Using Zotero to store all my pdfs?

I'm just starting out with zotero so apologies if this question has already been covered. I have lots of pdfs and epubs that are currently stored in various haphazard ways. I'm wondering if it makes sense to use Zotero not only to maintain the bibliographic information about the files but also to be the place to keep the working versions of the files themselves. In particular, I want to be able to open a pdf, make annotations (in, say, iannotate on my iPad), and have those annotations be maintained across several devices. Does it make sense to move all the files into Zotero for this purpose (meaning not just to put the metadata for the file into zotero but the file itself)? Also, I understand that I can have Zotero make a copy of the file in the Zotero database OR I can have Zotero store a pointer to the file elsewhere on my computer, yes? The latter option seems like it would give me the maximum flexibility and not use up tons of space in the Zotero database, but I'm wondering how robust Zotero is at handling broken links when a file is inevitably moved from where Zotero expects it to be? I hope this all makes sense and many thanks in advance for any advice. From what I've seen so far Zotero seems like a huge improvement from the bibliographic database I was using before.

thanks,
Abe Z.
  • edited February 11, 2014
    Generally speaking it'd be very odd not to use Zotero to also manage your files in some capacity.
    As you say, you can do that with links or by storing copies in Zotero. The main advantage of the latter is that, as you rightly recognize, there is no risk of links breaking. It's also the easiest set-up to make work with Zotero sync and iOS apps such as ZotPad or PaperShip (wether you sync those files across devices via Zotero File Storag or a WebDAV server).

    I'm not sure what you mean by robustness wrt broken links: If you move a file then the link breaks and there is no easy way to re-find the file. Not sure what Zotero could be doing there, so if you expect that to happen a lot, using links is probably not a good idea. That said, Zotero can store links relative to a base directory (see advanced tab of the preferences), so if this is just about moving between different computers with different directory stuctures, that's not much of a problem.

    The other issue is to think about what to do with new additions. One of Zotero's key features is that it automatically attaches files for new items you import from the web (when you have access to the PDF). By default those are stored in Zotero. You can use an add-on like ZotFile http://zotfile.com/ to automatically turn those into links if you want to, but what you probably want to avoid is to have a mix of files linked to Zotero and stored as attachments in Zotero, so you should pick one solution.
  • Thank you - this is very helpful. It sounds like there are significant advantages to just putting all the files into Zotero itself. Is there any reason *not* to do this? For example, does Zotero get very slow and clunky if it has thousands of pdfs stored in it?
  • There are two main reasons people prefer links:
    1. They want to have (or keep) a human-readable folder struture for their files outside of Zotero and
    2. They want to sync files through a sync-folder service like Dropbox.
  • Ok, thanks for the input. Both of those reasons you just gave apply pretty well to me so perhaps I should go with using links. I guess I need to experiment a bit with both options and try using them together with iAnnotate on my iPad, ZotPad or Papership, and Zotfile and see how they work together in practice. Thanks for the help!
  • Dan, any tips for how you organize the files outside of Zotero? I have a tendency to move my folders around a lot - using my folder structure to reflect my current thinking about any given project - so I'm worried that I'll be constantly breaking the links. On the other hand, I'm hesitant to put my 'working' copies of all my files inside Zotero.
  • (dannreinhart is a spam account, his post—and account— will be deleted)

    You can use links to a stable folder structure outside or inside of Zotero and do all the restructuring inside Zotero using collections and tags. There is really no reason to move files around your actual folder structure.
  • azablocki,

    Your use case sounds exactly like the reason to put all of your "working" copies of your files in Zotero. You need a way to keep your thoughts organized without worrying about lost or duplicated documents. That's what a reference manager like Zotero, Endnote, Mendeley, etc. is for.

    If you eventually get "finished" versions of something, you can always replace the working copies or keep both, as meets your needs.
  • Thank you both for your input. I think I need to play around a bit more to see how this works in practice. I'll post again if I have more questions after doing this. Thank you for the suggestions - I really appreciate it!
  • edited February 19, 2014
    hey!

    I find this thread very interesting, because i’m bothering with pretty much the same questions. Since quite a lot of my pdfs (or other files) are very big in terms of MB (mainly due to the lacking scan expertise of lecturers and tutors…) i prefer to store them on my harddrive and attach Links to them in Zotero.

    But i was wondering, how other people organise their files. At the moment i try to arrange every text in one main category and for these categories i have folders. Mostly this folders reflect my Zotero collections.

    I am aware of the possibility to multi-categorize or re-categorize the files in Zotero. Thats very helpful, because i can put them into a topic folder and at the same time in a working project folder.

    But i wonder if it makes sense to organize the texts in my harddrive in another way, because sometimes i would categorize a text in another folder after some time, because then other aspects are more important or because then i use a new category which I didn’t create before due to the little number of texts that would be in it. So I was thinking of an alphabetical order, or just one folder with all the texts in it. Therefore it would be very interesting to get some impressions of your organizing structure.
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