Recommendations for file (PDF) management decisions when starting with Zotero

DrCamTurner

I'm migrating myself and my organization from Mendeley to Zotero. As a disillusioned Mendeley Advisor, I'm impressed with Zotero's mission and features (particularly Zotero Groups) and look forward to it becoming so widely used that I never manually name or email another PDF. But Zotero presents some difficult decisions for how to approach file management when getting on board. For example, only the File Copies strategy is compatible with Zotero Storage, and Group File Sharing, but it requires all your PDFs to be stored by Zotero in their own individual subdirectories with random 8-character subdirectory names. The alternative strategy (File Links) is incompatible with those two features, but lets you store all of your PDFs in one directory of your choosing (with whatever subdirectory structure and names you choose).

@dstillman makes a good case in this discussion with @martijnende for how to use Zotero when finding and downloading articles online ...

That's just not really how you use Zotero. Zotero integrates tightly into the browser, so if you want to save something, you just click the Save to Zotero button while on the article page ...

... but I think many of us download articles online from platforms like ResearchGate rather than an article page on a publisher website. This makes the PDF, not the publisher's metadata, our starting point for managing an article with reference management (rm) software. Consequently, we've developed systems for naming and organizing PDFs on our computers and cloud storage. Even though we may subsequently interact with our articles through rm software, these systems remain useful for sharing articles (and their PDFs) with colleagues - particularly those who don't use rm software or don't use the same software we do.

It seems like getting new Zotero users on board would benefit from increased compatibility with their existing systems for PDF organization and sharing. Despite Mendeley's now fatal flaws, its "watched folder" feature seems ideal for this. Is there anything fundamental that prevents Zotero from offering an equivalent feature that's still compatible with the File Copies strategy, Zotero Storage, and Group File Sharing?

In this discussion with @ZenonMarko, @adamsmith makes a good case for why power users rely on Zotero's file organization ...

It's easier to setup, maintain, and provides more functionality.

...but how would a power user handle the following two scenarios:

I commonly need to share a small batch of PDFs with a colleague or client for a one-off request or project and she doesn't use any rm software. I need to 'export' copies of my Zotero-stored PDFs to a new folder on my computer so I can remove my PDF annotations from the copies and then email or cloud-share the batch to my colleague/client. I need the PDFs to all have consistent and informative filenames (e.g., Author_Year_Title) that I can refer to when I communicate with her, ideally the same filenames they already have within Zotero.

My organization understandably wants our collective library of PDFs to reside (or at least be duplicated) within its cloud storage, not just in Zotero Storage and individual's computers. But automating or streamlining the process of duplicating individual-acquired PDFs to the organization's cloud storage seems difficult when PDFs start out in random 8-character-named subdirectories on every individual's computer (i.e., the File Copies strategy). The process seems easier if individual computers each have one directory containing all their PDFs (i.e., the File Links strategy), but this prevents Zotero Group File Sharing.

Thanks in advance for your input - the Zotero Forums are proving very helpful!

bwiernik

Zotero can automatically retrieve metadata when you drag a PDF file into Zotero. If this is a recent publisher PDF, results will be as good or nearly as good as if you imported from the publisher web page. This will happen even if you view the PDF in your browser and then download it using the Save to Zotero button. Though I do suggest trying to get into the flow of importing using the the Save to Zotero button from the publisher web page. It is generally easier (1 step), and Zotero can even automatically retrieve the PDF if it is freely available on the internet or your institution has access to it from the publisher.

Regarding file management, I do suggest you try out just letting Zotero manage the file locations for you. I switched to this system many years ago and personally find it much easier than trying to worry about where files were being stored myself. If you later decide to change to another program, Zotero makes it easy to export your item data with the attachments in standardized formats. For groups, there are some pretty challenging technical hurdles that are the reason linked file or WebDAV support isn't yet available for Zotero Groups.

For your use case of sharing a set of papers with a colleague that doesn't use Zotero other other reference management software, there are two fast ways to do that. First, you can select the items in Zotero, right-click, and choose Export Items. Select RIS or BibTeX and check the 'Include Files' box. Zotero will export the item data to a file, along with all of the attachment files. By default, Zotero will rename PDF files using the authors, title, and year when you add them to Zotero, so the filenames will be readable. Second, you can use the 'Send to Tablet' function in the Zotfile plugin (http://zotfile.com) to send just the PDFs of selected items to a folder you specify on your computer.

To share some personal experience, I use about 20 Zotero Groups in my organization, and my organization is happy for us to use Zotero storage for these files. We use the institution cloud server for our manuscripts, data, etc., but the organization is happy for us to use Zotero for articles because of the great additional functionality Zotero provides beyond just cloude file storage.

It is possible for your organization to set up its own sync server to sync Zotero for its members and host files for organizational groups, but this requires a fair amount of technical setup and maintenance. (I think it will also prevent members from being able to be a member of or with Zotero groups outside your organization if that is a concern.) One alternative your organization might consider is Zotero Institutional Storage (https://www.zotero.org/storage/institutions), which will provide unlimited file storage for members of a lab or the entire institution.

DrCamTurner

Thanks for the detailed response @bwiernik - very helpful to hear your experience!

I do suggest you try out just letting Zotero manage the file locations for you. I switched to this system many years ago and personally find it much easier than trying to worry about where files were being stored myself.

I like this suggestion, particularly since you totally solved my use case of sharing a set of papers. Using Zotero's collections and tags is far more capable, flexible, and convenient. That said, I'm sure to encounter colleagues in my organization who feel the way @frucker described in this discussion:

As most of my colleagues right now do have a folder structure and do not use any library manager, it would be helpful for them to be able to keep their folder structure while using or starting to use Zotero. (In fact, some of them will not agree to use zotero if they cant access their pdf directly through a folder structure anymore, especially older professors :)

So while you've persuaded me free of my own PDF organization system (thanks!), I do think Zotero with comprehensive linked file or WebDAV support (i.e., compatible with Groups) would be much more easily adoptable for many potential users - creatures of habit and all that. Alternatively, an import tool that turns each sub-directory in a PDF's full path into a collection or tag in the Zotero library would address this. Anyone's meticulously crafted PDF organization system could be automatically replicated as a (better) Zotero collection/tag system. I feel like I've come across something like this while researching Zotero - will post it here if find it again.

Regarding my organization's file storage preference, I don't think the issues are cost, storage space, or functionality (Zotero wins those) but security and customer support. If (deities forbid) Zotero Storage were to get hacked, crash, etc., there doesn't appear to be any dedicated staff to call. Although it's still early days for me to discuss that with our IT director, I can't imagine him being comfortable without at least all of our organization's files backed up to our server.

It is possible for your organization to set up its own sync server to sync Zotero for its members and host files for organizational groups, but this requires a fair amount of technical setup and maintenance. (I think it will also prevent members from being able to be a member of or with Zotero groups outside your organization if that is a concern.)

Cutting all of our Zotero accounts off from other groups is definitely a concern, so thanks for mentioning that. Does that only apply if using a local server for both library data and attached files (sensu this)?

Thanks again for all the valuable input!

dstillman

For sharing a few PDFs, you can also just drag the attachment items straight from Zotero to a folder on your computer. Zotero will copy the files to that folder, and they'll already be named after the parent metadata.

If (deities forbid) Zotero Storage were to get hacked, crash, etc., there doesn't appear to be any dedicated staff to call.

We provide 24/7 direct support here. There are ways to exchange private info with us when necessary, but for the vast majority of issues, we can provide far better support here than you'll get pretty much anywhere else, for the reasons explained on that page. (And, obviously, the kinds of things you're describing are both extremely unlikely and would likely affect nearly all users, so it's not the kind of thing where phone support would really make any difference.)

Although it's still early days for me to discuss that with our IT director, I can't imagine him being comfortable without at least all of our organization's files backed up to our server.

Zotero is a local-first program, so that's as simple as having one computer set to download all files at sync time and keeping a backup of its Zotero data directory.

Cutting all of our Zotero accounts off from other groups is definitely a concern, so thanks for mentioning that. Does that only apply if using a local server for both library data and attached files (sensu this)?

Yes, bwiernik is talking about a local data server. But that's hardly the biggest obstacle. Just at a technical level, it's not really a realistic option for most organizations.

DrCamTurner

Thanks for the comment @dstillman. Your point about using one computer for the backup is a simple solution. If our IT director is comfortable with Zotero's at-rest and transit encryption, then maybe we'll even be able to include our organization's non-public reports in group libraries. My assumption is that IT folks will always prefer 'their' server to be the only cloud for all of the organization's data, but given the ubiquity of cloud storage I may be wrong.

AlexanderSavenkov

Hello @DrCamTurner , could you provide the details of the current setup at your organization? Have you managed to persuade the IT director? Have you all guys dropped the local folders?

Thank you.