Any edited volume has chapters by different authors (while the book itself doesn’t have any author but editors).
I’d be curious to learn what your main limitations are. I seem to be settling for Zotero, but still ready to move, in case any dealbreaker comes up…
OK The closest I can see in my own stuff are 2 classes of books: Short Story Anthologies and a curated special journal of papers on a specific topic.
I’ve never had a reason to cite a short story from an anthology. I can cite them by going back to the original publication, usually a magazine.
For the second class I have a single instance of that in my Zotero system. It’s a special publication on Textiles from Hallstatt. But in that case each individual paper is available separately and so the ones I care about are entered as individual items in Zotero and they all came in with the same book info.
What are you doing with PDFs within Zotero?
I’m asking because I’ve ended up doing all my PDF annotating outside of Zotero in a different application.
Apologies … I lost track of the thread for a bit.
I just reloaded Zotero. I tried to put my PDF attachments (from Bookends) in one folder. I wanted to add the folder to Zotero and share that folder with my research team. This is not possible.
I also much prefer working with PDFs through the UI of a “traditional” bibliography management app such as found in Papers or Bookends.
I am still tackling annotations. The problem I face is not HOW I will annotate (exclusively on my iPad with some iPadOS app or another). The question I am struggling to finally nail down is WHY I should bother.
Essentially, I have (over this next month) somewhat of a luxury to start from the ground up to redesign/improve my workflow to writing publications and proposals. Although I’ve bounced around with reference managers perhaps as much as @JohnAtl who started this thread, I am likely back to Bookends permanently. The primary reasons are that I can split my otherwise exhaustive library into more manageable libraries, that Bookends plays nicely with other PDF macOS apps (e.g. Devonthink), and that Bookends on the iPad promises to provide me with the least amount of headaches when I finally do get around to annotating.
Hope this late response still has some interest for you … (and adding a post-connection for @toffy who also asked specifically about my limitations with Zotero for PDFs).
–
JJW
How do you make this kind of decision? I have trouble here. I find I often cite across domains/disciplines. (Maybe that just tells me I should keep everything together…)
I have decided that data storage is cheap compared to my needs for the bibliography database to be a) rapidly transportable, b) rigorously focused, and c) cleanly sharable. I intend to keep a “global” master library and pull out (COPY not move) citations as desired to the sub-libraries.
Also, I have changed research sub-disciplines many times over in the past few decades of my career. So I have citations that are in sub-field A with, honestly speaking, not even a glimmer of a connection to my current sub-field K. I am getting rather weary of continually seeing files from sub-discipline A still hanging around in my bibliography database. I could just move to the cluttered attic (the full bibliography database) and prune out the old furniture (sub-discipline A/). Or, as I’ve decided, I could move to a totally clean room and methodically bring in the furniture that I think I want/need one piece at a time so to speak.
So, my current approach is born from a desire to be methodically collecting needles together and joyfully watching the haystack form rather than to be frantically building a haystack and exhaustively searching for the needles within it.
It is perhaps the luxury of a month to try.
–
JJW
Ohhh that makes sense. Genius! I especially like the idea of sharing a bunch of references this way…
Keep us in the loop.
Just to follow up, Zotero is working well for me.
I don’t miss Bookends, et al. at all.
This is an interesting strategy, particularly for the indexing of Bookends PDFs in Devonthink. My own approach involves a massive Bookends library, rather than several, but using PDF tags on major areas of my work, which I then have to manually index into my separate DTP databases. Like Ryan, I’ll be interested to hear any updates up in my dusty attic as you continue to populate your new room.
I also recently tried Zotero as I found I couldn’t sign into Bookends cloud (it was clearly another bug in a long list that I’ve experienced), and I immediately prefer it. Simpler, works well at detecting papers and does all I need. I’ll be keeping this in my research workflow and dropping Bookends. The Bookends interface really is awful and I’ve been putting up with it for too long!
I’ve been using an Alfred workflow called ZotHero to look up refs and open the PDFs.
I learned today you can set it up to insert the citation key in whatever app you have in the foreground (Scrivener for me). The workflow goes:
\\\ (My shortcut snippet)
Type part of the ref.
Up/down to select if needed.
Shift+Enter to insert the citekey.
I modified the workflow to add the @ before the citekey which is a Pandoc-style citation.
Super cool.
So far, I am also quite happy with Zotero. Can’t say if I’d be happier with Bookends, since I never really got very far in trying it, but I’m more and more coming to appreciate open source software in the long term and the possibility to share references with colleagues on windows seems like a big advantage.
Anyway, I just wanted to mention that Zotero also integrates quite well with Obsidian. There are two plugins for that, a n obsidian plugin called citations and a zotero plugin called mdnotes. It can be a bit confusing to understand how they relate to each other or which is “better”, so I asked the mdnotes developer on the obsidian forum and perhaps the short answer is that mdnotes is more powerful because it has access to all fields in the zotero database, but there are advantages to the obsidian citations plugin too so I eventually came up with this solution of combining the two for myself:
I haven’t quite developed a definitive workflow yet (because I’m trying to spend more time actually doing work that trying to organize it perfectly), but maybe it can inspire someone.
I’ve come from Bookends to Zotero, and I am extremely happy with it. I’m also using it with Obsidian and love the integration.
I’m a really heavy user of citation software as I publish around 10 papers a year at conferences and in journals. You absolutely made the right choice, Zotero is a pleasure to use in comparison. I think Bookends is a mess (the user experience is just frustrating), and that’s after a long time using it.
Endnote was also good, I used this when I was employed by a university that gave me a license. I just cannot justify the cost and prefer Zorero.
The macOS experience is frustrating still. The iPadOS experience is rather pleasant, especially to review and annotate PDF documents.
I am anxious to see whether Bookends iPadOS will provide a front-end to a Zotero database, as suggested in the user forum as being in consideration.
—
JJW
Almost a year on and are you all still using Zotero or Bookends? Any further advice for those of us trying to choose a reference manager?
I’ve stuck with Bookends over Zotero because it has excellent AppleScript support, and, as @DrJJWMac points out, annotating PDFs on the iPad through Bookends is quite pleasant.
I want to like Zotero because it seems far more intuitive. But for example, being able to integrate Bookends with TextExpander to output a formatted reference to the selected item in Bookends aids my workflow considerably.
Here’s the TextExpander Snippet:
(*
This script returns plain text formatted bibliography entries for the
selected publication(s) in the Bookends app.
*)
tell application "Bookends"
set _items to (selected publication items of library window 1)
set _text to ""
if _items is not {} then
set _text to format _items using "<Your desired format here>.fmt" as plain text
end if
return _text
end tell
Note: You’ll need to replace the <Your desired format here> section in the above script with the name of the Bookends format you’d like to use. I’ve defined a custom reference format that uses Markdown formatting, which I often use when adding references to my notes.
The new Zotero app on the iPad isn’t bad for taking notes and since I switched my file syncing for Zotero to WebDAV (making use of my Fastmail space), it’s been rock solid and easy to access on my iPad with no further need for additional plugins or software. I can then export the notes to markdown on the Mac to us in Obsidian.
I’m still on Zotero and since the recent update with the integrated pdf reader/annotator I’m sure it was the right decision.
For anyone who was sitting on the fence w Zotero 5, I’d recommend checking out Zotero 6 it also has an iOS app that works flawlessly for me annotating pdfs.
Note, though, that zotero 6 saves annotations to its database rather than the pdf file. But you can save the annotations to the pdf by “exporting” them there. To add new annotations, you’ll have to go back to database mode and then re-export. That’s probably the biggest issue and I thought it might be a dealbreaker, but so far I’m happy the way it works since I didn’t see any need to use other pdf editors.
Zotero all the way, My breakthrough was using Highlights as my PDF annotation tool on the iPad and I personally save the un-annotated and annotated PDFs in my Zotero system.
Perhaps my use case is unique. I have to chosen to manage about a half dozen separate citation libraries to work across as many different individual projects and team members. Everyone else uses Windows.
I am staying with Bookends. It offers the best all-around support for AppleScript, multiple libraries with their own attachments sub-folders (no other app appears to offer this), iPad annotation toolset (the Highlights app on the iPad is cumbersome by comparison), and integration with DevonThink.
I’ve dropped Papers. It is professional and very well-designed. I could use it for its ability to search for comparable articles. But this is not my primary need, and its limitations in other areas leave me stranded.
I use Mendeley solely to share PDFs with members of my research team.
I just completed a proof of concept test for how my workflow will run going forward on my projects. A team member marked three journal articles in Mendeley for me to review. I exported the PDFs from Mendeley to an > inbox folder at the Finder level. This folder was set as a Watch folder for a certain library in Bookends. When I open that library in Bookends, it imported the PDFs, completed all the meta-content, and moved the references to a Static Group called > to review. I synced only that category to Bookends on my iPad. I pulled up each PDF, annotated for highlights such as #why, #how, #result, and so on. I synced back to Bookends on my computer. I exported the annotated PDFs into a Finder folder > to Mendeley. I replaced the PDFs in Mendeley with the newly annotated files. The most difficult step in this was the last one. Mendeley is not well designed to swap out PDFs with any degree of ease. The biggest frustration in all of this is that Mendeley does not recognize any form of annotation or note from external apps. I tried annotating in Acrobat … Mendeley does not recognize it. Yes, you can see the annotation on the PDF. But you cannot see it in the notes list.
Otherwise, I’ve tried but not taken to Zotero. I get lost trying to set it up properly for citation management. I hear all the great things about Zotfile or the annotation options on the new iPad version. But … setting up Zotero and understanding how to get it to work always seems to cause me more friction compared to working with Bookends. I keep Zotero if only as an option to replace Mendeley for sharing in case one or the other of my team member prefers.
–
JJW
Another possibility is to set up the Zotfile plugin to automatically store files in cloud storage (so the database will just have the links).
Then PDFs can be annotated in any app with access to the cloud storage.
Notes can still be kept in Zotero itself.