That’s what I used to do (linked files) because I didn’t want Zotero manage my pdfs for me (Because I would still open them on various devices with a pdf tool to annotate them). I did this even though that meant that some Zotero features didn’t work because they were reliant on Zotero internal reference ID for each item.
But with version 6 I see no more need for this. Since the internal annotation works fine for me - and even works across devices - I am now letting Zotero handle my pdfs. This means I can no longer use cloudstorage like dropbox, onedrive etc to store and sync my pdfs (because Zotero doesn’t support these) but it does support webdav and because I have plenty of Webdav storage available, that’s where my pdfs now reside. But chances are, that in a year or so, I may have forgotten where they actually are, because from a user perspective they are just “in Zotero”…
I haven’t used it extensively yet, and I usually find some quibbles/bugs, but so far I haven’t.
Yes, you can do that if you want (and that’s what I’ve done for many, many years), but unless you have specific reasons why you want to store your annotations in the pdf file, there is no need for this any more.
Yeah, WebDAV storage is what I didn’t have — but I do have 2TB of iCloud storage.
I’m curious — which Zotero features rely on the internal reference ID? My reference manager needs are fairly simple, so I haven’t encountered those features so far as I know.
Tell you the truth I am now back to pencil and paper and a kind of ‘lab book’ system for references: all I really need. I used both Zotero and Bookends in the past and still do for formatting sometimes, LaTeX too which is my real favorite. I was interested in the comments regarding Legal citation here, I feel few lawyers use any of these?
I came to the conclusion with Bookends, which I like and I like the developer who was very helpful to me once, that one is expected really to design one’s own formats, that seemed to me to be the bottom line, unlike, for example EndNote which has built in nearly every citation format I know about when I looked. This is a kind of question out of sheer interest. What is your feeling on this?
I wanted to use Bookends on the iPad to read/annotate PDFs, but discovered that tags (not labels) do not stick when you « resync » with MacOS… Anybody experienced this? Or found a workaround?
I index the Bookends attachments folder in DT, and use tags extensively to classify the PDFs & search in DT. So that’s a dealbreaker for me…
Well, for the iOS app only. I still use the MacOS app, but I annotate in other apps on the iPad…
Personally, I don’t need much from this type of software. I read all my PDFs on macOS in Skim, for its inline annotations, which allow me to tag text (using a few tricks I developed long ago). For extensive note-taking, I use BBEdit (I hook the PDF to my BBEdit).
I’ve not written much academic stuff since switching to Bookends. What I mainly want that doesn’t seem to be in Bookends, as @ryanjamurphy metioned, is excellent ability to get the full reference from a PDF. So I’m having a look at Zotero given that Zotero 6 is out and seems to be getting good reviews. I’m also considering (finally) switching to LaTeX after all these years.
The key difference with your workflow and mine is that I read all my PDFs on my iPad in either Bookends or PDFExpert (for documents that are not bibliography journals).
Admittedly this can be a hit-or-miss in Bookends. I too would like to see some improvements in this front. The most frustrating limitation is the inability to fill the abstract field even with the DOI.
The decision may be whether you do not mind working with the format that Zotero uses to store the PDF and to store annotations to the PDF. I prefer the approach in all other citation managers where the PDF is not “hidden” in a subfolder. I prefer the standard where annotations are stored within the PDF not stored external. Since you mentioned Skim, you are already familiar with the processing needed using apps that store annotations external to the PDF.
I’d consider this a highly beneficial step when you work in the hard physical sciences or engineering fields. It beats Word for writing any long-form reports, especially when they include mathematical expressions and figures.
I’m in the process of moving my Bookends library wholly into DEVONthink. It’s experimental but I think it’ll work.
The process is to create a markdown file in DEVONthink for each reference item and then add all the Bookends metadata for that item as custom metadata. The markdown file itself contains any notes. Attachments are simply related as item links, having been already indexed.
I use Pandoc to process my citations, so that side is already taken care of. One benefit of moving everything into DEVONthink is that Pandoc uses CSL as a standard, which has a different and much wider range of metadata types. So I just have a bunch of custom metadata fields set up in DEVONthink, named and structured as per CSL. It’s much neater.
Translating the one data structure into the other is pretty easy, if time-consuming to set up. The challenge will be getting new references into DEVONthink without passing through Bookends or Zotero first. Getting book metadata from the Google Books API is straightforward, as is getting academic article metadata from DOIs via Crossref. I also plan to look into this at some point: GitHub - zotero/translation-server: A Node.js-based server to run Zotero translators
Another lawyer here. I use Zotero, but I don’t use it for giving me Bluebook citations in briefs. There is a Bluebook citation style, but it’s not very accurate in my opinion. I’ve toyed with the idea of creating my own, but it’s too ambitious a project for the moment. I do use Zotero for managing my library of authorities and precedent, and my annotations of them. It’s a gem of a tool.
P.S. Late to this party, I know. But this thread just showed up for me. Maybe because of the recent comment activity.
I’m a European, rather than an American, lawyer, so I typically use Oscola rather than Bluebook. From what I’ve seen though, there is no automated Bluebook solution. It’s just too idiosyncratic.
Oscola has a few problem areas (EU law and cases for example), but it seems much easier to automate.
[Insert rant about us having to deal with citation formats that can’t be fully automated 30 years after word processors became ubiquitous…]
