I’m an academic researcher. I’ve been using DEVONthink since the start of the year and really enjoying it.
I use it for lots of notetaking, saving news articles, storing and analyzing original research (images, pdfs, etc), legal research, etc. It was always a question for me how to incorporate academic literature that I keep in Endnote. I finally got around to trying out DEVONthink’s indexing function this morning to see if that would speed up keyword searches and linking ideas. I indexed Endnote’s “PDF” file that holds all of the actual PDFs.
I was really impressed how fast DEVONthink indexed the whole thing (~5,000 articles). It’s just astounding the speed and ease now of searching everything (like, everything everything) and viewing DEVONthink’s connections between documents.
Can’t believe I didn’t do this sooner! If you’re a researcher trying to figure out how to integrate lots of original notes and source material in DT with structured citations from a citation manager without blowing up the size of your DT, this method seems to work really well.
Hi there, I read this post with interest… I too am using DT3 to support my academic studies having just started on a new course. I have access to Endnote for free, so will intend to go with that. However, I have already massed lots of articles in DT3 as I am familiar with the app, whereas am not with EN.
So, to store in EN and index in DT3 and or to store in DT3 and link from EN records… which is the best and what are the things to look out for…? I use DTTG actively as well if that makes a difference? What will DT3 give me that EN doesn’t? Welcome perspectives before I head off full steam! Thanks.
I’m only involved in the writing of a few academic reports a year so I’m not a good case study, but I don’t use a cititation manager much nowadays. DT has my research and the original sources, and I cite manually. Each paper/source has at least one corresponding text file with my notes, and in there one of my first tasks is creating a full citation in my preferred format which I can then copy and paste as needed.
(Yes, it is a a bit of a faff doing this manually, but I found maintaining a citation manager was a faff too and for the amount of writing I was doing that required it, I figured I was just choosing my pain not eliminating it )
I’m very aware that people doing far more academic writing than I do probably should choose the pain of a citation manager over the pain of manually creating reference lists, but thought I’d mention this as I assume I am not the only one doing manual citations.
Yup, I’m using Bookends which is great for finding and schlurping papers, and great to read in (despite a really awkward sync implementation). Indexing the Bookends PDF directory in DEVONthink grants insane full-text search powers over those papers that Bookends can’t even begin to match. It’s ridiculous how good search is in DEVONthink, and again makes me glad for an ecosystem of applications that are happy to work with offline flat file structures.
Richyo, great to hear from you. The short answer to your question about Endnote is: Endnote is designed to be a home for academic references, which helps not only with having a structured source of information on articles, books, reports, etc., but also allows you to insert those references and bibliographies much easier than doing it manually (and it accommodates a variety of citation styles and allows your to adjust them to fit the journal).
DEVONthink doesn’t have anything close to this, so inevitably your academic references will not be stored in as structured of a format and will not be able to be automatically inserted into your work.
If you are pursuing an academic career or even a career that involves a lot of writing, I strongly encourage you learn how citation managers like Endnote work as early in your career as possible as it will ultimately save you enormous amounts of time.
The brilliance of Devonthink’s ability to index is that you can index your Endnote library and get the benefits of both a structured source of references AND Devonthink’s amazing search abilities, PDF editing, tagging, etc.
I understand your logic with the reference list and in fact do something similar myself.
I review medical records to prepare reports in a legal setting so I regularly need to search and reference academic literature but the topics can vary quite a bit; it’s a bit different from being an academic in one focused area.
But the issue I wonder how you resolve is - how do you create your bibliography in acceptable format, i.e. MLA format or whatever you require? Devonthink does not do that.
So I create my reference list in Zotero for each case, I store a link back to the applicable Zotero collection in Devonthink, and I use Zotero to create my bibliography in the desired format.
If you use a different workflow to achieve this, what is it?
The answer will make you die a little. I put on a pot of tea, and I do it manually…. It usually takes a few hours for <100 citations.
But, the answer makes more sense when you learn that my employer is a Google Workspace. Google Docs is rubbish at footnotes/references, and doesn’t handle them in a way that seems very compatible with other apps, so every time I export to a different format it all has to be manually checked anyway (the trick is to export to Microsoft Word first, which formats it properly, then convert that doc to whatever is needed. I often forget this until I’ve made a mess.). (Google Docs has other benefits, e.g. having multiple authors working on a doc at once is a breeze, but it definitely does not shine with referencing.)
Hoepfully your employer does not lock your ability to add extensions.
Google docs cannot handle references well out of the box but there are infinite extensions available or you can create one pretty easily with AppScript.
What do you think of Zotero?
Alas I don’t have the budget for Endnote because I’m a freelancer.
With Zotero I may use their software for free and use DevonThink to index and do the rest.
May I ask you how it can save time?
My content production is heavily related to papers, so every advice on how to save time is welcome.
The time saving comes in both document retrieval and citations. I haven’t written a manual bibliography since undergrad and every time someone says they do manual bibliographies I really question their sanity! LOL, JK, but not JK. If you submit to various peer review outlets, you likely have to conform to various citation styles. With a citation manager, that’s easy since you just adjust the output of the citations referenced in your article (although sometimes with a few simple mods) and viola, you’re done.
I don’t really like Google Docs for academic writing overall (at least not for finishing and submitting). I think Word works much better across the board with citation managers, including Zotero. I don’t personally like Zotero that much because it is quite limited as technical software (IMO), but it is free and it has a large user base, so I wouldn’t discourage anyone from using it. I don’t want to regurgitate a whole comparison between the two, but this is just my take.
I personally use Bookends. It’s Mac-only and has a one-time user cost, which is great. Customer support is excellent, actually, very responsive from the developers themselves. Good mobile app, simple file structure, iCloud syncing. It’s got a few aesthetic and interface issues, but nothing catastrophic, and besides, you have to remember that citation software is so niche and so hard to develop a business model around (see Mendeley getting gobbled up and abandoned).
Although Endnote is fairly mature as a citation software app, I just totally despise their marketing, their upgrade structure with essentially no new features in literally 10 years, etc. It’s really exploitative.
I also agree with Bluefrog that Devonthink is the way to go on PDF markup, although I find Bookends mobile (on iPad) to also be solid.
I would like to amend my initial post here and say that I have since moved on to Bookends after being frustrated yet again with Endnote’s just awful upgrade scheme, absurd pricing, and BS marketing. I do think it’s fairly good software with pro features and it’s cross-platform. But people here are Mac people anyways, and Bookends has been around for a long time and has a good business model with constant improvements and updates. I highly recommend Bookends, and if I could go back and change the post and the title, it would be Devonthink + BOOKENDS = WOW (not Endnote).
Thank you all for your super helpful and informative suggestions. I too am already frustrated with Endnote - it seems like basic database handling activities like tagging and the like are not great - I may be going mad, but it doesn’t seem like their advanced search includes the ability to search on tags, let alone combos of tags. I didn’t look much further… I will take the approach of using DT3 and DTTG to architect my database and only use EN to store the citation info (storing a DT3 link in the research notes field of EN - at least it displays correctly as an URL!).
This approach is strengthened even more by the fact my lecture notes (indexed from Obsidian), reference annotations, You tube vid links (plus annotations) and goodness knows how many other shapes and sizes of data can sit in DT3. More to the point…searched across… When developing my own analysis of the subject that is invaluable of course.
I havent stored the refs in EN at the moment (and indexed in DT3) as Im struggling to see the benefit since I have the DT3 link stored in EN… My OCD just likes to have all the ref material in the same database rather than one index and another in DT3 (apart from my Obsidian stuff). Actually, I wouldn’t be surprised if there was another way around that in DT3 given its flexibility.
Just a final few questions if I may, can you attach multiple annotation files to each item in DT3 or just one. Also, since getting onboard the Obsidian bandwagon, I like using markdown - but the annotation editor whilst it accepts .md, doesn’t seem to have the outlining functionality that say, Obsidian does… is that correct or am I missing something? Final one … can you zoom in on the annotations without changing point size?
Interesting to hear about your process, keep up the fun work!
To your questions…
I don’t really understand or use DT annotations and don’t see a use case for it in the context of what we’re talking about. I’d much rather either mark up the PDF and/or (in my case) I have a folder for “literature notes” where I store all of my notes and reflections on a given piece of academic writing (book, article, etc.), then link it to the indexed PDF file. Just my approach, not saying any other way is wrong. I guess I just prefer to have anything I’m writing as accessible as possible and annotations are just a little less visible than a standalone note.
On zoom, that’s easy to answer: go to View > Zoom (near the bottom), and you can absolutely change the display size without changing font size.
Thanks. I like the annotations personally as it is all displayed on one window, so easier to keep track of if multiple windows open and Im juggling… whatever works I guess
On the zoom, the menu command only zooms the main doc, Im after zooming of the annotation pane to the right… but if you don’t use, then not an issue for you!
Oh, I see what you mean about the zoom. Sounds like that might not work in the annotations pane. Creative use of annotations! That’s one of the wonderful things about DT, you can develop a system personalized to fit your needs and style. Love it!
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