you can’t duplicate it exactly in the “new” 3-pane view.
Which is why I used the ierm approximate 
However, I think this is pretty close…
Honestly, the only real difference here is there isn’t an isolated middle panel for the groups. However, those are still shown in the Navigate sidebar.
Does this include documents? Or just text type notes?
If the first database is an indication out of a DB of 2867 items I have 71 PDFs, 473 Rich text files, 14 Markdown files, 210 images and the rest are plain text files.
Oh wow. Are the PDFs in obsidian searchable?
I have had DevonThink (DT) for five years or more. I struggled to find a serious use for it until recently. I am now using it to cull documents collected from over two or more decades of teaching courses. My goal is to create a reference library of lecture slides, worked examples, demos, study guides, study problems, and additional resources for each topic in a given course. To that end, I have imported the source documents into a DT database and am working methodically to mark (and remove) duplicates as well as to categorize and sort the remaining documents (by topic followed by type).
Given this objective, I have not found any other app that allows me to work through my resources with the effectiveness that is provided by DT. This is not to say that DT could not do better (and I direct my comments to this end to the DT Forums). But, after 5+ years, I am finally appreciating the need for DT in my toolbox.
You did not ask directly, but implicit in your question might also be the inverse … “Why NOT DevonThink?”. To problem raised by @OogieM on data loss: I’ve not experienced it. You might decide whether her warning means that you should avoid DT entirely or whether it means simply that you should develop a stronger contingency plan for the potential that data loss could happen to you.
My one reply to the “NOT” based on the 5+ years of experience is: Do not get DT if you are thinking that you need it to be a more sophisticated way to do Finder-level actions. While DT is more sophisticated than the Finder in its ability to search, I think the overhead is too high to use it on a routine basis as simply a better Finder tool.
My one reply to the “NOT” based on recent advances in apps: Do not get DT if you are thinking that you want it to help you connect ideas across existing or as-yet-to-be-assembled collections of documents. Up to the point of Roam and Obsidian and comparable tools, DT may have been the best macOS app for such work. In the meantime, I am finding that, compared for example to Obsidian, the overhead is too high to use DT as a tool to generate and investigate connections between document content. However, see also the note (caveat) in the next paragraph.
Finally, what about the possible limitations with Obsidian (or Roam or others) compared to DT in the ability to search inside documents to expose the content that can then be connected? I take a neutral stand on this question. First, I am entirely naive about whether Obsidian or Roam or other (markdown-centric) apps can or cannot search content inside documents (e.g. PDFs). I cannot imagine that they absolutely cannot (or that eventually some plug-in will allow the search to happen). My comparable work here is that I read PDF documents in the science/engineering discipline for research developments. In this realm, I have a dedicated database app (Bookends), and I do the work manually (by annotating the PDFs as I read them). To continue the note in the previous paragraph, I am also exploring how to bring the annotations from the PDFs into Obsidian rather than DT. This said, I am aware that other folks post accolades about the ability of DT to search inside documents, reveal the content, and expose otherwise unseen correlations among the revealed content. So, as the saying goes … YMMV here.
Hope this provides some useful insights.
–
JJW
THIS!!! This is exactly what i use DT for! It really helps….
My biggest issue with the process is my “need” to keep stuff in google drive - and it’s mostly because that’s how I share and post stuff to students and colleagues and for a while desktop google drive didn’t work on the M1 …. But now it does. The other issue is tags … I love tags but google drive doesn’t. @DrJJWMac if you have time I’d love to hear your workflow with all your teaching documents 
My markdown notes are managed in obsidian, and I work with lots of links to files.
So, one critical use case for me, is to have a robust link to a file. DEVONthink links works on my Mac and iOS devices with DTTG.
Haven’t been able to do this with anything else. I did use private Dropbox links for a while, but they break when moving the files around.
Not that I know of, I never search within PDFs except when I open one so I’ve never tried that in Obsidian. FWIW I never used that feature in DT either.
I am not a teacher but I am also sorting, culling and linking materials collected over the last nearly 40 years. I find it interesting that in all the years I used DT I still had a pile of unsorted, un-annotated poorly named files of stuff and lots of duplicates. DT’s find duplicates feature was so unreliable, marking as duplicate things that weren’t and not catching some real duplicates that I could never depend on it to find stuff and eventually tuned out even using it. My workflow is evolving but now includes Zotero with Zotfile to deal with PDF documents and their annotations (most of the scientific papers and a lot fo my older material I generated and scanned from hard copy) Bookpedia for the paper and kindle book reference and Obsidian as the final repository for all the annotations taken in the PDF and e-book worlds plus using GoodNotes as my hand written capture tool because I can now get those items into Obsidian as typed text easily.
It may not be a seamless as using DEVONThink but it is far more versatile and fun to use which means I am using it more and enjoying it more.
I would seriously like to know what else I should or could have done to identify the problem earlier so I could recover. I had considered my backup strategy to be very solid, daily backups to a local system, time machine to both a local and raid server. Weekly backups to a RAID server, monthly backups on external drives rotating to 2 separate offsite locations, archive backups every 3 months, the oldest of which was 2 years old. Weekly verify and repair database, monthly optimize database, quarterly rebuild database operations in DT as per user manual suggestions. Yes, I could have implemented a rigourous checksum of every file at every backup and perhaps discovered the data loss before the 2 years had passed but that is a bit beyond what most people would expect to need to do for a software package designed to store and manage data for the long term. Now I do have scripts running to alert me to zero length files and so far I’ve been catching the problems as they resurface. What should I have done differently?
This is then where you and I differ fundamentally in our use case for DT. I depend on being able to search inside PDFs (as well as Curio projects and other resources) to find terms so that I can collate comparable content more effectively.
I agree. I gave up on tracking duplicates in DT almost soon after I started. I could never convince myself how to adopt the findings as anything more than some nebulous “these two files could have something in common”. I believe in retrospect that I was still stuck somewhat in a “DT is a smarter Finder” mentality. In the meantime, since I understand better what this feature is trying to do, I would be less negative today about it when the DT team would change it to “Closely-Matched” rather than Duplicate. I’d likely still find no immediate use for it, especially since I am not interested in searching for close matches on files as much as I am in searching for close matches on content (manually) extracted from the files.
With due respect, the DT forum is replete with postings from folks who sing praises about the Duplicate feature helping them in their workflow.
First, I do not mean at all to disrespect the extent of trouble that you faced. Nor do I mean to impose any statements about blame.
I don’t know if you will ever have a satisfactory answer to your question as you have posed it.
If it offers any consolation, your warning is a primary reason that I gave up indexing files with DT. I keep the source content separated (and routinely backed up). I work with imported copies in DT.
—
JJW
um the VAST majority of my losses were in imported files not indexed ones!
Yes. Apologies, I see now that you said that clearly enough.
So instead I can say that, while I have imported files into DT, I have every intent to keep the raw source files outside of DT both still locally accessible and stored as archives on a separate external drive.
I also am likely not to use DT to create new content and, if I do, I will also store it outside of DT (e.g in Obsidian).
In short, for me, DT is a tool to cull raw data effectively, not a tool to create new data.
If something in DT does go to zero as per your experience, I will have the raw data sourced elsewhere to replace it.
—
JJW
Dr. J,
You did it!!! You got me into my external hard drive and for that I certainly thank you!!! WTG!
Field Guide is up! Now I have to actually find time for it…
I’ve been thinking more about this and realized that I’ve been doing an extensive annotation of PDFs when I first add them to my system. My annotations are both highlights and my own notes. One of the good things about moving to Obsidian is that it’s forced me to consolidate all my sources and develop clean workflows for each type of resource. Part of that is at least briefly, visiting/reading/reviewing every item that is being linked or added to Obsidian. I have found duplicated scientific papers filed under multiple folders each with slightly different sets of annotations. So I use a manual process to move those into one copy and enter in that one into Zotero and the notes into Obsidian. I will highlight lots of potential search terms so that seems to have solved the search for me. I have found that in practice, I go back to a topic and if I’ve linked all the notes correctly I am finding evrything without doing a search again. But my reference material, while the sum covers a broad range, each individual item in it is pretty narrow in scope so there isn’t really a need to search if I’ve done my homework of proper entering in first. That could be a function of my own interest areas. I don’t know what Curio is, my other source material is usually Libre Office documents, spreadsheets or presentations. They tend to be narrow in scope enough that a good filename tells me all I need to know about the item. I do have some things in Scrivener and I still use that for long form writing but the notes and ideas for those items are in Obsidian now. They used to all be in DT.
One thing that I’ve realized is critical to me is that I have one true source for all items. I do not handle multiple copies of items well at all. I am having more problems with finding duplicated data in different DT notes or pieces of data in multiple notes. Now as I move them into Obsidian I create one note with the common data and add links into all the other notes where that item appears via transcluding the file. That way I have a single place to make chaneges and it’s reflected across the spectrum of the places I reference or use that item. I still get the benefit of having it appear all the places I may want to see it.
Just starting my DevonThink journey. I am a lawyer and the ability to do in-document PDF searches for terms is what sold me. I am slowly learning about all the other features, but that single feature was worth the $ to me.
There are numerous lawyers hanging out on the DEVONthink forum, and there some there hoping to do a spin-off forum for lawyers. Can search the DEVONthink forum to find those posts.
Alarming, taken out of context.
No bad at all. I was joking. Sorry if I appeared to be slapping you on the wrist—not my intent at all!
Don’t sue me!
I have to admit I couldn’t see anything arrogant or dismissive about that reply from you. I find this quite often though here. Sometimes one has to circumnavigate the truth so much that one loses course I find. By reassuring a person they have done nothing wrong as such… Most of my problems with tech, DEVONthink 3 especially have been user error frankly, same with apple over all actually. The biggest user error is not having proper back up. I consider that now a ‘user errror’ and have little patience with it. Same with ‘password1’ for a password.
Your use here is comparable to what I do with my PDF journal articles, Your struggles match somewhat those that I face now in trying to converge documents from three different citation management apps (Bookends, Papers, and Mendeley) into just one database and in finding a robust, reliable workflow to translate the annotations out to just one “brainstorming + reviewing” app (Obsidian).
The one reason that I am using DT is for my need to bring PDF, LaTeX, and other source documents from three decades into a single, trimmed-down collection where the documents are categorized (sorted) by type (PDF, Word, LaTeX, …), theme (assignment, exam, lecture notes, examples …), and topic (e.g. in materials science: composition, bonding, crystallography, phases …).
I appreciate the follow-up. It helps me to know that I am not alone in at least one of my expeditions.
–
JJW
