Seeking annotation-organizational approach for DTP

I’ve been trying to figure out the best way to annotate files, and organize my annotations in DTP – which is the final repository for my files & documents. I’ve tried various approaches that users have suggested here, and was advised by DTP staff to post this query so that others could trade ideas about their work process.

I should explain that I work on articles and books. So, I’m struggling to figure out an annotation and an annotation-organizational approach that allows me to group annotations for specific projects (e.g., articles - say, on the War of 1812), as well annotations that crossover my projects and contain global themes (e.g., for books - such as on early American history).

My annotation workflow basically involves:

b[/b] Clipping documents on Mac & on iOS (i.e., DTP & DTTG) – more specifically, saving documents as a PDF format (which seems better for annotation) – and saving them on a synced DTP database.

b[/b] Read and do a cursory annotation on files, with highlights, notes, etc.

b[/b] Review annotated files, and select annotated passages that were especially noteworthy and important.

I’ve been trying to figure out the best approach for organizing those “noteworthy and important” annotations in DTP.

Naturally, there are several ways to annotate, and various approaches for organizing annotations. DTP serves as one of my central apps, especially for storing, consolidating and organizing files. So, it’s important for me to incorporate an annotation approach that works with DTP.

Here are the three main approaches that I’ve tried…

b[/b] I was really impressed with the “one thought, one note” approach to annotation. That led me to to the “Make an Annotation with Links, Notes, Tags” script that was created and further developed by users @korm, @Frederiko, et. al. ([url]Annotation Pane (Annotation with Links, Notes, Tags v3)])

That script help isolate certain key annotations, affix notes to them, and organize them in multiple groups – in this case, tags. Furthermore, when clicking on “Page” link (created by the script) it refers back to the exact portion of the annotated text, and highlights it with an animated flash – making it easy to spot the original text, making it enormously convenient time-saver feature.

b[/b] @korm kindly suggested Marginnote as an alternative way to sync and annotate files. Marginnote is a terrific app with many creative and useful ways to annotate, such as allowing users to create outlines / MindMaps of notes within the margin (hence the name), as well as affixing hashtags to annotations (which kind of work like tags). Also, one can annotate and sync files within Marginnote’s Mac and iOS app interfaces, and that’s a huge plus.

b[/b] Highlights is a solid app for extracting the annotations from a document, and compiling them into a stand-alone file of consolidated annotations. It’s also possible to make further annotations in Highlights, or tweak existing ones, and export a file from Highlights into DTP tags (though it takes a bit of finagling).

All of the apps and approaches are really terrific; the users and developers put a lot of thought and care into their respective approaches. What follows isn’t a knock on any of them. Also, I might be misapplying these apps and approaches and/or ought doing something entirely different. But before I get to that, the larger limitations I’ve faced w/ the annotation - tag process include:

b[/b] I’ve been advised to maintain most of my work projects in a single work database (though I concede this might be a mistake). That can create a problem with tag systems since there are only one set of tags per DTP database. So, I struggle with either having a complicated tag system for various projects within a single database or creating multiple databases for each individual project. If I do the former, I’ve got a sprawling tag system that’s hard to navigate; if I do the latter, it means that each tag system is narrowly focused, yet segregated from other databases, and therein separated from work projects where there might be overlapping subjects.

b[/b] That problem of separate tag system also goes to one of the main problems that I mentioned above: I haven’t yet figured out how to create a DTP tag system for specific projects as well as for global / crossover themes.

b[/b] While I appreciate the tagging process, I’ve learned what people mean when they say they’ve come burdened with “tag farming.” Tags are definitely a handy tool. But I’ve also found that I often expend more energy organizing my annotations w/ them than actually reading, annotating, and synthesizing the material. Again, I could be doing tags all wrong – this is just my experience with them.

So, here are the limitations that I face with my approach when using the aforementioned script and apps…

b[/b] The “Make an Annotation with Links, Notes, Tags” script is truly remarkable, and @Frederiko’s latest incarnation of it is really smart and elegant. Unfortunately, I do my much of my first reading and annotating on an iPad (I’m dyslexic, so it’s much easier for me). That means, I have to add another layer of work when I take an annotated file from the iPad (even if it’s synced within a DTP/DTTG database), and then process the same file through with the script in DTP.

While I love the way the script highlights annotations through the Page links, and allows me to add a note to a particular annotation, I’d just refer to the above section on the problems I’ve faced with tags and tag management.

b[/b] Marginnote is an awesome annotation app, but…so far it doesn’t interface with DTP, so right now there’s no way to export the annotations it creates (along with their hashtags) into DTP. I’m told that Marginnote might soon integrate with DTP in some way, and might even be able to port over their annotations into DTP tags (perhaps via Highlights).

b[/b] Highlights is also a super app. Unfortunately, there isn’t an iOS version of it, like Marginnote. The Highlights creator was kind enough to create a better interface with DTP, and enable Highlights to export files so that it “splits documents into a folder of files with one annotation per file.” While the latter feature is a great way to segment annotations with DTP, I’d ideally prefer export annotations that have tags instead of every annotation. That means, when users export annotation files to DTP, one has to delete Highlight-exported files that don’t have tags. Also, Highlights can’t import DTP’s tags (or hashtags from Marginnote). That means users have to create a “pick-list” in order to select @tags while using Highlights – or just write in each tag for annotated files (which can be time-consuming).

Again, these are all great apps and approaches, and I’m grateful for the hard work that their developers invested in them. I’m totally happy to consider another approach or app. I’m just trying to figure out how best to solve the annotation process and the craddle-to-grave and annotation-organizational process with DTP.

So, what’s your annotation / annotation-organizational approach? Any suggestions for a better approach for what I’m aiming to do?

Thanks for your help.


See below

Everything you’ve said is perfectly fair and reasonable. I’m not necessarily trying to find another new tool – I’d be happy to work with existing tools, and just revise my approach. The thing is, exploring new approaches means creating new organizational architecture, and that’s exhausting to set up, revise, etc. I’m not looking for perfection, but am seeking some approach that will come closest to my desired goals.

To clarify, I’ve only gone so far with setting up @Frederiko’s scripts. I didn’t go all in because of the main problems I’ve had: the lack of iOS interface, causing me to effectively redo annotation-input from the iPad to the script, and how one has to silo tag systems per database, thus preventing crossover tags/groups/hashtags (whatever) for global themes.

I’m not going to revisit the points in my opus. You’ve made your point. So let me do this… I’ll try to succinctly answer your question: “But just what are you “aiming to do”, exactly?”

Ideally, I think that would involve:

-Easily clip articles and documents in a readable, annotatable format (e.g., PDF)
-To a secure service (important) that can synced for / between Mac and iOS platforms
-Annotate said articles and documents through a tool that’s similar to what Marginnote does, namely:
-Allowing users to create outlines of annotations, as well as affixing notes and hashtags (or tags, whatever) to those annotations, and then
-Export those annotations with hashtags / tags to be imported into DTP document libraries, so that
-The annotations with hashtags / tags would correspond with DTP groups (tags…whatever), and
-That there’s some way to have hashtags / tags for specific projects, as well for global themes.

Finally, I want to find an approach that doesn’t force me to expend more energy organizing my annotations – than actually reading, annotating, and synthesizing the material. My struggle to organize my annotations has been matched by my frustrations over the time consumed to curate them. I’m just trying to solve that so I can get back to the business of reading annotating, and not worry about that anymore. That was the purpose of laying it out in my opus.

Thanks again for your help.


You won’t find a simple, manageable, lower-energy workflow that accomplishes all those requirements simultaneously. You’ve got way too many goals going on at the same time.

The point of research and annotation is discovery – finding relationships and patterns in your notes. You can’t avoid curation.

But I think tagging is a rat-hole of work with very little benefit. You have to constantly be thinking about making notes fit into pigeonholes and wondering if you’re doing the right thing. Simply put: tags do not make research better. They make it worse because your mind isn’t focused on understanding what you are reading – it’s focused on managing a massive list of categories and hoping you don’t miss something. And then days, or weeks, or months later you can’t find something because you didn’t anticipate the right tags.

If you examined your requirements, above, and deleted everything to do with tagging and organizing tags – and gave up the tagging habit – you could be left with:

  1. Clip everything to DEVONthink and annotate it there – on the desktop and in DTTG.**
  2. If you want to break down your annotations into discrete notes then use Highlights when you get back to your DEVONthink desktop
  3. Use DEVONthink’s “see also”, “classify”, and (my favorite) the contextual menu’s “See Related Text” command when you’ve selected text in a document or note.

Here’s a trick: in a document select some text and use “See Related Text”. The right panel will open with “see also” suggestions of related documents. In the right panel choose these suggestions and then Data > Create Table of Contents – you’ll get a nice snapshot listing (with document links) of the related documents that you can save and browse, and annotation, and do whatever you want.

Finally – this seems obvious, but it’s a lot less stressful if you compartmentalize your effort and break your work into phases:

  1. I’m just browsing and reading and clipping
  2. I’m reviewing my clippings and taking notes / annotations
  3. I’m organizing my notes and looking for patterns, consolidating thoughts, taking additional notes

[size=85]** I’ve told you about MarginNote in the past, and I’ve also been clear about this: MarginNote is great, but it will never integrate well with DEVONthink. The two apps’ organizing metaphors are radically different. Integration will never be smooth, without numerous intermediate steps between the two. I use MarginNote a lot – as a stand-alone research environment. I gave up years ago trying to make it work seamlessly with DEVONthink. It just can’t.[/size]

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This. Is. Awesome!!!

Thank you so, SO much! Cannot tell you how much a relief this is…

I think I had to go through a series of convoluted annotation-organizational approaches to have a “coming to Jesus” moment where I realized that tags, while nice in theory, were ultimately a time suck that wasn’t helping me synthesize and retain relationships and patterns with my reading & annotating. So, this is…totally liberating. I might still use tags for certain task-based approached (e.g., follow-up reading, follow-up questions, further review) or where there are notable features in text (e.g., strong quotes, important point, etc.). Beyond that, I’m done w/ them. So, THANK YOU!

Super quick questions… (I’m honestly trying to be better.)

-I’ve always been operating under the assumption that it’s best to make annotations on PDF formatted documents. Is that still the case with this workflow?

-I’ve been reviewing posts, tutorials, and other texts (in this forum and beyond) re: setting up DTP so that it can optimally use “see also”, “classify,” etc. Are there particular posts on this topic that you’d recommend checking out? Thanks! It just seems like laying the right foundation could be a crucial step, so I’d love to get a better grasp of that.

-In that same vein, would you suggest selecting various docs, and then running Auto Classify? Or, in this instance of DTP’s A.I., do you think it works better to have users first set their own topical groups before running “see also”, “classify”, and “See Related Text”?

One small question, (now) unrelated to this process. You said, " I use MarginNote a lot – as a stand-alone research environment." Could you explain why & how you do so? I ask because it seems like our approaches to research are similar in some ways, and I seriously dig Marginnote, so I’m curious to hear about your approach.

And yeah, I hear you about “the two apps’ organizing metaphors are radically different.” In a sense, this whole process might compel me to finally get serious about learning Tinderbox, so I can utilize the mind mapping approach found in Marginnote. By the way, FWIW, I’ve heard that Marginnote is still trying to a way to interface w/ DTP. We’ll see.

  1. Things to read here re: AI. Anything on the topic from Bill DeVille. Bill’s take on using the AI is practical and based on his experience as a researcher. I can’t point to a specific post – there are too many.

  2. MarginNote standalone. Because I really like Sun Min’s implementation of notebooks (note taking and web research on topical groups of PDFs / ePUBS) . The notes are integrated across all the documents in the notebook. I can draw connections between clips / notes related to different PDFs. I cannot do this easily in DEVONthink. It’s not that MarginNote is better, it’s that it’s a different metaphor. I don’t need to research the same question in two places, so I pick the tool I want at that time.

  3. “it’s best to make annotations on PDF formatted documents” – I don’t think I understand the question. Because PDF’s can carry annotations with them easier than, say, webarchives, I guess it’s preferable. But when it comes to note taking, nothing is canonical – it’s always just about preference and what works for you. **

  4. Tinderbox is not a mind mapping app. Sure, you can create beautiful maps – I do this all the time – but just because it has some visual components does not make it a peer of iThoughts or the like. Before you dive into Tinderbox (there is no bottom to that ocean), spend time lurking on Eastgate’s old forum. (The new forum is only a few months old and the conversations are just developing – the old forum has been running for a very long time, with long-lived conversations about important use cases.) Also, get to know Mark Anderson’s aTbRef – the best user-contributed how-to.

** [size=85]Example: I am working through the Manzotti / Parks dialog on consciousness that NY Review of Books has published over the past several months. Six articles thus far. As they come out, I print them as PDFs and open in MarginNote (from the print dialog). There, I have a Notebook that combines the 6 articles in one study set, and I will add the newer articles as they come out. I can annotate and comment on the whole “Manzotti Notebook”, immediately create links between notes, bring outside references from the web into the notebook, sync the work up and down to my iPads, and work on the analysis wherever I am. Sure, I could do all of that with DEVONthink / DTTG, but I’d be forever fiddling with a group of files and couldn’t see the links that are important to following the dialog over time. Research of this sort is best done standalone in MarginNote, IMO, and there is no comparable app for all Apple platforms. If I didn’t care to have the source material with the notes, I would do this on Tinderbox, but there I would be limited to macOS only. I am not a big fan of DEVONthink for in-depth research / note taking of this sort.[/size]

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This is wonderful discussion.

I completely agree with Korm’s view of tags. I also do not organize my library with Tags. But, I use them for running projects.

After I use “see also” feature, for the pdf files that appear top on the right, I select them and assign my project Tag to them.

So, if I am writing an article on [causatives], I will assign that term to those top sources. I have a smart folder inside my project container which scans for sources containing that tag. It collect the sources there. There are false alarms in the AI: I remove the tag from that file. Causative can be used in non-techincal way in a paper for example. The AI cannot identify that. I have to remove the tag from that source manually.

Then, depending on the sources, the files collected in the project folder get dragged into Tinderbox. I map their relations; develop new directions on the map view inside Tinderbox. That makes me use the best of DT which is the AI; and the best of TB; which is the visual presentation of ideas. So, Tags basically feed into Tinderbox. They are my means of filtering out files for a specific project from the ocean of sources that I accrued over the years. AS soon as the project is done, everything is archived back in Devonthink and deleted from TB.

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Great tip.

The point is that you can do things with the list itself in See Also, not just look at it. @Dellu’s example is perfect for that.

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Korm: by the way. I would like to encourage you to write a Mac productivity book (=tips and tricks focusing on the knowledge management softwares–Devonthink; BE; TB; Curio etc). You are one of the most knowledgable persons in these forums I have every known. The tips and tricks you give us in the forums [Curiota forum and Devonthink forum;] could just make a book if you collect them. I don’t know how lucrative these books are–but, yah. I think you have the best tips and tricks out there. I would be the first to buy.

:neutral_face: Thanks, @Dellu. Someday. Maybe.

@korm - thank you!

Got it re: Bill DeVille & AI. I’ve already skimmed some of his posts on the topic an will give them a closer read.

Yes, got it re: Tinderbox. I misspoke in describing it as “mind mapping.” I’ve been knocking around on their forum (I guess it’s their old one), and the fellow users over there have been incredibly helpful. I do find it to be a rather daunting app - “bottomless ocean” perfectly sums it up. Hopefully, I’ll be able to conquer the basics, since it seems like a good approach with sort out some of the complex research I’m aiming to do. I’m familiar with the other forum as well - thanks!

Onto MarginNote…

You’ve perfectly summarized many of the reasons why I’m drawn to MarginNote. I feel like it’s annotations features are strong and pliant, allowing users to seamlessly make connections between notes and disparate documents. I genuinely want to continue using MarginNote because I feel it improves the way I read and form connections to the text, and other material. And it’s valuable to find an app that can genuinely improve your thinking.

I had hoped to bridge MarginNote and DTP because I’ve got a ton of existing material in DTP files, and even my archival files sometimes relates to ongoing projects. As much as I really like MarginNote’s notebooks, and want to build on links between new articles and old text, it doesn’t seem practical to port everything over to it from DTP to achieve that.

I suppose that’s sort of the conundrum I face with MarginNote vis-a-vis DTP: I want to continue to use MarginNote for annotations, though it doesn’t seem appropriate for managing high volume data (or integrating with my mass archival files in DTP, imported and indexed); alternatively, that’s one of DTP’s strengths (through A.I. and the various other amazing tools it provides). While DTP will remain an essential app for me, doing the kind of annotation workflow that we utilize in it requires, as you put it, “fiddling with a group of files” sometimes making a bit more limited to “see the links that are important to following the dialog over time.”

I’m not asking you to solve this for me, though I’d love any input you might have. You’ve clearly explained the reasons why MarginNote doesn’t interface with DTP, and that certainly makes sense.

Let me ask this: How do you archive your MarginNote notebooks and files? Even if you’re not using DTP for annotation, are you using it as a final repository for your files? It would be useful to understand your workflow in this context, just help glean ideas about how one might (perhaps) still use MarginNote’s annotation while aligning it with DTP storage in some way.

Thanks again. Really appreciate it.

This is a really ingenious approach, and I thank you very much for sharing it. I want to make sure I’m properly understanding it, though.

I understand that you run “See also” on a PDF, and ID files that it produces in the sidebar window, and then apply the [causatives] tag to the appropriate files. But I was confused about why (or how) you use a smart folder instead of just using the tag itself. Is it the location within the group for a particular project?

But I think I follow the rest, as far as using the collected files, dragging them into Tinderbox, and mapping their relations. I think I’m getting close to the point in which I’ll soon be able to do it!

Thanks so much again…

You beat me to the punch! I was going to make the very same recommendation.

@korm - I hope you take this recommendation seriously. Your posts have been enormously helpful, but they would benefit far more people if you could weave your knowledge and suggested approaches into a more comprehensive document. Please consider this – seriously.

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Yes, it is a location within a project group (=pCaustive).

The project group within Devonthink ( pCausatives) typically contains two types of items. It contains the PCausative project folder in finder where I run the Latex. I want the Latex drafts to be part of the search system in Devonthink. Plus, i want to open and edit the latex file inside Devonthink.

  • it contains the smart folders which scavenge for files tagged with the project tag [causative] (by the way; I do not use the braces in the tags: I m just using them here to make them distinctive). The files could be PDF files; indexed in Devonthink: or other types of files (rtf) typically snipped to Curiota (nvalt) or Devonthink inbox.

The tags feed the project folder in many different ways, from different directions. I assign the tags inside Finder; using Alfred: via Hazel…etc. They all hit the project folder ultimately. That is the function of the tags.

Then, as ideas grow in Tinderbox; when they mature enough for drafting (writing), I push them to Latex (have a system to copy the RTF and paste it in Latex).

I tried Marginnote by the way: here is my reflection on it (and other readers like PDF expert, highlights and Skim): … df-expert/

It’s useful to understand that MarginNote does not add the annotations to the PDF file itself. The PDFs are stored in one location (usually iCloud Drive) and the annotations in another (can be iCloud drive, or Dropbox). So, you could index the PDFs in DEVONthink, I suppose, but it’s not easy to index iCloud in DEVONthink and your notes would not be visible because of the way MarginNote stores annotations. The annotations are stored in .opf files, a binary format related to ePUB. When I’m finished with a project in MarginNote I export the notes to .mmap and .oo3 for “archival” purposes – I store these exports in DEVONthink. You can also export a PDF document from MarginNote – this is a bit misleading, since what is exported is an image of the annotations, it is not a PDF with editable annotations.

In a sense MarginNote is fragile (if Sun Min gives up on it, so do all of us), but not unusually so. There is no way to associate the notes to the PDF without MarginNote. Just as there is no sane way to reconstruct a Tinderbox map from the Tinderbox .xml file without Tinderbox.

You might already know that MarginNote can import annotated PDFs, but MarginNote does not recognize annotations made by DEVONthink. I usually use Acrobat for annotating files.


There is a lot of pushback against tagging so I think its worth reviewing when it is useful.

The important distinction to be made is that folders are for storing documents and tags are a way of storing metadata about those documents.

The purpose of adding metadata to a document is to make that document findable and classifiable in another context. If you are going to tag you have to have a clear understanding what those contexts are. Once you understand these contexts then things like tag categories and auto-complete of tags help keep the contexts consistent.

There are two approaches to adding metadata with tags:

  • You know actually what metadata you want to add to the document before you even start. There are obvious examples of this sort of metadata such as the date the document was created, the author of the document, the addressee of the document and so forth. In much the same way as I would not want a document in a database that did not have meaningful title, I would not a document in the database which reflected an interaction between people unless it properly reflected the sender and receiver as metadata.
  • You dont know what sort of metadata may be useful before you start working through the documents. A common example of this is the type of document. After reading through a bundle of document you realise that they are composed of invoices, handwritten notes, typed transcripts. etc. and you decide that these are useful categories to add to the document. This is the sort of metadata you might choose add on a second review of the documents

It may be that the type of work you do does not require metadata at all. For less than a 100 documents, the visual representation of the layout of the documents in DT combined with ones own memory means its almost not certainly worth adding any metadata. If you are dealing with documents that use clear and distinct terminology then the AI may also be good enough for you. Where however you are dealing with thousands of documents, meticulous metadata can be invaluable to finding connections or even in locating documents or annotations which you can only identify by a single feature.

Adding metadata can seem unproductive and boring and frequently is. I think if you have many documents and the resources it is worth employing someone to add the metadata for you. Its may not be directly worth your time to add the recipient, addressee and date to several hundred pieces of scanned correspondence but when its done for you, its invaluable. You can process the documents and see the connections between them in half the time it would otherwise take. Instantly you can choose to see only correspondence between two people of interest without laboriously searching through the documents. Expand this to thousand of documents and the benefits only multiple. If you export your notes to Aeontimeline (or I imagine something like Tinderbox), tags groups are the only real way to export the context of the notes.

I have written about tagging and metadata in other contexts which may be interesting if you are new to the topic:

Using annotations to build a chronology
Tags and folders are different

Whether tagging is useful to you will depend on what you need from your workflow.


(As a side note, in the legal field coding, as tagging is termed, has well established hierarchies and methodologies (Unitisation, Subjective, Objective, Physical, In Text) and whole software products in the windows world are built on making this process efficient and consistent. The procedure is that you code the first hundred documents and then the AI processes the remaining thousands of documents and codes them automatically for you (based on its interpretation of your initial coding), presenting you with only those that it has a low confidence about its code assignment, for review. The AI in these products is truly impressive but then so is their price!)

Sorry for being away from this thread for a while. Really appreciate everyone’s contribution – it’s been enormously helpful.

FYI: MarginNote now interfaces better with DTP through creating RTFD export notes. It’s a really nice development for those who use MarginNote & DTP, and I believe they’re still ironing out this feature.

Per @korm’s advice, I’ve broken up my work process into simplified tasks:

(1) clipping;

(2) taking notes / annotating clips, and;

(3) organizing notes & annotations.

I overhauled my DTP Inbox to create an easier way to clip articles & documents, and to create parity with DTP & DTTG’s clipping options, namely:

-A tag system to for grouping files (clips) into topics, and;

-2 raw articles & documents groups (clipped files), and;

-2 annotated articles & documents groups (read & annotated files).

(Quick request: I wish one could also add a Label to clips in DTP/ DTTG.)

After clipping files in DTP/DTTG, I can then select Open In… to read & annotated these files in MarginNote, and use their outline and mind mapping features.

In the past I tried to create a kind of cradle-to-grave system of annotating documents, and then saving discrete annotations (as well as the annotated files) into DTP groups (or tags).

Thanks to everyone’s advice here, I’m now relying on DTP’s AI to help organizing discrete annotations & notes vis-a-vis groups.

But now I’m trying to figure out the best way to retain files that I keep in MarginNote for ongoing projects – and when to export MarginNote-annotated PDFs and RTF exported notes to DPT.

More specifically, here’s the dilemma I’m trying to figure out, and would appreciate any ideas / suggestion…

I work on a number of ongoing projects, and their importance rises and falls depending on external demands (e.g., editors’ interest in certain projects). As I’m working on process that combines MarginNote & DTP, I’m trying to figure out how to long to keep files and annotations in MarginNote that relate to ongoing projects, and then when to migrate them to DTP. I can keep annotated files within MarginNote, esp. with they relate to high-priority projects I’m currently working on. But I wrestle with keeping everything within MarginNote v. porting discrete annotations, as well as annotated files (PDFs), over to DTP (not to mention keeping so much data floating on the iCloud for MaginNote) – even if they’re part of ongoing projects that involve continued reading and note-taking on particular topics.

(Perhaps there’s a way to retain some of the notes & annotations from MarginNote within a notebook, even after such files have been migrated to DTP…)

Anyway, I welcome any ideas, suggestions, and insight others users might have who use MarginNote & DTP together for annotations and organizing notes.

PS-I totally appreciate @Fredriko’s point about tags. For me, I just found that I was getting lost in tag curating, and that was impeding my annotations in the end. But I’m sure there are other effective ways of using them (e.g., some of the ways that @korm and other described strong approaches that seem efficient and powerful).

Thanks so much for everyone’s help & suggestions. I think I’m getting the hang of this new work process, which has been working out great. Just got some questions re: some fine tuning.

Like I said (above), I overhauled my DTP Global Inbox to create an easier way to clip articles & documents, and to create parity with DTP & DTTG’s clipping options.

After clipping files in DTP/DTTG, I then select Open In… to read & annotated these files in MarginNote, and use their outline and mind mapping features.

For now, I’ve been keeping the original PDF files in my DTP/DTTG Global Inbox (within raw articles & documents sub-groups) until I’ve completely finished annotation them w/ MarginNote. (Still trying to figure out a better temporary repository for these MarginNote-exported files that are in abeyance during my annotations - so that they’re in DTP, but not clogging up the Inbox…haven’t figured that out yet.)

@korm has been incredibly helpful w/ suggesting an amazing work process for further organizing discrete annotations and notes through exporting MarginNote Notebooks to iThoughtsX and then to Tinderbox.

Anyway, I’m trying to better understand @korm pre-MarginNote annotation process, and the “archival” saving formats since they seem integral to the cradle-to-grave annotation process. Here’s what I’m referring to…

This is very helpful. I’m just wondering:

(1) (Cradle) Why do you use Acrobat for annotating files? I understand what you mean when you said that MarginNote “does not add the annotations to the PDF file itself.” But it seems to me that one would be doubling the work by first annotating a PDF in Acrobat (or Skim or Preview), and then further reviewing and organizing annotations from within MarginNote. Is it just a way to ensure that the annotations are a more permanent part of the original PDFs?

(2) (Grave) An extension of that point, which reflects my ignorance on export formats… Could you explain a bit more about why one wouldn’t just “export a PDF document from MarginNote”? I (sort of) understand that “what is exported is an image of the annotations, it is not a PDF with editable annotations” but I don’t quite get the functional limitations of what that means. In my case, I mostly just want an archival file that shows the annotations - and, ideally, can link back to them in MarginNote. (It seems MarginNote is still working out the kinks w/ some of that functionality.) I don’t know much about .oo3 formats. Would saving MarginNote annotated files in that format (or some other format) allow me to see / access MN-created annotations and do additional edits to the file, should I need to do so in the future?

Thanks so much again!