Advice/best practice for accessing and connecting research and quotes for a book

I’d appreciate advice regarding best practices for connecting research for outlining and/or mind mapping ideas that will end up as the headings/subheadings of chapters in a book project.

I’m working on a large book project. I have collected a lot of digital research/resources. The material is primarily in one of three formats: PDFs, plain or markdown files, or archived web pages.

Currently all of the documents are in folders/sub-folders in iCloud and accessed through the Finder or through the Files App. They were originally in DEVONThink but I was having syncing issues on iOS so I moved everything out of DT to iCloud.

Currently Used Primary Apps

  • Scrivener–my long form writing app on iPad Pro and the MBP
  • Scapple
  • MindNode
  • PDF Expert
  • I’ve downloaded a trial version of Curio but have only tried a few ideas in the app. I don’t have an opinion on this app yet.

Possible Other Apps to Use

  • Curio?
  • Coda?
  • Notion?
  • Roam (the subscription price is too high for my tastes)
  • Other?


  • Cross platform MBP and iPad syncing in iCloud
  • No subscription required – though if the application is strong enough and cross platform I’d consider ~$60/year as reasonable

My struggle
I may be making this much harder than it needs to be. What I’m trying to do is review each research document related to a particular topic, say team dynamics and cull out the important ideas from the document into a system so I can manipulate the information around and connect it to create final headings and subheadings for each chapter I’m working on.

I’m trying to capture a visual outline or mind map of the ideas/concepts/quotes so I can connect them by copying/pasting/dragging them into an application so that the resulting content does not require reopening the source file. If I use a mind mapping app or free form canvas app like Curio, Coda or Notion, then I only want to type (or cut/paste) a few words with the remainder of the content embedded in the app or branches of a mind map for quick reference.

Ideally I want to be able to export the results into each chapter in Scrivener as headings/subheadings. From there I’ll start the writing. I’m looking for a “bridge app” between the research documents and Scrivener to ensure I capture and connect all of the major ideas, facts, and concepts from the research into appropriate conceptually connected headings/subheadings for each chapter in the book.

Now here is where I may be making this harder than needed. In the “good old days” I had a stack of books and research literature for my dissertation stacked everywhere and I took notes, arranged them in legal pads or note cards, and then started writing. I can certainly do something similar again but I’m hoping there is a better way given all of our new digital tools.

Any best practice advice will be appreciated!


The OPML export/import described here also works with Mindnode:

I’d stick with the tools you have.

By this do you mean creating a link/alias to the original source file? You could create an outline like this using Evernote, as you can create links for a given individual note, but I’m not sure how you’d extract this into an outline for another application like Scrivener.

I don’t use Scrivener, but isn’t this an inherent feature of the app?

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Yes, Scrivener has a good outline feature and I can import mind maps but my only option seems to be to copy/past text from a mind map into the notes field of each outline heading which is a chapter in Scrivener. If I import a mind map it creates a sheet/doc from each node. This is perfect when outlining a project from the beginning (in fact this is precisely how I created the chapter outline to begin the project) but this does not work for headings/subheadings within a chapter.

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It does and this is how I created the overall book outline by chapter. But, I’d like a way to do the same for headings/subheadings within each chapter, which as far as I can determine is not possible with a mind map import.

Did you enjoy using devonthink? If the issue was sync, then the forum is particularly helpful in fixing sync issues. I sync via bonjour and have been happy with it.

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Yes, I like DT a lot but there are two issues that have caused me to sideline it for a while:

  1. The iOS version is very bad for any editions work, especially when using the new Smart Keyboard on the iPad
  2. I was having a lot of syncing issues on the iOS/iPadOS devices. Because I use the iPad a lot, this is a problem.

Hopefully, the upcoming iOS/iPadOS versions of DT will resolve some of these issues.

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It’s been a while since I’ve touched Scrivener, but this sounds like a good use of Scrivener’s ring binder and index card paradigm. Copy/paste to an index card, rewrite in your own words, then rearrange on the corkboard to structure whichever part of the book you’re working on.
I believe the scrivenings mode would apply here too, as you can move chunks of text around for better flow, or to suit other needs.

Essentially, Scrivener has the digital tools to emulate your analog system used in your dissertation.

Have you done any training on Scrivener? It sounds like rather than trying a new tool, the existing one would serve your needs, without the need to bridge between apps.

Reports on this forum and elsewhere indicate that switching to Bonjour/WebDAV for iOs sync seems to solve most if not all those issues.

I’m glad humility is a virtue because I’m about to demonstrate humility—I really don’t understand hat Bonjour or WebDAV are. I’ve never had a need to use those syncing options.

Liquid text does some of this. It’s a very cool app though for extracting pieces and linking them together. They are still working on iCloud sync, but you can easily export the file and open on another device.
Highlights is cross platform with good export options but is more of a reading/annotation app than a mind map tool.

From Joe Kissell’s free Devonthink ebook (which I recommend DevonThink users read cover-to-cover)

For direct Mac-to-Mac (or Mac-to-iOS/iPadOS, or iOS/iPadOS-to-iOS/iPadOS) syncing to work, DEVONthink must be running on both devices, which must also be on the same network. If this arrangement is possible, direct syncing is the fastest and most efficient option, and has the lowest risk of conflicts.

Bonjour (direct connection): This option lets you sync directly with a copy of DEVONthink running on another Mac or iOS/iPadOS device on your local network (or even over a USB cable; see How to Sync by Wire). Although the syncing is bidirectional, one device effectively acts as a server and the other(s) as client(s). You must set up a password on the server and then authenticate with that password on your other devices; this prevents unauthorized users from syncing with your databases.

WebDAV Server or CloudMe: You can sync your database to a WebDAV server on your local network or on a remote network. You’ll have to specify the server address, the path to the desired location on the server, a Store Name (the filename you want to use on the server), your username, and your password. (DEVONthink uses HTTPS and/or a custom port if those are included in the URL.) Because the cloud storage offered by CloudMe is accessible over WebDAV, you can use those as locations for a sync store, and DEVONthink even offers shortcuts to set up those services.

A lot more on the subject, and the ebook describes step-by-step instructions for syncing DTTG.

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FYI since working from home I’ve switched all my DT syncing from iCloud to Bonjour & it’s way better.

I’m never tired of recommending Qualitative Data Analysis (QDA) software (like MAXQDA, Nvivo, ATLAS.ti) to do literature review, especially for a big project. Myself is using MAXQDA to my thesis project. I can imagine my lit review would have been a disaster without it. Here is the reason why👇

An additional reason I can think about is that QDA software is one of the closest instruments to achieve what so-called Syntopical Reading, proposed by Mortimer J. Adler and Charles Van Doren in his famous book—How to Read a Book. :point_down:

I also mentioned the same thought on a Twitter thread. :point_down:

In the same tweet thread, I add a reference to a blog about how to use QDA (Nvivo in this case) to do lit review. The blogger even made a video demo. Highly recommended to have a look! :point_down:

ps. @msteffens 's in-progress app—Keypoints—might be a powerful tool to do research👇


Our host @macsparky inteviewed someone about a similar academic workflow:

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First a big THANK YOU for the excellent advice and help. I have finally figured out what will work. I’ve spent all weekend on this issue but I do believe I have it resolved to my satisfaction. I have one follow-up question and then below is a simple summary of what I have done–I’ll spare you the gory details. :slight_smile:

The Question:
All of my research files that are not already PDF’s or webpages have been converted to plain text. The iPad, which I use for a substantial amount of my writing, does not have the Mac’s TextEdit app.

I would like a consistent experience in opening and using the plain text formatted research files in DEVONThink (see below) and Scrivener on my Mac and iPad. I have Drafts and iA Writer.

Do you recommend that I set the Mac to use one of those (and if so which one) or another app for opening and managing the content of these files on my Mac and iPad for a consistent experience?

What I did to solve my dilemma

  • I converted all non-PDF/Web files to plain text
  • I deleted my old DT databases (after backing up) and created a new research database that indexes files from iCloud. The result is faster and so far…provides trouble free syncing between MBP and iPad. I think I can avoid dealing with Bonjour.
  • I discovered that I can bookmark internal and external links within Scrivener to iCloud, DT, etc., as well as to internal Scrivener documents. Using the Scrivener Index card synopsis feature I believe I can make the necessary conceptual connections I’m seeking and avoid using another application.
  • I have used Bookcision to download as plain text files all of my Kindle notes and annotations, which are then indexed to DT and indexed as needed in Scrivener from iCloud and/or DT.

I cannot thank everyone enough for taking time to give advice. Because of folks like you this forum is indispensable! Thank you!


As a fellow academic, I love good follow-up :slight_smile:

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John, you hit the nail on the head! Scrivener certainly sounds like it could help get the job done as it is apparently the closest thing to the “good ol’ days”!

I, myself, could easily get caught up trying to reinvent the wheel when the solution is staring me in the face. I can apply that to my own writing. And I thank you!

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Seeing as you have DEVONthink, I’d give it another chance because it is the ideal tool for organising research, it’s designed for what you need. You still have to devise a system yourself but it is easy to organise, tag and then search through your material once it is indexed. The AI suggestions are amazing for linking the different documents and seeing connections.

I would leave the files in iCloud and index them with DEVONthink, then use WebDAV to sync to your iOS devices.

Sync in DEVONthink requires that the app is open to complete. This can take a long time, a few hours with a lot of material if it is being downloaded locally. I turned off the auto-lock on the iOS device and allow it to complete in one session last time I set up an iOS device and it worked perfectly with tens of thousands of documents. Personally, I use iCloud and have no issues but if that didn’t work for you maybe you’re better off with WebDAV as everything is synced locally between your devices, as other posters have pointed out.

@Rob_Polding thanks for the input. That is in fact what I decided to do. So far it seems to have resolved most of my issues. I believe the combination of Devonthink and Scrivener is going to work fine in the long run. I do not believe I need another app to accomplish this project. Thanks again.