Organizing Reference Library - Filesystem; DevonThink; Other Options?

@JohnAtl - Thank you for this and for drawing @beck into this post. I think the benefits of DT incorporated into a system where it’s as

May be very useful to me. I don’t really want to let go of my PDF Expert annotation process.

This is very helpful. Thank you.


@beck - you are one of my new favorite people. I’ve scoured your website and while my current system is different than yours in some respects, our foundations seem identical. The ability to search my own curated list the ways you describe is important to me. Thanks to you and @JohnAtl, I’ve now spent hours reading about this curious note-taking system known as zettlekasten. It’s fascinating. I’ve been a die-hard outliner since I learned about them in fourth grade. But, again, the process I use is similar to what you zettlekasten practitioners do. I capture notes in an temporary place and then capture them permanently into an appropriate home in my outline. Anyway, I was encouraged to hear that your very well-thought out system has redundancies and inefficiencies. I, too, can live with those, as long as the system itself has minimal friction points. Your posts and your website are extremely helpful. Thank you.


@DrJJWMac - Thank you for understanding the “problem domain” and your synthesis.

I think this was right on.


@OogieM thank you for sharing more about your usage. I am starting to feel like, if I use DT, a mix of imported (archives) and indexed materials (like the mutable content @JohnAtl mentioned) may be the right solution.


Thanks again, all of you referenced here or not, for your helpful contributions as I work through this.

-Tom

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Have you rebooted since the OS change?

Tom (@iPersuade), thanks for your kind words and I’m so glad you created this thread as it 1) helped me articulate a bit of my system and 2) helped me learn from others who have concocted their own. :slight_smile:

I, for one, would love to hear more from you on outlining. I’ve never been much of an outliner and imagine that I’d benefit from it in my writing. Do you have any practices or nuggets of wisdom you’ve shared elsewhere or might share here with us?

— Beck

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I think of an outline as “a family of statements that is looking for flow”. Like, writing thoughts, or assertions, or facts, or questions, etc., on index cards and then sorting them and editing them until the statements fit together from top to bottom / beginning to end. Except outlines are more efficient than index cards.

When I start an outline I don’t know as much as I will when I finish it. It’s the act of thinking about the subject while writing about it. Thoughts come to mind, and can be fit back into the outline – or taken out – as the outline develops.

Outlines can have complications in some software – like Tinderbox which really isn’t for outlining – such as attributes or metadata and so forth. For me the best outlines are the ones that take 15 or 30 minutes start to end, until there is enough of a framework to segue into the next exercise: writing.

I never outline on paper – too slow and constricting. I never use mind mappers to outline – too much busy work fiddling. My favorites: Outlinely and Dynalist. Just the right amount of extra features without making the act of outlining all about playing with software.

I have to mention Gingko here, as we’re discussing outlining, writing, and thinking.
I’ve purchased it, but haven’t put it too good use yet (working on other things).

I agree with you on outlining on paper and I don’t think in pictures so mind mapping fails for me most of the time. What I’ve been testing and loving as a way to outline is use Scrivener in corkboard mode and put each main topic as a card and then just keep adding. I get the benefits of text entry but can move them around and combine and split topics easily. When I’m done I have my structure all ready to go in the app I am now using for almost all medium and long form writing.

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Personally I’d love to hear @beck on the MPU podcast, @iPersuade please put her in the queue.

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I totally agree with you, but I think you wanted to call out @ismh!

My fault yes @ismh and @MacSparky get Beck on the podcast

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I’m happy to share my thoughts on outlining for you; although, my process is not documented nearly as thoroughly as yours are. So let me give you…well…the outline.

What do I outline?

At the outset, understand that I outline for three purposes (the first two perform essentially the same function). First, like many people, I outline as a precursor to writing something. I might outline a brief, a presentation, a speech, a paper, an article, a book, etc. This is essentially the same as what @anon41602260 described, although my outlining process may take days or weeks depending on how complex the topic is:

Second, generally speaking, outlining is my preferred method of planning. Whether it’s my “to dos,” or as they call them in OmniFocus, action items; the way I’m setting up my office; a trip I’m planning, I organize in hierarchical lists.

Third, and most important for this discussion, my outlines are often “the final product” of something. I.e., I outline for the outline’s sake. The typical basis for this is any synthesized reference material that is meant for my periodic review, analysis, and reference. Think of it this way, one can throw all sorts of things – documents; web pages; articles; scraps of thoughts – into a program like Evernote. But storing information in a repository like Evernote is only half the work. The real work is extracting the valuable information on the topic, relating it to other important information on the topic, and making it easily digestible in the future.

For example, my job requires me to communicate both in speaking and in writing. So, I read lots of books and articles on speaking and writing skills. I could just highlight the books and put them away. But then I need to remember the right book and leaf through that book again to find some information I might need. Or I can highlight a bunch of articles, put them in my note database, and leave them there for reference. But, once I want to get information on a topic, I have to use search tools to find it.

Instead of doing that, I capture all my notes and thoughts and put them into a comprehensive outline. I wrestle with the material to develop a hierarchy of information that relates it all together and makes it easy to find. I can refresh myself on everything I’ve read on a topic by looking at one document and it takes me only a short time to do it. Then, since my outline is tagged to the references, I can always go back and read the source material if I need to dig deeper.

Again, this is much like the nice way @anon41602260 explained it:

I have outline for legal topics. If I’ve researched something once, I don’t want to re-do that work. Certainly, I have to update my research from case-to-case, but it’s nice to have a starting place. I have outlines for skills I’ve learned, like speaking skills. I have outlines for my hobbies, like classical music and rock music. I even have a series of outlines I’m putting together for things that I’ve learned that I want to be able to pass on to my kids.

Why do I use outlines?

For me this is simple. I outline because this is how I process and make sense of information. I capture it, I analyze it in my mind, and then I try to organize it in lists that help me understand and retain it. Those lists turn into hierarchies that we know of as outlines.

I don’t think in mind maps. Often, a visual can help comprehension and I include diagrams or pictures in my outlines from time to time. Generally speaking, though, I think in words. Like @OogieM, I don’t think in pictures.

What is my process?

My process comes in five parts: capture; organize; re-organize as new information comes in; review; and repeat.

When I read something, I annotate it. I take those annotations, which consist of the piece of information, quotation, thought, or the like and a reference to the source, and I dump them in the bottom of my outline. They are un-organized, just captured so I don’t forget them later. In the second phase, I will work directly in the outline and start processing the information. That process generally results in moving components around into different places in the outline. While the author may have put six points together in one chapter, those concepts may be spread through different topics on my outline.

In the third phase, I end up reorganizing things even more as I learn more, relate concepts from one author to those of another.

Finally, I have a reference tool that I can go back to for a quick review of the material I’ve studied.

It is this process that enables me to synthesize large bodies of information in a way that works with my brain.

What tools do I use?

I used to outline just in WordPerfect and later Word. Like @OogieM and @anon41602260, except in the case of taking live notes, I would never outline something complicated on paper alone. I primarily use OmniOutliner, which is about perfect for this process. I can have simple or highly-formatted outlines, the tool makes it so easy to move things around, the columns feature allows me to separate references from concepts and add other metadata-like things to my outline, the search tools is robust and I can even drill down to find all my notes from one source; and the apps are just as useful on iOS as on macOS.

I use Scrivener for outlining any material that will end up in a more formal writing (i.e., where the outline is not the end in and of itself). I also love the corkboard feature and find it just as efficient at re-organizing things as OO is.

I use Word if I have to, but usually only for ephemeral things, such as a pre-writing outline for a letter. Outlining in Word–which has improved over the years–is still not great for moving things around. If you use outline view, you can make do. It’s not ideal, though.

If I have to give a presentation, I sometimes create an outline in Keynote by creating all the main topic slides and then filling in the detail as I develop the presentation. But often when I present, I just display various source documents, but I organize them in an outline using a naming convention. Then I can just click to the document I want to pull up as I progress through the talk.

Finally, for other less intensive outlines, an Apple Note with formatted text will work. I have a great outline on all the features of LaunchBar that I learned from the Take Control Book and other places that I use as a quick reference to LB features that I don’t use regularly enough to remember. I have outlines for command line tools for Terminal in Apple Notes, etc.

I hope you don’t regret having asked, @beck!

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Great post.

I pretty much think and expand on ideas in outline and checklist form. I too use OmniOutliner, but grudgingly. The app remains stuck with a clunky user interface and set themes that I don’t like much. That said, it’s better than any other Mac outliner I’ve used since Symantec’s ‘MORE’ from the early 90’s. MORE still has features that modern (ahem) outliners still don’t have, like cloning (alias-text that when edited simultaneously edits all clones).

TaskPaper, OutlineEdit, CloudOutliner Pro - I’ve bought them all, but they all have their own disadvantages for me.

For some forms of longer writing I loved the now-defunct Tree app, which was a horizontal outliner

That type of horizontal outline writing structure with ‘folding’ can be seen today in Gingko, which is both a moribund web app with no further development devoted to it, as well as a (fairly primitive) desktop app that’s being actively coded. I bought the Mac app - it has promose, but I don’t trust it yet because of some general bugginess.

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I agree w/ your criticisms of OO. The app is not perfect from a UI standpoint, but it’s the best outlining tool from a functionality standpoint for my purposes. I also get nervous about longevity. What happens if Omni stops developing the app? (Thankfully, it has a comprehensive set of export-format options, so there should never be risk of data loss from ). I flirted with the idea of trying to use some kind of personal wiki system at one point, but it seemed like it required too much scaffolding to suit my needs.

More importantly, I love that you have an outline for BSG. If you have it fully fleshed-out, please post more!

It was always hard to get past ‘Pa’ being captain of a starship.

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HA!! I was more a fan of the re-boot than the original.

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You’ve inspired me not only by the effortful and thoughtful post but all the good ideas it contains. Thanks both @ipersuade and @anon41602260 for your reflections.

I have to know, Tom, did you create an outline before writing this post?

What strikes me about both of your approaches is how important thinking is when outlining. I suppose that sounds a bit obvious when typed out, but I sort of saw it as a shortcut before. It’s now clear to me that it’s not. Outlining is synthesis, organization, trial and error, further articulation, follow up, and so on.

This level of detail is especially appreciated. It gives me a way to play with outlining for myself. I imagine if I had this mode of notetaking, I might capture different notes, realizing they will ultimately appear in outline form.

As a side note, I could see this paste then organize/re-organize process being very handy for qualitative research, esp when theming coded interviews and the like.

I have OO and have been playing with it a good bit recently. Thanks for giving me a more robust use case to explore!

Beck

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It’s not truly that big of a hassle.

  1. Download PDF
  2. Download .ris (or .bib) or whatever (or use your reference manager’s browser extension)

Hazel runs a script to import the reference file into your reference manager, you put the PDF into DTPO in whatever way you like (manually, by script, whatever) and you’re done!

For me, in most cases, getting references into my manager and files into DTPO is 2-3 clicks.

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Not sure if this is the sort of thing you are looking for, but I have stored my reference library in EndNote for years. Currently 5000+ publications, easily searchable, PDFs can be open from within the software via default PDF reader, changes to the database sync reliably across all my devices, custom local folder organization, and the cite-as-you-write feature will build bibliographies in just any format. I am an academic so the software might not be for everyone, but I love it.

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I DID! For this I just created it in Drafts; I would have done it directly in the draft reply within forum but my impatient fingers may hit the reply button too soon. As it is, I probably edited the post six times after I published it.

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:clap::clap::clap:

(Post must be twenty characters)

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If there’s a .ris/.bib. Academic papers are very easy. I just need the search feature in Papers and can pull the bibliographic information from PubMed or whatever.

But I deal with a lot of stuff that’s not in databases or with downloadable .bib files. Contracts, agreements, internal (closed) publications, etc. So, when I state “it costs $x per year”, I add the source of that information (contract y, supplement z) so it can be cross-checked. It’s a hassle, but worth it, since I save a lot of time (no questions on where it can be found, etc.).