Devonthink and Bookends (and possibly Mellel)

OK, so I’ve been using DTPO for a few months now, cleaning out and scanning old paper files. When I come across a journal article, I want to add it to my Bookends DB at the same time, and attach the .pdf file to the Bookends record.

I also work with two computers, one at work and one at home.

What’s the best way to set up the whole enterprise so that

  1. I don’t have to duplicate article files for each program
  2. I can share one database both at work and at home (here, I’m thinking of a thumb drive, with backups routinely to both home and work machines).

Is there any tutorial to teach this sort of thing? (I wish there were a locally-offered or even web-based class, say for $50 or so, that would teach me all the ins and outs of the program and allow me to pose questions in real time…)

Thanks in advance!

Charles Hogg, Dept. of Philosophy
Grand Valley State University

Index the folder where you store your bookends PDF files.

I’m thinking about this too.
It seems sensible to put as much as possible into DTPO to get the maximum benefit, so I was thinking of storing the pdfs directly in DTPO, annotating/highlighting them there, and then pasting a hyperlink in the notes field of the bookends record - i.e. citations only in bookends.
Also some people suggested DTPO has better annotation facilities. And the bookends people stated somewhere on their blog that full featured annotation was not a priority for them, many people seem to use other apps for annotations.
I guess another way would be to specify a DTPO database location (the actual file location) as the attachments folder in bookends, if this is possible.

I have indexed the Bookends PDF folder into Devonthink, it works nice. Another option is to link the PDFs to DTPO, but it is much easier to index the folder where you store the PDFs.

Yes that’s the best solution. I tested after my comment above and annotations made in Bookends (using pdf editor of your choice, mine is Skim rather than Preview) show up instantly in indexed DTPO folders. So finding, annotating and managing citations and attached pdfs stays within Bookends. Actually, editing the pdf with Skim from DTPO will get me to the exact same place.
There is apparently also a way to export skim annotations as an attached (to the pdf) file, which means you can index and search those within DTPO also. I’ve yet to make this bit work!

EDIT: It’s as simple as turning on ‘Automatically save Skim notes backups’ option in Skim Preferences. The skim file holds just the annotations shows up in the indexed database and can be searched, tagged etc. like any other file.

…"There is apparently also a way to export skim annotations as an attached (to the pdf) file, which means you can index and search those within DTPO also. I’ve yet to make this bit work!

@anon2998708 I am planning on using either Goodreader or Highlights for my highlighting and annotations. Do you, or anyone else on the forum, know if either of my prefered PDF apps will offer the same result? I.e. being able to search annotations?

To my knowledge Highlights does not attach the annotations exported file to the original pdf.

However, you can export the annotations in another format (markdown, html, pdf) and either place that file on DT3 (with a link to the annotated pdf file) or as second attachment to Bookends. Also, keep in mind that all the annotations made with Highlights (and I’m guessing Goodreader as well) can be seen on Bookends (see image below and notice red arrow on lower right).

I use Bookends as as reference manager, DT3 as a knowledge/research organizer, and either Highlights or PDF Expert to annotate pdfs. The annotations that I make are not my endgame: my endgame is use them (and them discard them) to process my own reading notes.

My workflow is as follows:

  1. Catalog pdfs in Bookends.
  2. Read and annotate them in Highlights (iPad).
  3. Export the annotations to DT3 as html or markdown file and, from it, process that note within DT3 (make a reading note, i.e. write the main ideas in my own words, following Zettelkasten system; this allows me to create links to other notes using DT3 wiki links).
  4. Connect the reading note to the Bookends URI and delete the original annotations file.

In the end, I have two files: the annotated pdf, that stays in Bookends, and my own reading note which is in DT3 with an easy to follow connection (in the image below, that link is the Bookends ID). From them on, my research relies on my reading note. The annotated pdf will be used only if my note fails to be understood in the future (hopefully that will not happen).

Back to your question:

If you keep the annotation file in DT3, yes. (Bookends, alas, is not very capable re: searching the annotations.)

You can also attach a pdf copy of the annotations to the original pdf, but that has to be done after exporting them from Highlights.

@valente thanks for sharing this looks cool! Just out of interest, do these numbered points follow the thread of the argument as Henriques writes about them or do you gather the ideas from various points of the essay and bring them together under these headings. Also – does every numbered ‘Idea’ link to its own Zettel? If you would be willing, it would be interesting to see what one of these notes would look like when you follow the link. Finally, maintaining this sort of reading and noting practice looks intense and time-consuming if each chapter or articles might spark 10s of smaller Zettels. Do you script this or work from templates, or manually compile the MD files as you go?

Excuse all the questions, I’m trying to learn from people’s practice here and this seems a very sound approach that really harnesses the power of Wikilinks and opportunities for atomic note-taking in DT3. My system is still very much in development in this regard. Cheers!

I am sure what you mean. Isn’t it DT that search the annotations?

In my previous post, I suggested two places to keep the annotations:

  1. On the original pdf (annotated in Highlights) and stored on Bookends. Your annotations are kept there, you can see them in Bookends notecard as showed here, but are not searchable (as far as I know). [Note: this was the one referred by my quotation.]

  2. The exported file (html, markdown, pdf) of the annotations. This one you can store on DT3 (in any format) and be searched.

Thank you for helping, Valente. Just a quick Q: how do you connect reading note with bookends URL?

First let me explain the type of notes I take…

  • Snippet notes (SNxxxx): Normally copy+pasted from diverse sites, papers, books. They tend to be short or middle sized, and always have the source. Most of the time they are temporary notes, since after I process them to a conceptual note, I discard them.

  • Reading notes (RNxxxx): They are what they say: my notes after reading something. They can be extremely detailed and long if the reference is long and complex; or they can be shorter and focused in one or two ideas that caught my attention. The one I posted here is an example of a very long one. What you see in it is my Table of Contents {{TOC}} of the note. They generally follow the author’s text order, but not always. I often reorganize ideas and merge some (complementary) information that can be from p. 38 and p. 49, for instance. Here is the same Reading Note on Idea #6–8:

  • Concept notes (CNxxxx): These are the core of my Zetterkasten. They mix different sources, quotes, ideas, my reflections, references, back and forward links. I try not to make them too long. If they become too long I split them in different subtopics and link the new CN to the original one.

As you can see, I adapted the Zettelkasten system to my own needs and workflow. I don’t think I follow it in its “pure” form. The one note per idea doesn’t really work with my research method, although I sometimes use that kind of note too. I think I mostly do one note per topic (a slightly different approach that leads, I think, to longer notes; i.e. the concept notes). Each topic (i.e. concept) note contains several ideas. If the idea becomes too complex/important/full of data, I process it into another topic (concept) note.

I also prepend a code (SN, RN and CN) to DateHour Topic so I can easily see what kind of note I’m working on/consulting/searching.

… does every numbered ‘Idea’ link to its own Zettel? If you would be willing, it would be interesting to see what one of these notes would look like when you follow the link. Finally, maintaining this sort of reading and noting practice looks intense and time-consuming if each chapter or articles might spark 10s of smaller Zettels. Do you script this or work from templates, or manually compile the MD files as you go?

  • In this case, the idea is written in the same note further ahead (a Zettel within the Zettel).
  • Re: time consuming: it depends on the reference and how highly I value its contents. Sometimes, yes, I may take more than one day in a good book chapter (as is Henriques 2017). Also because from it I processed a large amount of Concept Notes (basically it was great fuel for my Zettelkasten and my research mind).
  • Re: the last question. I use templates in DT3 or placeholders automation in Keyboard Maestro. As for the writing content (with exception of the SNs or quotes in CNs or RNs) they are manually compiled, but I do automate some tasks for links.

Templates for notes (I also have a Keyboard Maestro palette to speed this; note: in the near future I might set up shortcuts for each of the templates so the workflow may be even faster):

The Keyboard Maestro palette for markdown speed up process (most are string typed actions, as showed in between parentheses):

In the end, I do think is a lot of work, but a very useful type of work. In the process one learns a lot and prepares much of what can be used later in writing articles, debating ideas with colleagues, teaching classes, advising students, etc. Plus, it makes knowledge very fluid since you can revise, adapt and append new ideas/sources/etc.

Nonetheless, we must learn to be focused on what is essencial for our research, what is accessory, and what it superfluous. And use time and effort accordingly.

2 Likes

Valente. Thank you so much for sharing your workflow. I have three questions: 1) Do you use markdown or rtf for you notes? It seems you are using markdown, but I want to be sure; 2) Do you use the wiki link available in DT? It seems you prefer to use cross-links between your notes; 3) Do you see any advantage to add the creation date in the title of your notes? Do not you think this information can be part of the note but not part of the title?

You are welcome.

I have three questions: 1) Do you use markdown or rtf for you notes? It seems you are using markdown, but I want to be sure; 2) Do you use the wiki link available in DT? It seems you prefer to use cross-links between your notes; 3) Do you see any advantage to add the creation date in the title of your notes? Do not you think this information can be part of the note but not part of the title?

Re: 1) Markdown all the way for my own notes. :slight_smile: (see interesting debate here)

Re: 2) Yes. I find wiki links faster than the item links (also they are automatic to read). I prefer the Square Brackets [[…]] syntax to the Name and Alias since I seem to have more control on their usage. I even customised the automatic template. (Note: in a future I hope never happens, if DT stops to exist the usage of Square Brackets is quite common in markdown applications, so, hopefully, I can maintain my connections between notes).

Re: 3) Yes. Because of that “code” I very easily spot my own notes on any search, list, or when I’m setting the wiki links.

I sometimes use easier alias names for those links; for instance CN202006071755 On the usage of DT3 as Zettelkasten, may have an alias name of DT3 as Zettelkasten and the wiki link could either be [[CN202006071755 On the usage of DT3 as Zettelkasten]] or [[DT3 as Zettelkasten]]). [Note: there’s a great set of posts about wiki links and aliases in here.)

Valente. Wonderful! Thank you.

Valente, thanks for your time and laying out your use of DT so clearly here. Massively useful to me. I’ve never ventured in to KM but will check it out. Without it, there’s still plenty to go on in terms of your structure. I have a few different types of notes (also including ‘manuscript notes’ which contain physical descriptions and contents of manuscripts, and ‘people’ notes on historical figures of interest or well as a few plots of relations between people (often families) – these aren’t at present in md so I may have to keep them apart.

I otherwise also maintain Reading notes and what I call ‘Themed notes’, or your Concept notes. Mine aren’t half as nicely styled or organised as yours, though!

I’m still leaning towards x-devon style internal links as the Wikilinks are so depending on file names, and at present all my types of notes are in different folders. I may simply settle on a naming convention that I stick with (and convert my historical notes to such a convention, ouch), and then the power of Wikilinks is really evident.

I totally agree with your remark above of course, I wasn’t suggesting that time isn’t well invested. I’m a fellow academic here and what you describe is the bread and butter of our existence :). Thanks again, and happy researching!

Thanks. And the same good wishes to you.

Re:

I’m still leaning towards x-devon style internal links as the Wikilinks are so depending on file names

Don’t forget that even if you change a name to a file that already was being used in a wiki link, that wiki link will maintain if you place the old file name as an alias.

This quote is perfect. This is so great. Thank you.
And this whole forum has been a learning experience. Thank you all. It helped me find use of WikiLinks here. I now get it.