An academic workflow in DT: note-taking, references/bibliographies, and knowledge organization

Hello members of the DT community,

I’m new to the forum, but not to the software, which I used to write my dissertation in the past year and a half. I greatly benefited from this community, silently reading other users’ posts, questions, and comments, and I now want to give back sharing my academic research workflow :relaxed:.
I am a researcher in the field of ancient history, so I have some particular needs (I often deal with dead languages), but as others researchers I mainly read and annotate papers, take notes, link pieces of knowledge, organize them, and write. I discovered DT Pro Office after learning about Luhmann’s Zettelkasten: I started using it to organize my research while writing my dissertation and I will probably stick with it for the rest of my life. I am now on DT3, and could not be any happier with the new update. I am a paper enthusiast, but I also must acknowledge the fact that my life routines (commuting, moving between libraries, etc.) do not get along well with paper support. I thus went 90% digital: most of my research is on my computer.

There are several different pieces of software that I somehow integrated with DT and I use in my workflow: I am going to list them below, along with a description of how I use them.

First comes the reference management software. I tried almost all free(mium) reference management softwares (Mendeley, Paper, Bookends, JabRef, BibDesk), and Zotero has been my final choice mainly for two reasons: plugins and the community, which is very active. I add my references to Zotero, using ZotFile to rename them, and BetterBibTeX to produce customized citation-keys. As all of you know, DT integrates with Bookends but I still prefer Zotero’s flexibility and the possibility to also share my group libraries online (mainly for didactic purpose). Furthermore, Zotero goes well with other two tools I massively use: Atom and pandoc.

I use Atom to write markdown notes; my Atom setup includes Markdown Preview Enhanced package (to preview my notes when needed) and the zotero-citations package by retorquere. This last one is amazing, because it uses the BetterBibTex extension for Zotero to add citations pandoc-style in Atom via Zotero interface.[^1] For those who are not familiar with pandoc-citeproc (see below), it is a very useful way to add bibliographies/references to a document simply typing the citation key that has been generated by Zotero, and let pandoc do the dirty job. I created three DT templates (which I can quickly call with keyboard shortcuts) for my notes:

  • bibliography: to collect bibliographic references on a given topic;

  • quote: to archive pieces of things I read; this might seem an unnecessary or even detrimental habit, since I don’t re-elaborate the concepts I read writing a new note. However, it’s a fast and effective way of collecting materials: then I can stare at my quote-notes for hours while I elaborate concepts in my mind, quickly moving from a piece of knowledge to the other.

  • note: this is the most important (although most hard-working) part of my note taking system. I craft a note of my thoughts (complete with references), which in most cases I am then able to “recycle” when writing a scientific paper.

All notes have a similar title, such as 20200506-11:43:34-Main (= %year%%month%%day%-%time%-title), but three different tags (bibliography, quote, note, attached to the template file, so that I don’t have to manually add them). Date and time in the title have the only goal of creating unique file names, even when two notes are about similar topics. In addition, it is important for me to see at later moments which path I followed (what I read, in which order, on which topics my attention was focused), and it is easier to do so if my files are stored in such a way.

The content of the template is quite simple:

link-citations: "true"
urlcolor: "red"
- a5 paper
- landscape
- margin=1.5cm
# title

The YAML gives some additional information to pandoc (using LaTeX packages), like the A5 paper format that resembles the size of a real index card (just because I like it, there is no particular need for it actually :grin:).

As I said, I am a paper enthusiast, and I have some sort of eidetic memory for reading scientific papers; I thus use Goodnotes for iPad to annotate PDFs. I keep my annotated PDFs synced in a different folder: it happens often that I share my materials with colleagues and I want to have the possibility to share a clean copy of my files. These annotated PDFs are not in DT, since with time I noticed that I used them mostly through GoodNotes.

After a note is complete (bibliography and notes usually take some time to be finished) I run pandoc-citeproc: I use it both to export my notes inside DT and while writing scientific papers, since it frees me of the burden of writing never ending bibliographies and bibliographic references. I slightly modified a script I found in this forum to run pandoc-citeproc on my notes and export them to PDF. pandoc uses a .bib file I constantly update via Zotero to compile the references, while using a specific citation language style (I am a Chicago Style aficionada).
You might wonder why I write a note in markdown and then export it in PDF; it is mainly because I endlessly take notes on notes: I add comments, highlight text, and so on. Furthermore, the automatic WikiLinks feature with markdown files is are not very effective (in some cases is even misleading) because of the content of my notes (dead languages most often). I thus prefer to link documents using the “Link to” feature. Last but not least, I make large use of all possible formatting while studying documents written in ancient languages: superscript, subscript, italic, small caps, small caps italic, you name it. All this in markdown is fast to type, but hard to read.

After exporting a note to PDF I add tags, and archive it in a folder on the topic I am researching on. If I later discover that one note is interesting for more than one topic, I create a replicant and store it in another folder. I also create a Smart Group using tags if I want to quickly see all the material I collected on a specific topic.

After this whole workflow, the real job is done through DT: I archive my PDFs in a folder managed via Zotero using ZotFile. This same folder is added to DT via indexing, so that when I have a “question” I simply search into DT to find answers. I also index the folders in which I store my paper drafts, so that often DT suggests me note/scientific literature that it considers relevant for that particular topic. This last is for me the most important feature of DT.

I hope this might give other DT users new ideas on how to adapt DT to specific needs. And if you have suggestions, observations, or questions, please share.

All the best,


[^1]: Previoulsy to switching to Atom, I used Sublime Text which is a very good software. There is a very interesting package for ST which mimics Luhmann’s Zettelkasten features (sublime_zk), but I stick to Atom mainly thanks to the amazing zotero-citations package.


Welcome @palapapanda

Thanks for the thorough explanation of your use and process. I’m sure there are people here that will find inspiration in it.