From references to fleeting notes: Zotero and Zotero plug-ins

This is the first step of my research workflow. For the rest of the series, see:

In the last nine months alone, I have come across seven hundred references that were relevant to my research: not only books, chapters, or articles, but also websites, images, letters, historical documents, artworks, etc. Previously, I would store all these references in bookmarks in my web browser or in folders across my computer. This worked well when I was an undergraduate or even graduate student, but as a full-time researcher it was a recipe for disaster: creating bookmarks for internet websites did not guarantee I would look at them when I needed them; saving images to a folder makes it very hard to record the metadata you would need to reference them, and just saving hundreds of files in different folders made it very hard to keep track of them all. A reference manager solves all these problems and has the added benefits of creating citations and bibliographies for you, organizing your references with tags, collections, related items, and more, and integrating nicely with text editors such as Microsoft Word, LibreOffice, or, as is my case, with Obsidian.

Every time that I come across a reference, whether I have immediate access to it or not, I immediately store it in Zotero. In the past I was a bit more lazy, but I have learned the hard way that importing a reference takes less than a minute but searching for a lost reference can take up a lot of time and mental energy.

I use six ways to import a file and/or reference into Zotero:

  • If I have a physical book, I use this iOS shortcut to save the reference to my Zotero database by scanning the barcode.
  • If I come across a resource online, I import it using the Zotero Connector plug-in;
  • If I have a PDF with embedded metadata, I simply import (i.e. “drag and drop”) the document into Zotero;
  • If I have a PDF but it does not contain metadata, I look up the .bibtex reference on Google Scholar and use the Zotero import from keyboard;
  • If I only have an ISBN or DOI, I use the “Add Item by Identifier” option in Zotero;
  • If none of the above applies, I fill out the metadata manually.

As soon as I import a new file into my database, I make sure to revise and correct the metadata. Then, I file the reference in the relevant collections and add the relevant tags if necessary. My folders are theme-based, for the moment, but I plan to change their names so that they correspond with the Maps of Content that I use in my Obsidian vault. My collections serve two purposes: it makes sure that I always have an up-to-date bibliography of main research topics, and it makes sure that my literature notes contain backlinks to the most relevant MOCs and/or permanent notes when I export them with the Mdnotes plugin (see the function of collections placeholders).

This is a screenshot of my Zotero database:

I do most of my reading on my computer or on my tablet (using a styles and Zotfile): I find it more convenient to have all my references digitally than having to deal with piles and piles of photocopies and books. In both cases, I highlight relevant sentences or paragraph, write summaries, and/or add reflections as I read. If I am on my computer, I generally type notes on the PDF document itself, and alternatively in the “notes pane” in Zotero. If I am on my tablet, I take handwritten notes in the margins of the PDF document. I call these initial notes “fleeting notes”, following the Zettelkasten terminology.

Generally, I avoid taking notes directly in Obsidian because I find that this is a much more distracting environment. This is a screenshot of my PDF viewer, where you can see how I take fleeting notes on the file:

A close up of the sticky note:

As you can see, my fleeting notes already contain wikilinks (with double square brackets) as well as BetterBibTex cite keys (within single square brackets). The backlinks or the cite keys do not do anything in the PDF itself, but they will later on: everything that is inside double brackets will be turned into a backlink to another note in my Obsidian vault, while BetterBibTex cite keys will be turned into formatted citations when I convert my Markdown notes using Pandoc. Being very mindful of inserting citation keys in my fleeting notes saves me a lot of time later (because I do not need to constantly check the source document when I process my notes) and makes a crystal clear distinction between the source’s ideas and my thoughts.

Although I am not too fussed about structuring these notes, I do try to write self-contained and well-written notes: if an author gives a short list of reasons/examples/references, I capture these all within one and the same note; I write out the author’s complete name in every note, and use at least one cite key; I write in full sentences and avoid ambiguous language, etc. As you can see, however, there are still plenty of typos and grammatical mistakes, as well as some issues with consistency. These flaws are corrected once I turn these fleeting notes into literature notes.

16 thoughts on “From references to fleeting notes: Zotero and Zotero plug-ins

  1. Dear Miss R. Martinez Ponciano,

    Your writings are elements in a Zotero-map named Academic Writing. I used Zotoro’s reporting-tool to cite your articles. At the end of this letter I have formulated a question.

    Martínez Ponciano – 2021 – From references to fleeting notes: Zotero and Zotero plug-ins [Snapshot].html
    Small2015, pp. 2-5
    As you can see, my fleeting notes already contain wikilinks (with double square brackets) as well as BetterBibTex cite keys (within single square brackets). The backlinks or the cite keys do not do anything in the PDF itself, but they will later on: everything that is inside double brackets will be turned into a backlink to another note in my Obsidian vault, while BetterBibTex cite keys will be turned into formatted citations when I convert my Markdown notes using Pandoc’.

    Ponciano – 2021 – Research methods and tools for a Humanities PhD [Snapshot].html
    Having “wasted” so much time and resources, however, has made me realize that many of the “rules” that govern this workflow, are not tiresome steps but rather simple techniques which will make my life easier

    Ponciano – 2021 – Research methods and tools for a Humanities PhD [Snapshot].html
    2nd paragraph
    “”If you know a bit about … “” methods/apps.
    This is an understatement.!!!! Your articles are sophisticated.

    But I am wondering. The structure of your PhD-project is “rigid” (tagging, linking, the maps of content(s? plural?) although you can change them according to the developments in your project) and your use of the Zettelkast-method is very flexible and fluid.
    My facsination: at which stage of your research it became obvious to you, that you could use [[Wiki-links]] and [bibtex-links] in your fleeting notes/PDF-post-its? This is not a methodological fallacy. Is it serendipity? Or is it traceble in your researchjournal (e.g. Zotlog Pascal Martinolli, historian/liberian @ Uni of Montreal)?
    Could you reveal this secret?
    Greetings, good look and happiness writing your dissertation,

    HJJ van Nieuwkuijk
    Dutch pensonado, and student of education permanente, studying the Zotero-ecosystem.

    P.S. the Macintosh automation software (keyboard) is more evolved than its counterpart Windows.


  2. Love your writing workflow series! I’ll try it on my own thesis. But in my campus, most of us use Mendeley as reference manager, instead of Zotero. Do you have any experience with Mendeley? I expect some insights from you. Keep it up!


    1. Thank you so much! My apologies for not replying sooner.

      I used Mendeley but I moved to Zotero because it is open source and (therefore?) had much better plug-ins, such as BetterBibTex (Mendeley gave me trouble with .bib files) and Zotfile, and when I was still using Microsoft Word it was less likely to crash. Now that I’ve switched to this workflow, I really can’t imagine doing the same with Mendeley in an efficient and effortless manner. The only thing I “miss” in Zotero is the in-app PDF viewer, but that’s going to be included in the next updated so I’ll stick around.


  3. Thank you so much for this series of blog posts. After reading Ahrens’ book on Smart Notes, I felt well equipped to start building a paper-based Zettelkasten but was struggling to make it work with Obsidian and Zotero. Your example-based approach was perfect for filling the gap in my understanding. In particular, I appreciated that you related what you were doing to the purpose and principles of the Zettelkasten method. It gave context to your technology workflow in a way that is missing from many other tutorials.


  4. This is a great explanation of your workflow. I follow a similar process, but I’m still refining it. It helps to get ideas from others. You mentioned that you sometimes make handwritten notes on your PDFs. Are you able to extract those annotations using Zotfile? I’ve tried using a few different PDF readers, but whenever I take handwritten notes they are saved as images and don’t get extracted with the rest of the annotations. I’d love to be able to take handwritten notes directly on PDFs, but I haven’t found a way to make them work.


    1. Hi there! Thank you for your kind words. I have actually found a workaround for handwritten notes, but it involves an iPadOS feature.. It’s fairly simple, really, and it just involves activating the “Scribble” ( feature for the Apple Pencil in the Settings, which activates automatic conversion of handwritten notes into text (as well as a bunch of other neat little features). The only “trick” to it is that you have to create a “Note” box rather than just a freeform-type of annotation too l for it to be picked up as a note rather than an attachment. I hope this helps or at least gives you an idea for an alternative on your machine if you aren’t in the Apple ecosystem!


  5. Thank you for the write-up! I’ve read this series of posts a few times already and am starting to think of how I could implement/adapt your system so that it suits my needs. One question that I was unable to find an answer to, is how you deal with your fleeting notes. I understand you keep these in Zotero and in the PDFs, but in part 2 of this series you mention that fleeting notes are extracted and imported into Obsidian. Is this just to have the fleeting and literature note side-by-side in a similar format, so that you can manually populate the literature note?

    I am wondering what is done with the fleeting note in Obsidian after you have the literature note completed. Is it deleted? Similarly, where do you then store the literature notes? Do you have folders for fleeting, literature, and permanent notes, or are they all stored in the top-level of Obsidian? Apologies if I read over this in your posts!


    1. I’m so glad it was of use!

      When I refer to “Fleeting notes” I refer to those which are taken within the PDF or in the Zotero “Notes” pane. They are fleeting because they were never meant to be useful-as-is but rather taken as I was reading the text in order to ensure my comprehension and summarise arguments. Once I am finished with this initial note taking stage, I copy-and-paste these fleeting notes into Obsidian but extensively rewrite them for the sake of coherence. The original “fleeting” notes thus remain in my Zotero database, and a polished “Literature Notes” lives on in Obsidian. I can always refer back to my fleeting notes, but I hardly do so because they are so “rough”. I don’t delete the Fleeting Notes because I don’t mind them being in my Zotero database, but there’s no real reason to keep them either: I do find it useful, as you suggest in your comment, to keep the fleeting note in Zotero and the literature note Obsidian side-by-side while processing. I also end up reopening the PDF a couple of time to reread some passages.

      The fleeting notes, then, remain in my Zotero database. The literature and permanent notes are stored in my Obsidian, where I have a folder system:

      – 000 Organization (Inbox, To-Do, Templates, Planner, Attachments…)
      – 100 Index Notes (this is a “new” idea I’m trying out where I write stand-alone notes such as “Oscar Wilde”, “Short Fiction”, or “Ghosts”, which are not original per se but nonetheless contain useful information for me to record)
      – 200 Literature notes
      – 300 Permanent notes
      – 400 Project notes (for completed and archived drafts)

      I don’t really use sub-folders in the case of index, literature, or permanent notes but I do use emojis to distinguish between sub-types of these notes: a concept is prepended by a tulip-emoji, a definition by a magnifying glass emoji, etc; literature notes follow a strict YEAR-AUTHOR naming convention. This provides some sort of oversight/structure within the folder but does not require the same maintenance as having a series of sub-folders. I do this because I have 1300+ notes in my vault and keeping everything top-level would just be a nightmare, but I don’t want to spend too much time reorganising everything all the time.

      I hope this was helpful!


      1. I see, thank you very much for the elaborate response! I understand correctly that you keep all of your literature and permanent notes in the same folder, regardless of project? Do you use the names or tags, then, to narrow down topics when searching for something specific? I’ve experimented with this idea of note-taking in the past week and have adapted a similar folder structure. I only worry that it may get out of hand without further folders for specific projects (your mention of 1300+ notes is something that I truly dread).


      2. Embrace the chaos! It is pretty much impossible to keep track of every single not so I have let go of that expectation and am honestly no longer bothered by the number. I do use some tricks to make my notes easy to find, some of which I detailed in the post and some of which are new:

        – For “high level” permanent notes I use pretty consistent naming conventions that are more theme-based and function as a type of Map of Content: e.g. Oscar Wilde’s Short Fiction, Monstrosity, Oscar Wilde’s Journalism. I use Dataview to generate tables/lists of all the notes that have backlinks to these general topics.
        – In the case of permanent notes, I expand these theme-based notes in a pretty consistent manner: to continue with the previous example: Oscar Wilde’s Short Fiction and Monsters, Oscar Wilde’s Short Fiction and Oscar Wilde’s Journalism, etc. This has the considerable advantage that it makes it easy to find notes where I can put my thoughts about the intersection of two (or more) ideas/topics. It has the disadvantage that these notes can become a bit long, and therefore sometimes a bit more hassle to find the particular sub-idea that I’m interested in.
        – All my notes are populated with front matter. I mostly use it to create aliases, to tag information I find relevant and would like to display through a Dataview query, and to tag projects (e.g. PhD/Chapter 1) and primary sources (e.g. Oscar Wilde’s collection *The Happy Prince and Other Tales*) so I can pull a sort of bibliography with Dataview when needed.
        – Dataview, dataview, dataview. All my new templates (I use the Templater plugin to automate much of this process) include a basic Dataview list which keeps track of the backlinks to that particular file: I distinguish between backlinks from literature notes, which I track under “Bibliography”, and backlinks from index notes and permanent notes which I track under “Related to [this note]”.

        As you can see, I am more preoccupied with tagging things correctly so I can find them (through simple searches or Dataview queries) rather than tagging them according to a project. By applying consistent naming conventions and using templates I make sure that everything can be easily connected either through general topics or through metadata.

        When I am writing a draft (for a project), I use my Literature notes and Permanent notes as I would use a dictionary or a secondary source: they contain the nuggets of information of insight that I can consult as many times as I want while I write, but the draft is necessarily a separate beast altogether. In the beginning I though my permanent notes “should be” ready to copy-paste in a draft as is, but this inevitably led me to writing permanent notes which were only useful in one particular context (i.e. the draft I had in mind while writing it). This means that, by default, my draft is always a reflection of my insights at a particular moment in time, while my permanent notes are continuously evolving. This makes sense to me because I can keep writing about a certain topic on several occasions throughout my life, but the knowledge I have on that topic will (I hope) increase as time goes by.

        I do struggle with the fact that it’s very difficult to keep track of what you have put into a draft and what you haven’t. Right now, my priority is to write a manuscript that I can easily export to Word, so I keep my drafts without any single backlink. My other priority is to create a system that is future proof, which is why I have been experimenting with the trick I’ve mentioned above. Is it perfect? No. But I keep improving it little by little, constantly tweaking workflows and adjusting my templates, etc. You can do the same!


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