What about citations/notes you’ll be taking upon covering the pdfs?

Presently, I am just pasting the formatting citation on the top of each md file so I can search the journal article later, such as using google scholar in case I cannot find my PDF. If you are talking about the inline citations in the article itself (such as [11][12]), I dont have a robust system yet. I just copy paste the relevent text from the PDFs and if I need to go back to the references (eg. [11]) I will search few words in the PDF and then can locate the citation from there.

Are you going to create a separate note for each? Or are you including them in your individual md file for each paper?

right now I just make one single md file for each article I read. For instance, I have 6 md files in my literature review vault as I have read 6 articles

Also, are you going to have a separate stack of notes for your citekeys and quick references and a separate stack for more extended writing based on the earlier quick notes?

I think it doesnt matter if you are doing a thorugh reading or a quick read of an article. Just make a separate md file for each work you read and its upto you if you want to write lots of notes in it or just few lines. Personally, I even have some notes with just few sentences from the conclusion of the paper for the work I just skimmed. I agree that naming the md file might take 10-20 seconds more but its worth doing it to ease your searching for the notes later.

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its okay to have empty md files, even I have empty notes for the links.
You can change the default location of the newly “autocreated” files to a folder something like Nodes. As you take notes and make more and more [[ ]] type links, your Nodes folder will populate with the internal links.

you might as well use #tags to achieve your goal, but then they will not appear in your graph view.

Thank you for your reply!
Let me see if I understood correctly:

Step 1
A. I have a Book talking about healthy meal
- I take a note from page 18 and name it (for ex) - Organic food
- the note look like this: [[Author X]] claims that a [[healthy meal]] is always based on fresh products, preferably bought in the same day, and also organic
B. I have a another Book talking about being productive
- I take a note from page 23 and name it (for ex) - Maintaining productivity
- the note look like this: [[Author Y]] claims that a productivity is closely related with a good sleep and it also with a [[healthy meal]].

Step 2

A. I click on [[healthy meal]] and fill it with my reflections?
- Healthy meal is not fundamental for a [[healthy body]], but it seems that in some cases is a [[trigger for increasing productivity]].

what if I read another book about taking best grades at school and somewhere in a page there is a remark about being healthy is always a step forward to be more productive and in this way students increase the chance to take better grades in school? Whare should I fill it? on [[healthy body]] or on [[steps to take better grades in school]]?

Step 3
A. fill the [[healthy body]] & [[trigger for increasing productivity]] in the same way?

They don’t have to be filed anywhere. They will be linked to the other notes. If you synthesise another reflection that will be linked too. They don’t have to fit preordained categories.

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can anyone share your experience of attaching the PDFs to your md notes.

Is the referencing fluid or tedious ?

Presently I am mostly refering to my PDF articles either using Mendeley or straight from my hard drive which are not in my vault. The only issue is that I have to leave the obsidian app if I need to refer back to the PDF.


Hey there,

I’m an Australian academic in the field of education. I read the How to take smart notes book and a couple of Luhmann’s articles which were translated into English. I also would recommend looking at the writing of Andy Matuschak on how to label your notes, what to include in them, and so on. Here’s the process I’ve come up with (which continues to evolve):

  1. Initial highlighting: Read journal article via Zotero. Highlight the parts that are relevant to you using the default PDF viewer on your computer. Use Zotfile to extract the highlights (and any notes) in Zotero, then paste them into Obsidian in a new note. I have a template I copy and paste to start each new highlight note with relevant details like the author names, date of publication and so on before the highlights.

  2. Refine highlights: Look through your highlights from the article and use the Obsidian highlighting feature (==like this==) to pinpoint what’s valuable in each highlight. This makes it easier to complete the next step, particularly if it’s a long paper or you have to come back to it. Skip if necessary.

  3. Process highlights into literature notes: Summarise the highlights into your own words. Add any personal insights. Each literature note should relate to one idea. I do this directly above the highlight notes using bullet points and a L - for literature notes and a H - for highlight notes. Try to write the literature note as if it was part of a journal article.

  4. Add a label to each literature note: Above each literature note, I add a label, which should be the briefest possible summary of the literature note. Have this label inside double square brackets. Avoid labels like “Definition of X”. Instead, write “X is y and z”. Try to be specific. I mainly use the bracket links in this way. An example label might be [[E - X is y and z]]. I use E - because it will soon be an evergreen note.

  5. Add each label to an index: The index will be a long list of all your literature note labels. Categorise the labels in a logical manner.

  6. Create evergreen notes: Click the label (which is a link to a new note) and copy/paste the literature note text (which will be quite short) into this new evergreen note. Add connections to other notes categorised in the same place in your index plus any other relevant evergreen notes. Add relevant tags. The index may not be overly important in the long run, but it definitely helps at this point with connection making. I also add the reference details at the bottom of each evergreen note. Next it’s time to create your paper.

7a. (Top down approach) Create journal article outline: Create an outline for your article, chapter, application, or whatever you’re working on. You can make a quick template with the relevant stages of the genre (e.g. introduction, literature review, and so on). Then, drag relevant evergreen notes into the sections. You’ll need to massage the gaps between notes to make it cohesive. If you use a note, add a tag to say so. You’ll need to reword the note if you use it again in another paper to avoid self-plagiarism.

7b. (Bottom up approach) Add evergreen notes to papers: Instead of starting with a paper outline, you might look at your notes in the index and consider what kind of interesting questions they might help you answer, then build your paper from there.

I hope someone out there finds all this useful. One of the best things I’ve done is create a note called master production line which includes these numbered steps as headings, and then I can add my highlight notes as they’re created and move them down the production line as they’re processed. I also organise them in certain steps (like 2 and 3) as high, medium and low priority. It means you never lose track of notes and there’s always something you could be working on. The bit I’m still figuring out is the last step: how to go from evergreen notes to paper drafts as efficiently as possible. I’m a little old fashioned, so I’ll probably so the final edit in Word once everything else is done in Obsidian. The multiple window support in Obsidian is great, but still a bit janky, and this method requires multiple windows to be open at a time. Hopefully a future update keeps the windows in the one spot.

Anyway, take care everyone and good luck.


Thanks that’s an interesting setup and a nice way of doing things!

I just started. Hunting for best practices too. First idea is mechanical, paste Endnote record number = {Manfredini, 2008 #10746} into Obsidian note. Replace # with ^ or something else that is a simple quick keystroke. The reason is the extra # in the middle of the record number will screw of tags and linking in Obsidian. I paste the abstract in and then collapse it. This is the reference material you turn to for confirming the accuracy of your finished sentences. I struggle with writing 3 or 4 sentences that meet the criteria for the different ways I might want to use the sentences in a manuscript. Is it a reference that answers a question? Does the reference confirm other people’s work? Does the reference contradict someone’s work? The list goes on and on. So what I am struggling with now is what are the questions that I think the reference can answer? One sentence (idea) cannot answer all the questions? And, each reference has more than one idea, as well as implications. How do you write a sentence for all of the good ideas or findings? I an leaning towards multiple ZK notes for a single reference. I decided not to use Obsidian alone for my references. I think it is better to use it in conjunction with a bibliographic program, like Endnote which the school pays or Zotero which is free. Notes that contain facts are boring science but are the brick and stones that lay the foundation. Articles that break new ground - how do you describe them in a single sentence? This an area that I am struggling with considerably. I am trying to stick close to the teachings in “How to take smart notes” by Sonke Ahrens.

How would you go about processing review articles? All the ideas are in reference to other articles so is it better to just read the primary source material and not make a note of the review article itself? Or perhaps use the review article as a sort of table of contents to those primary articles?

I think you’d be ok to process the review article. Each idea is basically their summary of someone else’s research, so if you carefully transform their summary into your own words, integrating in other relevant ideas/connections of your own when you use the processed notes in your own writing, I can’t see an issue with this. Good luck with it!

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Glad I could help!


I only have 1 vault: the single folder I keep all my markdown notes in. I may make a separate one in the future just for personal stuff, but as of right now 90% of my notes are academic. I don’t want any in separate folders because then I can’t connect them!

Finding Authors

I’m not sure I understand what you’re asking exactly. The plain search function works great for finding references, or making it a link like you said would work too. Could you rephrase? Mostly I just do A LOT of direct links (it takes time, but they’re really solid).


I’ve changed my mind about tags actually, they work just like my underscore does: they make sure the search function only looks for the author _doe #doe and not any references to the animal “doe” in my files. So you could also phrase the references as #jdoe1977. Nevertheless, I’m gonna keep using links because they are a solid and true way of linking files.

Let me know if I could say more!

Hi all!
Great to see so many interesting and thoughful posts on this forum.

I am the director of a charity that works to protect biodiveristy and operates in various fields (like economics, politics, agriculture etc) to do so. I am still at the early stages of testing out Obsidian. I am looking at how well it functions as tool for a single research project – in this case a book.

I use Roam, Evernote and Devonthink but find them unsatisfactory for different reasons.

My workflow in Obsidian has pretty much turned out to be a series of work-arounds to a number shortcomings that Obsdian has in its beta form. I should say that I think Obsidian has great potential and there is much that I really like about it. I am sure those shortcomings as a research tool will disappear over time. So, much of the workflow I have set up using Obsidian will change when those improvements come into effect.

In terms of overall structure, I have a main index page, with a series of sub-indexes listed on it. I think these are similar to what are sometimes called MOCs in the forum. I found that when the number of notes goes over a few hundred an intelligent structure becomes essential.

I also found that individual notes themselves need to have common structures. So I have created a series of templates which I star so that I can easily access them. To create a new note I copy the template and paste it into a new note. The template I use most is a temporary note template. This is a seed form of a note. Because I do not find the information displayed on the backlinks pane particuarly useful, I have created a space for backlinks on each template. I add a link to any semantically connected note in that section. I find it visually a more intelligent than what I see in the backlinks pane. It does mean I have to link each page manually, which ends up being a lot of work. Another section in the template connects notes structurally. For example, a temporary note has a link to the temporary note index. I also add a link to each note, to its relevant index page after creating that note. I also sort those note links on the index page alphabetically.

The result that one ends up with, I was surpised to see in the midst of all this amazing tech, is something very like a good contents page and good index section in a traditional book. I find this combination works very well. I can find anything I want. But it is labour intensive to create it.

On the creative side, those structures are not particularly useful. Semantic connections are useful creatively. So the graph is the feature that interested me most about Obsidian and Roam. I was hoping the graph on Obsidian would provide a parallel approach to the structured organisational contents-index system noted above. However in it’s present incarnation I find the graph fascinating but actually not useful! This is because there is no filter on what one sees. When we get filter functions, I think the graph will be amazingly useful. But for now, with about a thousand notes in the vault, the graph is an inpenetrable spiders nest. I am waiting in hope for the day when that feature appears! I also hope that in the future, some means of distinguishing structural ties ( for example the link that ties a note of a certain type to an index of that type of note) from semantic links between notes will be a feature. I’d like to be able to toggle one or other of those off. Most of the time I don’t need to see tens of thousands of links to structural index pages. I hope at some point it will also be possible to create links on the graph itself, for example by dragging a node and placing it on another node. I often see new connections between notes on the graph, but then I have to create them off the graph.

I have not explored citations yet. I am reading with interest how others are handling that!


Thanks a lot for sharing your working strategy, I realized that I was never going beyond the step 2 you mentioned.

I did not grasp your idea of labels and index . Would you mind ellaborating more on that ?
Or if lazy, can you share some resources talking specifically about the index and labels ?

Many thanks !

Thank you! I think I understood how finding references works in your case.

Sorry if I’m stating something obvious, but when you have a blank note called [[healthy meals]] and you have “[[healthy meals]]” in other notes, then on the blank note, open up the links to it (usually on the right-hand side of your Obsidian window), and that will reveal all the notes that the blank note is connected to.

For those looking to get close to EvergreenNotes/Zettelkasten, particularly when starting out without your own system in place - this is one of the clearest encapsulation of the main workflows I have seen written.


I would add that recognizing that there are different note types and statuses is crucial. But also that any low-level note can/will be transformed to others.


Yes. This is the nature of the backlinks. Page references can simply be aggregators. Tags on the other hand would be used differently.

Thanks for sharing. I am taking notes and doing my papers in this similar way, but since I am new in Obsidian my workflow is not clear like yours. This helps me a lot and makes me to rethink my method.
Hopefully I will share my method in the near future.

Great idea! So curious about your templates, which should be a very creative and laborious job!
Can you share your thoughts about the templates, or give a simple example?