Research/PhD/Academics

[verma]

To all research scholars using obsidian, I would like to know how are you utilizing obsidian to read vast amount of literature in your field. I would appreciate if you can share your hacks to manage literature reading/ note taking in obsidian.

Also, since .bib or referencing is not yet a reality in obsidian for now, how are you managing the refernces you are reading ?

Will be more precise if you can touch on:

• do you take all your notes in a single md file or multiple files or one md file for each journal paper
• do you take notes while you read the articles or you annotate and take notes later
• how do you make connections between the journal articles backlinks/tags etc.

Thanks a lot

[robotsheepboy]

I’m a mathematics PhD, I’m using obsidian and the latex support to type up a more polished version of my notes and crucially to make lots of links between them. I use zotero and better bib(la)tex for my references, currently I treat references as I would treat them for making a latex file (that is I export a better bibtex .bib file and point to it at the end of my note) so that if I ever want to make an actual pdf of my note I can just copy and paste it into Texmaker and take a copy of the .bib file and the edits necessary are minimal.

[verma]

@robotsheepboy

point to it at the end of my note

If I understood correctly, you write your notes in Obsidian and then paste the cite key from your .bib file inside your notes. Isnt it ?

Also, can you shed some light on the process you take notes in obsidian when reading journal articles ?

Will be more precise if you can touch on:

• do you take all your notes in a single md file or multiple files or one md file for each journal paper
• do you take notes while you read the articles or you annotate and take notes later
• how do you make connections between the journal articles backlinks/tags etc.

Thanks a lot

[robotsheepboy]

To your first question, yes, that’s correct, for me I usually know what the source is so just using the cite key in my note is sufficient. I was also contemplating copying the relevant pdf files into my vault folder and then also explicitly linking to them next to my citekey, but I’m undecided on this at present as it’s slightly more work.

Usually when I read journal articles I like to physically print out and write on the articles themselves, because at that point I’m usually working through them and trying to understand them. Then later if I happen to be writing about something that uses information or understanding I gained from an article I’ve read I’ll just link to it as described above using bibtex and the citekey. I tend to use my vault for things that I’m trying to write in a more polished way (I have a drafts and complete folder and no others) so by the time I make a vault note about something in an article I’ve read I have already developed some idea about how it works and what it connects to. My idea is that my vault is used to see links between subjects and to act a central store for ideas I may want to return to later, or use to write a paper, I think this is where the digital side of things flourishes, whereas for actually working through the content and gaining an initial understanding I think having physical copies and writing things out with a pencil and paper is most helpful for me.

I try to keep my notes fairly specific, so I have lots of notes on specific things and I intentionally try to include as many link and tags as possible, on anything even remotely relevant. Often I will just add links and tags at the bottom of my note; if the links don’t naturally fit into the main body of the text, I’m not trying to force them, but I do want clear links between related concepts to form a kind of ‘web of understanding’ which I can refer to and traverse later.

[verma]

That is a great working strategy in my opinion.
Unlike your case I face a totally different dilemma.

I am a PhD student in materials Science. When writing journal articles, we often have to “recollect” lots of ideas, facts, numbers from a ton of PDFs you read to design your study or experiment. I am struggling to build a good system in obsidian to accomplish the same.

In short, I need a good hack to store all the information overload in a fairly accessible way.

[robotsheepboy]

Thanks, it’s currently working well for me, but I tend to review my working method every so often (about every few months) to see if there’s anything I want to change.

I think if I were in the position you’re describing I’d do something like the following:
For each journal article I intended to write I would have one note in my vault. In this note I would list the zotero/betterbibtex citekeys for the relevant pdfs I’ve read, in the order that I would be referencing them in my article. I would then include a (very) brief summary of the key point from that reference under each citekey. The idea would be that this note is a kind of skeleton of all of the background material for the article I intend to write.

e.g. (something like)

note name:
article for journal x on topic y

note contents:
citekey_1
describes the Haber process on line 17

citekey_2
has the value for the molar gas constant on page 7

etc.

I imagine that it may take a little time to actually put together this document, but equally I think it would be useful for a variety of reasons (helping with structuring your article, making explicit exactly what you need to reference and from where, ensures familiarity with the key points, certain entries can be later recycled if needed for future articles etc.)

[Frederick_Lost]

1. Reference Form

I use the following style in my .md notes and in the titles of my files in my cloud drive.

Ex. A Book by John Doe, published in 1977: (j_doe1977)
When I want to reference a page: (j_doe1977p22)
If there are multiple authors or editors, I just use the first one named.

This form makes it SUPER easy to search for files and through my .md vault. If i remember the author’s last name only, I can just search _d and I almost always find it because few other documents or files have that.

2. Notes & Connections

I make a file for each work, ex, (j_doe1977).md. I’ll then take notes in that file while reading, making links to other files as I go along. Later I’ll move those notes from that author file to their proper place in a topics file, for example, indo_iranian_history.md. I usually work with particular articles, so I use this kind of focused form, but you could also just make a file called (j_doe).md or one called scholars.md if you want to be more vauge. I do this is some cases where I want to say something about the scholar as a person. You could also keep tabs on which books your finished taking notes on in the broader files like:

(j_doe1977) DONE
(j_doe1985) IN THE PROCESS
(j_doe1994) NEED TO READ

3. Other Ideas

• I prefer links over tags, just because they work on all platforms and work just like wikipedia (which I’m use to). The more the merrier, you’ll never have too many.

• It’s better to have a flat, rather than pyramid shaped wiki, since too much hierarchy leads to forgetting.

Let me know what you think!

[Frederick_Lost]

THIS

robotsheepboy: "I try to keep my notes fairly specific, so I have lots of notes on specific things and I intentionally try to include as many link and tags as possible, on anything even remotely relevant."

[verma]

I made a working strategy now as follows:

• make a single md file for each paper I read, use the file name as citekey (usually as lastname and Year)
• use the md file heading as the formatted citation (eg MLA or other equivalents, to search them later)
• copy and paste the full abstract of the paper
• read the PDF and annotate
• once done with PDF copy and paste the required text into the md file.
• highlight the selected keywords and enclose them in [[ ]]
• change the default folder location of the new file created to a new folder named interalLinks

I then have all my keywords in the internalLinks folder and each of my PDF file in a separate md file. This way I can see all the files in the graph view and all the keywords or internal links will appear as connection between the md files I created.

[ashwinbalaji]

1. i take notes of a single paper in single .md file.
2. i take notes in a paper, then i type it down in obsidian.(increases retention)
3. i’m figuring ways to make connection between journal articles(may come up with a quick script which will replicate the citations in notes)

You can quickly script it as it is just some bunch of markdown files.

[Miah]

@Frederick_Lost

(j_doe1977p22)

Frederik_Lost, thank you for your post, I found it helpful for my case. I have a couple of questions:

1. I’m trying to understand how you find your authors later. Your example for (j_doe1977) do you mark it as internal link so that the system later founds it instantly?

2. The file for each work: is that a file within a vault on a project you are working?

3. Links over tags, does it mean that you skip the tags part concentrating on links?

I just started diving into the knowledge management and obsidian, therefore, working on understanding the basics. Thank you once again.

[metemxi]

Not that I can answer for Frederik_Lost, but you could use also a citekey (autogenerated or not by many reference manager apps) and use it as a unique identifier of a publication you are referring to. Since you could have more references from the same author for the same year or different authors with the same name, having two letters after the year is important. Thats generally generated by your ref. manager. eg. citekey: [Doe1977ab] different from [Doe1977cs]…

[Miah]

Your reply does make sense, nevertheless, metemxi. Thank you!

[Miah]

Your strategy looks neat. What about citations/notes you’ll be taking upon covering the pdfs? Are you going to create a separate note for each? Or are you including them in your individual md file for each paper? 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? Trying to understand how Zettelkasten works in obsidian and develop my own system, hence asking. Thank you.

[metemxi]

At the moment, I have all the citations of a paper in the reference note of the paper, but just do what works for you. I might move in the future in having one citeable quote per note if I find this system easier to use/retrieve. If you can get a hand onto Sönke Ahrens’ book how to take smart notes go for it as the Zettelkasten method is very well explained.

[Miah]

Thank you for getting back in perfect time Just about to start another paper. I’ve read Ahrens book, in which, if you remember Luhmann had two stacks for quick notes and for more extended notes, hence was asking. In Obsidian, it seems quite possible to put quick notes in the reference file, marking each with internal link (?), which is quite handy. Yesterday, I tried to create Zettelnotes for each quotation in a different book I was reading, it was quite time consuming. In Obsidian it does seem to make a more sense to avoid doing that. Thank you once again, your replies helped a lot.

[metemxi]

Happy to help. And thanks for mentioning about marking each note with an internal link. Sounds like an interesting idea.

[mafsi]

Hi,
I still don’t get the main idea of having a Zettlekastel method of my notes. If anyone is willing to help me I’ll be very happy.

Here is my method: (please feel free to discourage it if it is wrong)

In Obsidian I have the following structure:

1. root

2. media files (images inserted on my notes)

3. Notes on Literature (main folder of my notes)

   • Notes on Book 1 (each chapter on separate .md)
     • notes on chapter1.md
     • notes on chapter2.md
     • etc.
   • Notes on Book 2 (each chapter on separate .md)

4. Index of Books with Notes (the .md paper looks like this)

   Books

   1. Author - Book1
   2. Author - Book 2

   Articles

   1. Author - Article 1
   2. etc

Inside every note that I took I made [[links]] on what concepts I’m interesting in.
For example: [[narrator]], [[figure]], [[Aristotle]], [[chronology]], [[plot]], [[Story]] etc

Here is my problem. All the links above are blank_pages.md. There is no note on them. I only made these links to see where the word Narrator, Aristotle etc. appear in all of my notes. If in a note taken words Aristotle & narrator meet then those notes become interconnected. There is something wrong with my system… Is functioning like a word search in Microsoft Word or in best case like a saved search: “Aristotle” AND “Narrator”.

Please advise.
Thanks in advanced!

[Miah]

I’m definitely not an expert in Zettelkasten and not even authorized to advise. Waiting for a tutorial on Zettelkasten in Obsidian at the moment. From what I have been trying since yesterday, I learned the following (though again I might be wrong, just started learning about both Zettelkasten and Obsidian):

• I think there is nothing wrong with what you are doing. I had similar case and I was frustrated when I saw that my links were empty, but when I added tags, my notes became visible and kind of connected because I could see them in one list.

What I’ve decided to do, I am creating two separate folders, one for quick notes and internal links that I generate from my readings. In the graph, it will be showing the connection between the links. The other folder is for more extended Zettelnotes based on the quick notes and links. Graphically, notes will become visible. That will allow me a) to sift ideas pertinent to the project I am dealing at the moment; b) to see the links I wouldn’t see otherwise. Both folders contain tags, which lets me see relevant notes in a list.

I hope it makes sense. I believe as long as your system works for you, there is nothing wrong with what you are doing.

[Dor]

@mafsi

I still don’t get the main idea of having a Zettlekastel method of my notes.

Following a zettelkasten isn’t compulsory, or even a gold standard, unless you believe in it.
What you have is effectively stage one notes.
You could simply regard the empty notes as reminders that you haven’t completed stage two.

Luhmann’s system is designed to make publishing easier, by having notes in publishable text.
And it’s based on noted iterative reflections.
You don’t seem to have the rewriting into crafted prose or the iterative reflection driven by your notes.
Also unclear whether you have actually moved on from the original structure around the source material to atomic thoughts of your own.