#74

Have you tried Diigo for annotating ?

#75

Hello and thanks for your message. I’m glad to hear you think my tags-first, crucible notes approach might help to speed up your workflow. Regarding your questions:

  1. In obsidian, I title each highlight note with the surname of the author plus the date. They are almost always academic sources so this works well. I use et al. for references with three or more authors. For example, an article by John Smith in 2021 would be titled [[Smith, 2021]]. An article by Smith and Holloway would be [[Smith & Holloway, 2021]], and an article by Smith, Holloway and Jones would be [[Smith et al., 2021]].

  2. For note names, it depends on what type of note. Probably the most relevant for importing highlights and generating new outputs would be highlight notes, paper ideas, and crucible notes. Highlight notes are literally just the highlights taken from other people’s articles. Each point or idea includes between two and ten tags. I don’t rewrite any of these highlights yet because I save that part for when I’m creating a new article of my own. Paper ideas are notes where I can bring together quotes from highlight notes. In a sense, I construct as much of a new paper as I can from the papers I’ve read. I still don’t rewrite the points at this stage. I add a checkbox to each point or idea. This way I can easily keep track of which points have been rewritten in the following step in the process. I name each paper idea note whatever I’ll name the final article but with a P - at the start. For example, I’m writing a paper at the moment which proposes a new argument genre, and I’ve named the relevant paper idea note [[P - Elaborating a new argument genre]]. That’s it for paper idea notes. Third, I have crucible notes. This is where I’m now ready to rewrite or summarise what other people have said, mixing in my own ideas and insights as I go. I have the crucible note open in one pane and the associated paper idea note beside it. As I rewrite or summarise an idea in the paper idea note into the crucible note, I check the checkbox and move to the next one. My use of highlight and paper idea notes means I already know which other work I’m citing and what the structure of my final article will be. This makes the process easy and, dare I say, fun. I name my crucible notes the same as the associated paper idea note but with a CN - at the start for crucible note. For example [[CN - Elaborating a new argument genre]]. When the crucible note is done, I use Word for the final edit.

  3. You could use the workbench plugin for the stage in the process where you search your vault for given tagged ideas (using the line search ability) and then want to pull together and structure the notes of others into your paper idea note. The paper idea note can start as the workbench and be renamed when it’s ready, but you don’t have to do it this way.

I hope this is helpful. The tags-first, crucible notes approach only uses particular aspects of obsidian, so it may not seem appealing to some people at first glance. But for academics or HDR students who need to read regularly and can’t afford to waste time summarising or reworking ideas that you may not use in your own outputs, this approach works very effectively.

Good luck and I look forward to hearing how you go.

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#76

Hello Expeditioner. Thanks for this. I’ll have to check out Jason Yuh’s ideas (haven’t come across them yet but I’m glad to hear others are promoting a tags-first approach). I’ve outlined my crucible notes process to sharulhafiz so that might help answer your question in more detail, but in short, no tagging is necessary in the crucible notes stage; by then, you should already know which authors you’re citing, what ideas will make up your new article or chapter, and what structure it will take.

Working very well for me but I acknowledge there are many ways to use this app and achieve similar outcomes.
Take care!

#77

Thank you so much for your time for the very long elaboration. My notes organization is different, which needs a revisit.

#78

Thanks for answering. You can check out Jason Yuh’s interview on Obsidian Office Hours YouTube channel.

Two more questions. How do you pull relevant highlights into the paper note ? And, how do you cite in the crucible notes ?

Cheers

#79

Hi mate,
For the first question, it depends on where I read the original source. I have the Roam Highlighter Chrome extension for any online sources or Kindle book highlights that I access via Chrome. Lately, I’ve been reading a lot of PDFs on the kindle app, either on my phone or actual kindle. I email the PDFs to my kindle email with the message title ‘Convert’ so I can read and format the PDFs like kindle books. Then, you can use the kindle app to export your highlights to your normal email, and from there copy and paste into obsidian.

For your second question, I write the crucible notes like a journal article, so I cite any reference using APA 7 format (for example: Smith, 2021).

Thanks for the tip re Jason Yuh. I’ll look him up!

Cheers

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#80

@Dpthomas87 I just ran across your October post. I’m new to Obsidian and I’m intrigued by your approach to literature notes. Would you be able to add a screenshot as an example? That would be helpful as I begin rebuilding my academic workflow around Obsidian. Thanks in advance for your consideration.

2 Likes
#81

Hey there,

Sure thing. Here are a couple of screenshots from one of my highlight notes.

Screenshot_20210720-214117_Obsidian
Screenshot_20210720-214117_Obsidian1536×2152 367 KB

Screenshot_20210720-214125_Obsidian
Screenshot_20210720-214125_Obsidian1536×2152 576 KB

The first shows the metadata I capture, plus some of the information I typically include before the highlights. The second shows some tagged highlights. These highlights are a bit long (they’re often shorter), but this should show you roughly what I do. Being able to search by multiple tags allows me to find specific highlights about the same topics across my notes.

Happy to answer any other questions and find luck with your workflow.

Damon

3 Likes
#82

Thanks! May I ask one last question? What application to you use to compose your writing? I’ve gone back and forth a bit between Scrivener, Ulysses, and most recently Obsidian. I don’t want to presumptuous with your time but I thought I’d go ahead and ask. Thanks for your kind assistance!

#83

As a Historian, i’m trying to use Obsidian as a Knowledge Discovery theory experiment.
Working with historical documents (scanned, mostly) needs a lot of pre-processing. So, before creating notes, i’m trying to OCR those documents to find Named Entities, and that I decided to turn into single .md files. Each person, place, idea, scientific concept, I turned into a .md so the Graph can be populated and interpreted, to find new narratives using the Journey plugin maybe, or any other possibilities. About articles, books and note-taking, I just go with the flow. I read, if I identify an important entity, I turn it into a .md, after that I try to populate some information about it, to enrich the whole graph view. So, the process of knowledge and narrative discovery is basically a loop.

Hope you liked my way of working with Obsidian as a Scholar. Thanks for this post.

1 Like
#84

Hello again,

I try and do as much in Obsidian as possible. It’s also where I manage my daily tasks, meeting notes, and where I develop lectures and tutorial content for my teaching too. The final version of my work depends on what I’m writing. If it’s a journal article/chapter, I’ll do the final edit in Word. If it’s a Tweet, I typically use the Twitter website or Typefully.

Really the key to my workflow is getting the best bits of what I read into my vault as efficiently as possible and in a way that makes them easily retrievable when I need them. I don’t write my own summaries of what I read before putting the highlights into my vault because this takes a long time. I need to read multiple papers each day in my job (if possible), so spending a whole day or longer on one reference is a poor use of time when I may not even end up using that reference in my own writing. I do summarise and recontextualise what others have written into my own words, but not until I know I want to use their specific points in my outputs.

I’ve used Obsidian for 12 months now, and in that time, I’ve read and processed 235 articles/book chapters. My outputs have increased considerably too, which I put down to the system. In the past, I found it a real chore to read any academic articles. In fact, I’d only ever do so as I was writing because I needed to find a quote to support what I was already arguing. This obviously limited my writing to my own ideas, whereas now, I’m reading, learning, and thinking every day, I’m reading widely in my own field and into other fields, and all these practices are improving my writing.

There are many PKM workflows you can try with a tool like Obsidian, and different workflows suit different people and needs. If anyone wants to increase the amount of reading they do and have more to write about when they need it, the workflow I’ve developed seems like a good way to go.

Good luck!
Damon

5 Likes
#85

Shhhh. Don’t reveal our secrets…

More seriously: how long did it take you to kick this habit? I feel like I’m constantly playing catch up with the deadlines/projects I already have, so I don’t have the freedom for this kind of “freedom.” But maybe that’s just PhD life (plus being a new parent) and I’ll be able to shift gears in the future…

1 Like
#86

Haha! Your joke is both funny and sad at the same time.

I’ve been an academic since 2014 (PhD conferred in 2015), and things only really changed for me when I started using Obsidian around a year ago. The key wasn’t really using Obsidian, it was in changing my mindset from ‘publish or perish’ to a sense of just wanting to learn and grapple with the ideas in my field that I find most interesting/pressing. I had to be able to trust that focusing almost exclusively on thinking and learning (as serviced by reading and writing), all the publications, grant applications, and other academic activies would be addressed as byproducts. In my mind, my identity as an academic is now to be a prolific reader, writer, thinker, and learner, and all the other stuff is just the fruit of these core practices. Obsidian (and similar tools) help with this since you know that you only need to read a paper/book/whatever once. It’s funny to admit this since I really wasn’t motivated to read in the past, but now I literally go to bed asking myself if I can fit in reading a little more of the latest paper before I go to sleep. As I sit there watching a movie with my wife (after the kids are asleep), I’m also reading a paper on the side, chuckling occasionally so she thinks I’m fully engaged in the movie. If I didn’t know that all the good bits of what I read are stored safely and easily accessed in my Obsidian vault for all eternity, I wouldn’t be motivated to read, since I know I’d just forget it all in a heartbeat. It’d be too much work. But by largely forgetting about the outputs you’re working on, and focusing on just learning about your field, it changes not only how much you get done but who you are as an academic/PhD student. Or, it has for me at least!

A book that helped me realise this stuff is ‘Essentialism: The disciplined pursuit of less’ by Greg McKeown. It’s not really about academia at all, but it helped me trim away the stuff in my life that was taking up my time in unhelpful ways. When there’s not as much ‘fun’ or ‘distracting’ stuff to do, your genuine interest in your field and the knowledge that whatever you read is ‘safe’ in your vault will prompt you to pick up the next paper. In a nutshell, this mindset to be a prolific reader, writer, thinker, and learner, coupled with Obsidian, has allowed me to feel happy about being an academic for the first time. I’m not stressed at all - I’m just focused on learning. This is a pretty positive step for someone who literally burnt out in the first few years as an academic.

Good luck with the PhD and the much more important task of being a parent :+1:

16 Likes
#87

What a wonderfully helpful and kind response. Thank you! You just pushed me over the edge, in a good way. :slight_smile:

I’m going to work to finish my book project in Obsidian and then export the near finished product to Word or Scrivener for final editing.

Thanks again for taking time out of your busy schedule to respond in such a thorough and helpful way.

Blessings to you.

5 Likes
#88

I also enjoyed this post - thanks for your comments on this thread (as another academic using Obsidian, I find it very encouraging to know that others are finding it as useful as I am). If you do have a moment, I’d be very interested to hear how you gain an overview of your notes (as I understand your workflow, you don’t have ‘atomic zettals’). This is where I have found Obsidian quite useful - having markdown files with relatively long file names (say Professor Smith made this comment about this text) - and then using graph view/the side bar to replicate the experience one would have with spreading notecards across a desktop. Do you mainly use your tags when searching through your notes and constructing outputs? (Thanks again! - And, just to say, it is wonderful to hear from an academic really enjoying their work for once!)

1 Like
#89

Hi Ryan,

Thanks for your reply. Hmm, great question. I’d say I don’t really use atomic notes, as such. I have my highlighted notes, which are long notes with highlights from books with tags added to each quote to suit the quote’s topic (e.g., writing, assessment, phonics, etc.) and rhetorical purpose (e.g., definition, example, solution, etc.), and then I trust the search functionality to find each quote when I need it. I initially followed the How to take smart notes approach, with fleeting, literature and permanent notes, but once I could search for a specific quote so easily, I figured it was adding an extra step to take the quote and put it in an atomic note. I also initially had an index note with a similar set up to what you explained (descriptions of the quote/note), which let me see quickly what I had on different topics, but I haven’t missed it in the months that I’ve stopped using it and not having to write the descriptions has saved a lot of time. In a way, my current approach has the potential to limit my vault from being a ‘conversation partner,’ since I now have to know what I’m looking for before searching for it. But I usually know what I need next, so it hasn’t really been an issue. In a way, the use of tags and searching allows each quote to operate a bit like an atomic note, even though it’s just there, in the long highlight note with all the others.

I would be incredibly happy if someone developed a plugin that allowed the tag system to work like it does in Roam (filtering the tag list based on what tag you select to only show other tags that are used on the same lines/blocks - the more tags you select, the shorter the list of tags becomes). I’d probably pay money for a feature like that, since it ‘would’ allow for conversations with my vault, revealing connections I never knew were there.

Anyway, yes, I try and get multiple papers into my vault each day, filled with highlights and tags, then, when I’m ready to write about a topic, I create what I call an ‘ideas note’ where I dump and reorder all the direct quotes I need for an output, then I create what I call a ‘crucible note’ which is where I summarise and recontextualise the quotes in the associated ideas note into my own words and mix in original thoughts. So, all the novel thinking and connecting still happens, but not until I’m actually ready to write an output. Initially I was summarising and putting quotes into my own words after highlighting every source, which was very time consuming and frankly unsustainable since I may not even need it for an output. It took so long to process a single article, so while it did help me to think in new and interesting ways, it didn’t really keep up with my workflow as an academic. My current approach is much more streamlined and I’m sure wouldn’t appeal to many people using Obsidian because it doesn’t really rely on many of Obsidian’s key features. But it’s helped me to become a more prolific reader, writer, thinker and learner, so that’s good enough for me.

All the very best with everything. I’d love to hear about your approach to this PKM work. How brilliant that you’ve found this while working on your PhD. I feel like all the reading I did for my PhD back in 2021-2014 is largely forgotten and wasted now. Oh well!

Cheers,
Damon

8 Likes
#90

I do things similarly to @Dpthomas87. (I’m in philosophy, but read a lot of old texts, medieval manuscripts etc., so lots of pre-processing there too.) I keep my references organized in BibDesk (which I can really, really recommend if you’re on the Mac), including my pdfs.
When I read and highlight a pdf article or book, I export the highlights to markdown, which goes into Obsidian. I name my lit notes by their citekey, and use tags pretty much the way Damon described it.
If I come across something that I think is very important, or just very well put, I tend to create a separate note for it (and link it to the main lit note). All these “snippets” get their yaml field with the author and the parent note, so that I can parse them later.

When I write, I have an “ideas” note as well, where I collect all kinds of things that come to mind about the project, as well as link to all the lit that may be relevant.
Nowadays I do my first draft writing in Obsidian and then export to latex for final editing and compiling.

Good luck with the PhD!

2 Likes
#91

Amen and a thousand upvotes. I left Roam for the Obsidian beta at least 18 months ago and this is the main feature I still pine for…I love writing in Obsidian but searching for and resurfacing information is still a significant concern. This adds a LOT of friction to my workflow. Using search in Obsidian is high friction as well (as it was in Roam). For my use cases this (ease/certainty of resurfacing) is by far the biggest remaining issue with Obsidian.

2 Likes
#92

Thanks for all this - absolutely fascinating.

Might experiment a bit with my workflow (basically at the moment my Kindle highlights are copied into Obsidian atomic note by atomic with tags which I then use on the graph view to get an overview of a topic and start building an outline).

Experiencing a lot of friction creating a new note for even quite small pieces of information (which I already probably have from other scholars in the vault anyway) and adding similar set of tags again and again (though like you I find rhetorical purpose tags exceptionally useful). Something nice too about having the atomic note title to force you to get to the point and think ‘how will I actually use this in future’. But it is very time consuming, especially when a text is very dense and complex (just been going through an edition of a primary source where I was making multiple atomic notes even from just a single footnote). I’ve seen a new plugin which may help provide best of both worlds - going through one document of highlights, adding tags and headings, and then running the plugin to split the highlights into those atomic notes.

Glad to hear how well everything is going though - it is always a pleasure to read and hear from people who are becoming more productive (and, crucially, enjoying their work at same time).

Take care,

Ryan

1 Like
#93

@Dpthomas87 not sure if you are aware, but there is a discord role to make these sort of requests: @dev for hire. Hope that helps!

1 Like