This thread has compelled me to make an account just so I can join in after being a lurker on the forum for months.
I mostly wanted to post because:
a) some systems seem more complicated than others and I wanted to share my super-bare-bones system that works for me
b) I’m only recently an Obsidian user, and my system was originally built using pen and paper (I should add I’m a millennial and this was a choice because it’s how I liked to work!) - my point here is the process is app-independent.
Background: I’m an ecologist, working for an NGO (shoutout to @Satya who I spotted in this thread and works in the same field, nice to see another conservationist “in the wild”!). I need to keep up with several fields (ecology & conservation, politics, economics, etc.), but also I don’t have time.
My focus with reading is 4 things:
- Latests stats
- Latest research
- Latest best practice (with evidence)
My process with reading requires 3 tools:
- Citation manager
- “Personal library” (I.e. literature manager)
- Note manager
I won’t discuss a citation manager here, but y’all know you need a manager that stores your citations and that will compile bibliographies when it comes to writing papers.
I use DevonThink Pro for my literature manager. It stores all my PDFs, which are highlighted etc. Files are named “author, year, full title”. I put them in some loose folders based on main topic; this isn’t necessary really given the search abilities in DevonThink, but I like folders.
This is where Obsidian comes in. I have two types of note:
I keep paper notes in a folder called “Papers”. That’s the only folder I have in my vault. Topic notes are loose.
My plan is to only touch papers twice.
- I read my papers in DevonThink, highlighting as I go and adding notes as needed. This will take an hour or two, or perhaps longer if it’s complex or on a topic I’m unfamiliar with. I want to understand what I’m reading, but I don’t need to be an expert on the paper at this pass.
- Using DevonThink’s ‘summarise highlights to markdown’ function, I turn all my highlights and notes to a markdown file. I copy and paste this to Obsidian (deleting the original in DevonThink) and now the real work begins!
- The markdown file is named the same as the paper in DevonThink, and is put in my “papers” folder. It automatically has a backlink to the pdf in DevonThink, but I do add a full citation to the file at this point (2 reasons: for future proofing but also so if I need to share the paper with someone I can just quickly copy and paste the citation without opening my citation manager).
This step is where the thinking occurs: I format the file how I like as I go, add deeper comments to the quotes/highlights I marked up, add tags as needed, and…
- Add quotes and thoughts to “Topic notes”. Topic notes are notes I keep on specific themes, e.g. “lynx” or “kelp forests”. I try to be specific enough that the notes are focused, but not so specific that I end up with a million notes. I add relevant bits of my reading to these notes, rearrange and add new sections to these notes, etc. It’s where the thinking happens. I also use data view to show a list of backlinks to these notes. I usually do this step with the original pdf open as well: I can add bits that I might have missed on my first read and dig out any references I want to follow up. I have a keyboard shortcut that keeps a basic template for all new topic notes (it creates a title, a tag section for me to add a list of tags, and the data view for backlinks).
In theory, once I’ve finished updating my paper note and topic notes, I don’t revisit the pdf in DevonThink. Day-to-day I mostly work from my topic notes, but I do dip into the paper note when I need something more specific. Otherwise, the topic notes are where my work takes place.
It might take 3-5 hours to work through this process per paper, but much of this is my thinking and linking up research, and after that I rarely re-visit a paper and lift most the things I need for my work straight from my topic notes.
Pre-Obsidian, my topic notes were actual “themed” notebooks or notebook sections where I handwrote quotes and thoughts on the papers I read. I printed papers and kept them filed, with highlights, comments and post-it’s for longer thoughts attached. I rarely revisited them as my notebooks had what I needed, but I kept them in case I needed to refer back. Wanting to streamline my shelving made me move to a digital system.
Not all of my ideas/research comes from academic papers of course. When I get ideas, spot interesting comments in news articles, discuss things with peers, etc., I add them to the relevant topic note. I might also save the original source in DevonThink (I try to do this for news articles and websites at least - I save as a PDF and add a link to the relevant section in Obsidian). This thread isn’t about books, but for interest I have exactly the same format for books as I do for papers, except that I either download my highlights from Kindle or add them manually if it’s a paper book. As these are big files, I leave the highlights in DevonThink and only add the quotes and my comments to topic notes in Obsidian.
If I have a new question or topic that I’ve not thought about before, my first step is a search in DevonThink to see what I might have read about it already. Then I can start a new topic note in Obsidian and starting bringing together new ideas. My obsidian vault is indexed in DevonThink too so if I wrote anything in a note that is relevant it will be found by DevonThink.
In an perfect world we’d just download this knowledge to our brains without having to read it first, but since we’re not robots I like my stream-lined process for accumulating new research and integrating it into my thinking.