Research/PhD/Academics

Assuming you mean the PDF reading app for macOS and iOS, it is not designed to support literature searching/discovery. It is an excellent highlighting app, though, and plays well with note-taking as you can export annotations in Markdown format.

Thank you so much for the elaborated explanation. Instead of Zotero, I’m using Paperpile, which have built-in annotation, and highlight. Once I’ve finished reading and annotating the article, I can export them in Markdown format and paste it into the notes

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For those using Zotero (or those not on Mac), I added a few tips over here on how to use your standard PDF reader similar to the Highlights app: Zotero best practices

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Amazing tips here. Thanks arg

Thanks for your thorough explanation! I have been following a similar approach, based on your experiences for three days now (I know, not that long).

But processing the ~50 notes I took from a single article is taking me over 2 days now. Whereas i used to shortly summarise a finding from a paper in one sentence, which took 15 mins for a paper tops.

Do you think it will be worth the effort in the long run or am I taking the wrong approach here? I am intrigued to see whether I will start seeing a bigger picture more easily with this method but if I can read a fifth of the amount I otherwise would, I’m not sure if it will be worth it. Though perhaps these are just startup costs and it will get faster?

I am interested to hear your guys’ opinions on the matter!

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Hi mate. I’m totally with you on this. In academia it’s critical to have a system that allows us to read and mine important ideas from papers into your vault as efficiently as possible. My method has continued to evolve and I’m finding it more efficient now.

In a nutshell, I’m now adding the one-sentence summaries to highlights as I’m reading (and the tags where possible). This means I don’t need to read the source more than once; instead I’m processing them as I’m reading because that’s when I discover them as important points in the first place. I then bring them into Obsidian in a single note per paper/source. I title each note Surname, date (e.g., Smith, 2018). It’ll make sense why in a moment. Each idea within the note is structured like this:

One-sentence summary of idea

|
Original idea in the author’s words (Reference, date, page number).
T: #tags #go #here
C: Any connections to other notes or ideas - not necessary to include for every idea but it’s useful to think of connections where possible

If you structure all the notes this way, it means you can then add the ideas straight into your index with transclusion without needing to create any additional notes (in the past I created a new evergreen note for each idea).

An example of a transcluded idea to pop into your index would be like this:

![[Smith, 2018#One-sentence summary of idea]]

This allows you to see the source and the summary of the note in edit mode and just that idea transcluded from your note page in the preview mode.

I have another approach for actually turning those ideas into publications, but this is the main approach for processing notes into my index. There may be even more efficient ways to do this. The key I think is being able to process ideas into your vault as quickly as possible while still tagging and making connections to help with later retrieval of ideas.

Since changing to this approach I’ve written a couple of book chapters with very little cognitive strain and I’m reading more than in the past (it’s addictive because every paper has the potential to be used to level up your knowledge base).

Hope this is somewhat helpful to others. The evolution will undoubtedly continue. I know there are awesome examples of how to do all kinds of things in Obsidian but all I’m really aiming for is being more productive in my academic role. The rest is all interesting but additional to my main purpose for this wonderful app.

Good luck!

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This really seems to be a step in the direction that would work for me as well, I must say!
I did not really index (every) note yet, which may be a good idea to start and may well speed up the process.

However, upon trying your latest approach I found the resulting index to be somewhat cluttered. The main ideas are only the small title/summary, whereas the content, tags, and links below it takes up the most space.
I tried using the raw internal link (not transcluding) but here the “Smith, 2018#” was distracting me a bit. Do you not find this bothersome or have you also found a good solution for this?

What also may make the workflow less compatible is that my research is in chemistry, where I have very dense papers (virtually every sentence in a good paper expresses an important idea). As such a lot of paragraphs have to be highlighted and some paragraphs contain 3 or 4 important ideas.
Of course, I do not know in which field you are active, but I imagine fields with longer and less dense books/articles that centre more around developing arguments may work better with this system.

Perhaps I also need to loosen the atomicity principle a little, as I don’t yet see how Obsidian could work currently, as I am now expecting to require 4 days to process the paper I read last. (Although it was a great paper with a lot of useful info, making it more time-consuming).

This reference system is brilliant. Stealing the format if you don’t mind, but using it in the context of my own system.

Moved away from Papers before they were bought by Readcube. Currently using Mendeley but seriously considering the move to Zotero. Papers gets bogged up pretty fast and the library then is very resource hungry. Mendeley also provides a sturdy iPad app for reading and when I need to extract highlights I mark it up in PDFExpert. Similar to you I am interested in simplifying and consolidating my workflows. Zoteros would enable me the automatic import of highlights into Obsidian (as far as I understand until now), so that would help. What was you reason for using Papers?

Mendeley is a low-quality, reluctant to improve, adaptation of Zotero (based on some/many of its libraries afaik) and has sold its soul to the Elsevier capitalist devil—and is just a terrible app. I would really encourage you to make the transition sooner.

Regarding this:

You can organize your PDF library using Zotero plugin ZotFile and put it on the cloud. Follow this excellent tutorial. Then, use Xodo PDF reader to read your files on your iPad right off your cloud drive. Per my experience on my Android phone, it does the whole syncing stuff for you very smoothly with OneDrive.

Xodo does not have a Mac desktop app. But in case you are on Windows, it has an awesome desktop app for you. I have had a great experience using it in tandem with OneDrive. With some black magic, whatever annotations you make on the files in Xodo are saved right away and you do not get OneDrive errors like “could not sync that file as it’s open somewhere.”

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Hi @psyguy, thanks for the encouragement to move on, I especially enjoyed the religious attitude in your passionate dismissal of Mendeley. As it mostly is with regards to the devil I have some things that currently make it necessary to continue to use the app (sharing groups with my PhD and MD students). Meanwhile I will organize my escape to Zotero and check out the links an apps you mentioned. Thanks! I’ll report back.

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If it helps, I’ve worked with Zotero in teams and it’s been pretty nice. I can’t compare with the Mendeley experience though.

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Others on the page here (specifically @Dpthomas87’s A, B, C) have done a great job at outlining their methods which I’m generally following. So I’ll focus a bit more on the mechanics.

I rely pretty heavily on Hypothes.is for most of my note taking, highlights, and annotations. This works whether a paper is online or as a pdf I read online or store locally and annotate there.

Then I use RSS to pipe my data from Hypothes.is into a text file in OneDrive for my Obsidian vault using IFTTT.com. I know that a few are writing code for the Hypothes.is API to port data directly into Roam Research presently; I hope others might do it for Obsidian as well.)

Often at the end of the day or end of the week, I’ll go through my drafts folder everything is in to review things, do some light formatting and add links, tags, or other meta data and links to related ideas.

Using Hypothes.is helps me get material into the system pretty quickly without a lot of transcription (which doesn’t help my memory or retention). And the end of the day or end of week review helps reinforce things as well as help to surface other connections.

I’m hoping that as more people use Hypothesis for social annotation, the cross conversations will also be a source of more helpful cross-linking of ideas and thought.

I prefer to keep my notes as atomic as I can.

For some smaller self-contained things like lectures, I may keep a handful of notes together rather than splitting them apart, but they may be linked to larger structures like longer courses or topics of study.

If an article only has one or two annotations I’ll keep them together in the same note, but books more often have dozens or hundreds of notes which I keep in separate files.

For those who don’t have a clear idea of what or why they’re doing this, I highly recommend reading [[Sönke Ahrens]]’ book Smart Notes.

I do have a handful of templates for books, articles, and zettels to help in prompting me to fill in appropriate meta data for various notes more quickly. For this I’m using the built-in Templates plug-in and then ctrl-shift-T to choose a specific template as necessary.

Often I’ll use Hypothes.is and tag things as #WantToRead to quickly bookmark things into my vault for later thought, reading, or processing.

For online videos and lectures, I’ll often dump YouTube URLs into https://docdrop.org/, which then gives a side by side transcript for more easily jumping around as well as annotating directly from the transcript if I choose.

I prefer to use [[links]] over #tags for connecting information. Most of the tags I use tend to be for organizational or more personal purposes like #WantToRead which I later delete when done.

When I run across interesting questions or topics that would make good papers or areas of future research I’ll use a tag like #OpenQuestion, so when I’m bored I can look at a list of what I might like to work on next.

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Hello fellow researchers,

I’ve been receiving some emails from people wanting to know more about ideas in my old posts so I thought I’d write an update outlining my current system. For context, I’m a senior lecturer in English education working at the University of Tasmania. My current system is quite different to what I’ve written about here before. I’m now using what could be termed a ‘tags-first approach’, which is very simple in order to keep up with (and speed up) my workflow: I no longer bother with indexes, headings or summaries of any kind.

Now, I simply (1) highlight what I find relevant and useful in journal articles or book chapters, (2) tag each highlight as I go in Acrobat Reader for articles or Kindle for chapters, (3) import them into Obsidian in a folder called ‘Highlight notes’, and (4) rework them with my own ideas into outputs. Perhaps the key to this system is that I not only tag each highlight for its key concepts, I also tag their ‘rhetorical purposes’ which will help me to find them again later. So, an example for a useful quote that defines the writing prompts used in an assessment like NAPLAN (Australia’s national writing test) might be:

#writing #assessment #standardised #tests #NAPLAN #prompts #definitions

In this case, tagging #definitions is crucial because, later on, I might want to see what I have in my vault that defines the topic so I can include them in my own writing. Another example might be:

#reading #phonics #primaryschool #differentiation #teachingapproaches

In this case, I’d easily be able to find the highlighted quote with these tags if I needed to locate previously encountered research about methods of differentiating phonics instruction in the primary school grade levels.

The key with the system is to get the useful highlights into Obsidian as quickly as possible in a way that they can be easily found again. In the past, I was spending ages summarising other people’s ideas but with the amount I read there was a high likelihood that I’d never use those ideas in my own papers. In other words, it was wasted time. Now, if I have to write about a specific topic, I can use the line:(#tag1 #tag2 #tag3) search command to find previously encountered ideas I need for a given purpose.

While you could achieve this in a number of ways, I use the workbench plugin to quickly copy the useful highlights into a workable space, then create a separate note for that topic which I call a ‘Crucible note’. This is essentially a place for me to recontexualise the quotes of others into my own words, mixing in my own ideas as I go to create a new piece of writing (like a crucible). This is where the summarising/reworking of other people’s ideas happens, when I’m ready to use the original highlight for an output. I then use Word for the final edit.

As you’ve probably surmised from this post, I now don’t use many of the features of Obsidian; there is no backlinking and no graph view. Perhaps my system will evolve to make use of these, but right now I’m quickly able to read and write so I’m happy.

I hope this is useful to people and I’d love to hear your thoughts. Cheers.

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@chrisaldrich - appreciate sharing your workflow. About Hypothes.is:

Would you have any interest in breaking this down a little? Is the RSS feed native to Hypothes.is? I understand IFTTT a little, but I’m not sure how to incorporate a feed.
I’ve been experimenting with Hypothes.is lately and love it, but the friction of getting things out is frustrating me.
If it matters my vault is just in local storage, backed up to GitHub.

Thanks!

Hypothes.is has both RSS and Atom Feeds. So the IFTTT “if” is a new item in your feed which creates a text post in some appropriate storage account. I use OneDrive as the “that” target, but I’m sure you could potentially use others with some experimentation. If you have something that only saves as .txt files, that’s fine, you can simply rename them as .md files for your vault later.

I’ve described some of this before at https://boffosocko.com/2020/08/29/a-note-taking-problem-and-a-proposed-solution/ for those interested in further details.

Hopefully this helps (until someone has a more automated version).

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@chrisaldrich - Thank you very much. I recall reading your post when I first discovered Hypothes.is - in fact, it may have been the reading that caused me to discover it. Perhaps if I had taken notes at the time I would have this set up already…
Even only partially automated, this will greatly improve my workflow.
Thanks again for your help, and for sharing your experience and wisdom. I hope to put it to good use.

Many thanks for such a detailed introduction to your workflow! Very nicely written! I benefited a lot from it!

No worries! Good luck with your note-taking.

org-noter with org-mode.