Research/PhD/Academics

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.

Me myself did trying to create notes when reading them in my own thought, which is what most of youtube videos and others said. And as you experienced, this taking a lot of times, and to my surprise, I have not using any of my written thoughts, and I’ve been doing this for almost 2 years now. THANK YOU.

I’ll try your new system and see if it fits me.

Some question:

  1. How do you title the article/md file the highlights are from?
  2. How do you name your notes?
  3. Workbench plugin?

Thanks for sharing your process. I would like to know more about your “crucible notes” . It seems to me you use in line tagging, like Jason Yuh. Do you tag the crucible notes too or just the highlights ?

Have you tried Diigo for annotating ?

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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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!

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

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