Working with PDFs in Obsidian: Annotation masterclass


Dear Scholar,

The number of yearly published papers increased by > 47% since 2016, strongly outpacing the growth in PhDs awarded per year, as this 2024 study found. AI is expected to "fill the gap", making us read more, publish more and be more productive. If this feels daunting, you're not alone.

Writing with AI feels magical, yet often unsatisfying because the depth of understanding is missing. Those who use AI for coding, for example, know the experience of being able to follow the result and the certainty of being unable to produce the solution themselves. Fully trusting AI, therefore, might take away our agency and satisfaction.

A way out is to use AI to augment our knowledge and access the information we have processed and understood, focusing on the access/search part rather than the understanding part.

I am currently working on developing an approach to using AI on my notes and on ways to create better AI-ready academic notes. The first step of this journey are PDF annotations because they link my interpretation (i.e. notes) to the facts (i.e. papers), and together, they form a unique fingerprint of my thinking, that AI can help me access. In this week's article, you can learn how to do it in Obsidian:

Additionally, this article dives into AI-driven full-text PDF search and a few hacks for academic note-taking in Obsidian.

(If you aren't yet taking digital notes in Obsidian, join the free 8-day note-taking course, where I explain how to get started and what you miss out on.)

Reminder: Note-taking Course 2.0 update

In case you missed the announcement last week on the update of the note-taking course, here is a reminder to check your email if you previously purchased the course and want the free update. The update includes:

  • Merging your PDF annotations and digital notes
  • Working with Zotero7 (newest update)
  • Connecting Paperpile with Obsidian (my favourite reference manager)
  • Working with Obsidian in 2025
  • Synchronizing across multiple devices
  • Advanced mind maps for academic projects
  • Updated starter vault with explanations and examples

Wishing you a wonderful weekend,

Ilya Shabanov, The Effortless Academic

You received this email because you signed up on EffortlessAcademic.com or Substack
Don't want to receive emails:
Unsubscribe only from the weekly newsletter (keeping only new webinar announcements every 3-4 months) or Unsubscribe from everything (You won't hear from me unless you sign up again).

The Effortless Academic

Literature Review Tools, Note-Taking Strategies and AI tutorials for the modern academic. Publish more with less effort and supercharge your career.

Read more from The Effortless Academic

Dear Reader, Last week, I made a post on using AI for academic writing, which enraged the community like nothing I have ever written. 4 Million views & about 400 hate comments. A dozen people even took the time to reach out to the dean of my university & my supervisors (yet none to me personally). I don't think even 1% read past the hook ("I wrote 4000 words for my thesis with AI") and ignored that the basis for the entire process were my own papers, the workflow included deep-reading &...

Obsidian Bases for Idea Generation Dear Reader, Generating new ideas is the currency in academia: The more impactful your ideas, the more impactful your research, and the better your chances of success. But what are ideas? Ideas are connections between two related concepts. For instance, if someone finds a link between a vegetarian diet and hip fracture rates, that's novel and vital research that could improve people's lives. But these two concepts are not necessarily related. Nutritionists...

Sourcely.net (Sponsor) Your AI-powered academic search assistant, offering access to over 200 million papers. Sourcely finds papers matching an entire manuscript rather than a short query, providing scientific evidence for every sentence and enabling the so-called "reverse literature review": Write first, cite later. Discount Codes:Effortless40 (40% off annual)or Effortless20 (20% off monthly) Which Reference Manager To Choose For AI Dear Scholar, Reference Managers are the workhorses of...