Reading and annotating PDFs

Graduate research involves reading a lot of PDFs, and where you read them affects whether your notes are still useful a year later. Tools in this category help you highlight, annotate and organize papers, and some add an AI that answers questions about a document.

Many reference managers now include a reader, so start by asking what a separate app would add. LiquidText lets you pull excerpts into a workspace and link ideas across documents, which suits close comparison of several papers. MarginNote turns highlights into outlines, mind maps and flashcards on Apple devices. Readwise Reader brings articles, PDFs and newsletters into one reading queue and syncs highlights to note-taking apps. Hypothesis adds shared annotation on web pages and PDFs, which is popular for reading groups and teaching.

AI question answering is where care is needed. Adobe Acrobat's AI Assistant and ChatPDF let you ask about a document and point to the passages behind their answers. That helps you find where a method is described or which table holds a result. It does not replace reading the paper, and answers can misstate numbers or mix up conditions. Use the answer to locate the passage, then read the passage.

Think about where your annotations live. Highlights stored only inside one app are hard to move later, so check whether the tool exports notes as Markdown, plain text or into your reference manager. Also check data terms before you upload unpublished drafts or confidential reports, since some tools process documents on remote servers.

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6 AI research tools in reading and annotating pdfs

ChatPDF

Upload a PDF and ask questions about it in chat; answers point to the pages they came from.

  • Free plan or free tier
  • Shows sources for its answers

Hypothesis

Open source tool for annotating web pages and PDFs, privately or in shared groups, often used in reading seminars.

  • Free plan or free tier
  • Open source

Adobe Acrobat

by Adobe

Adobe's PDF app, with an AI Assistant that summarizes documents and answers questions about them as a paid add-on.

  • Mobile app

Readwise Reader

by Readwise

Reading app for articles, PDFs and newsletters, with highlights that sync to notes apps and an AI that answers questions about a document.

  • Mobile app

LiquidText

PDF reading app for tablets and computers where you pull excerpts into a workspace and link them across documents.

  • Mobile app

MarginNote

Reading app for Apple devices that turns PDF and ebook highlights into outlines, mind maps and flashcards.

  • Mobile app

It helps to decide on a reading routine before choosing an app. Some people skim abstracts and figures in one pass, mark papers to read closely, then return for full annotation. Others read every paper once, in depth, and write a short summary in their own words straight away. A tool that fits your routine will get used. One that forces a new routine usually ends up abandoned after a few weeks, with notes scattered across apps.

Accessibility matters too. Some readers offer text to speech, adjustable fonts and reflow for small screens, which help with long reading sessions and for readers with dyslexia or low vision. If those features matter to you, test them on a real paper with equations and tables before you commit.

The tools below are listed in no particular order, each with a short description we wrote and a link to its official site.

Questions about reading and annotating pdfs

Can I trust an AI summary of a paper?

Treat it as a guide to where to look. Summaries can leave out limitations or misstate numbers. Read the relevant sections yourself before you cite anything from the paper.

Should my PDF annotations live in my reference manager?

Keeping them there means notes stay with the reference and travel into your writing workflow. A separate reading app makes sense when it offers something your manager lacks, as long as it can export your notes.

Is it safe to upload a manuscript under review to a PDF chat tool?

Usually not. Peer review material is confidential, and many publishers forbid uploading it to AI tools. Check the publisher's reviewer guidelines and the tool's data terms first.

Which tools work for reading groups?

Hypothesis is built for shared annotation, with private groups so a class or lab can comment on the same paper. Shared libraries in reference managers also let a group read and annotate one PDF.

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