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Tablet Workflow: Notero, Papership & Zotero for organised note taking

Nothing beats reading on paper but relying on hand-written annotations means missing out the massive benefits digital notes offer for synthesis and searchability. Using a tablet is the sweet spot in between, especially if you have a pencil for it. This workflow uses 3 apps: Zotero, Papership and Notion that work together to annotate your PDFs using a a tablet and store your notes across all devices.

IPad annotation and note-taking workflow: Apps and integrations notion zotero papership

We will focus on 3 apps here: Notion, Zotero, and Papership together for smoother note-taking.

  • Notion is a web and desktop based note-taking and organisation app. It is used in the workflow shown today because of its customisable nature, which allows us to link it to Zotero. This is where the note-taking will happen.
  • Zotero is a reference manager. This means that papers can be directly downloaded and stored here. This will be the home base of the note-taking system and will be further linked to Papership.
  • Papership is designed for reading and annotating academic papers. It allows for a seamless no-frills annotation and storage system. This is where the reading of papers will happen.

Notion is used in this case for note-taking, it is an alternative to Obsidian. To take good notes apply the same principles introduced in the in-depth Effortless Note Taking Course.


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We will outline in four steps some of the best iPad apps for researchers, and a way to link them up for an efficient paper reading process:

  1. Download papers into Zotero (using the Zotero Chrome plugin)
  2. Have Notion + Zotero integration (Notero) automatically create notes for every new paper
  3. Connect Zotero to Papership and annotate your paper
  4. Annotate papers in papership (on iPad) and take notes using Notion

1. Getting all of your papers into one place: Download papers to Zotero

Add your papers to your primary computer. The Zotero plugin for chrome is an efficient way to find papers and download them with a single click. Zotero will usually download the PDFs for you as well. Paywalled content might need to be added manually.

After adding your papers to Zotero you will:

  • Have all of the papers readily available when you need them in a centralised database
  • Have access to these papers through a desktop/offline, online, and mobile interface.
  • Have the ability to connect Zotero with other apps, allowing the papers to exist on other devices without needing to re-download them.
  • Have all of your papers aligned across your devices with Zotero Sync, a free tool which automatically updates your library.

Zotero is therefore a perfect base for our use-case. From here we can branch off in two directions to create:

  • An automatic note-filing system (Step 2a, Notero)
  • A distraction-free space to annotate and read papers (Step 2b, Papership)

2a. Notero automatically creates Notion notes for new papers in Zotero

Once this integration is set up, it remains fully automated and you can forget about it. Setting it up does require a few steps. Allow about 10 minutes to get everything up and running, but it is absolutely worth it. The end result looks like in this video. Any papers added to the Inbox folder in Zotero (right) automatically sync to Notion (left). Note that this Notion note automatically syncs to your iPad as well:

Source: https://github.com/dvanoni/notero
Source: https://github.com/dvanoni/notero

To set this integration up you will need to do these steps in Notion:

  1. Download Notion and Zotero (if you don’t already have them)
  2. Create a Notion page with a table (called “Inbox”)
  3. Add a Notion “internal integration” in your Inbox note. This yields a database key. Store it
  4. Download the github file.
  5. Drag and drop file into Zotero Add-ons
  6. Add the database key(from 3.) to the add-on

This video has more details:

Using Notero

Now, whenever you download a paper to your Zotero, a note file will automatically be created in your notion database.

This note file will include:

  • The title of the paper
  • The author(s)
  • The abstract
  • A link to where you got the paper
  • And any tags that you add to it

The real shining star is that your papers database in Notion is extremely customizable. It acts as a digital filing system for all of your papers, which can be sorted by any tags you’d like and displayed as tables or boards:

I personally find it very useful to tag papers I need to read and treat it as a to-do list. Additionally, sorting papers by topic is a game changer, allowing you to quickly refresh on any topic and see the most relevant publications.

Since it automatically creates the file when I download the paper to Zotero, I don’t need to put any extra energy into finding the file and creating a space for notes; it’s all done on auto-pilot.

You can go on and start taking notes on your sources directly in Notion.

2B. Papership: A dedicated place just for reading and annotating papers

Now this is where using a tablet or iPad comes in. You have your dedicated space set up for note taking (Notero), now you need a distraction free and engaging medium for reading the papers.

This is where the iPad really shines. It is much more engaging to read a text when you can highlight, annotate, and make notes in the margins. Doing this on paper would be great, but it is unrealistic and inefficient to organise 100s of PDFs. By having your PDFs on an iPad, you can highlight, annotate, add notes, and more.

Papership syncs directly with Zotero and mimics the folders that already exist in your account, so once it is downloaded and synced up you will be ready to use it, without any additional steps:

You can see that by using Papership, reading a paper requires active engagement. This means you’ll be more likely to absorb the information the first time and with an annotated PDF, looking back to find the key points of the paper will be easier.

Zotero vs Papership for annotations

While there is a Zotero app for iPad available, here is why you may not use the Zotero app with a built in annotation feature.

There are three main reasons:

  1. The Papership app offers more possibilities for annotation (such as adding images and selecting text) .
  2. Zotero is not available for Android tablets.
  3. In the Papership app, the files can be hosted by Zotero and synced in. Meaning the PDFs are not downloaded onto the iPad, leaving less room for syncing problems. The Zotero app for iPad requires you to download all the PDFs, which for most academics, would simply take up too much storage and be an unnecessary repetition.
  4. Once Papership is linked up to Zotero, it will automatically sync the annotations and highlights back to the Zotero PDF. Since this is process requires no effort beyond setup, using the seperate Papership app is worth it.

If you do want to annotate offline, you can choose to download the PDF into Papership.

Summary: Academic iPad Annotation Workflow

The coupling of Papership and the Notero integration creates a naturally organised note-taking system:

  1. You can have your note file open on your computer Notion and Papership open with a tablet.
  2. Now you can focus on reading and annotating on one device without switching windows, and taking down the big ideas on your computer (with a physical keyboard).
  3. When you want to go back and remember the big details of a paper, you can jump to Notion and find it easily, because your notes are now organised by ideas and searchable.

Using this integration will provide you with a working digital filing system that takes your note-taking and organisation to the next level.