I prefer to annotate my PDFs and papers in Zotero rather than Reader for a couple of reasons. First of all, when saving a document to Zotero, it often has a PDF attached so I am not duplicating files. Secondly, I use colours when annotating and Reader does not provide this feature as yet. They suggest using highlight tags instead, but that does not suit me.
My workflow when doing research and working with academic papers is to write all my notes in Obsidian. I save all my references to Zotero with PDFs attached wherever possible. If they are not downloaded with the reference, as in a web page for example or an online PDF, I will save them to Reader/Readwise.
The object is to do all annotating in Zotero rather than involving Reader in the mix as well. Mind you, I absolutely love Reader and use it daily, but for academic papers, I prefer to keep them all in the one place and that is Zotero. If you are not already using Reader/Readwise, you can get two month’s free trial by following this link.
The process is listed here in step form, but you may find it easier to follow in the accompanying video.
- Locate source page for keeping
- Save to Zotero
- Save the web page to Reader
- Open page in Reader
- Click on the ellipsis top right (…) and select Print with Annotations
- Window will pop up, click Save
- Select the location for saving the file and Save
- Go back to Zotero
- Select the Source reference listing, right click and Add Attachment/ Stored copy from File
- Browse the file manager and select the PDF document
- Once in Zotero, click on the document and it will open in editable form in Zotero.
In case anyone is interested, here are the colour codes I use when annotating. When scanning a document, they immediately alert me to the significance of the highlight.
Colour and Meaning
Figure 1: Colour codes used in note annotation
This has been another one of those things that has been annoying me with my workflow between Zotero, Reader, and Obsidian. It has taken time and experimentation to develop a working system. Hopefully, this will save you a lot of time in trying to work out a system to achieve this or may find this system a more suitable way of doing things. Naturally, if you have a better system or suggestions for improvement, I would love to hear about them in the comments.