Paper Annotation in Obsidian

I’ve started keeping notes on papers in Obsidian and I thought I’d share the workflow, which so far is pretty straightforward and easy to set up. This uses the binary file manager plugin and the annotator plugin. Annotator uses with local storage (in markdown) of the annotations.

I set up a folder, attachments/papers, which is where I’ll be putting all my PDFs. I have this template, templates/pdf-annotation:

aliases: ["{{NAME}} - Annotation"]
type: pdf
fileClass: pdf-annotation
- pdf
- notes 
- paper 
created: {{NOW:YYYY-MM-DD}}
modified: {{NOW:YYYY-MM-DD}}
annotation-target: "{{PATH}}"


In the binary file manager plugin, I turn off all the file extensions except PDF, and I have the “New file location” set to reviews/papers. That’s where the metadata markdown files will go. I point at templates/ for the template file location, and I turn on ‘watch.’ (Note that there’s an open issue about having it only watch one particular directory, which I am going to enable if it gets implemented. Not sure I will try implementing it myself.) Whenever I have a PDF I want to store a local copy of, I drag it into the attachments/papers directory, and the metadata file gets created. Then I open up the newly created file, and I have a side-by-side annotation view!

A screenshot of an annotation view in Obsidian

I think, but I’m not totally sure, that with a little bit of work it should be possible to make this work without much change (using the same template, location, etc) for online annotations too, which I’m going to have a shot at. Annotator supports remote URLs, so the work would just be in making sure I can use the same template both ways.

Matthew Turk
Matthew Turk
Assistant Professor of Information Sciences

I am interested in the intersection of data analysis, visualization and open source in the sciences.