Zotero is a great free tool for managing any kind of references and citations.
In this video Bryan Jenks demonstrates his workflow to enable initial annotation of PDFs in Zotero to be flowed through into Markdown comments that can be imported into Obsidian, Foam or any other plaintext notes system. The notes include links back to the source via Zotero.
Key steps are:
- have a working installation of Zotero
- install necessary Zotero plugins
- import the PDF source material into Zotero
- open the PDF from within Zotero
- annotate and save the PDF
- in Zotero right click on the PDF and select
Manage Attachments > Extract Annotations
- in Zotero right-click on the extracted notes file and select
Mdnotes > Export to markdown
- save the markdown file somewhere you can easily import into your notes system for further processing