Import notes with extracted annotations from Zotero

[Bubblbu]

With the recent update that annotations are extracted properly, this feature is becoming a lot more interesting. A possible Zotnote workflow:

1. Import article into Zotero
2. Read and annotate using compatible PDF reader
3. Extract annotations into a Zotero internal note
4. Use Zotnote to import that article and run some basic processing of the note to get to a nice literature note
5. Use Zotnote to create reports, annotated bibliographies etc.

BBT (starting v5.2.22) is now also providing an option to directly import notes from Zotero. This could be interesting for anyone wanting to import notes and access advanced features with those notes.

[Bubblbu]

Extraction of PDF notes is working in Zotero now that I am using a different PDF Viewer (Okular for Ubuntu seemingly has issues with annotations).

[Bubblbu]

The default format for extracted annotations is functional, but not what I would like at all. The notes can be imported as the plaintext html. The question now is to nicely convert that markup to a cleaner, nicer look in Markdown.

Some of the annotation extraction markup can be tweaked in the advanced tools of Zotero/Zutilo, but I am currently leaning towards leaving the markup untouched and running the conversion in Zotnote.

[Bubblbu]

Some of the required changes:

• Import notes
  • BBT endpoint implemented already
• Edit note using Beautiful Soup
  • Convert highlights to quotes
  • Regular notes should become regular notes instead of the quoted passages.
  • Should the page references be retained? Probably no as this opens the door to basically take markdown notes (headers, links, etc.) in the PDF and have them as functioning files in the final note.
• Convert to md using https://github.com/bebraw/pypandoc