Pasting part of my reply from New Native Annotations in Zotero (Currently on Beta) · argenos/zotero-mdnotes · Discussion #77 · GitHub :
I took a little time to set up a profile to test with the beta over the weekend, and the beta simply has too many limitations currently. I’ll add my summarized comments from discord and other issues below. As you say, this will likely be addressed later, and I remain to be convinced that the annotation lock-in is worth it.
The main limitations I found:
- Limited amount of colours (5 max, predefined)
- It only does highlights (no underlines, which are essential to me, others might use other PDF viewers that support other types of annotations too).
- The extracted annotations when saved as a note don’t have the zotero:// link to the page. They have added something similar that works within Zotero, but that makes it useless right now if you want to export/copy-paste that note somewhere else.
The advantages:
- image-style clipping - images stored in the DB might not be easy to get out (see Support the export of images to markdown? · Issue #62 · argenos/zotero-mdnotes · GitHub)
- individual tagging of the annotations, I however couldn’t get Zotero to show my annotations by filtering tags
- annotation searching - this was already possible IMO
- others have mentioned categorization, but I found no way to do that
Other things missing that Zotfile offers (Most likely some of those gaps can be covered by mdnotes possibly during export):
- Grouping annotations by colour
- Custom formatting for the note title, highlights and annotations (particularly relevant if you want to make distinctions between the latter two)
- Wildcards
- Using the colour and colour category wildcards to format the note’s contents
- Formatting the date as you see fit
I understand the appeal for some to have everything under a single app (Zotero), but the viewing/annotating experience is still very limited and any PDF viewer can do a lot more. I assume this will get better with time, but for now I’m not convinced.
Please note that if you use the beta the mdnotes workflow is limited to the way Zotero processes your annotations. The annotations are not saved on your PDF, they live in Zotero’s DB, so you won’t be able to extract them with Zotfile (or view them somewhere else). The workaround for now (strike-through is mine):
in desktop in the right hand side if you click “new note” it gives option to select “from annotations” and then it basically enables the
entirezotfile/mdnotes workflow. The note is made from the annotations and i can convert to markdown successfully.
The note created from your annotations by Zotero do not contain zotero:// links to your PDF (these were obtained by Zotfile in the stable/previous workflow). If you rely on this, or on custom formatting for differentiating between highlights and notes, I recommend holding off until I update mdnotes.