I’m late to this party, but I just discovered this feature and am sharing it here because there may be others who will find this helpful.
Using DEVONthink, you can convert your PDF highlights into clean Markdown text with just a couple of clicks. Go to Tools → Summarize Annotations, and select the format. DEVONthink pulls all your highlights into a Markdown file (or Rich Text if you prefer). The extracted Markdown includes links to the highlighted section of the PDF. The attached screenshots show how this works.
NOTE: After experimenting with this, I determined that this works best if you use DEVONthink or DTG to make your highlights.
Alternatively, if you prefer individual Markdown notes (i.e., one note per PDF annotation) as these can then be individually tagged, flagged, color labelled, commented on, linked, etc, you could also use my recently developed script:
The script can be called from the DEVONthink scripts menu, and can also be triggered via a keyboard shortcut or automatically from a DEVONthink smart rule.
The script can match the PDF annotation highlight color to your DEVONthink labels, supports markup in PDF annotation notes to directly set the note’s title, flag, rating, tags & custom metadata, can auto-fetch bibliographic metadata, and also creates deep links that directly point back to the PDF annotation.
Been using DEVONthink continuously since about 2010 … despite that long time I still learn new things from doing a scan of the outstanding DEVONthink Manual. As I’m using Markdown a bit more now than in the past, I ran across this feature a while back from reading the manual. Other nuggets there, and in “Tips and Tricks” inside the app, remaining to be discovered and used.
Another cool trick I recently learned was to drag multiple screen shots of text — this was for getting notes from slides in an online presentation — into Devonthink, OCR them, convert them to rich text (or markdown), and then merge the individual quotations into one document. I felt like a kid who’d just realized he could pop a wheelie on his bicycle.
