[davidfor]

Originally Posted by MHaensel

Hopefully others will fact-check me if I've found something incorrect. Based on my reading, and experiments with the Kobo desktop reader:
1. All highlighted text and annotations are stored in the Kobo.sqlite file.

Correct. But, if the book is an epub in the main memory of the device, it is also written to a file.

2. The text is stored in the file (essentially) by book, so you do need to click through each book to extract the annotations. This may work differently in Calibre.

Correct to both places.

3. The annotation information isn't as extensive as the Amazon setup. You get text and no location information.

Where do you mean? The annotations list shows the chapter where the annotation is. Plus a percent. For epubs, the percent is from the start of the book but for kepubs, it is from the start of the chapter.

The database has the exact location of the start and end of the annotation.

I'm not knocking either platform; Kobos have several other advantages that may outweigh the inconvenience of this for me. It's more a FYI for others considering the jump.

For others with the same question, I found some helpful threads:
How to save highlighted portions of books, which includes a link to a stand-alone program that extracts highlights and annotations from the Kobo.sqlite file.
A Kobo Utilities plugin for Calibre is also available, that has somewhat similar functionality among other stuff.

The annotations display in the utilities plugin was something I did quickly and intended to improve but could never come up with a better way. The Annotations plugin is the better way. Still not ideal as it is only one way and doesn't have an export function.