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Is there any open or semi-open standard for ebook and notes/highlighting storage/format which is used by multiple ebook reader vendors and/or ebook reader software?

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The short answer, no.

Kindle uses what is called a My Clippings.txt file using standard text formatted in a particular way. Here is an example that was taken from this readme file on a GitHub project (modified slightly to remove leading comment characters).

97_Things_Every_Programmer_Should_Know
- Highlight Loc. 250-51 | Added on Wednesday, December 29, 2010, 06:10 AM

As soon as you make the decision to compromise, write a task card or log it
==========
97_Things_Every_Programmer_Should_Know
- Highlight Loc. 298 | Added on Wednesday, December 29, 2010, 06:19 AM

the best way to capture requirements is to watch users.
==========
97_Things_Every_Programmer_Should_Know
- Note Loc. 1453 | Added on Sunday, January 02, 2011, 09:40 PM

this is a personal note
==========

Sony Reader provides .note files. These are just wrapped .svg files (scalable vector graphics, an XML based image format). I believe this is because the Sony Reader notes can be annotations, doodles via a stylus and text highlights. You can find out more information about extracting them here.

Kobo, according to this thread, stores annotations in [epub-filename].annot, which is a standard XML file. I'm not sure if this differs for other eBook formats.

You get the point. There is no single standard format or way to handle annotations. That being said, perhaps someone could take various open source tools and create a single utility for exporting and/or importing annotations to various devices (sounds like an interesting side project...).

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