How to manage Skim Notes within DevonThink?
In Skim preferences, select "Automatically save Skim notes backups." This will ensure that a .skim file is saved next to the PDF. Now, index the PDF &amp; its .skim companion in DevonThink. Select the .skim file and DevonThink will show its contents, i.e. the annotations alone without the PDF. 

Use the "see also" feature in DevonThink on this .skim file.