Is there a way to limit See Also & Classify to only look in the database I have currently selected?
That used to be the default. (I know many wanted it to look across all open databases, but I would like the choice if possible).
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That is not currently possible. We are considering options but it’s not necessarily a simple thing to implement to cover potential use cases. Thanks for your patience and understanding.
I’m also interested in having flexibility with regards to See Also & Classify. I set up my database structure with DTPO’s one-database-only limitation in mind, and have been struggling to figure out how to adapt to DT3’s new all-databases behavior. Jim, the idea you mentioned here, to toggle between all databases and the current database, sounds great. But I look forward to seeing what the team works out. Thanks.
Another (more complex?) option could be a dropdown menu at the top of the See Also pane to allow filtering of databases from which the suggestions are to be drawn.
For example, I’m viewing a PDF in my “Sources” database (full of articles, book chapter, etc.). Sometimes I use See Also to find related PDFs in this same database. But right now I would like to find related documents from my “Notes” database (full of shorter text notes). Being able to toggle on/off datases right from the See Also pane would be very helpful.
(Always feels weird to “toss out” suggestions and shout “build this!” to the creators… Thanks at least for considering this.)
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to “toss out” suggestions
This is fine.
shout “build this!” to the creators
This is not nice, so I’m glad you’re making civil suggestions 
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I support this request, because I use my databases for quite different approaches and would like to have an option to have a clear line between them.
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I know this is an old thread, but I would like to add two things here:
The first is to point out the obvious: Since “See Also & Classify” only works across open databases, a workaround — albeit a slightly onerous one — is simply to close the databases you do not want to classify to.
Secondly and more importantly, I personally have found that when I get a lot of cross-database recommendations for classification, it is often an indication that two databases actually need to be merged (or at least that a section of one database should be moved to another). That’s just my experience … of course YMMV.
Of course, I would certainly not object if the ability to choose whether classification only affects the local database is added!
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That’s an interesting point. Thanks for bringing it up.
+1
Dreaming: A default (e.g. the last chosen databases for a given database in such a dropdown) that a database would be drawn against.