Upgrade Storageadd an extra option to "add note from annotations" to automatic overwrite previous extracted note
I use "add note from annotations" to create a note, which will be imported into obsidian to take further notes there. The reason of doing this is: obsidain offers more flexible ways to query highlights/notes/tags, and these functions can be stored in obsidian md notes, so that one can come back to these searches easily.
The above transfer can be realized upon 1. extract the pdf annotation using the "add note from annotations" button in zotero 2. automatically exporting the zotero library using better bibtex of zotero 3. import the note into obsidian with the aid of, e.g., bibnote formatter.
The problem is, each time I make new comments in the pdf and then again choose "add note from annotations", another zotero note will be created, rather than overwriting the previous note. I believe that this behavior has its own benefits, but for the application I just described, one doesn't need multiple such zotero notes, so one has to manually delete the old ones, to avoid that obsidian retrieves all of these notes, which leads to information duplication in obsidian note, created by bibnote formatter.
So I suggest zotero to offer an option similar to "update the latest zotero annotation note", so that one can use this option when he makes more notes in the pdf, and don't want to create extra zotero notes.
The above transfer can be realized upon 1. extract the pdf annotation using the "add note from annotations" button in zotero 2. automatically exporting the zotero library using better bibtex of zotero 3. import the note into obsidian with the aid of, e.g., bibnote formatter.
The problem is, each time I make new comments in the pdf and then again choose "add note from annotations", another zotero note will be created, rather than overwriting the previous note. I believe that this behavior has its own benefits, but for the application I just described, one doesn't need multiple such zotero notes, so one has to manually delete the old ones, to avoid that obsidian retrieves all of these notes, which leads to information duplication in obsidian note, created by bibnote formatter.
So I suggest zotero to offer an option similar to "update the latest zotero annotation note", so that one can use this option when he makes more notes in the pdf, and don't want to create extra zotero notes.
Also worth noting that an Obsidian integration plugin arguably should just pull in the PDF annotations directly and offers its own note templates, with whatever makes sense for the Obsidian data model. There's no particular reason people using another note editor with plugins written specifically for Zotero should need to create intermediate notes in Zotero just for the purpose of transferring them out.
Moreover, I'd like to point out that, the users may often want to extract notes for multiple zotero items in one shot; as a result, the above extra option and the potential warning should take into account of handling multiple items.
Finally, since the said obsidian plugins rely on a database created by better bibtex, and the said database can be generated based on a specific collection or a whole library of zotero, it would be even better if zotero provides an option to the collections, such that, when enabled, all the items within that collection (or also within the subcollections) will automatically "add note from extracted annotations". In this way, the obsidian users don't have to make any extra effort on the zotero side.
As for the second point regarding Obsidian, I totally agree that it would be great if one doesn't have to manually extract notes from within zotero, but seems that none of the existing approaches work in such a way so far. The only plugin that offers a similar function seems to be "obsidian-zotero-integration", which is capable of extracting notes within pdfs automatically, with the aid of the tool called "pdf utility". However, I suspect that it can't handle tags of individual comments within the pdfs in zotero. Moreover, I tried this plugin out yesterday but failed to import zotero items into obsidian successfully. So I couldn't test this out, and give this plugin up.
For those obsidian plugins such as the "bibnote formatter" or "citation", I guess the reason for the need of the "manual extraction of pdf note" is probably that, they rely on json files exported from zotero via better bibtex, and the items in this database do not contain the information of the comments made within zotero pdf reader.
To conclude,
1. if "add note from extracted annotations" can handle multiple items in batch while avoiding creating unnecessary duplicated notes, the workflow above can work without requiring too much effort;
2. if zotero also offers the option of "automatically add note from extracted annotations for all items within this collection/library", the above workflow can become even better.
3. Otherwise, the obsidian plugins have to find a way to extract the pdf notes and tags by themselves, which seems more difficult; I'm not sure if such a tool exists or not so far.
Since one may merge items later on in zotero, I wonder if the above link can still retrieve the correct item and pdf, when the said item is merged with another? As far as I remember, the itemkey that was abondoned will not be deleted, but will be stored within the item info, so this seems doable.