Feature Request: export multiple annotations as single markdown files

At present I can export from the beta all the annotations and highlights in a long PDF as markdown with a couple of mouseclicks. This is great. But the result is one long file containing all the annotations etc from the document. I don't think it's possible to export all the annotations and highlights into separate files unless this is done one by one.

For some styles of note-taking and for some markdown editors, it is more natural to handle each annotation/highlight as a single file, with its own tags. Could this be made an option in the future, please.
  • edited February 6, 2022
    Yes, it should be possible to just select and drag several annotations (from the left side of the pdf view) to the desktop or app and create separate files (with a shortkey combination maybe?). But I think this is planned:

  • #2289 (and my understanding of your request, @erazlogo) was for Quick Copy of annotations, with one or more selected annotations simply copied to the clipboard or target text area the same format they'd be exported to a single Markdown file from a Zotero note.

    Exporting individual annotations as multiple files would be a different request, and wouldn't be related to Quick Copy. If we supported that, it would be handled (at least in its primary form) via an export option in the File menu of the PDF reader and an options dialog to choose between a single output file and multiple files. In the latter case, you'd select an output directory rather than a filename.

    @seatrout, could you say more about that workflow, and what tools you're familiar with that use it? How would you expect the files to be named?
  • edited February 6, 2022
    @dstillman yes, in my request I was mostly interested in the drag-and-drop of one-two notes together, but potentially exporting several annotations separately could also be useful.

    A lot of Obsidian users want to export all their annotations as separate markdown files directly into the Obsidian directory. Here is a workflow description that describes how to do it with Zotfile. But now that Zotfile is being phased out, some of this functionality may be useful to include in Zotero:


    BTW, this workflow also describes why one would need several different highlight colors in the exported note, as requested here:

  • @dstillman My workflow is at present to read PDFs in the Zotero Beta, highlighting and annotating as I go, and then export to Obsidian. The various annotations and highlights from a long PDF will often have different uses, and destinations, in the final product. So I'd like to tag them and indeed access them individually.

    This is much easier in Obsidian if they are stored as discrete files. Although it is possible in the latest versions to refer and link to individual paragraphs ("blocks") within a long note/file this is still a clumsy process. More than that, you can't, I believe, use tags on a block-by-block basis. Any tags attached to a note applies to the whole file and not just one section but I find tags more useful on a much more granular basis. So when it becomes possible to export the tags on Z annotations to Markdown files, it would only be really helpful to Obsidian users if the annotations themselves were exported as discrete files and not as one huge block.

    As for naming the results — either do it by the first line, or in sequence according to their position in the document, as in "Annotation extracted from {citation} #1"

    The difficulty with both cases is that you might get duplicates. This could be avoided by sequencing the annotations by their creation time, which could only be broken, I think, by users travelling across time zones at exactly the right moment.

    The burden is then on the user to rename them to taste, but I don't think there is any conceivable telepathy that could be automated to know what filenames would be most useful to any particular user.
  • @dstillman And I know this is something that could just as well be done "at the other end" with an Obsidian extension to split and if needed reformat the Zotero export.
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