Annotation workflow including Obsidian

Hunzen
Hello to the forum,

I started using Zotero with the goal to have referenced annotations in Obsidian. My workflow is simple:
annotate PDFs in Zotero → Import annotations as references in Obsidian so I can click on the reference and it takes me to the exact location of the source.

Despite my use case being simple, I have encountered several impediments, and I cant tell whether it is me doing something wrong or this being the intended way of working with Zotero:

- I would like to do both in parallel: As I am writing my summary note in Obsidian I want to insert references according to the section of the PDF I am currently summarizing. Since the import deletes/overrides the note, this is not feasible. Importing into a different note doesnt seem like a good option to me as well. I cant imagine being the only person having experienced this?

- I dont use any tags, the unique filenames are completely enough for my use case (non-scientific PDFs for PKM). However for the Obsidian import to work I have to create a "parent" item and enter metadata. Is this correct? I can not enter the metadata at the PDF level?

(optional) (- Ideally I want the annotations persistent inside the PDF so I can see them with any PDF reader or even when I am on mobile)

Thanks in advance and I hope someone has made the same experiences and/or found a workaround for themselves!
  • FeralFlora
    You should probably ask this in the Github repo of the Zotero Integration / Citations plugin for Obsidian, or on the Obsidian forum / Discord (#academic-tools channel).

    Anyway, I think your best bet is to switch to the Zotlit plugin, which has an annotation sidepanel that live-updates as you add annotations in Zotero. From there, you can drag and drop annotations into Obsidian. This includes a URI backlink to the annotation in Zotero.

    Or, since you don't seem interested in a reference manager, just do your annotation directly in Obsidian with the Annotator plugin.
  • Hunzen
    Thanks for the Zotlit tip, I installed it immediately. The import worked out of the box (what took me 3 days with the "Zotero Integration" plugin)! It seems fitting for my use case! However I cant reproduce the other features you mentioned:
    The annotation sidepanel stays empty displaying the message "active file not literature note", even tho the file was created via right click "obsidian actions → create literature note"

    A drag and drop of the zotero annotation into obsidian creates a text with the structure " (author, page x)", there is no link to the annotation. Same applies to all other annotations that were created via "create literature note". Zotlit only creates a link to the PDF item "zotero://select/library/items/BGIMS5MJ".

    I activated "overwrite existing note", "inplace update of existing annotations" and left the import templates at default and didnt touch the contents of the imported obsidian note.
  • FeralFlora
    Does the created note have the item key in its properties? That's a prerequisite for the annotation sidepanel to regard the note as a literature note.

    If not, you may have to change the properties template in the plugin settings. You may also need to update Better Bibtex.

    Lastly, you can also just choose which Zotero item you want the annotation panel to be connected to, regardless lf the active note.
  • Hunzen
    Yes, the created note has a zoterokey and a citekey pointing to the correct PDF in Zotero. When I "open the note in obsidian" in Zotero it also takes me back to the correct note.
  • FeralFlora
    Check if Zotlit is up to date. If it is and the issue persists, raise an issue here: https://github.com/PKM-er/obsidian-zotlit/issues

    Remember to check the console logs for relevant errors that might be worthwhile to mention.
  • edmolo
    Hi Hunzen,

    I don't know if I am understanding you correctly, but I can offer my workflow as a suggestion. Basically, I read and annotate in Zotero but reference and revisit from obsidian. To do this, I import notes from annotations in Zotero.

    When making my annotations in zotero, I apply MD formatting to them. I highlight all article titles in Orange, and then add ## _title of section_ to the annotation. When I import notes from annotations, it automattically creates a section in the note in obsidian, containing that sections content. Then, you can link other notes to that specific heading, [[Your Note Title##_title of section_]].

    Once imported, I add a level one heading labelled "Article summary". You can also use the ^ caret key to link to specific blocks of text.


    As for your other questions, you do indeed need to have a zotero parent item for obsidian integration to work because that is how betterbibtex (i think) identifies which item to import.

    Theoretically, I think you could make it such that your annotations appear in any PDF viewer. However, this is going to require some effort on your end to make work. Zotero stores pdfs and the annotations that you make in different locations. Your pdfs are stored in a 'storage' folder, and your annotations are stored in your zotero database–different from the storage folder. I believe these are going to be in the sql file labelled zotero.sqlite. This is for ease of use for zotero across devices (i think). I don't reccomend messing with it, nor does zotero. What you could do if you really want to solve this is make a copy, and then interact with that copy so that you don't corrupt the original by mistake. For vanilla persistent annotations, you would have to use save as or export as a file
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