Workspace/notebook with file annotation references

Let me please introduce our scenario. In our library of papers in JabRef, we add a new paper, read it, put it in some groups, and annotate some sentences directly in PDF.

Currently, we can see these annotations in the File annotations tab. Now, we have a research idea, and we would like to reference annotated sentences across different papers in some workspace or in a notebook.

For example, we create a workspace called Requirements Quality, and we would like to reference here all cool sentences that we found across papers. Then, we can simple click on the referenced sentence and we will be navigated to the concrete paper.

What do you think?

I can’t create a voting poll, so please edit my post to add the poll if you wish.


current workaround in Jabref 5.5:

manually use fulltext index search for linked files and search for the annotated sentence.


  1. Optional: Whenever a sentence is annotated, write the sentence down within the annotation.


    Sentence to be annotated: The sky is blue.
    Annotation: The sky is blue. These two sentences here are the annotation.

  2. Create a group Requirements Quality with free search expression: annotation=.+

  3. Navigate to group requirements quality if you only want to search within annotated entries or go to any other group if non annotated entries shall be included within the search; e.g. the group all entries.

  4. Go to File annotations tab

  5. Select and copy (strg + c) the sentence that is desired to be searched within entries. e.g. the sky is blue

  6. activate full text search within linked entries.

  7. Paste (strg + v) the sentence into the search field and press enter.

This should (ideally) result in finding all entries that fulfull all three conditions:

  • includes the sentence the sky is blue
  • are annotated
  • the annotation is about the sentence the sky is blue.
    → This condition is the most bothersome one and it requires you to write the sentence into the annotation or at least somewhere else into another field in your library, because Jabref currently does not have a user interface (UI) that is built around referencing specific annotated sentences, but as you can see it technically is possible to do it. Of course, a better UI would be nice to have to ease the workflow :grin:

Christoph mentioned (here) that annotations are not stored within the library file, but rather in memory. I think this breaks my workaround posted above.

(Because user annotations and comments within Jabref are not in sync with annotations made directly in attached (pdf) documents.)

Thank you very much for showing your workflow. Yes, it should be better to save it together with a papers collection.

Mendeley has something similar called Notebook. It can be taken as inspiration if somebody finds it useful for JabRef, too.

Maybe it’s out of the scope of reference manager; however, I see really cool to click on saved sentence and be navigated directly to a concrete paper (and in the best page to a concrete page).