Upgrade StorageZotero 7 Beta - Can not extract Ink Annotations to Notes
Hey Zotero-Community,
i was playing around with Zotero 7 Beta lately. I really like the ink annotations in Zotero's internal PDF reader.
I want to add ink annotations to my workflow, which involves transferring annotations to Obsidian. In order to make all annotations visible for the Obsidian plugins (Citations + Zotero Integration), i need to extract them to notes.
However, i haven't been able to extract ink annotations to notes. But they appear in the 'Annotations' section of the attached file. 'Select Area' on the other hand can be extracted to notes.
Without any further knowlegde of implementation details: Selecting areas seems to me like a similar use case. Both ink and area annotations are boxed and recognized as individual annotations. Only difference i can think of is the file format of saving. SVG instead of jpg would be more convinient for zooming into small ink annotations.
Was extracting ink annotations to notes an intended feature in the first place?
If so, what is the correct workflow of extracting? Simply making ink annotations and then pressing 'Add Note from Annotations'?
Thanks in advance for your time.
i was playing around with Zotero 7 Beta lately. I really like the ink annotations in Zotero's internal PDF reader.
I want to add ink annotations to my workflow, which involves transferring annotations to Obsidian. In order to make all annotations visible for the Obsidian plugins (Citations + Zotero Integration), i need to extract them to notes.
However, i haven't been able to extract ink annotations to notes. But they appear in the 'Annotations' section of the attached file. 'Select Area' on the other hand can be extracted to notes.
Without any further knowlegde of implementation details: Selecting areas seems to me like a similar use case. Both ink and area annotations are boxed and recognized as individual annotations. Only difference i can think of is the file format of saving. SVG instead of jpg would be more convinient for zooming into small ink annotations.
Was extracting ink annotations to notes an intended feature in the first place?
If so, what is the correct workflow of extracting? Simply making ink annotations and then pressing 'Add Note from Annotations'?
Thanks in advance for your time.
Image annotations ("Select Area") are just rectangular sections of the document, so it's straightforward to generate an image and insert that into the note, and there's a reasonable expectation that you want that when running "Add Note from Annotations".
With ink annotations, the annotation itself is a just a path, so first we'd have to decide whether the inserted images were also just the paths (in which case SVG would make sense) or if they should be rectangular sections of the document like image annotations (in which case they'd have to be PNGs). And since people could easily have hundreds of ink annotations in a document — potentially just stray marks here and there — we couldn't really have "Add Note from Annotations" include them by default, and so things just get complicated.
It totally makes sense that image annotations are easier to handle. Thanks for clarifying that.
Is there a limit on the amount of image annotations per file? If not, they could also lead to overcrowed notes when extracting them, or am i missing something here?
May I state my humble view here on possible use case(s) regarding the use of ink annotations in notes:
1. When I read papers, I sometimes add conceptual drawings, which most likely are diagrams rather than text. Such diagrams can usually convey a deeper understanding in a very compact form, for me at least. Besides my workflow with Obsidian (extracting all annotations via the notes) summarizing the ideas of a paper in a note seems reasonable to me even with a Zotero-only workflow.
2. That said, adding comments to ink annotations analogously to the image annotations would make sense, if the ink drawing is just a diagram. Comments could help to link the drawing to text of the paper or the other annotations (in the summary note) on a semantic level.
3. The option to manually group multiple ink annotations to one single ink annotation would allow users to reduce unintended stray ink annotations. (Something like rectangular select with merge option.)
4. Adding extra empty pages to the file via Zotero's interal reader would increase the ease of use even further, considering the limited space in the PDFs.
(2., 3. and 4. would possibly require a separate thread, but I have added them here to give a more comprehensive sketch of my (desired) workflow. Let me know if I should start new threads for those features to keep content and thread titles aligned.)
Regarding the design/implementation:
1. Using SVGs instead of PNGs probably comes with the advantage of having no distracting background as well as zoom-in abilities. SVGs would probably also yield a decreased storage size compared to PNGs.
2. To further allow moving around already existing ink annotations - in contrast to image annotations - there is probably a need to separate the storing of positional information from the content storing. I don't know whether or not this can be easily implemented in your current design.
One may use the plugin 'Zotlit' (https://zotlit.aidenlx.top/) both in Zotero and Obsidian to handle data transfer from Zotero to Obsidian. Reduces the transfer process from 2 plugins and 2 commands to just 1. This plugin is also able to extract annotations from the Zotero database directly without the need to use Zotero notes ('Add Note from Annotations' command in Zotero). And you have more control on how design the Obsidian literature note (with markdown inline JavaScript commands).
But still, the content of ink annotations is not transferred to Obsidian.
Update: I took a deeper look into the ZotLit Source Code (Obsidian Plugin) and found that ink annotations are not displayed in Obsidian because the plugin is not loading it. So no problem on the Zotero side here.
But saving ink annotations as SVGs would still be more convenient from my point of view.
It would be really useful to be able to annotate graphs and then use the rectangle tool to highlight the annotated area. However, as you mentioned this is currently only showing the raw pdf content selected by the rectangle tool without the annotation.
After discovering that the simple solution would only require to update ZotLit, I tried that one, but wasn't able to run the build process of the ZotLit repo. Therefore I couldn't test my hacky implementation.
After that, I decided to stick to Obsidian and started to write a plugin there, which updates PDF annotations back and forth between a markdown note and the PDF file. This is now nearly finished. Bonus: Allows any external PDF reader to be used for annotating PDFs, as long as they are not flattened out in to the page, but rather stored as an additional layer using one of the major advantages of the PDF standard. I currently use PDF Pro for my IPad.
So current workflow for me is:
- Use Zotero as plain literature database + PDF collection
- Use ZotLit to extract paper metadata to Obsidian note and move corresponding PDF files to a specified place in my Obsidian vault
- Use my plugin to extract/update PDF annotations from that PDF to the note created by ZotLit
So it boils down to just 2 commands:
1. ZotLit extracting the paper to Obsidian
2. Extracting my annotations
I can think of chaining those to together. Making all of this just one command.
Regarding your specific use case: This is possible with my plugin as it renders rectangular sections of a page as is, with all visible layers including other annotations.
P.S.: Sorry for the late response, I somehow didn't get notified when you posted your comment to my thread
- Maybe this could be done on an individual basis (ink annotations wouldn't be included in add item notes from annotations)
- Also it would be nice to be able to export the pdf with the ink annotations. Using export library as file hierarchy and including annotations would also include ink annotations.
- We should be able to copy an ink annotation and paste it in another document (such as word or other)
- While I am at it, in the side pane it would be nice to be able to select annotations based on type (images, text, comments, ink annotations)