Foxit Reader works really well with this method (when I tried it out the other month haha).
Colored highlights are really great.
I compared it with Adobe Reader, and surprisingly for exporting highlights Foxit Reader works better. On Mac that is.
Thing is I can’t remember why I found it to be better I think it was something due to colors being a bit incompatible with exporting the highlights(?) despite changes to the config file for zotero colors that is.
Tbh I’m really not sure hahaha. It’s also possible that it’s just I make extensive use of the “rectangle area highlight” which works well with this.
And then again, it’s been some time since I used the export highlights functionality with Zotero since I primarily use MarginNotes for all PDFs that I study.
I am trying to setup a similar workflow, right now my major issue is figuring out how pdf annotation works . When I read a book I also try to make a outline of mine for the book beside highlighting. I’ve noticed that zotfile only extracts highlights and underlines, not sticky notes and text boxes and other useful tools like drawing tools that Adobe provides, I also can’t find some of these tools in the new zotero local pdf reader, and I suppose other pdf readers. I don’t know it is lack of standard or what. Also highlighting and reading a passage in a book which has multiple highlights is a bit annoying. I think it would be very handy if we could extract more that just highlights and underlines from the text. Do you know is that possible with the zotfile or not? I could not find anything useful in zotfile’s setting to this end.
Hi @argentum
Yeah I thought the sticky notes were included before i separated notes by the color. I am not sure tho.
What do you mean by “custom Adobe note”. I will certainly send a screenshot if you tell me where I should look.
After a bit of experimentation, I managed to get the Zotero-Zotfile-MdNotes workflow (with a patch-up script that does some regex on the MdNotes export) to do what I needed. A few things that may interest others playing with the workflow described by @Cat (they/them) in the pinned post:
the Admonition plugin is helpful to hide metadata and other information by setting the default as “closed”
I have assigned a colour to highlight keywords and used some regex to build an index of the topics covered
it is possible to add a link in the literature note to the local file as well as any version stored on the cloud by giving it the same name as the bibtex key (and a bit of regex), thus bypassing zotero in accessing the pdf and making it accessible also from the mobile version
In addition to presenting the annotations next to the original piece of highlighted text, I find it helpful to gather all the comments in a separate block (created with the same manipulation of the md file)
This is great! I would really like to poach your setup for my own use. Can you expand some regarding at what point you deviated from and/or appended to the setup instructions above?
I’ve mostly followed the setup in the post. The only main difference is that I configured one highlighted colour (Magenta in my case) to identify keywords that I wanted to collect in a separate section. I’ve tweaked the Zotfile setting so that all keywords highlighted in that colour would be given a prefix, which I later removed. Once I have exported the attachment (with zotfile) and created the note (with mdnote), I run a hacky script (written in R because that is the only language I know, but the same can be done in most other programming languages) that edit the md file (e.g. move the comments made on a highlighted section at the beginning of the highgliht rather than at the bottom, gather all the keywords highlighted in magenta in a separate block)
@Cat Thank you for sharing this creative workflow！ I try to rebuild it, but I still meet one problem just as below.
The blockquote style of annotation note is correct in Zotero, but incorrect in Obisidian, in fact, it has been incorrect since step 3.2.3 all the time…
I would be grateful if you could give me some advice on it
This setup (and mdnotes generally) are a godsend for keeping my research together. As a finishing touch, I set up Zotfile to format extracted annotations in a way that I can pair with the Admonitions plugin. For instance, following the OP, I have cyan highlights tagged as “Important,” and I have a matching custom Admonition so the annotations appear with a nice, colorful icon, and I can use the Admonition copy button to quickly copy quotations as I’m writing.
I think it was something due to colors being a bit incompatible with exporting the highlights(?) despite changes to the config file for zotero colors that is.
. my version is 0.1.3, I will try it again