Zotero -> zotfile -> mdnotes -> obsidian -> dataview Workflow

[a.u]

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.

[Archie]

Thank you for this awesome thread.

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.

[argentum]

Hi @Archie, unfortunately no, Zotfile only recognizes highlights and underlines. In case this helps: Zotero best practices - #57 by argentum

[argentum]

@Archie also to add, sticky notes should work too. Are you using a custom Adobe note? Could you maybe share a screenshot?

[Archie]

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.

[argentum]

I meant this part specifically:

@Archie

not sticky notes and text boxes and other useful tools like drawing tools that Adobe provides

What kind of sticky notes are you using? If you share a screenshot of that we might be able to tell if Zotfile will recognize it.

This is an example of is what this looks like and what works for me in Linux:

@argentum

Keep in mind that if you annotate your PDFs, Zotfile is also able to extract “pop-up notes”, but not inline notes. These highlights:

End up in this note:

[Archie]

it says ‘sticky note’. I can’t find pop up note like what is in your post

It looks like this:

It’s content is only visible in side pan for comments

[Markus0000]

Just wanted to refer to my latest posting: pdf.js is integrated in zotero (amazing NEWS!)

Could change workflows…

Zotero with integration of pdf.js - already available in Beta

Zotero is integrating pdf.js - already available in Beta version Zotero just announced, that it is integrating pdf.js - already available in Beta version dev builds [Zotero Documentation] Features of pdf.js integration in zotero Discussion about the beta state can be found here: Recent Discussions - Zotero Forums #announcement #zotero #pdf.js

[Erisred]

@Markus0000

pdf.js is integrated in zotero

Be careful. Some of the beta is reportedly unstable, and Mdnotes is not quite set up to accept it yet.

Zotero best practices

@PedroSilva yes, that’s what the docs above say. For example, this is what I have on mine: [image] Indeed! That’s what the demo showed, and afaik it is not possible to use both simultaneously. Either you split by colour or you get the tags. I don’t personally use this, but maybe you can try what Archie mentioned above. Eventually, yes. I can’t update to the beta at the moment (I’ll wait until it’s a bit more stable, especially for Linux). I’ve added a discussion for this in the GitHub rep…

I’m patiently waiting, though!

[argentum]

@Markus0000 I have replied to your post with my current observations of the beta. For those on this thread, here is what to keep in mind:

@argentum

Please note that if you use the beta the mdnotes workflow is limited to the way Zotero processes your annotations. The annotations are not saved on your PDF, they live in Zotero’s DB, so you won’t be able to extract them with Zotfile (or view them somewhere else). The workaround for now (strike-through is mine):

in desktop in the right hand side if you click “new note” it gives option to select “from annotations” and then it basically enables the entire zotfile/mdnotes workflow. The note is made from the annotations and i can convert to markdown successfully.

The annotations created by Zotero do not contain zotero:// links to your PDF (these were obtained by Zotfile in the stable/previous workflow). If you rely on this, or on custom formatting for differentiating between highlights and notes, I recommend holding off until I update mdnotes.

[stpag]

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)
  

[MarkC]

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?

[stpag]

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)

[TelsaMJ]

@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

[Cat]

Which version of mdnotes are you using? it needs to be the 0.2.0 alpha 4 build (Releases · argenos/zotero-mdnotes · GitHub) for this to work

[TelsaMJ]

Thank you very much . my version is 0.1.3, I will try it again

[OogieM]

@davecan

Are there any really good PDF highlighting/annotation apps out there that work on both MacOS and iOS? So the colors/etc will be consistent.

I tried PDF Expert but found Highlights to bee much much better for me.

[JordanMO]

I have now set this up, thanks for the useful guide.

Though I cannot seem to get {{yamlbooktitle}} to populate at all. Any ideas?

[tomhaley]

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.