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

What I need now is a decent PDF annotation tool that actually works well.

When I double click the PDF in Zotero it just opens in Preview. EDIT: Ok I got the new pdf.js viewer to work but the annotations appear to not be detected by zotfile. :frowning:

I have Skim but it requires jumping through hoops to get the annotations back into the PDF properly.

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.

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I really like PDF Expert,other nice editor is pdfPEn (it integrates really nice with Hook)

PDF Expert is free for annotationg on iOS, on Mac it may be quite expensive but I bought it together with VPN and other apps bundle in less than half of normal price

I like Highlights too (the pane with annotation is really nice and it offers export to markdown)


@davecan - I’ve pretty much figured out that Zotero uses the first ‘block’ from the note to create the title for the note - that’s why I was surprised the extraction name had things from the next block(s) in it. I can only assume that if it’s a known bug, and has been reported to Zotfile.

This being the only hang-up in the whole Zotero - Zotfile - Mdnotes process, I’m happy to oblige with an extra click or two.

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 :sweat_smile: 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.

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.

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

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

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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.

I meant this part specifically:

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:

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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

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

Could change workflows…

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

I’m patiently waiting, though!

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@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:

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A post was merged into an existing topic: Zotero with integration of pdf.js - already available in Beta

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?

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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 :sweat_smile:

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

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