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

[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.

[Caffae]

Really awesome writeup

I found that it was slightly confusing for me in regards to the templates, so I think the usual workflow is to extract annotations from the pdf using zotfile, then go to the main zotero item (not the extracted Zotero note item but the parent) then do full export of the note in order to get the metadata to work.
For my Mdnotes Default Template.md file I use:

---
aliases: 
	- {{title}}
	- {{citekey}}
---
type:: #Source #Paper
authors:: {{author}} 
source:: {{pdfAttachments}}
year:: {{year}}

## Abstract

{{abstractNote}}


## Summary


## Notes

{{notes}}

so I usually fill in the summary when I import the note into obsidian, hence it is just an empty field here.

For my Zotero Note Template.md I just have:

{{noteContent}}

In terms of annotations, for me:

• yellow is the key contribution of the work / findings / key argument
• cyan is talking about the field of the problem or approach
• magenta is experimental stuff i might want to look into doing too
• green is to follow up literature

I followed OP for the rest, so my colorCategories in Zotero are:
{"Black": "", "White": "", "Gray": "[[Argument]]:", "Red": "[[Disagreement]]:", "Orange": "[[Critique]]", "Yellow": "", "Green": "- [ ] #litreview", "Cyan": "[[Field]]", "Blue": "[[Confusion]]:", "Magenta": "[[Useful for Research]]:"}

---

I have had issues with the exported note having escaped characters like

\[\[Field\]\] and \- \[ \] although I have disabled HTML conversion in obsidian and am using mdnotes 0.2.0-alpha4. Is there a setting I am missing?

[Badjer]

Trying to figure out Zotero so I really appreciate this thread. So before I ask anything let me say TY very much for posting all this info

You can also choose to sync your library through a different cloud storage

If I plan to use Dropbox for my storage do I still set up the Zotero Sync as outlined in step 1.2?

5. Once you have an account, if you don’t plan on using zotero sync, unselect “Sync full-text context” as seen in the screenshot

I do not see the “Sync full-text context” in any screenshot

So if I am wanting Dropbox at some pt I would go to

If you’re not planning on using zotero file storage but want to use another cloud that isn’t WebDAV, go to the “Advanced” Tab, and then to the “Files and Folders” subtab (screenshot 04)

I am just not sure about the steps listed above. I am a noob to zotero & a non academic so forgiveness if these things seem obvious

TY in advance for all the help

[echej]

Zotero sync is need to sync metadata (the storage is for syncing zotero items (like authors, year and other things), even if you use dropbox for syncing pdf
Here is the tutorial how to set up zotero and zotfile This is how I did it: created the best reference manager set up for research & writing – Natural Resource Ecology Laboratory at Colorado State University

[tomhaley]

In the mdnotes preferences, do you have Wiki Style selected under “Internal Links”?