Zotero integrations

Please Could you add some feature to use zotero like reference manager with Obsidian. My detailed suggestions are below.

My planing workflow is collecting PDFs on zotero, annotate them on default pdf reader. After reading finished, extract annotations from pdfs by the help of zotfile in Zotero. And use this annotations to write new article. It should be ideal to copy this excerpts ( with linked to pdf in zotero) paste to obsidian and make new notes for each pdf or may be for each annotations. Then while writing use this notes to develop ideas. And if it is possible with new obsdian version, insert reference through ( bibtext addon of zotero) .bib file into obsidian. At the end stage manuscript, styling reference depending on journal with .css styling styles. After all, print as pdf or word files.

Best part of creating this annotation as a note is, you can easliy convert to them permenant or zettel notes ( my suggestion even this notes can be different color to recognize easily ). After 2 or 3 year later you will have a great library to write. By this way you learn more from your read past article also you dont need to read the same article again and again.

Zotero is best for our purpose because it open source, free, annotations have links ( which is very important feature, because after 2 year you want to read this article pdfs so by clicking the link in your permenant note and open the pdf) and betterbibtex addons which is ideal for reference insertion to the markdown files.

To be honest, Zettlr have similar features but dont have graph view. And I think obsidian note system is much better. I hope it will become more excellent with plugins.

I dont know may be my workflow is not so good but may be we can learn more if other users also share their workflows. I hope Obsidian become better than other markdown wiriting tools.

I also suggested Anki plugin especially to memorize some notes easly.

Thanks

Some links may be helpful for researcher

1- https://ikashnitsky.github.io/2019/zotero/
2- https://an-ancient-academic.com/2019/05/22/using-zotero-zotfile-and-scrivener-to-carry-out-research-annotate-pdfs-and-extract-the-annotations-as-notes/

83 Likes

Yes, Zettlr does this and it is extremely helpful. In the end, a good knowledge management system should always make it possible to quickly get to the source. Not only for copyright-reasons, but also for being able to follow an interest at a later point in time without having to find new sources.

7 Likes

As a researcher, I totally see the value in a Zotero/Bibtex integration. Right now, the devs are focused on building the foundations. However, this is a great idea for a plugin later.

Edit: moved to plugins.

19 Likes

The integration of bibliographies would be excellent. The SublimeZK plugin for SublimeText implemented some excellent ideas in this regard, e.g. counting number of citations for sources within the Zettelkasten. But since other apps already do this, perhaps the devs should focus on the more foundational elements for now.

6 Likes

just a normal feature to read and use a citation from .bib file is already quite good.

4 Likes

@drsn Author of Zettlr implemented something like you describe (collecting annotations to notes) with python script https://forum.zettlr.com/discussion/comment/272#Comment_272

For Obsidian plugin to autocomplete citation from database and render it in the note would be enough for me

11 Likes

If we get a bib plugin or two (or more) implemented the academia will indeed be very interested in Obsidian. This world is wide open concerning updating .bib resources from the web and so on.

12 Likes

With enhanced exported libraries (like Better CSL JSON) is even possible to open the cited file from Markdown editor. With one of Zettlr libraries (Citr, released as GNU-GPL) parsing citations between Markdown and CSL JSON is really easy, I am giving this as an example

4 Likes

Someone already made a plugin integrating Roam with Zotero

5 Likes

I just found out today that you can work both in zettlr and obsidian with the same vault folder. All the changes you make in one editor will reflect in the other app almost instantaneously.

presently the editor of zettlr is more polished and have the citations support, but obsidian has the graph view.

You can get the best of both worlds, might give a try if you are familiar with zettlr.

18 Likes

can this be made for obsidian?

1 Like

Hello guys,

I played with a script for Scrivener by a lady called Emilie and here’s the result. It is slow but it’s better than copying and pasting for Zotero. I hope Obsidian has Zettlr-like blazing fast citation insertion soon, meanwhile you can try this quick and dirty solution here: https://github.com/AlexanderSavenkov/Zotero-Obdisian-Picker-Windows

6 Likes

+1 from me. Zotero support would be great.

5 Likes

I think the best way would be to have pandoc citeproc compatible citations that look like [@citekey]. Maybe one vault can be associated with a .bib or CSL JSON file, so citekeys can be autocompleted. We can also have clickable links from the citation to the bibfile, link to other notes where the same citation has occured etc.

This is how Zettlr processes citations as well. The pandoc compatibility allows automatic generation of LaTeX and PDF artifacts from the note using the same .bib file.

The workflow would be: Zotero export to .bib/CSL JSON -> Add .bib/CSL JSON to Vault through plugin -> Write note using Obsidian with citations -> pandoc with same .bib file exports to LaTeX/PDF with references.

https://docs.zettlr.com/en/academic/citations/
https://pandoc.org/MANUAL.html#citations
https://pandoc.org/demo/example19/Extension-citations.html

12 Likes

Totally agree. Already started referencing Zotero database with [@citekeys] all over the place. Eager to see Zettlr-like support.

4 Likes

is it possible write a script which can:

  • read a .bib file and convert it into md file
  • inserts [[ ]] in every cite key, for example [[@verma2020am]] ?

If yes, then everytime you begin writing anything, just run the scirpt in your latest .bib file, get the md into the obsidian vault. fFrom there citations will be as easy as making any other internal links.

This is a crude way I can think on the top of my head.

2 Likes

Nice idea, @verma, could be very convenient. There’s no need to convert a .bib to .md though, since it already is a textual document and Obsidian can parse it as-is.

I agree with @AlexanderSavenkov. There is no need to have any .bib to .md conversion. Nowadays most reference managers directly export CSL JSON which can directly be parsed by the plugin.
Even if you only have a .bib file, aristocrite, a Javascript library can convert it to JSON on the fly. This is the library used by Zettlr as well.

@verma, is your motivation to convert to .md because you’d like to see the cite key as a node in the graph?

2 Likes

Oh nice to see tools to convert like this. Thanks for sharing.

@verma, is your motivation to convert to .md because you’d like to see the cite key as a node in the graph?

Partially yes, but I was more worried if obsidian cannot read a text file which is not md. If it can read, then its already quite good.

I just want to see the list of citations popping up as soon as we press @, the way you see in overleaf or in zettlr… Making a node manually should be easy by adding [[ ]] around the cite key.

1 Like

I just want to see the list of citations popping up as soon as we press @

This is how this library works