Two-way Markdown Sync With Obsidian and Zotero Better Notes Plugin

You know that feeling when you’re trying desperately to find something and you realise you are looking in the wrong place?

Well that was me.

OK, maybe read ‘desperately’ as ‘something semi-obvious’, but I’ve been looking (hoping) for a sync between Zotero and Obsidian for as long as I have been using Obsidian … so about 13 months. The Obsidian Citations and Zotero Integration plugins work excellently at importing bibliographic information and research paper notes. That’s cool.

But what about exporting and syncing?

What if I make notes in Obsidian I also want to show up in the notes file in Zotero, say if I wanted to make a note to check something? If Zotero can write, export and read Markdown files and Obsidian can write, export and read Markdown files, then as long as that file was in the same place, surely it’s not that hard to set up a two way system?

[Note: At this point it may be evident I am not a software developer. I’m sure it’s very hard to do such a thing…]

Well it turns out there’s a plugin for note syncing. Except it’s not in Obsidian, it’s in Zotero. Turns out I was looking in the wrong place.

Welcome to the Better Notes plugin by windingwind

Even without Obsidian, the Zotero Better Notes plugin is an extremely capable and powerful plugin. One powerful enough to even negate the use of Obsidian for dedicated reference management users who don’t want the additional Obsidian use cases. In fact, even Zotero alone is more powerful than most people realise.

That’s the beauty of an open source software like Zotero; it’s free to use and does what it says on the tin. Like Obsidian too, I guess.

That aside Better Notes was envisaged to improve the note-taking and note-linking process within Zotero. I get the impression, the sync aspect came as a result of user requests rather than it being the primary purpose of the plugin. This is worth bearing in mind.

I haven’t explored its use in Zotero fully yet but it has some seriously cool functionality, like linking between notes and mind maps of those notes.

The Better Notes GitHub page tells you everything you need to know about use and installation so I won’t go into that here.

Zotero Better Notes can export and sync notes as Markdown files

What we are really interested in here is the note export option. Better Notes permits us to export a note we create as a standalone Markdown file, as demonstrated in the screenshot below.

And thanks to the sweet little ‘Auto-Sync’ option, if we save the file in our Obsidian vault, it updates regularly whenever we write something in the Zotero note. Cool eh?

Then, if we make a change in Obsidian, by the magic of software development I know nothing about, that change appears in the Zotero note. Even better, if you’re not an Obsidian user, this should work with any Markdown editor.

Some of the finer points on this plugin

Below I’ve shared a screenshot of a few notes on a paper by Bachman et al (2015). It’s an ecology paper. If you’re curious, the research concerns whether the number of plant species in a community influences where those plants use water from in the soil. The suspicion was if there were more types of plants, they would use water in more ‘hard-to-get’ places. Turns out they don’t.

Back to the point of this article.

The Zotero note allows us to give the note tags which transfer across to a ‘tags: [ ]’ YAML, along with the paper title and any collections the paper is in. I like that Zotero tags can be transferred. Version, libraryID and itemKey are all defined by the plugin and can’t be changed.

It takes the note first line as the name of the note and appends the itemKey. A bit messy, but I can work with that.

This arbitrary allocation makes it less streamlined to use transclusions in my main Obsidian literature import note. As I can automagically when I use Omnivore to read research papers.

The quote I’ve taken, highlighted in pink, links directly back to the highlight in Zotero, but the code behind that link, is well, not pretty.

The Obsidian Zotero Integrations plugin does a way nicer job of encoding the location:

At the bottom of this note, you’ll see ‘Jena experiment’. Ideally, I would like this to be a wiki link to link to the separate Obsidian note I have on this big international grassland ecology experiment. Unfortunately, Better Notes cannot do a one or two way sync of a wiki link (Zotero Integration can do one way) as it adds in a couple of forward slashes making it unusable.

Annoying, yes. End of the world, no.

That all being said, there’s some nice stuff to build on here and I look forwards to experimenting with it more and following the journey as it develops.

Better notes isn’t perfect but its a starting point

Better Notes in general has a bit of a learning curve (at which I am definitely at the bottom) and I would only use the sync for really basic text changes at the moment. It can’t sync the fancy pants stuff like highlights nor do wiki links transfer properly, but it’s a system unto which we can potentially build a new note-taking empire!

Rome wasn’t built in a day. There’s no reason to expect any different here!

If you’re curious about everything Obsidian and research, I’ve just started a new free newsletter called 🧠 Brain STREAM. I’d love to have you on board!