Tag: zotero

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Bookmarked Research Rabbit

Research Rabbit is a tool that, when provided with some academic paper you already are familiar with, can suggest other related material as well as provide that material. By looking for material from the same authors, by following the references, and by looking at the topics. This can speed up the discovery phase quite a lot I think. (And potentially also further increases the amount of stuff you haven’t looked at but which sounds relevant, thus feeding the collector’s fallacy.).

I’ve created an account. It can connect to Zotero where you already have your library of papers you are interested in (if you use Zotero with an account. I use Zotero standalone at the moment I added a Zotero account and storage subscription to sync with Research Rabbit).

Looks very useful. HT to Chris Aldrich for in Hypothesis pointing to a blogpost by Dan Alloso which mentioned Research Rabbit.

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I’ve been using Zotero for over a year now. It is one of the elements that allowed me to leave Evernote, as it can automagically fetch scientific papers and their metadata for me, store web pages, clip PDFs from my browser etc.

Thanks to Nick Milo and Eleanor Konik discussing Eleanor’s Zotero/Obsidian workflow on YouTube, I found Bryan Jenks’ video on the same topic. Bryan Jenks’ nicely explains something I had seen other people reference.

First he discusses two Zotero plugins that are very useful to me:

  • Zotfile, this allows me to annotate and comment an article, and then extract and store that inside Zotero, with links back to the paper and the location in the paper the annotations and articles belong to.
  • MDnotes, which allows you to export material from Zotero in markdown.

Together they allow me to higlight and annotate an article, and export that as notes into my Obsidian notes. Even better, those notes have the links to the paper and page of an annotation still in them. Clicking them opens up Zotero in the right article, in the right spot. This way context is maintained while I further process my notes, and the actual reference is just a single click away.

This is already very nice and smooth.

Then towards the end he mentions another very useful thing: Dean Jackson‘s Alfred workflow for Zotero, Zothero, which a.o. allows fancy search methods of my Zotero database right from my main screen.

Half an hour very well spent, thanks to Bryan Jenkins.

Yesterday I wrote in Getting to Like Obsidian

The combination of Obsidian and Zotero, which I started using for reading references, even looks like something to replace Evernote with. This is the first time I’ve thought that in the past 4 years for longer than an hour.

Coincidentally today was my annual renewal of my Evernote subscription. I guess that I now have a year to remove myself from Evernote 😀

Today I moved my daily notes (a bullet list of things I do during the day) to Obsidian from WP. It was a frictionless change. A next experiment will be to take a random recent note and a random recent bookmark from my Evernotes and see how I can add them to the Obsidian/Zotero combination in a meaningful way.

Start the count down! 😉

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In the past days I have been both exploring my process for second order note taking, and part of that is evaluating tools. I’ve been trying the note taking process in both WordPress and Evernote. In parallel I have also been looking at other tools for note taking. I’ve looked at a few tools that say to have implemented the Zettelkasten method, but I don’t want tools that assume to shape my process. I want to shape my tools, based on my routines.

In terms of tools that support me, I want tools that increase networked agency. Tools that treat data as fully mine, the tool itself as a view on the data, and its interface(s) as queries on that data.

Between WP and Evernote, the first does that, the second most definitely not. At the same time Evernote makes note taking much easier than WP can ever do. This is not surprising as WP is a blogging tool that I am using as a wiki on my local host while Evernote was designed for note taking. From the other tools I looked at, Joplin and Obsidian stood out, both tools that use markdown. Joplin because it is open source, allows easy import from Evernote, and can save webpages locally, can sync with Nextcloud allowing easy mobile access. It does store notes in a sqllite database which makes accessing my data more difficult.

Obsidian is still in beta but already looks pretty amazing to me (similar to Roam it seems). It operates on text files in a folder, thus allowing direct access through my file system to any data I add. It provides a view on that data that allows easy linking between notes, and you can split off any number of panes in the interface with whatever content or query. This means you can have a variety of notes open, pin them, see what links to what etc. There is also a graphical view, that allows you to explore notes based on the cloud of links they form. That makes it look a bit like the Brain of old. It’s all in markdown, so easy to use on mobile with a different client if I sync it through Nextcloud. I added the same notes I previously added to WP and EN in Obsidian, to experience differences and commonalities. In comparison with the other notes tools I tried a key difference is that I left this app open since I started it up this morning. A key difference with WP and EN is that I want to add notes to this tool. It does mean I need to relearn markdown, which has gone rusty since I last used markdown (in a locally hosted wiki), but of course it was easy to make a note and pin it to use as cheat sheet.

Obsidian screenshot, list and search pane on the left, a graphical overview middle top, a note middle bottom, and my markdown cheat sheet on the right

Having used Obsidian for a day, I am now wondering if I still need my local WP instance. The combination of Obsidian and Zotero which I started using for reading references even looks like something to replace Evernote with. This is the first time I’ve thought that in the past 4 years for longer than an hour.