Research and Writing Using Obsidian and Zotero

Articles on this site often rely on multiple sources and effective consolidation of that material. I’ve put together a simple system that meets my needs.

The developers of Obsidian promote it as “the private and flexible writing app that adapts to the way you think.” The developers of Zotero promote it as “a free, easy-to-use tool to help you collect, organize, annotate, cite, and share research.” Both achieve their objective and both have a system of plugins to customize their behaviour to address a wide range of needs.

This is not a tutorial about how to use either app. There are lots of resources out there for that. It is a description of how I’ve set up both apps and how I use them to meet my needs. I’ve installed both apps on my desktop and iPad.

Setup

The only add on I’ve installed for Zotero is Better Bibtex. That provides bibliographies and citations.

In Obsidian I’ve installed Zotero Connector, Outliner, Text Format and Obsidian Clipper. The Zotero Connector obviously facilitates getting data from Zotero into Obsidian. The Outliner plugin extends the basic outliner in Obsidian to provide a really useful tool. I use Text Format to format annotations from Zotero so they will work better with the Outliner. The Obsidian Clipper allows me to copy a selection on a web page to a daily note in Obsidian.

Research and writing

When I’ve identified a potential resource I’ll visit it online, review it quickly and if it looks like it might be relevant I’ll use the Zotero Connector to download it to the app. I usually create a “resources” folder into which all the downloaded documents go. If I’ve identified a few resources I’ll repeat the process.

In Zotero

Review and highlight documents: 1. Open each of the documents and highlight relevant relevant information. 2. When review is complete “move” the file to a “references” folder. 3. When the process is complete I have a references folder containing all the relevant highlighted documents.

Create a file containing all the annotations

1. Select all the files in Zotero, right click and “Create Note from Annotations”. That creates a file “Annotations” in the references folder.
2. Right click on that file, select “Export Note”, choose Markdown as the format, give the file an appropriate name and save it.

In Obsidian

Preparing the Outline

1. Drag and drop the saved file to an appropriate folder in your Obsidian vault.
2. Open the file and delete the headings so that only the annotations remain.
3. Select all the text, open the Obsidian command palette and select “Text format: Remove blank line(s)”.
4. With the text still selected open the command palette again and select “Toggle bullet list”.
5. Enter a few generic headings (like “Intro”, “Body”, “Conclusions” at the top of the file to provide some initial structure for the outline. Of course if you already have some specific sections in mind for the document use those.
6. Using the keyboard options for Outliner select and move the bullet points to the appropriate section.

The Writing Process

1. With the outline still open create a new note in a second tab.
2. At the top of the Obsidian window click on the “▽” and select “Stack tabs”. You will now be able to view the outline and document you’re writing side by side.
3. If you want to cite a document while you’re writing place the cursor where you want the citation to appear, select “Zotero integration: cite” from the command palette and enter the author information in the popup.

It’s likely that during the writing process you’ll come across new references:

1. Repeat the highlighting process for the new document(s).
2. When complete select the new document(s), right click and “Create Note from Annotations”.
3. Export the file as Markdown and drag it into Obsidian.
4. Use the “Merge current file with another file” in the command prompt to add the new annotations to your existing file.
5. Repeat the remove headings, remove blank lines and convert to bullet points steps above.
6. Restructure your outline as appropriate.

Creating the bibliography

1. Make sure you’ve deleted any annotations files from the references folder.
2. Select all the items in the references folder, right click and choose “Create Bibliography from items”.
3. Select the appropriate style and choose “Copy to clipboard” for the output method.
4. Return to the article you’ve created and paste the bibliography.

A simple — some would say simplistic — process that gets the job done for me. Perhaps it’s of use to you as, if nothing else, a starting point. There are many ways the process could be improved not the least of which is using Obsidian’s hot keys feature (which I’ve done) to avoid having to use the command palette (which isn’t really that onerous) but hotkeys do speed up the process.