Using Obsidian with Zotero and Converting Citations for LibreOffice

As anyone who knows me knows, I'm a big fan of both Obsidian and Zotero. Obsidian is where I write all of my notes, reflections, and publishable work, while Zotero is where I maintain my bibliographies, annotate manuscripts, and organize PDFs of articles and other documents. One of Zotero's advantages is that I can work with my documents directly within the application, whether on my MacBook or iPad. I can even use the Apple Pencil to annotate PDFs in Zotero on my iPad.

I moved to Obsidian about two and a half years ago from another favorite application, Scrivener. I made the switch because I wanted more control over my documents and how I organized them. Although Scrivener stores individual documents as RTF files, it manages them within a project structure that makes their organizational relationships difficult to discern outside the application. Obsidian, by contrast, works directly with my own file and folder structure. I can organize and manage my documents in Finder, independently of Obsidian, while retaining that same organization within the application. I also wanted a more minimal writing environment, which Obsidian provides through its use of Markdown.

Markdown is central to my writing. At its core, a Markdown file is a plain-text document that remains human-readable, even with its formatting syntax. The format is relatively simple, works across operating systems and applications, and produces small files that are easy to store and manage. Because the formatting doesn't obscure the text, I can open and read my documents in almost any text editor without depending on a particular application. This differs from Microsoft Word's DOCX format, which packages a collection of XML files and other resources into a compressed archive. Although DOCX is a documented, standardized format, its underlying structure is considerably more complex than Markdown and is not intended to be read directly in a text editor.

The challenge, of course, is that most people don't use Markdown. When sharing manuscripts, articles, or other documents, I generally need to convert my Markdown files into a format that others can open, read, and edit. Whenever possible, I prefer open-source software, so I usually turn to LibreOffice rather than Microsoft Word. LibreOffice provides the document-editing and formatting capabilities I need, and it works well with Zotero, which allows me to manage citations and bibliographies directly within my documents.

This brings me to one of the challenges of my writing environment. As with Scrivener, integrating Obsidian with a bibliographic reference manager such as Zotero requires some additional configuration. Obsidian offers considerable flexibility, but establishing a workflow that connects notes, bibliographic references, citations, and finished manuscripts takes some work. Converting Markdown into a LibreOffice document introduces an additional consideration: citations written in Markdown do not automatically become editable Zotero citations. Managing that transition requires a workflow that preserves bibliographic information while moving between applications.

A number of solutions are available online, many developed by scholars who use Obsidian and Zotero in their research and writing. I thought it would be useful to share my own setup and workflow in an approachable way, particularly for others who want to integrate Obsidian, Zotero, and LibreOffice into their writing process. I use a Mac, and while it should work, I have not verified that this setup works on Linux or Microsoft machines.

You can see my workflow, get directions to replicate it, download the script I use on Github.