Markdown for knowledge management

Markdown files can form the basis of a personal knowledge-management system. Instead of keeping all of your material in one long document, you can maintain smaller notes for chapters, sources, reading notes, and individual ideas, then connect those notes with links. This approach can help organize a long research project such as a dissertation while keeping its written content in portable plain-text files.

Obsidian

Obsidian is a note-taking and knowledge-management application that stores notes as local Markdown files. It supports links and backlinks between notes, and its graph views provide a visual way to explore those connections.

An Obsidian vault is a directory on your computer. You can create a new vault or open an existing directory of .md files as one. A vault can contain Markdown notes, subdirectories, images, PDFs, and other attachments. Obsidian adds a hidden .obsidian directory containing vault-specific settings; the Markdown notes remain ordinary files that can be opened in other text editors.

Obsidian’s wiki-style syntax links to another note with [[Note name]], directly to a section with [[Note name#Section heading]], or to a non-Markdown file in the vault with syntax such as [[Article.pdf]]. Prefixing a link with !, as in ![[Article.pdf]], embeds supported files in a note.

Wiki links are not part of standard Markdown. Some knowledge-management applications support them, while other Markdown applications display them as plain text. When compatibility with other Markdown tools is important, Obsidian can also use standard Markdown links such as [Note name](Note%20name.md), where %20 represents the space in the filename Note name.md.

Example vault

Professor Inger Mewburn, creator of The Thesis Whisperer, has shared Coffee, an example Obsidian vault based on a fictitious research project about coffee. The repository demonstrates folders, tags, backlinks, graph views, images, Zotero integration, and the Dataview plugin. Its README notes that the example text was generated with AI and should not be treated as factual research content.

Download the Coffee vault as a ZIP file, extract it, then open Obsidian and select Open folder as vault. Choose the extracted Coffee-HEAD directory to explore the example.