Thursday, April 07, 2022

Obsidian, markdown, and taxonomic trees

Returning to the subject of personal knowledge graphs Kyle Scheer has an interesting repository of Markdown files that describe academic disciplines at (see his blog post for more background).

If you add these files to Obsidian you get a nice visualisation of a taxonomy of academic disciplines. The applications of this to biological taxonomy seem obvious, especially as a tool like Obsidian enables all sorts of interesting links to be added (e.g., we could add links to the taxonomic research behind each node in the taxonomic tree, the people doing that research, etc. - although that would mean we'd no longer have a simple tree).

The more I look at these sort of simple Markdown-based tools the more I wonder whether we could make more use of them to create simple but persistent databases. Text files seem the most stable, long-lived digital format around, maybe this would be a way to minimise the inevitable obsolescence of database and server software. Time for some experiments I feel... can we take a taxonomic group, such as mammals, and create a richly connected database purely in Markdown?