Notes ecosystem
Turn the literature into reusable knowledge.
CardiOX Atomic is an Obsidian plugin that connects Zotero to an atomic-notes system. Every article you read becomes a network of classified, deduplicated and linked notes — not a dead archive.
Tips & tricks Soon
Obsidian + Zotero setup and tricks, step by step.
Build a clinical second brain.
Electrophysiology content, a note-taking method, and open-source tools.
Base tools
Obsidian + Zotero
The whole method and the plugins build on these two free applications.
The pipeline
From Zotero to the summary map.
15
taxonomy dimensions
3
in-house plugins
2
base apps
01
Zotero
Read and highlight PDFs. References are managed via Better BibTeX.
02
Highlights 🧠
Highlights become sourced fragments, ready to cite.
03
Notes 🤖
Generated and classified along a 15-dimension taxonomy.
04
MOC
One Map of Content per article links all of its notes together.
CardiOX Atomic
One idea, one note.
- One idea = one note: truly atomic notes, reusable across many contexts.
- A 15-dimension taxonomy to classify each note (type, level of evidence, theme…).
- Origin prefixes 🧠 (highlight) / 🤖 (AI) with deduplication — “the highlight wins”.
- A Map of Content (MOC) per article: a single entry point to all its notes.
- Per-article analysis cache for fast, reproducible regeneration.
Synthesis
One map per article.
The MOC (Map of Content) gathers each publication’s conclusions, concepts and figures into a single entry point. It is the bridge between reading and reuse: find an idea, cite it, link it to another.
Highlight processing tracks the origin of every note — 🧠 highlight 🤖 AI — and deduplicates automatically.
The ecosystem
Three plugins, one workflow.
CardiOX Atomic
The core of the system: Zotero → classified atomic notes + a MOC per article.
CardiOX RefNotes
References and citations: clean links between notes and their sources.
CardiOX Sketchnote
Sketches and diagrams to visualise mechanisms and decision algorithms.
Obsidian plugins built for the CardiOX project, currently being consolidated. The content they produce is for educational purposes and does not constitute medical advice.