Daily workflow

Six steps per paper.

1. Capture

Browser → click the Zotero Connector button on the paper page. Zotero saves metadata and PDF.

2. Read & annotate

Open the PDF in Zotero. Highlight:

Yellow for claims, facts, useful prose.
Green for terms and definitions to remember.
Blue for figures, tables, and other media worth revisiting.

Add inline comments to highlights for reactions or open questions.

Zoteros built-in PDF reader, with yellow general highlights and green key-term highlights ready for import.

3. Import to Obsidian

Cmd+Shift+I (or Option+T → Import Paper from Zotero) → search title → Enter.

Zotero Integrations import modal in Obsidian — start typing the title to fuzzy-search your library.

Creates 1 Literature/.md with metadata, an abstract, highlights split by colour (General / Key terms / Media), a reading-status tag, and empty synthesis blocks.

The freshly-imported literature note: frontmatter, abstract, highlights grouped by colour, and empty persist blocks ready for synthesis.

Optional. Run Refresh TOC (Launcher) to pull the PDFs table of contents into the note. Once a note has a TOC, Refresh All Literature also regroups its highlights under the matching chapter headings. Needs the one-time helper venv.

4. Synthesise

Fill the persist blocks in your own words:

Block	Content
Summary	3–5 sentences: what the paper does
Key findings	bulleted concrete results
Connections	wikilinks to other papers and concept notes
Open questions	what you did not understand, what to investigate

Highlights are raw input. The synthesis is yours, and it survives Zotero re-imports.

Tip. When a green-highlighted key term deserves its own atomic note, select it and run Promote selection to concept note from the Launcher. One keystroke creates 2 Wiki/Concept Notes/<term>.md from the Concept Note template and replaces the selection with [[<term>]]. See Templater commands for details.

Mark where the paper stands with Set Reading Status (Launcher) — to-read, skimmed, referenced, or fully-read. The Reading Queue dashboard groups your whole library by that status, so nothing stays half-read by accident.

5. Cite in your draft

Draft your chapters in 3 Writing/. The Draft Section Block template gives each section a heading plus collapsible callouts for sources, open decisions, and a changelog.

As you write, type citations in plain (Author Year) form, then run Link In-Text Citations (Launcher) to turn them into [[wikilinks]] that resolve to your paper notes via their aliases.

When you move text into the final document:

Word: Zotero toolbar → Add Citation → search → insert. LaTeX: \parencite{citekey}. Same citekey thats in Obsidian.

6. Backup

Nothing manual. Obsidian Git auto-commits every 30 minutes and pushes to your private GitHub repo.