Obsidian for researchers: papers, Zotero, Dataview and the graph

How the research workflow fits together

• Zotero for the library: papers, PDFs and citations live in Zotero — the reference manager built for academic work.
• Literature notes in Obsidian: one note per paper, linked from Zotero, holding your summary, quotes and criticism in your own words — in plain Markdown files you own.
• Dataview for the overview: queries that pull every note tagged by project, method or theme into live tables — a literature review that updates itself as you add notes.
• Links and graph for the argument: ideas link to the papers behind them and to each other; the graph shows clusters and gaps when you are shaping a thesis or a review.

What needs plugins — said plainly

↔ Scroll this table sideways — the rest of the page stays put.

What breaks if you move

Your Markdown notes travel anywhere — that part is safe by design. The plugin layer does not: Dataview queries must be rebuilt in another tool’s query language (Logseq has its own), Zotero plugin links are Obsidian-side wiring that a new app will not read, and graph-shaped habits survive only where the new app has a graph. The vault checker scores exactly this damage for your vault before you move. Researchers hit hardest are those whose literature tables are pure Dataview — budget real rebuilding time, and keep the Zotero library itself untouched: it is independent of whichever notes app sits in front of it.

Who Obsidian fits — and who it does not

• Fits: qualitative researchers, literature-heavy PhDs, anyone building an argument from many sources over months or years.
• Harder fit: work that lives in shared team databases or needs real-time collaboration — see Obsidian alternative for teams.
• Students doing research-lite? Start with Obsidian for students — the same ideas at coursework scale.