Concept
Research organization tools, evaluated honestly.
Research means many small reads that later need to combine into bigger writeups. A research organization tool keeps every source, every annotation, and every working hypothesis findable months later. Here's what to look for.
What the job actually looks like
- Capture: papers, articles, web clips, conversation excerpts.
- Annotate: highlight, comment, summarize.
- Connect: link each source to the project, paper, or hypothesis it speaks to.
- Synthesize: write outputs (literature reviews, decision memos, papers) that draw on dozens of source notes.
- Revisit: come back six months later and still be able to find what you read.
What to look for in a tool
- Plain-text format you can leave with. Anything that locks your reading notes in a proprietary store is risky for long-running research.
- Per-page properties (citation, author, year, status) so you can filter and group sources.
- Wikilinks + backlinks: every source page knows which writeups depend on it.
- Search that handles fuzzy phrases — you'll often remember the gist, not the title.
- An AI surface so a model can pull the right sources without you re-pasting them.
How MindWiki maps onto research workflow
- Source pages: one markdown file per source under a sources/ folder. Properties for title, authors, citation, year, status.
- Capture inbox: drop highlights via email, web Quick Capture, or the mindwiki_capture MCP tool. Triage them weekly.
- Cross-links: write your project page, link to source pages, and the source pages automatically show backlinks.
- Graph view (macOS): see whole sub-areas of research as one cluster.
- AI: connect Claude/ChatGPT and ask "what sources do I have on X?" — the AI uses the same vault.
Frequently asked questions
Does MindWiki manage citations like Zotero?
Not as a dedicated citation manager. You can keep citation metadata in YAML frontmatter and use Zotero (or similar) as the system of record for bibliographic data, then link MindWiki source pages to Zotero entries.
Can AI summarize a literature cluster?
Yes — point your Claude or ChatGPT client at MindWiki via MCP and ask "summarize the sources tagged thermodynamics, grouped by year." The model uses the live vault, not a stale dump.
Is it fine for solo researchers?
Yes. MindWiki is a single-user product today. There's no shared workspace overhead.