How to use ScholarThread
Step-by-step guides for managing a research library, reading and taking notes that connect, searching and asking your library, and linking your other tools — plus the thinking behind how it all works.
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New to ScholarThread? Read these in order.
- A tour of the ScholarThread web workspaceThree panes, one job each: how Library, Notes and the tabbed workspace fit together — plus resizing, multi-select drag-and-drop, and Trash that goes all the way down.
- Add a paper: from a PDF, a DOI or a BibTeX entryThree quick ways to put a paper in your library: drop in the PDF, look it up by DOI, or paste its BibTeX entry. What each one does, what to expect afterwards, and when to use which.
- Inside the ScholarThread readerOne reading surface for PDFs and EPUBs, five highlight colors with an inline note on every highlight, and deep links that take you from a note back to the exact passage it came from.
- A repeatable literature-review note-taking workflowHow to move from a folder of unread PDFs to a connected set of notes you can actually write from — a practical, repeatable system for reading at scale.
- One search box for your library and the open webSearching your own papers and discovering new ones are two different jobs. Here is how ScholarThread splits search into just two tabs — Your library and OpenAlex — and why that beats a wall of filters.
- Ask your library: grounded chat with a citation trailHow ScholarThread's chat answers questions from across your whole library, cites the exact passage behind every claim, and what to expect when a paper isn't fully indexed yet.
Getting started
- 13 August 20265 min read
A tour of the ScholarThread web workspace
Three panes, one job each: how Library, Notes and the tabbed workspace fit together — plus resizing, multi-select drag-and-drop, and Trash that goes all the way down.
Product tourWorkflowLibraryNotes - 23 October 20264 min read
Add a paper: from a PDF, a DOI or a BibTeX entry
Three quick ways to put a paper in your library: drop in the PDF, look it up by DOI, or paste its BibTeX entry. What each one does, what to expect afterwards, and when to use which.
Getting startedLibraryBibTeXOpenAlex
Library & reading
- 29 September 20263 min read
Add a paper by pasting its BibTeX entry
Skip the manual-entry form entirely — paste a BibTeX record from your LaTeX file, a citation manager export, or a publisher page, and ScholarThread adds the paper and classifies it in the background.
BibTeXOpenAlexGetting started - 16 September 20265 min read
Inside the ScholarThread reader
One reading surface for PDFs and EPUBs, five highlight colors with an inline note on every highlight, and deep links that take you from a note back to the exact passage it came from.
Product tourReaderNotes - 15 October 20265 min read
Write on your PDFs with Apple Pencil
ScholarThread's iPad and iPhone app now lets you write directly on the PDFs in your library. Your handwriting stays exactly where you put it at any zoom, syncs between your devices, and shows up in the web reader too.
Product touriPadApple PencilReader
Notes & writing
- 16 July 20265 min read
A repeatable literature-review note-taking workflow
How to move from a folder of unread PDFs to a connected set of notes you can actually write from — a practical, repeatable system for reading at scale.
Literature reviewNote-takingWorkflow - 17 September 20265 min read
Your note templates are an ontology (and why that helps)
What ScholarThread's literature and concept templates actually define, how claims attach to a concept note, and how the AI-assisted drafting tools fit in — you always review before anything is written.
Note-takingNotesPro - 20 July 20263 min read
Export your notes as an Obsidian-compatible Markdown vault
ScholarThread notes round-trip cleanly with Obsidian: every note becomes a Markdown file with YAML frontmatter, and note links become [[wikilinks]]. Here are the three ways to export.
ObsidianNotesExport - 20 July 20262 min read
Import a Markdown vault into ScholarThread
Bring notes in from Obsidian or a ScholarThread export: any .md or .zip with [[wikilinks]] imports through one button, idempotently, with links reconstructed. Here's how it behaves.
ObsidianNotesImport
Search & chat
- 6 August 20266 min read
One search box for your library and the open web
Searching your own papers and discovering new ones are two different jobs. Here is how ScholarThread splits search into just two tabs — Your library and OpenAlex — and why that beats a wall of filters.
SearchLiterature reviewWorkflow - 15 September 20265 min read
Ask your library: grounded chat with a citation trail
How ScholarThread's chat answers questions from across your whole library, cites the exact passage behind every claim, and what to expect when a paper isn't fully indexed yet.
ChatAI creditsGetting started - 20 October 20264 min read
Choose the model behind your chat, and what changes if you pick a global one
ScholarThread's chat now lets you pick the model that answers, per chat or as your default. Three optional models run on global infrastructure that may be outside the EU, so they stay locked until you give your consent, which you can withdraw at any time.
Product tourChatPrivacyAI credits
Integrations
- 15 July 20265 min read
How to sync your Zotero library with ScholarThread
A step-by-step guide to connecting Zotero, finding your collections in the Library sidebar, keeping them fresh with background sync, and (on Pro) pushing individual papers back to Zotero.
ZoteroIntegrationsGetting started - 20 July 20263 min read
Set your own OpenAlex API key for literature search
ScholarThread's literature search runs on OpenAlex. Adding a free personal key gives you your own search allowance instead of sharing ScholarThread's default. Here's how, and when it matters.
OpenAlexIntegrationsGetting started - 19 July 20266 min read
Connect a private Git repo — and get two-way Obsidian sync
Why syncing your notes to a private GitHub or GitLab repository is the most durable, vendor-neutral way to own them — plus how to set it up and bridge to Obsidian with the Obsidian Git plugin.
Git syncObsidianIntegrations - 21 August 20265 min read
Connect your AI assistant to ScholarThread (MCP)
Give Claude Code, Claude Desktop, or any MCP-compatible assistant direct access to your ScholarThread library and concept notes — how to set up a key and what the assistant can actually do with it.
MCPClaude CodeIntegrationsGetting started
Account & billing
- 20 July 20262 min read
Who can use ScholarThread? Age and eligibility
ScholarThread is intended for users aged 16 and over. Here's why — consent law, contracts, sign-in providers and AI features — and what to do if you're a parent or teacher.
AccountPrivacyPolicy - 20 July 20262 min read
How to cancel your Pro subscription
Cancel ScholarThread Pro any time from your account settings — no email, no form, no retention call. Here's the exact process, what happens to your data, and how refunds work.
ProBillingAccount
Background
- 10 October 20266 min read
Why we built the knowledge graph
Reading, notes and sources usually live in separate places, so the connections between them stay in your head. The ScholarThread knowledge graph draws those connections for you, and shows what's still unconnected.
Product tourKnowledge graphResearch workflow - 6 August 20265 min read
Semantic search that runs on your device
Search-by-meaning usually means shipping your library to someone else's server. ScholarThread can do it on your own device instead — private by default, and it works offline.
SearchPrivacyOffline - 18 July 20266 min read
BibTeX, RIS and CSL explained: the reference formats that actually matter
What BibTeX, RIS and CSL are, how they differ, and which one to reach for when importing, exporting or citing — a plain-language guide for researchers.
Reference managementBibTeXCSL - 6 October 20266 min read
How ScholarThread's chat assistant stays on the right side of academic integrity
A look at the six safeguards built into ScholarThread's AI assistant — from a deterministic input gate to a tamper-evident disclosure log — designed so the assistant helps with research without ever producing submittable coursework.
Trust & safetyPolicyChatAcademia - 17 July 20266 min read
Preparing for your PhD viva: a practical checklist
A grounded, week-by-week approach to viva preparation — knowing your thesis, anticipating questions, and walking in able to defend every claim you made.
VivaPhDResearch