paperKB
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Getting Started

paperKB helps you build searchable, queryable knowledge bases from scientific literature. Here's how to get up and running.

1. Create your first knowledge base

  1. Sign in to your account (or ask an admin to create one for you).
  2. Click New KB from the user menu in the top right.
  3. Choose an owner (your personal account or a group you belong to).
  4. Pick a short slug (e.g. my-research) and an optional description.
  5. Click Create — you'll land on your new KB's overview page.

2. Add papers

Navigate to your KB and click Docs → Import. You can add papers in several ways:

  • PubMed IDs — paste one or more PMIDs. Full text is automatically fetched from PMC when available.
  • DOIs — paste DOIs to import from CrossRef / PubMed.
  • PDF upload — drag and drop PDF files. Text is extracted automatically, and if a DOI is found inside the PDF, metadata is fetched.
  • Zotero sync — connect your Zotero library from Settings → External Keys and import collections directly.

After import, a background worker will extract text, compute embeddings, extract structured observations, and build the citation graph. You can monitor progress on the Status tab in KB settings.

3. Search your KB

Use the Ask KB tab to run semantic queries against your knowledge base. paperKB expands your query, searches across all papers, and returns the most relevant passages with citations.

You can also browse by Docs, Authors, or Observations using the navigation tabs.

4. Chat with your KB or a paper

If chat is enabled for your instance, you'll see a 💬 Chat with KB button in the navigation bar and a 💬 Chat with this paper button on individual paper pages.

  • Chat with KB — ask questions across your entire knowledge base. The assistant automatically pulls in relevant passages and facts from your papers as needed to answer your question.
  • Chat with a paper — focus the conversation on a single paper. The assistant draws from that paper's full text, figures, and extracted observations.

During a conversation, the assistant cites specific passages from your KB. You can see the references it's drawing from inline in the response — click through to read the original source.

Your chat history is saved automatically. You can return to previous conversations to pick up where you left off or review past answers and their references.

5. Connect via API or MCP

Generate a personal API key from Settings → API Keys. Each KB exposes an MCP (Model Context Protocol) endpoint that AI tools like Claude can connect to directly:

Endpoint: https://paperkb.org/{owner}/{kb}/mcp
Header:   Authorization: Bearer sk-…

See the API & MCP docs for more details.