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Zotero Integration

The Agent Bayes Zotero plugin lets you include items from your Zotero library — together with their PDF attachments — into Agent Bayes libraries, without leaving Zotero.

Requirements

  • Zotero 7, 8, 9 or 10 installed.
  • An Agent Bayes account with an API key (available in your account settings).
  • The Agent Bayes Zotero plugin XPI downloaded from settings or the website.

Install the plugin

  1. Download the latest agent-bayes.xpi from your account.
  2. In Zotero, open Tools → Plugins.
  3. Click the gear icon → Install Plugin From File… and select the XPI.
  4. Restart Zotero.

Connect your account

  1. Open Settings → API Keys in the Agent Bayes web app and create a new key. Copy it immediately — it's shown only once.
  2. In Zotero, open Preferences → Agent Bayes.
  3. Paste the key into the API key field.
  4. Click Test Connection. You should see a success indicator inline.

Include items in an Agent Bayes library

Select any regular item in your Zotero library. An Agent Bayes panel appears in the item pane on the right (see screenshot above). This panel lets you include any attachment in any of your Agent Bayes libraries:

  • The library dropdown lists every Agent Bayes library on your account. Select one to index into.
  • The file list shows all PDF attachments on the item, along with their page count and estimated indexing credit cost.
  • Clicking Index starts indexing the file into the selected library. You can index multiple files from the same item — they will be grouped under the same document record, mirroring Zotero's data model.
  • Once indexed, click Remove to remove the file from the library.
  • Removing the last file from a document removes the document record from the library too.
  • A single item can live in multiple libraries at once, with no additional indexing cost.

Add many items at once

To bring in a whole reading list, select the items in Zotero (or right-click a collection) and choose Add to Agent Bayes library… (for a collection, Add collection to Agent Bayes library…, which includes its subcollections). A window opens with:

  • The library to add them to.
  • How many PDFs will be indexed, their pages, and the estimated credits, next to your credit balance.
  • The items that are skipped and why: already in this library, missing a title, author, or year in Zotero, or without a PDF file.
  • PDFs already indexed in another of your libraries, which are copied at no cost.

Click Send to start. Three items upload at a time. Stop sending pauses the queue, and Retry sends anything that didn't go through. If you run out of credits or the library reaches your plan's file limit, sending stops and the remaining items are marked as not sent.

The same window, Tools → Agent Bayes Indexing, follows every PDF you send to Agent Bayes in this Zotero session, from the bulk window or from the item pane. In progress shows each PDF as it's sent, queued, and indexed, with its progress. Finished PDFs move to Completed, a log you can fold away, with the date and time, the library, and the credits each PDF used, plus the total. Log entries stay even if you later remove the document, and sending the same PDF again adds a new entry. The log starts fresh each time Zotero starts.

Indexing happens server-side and may take anywhere from several minutes to a few hours (for a 1,000-page dissertation). The panel streams progress while files are processing. Canceling an in-progress indexing job is possible from the library's page in the web app, but not from the Zotero plugin.

Keep metadata in sync

Each time Zotero starts, the plugin audits all indexed items against Agent Bayes and flags any divergence in metadata — title, authors, or year. When you focus a flagged item, the Agent Bayes panel shows a button to resolve it inline. For a broader view, open the Sync Issues dialog to review and resolve all issues at once. Sync is bidirectional — you can apply Zotero's values to the server or the server's values back to Zotero.

The plugin detects two kinds of issues:

  • Metadata diverged — local item and server document disagree on title, authors, or year. Resolve individually with Use Zotero / Keep Server, or in bulk with All Zotero / All Server.
  • Orphaned on server — the server references a Zotero item key that no longer exists locally. Resolve with Delete from Server (permanent) or Disassociate (keeps the server document but unlinks it from Zotero).

Acknowledged issues stay dismissed unless either side changes again.

Credit balance in Zotero

The item panel shows your current Agent Bayes credit balance, which refreshes after every upload. If your balance is running low, a warning label appears next to it. Each file in the list shows its estimated indexing cost — if that estimate exceeds your available balance, the Index button for that file is disabled until you top up.

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