Zotero integration
Connect your Zotero library so the agent can research over the papers you have already curated — importing collections, syncing discoveries back, and surfacing the foundational references your reading list quietly shares.
Zotero is where many researchers keep the literature that actually matters to their work: the collections they build by hand over months and years. BioSkepsis treats that library as a first-class corpus. Once connected, the agent can reason over your collections directly — answering questions, extracting data, and synthesizing findings across your curated papers without you re-downloading a single PDF.
#Connecting your Zotero library
The connection is authenticated with a Zotero API key that you generate yourself and paste into BioSkepsis. There is no account-linking pop-up and no third-party redirect — you stay in control of the credential and can revoke it at any time from Zotero.
- Create an API key in Zotero. Sign in at zotero.org/settings/keys and choose Create new private key. Give it a recognizable name (for example, “BioSkepsis”) so you can identify it later.
- Grant read — and write, if you want sync back. Enable read access to your personal library so the agent can import collections. If you want the agent to write newly discovered references back into Zotero, also enable write access. Scope the key to specific group libraries as needed.
- Copy the key and your library ID. Zotero shows the generated key once — copy it immediately. Your numeric userID is listed on the same settings page.
- Paste it into BioSkepsis. Open the Zotero settings panel in BioSkepsis, paste the API key, and save. Your library and its collections appear inside BioSkepsis as soon as the key is validated.
#Importing collections for the agent to work over
Once connected, your Zotero collections are browsable inside BioSkepsis exactly as they are in Zotero — nested folders, group libraries, and all. You choose what the agent should treat as its working corpus for a given research session.
- Pick a collection or individual papers. Import an entire collection to hand the agent a ready-made corpus, or cherry-pick specific items when you only want the agent focused on a handful of key papers.
- Combine multiple collections. The agent can work over papers drawn from several Zotero collections at once, so a single session can span, say, your “mechanism” and “clinical” folders together.
- Full-text reasoning. Where the underlying full text is available, the agent reasons over the complete papers — not just titles and abstracts — so you can ask detailed methodological and quantitative questions and get answers grounded in what the papers actually report.
From there the agent behaves as it does over the broader life-science literature: you ask a question, it reads across the imported papers, extracts the relevant evidence, and synthesizes an answer with the specific papers cited. The difference is that the corpus is yours — the collection you trust — rather than an open search of the literature.
#Bidirectional sync
The integration moves in both directions, so your library and your BioSkepsis research stay in step.
| Direction | What happens |
|---|---|
| Zotero → BioSkepsis | Import existing collections and individual items so the agent can research over your curated papers. |
| BioSkepsis → Zotero | Push newly discovered, citation-backed references the agent surfaces during a session back into your Zotero library in one click. |
The write-back path is what keeps your library growing rather than fragmenting across tools. When the agent turns up a paper you did not have — a foundational reference, a newer follow-up, a study you missed — you can add it to the relevant Zotero collection without leaving BioSkepsis, complete with its metadata. Your next reading session in Zotero already has it.
#Discovering shared foundational references
A curated collection usually rests on a bedrock of seminal work — the papers that everything in the folder cites, even when you never added those papers to Zotero yourself. After importing a collection, the agent can trace those shared roots and surface the foundational references that underlie your reading.
This reveals the intellectual scaffolding of a collection: the handful of studies that a large fraction of your papers depend on. It is a fast way to spot a landmark you have been citing second-hand, to onboard into a subfield by reading its foundations first, or to sanity-check that a collection is built on the literature you think it is.
- Surface the seminal works. The agent identifies references shared across many papers in the imported collection and ranks the ones that recur most.
- Fill the gaps. Any foundational paper you do not already hold can be written back into your Zotero library, closing the gap between what you cite and what you have.