> ## Documentation Index
> Fetch the complete documentation index at: https://docs.openbio.tech/llms.txt
> Use this file to discover all available pages before exploring further.

# Zotero Support

> Integrate your Zotero reference library with OpenBio research workflows

OpenBio integrates with **Zotero**, the popular reference management system, allowing you to search, manage, and cite your research library directly within your research conversations. Access your citations, collections, and notes without leaving OpenBio.

<Info>
  **What is Zotero?**

  Zotero is a free, open-source reference management tool that helps you collect, organize, cite, and share research sources. OpenBio's Zotero integration lets you access your Zotero library directly from your research conversations.
</Info>

Watch a demo of Zotero integration in action:

<iframe className="w-full aspect-video rounded-xl" src="https://www.youtube.com/embed/J5zTULYlSBo" title="Zotero Integration Demo" frameBorder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerPolicy="strict-origin-when-cross-origin" allowFullScreen />

## Overview

With Zotero integration, you can:

* **Search your library**: Find papers, books, and other references
* **Manage collections**: Organize references into collections
* **Access metadata**: View titles, authors, abstracts, and more
* **Create citations**: Add new references to your library
* **Download attachments**: Access PDFs and files from Zotero
* **Manage notes**: Create and search notes linked to references

## Setting Up Zotero

### Connecting Your Account

<Info>
  **Location**: Profile Settings → Zotero Settings tab
</Info>

<Steps>
  <Step title="Open Zotero Settings">
    Navigate to Profile → Settings → Zotero Settings
  </Step>

  <Step title="Connect with Zotero">
    Click the **"Connect with Zotero"** button
  </Step>

  <Step title="Authorize Access">
    You'll be redirected to Zotero to authorize OpenBio

    * Log in to your Zotero account
    * Review permissions requested
    * Click **"Authorize"** to grant access
  </Step>

  <Step title="Verify Connection">
    Return to OpenBio settings

    * Status should show "Connected"
    * Your Zotero user ID and display name appear
    * Last verified timestamp is shown
  </Step>
</Steps>

### Connection Status

The Zotero settings page shows:

* **Connection status**: Connected, configured but not verified, or not connected
* **User information**: Your Zotero user ID and display name
* **Last verified**: When the connection was last checked
* **Library access**: Which libraries are available

### Disconnecting

To remove Zotero integration:

1. Click **"Disconnect"** button
2. Confirm disconnection
3. Zotero tools will no longer be available

### Reconnecting

If your connection expires or needs refreshing:

1. Click **"Disconnect"** button
2. Complete the authorization flow again
3. Your connection is restored

## Using Zotero in Chat

### Searching Your Library

Ask OpenBio to search your Zotero library:

```
Search my Zotero library for papers about CRISPR
Find references related to protein folding
Show me recent items added to Zotero
```

### Accessing Collections

Work with your Zotero collections:

```
Show me items in my "CRISPR Research" collection
List all collections in my library
Get items from the top-level collection "Biology"
```

### Creating References

Add new items to your library:

```
Add this paper to my Zotero library:
Title: "Novel Protein Design Methods"
Authors: Smith, J. and Jones, M.
Year: 2024
```

### Managing Items

Update and organize references:

```
Update the tags on the paper about kinase inhibitors
Add a note to the CRISPR paper about key findings
Delete the duplicate entry for the protein structure paper
```

## Zotero Features Available

### Search and Discovery

* **Quick search**: Search across titles, authors, and abstracts
* **Advanced search**: Filter by item type, tags, collections
* **Recent items**: View recently added references
* **Item type filtering**: Find specific types (journal articles, books, etc.)

### Collection Management

* **View collections**: Browse your collection hierarchy
* **Collection items**: See items in specific collections
* **Create collections**: Organize references into new collections
* **Update collections**: Modify collection names and structure

### Item Operations

* **View details**: See full metadata for any reference
* **Create items**: Add new references manually
* **Update items**: Modify existing reference information
* **Delete items**: Remove references from your library
* **Batch operations**: Perform actions on multiple items

### Notes and Tags

* **Create notes**: Add standalone or item-linked notes
* **Search notes**: Find notes by content
* **Manage tags**: Add, remove, and search tags
* **Tag filtering**: Filter items by tags

### File Attachments

* **View attachments**: See files attached to references
* **Download files**: Access PDFs and other attachments
* **Create attachments**: Add files to references
* **Update files**: Replace or modify attachment files

## Common Use Cases

### Literature Review

```
1. Search Zotero: "Find all papers about protein design from 2023"
2. Review results and identify key papers
3. Create a collection: "Protein Design Review"
4. Add selected papers to the collection
5. Create notes summarizing key findings
```

### Citation Management

```
1. Ask: "Add this paper to Zotero: [paper details]"
2. OpenBio creates the reference with metadata
3. Add to relevant collection
4. Attach PDF if available
5. Tag with relevant keywords
```

### Research Organization

```
1. Search library for specific topic
2. Review items and organize into collections
3. Add tags for easy filtering
4. Create notes with key insights
5. Export bibliography for papers
```

## Best Practices

<AccordionGroup>
  <Accordion title="Keep Library Organized">
    Use collections and tags consistently to make searching easier.
  </Accordion>

  <Accordion title="Add Rich Metadata">
    When creating items, include as much information as possible (DOI, abstract, keywords).
  </Accordion>

  <Accordion title="Use Tags Strategically">
    Tag items with relevant keywords for easy filtering and discovery.
  </Accordion>

  <Accordion title="Create Notes">
    Add notes to important papers with key findings and your thoughts.
  </Accordion>

  <Accordion title="Regular Syncing">
    Keep your Zotero library synced to ensure OpenBio has the latest references.
  </Accordion>
</AccordionGroup>

## Troubleshooting

<AccordionGroup>
  <Accordion title="Connection not working">
    **Solutions**:

    * Click "Reconnect with Zotero"
    * Verify Zotero account credentials
    * Check internet connection
    * Try disconnecting and reconnecting
  </Accordion>

  <Accordion title="Library not syncing">
    **Solutions**:

    * Ensure Zotero sync is enabled in Zotero desktop app
    * Wait a few minutes for sync to complete
    * Try refreshing the connection in OpenBio
  </Accordion>
</AccordionGroup>

## Library Permissions

Zotero supports different library types with varying permissions:

### Personal Libraries

* **Full access**: Read, write, files, notes
* **Your library**: Complete control over all operations

### Group Libraries

Permissions depend on your role:

* **Owner/Admin**: Full access
* **Member (write)**: Can create/edit items and collections
* **Member (read)**: Can view items but not modify
* **Member (files)**: Can access file attachments

<Info>
  Some operations may be limited based on your permissions in group libraries. OpenBio will show helpful error messages if an operation isn't allowed.
</Info>

## Integration with Research Workflow

### During Literature Search

1. Search PubMed or other databases in OpenBio
2. Add interesting papers directly to Zotero
3. Organize into collections
4. Create notes with key findings

### While Writing

1. Search Zotero for relevant citations
2. Get formatted citations
3. Export bibliography
4. Access PDFs directly

### For Project Organization

1. Create collections per research project
2. Tag items with project identifiers
3. Add notes linking to OpenBio analyses
4. Track research progress

## Next Steps

<CardGroup cols={2}>
  <Card title="Chat Guide" href="/user-guide/features/chat">
    Learn how to use Zotero tools in conversations
  </Card>

  <Card title="Profile Settings" href="/user-guide/getting-started/authentication">
    Manage your Zotero connection
  </Card>

  <Card title="Tools Reference" href="/user-guide/tools/overview">
    Explore all available tools
  </Card>

  <Card title="Notebooks" href="/user-guide/features/notebooks">
    Document your research findings
  </Card>
</CardGroup>

<Tip>
  **Pro Tip**: Keep your Zotero library well-organized with collections and tags. This makes it much easier to find relevant papers when you need them during your research conversations!
</Tip>