Protocols.io Integration

Core Capabilities

This skill provides comprehensive guidance across five major capability areas:

1. Authentication & Access

Manage API authentication using access tokens and OAuth flows. Includes both client access tokens (for personal content) and OAuth tokens (for multi-user applications).

Key operations:

• Generate authorization links for OAuth flow
• Exchange authorization codes for access tokens
• Refresh expired tokens
• Manage rate limits and permissions

Reference: Read references/authentication.md for detailed authentication procedures, OAuth implementation, and security best practices.

2. Protocol Operations

Complete protocol lifecycle management from creation to publication.

Key operations:

• Search and discover protocols by keywords, filters, or DOI
• Retrieve detailed protocol information with all steps
• Create new protocols with metadata and tags
• Update protocol information and settings
• Manage protocol steps (create, update, delete, reorder)
• Handle protocol materials and reagents
• Publish protocols with DOI issuance
• Bookmark protocols for quick access
• Generate protocol PDFs

Reference: Read references/protocols_api.md for comprehensive protocol management guidance, including API endpoints, parameters, common workflows, and examples.

3. Discussions & Collaboration

Enable community engagement through comments and discussions.

Key operations:

• View protocol-level and step-level comments
• Create new comments and threaded replies
• Edit or delete your own comments
• Analyze discussion patterns and feedback
• Respond to user questions and issues

Reference: Read references/discussions.md for discussion management, comment threading, and collaboration workflows.

4. Workspace Management

Organize protocols within team workspaces with role-based permissions.

Key operations:

• List and access user workspaces
• Retrieve workspace details and member lists
• Request access or join workspaces
• List workspace-specific protocols
• Create protocols within workspaces
• Manage workspace permissions and collaboration

Reference: Read references/workspaces.md for workspace organization, permission management, and team collaboration patterns.

5. File Operations

Upload, organize, and manage files associated with protocols.

Key operations:

• Search workspace files and folders
• Upload files with metadata and tags
• Download files and verify uploads
• Organize files into folder hierarchies
• Update file metadata
• Delete and restore files
• Manage storage and organization

Reference: Read references/file_manager.md for file upload procedures, organization strategies, and storage management.

6. Additional Features

Supplementary functionality including profiles, notifications, and exports.

Key operations:

• Manage user profiles and settings
• Query recently published protocols
• Create and track experiment records
• Receive and manage notifications
• Export organization data for archival

Reference: Read references/additional_features.md for profile management, publication discovery, experiment tracking, and data export.

Getting Started

Step 1: Authentication Setup

Before using any protocols.io API functionality:

1. Obtain an access token (CLIENT_ACCESS_TOKEN or OAUTH_ACCESS_TOKEN)
2. Read references/authentication.md for detailed authentication procedures
3. Store the token securely
4. Include in all requests as: Authorization: Bearer YOUR_TOKEN

Step 2: Identify Your Use Case

Determine which capability area addresses your needs:

• Working with protocols? → Read references/protocols_api.md
• Managing team protocols? → Read references/workspaces.md
• Handling comments/feedback? → Read references/discussions.md
• Uploading files/data? → Read references/file_manager.md
• Tracking experiments or profiles? → Read references/additional_features.md

Step 3: Implement Integration

Follow the guidance in the relevant reference files:

• Each reference includes detailed endpoint documentation
• API parameters and request/response formats are specified
• Common use cases and workflows are provided with examples
• Best practices and error handling guidance included

Base URL and Request Format

All API requests use the base URL: