API Documentation

Integrate KRT generation into your workflows

Version 1.0

Quick Start

The KRT Maker API allows you to programmatically generate Key Resource Tables from bioRxiv preprints. All endpoints return JSON responses.

Base URL: https://krt.xeradb.com/api/

Available Endpoints

GET Check DOI Availability

Check if a DOI is available in our local database.

Endpoint

GET /check-doi-local/

Parameters

Parameter	Type	Required	Description
`doi`	string	Yes	The DOI to check (e.g., "10.1101/2025.01.01.123456")

Example Request

curl -X GET "https://krt.xeradb.com/api/check-doi-local/?doi=10.1101/2025.01.01.123456"

Example Response

{
  "success": true,
  "available": true,
  "doi": "10.1101/2025.01.01.123456",
  "title": "Example Research Paper",
  "file_size": 245760,
  "downloaded_at": "2025-01-15T10:30:00Z"
}

GET Get DOI Suggestions

Get random or filtered DOI suggestions from the database.

Endpoint

GET /doi-suggestions/

Parameters

Parameter	Type	Required	Description
`q`	string	No	Search query to filter suggestions
`limit`	integer	No	Number of suggestions to return (default: 10, max: 50)

Example Request

curl -X GET "https://krt.xeradb.com/api/doi-suggestions/?q=cancer&limit=5"

Example Response

{
  "success": true,
  "suggestions": [
    {
      "doi": "10.1101/2025.01.01.123456",
      "title": "Cancer Research Example",
      "authors": "Smith J, Doe A",
      "publication_date": "2025-01-01",
      "file_size": 245760
    }
  ],
  "total_available": 15420,
  "query": "cancer"
}

GET Get KRT Data by Session ID

Retrieve detailed KRT data for a specific extraction session.

Endpoint

GET /api/krt/{session_id}/

Parameters

Parameter	Type	Required	Description
`session_id`	string	Yes	The session ID from KRT generation

Example Request

curl -X GET "https://krt.xeradb.com/api/api/krt/abc123def456/"

Example Response

{
  "success": true,
  "session_id": "abc123def456",
  "krt_data": [
    {
      "RESOURCE TYPE": "Antibody",
      "RESOURCE NAME": "Anti-GFP antibody",
      "SOURCE": "Abcam",
      "IDENTIFIER": "ab13970",
      "NEW/REUSE": "reuse",
      "ADDITIONAL INFORMATION": "1:1000 dilution"
    }
  ],
  "summary": {
    "total_resources": 15,
    "new_resources": 3,
    "reused_resources": 12,
    "processing_time": 45.2,
    "provider": "anthropic",
    "model": "claude-3-5-sonnet-20241022"
  }
}

GET Get KRT Data by DOI

Retrieve the best KRT data for a bioRxiv paper by DOI.

Endpoint

GET /api/krt/doi/{doi}/

Parameters

Parameter	Type	Required	Description
`doi`	string	Yes	The DOI of the bioRxiv paper (e.g., "10.1101/2025.01.01.123456")

Example Request

curl -X GET "https://krt.xeradb.com/api/api/krt/doi/10.1101/2025.01.01.123456/"

Example Response

{
  "success": true,
  "doi": "10.1101/2025.01.01.123456",
  "session_id": "abc123def456",
  "krt_data": [...],
  "summary": {
    "total_resources": 15,
    "new_resources": 3,
    "reused_resources": 12,
    "total_sessions": 3
  },
  "article_info": {
    "title": "Example Research Paper",
    "authors": "Smith J, Doe A et al.",
    "publication_date": "2025-01-01",
    "is_biorxiv_paper": true
  }
}

GET Export KRT

Export a generated KRT in various formats.

Endpoint

GET /export/{session_id}/{format}/

Parameters

Parameter	Type	Required	Description
`session_id`	string	Yes	The session ID from KRT generation
`format`	string	Yes	Export format: "json", "csv", or "excel"

Example Request

curl -X GET "https://krt.xeradb.com/api/export/abc123def456/json/" -H "Accept: application/json"

AI Enhancement Features

Advanced AI-powered endpoints for intelligent resource identification, validation, and recommendations. These features address the 54% resource identification failure rate in biomedical literature.

POST AI RRID Suggestions

Get intelligent RRID suggestions for research resources using advanced AI analysis.

Endpoint

POST /api/ai/suggest-rrid/

Request Body

Parameter	Type	Required	Description
`resource_name`	string	Yes	Name of the research resource
`resource_type`	string	No	Type of resource (antibody, cell line, software, etc.)
`vendor`	string	No	Resource vendor/manufacturer
`catalog_number`	string	No	Catalog or part number

Example Request

curl -X POST "https://krt.xeradb.com/api/api/ai/suggest-rrid/" \
  -H "Content-Type: application/json" \
  -d '{
    "resource_name": "anti-beta-tubulin",
    "resource_type": "antibody", 
    "vendor": "Abcam",
    "catalog_number": "ab6046"
  }'

Example Response

{
  "success": true,
  "suggestions": [
    {
      "id": 123,
      "suggested_rrid": "RRID:AB_2138153",
      "confidence_score": 0.95,
      "reasoning": "Exact match found in Antibody Registry",
      "vendor": "Abcam",
      "catalog_number": "ab6046"
    }
  ],
  "total_found": 1,
  "response_time": 0.85
}

POST AI RRID Validation

Validate RRIDs across multiple scientific databases with real-time consistency checking.

Endpoint

POST /api/ai/validate-rrid/

Request Body

Parameter	Type	Required	Description
`rrid`	string	Yes	The RRID to validate (e.g., "RRID:AB_2138153")

Example Request

curl -X POST "https://krt.xeradb.com/api/api/ai/validate-rrid/" \
  -H "Content-Type: application/json" \
  -d '{"rrid": "RRID:AB_2138153"}'

Example Response

{
  "success": true,
  "validation": {
    "rrid": "RRID:AB_2138153",
    "is_valid": true,
    "status": "valid",
    "confidence_score": 0.98,
    "recommendations": [],
    "last_checked": "2025-01-15T10:30:00Z",
    "source": "fresh"
  }
}

POST Smart Resource Recommendations

Get intelligent alternative resource recommendations based on functional similarity and availability.

Endpoint

POST /api/ai/recommend/

Request Body

Parameter	Type	Required	Description
`resource_name`	string	Yes	Name of the original resource
`resource_type`	string	No	Type of resource
`context`	object	No	Additional context (applications, requirements, etc.)

Example Request

curl -X POST "https://krt.xeradb.com/api/api/ai/recommend/" \
  -H "Content-Type: application/json" \
  -d '{
    "resource_name": "DAPI",
    "resource_type": "chemical",
    "context": {
      "applications": ["nuclear staining", "fluorescence microscopy"]
    }
  }'

Example Response

{
  "success": true,
  "recommendations": [
    {
      "id": 456,
      "recommended_resource": "Hoechst 33342",
      "recommended_vendor": "Thermo Fisher",
      "recommended_catalog": "H3570",
      "recommendation_type": "functional_equivalent",
      "confidence_score": 0.92,
      "reasoning": "Alternative nuclear stain with similar spectral properties",
      "availability_status": "in_stock"
    }
  ],
  "total_found": 1,
  "response_time": 1.2
}

POST Conversational KRT Creation

Create KRT tables through natural language conversation with AI assistant.

Endpoint

POST /api/ai/chat/

Request Body

Parameter	Type	Required	Description
`message`	string	Yes	Natural language message about resources
`session_id`	string	No	Conversation session ID (auto-generated if not provided)

Example Request

curl -X POST "https://krt.xeradb.com/api/api/ai/chat/" \
  -H "Content-Type: application/json" \
  -d '{
    "message": "I used anti-beta-tubulin antibody from Abcam, catalog ab6046",
    "session_id": "chat_session_123"
  }'

Example Response

{
  "success": true,
  "session_id": "chat_session_123",
  "response": "I've added the anti-beta-tubulin antibody to your KRT. Would you like to add any more resources?",
  "intent": "add_resource",
  "krt_entries": [
    {
      "RESOURCE TYPE": "Antibody",
      "RESOURCE NAME": "anti-beta-tubulin",
      "SOURCE": "Abcam",
      "IDENTIFIER": "Cat# ab6046",
      "NEW/REUSE": "new",
      "ADDITIONAL INFORMATION": ""
    }
  ],
  "needs_clarification": false,
  "clarifications": [],
  "response_time": 1.5
}

POST Browser Extension APIs

Specialized endpoints for the KRT Maker browser extension providing real-time assistance.

RRID Suggestions for Browser

POST /api/browser/suggest-rrid/

RRID Validation for Browser

POST /api/browser/validate-rrid/

Note: These endpoints use the same request/response format as the main AI endpoints but include additional browser-specific optimizations and CORS headers.

Supported Platforms

Overleaf & ShareLaTeX
Google Docs
Notion
Editorial Manager
PubMed Central

Authentication

Currently, the API endpoints are publicly accessible for read-only operations and AI enhancement features. Authentication will be required for KRT generation endpoints and advanced AI features in future versions.

AI Enhancement Features: The new AI endpoints are currently available without authentication for testing and demonstration purposes.

Coming Soon: API key authentication, rate limiting, and usage quotas for production use.

Rate Limiting

To ensure fair usage and system stability, the following rate limits apply:

DOI Checks: 100 requests per minute
Suggestions: 50 requests per minute
Exports: 20 requests per minute
AI RRID Suggestions: 30 requests per minute
AI Validation: 60 requests per minute
AI Recommendations: 20 requests per minute
Conversational AI: 10 requests per minute
Browser Extension: 100 requests per minute

Rate limit headers are included in all responses for monitoring your usage.

Error Codes

HTTP Code	Error Type	Description
`200`	Success	Request completed successfully
`400`	Bad Request	Invalid parameters or malformed request
`404`	Not Found	Requested resource not found
`429`	Rate Limited	Rate limit exceeded, try again later
`500`	Server Error	Internal server error occurred

SDKs & Libraries

Official SDKs and client libraries are coming soon!

We're working on Python, R, and JavaScript libraries to make integration even easier. Follow our GitHub repository for updates.

Python SDK R Package JavaScript Library

Code Examples

Python Example

import requests

# Check DOI availability
response = requests.get('https://krt.xeradb.com/api/check-doi-local/', 
                       params={'doi': '10.1101/2025.01.01.123456'})

if response.status_code == 200:
    data = response.json()
    if data['success'] and data['available']:
        print(f"DOI available: {data['title']}")
        
        # Get KRT data for this DOI
        krt_response = requests.get(f'https://krt.xeradb.com/api/api/krt/doi/10.1101/2025.01.01.123456/')
        if krt_response.status_code == 200:
            krt_data = krt_response.json()
            print(f"Found {krt_data['summary']['total_resources']} resources")
    else:
        print("DOI not available in database")
else:
    print(f"Error: {response.status_code}")

JavaScript Example

// Get DOI suggestions
async function getDOISuggestions(query) {
    try {
        const response = await fetch('https://krt.xeradb.com/api/doi-suggestions/?q=' + 
                                   encodeURIComponent(query));
        const data = await response.json();
        
        if (data.success) {
            console.log('Found suggestions:', data.suggestions);
            return data.suggestions;
        }
    } catch (error) {
        console.error('Error fetching suggestions:', error);
    }
}

getDOISuggestions('cancer research');

cURL Example

# Get random DOI suggestions
curl -X GET "https://krt.xeradb.com/api/doi-suggestions/" \
     -H "Accept: application/json"

# Check specific DOI
curl -X GET "https://krt.xeradb.com/api/check-doi-local/?doi=10.1101/2025.01.01.123456" \
     -H "Accept: application/json"

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