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API Reference

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Conner Groth edited this page Jul 3, 2025 · 3 revisions

API Reference

Core Endpoints

  • GET /api/boot - Initialize server and load feature libraries
  • POST /api/annotateSequence - Get sequence annotations using SYNBICT
  • POST /api/annotateText - Get text annotations using BERN2 NLP
  • POST /api/convert/genbanktosbol2 - Convert GenBank to SBOL
  • POST /api/cleanSBOL - Clean and normalize SBOL URIs
  • POST /api/findSimilarParts - Find similar parts in databases
  • POST /api/importUserLibrary - Import custom feature libraries from SynBioHub
  • POST /api/deleteUserLibrary - Remove custom feature libraries

Request/Response Examples

// Sequence Annotation
POST /api/annotateSequence
{
  "completeSbolContent": "<sbol xml>",  
  "partLibraries": ["cello_library.xml"],
  "cleanDocument": true
}

// Text Annotation  
POST /api/annotateText
{
  "text": "This promoter regulates gene expression"
}

Boot Endpoint and Setup Behavior

When a user first visits the SeqImprove site, the frontend calls:

@app.get("/api/boot")
def boot_app():
    return "Rise and shine"

This endpoint triggers the setup() function, which loads feature libraries required by SYNBICT for sequence annotation. This loading step is time-consuming, so preloading on the first visit ensures users won’t experience delays when requesting annotations later.

Local vs Cloud Behavior

Local Development: setup() runs once on the first API request, then stays loaded until the server restarts.

Cloud Deployment: Servers may spin down when idle, so /api/boot is used to proactively reload libraries as soon as the site is opened.

SYNBICT performs sequence annotation using part libraries and internally leverages flashtext for fast string matching.

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