Biomedical Translator Data Summarization API

This repository contains a Flask-based API that generates summaries of structured responses from the Biomedical Data Translator system in natural language.

Summary Endpoint

API has the summary endpoint called "/summary".

It currently accepts JSON structured data which holds the user "query" and the "results" which has the following structure (Eg. refer this sample data):

{
  "query": "<a question of string datatype>",
  "results": [
    {
      "name": "<name of a biomedical concept>",
      "paths": [
        "<biological path 1>",
        "<biological path 2>",
        "<biological path 3>"
      ]
    }
  ]
}

The list of biological paths represents the mechanistic explanation of how that answer (i.e., the biomedical concept) relates to the query.

Make an API call

/summary endpoint accepts POST request. Here is a snippet for calling the endpoint from python:

import requests

api_endpoint = "https://ncats-llm-summarization.onrender.com/summary"

def stream_response(url, data):
    headers = {'Content-Type': 'application/json'}
    response = requests.post(url, json=data, headers=headers, stream=True)
    
    if response.status_code == 200:
        for chunk in response.iter_content(chunk_size=1, decode_unicode=True):
            if chunk:
                print(chunk, end='', flush=True)
    else:
        print(f"Error: {response.status_code}")
        print(response.text)

stream_response(api_endpoint, data)

Note: 'data' is the JSON data as mentioned above

Refer demo notebook for more details.