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Validates whether a given keyword is a valid chemical compound, biochemical concept, or drug-related term using GPT-4, and returns alternative names/synonyms if valid.

Purpose

This function leverages OpenAI's GPT-4 model to validate scientific terminology in the context of chemistry and biology. It determines if a keyword represents a legitimate chemical compound, biochemical concept, or drug-related acronym/tradename. If validated, it also retrieves alternative names and synonyms for the term. The function is designed for scientific literature processing, drug research applications, and terminology standardization workflows.

Source Code

def validate_and_alternatives(keyword):

    os.environ["OPENAI_API_KEY"]='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'
    llm = ChatOpenAI(model="gpt-4o")
    response = llm.invoke("""
    System: You are a specialist chemist and biological expert with deep knowledge of terminology and compounds used in biological science.
You are asked to validate specific scientific terms enclosed in backticks to determine if they describe a chemical compound, a biochemical concept, or an acronym/tradename/product name used in drug research and development.
Your role is to strictly answer "yes" or "no."

In a second step - if the answer is "yes," provide a list of alternative names or terms for the same compound or concept. You must validate specific scientific terms or abbreviations precisely based on known scientific uses and meanings.

Respond strictly in the following JSON format:
[
    {
        "result": "yes" or "no",
        "alternatives": [list of alternative terms or synonyms, or an empty list]
    }
]
For clarity, if a term includes abbreviations such as "ALN," "TTR," or "sc," expand and match these components to specific scientific or medical contexts (e.g., RNAi therapies, transthyretin protein, subcutaneous administration) to ensure accurate validation.                         
 User: ```"""+str(keyword)+"```")

    #print("submitted term ",i)
    #response.pretty_print()
    try:
        s=json.loads(response.content.replace('```','').replace('json','').replace('\n',''))
        alternatives=[]
        if isinstance(s,list):
            for x in s:
                if x['result']=='yes':
                    validation=True
                    alternatives.extend(x['alternatives'])
                else:
                    validation=False
        else:
            if s['result']=='yes':
                alternatives.extend(s['alternatives'])
            else:
                validation=False
        alternatives=[x.replace("'","`") for x in alternatives]
        return validation,alternatives
    except:
        return False,[]

Parameters

Parameter Details

keyword: A string containing the scientific term, chemical compound name, biochemical concept, acronym, or drug name to be validated. Can be a full name, abbreviation, or tradename. Examples: 'ALN', 'transthyretin', 'RNAi', 'aspirin'

Return Value

Returns a tuple of (validation, alternatives) where 'validation' is a boolean (True if the term is valid, False otherwise) and 'alternatives' is a list of strings containing alternative names, synonyms, or related terms for the validated keyword. Returns (False, []) if validation fails or if JSON parsing encounters an error. Alternative names have single quotes replaced with backticks.

Dependencies

• langchain_openai
• openai
• json
• os

Required Imports

from langchain_openai import ChatOpenAI
import os
import json

Usage Example

import os
from langchain_openai import ChatOpenAI
import json

# Set API key (should be done securely via environment variable)
os.environ['OPENAI_API_KEY'] = 'your-api-key-here'

# Validate a chemical compound
keyword = 'aspirin'
is_valid, alternatives = validate_and_alternatives(keyword)

if is_valid:
    print(f"'{keyword}' is valid")
    print(f"Alternative names: {alternatives}")
else:
    print(f"'{keyword}' is not a valid scientific term")

# Example with abbreviation
keyword = 'RNAi'
is_valid, alternatives = validate_and_alternatives(keyword)
print(f"Valid: {is_valid}, Alternatives: {alternatives}")

Best Practices

• CRITICAL SECURITY ISSUE: Remove the hardcoded API key from the function. Use environment variables or secure configuration management instead.
• The function overwrites the OPENAI_API_KEY environment variable on every call, which is inefficient and potentially dangerous.
• Consider adding input validation to check if keyword is a non-empty string before making API calls.
• The broad try-except block catches all exceptions silently, making debugging difficult. Consider logging errors or using more specific exception handling.
• The function makes an API call for each invocation, which can be slow and costly. Consider implementing caching for frequently validated terms.
• The JSON parsing logic handles both list and dict responses, but the prompt should be refined to ensure consistent response format.
• The function replaces single quotes with backticks in alternatives, which may not be appropriate for all use cases. Document this behavior clearly.
• Consider adding a timeout parameter for the LLM invocation to prevent hanging on slow API responses.
• The validation variable may be undefined if the response is a list with no 'yes' results. Initialize validation=False at the start of the try block.
• Consider adding rate limiting to prevent API quota exhaustion when processing large batches of keywords.

Tags

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