🔍 Code Extractor

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 scientific term (chemical compound, biochemical concept, or drug-related acronym/tradename) and, if valid, retrieves a list of alternative names or synonyms. 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, compound name, acronym, or tradename to be validated. Can be a chemical name (e.g., 'aspirin'), biochemical concept (e.g., 'apoptosis'), drug acronym (e.g., 'ALN-TTRsc'), or product name. The term will be evaluated by an LLM for scientific validity.

Return Value

Returns a tuple of (validation, alternatives) where 'validation' is a boolean indicating whether the term is valid (True) or not (False), and 'alternatives' is a list of strings containing alternative names, synonyms, or related terms for the validated keyword. If validation fails or an error occurs, returns (False, []). Single quotes in alternatives are replaced with backticks for safety.

Dependencies

• langchain_openai
• openai
• json
• os

Required Imports

from langchain_openai import ChatOpenAI
import os
import json

Usage Example

import os
import json
from langchain_openai import ChatOpenAI

# Set your API key (remove hardcoded key from function first!)
os.environ['OPENAI_API_KEY'] = 'your-api-key-here'

# Validate a chemical compound
is_valid, alternatives = validate_and_alternatives('aspirin')
print(f"Valid: {is_valid}")
print(f"Alternatives: {alternatives}")
# Expected output: Valid: True, Alternatives: ['acetylsalicylic acid', 'ASA', '2-acetoxybenzoic acid']

# Validate a drug acronym
is_valid, alternatives = validate_and_alternatives('ALN-TTRsc')
print(f"Valid: {is_valid}")
print(f"Alternatives: {alternatives}")

# Invalid term
is_valid, alternatives = validate_and_alternatives('randomtext123')
print(f"Valid: {is_valid}")
print(f"Alternatives: {alternatives}")
# Expected output: Valid: False, Alternatives: []

Best Practices

• SECURITY CRITICAL: Remove the hardcoded API key from the function. API keys should be loaded from environment variables or secure configuration files, not embedded in code.
• The function overwrites the OPENAI_API_KEY environment variable on every call, which is inefficient and potentially problematic in multi-threaded environments.
• Add input validation to check if keyword is a non-empty string before making API calls.
• Consider adding retry logic for API failures due to rate limits or network issues.
• The broad try-except block catches all exceptions silently, making debugging difficult. Consider logging errors or using more specific exception handling.
• The JSON parsing logic handles both list and dict responses, but the prompt should be refined to ensure consistent response format.
• Consider adding a timeout parameter to the LLM invoke call to prevent hanging on slow API responses.
• The function makes an API call for each keyword, which can be expensive. Consider batching multiple keywords in a single request for efficiency.
• Add type hints to improve code maintainability: def validate_and_alternatives(keyword: str) -> tuple[bool, list[str]]:
• 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.

Tags

Similar Components

AI-powered semantic similarity - components with related functionality:

• function validate_sharepoint_url 38.8% similar

  Validates that a given URL string conforms to SharePoint site URL format requirements, checking for proper protocol, domain, and path structure.

  From: /tf/active/vicechatdev/SPFCsync/validate_config.py

• function validate_azure_client_secret 36.6% similar

  Validates an Azure client secret by checking for placeholder values, minimum length requirements, and common invalid patterns.

  From: /tf/active/vicechatdev/SPFCsync/validate_config.py

• class RegulatoryExtractor 36.4% similar

  A class for extracting structured metadata from regulatory guideline PDF documents using LLM-based analysis and storing the results in an Excel tracking spreadsheet.

  From: /tf/active/vicechatdev/reg_extractor.py

• class MeetingMinutesGenerator_v1 36.3% similar

  A class that generates professional meeting minutes from meeting transcripts using either OpenAI's GPT-4o or Google's Gemini AI models.

  From: /tf/active/vicechatdev/advanced_meeting_minutes_generator.py

• function allowed_file 35.1% similar

  Validates whether a filename has an allowed file extension by checking if it contains a dot and if the extension (after the last dot) exists in a predefined ALLOWED_EXTENSIONS collection.

  From: /tf/active/vicechatdev/leexi/app.py