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Open Data with GPT

Overview

This project provides a set of Python scripts for analyzing scientific papers using XML data extraction and generating language model reviews. It includes functions for parsing XML documents related to scientific papers and a GPT (Generative Pre-trained Transformer) wrapper for querying OpenAI's GPT API.

Adapted from the work of Weixin-Liang et al.

Features

  • XML Processing:

    • Functions for extracting information from scientific papers in XML format, including title, abstract, introduction, figure and table captions, section titles, and main content.

  • GPT Wrapper:

    • A wrapper class for interacting with GPT API.
    • Tokenization and API calls for generating language model reviews based on parsed paper information.

  • Workflow Steps:

    • Functions for creating a truncated prompt for the GPT model based on parsed XML data.
    • Steps for evaluating whether a scientific paper includes information on obtaining reported data.
    • Task-specific questions and CSV formatting instructions for user interaction.

Getting Started

  1. Dependencies:

    • Install required Python libraries (openai, tiktoken, etc.). Ensure the API key is available in a file named "key.txt" in the project folder.

  2. Example Usage:

    • Use provided functions like step2_parse_xml to extract information from XML.
    • Generate language model reviews with step3_get_lm_review.

  3. Customization:

    • Adapt the number of tokens and modify functions as needed for specific use cases.

Usage Example

# Example usage of XML parsing and language model review
parsed_xml = step2_parse_xml(xml_data)
review_result = step3_get_lm_review(gpt_wrapper, parsed_xml)
print(review_result)

License

This project is licensed under the MIT License.