SciKG_Extract: An Agentic Workflow for Structured Scientific Knowledge Extraction

📋 Overview

SciKG_Extract is a comprehensive agentic framework designed to extract structured scientific knowledge from research papers based on a semantic schema representation of the target domain. The framework leverages Large Language Models (LLMs) to interpret and extract relevant information based on a schema and incorporates various tools and techniques like JSON validation, normalization using external data sources etc. to ensure accuracy and semantic consistency of the extracted data.

📁 SciKG_Extract Structure

scikg_extract/
├── agents/                                     # LangGraph agentic workflow components
│   ├── extraction_agent.py                     # Main extraction agent orchestrator
│   └── states.py                               # State definitions for agent workflow
├── config/                                     # Configuration management
│   ├── envConfig.py                            # Environment variables and settings
│   ├── normalizationConfig.py                  # Chemical name normalization configuration
│   └── processConfig.py                        # Process-specific configurations
├── models/                                     # LLM model adapters and interfaces
│   ├── model_adapter.py                        # Base adapter interface for LLM models
│   ├── openai_adapter.py                       # OpenAI API adapter (GPT-4, GPT-3.5)
├── prompts/                                    # Prompt templates for LLM interactions
│   ├── agents/                                 # Agent-specific prompts
│   └── tools/                                  # Tool-specific prompts
│       └── structure_knowledge_extraction.py   # Prompts for structured extraction
├── services/                                   # External service integrations
│   └── pubchem_cid_mapping.py                  # PubChem API integration and CID mapping
├── tools/                                      # Tools for agent workflow
│   ├── json_cleaner.py                         # Clean and normalize JSON data
│   ├── json_validator.py                       # Validate JSON against schemas
│   ├── pubchem_normalization.py                # Normalize chemical names with PubChem
│   └── structured_knowledge_extraction.py      # Main structured extraction tool
└── utils/                                      # Utility functions and helpers
    ├── dict_utils.py                           # Dictionary utilities
    ├── evaluation_utils.py                     # Evaluation metrics and comparison tools
    ├── file_utils.py                           # File I/O operations
    ├── json_utils.py                           # JSON-specific utilities
    ├── log_handler.py                          # Logging configuration and management
    ├── rest_client.py                          # REST API client utilities
    └── string_utils.py                         # String manipulation utilities

👥 Contact and Collaboration

For questions, suggestions, or collaboration opportunities, please reach out to the project maintainers.

• Issues or Bug Reports: Please use the GitHub Issues section of this repository to report bugs or request features.

📃 License

This project is licensed under the Apache License 2.0. See the LICENSE file for details.