monarch-initiative/ontogpt
LLM-based ontological extraction tools, including SPIRES
Extracts structured information from free text using instruction-based prompts grounded in ontologies, then maps results to standardized knowledge representations. Supports multiple LLM APIs via litellm (OpenAI, Anthropic, Azure, Mistral, local Ollama models), with command-line and web interfaces for interactive use. Designed for biomedical information extraction tasks like drug-disease relationships, leveraging the SPIRES method for zero-shot semantic extraction.
811 stars. Actively maintained with 9 commits in the last 30 days.
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Jupyter Notebook
License
BSD-3-Clause
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Last pushed
Feb 05, 2026
Commits (30d)
9
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