monarch-initiative/ontogpt
LLM-based ontological extraction tools, including SPIRES
This tool helps scientists and researchers automatically extract specific, structured information from scientific texts like research papers or clinical notes. You provide it with unstructured text and define the type of information you're looking for (e.g., drug names, disease symptoms), and it outputs that information in a structured, organized format. A bioinformatician, medical researcher, or anyone dealing with large volumes of biomedical literature would find this valuable for populating knowledge bases or categorizing data.
811 stars. Actively maintained with 26 commits in the last 30 days.
Use this if you need to transform large amounts of unstructured text into structured, categorized data for analysis or database entry, especially within biomedical or scientific domains.
Not ideal if you need to analyze highly complex relationships between extracted entities without further processing or if you are looking for a fully automated, hands-off knowledge base construction tool.
Stars
811
Forks
101
Language
Jupyter Notebook
License
BSD-3-Clause
Category
Last pushed
Feb 05, 2026
Commits (30d)
26
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