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monarch-initiative /ontogpt

LLM-based ontological extraction tools, including SPIRES

nlp ai information-extraction named-entity-recognition language-models ner data-modeling relation-extraction monarchinitiative obofoundry gpt-3 linkml large-language-models llm oaklib chat-gpt

UpdatedApr 16, 2025
Jupyter Notebook

INCATools /ontology-access-kit

Star138

Ontology Access Kit: A python library and command line application for working with ontologies

python rdf semantic-web owl ontology apis geneontology monarchinitiative obofoundry ontology-api oaklib

UpdatedApr 10, 2025
Python

INCATools /semantic-sql

Star44

SQL and SQLite builds of OWL ontologies

sql sparql owl ontologies obofoundry linkml relation-graph oaklib

UpdatedFeb 25, 2025
Python

cmungall /semantic-llama

Star28

A knowledge extraction tool that uses a large language model to extract semantic information from text

ai language-models obofoundry knowledge-extraction linkml oaklib

UpdatedJan 3, 2023
Python

Knowledge-Graph-Hub /kg-microbe

Star17

nlp go robot media knowledge-graph named-entity-recognition microbiology metabolism traits phenotypes data-modeling environments chemicals chebi envo oaklib anatomical-knowledge ncbitaxonomy cell-shapes

UpdatedMar 31, 2025
Jupyter Notebook

INCATools /oakx-plugin-cookiecutter

Star2

cookiecutter for OAK plugins

plugins cookiecutter oaklib

UpdatedJan 11, 2023
Python

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