I wanted to announce our python package, OntoGPT (GitHub - monarch-initiative/ontogpt: GPT-based ontological extraction tools, including SPIRES). This provides a number of different tools for doing various things related to ontologies and knowledge bases using the OpenAI API.
Two of the main applications have pre-prints up:
- SPIRES: an approach for extracting data from unstructured text, https://arxiv.org/abs/2304.02711
- SPINDOCTOR: interpreting genomic data [2305.13338] Gene Set Summarization using Large Language Models
We are also working on integrating LLMs with reasoning and ontology matching pipelines.
All code is on GitHub and contributions are welcome!