Info: Zenodo’s user support line is staffed on regular business days between Dec 23 and Jan 5. Response times may be slightly longer than normal.

There is a newer version of the record available.

Published August 24, 2023 | Version v0.3.1
Software Open

OntoGPT

Creators

Description

Highlights Access to open models through the llm package

llm provides easy access to LLMs from OpenAI and beyond, including the GPT4All set of open models. You may now specify one of these models by using the -m or --model option with most commands. When calling a model for the first time, llm will download a local copy.

Example:

ontogpt extract -t mendelian_disease.MendelianDisease -i tests/input/cases/mendelian-disease-cmt2e.txt -m nous-hermes-13b

Or extract from PubMed abstracts:

ontogpt pubmed-annotate -t drug "propranolol mode of action" --model nous-hermes-13b --limit 5

Or generate clinical case report text:

ontogpt clinical-notes -d "patient with chronic muscle pain and hypoplastic toenails" --sections "Past Medical History" -m nous-hermes-13b

See the full list of model options with

ontogpt list-models
Updated dependency requirements

OntoGPT should now be compatible with Pydantic versions less than, equal to, or greater than 2. Many of these changes happened upstream within the broader LinkML ecosystem.

What's Changed

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.0...v0.3.1

Notes

If you use OntoGPT, please cite it as follows.

Files

monarch-initiative/ontogpt-v0.3.1.zip

Files (4.9 MB)

Name Size Download all
md5:019fee144467ebf9b6d7c8ee8c39eae2
4.9 MB Preview Download

Additional details

Related works

Is supplement to
https://github.com/monarch-initiative/ontogpt/tree/v0.3.1 (URL)