v0.3.1

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

• Implement llm api by @caufieldjh in #167
• Update documentation by @caufieldjh in #170
• Fix #174 - add missing CLI parameters by @caufieldjh in #175
• A fix for encountering missing PubmedData fields by @caufieldjh in #178
• Dependency updates for llm (and pydantic compatibility, in particular) by @caufieldjh in #182

Full Changelog: v0.3.0...v0.3.1