OntoGPT

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 https://github.com/monarch-initiative/ontogpt/pull/167 Update documentation by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/170 Fix #174 - add missing CLI parameters by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/175 A fix for encountering missing PubmedData fields by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/178 Dependency updates for llm (and pydantic compatibility, in particular) by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/182 Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.0...v0.3.1If you use OntoGPT, please cite it as follows