OntoGPT

This release includes a variety of bugfixes and new options for running evaluations.

What's Changed

• Bump project version to 0.3.3 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/218
• Name params in call to complete by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/225
• Fixes for the BC5CDR evaluation by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/226
• Catch requests errors when call to NodeNormalizer endpoint fails by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/234
• Reduce redundancy in named entity list in evals by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/236
• Update documentation by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/220
• Repair clinical note generation and basic completion in CLI by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/239
• Parameter mis-usage fixes for CLI, OpenAI client, SPIRES engine, and gene set utils by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/241
• Add medical action extraction template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/208
• Bugfixes for Wikipedia extract and search commands by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/242
• Add a template specifically for extracting human phenotypes by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/214
• Add parameter to disable chunking in SPIRES evals by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/245
• fix typo by @andrewsu in https://github.com/monarch-initiative/ontogpt/pull/247
• Add model parameter to evaluation engine by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/249
• Fix #250 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/251
• Add NER eval for BC5CDR by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/252
• Fix #253 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/254
• Add gpt-4-1106-preview by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/258
• Add two more items to troubleshooting doc by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/263
• Add MAXO annotation evaluation by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/259
• Update dependencies for OpenAI API client and Pydantic compatibility and GPT4All by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/271

New Contributors

• @andrewsu made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/247

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.3...v0.3.4