v1.0.7

What's Changed

• Add initial version of micronutrient extraction template (and other new templates) by @caufieldjh in #469
• Add --target-class option to web_extract command by @ptgolden in #470
• Update pathology extraction template by @caufieldjh in #472
• Prep for v1.0.7 by @caufieldjh in #473

New Contributors

• @ptgolden made their first contribution in #470

Full Changelog: v1.0.6...v1.0.7

v1.0.6

What's Changed

• More updates for pathology report extraction by @caufieldjh in #461
• Add BioEPIC demo notebook by @caufieldjh in #463
• Provide spans of named entities by @caufieldjh in #464

Full Changelog: v1.0.5...v1.0.6

v1.0.5

What's Changed

• Suppress litellm debug messages by @caufieldjh in #448
• Expand option to set token/context limit by @caufieldjh in #449
• Dependency updates and adaptations by @caufieldjh in #453
• Improvements for pathology report extractions by @caufieldjh in #452
• Remove hardcoded values and references to gpt-3.5-turbo models by @caufieldjh in #458
• Removed pydantic_version keyword in template_loader.py by @gkreder in #459
• Prep for v1.0.5 by @caufieldjh in #460

New Contributors

• @gkreder made their first contribution in #459

Full Changelog: v1.0.4...v1.0.5

v1.0.4

What's Changed

• Add system-message command by @caufieldjh in #435
• Add topic classifier by @caufieldjh in #437
• Add new food extraction template by @caufieldjh in #441
• Further development of the pathology extraction template by @caufieldjh in #444
• Update output options for multilingual analysis by @caufieldjh in #442
• Refactor file loading/parsing; add support for spreadsheets as input by @caufieldjh in #447

Full Changelog: v1.0.3...v1.0.4

v1.0.3

What's Changed

• Add template for MIRO checklist extraction by @caufieldjh in #432
• Add caching for mapper by @caufieldjh in #433
• Prep for v1.0.3 by @caufieldjh in #434

Full Changelog: v1.0.2...v1.0.3

v1.0.2

What's Changed

• Added CSV exporter by @timalamenciak in #426
• Handle HTTP 500 errors with PubmedClient by @caufieldjh in #428
• Move eliminate_empty function into utils by @caufieldjh in #429
• Replace textract with pymupdf by @caufieldjh in #430
• Prep for V1.0.2 by @caufieldjh in #431

New Contributors

• @timalamenciak made their first contribution in #426

Full Changelog: v1.0.1...v1.0.2

v1.0.1

What's Changed

• Add docs section on OpenAI-compatible Proxy Servers by @caufieldjh in #419
• Partial fix for #417 by @caufieldjh in #422
• Add JSON writer by @caufieldjh in #423
• Updates for v1.0.1 by @caufieldjh in #424

Full Changelog: v1.0.0...v1.0.1

v1.0.0

🎉 Highlights 🎉

• LLMs are now accessed through litellm, meaning OntoGPT may now be used with a large collection of API endpoints and local or alternative model providers. See the full list with the ontogpt list-models command.
• Local, open models may be downloaded and used through the ollama package.
• Numerous bugfixes
• Documentation updates
• Updates for the webapp

If something seems broken, please let us know! Open an issue here: https://github.com/monarch-initiative/ontogpt/issues

What's Changed

• Fixing failure to parse markdown, JSON formatting, and numbered lists by @caufieldjh in #394
• Add template for summarizing LinkML data validation reports by @caufieldjh in #400
• Improvements for the alzrd template by @caufieldjh in #399
• Further updates to the ADRD extraction template by @caufieldjh in #403
• Restructure Alz extraction template; split into two variants by @caufieldjh in #405
• Additional updates to the Alzheimers extraction template by @caufieldjh in #406
• Fix issue with early termination of multilanguage analysis runs by @caufieldjh in #408
• Add support for more models by @caufieldjh in #373
• Tests for new LLMClient by @caufieldjh in #410
• General cleanup: docs, code optimization, and project structure by @caufieldjh in #411
• Add option to truncate input_text in outputs by @caufieldjh in #413
• eliminate hardcoded gpt4-turbo from multilingual function by @leokim-l in #415
• Misc changes for 1.0.0rc2 by @caufieldjh in #416
• Prep for v1.0.0 release by @caufieldjh in #418

New Contributors

• @leokim-l made their first contribution in #415

Full Changelog: v0.3.15...v1.0.0

v1.0.0rc2

What's Changed

• Add option to truncate input_text in outputs by @caufieldjh in #413
• eliminate hardcoded gpt4-turbo from multilingual function by @leokim-l in #415
• Misc changes for 1.0.0rc2 by @caufieldjh in #416
• Enabled using alternative source for textract (#412)
• A small fix for pubmed-annotate

New Contributors

• @leokim-l made their first contribution in #415

Full Changelog: v1.0.0rc1...v1.0.0rc2

v1.0.0rc1

This is a pre-release. See below for a preview of changes.

What's Changed

• Fixing failure to parse markdown, JSON formatting, and numbered lists by @caufieldjh in #394
• Add template for summarizing LinkML data validation reports by @caufieldjh in #400
• Improvements for the alzrd template by @caufieldjh in #399
• Further updates to the ADRD extraction template by @caufieldjh in #403
• Restructure Alz extraction template; split into two variants by @caufieldjh in #405
• Additional updates to the Alzheimers extraction template by @caufieldjh in #406
• Fix issue with early termination of multilanguage analysis runs by @caufieldjh in #408
• Add support for more models by @caufieldjh in #373
• Tests for new LLMClient by @caufieldjh in #410
• General cleanup: docs, code optimization, and project structure by @caufieldjh in #411

Full Changelog: v0.3.15...v1.0.0rc1