Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of ontogpt

ontogpt - v1.0.17

What's Changed

  • Switch to uv from poetry by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/535
  • Fix issues with caching: repair specifying cache db path, add tests, update docs by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/536

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.16...v1.0.17

- Jupyter Notebook
Published by caufieldjh 6 months ago

ontogpt - v1.0.16

What's Changed

  • Updates for the MIC extraction template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/530
  • Fix KeyError from map_identifier function by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/532
  • Prep for 1.0.16 and fix import of LiteLLM's getmodelcost_map by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/533

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.15...v1.0.16

- Jupyter Notebook
Published by caufieldjh 7 months ago

ontogpt - v1.0.15

What's Changed

  • Remove urllib3 dependency by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/525
  • Prep for 1.0.15 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/526

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.14...v1.0.15

- Jupyter Notebook
Published by caufieldjh 8 months ago

ontogpt - v1.0.14

What's Changed

  • Add template for AOP extraction by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/522
  • Small fix for errors in template loading by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/523

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.13...v1.0.14

- Jupyter Notebook
Published by caufieldjh 9 months ago

ontogpt - v1.0.13

What's Changed

  • Fix for edge cases with creating new LLMClient and SPIRESEngine by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/520
  • Prep for 1.0.13 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/521

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.12...v1.0.13

- Jupyter Notebook
Published by caufieldjh 10 months ago

ontogpt - v1.0.12

What's Changed

  • Improve handling of missing root class definition by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/514
  • Prep for v1.0.12 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/515

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.11...v1.0.12

- Jupyter Notebook
Published by caufieldjh 11 months ago

ontogpt - v1.0.11

What's Changed

  • draft schemas for table extraction by @realmarcin in https://github.com/monarch-initiative/ontogpt/pull/501
  • Improvements for the biotic interaction extraction template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/503
  • CLI cleanup by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/506
  • Refresh dependencies and update re: poetry dev group by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/508
  • Fix errors in CLI by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/509
  • Updates to MIC extraction template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/504
  • Bump version to 1.0.11 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/510

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.10...v1.0.11

- Jupyter Notebook
Published by caufieldjh 11 months ago

ontogpt - v1.0.10

What's Changed

  • Catch ValueError in SPIRES engine when returned value is empty in a single line by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/491
  • Add phenopacket extraction template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/484
  • Add codespell support (config, workflow to detect/not fix) and make it fix few typos by @yarikoptic in https://github.com/monarch-initiative/ontogpt/pull/493
  • Move codespell into main qc workflow by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/494
  • Build out MIC extraction template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/495
  • Prep for v1.0.10 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/496

New Contributors

  • @yarikoptic made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/493

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.9...v1.0.10

- Jupyter Notebook
Published by caufieldjh about 1 year ago

ontogpt - v1.0.9

What's Changed

  • Explicitly load key for groq when needed by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/486
  • Fix openapi key required for loading ollama models by @dnlbauer in https://github.com/monarch-initiative/ontogpt/pull/488
  • Prep for v1.0.9 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/489

New Contributors

  • @dnlbauer made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/488

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.8...v1.0.9

- Jupyter Notebook
Published by caufieldjh about 1 year ago

ontogpt - v1.0.8

What's Changed

  • Fix #475 - Handle templates without descriptions by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/476
  • Update dependency on python-multipart and fastapi by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/478
  • Expand test matrix to include Python 3.9 to 3.12 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/479
  • Add more error handling by catching specific litellm exceptions by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/481
  • Cleanup for v1.0.8 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/483

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.7...v1.0.8

- Jupyter Notebook
Published by caufieldjh over 1 year ago

ontogpt - v1.0.7

What's Changed

  • Add initial version of micronutrient extraction template (and other new templates) by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/469
  • Add --target-class option to web_extract command by @ptgolden in https://github.com/monarch-initiative/ontogpt/pull/470
  • Update pathology extraction template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/472
  • Prep for v1.0.7 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/473

New Contributors

  • @ptgolden made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/470

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.6...v1.0.7

- Jupyter Notebook
Published by caufieldjh over 1 year ago

ontogpt - v1.0.6

What's Changed

  • More updates for pathology report extraction by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/461
  • Add BioEPIC demo notebook by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/463
  • Provide spans of named entities by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/464

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.5...v1.0.6

- Jupyter Notebook
Published by caufieldjh over 1 year ago

ontogpt - v1.0.5

What's Changed

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

New Contributors

  • @gkreder made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/459

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.4...v1.0.5

- Jupyter Notebook
Published by caufieldjh over 1 year ago

ontogpt - v1.0.4

What's Changed

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

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.3...v1.0.4

- Jupyter Notebook
Published by caufieldjh over 1 year ago

ontogpt - v1.0.3

What's Changed

  • Add template for MIRO checklist extraction by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/432
  • Add caching for mapper by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/433
  • Prep for v1.0.3 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/434

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.2...v1.0.3

- Jupyter Notebook
Published by caufieldjh over 1 year ago

ontogpt - v1.0.2

What's Changed

  • Added CSV exporter by @timalamenciak in https://github.com/monarch-initiative/ontogpt/pull/426
  • Handle HTTP 500 errors with PubmedClient by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/428
  • Move eliminate_empty function into utils by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/429
  • Replace textract with pymupdf by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/430
  • Prep for V1.0.2 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/431

New Contributors

  • @timalamenciak made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/426

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.1...v1.0.2

- Jupyter Notebook
Published by caufieldjh over 1 year ago

ontogpt - v1.0.1

What's Changed

  • Add docs section on OpenAI-compatible Proxy Servers by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/419
  • Partial fix for #417 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/422
  • Add JSON writer by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/423
  • Updates for v1.0.1 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/424

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.0...v1.0.1

- Jupyter Notebook
Published by caufieldjh over 1 year ago

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

New Contributors

  • @leokim-l made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/415

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.15...v1.0.0

- Jupyter Notebook
Published by caufieldjh over 1 year ago

ontogpt - v1.0.0rc2

What's Changed

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

New Contributors

  • @leokim-l made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/415

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v1.0.0rc1...v1.0.0rc2

- Jupyter Notebook
Published by caufieldjh over 1 year ago

ontogpt - 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 https://github.com/monarch-initiative/ontogpt/pull/394
  • Add template for summarizing LinkML data validation reports by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/400
  • Improvements for the alzrd template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/399
  • Further updates to the ADRD extraction template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/403
  • Restructure Alz extraction template; split into two variants by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/405
  • Additional updates to the Alzheimers extraction template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/406
  • Fix issue with early termination of multilanguage analysis runs by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/408
  • Add support for more models by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/373
  • Tests for new LLMClient by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/410
  • General cleanup: docs, code optimization, and project structure by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/411

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.15...v1.0.0rc1

- Jupyter Notebook
Published by caufieldjh over 1 year ago

ontogpt - v0.3.15

Highlights

  • Four new templates: alz_treat, gene_extraction, storms, and onto_usage - see below for more details.
  • The pubmed-extract and pubmed-annotate commands now allow setting the text segment size (in number of characters) with the max-text-length option. Many LLMs now allow for large contexts, so set this to 100000 or so to parse the full text of a scientific article (along with the --get-pmc option).
    • Example: ontogpt -vvv pubmed-annotate -t storms --get-pmc --model gpt-4o --limit 1 --max-text-length 100000 -o storms_test.yaml "36598999"

What's Changed

  • Add template for alternate gene symbol extraction strategy by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/390
  • Template for Alzheimer's Disease extractions from literature; expose the max-text-length option for pubmed_annotate by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/392
  • Add ontology usage extraction template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/393
  • Fixes #396 by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/397
  • Adding STORMS checklist by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/395
  • Bump version to 0.3.15 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/398

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.14...v0.3.15

- Jupyter Notebook
Published by caufieldjh over 1 year ago

ontogpt - v0.3.14

What's Changed

  • Add custom template loader by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/388
    • Custom templates in yaml may now be passed directly to ontogpt commands - no make needed.
  • Updates for docs by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/389

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.13...v0.3.14

- Jupyter Notebook
Published by caufieldjh over 1 year ago

ontogpt - v0.3.13

What's Changed

  • Include only input-relevant named entities when producing output by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/382
  • More webapp updates - more models and all templates by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/385
  • Add notebook with two quick CLI and webapp examples by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/386

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.12...v0.3.13

- Jupyter Notebook
Published by caufieldjh over 1 year ago

ontogpt - v0.3.12

What's Changed

  • Part of a process for evaluating model performance in multi-language prompt situations.
    • Multilanguage gpt by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/369
    • Started on command extractcasereport_info() by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/141
    • Ground multilingual to MONDO only by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/372
  • Much-needed updates for the demo webapp.
    • Updates for the webapp by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/375
    • More fixes for the webapp by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/377
  • Add support for gpt-4o by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/378
  • Update options for embedding models by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/380

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.11...v0.3.12

- Jupyter Notebook
Published by caufieldjh almost 2 years ago

ontogpt - v0.3.11

What's Changed

  • Add template suggestion command by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/365
  • Update default model for OpenAI to gpt-4-turbo by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/366
  • Documentation updates, mostly to the README

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.10...v0.3.11

- Jupyter Notebook
Published by caufieldjh almost 2 years ago

ontogpt - v0.3.10

What's Changed

  • Functions to parse YAML output to KGX-compliant CSV by @serenalotreck in https://github.com/monarch-initiative/ontogpt/pull/349
  • Debug relation formatting in csv_wrapper by @serenalotreck in https://github.com/monarch-initiative/ontogpt/pull/354
  • Make azuresettings import conditional on using the azureselect flag by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/359
  • Fixes for #355 - more parsing for KGX output by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/360
  • Expand the MAXO annotation extraction schema by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/283

New Contributors

  • @serenalotreck made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/349

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.9...v0.3.10

- Jupyter Notebook
Published by caufieldjh almost 2 years ago

ontogpt - v0.3.9

What's Changed

  • Add new OpenAI model endpoints by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/331
  • Further updates to dietitian notes extraction schema by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/335
  • Add rdf to prefixes on templates to avoid extra warnings by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/339
  • Update citation metadata for repository by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/341
  • Further updates to dietitian notes schema to restructure nutritional support extraction by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/342
  • add azure openai api support to ontogpt by @k-bandi in https://github.com/monarch-initiative/ontogpt/pull/322
  • Repair synonym and diagnose functions by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/345
  • General cleanup; bump version to 0.3.9 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/350

New Contributors

  • @k-bandi made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/322

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.8...v0.3.9

- Jupyter Notebook
Published by caufieldjh almost 2 years ago

ontogpt - v0.3.8

Highlights

Try out ontogpt list-templates to see all the available extraction templates, including the new datasheetsschema and updated clinical dietitian notes schema.

What's Changed

  • Updates for dietitian notes extraction by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/313
  • Add datasheetsschema template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/310
  • Add further context to dietitian notes schema by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/319
  • Add list-templates command by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/326
  • Fix for errors on OWL write by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/327
  • Update prefixes defined in schemas by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/328
  • Version changes for v0.3.8 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/329

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.7...v0.3.8

- Jupyter Notebook
Published by caufieldjh about 2 years ago

ontogpt - v0.3.7

What's Changed

  • Documentation updates by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/302
  • First draft of dietician notes extraction schema by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/288
  • Dentin dysplasia by @sierra-moxon in https://github.com/monarch-initiative/ontogpt/pull/187
  • Testing figures template. by @balhoff in https://github.com/monarch-initiative/ontogpt/pull/171
  • Start on kidney template by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/150
  • Try extraction to nmdc-schema by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/148
  • Rebuild all templates by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/303
  • Enable running extractions on all files in a directory by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/304
  • Remove TALISMAN functions by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/309
  • Restructure SPIRESEngine to accomodate abstract model by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/306

New Contributors

  • @balhoff made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/171

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.6...v0.3.7

- Jupyter Notebook
Published by caufieldjh about 2 years ago

ontogpt - v0.3.6

What's Changed

  • Make introspection pydantic v2 compatible, fixes #294 by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/295
  • Add three simple extraction templates by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/296
  • Create draft template for extracting metadata to Datasheets by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/231
  • Use correct pydantic-version parameter with gen-pydantic by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/299
  • Dependency updates; bump version to 0.3.6 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/300

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.5...v0.3.6

- Jupyter Notebook
Published by caufieldjh about 2 years ago

ontogpt - v0.3.5

Minor updates plus new templates for Gene Ontology term extraction (go_terms and go_terms_relational).

What's Changed

  • Add section to docs on starting with OWL by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/274
  • Expand docs re: OWL templating by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/286
  • Added links to a tutorial and a presentation about OntoGPT and CurateGPT by @nlharris in https://github.com/monarch-initiative/ontogpt/pull/285
  • Proposing main OntoGPT logo by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/275
  • Add GO terms extraction templates by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/292
  • Bump version and update lockfile by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/293

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.4...v0.3.5

- Jupyter Notebook
Published by caufieldjh about 2 years ago

ontogpt - v0.3.4

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

- Jupyter Notebook
Published by caufieldjh over 2 years ago

ontogpt - v0.3.3

This version includes a bugfix, an updated OpenAI model list, and more clearly delineated documents in YAML output. See more details below!

What's Changed

  • Replace deprecated OpenAI models by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/210
  • Tidy up the CLI's write_extraction function by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/213
  • Fix for #215 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/216

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.2...v0.3.3

- Jupyter Notebook
Published by caufieldjh over 2 years ago

ontogpt - v0.3.2

This release primarily concerns bugfixes. Thanks to all users who have provided feedback!

What's Changed

  • Add option to show prompt by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/183
  • Quick fix for type mismatch in embed command by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/185
  • Updates for pydantic 2 compatibility by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/189
  • Repairs for incorrect model specification by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/192
  • Add SPIRES logo by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/196
  • Improve intro based on more up-to-date main/docs/index.md by @nlharris in https://github.com/monarch-initiative/ontogpt/pull/194
  • Fixed bug where named arguments did not match up in recurse function. by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/198
  • adding more prompts and example text to improve results by @diatomsRcool in https://github.com/monarch-initiative/ontogpt/pull/116
  • Address errors in using gene requests cache by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/203
  • Make kgx tsv by @hrshdhgd in https://github.com/monarch-initiative/ontogpt/pull/149
  • Fix #204 and the remainder of the HPOA evaluation by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/207
  • Run mypy through tox and address type check errors by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/202

New Contributors

  • @nlharris made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/194

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.3.1...v0.3.2

- Jupyter Notebook
Published by caufieldjh over 2 years ago

ontogpt - 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 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...v0.3.1

- Jupyter Notebook
Published by caufieldjh over 2 years ago

ontogpt - v0.3.0

Highlights

Generate-and-Extract Command

This release adds a new command generate-extract that composes two operations.

  • generate a natural language description
  • parse the NL description using SPIRES

Cell Type Use Case

(This use case based on a conversation with @dosumis)

For example, given a cell type such as Acinar Cell Of Salivary Gland , generate a description using GPT describing many aspects of the cell type, from it's marker genes through to its function and diseases it is implicated in.

After that use the cell-type schema (https://w3id.org/ontogpt/cell_type) to extract this into structured form. As an optional next step use linkml-owl to generate OWL TBox axioms

Iterative generate-extract

The command can be executed in iterative mode - this will traverse the extracted subtypes with each iteration, gradually building up an ontology that is entirely generated from the "latent knowledge" in the LLM

Here is a screenshot of an ontology generated entirely using OntoGPT by traversing from "Interneuron" downwards:

image

There are many oddities about it, currently each iteration is independent so it has no way of knowing if it is has already made a concept, but an interesting proof of principle. The ugly pct-encoded labels indicate cases where it couldn't match to an existing concept in CL or other ontology, and may represent KB gaps to be filled

More thoughts here: cell type summaries

What's Changed

  • Playing around: adding a phenotype extractor by @matentzn in https://github.com/monarch-initiative/ontogpt/pull/14
  • add unit test to makefile by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/16
  • Linted and minor flake8 edits by @hrshdhgd in https://github.com/monarch-initiative/ontogpt/pull/15
  • Add linter to workflow by @hrshdhgd in https://github.com/monarch-initiative/ontogpt/pull/17
  • Improve dependencies, add a web optional by @vemonet in https://github.com/monarch-initiative/ontogpt/pull/21
  • add recipe for test by @sierra-moxon in https://github.com/monarch-initiative/ontogpt/pull/23
  • added pad krapow recipe by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/25
  • Add recipe URL by @pkalita-lbl in https://github.com/monarch-initiative/ontogpt/pull/24
  • Add Walforf Salad URL by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/26
  • Add rajma pulao to recipe-urls.csv by @turbomam in https://github.com/monarch-initiative/ontogpt/pull/27
  • Adding gene set enrichment by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/30
  • enrichment by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/31
  • README updates; add project.Makefile by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/32
  • allow use of different models, entailing different API endpoints. extending enrichment comparison. by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/34
  • Add CITATION and version updater by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/35
  • Ingest and extract things from literature about inflammatory bowel disease by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/36
  • eval enrich by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/37
  • Create dental-restoration-material-composite-polymer-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/53
  • Create dental-restoration-material-composite-resin-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/52
  • Create dental-restoration-material-ceramic-composite-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/51
  • Create dental-restoration-material-ceramic-composite-resin-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/50
  • Create dental-restoration-material-ceramic-composite-polymer-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/49
  • Create dental-restoration-material-ceramic-composite-polymer-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/48
  • Create dental-restoration-material-ceramic-composite-polymer-resin-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/47
  • Create dental-restoration-material-ceramic-composite-polymer-resin-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/46
  • Create dental-restoration-material-composite-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/45
  • Create dental-restoration-material-composite-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/44
  • Create dental-restoration-material-polymer-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/42
  • Create dental-restoration-material-resin-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/41
  • Create dental-restoration-material-ceramic-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/39
  • Create dental-restoration-material-ceramic-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/38
  • Create dental-restoration-material-resin-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/40
  • Create dental-restoration-material-polymer-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/43
  • similarity by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/57
  • Add option to provide path to input file by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/56
  • Bicluster enrichment by @realmarcin in https://github.com/monarch-initiative/ontogpt/pull/62
  • Added command and code for computing euclidian distances between embeddings by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/58
  • Flake8 fixes + lint by @hrshdhgd in https://github.com/monarch-initiative/ontogpt/pull/63
  • enrichment changes by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/65
  • Missed parenthesis for random.SystemRamdom() by @hrshdhgd in https://github.com/monarch-initiative/ontogpt/pull/67
  • Change citation updater in Makefile to get_version by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/68
  • Raise FileNotFoundError if filepath for extract is missing by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/72
  • Makefile uses all templates by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/69
  • interactive-mode by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/71
  • Added command to generate mock clinical notes by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/74
  • Bump version of oaklib by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/73
  • msigdb hallmark gene sets by @realmarcin in https://github.com/monarch-initiative/ontogpt/pull/78
  • use prompts for enrichment by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/80
  • fixing gene sets and updating analysis by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/81
  • Adding schema for ontology issues in github. refactor enrichment by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/83
  • p-value templates with edited end markers to run multiple independent… by @realmarcin in https://github.com/monarch-initiative/ontogpt/pull/82
  • Add diagnostic_procedure template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/29
  • Fix for web-ontogpt not working on new install by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/85
  • geneweaver format by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/89
  • re-ran notebook by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/90
  • re-ran notebooks for enrichGPT by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/95
  • Update documentation by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/92
  • Autogenerate docs by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/98
  • Fix for doc generation by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/100
  • Added streamlit app for spindoctor by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/101
  • Study class as tree root in environment_sample template by @sujaypatil96 in https://github.com/monarch-initiative/ontogpt/pull/104
  • update sections in README by @sujaypatil96 in https://github.com/monarch-initiative/ontogpt/pull/105
  • Fixed a bug where the 'skip_annotators' option was being ignored by @daikiad in https://github.com/monarch-initiative/ontogpt/pull/108
  • first trait commits by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/109
  • first draft of biotic interaction template by @diatomsRcool in https://github.com/monarch-initiative/ontogpt/pull/107
  • One more fix for biotic interaction template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/113
  • Adding a GPT-based reasoner, for evaluation purposes. by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/112
  • more prompt language and adding ENVTHES ontology by @realmarcin in https://github.com/monarch-initiative/ontogpt/pull/118
  • Add general framework for specifying models by name and source by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/99
  • Adding a MappingEngine by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/121
  • removing importlib dependency by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/122
  • very small typo fix by @PR0CK0 in https://github.com/monarch-initiative/ontogpt/pull/124
  • Init environmental metadata template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/117
  • use latest rueaml. Avoids problems like this: https://github.com/monarch-initiative/enrichgpt-results/issues/4 by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/126
  • Add a command 'pubmed-annotate' to retrieve PMIDs for a search term, then apply a template to all of them to extract info by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/127
  • relaxing pinning by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/129
  • reasoner gpt changes by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/128
  • Retrieve remote models for local use and pass extract prompt to them by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/123
  • First pass at PhenoEngine by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/130
  • New PubMed eutil functions by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/131
  • Cleanup and documentation updates by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/115
  • Start of PR for IBD literature project by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/120
  • Fixes for #139 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/142
  • Add interface for HuggingFace Hub by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/145
  • Dependency updates by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/151
  • Adding generate-extract command, 158. Add cell type templates #159 by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/162
  • Removed temporary hack when generating documentation. Adding cell type to docs by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/163
  • Adding to cell/neuron template by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/164
  • Fix 157 - make webapp work, expand set of available data models by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/165
  • Add functionality for PubMed Central text retrieval by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/156
  • Improvements to iterative generate-extract. by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/166

New Contributors

  • @matentzn made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/14
  • @vemonet made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/21
  • @sierra-moxon made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/23
  • @justaddcoffee made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/25
  • @pkalita-lbl made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/24
  • @turbomam made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/27
  • @wdduncan made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/53
  • @sujaypatil96 made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/104
  • @daikiad made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/108
  • @diatomsRcool made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/107
  • @PR0CK0 made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/124

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.2.0...v0.3.0

- Jupyter Notebook
Published by cmungall over 2 years ago

ontogpt - v0.2.11

Highlights

  • Add a combined generate-extract command, fixes #158
  • Adds cell type templates, fixes #159

Generate-Extract

ontogpt generate-extract -m gpt-4 -t cell_type "Acinar Cell Of Salivary Gland"

This does two things

  1. asks GPT to generate a summary of the cell type
  2. parses/extracts knowledge from that cell type

This rescuscitates the original HALO idea. We could in principle directly generate an entire knowledgebase in structured form from the latent GPT KB

Example output:

yaml extracted_object: cell_type: Acinar cell of a salivary gland parents: - CL:0000066 subtypes: - CL:0000313 - CL:0000319 localizations: - UBERON:0001044 - UBERON:0009842 diseases: - AUTO:Sj%C3%B6gren%27s%20syndrome - MONDO:0021357 named_entities: - id: CL:0000066 label: Epithelial cell - id: CL:0000313 label: Serous cells - id: CL:0000319 label: Mucous cells - id: UBERON:0001044 label: Salivary gland - id: UBERON:0009842 label: Acinus - id: AUTO:Sj%C3%B6gren%27s%20syndrome label: Sjögren's syndrome - id: MONDO:0021357 label: Salivary gland tumors

Cell Type Templates

This PR also demonstrates using subclasses for more refined subtypes

Compare the two:

  1. ontogpt generate-extract -m gpt-4 -t cell_type "L2/3 Intratelencephalic Projecting Glutamatergic Neuron Of The Primary Motor Cortex"
  2. 1ontogpt generate-extract -m gpt-4 -t cell_type.InterneuronDocument "L2/3 Intratelencephalic Projecting Glutamatergic Neuron Of The Primary Motor Cortex"`

The first uses the generic base class. the second uses a subclass designed for interneurons, which has an extra slot for projection fields

Example output:

yaml extracted_object: cell_type: L2/3 Intratelencephalic Projecting Glutamatergic Neuron of the Primary Motor Cortex range: Not mentioned parents: - AUTO:excitatory%20neuron subtypes: - AUTO:Not%20mentioned localizations: - UBERON:0000956 - UBERON:0001384 genes: - AUTO:Not%20mentioned diseases: - MONDO:0005180 - MONDO:0020128 projects_to_or_from: - UBERON:0001893 named_entities: - id: UBERON:0001893 label: telencephalon - id: AUTO:excitatory%20neuron label: excitatory neuron - id: AUTO:Not%20mentioned label: Not mentioned - id: UBERON:0000956 label: cerebral cortex - id: UBERON:0001384 label: primary motor cortex - id: MONDO:0005180 label: Parkinson's disease - id: MONDO:0020128 label: motor neuron disease

What's Changed

  • Adding generate-extract command, 158. Add cell type templates #159 by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/162

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.2.10...v0.2.11

- Jupyter Notebook
Published by cmungall over 2 years ago

ontogpt - v0.2.10

What's Changed

  • very small typo fix by @PR0CK0 in https://github.com/monarch-initiative/ontogpt/pull/124
  • Init environmental metadata template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/117
  • use latest rueaml. Avoids problems like this: https://github.com/monarch-initiative/enrichgpt-results/issues/4 by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/126
  • Add a command 'pubmed-annotate' to retrieve PMIDs for a search term, then apply a template to all of them to extract info by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/127
  • relaxing pinning by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/129
  • reasoner gpt changes by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/128
  • Retrieve remote models for local use and pass extract prompt to them by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/123
  • First pass at PhenoEngine by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/130
  • New PubMed eutil functions by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/131
  • Cleanup and documentation updates by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/115
  • Start of PR for IBD literature project by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/120
  • Fixes for #139 by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/142
  • Add interface for HuggingFace Hub by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/145
  • Dependency updates by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/151

New Contributors

  • @PR0CK0 made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/124

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.2.9...v0.2.10

- Jupyter Notebook
Published by caufieldjh over 2 years ago

ontogpt - v0.2.9

What's Changed

  • removing importlib dependency by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/122

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.2.8...v0.2.9

- Jupyter Notebook
Published by cmungall over 2 years ago

ontogpt - v0.2.8

What's Changed

  • first draft of biotic interaction template by @diatomsRcool in https://github.com/monarch-initiative/ontogpt/pull/107
  • One more fix for biotic interaction template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/113
  • Adding a GPT-based reasoner, for evaluation purposes. by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/112
  • more prompt language and adding ENVTHES ontology by @realmarcin in https://github.com/monarch-initiative/ontogpt/pull/118
  • Add general framework for specifying models by name and source by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/99
  • Adding a MappingEngine by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/121

New Contributors

  • @diatomsRcool made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/107

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.2.7...v0.2.8

- Jupyter Notebook
Published by cmungall over 2 years ago

ontogpt - v0.2.7

What's Changed

  • Fixed a bug where the 'skip_annotators' option was being ignored by @daikiad in https://github.com/monarch-initiative/ontogpt/pull/108
  • Microbial trait template by @realmarcin in https://github.com/monarch-initiative/ontogpt/pull/109

New Contributors

  • @daikiad made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/108

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.2.6...v0.2.7

- Jupyter Notebook
Published by cmungall almost 3 years ago

ontogpt - v0.2.6

What's Changed

  • Added streamlit app for spindoctor by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/101
  • Study class as tree root in environment_sample template by @sujaypatil96 in https://github.com/monarch-initiative/ontogpt/pull/104
  • update sections in README by @sujaypatil96 in https://github.com/monarch-initiative/ontogpt/pull/105

New Contributors

  • @sujaypatil96 made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/104

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.2.5...v0.2.6

- Jupyter Notebook
Published by cmungall almost 3 years ago

ontogpt - v0.2.5

What's Changed

  • Add diagnostic_procedure template by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/29
  • Fix for web-ontogpt not working on new install by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/85
  • geneweaver format by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/89
  • re-ran notebook by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/90
  • re-ran notebooks for enrichGPT by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/95
  • Update documentation by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/92
  • Autogenerate docs by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/98
  • Fix for doc generation by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/100

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.2.4...v0.2.5

- Jupyter Notebook
Published by cmungall almost 3 years ago

ontogpt - v0.2.4

What's Changed

  • Adding schema for ontology issues in github. refactor enrichment by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/83
  • p-value templates with edited end markers to run multiple independent… by @realmarcin in https://github.com/monarch-initiative/ontogpt/pull/82

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.2.3...v0.2.4

- Jupyter Notebook
Published by cmungall almost 3 years ago

ontogpt - v0.2.3

What's Changed

  • Added command to generate mock clinical notes by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/74
  • Bump version of oaklib by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/73
  • msigdb hallmark gene sets by @realmarcin in https://github.com/monarch-initiative/ontogpt/pull/78
  • use prompts for enrichment by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/80
  • fixing gene sets and updating analysis by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/81

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.2.2...v0.2.3

- Jupyter Notebook
Published by cmungall almost 3 years ago

ontogpt - v0.2.2

What's Changed

  • Adding gene set enrichment by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/30
  • enrichment by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/31
  • README updates; add project.Makefile by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/32
  • allow use of different models, entailing different API endpoints. extending enrichment comparison. by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/34
  • Add CITATION and version updater by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/35
  • Ingest and extract things from literature about inflammatory bowel disease by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/36
  • eval enrich by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/37
  • Create dental-restoration-material-composite-polymer-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/53
  • Create dental-restoration-material-composite-resin-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/52
  • Create dental-restoration-material-ceramic-composite-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/51
  • Create dental-restoration-material-ceramic-composite-resin-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/50
  • Create dental-restoration-material-ceramic-composite-polymer-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/49
  • Create dental-restoration-material-ceramic-composite-polymer-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/48
  • Create dental-restoration-material-ceramic-composite-polymer-resin-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/47
  • Create dental-restoration-material-ceramic-composite-polymer-resin-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/46
  • Create dental-restoration-material-composite-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/45
  • Create dental-restoration-material-composite-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/44
  • Create dental-restoration-material-polymer-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/42
  • Create dental-restoration-material-resin-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/41
  • Create dental-restoration-material-ceramic-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/39
  • Create dental-restoration-material-ceramic-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/38
  • Create dental-restoration-material-resin-1.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/40
  • Create dental-restoration-material-polymer-2.txt by @wdduncan in https://github.com/monarch-initiative/ontogpt/pull/43
  • similarity by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/57
  • Add option to provide path to input file by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/56
  • Bicluster enrichment by @realmarcin in https://github.com/monarch-initiative/ontogpt/pull/62
  • Added command and code for computing euclidian distances between embeddings by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/58
  • Flake8 fixes + lint by @hrshdhgd in https://github.com/monarch-initiative/ontogpt/pull/63
  • enrichment changes by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/65
  • Missed parenthesis for random.SystemRamdom() by @hrshdhgd in https://github.com/monarch-initiative/ontogpt/pull/67
  • Change citation updater in Makefile to get_version by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/68
  • Raise FileNotFoundError if filepath for extract is missing by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/72
  • Makefile uses all templates by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/69
  • interactive-mode by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/71

New Contributors

  • @wdduncan made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/53

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.2.1...v0.2.2

- Jupyter Notebook
Published by cmungall almost 3 years ago

ontogpt - v0.2.1

What's Changed

  • Playing around: adding a phenotype extractor by @matentzn in https://github.com/monarch-initiative/ontogpt/pull/14
  • add unit test to makefile by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/16
  • Linted and minor flake8 edits by @hrshdhgd in https://github.com/monarch-initiative/ontogpt/pull/15
  • Add linter to workflow by @hrshdhgd in https://github.com/monarch-initiative/ontogpt/pull/17
  • Improve dependencies, add a web optional by @vemonet in https://github.com/monarch-initiative/ontogpt/pull/21
  • add recipe for test by @sierra-moxon in https://github.com/monarch-initiative/ontogpt/pull/23
  • added pad krapow recipe by @justaddcoffee in https://github.com/monarch-initiative/ontogpt/pull/25
  • Add recipe URL by @pkalita-lbl in https://github.com/monarch-initiative/ontogpt/pull/24
  • Add Walforf Salad URL by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/26
  • Add rajma pulao to recipe-urls.csv by @turbomam in https://github.com/monarch-initiative/ontogpt/pull/27

New Contributors

  • @matentzn made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/14
  • @vemonet made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/21
  • @sierra-moxon made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/23
  • @justaddcoffee made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/25
  • @pkalita-lbl made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/24
  • @turbomam made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/27

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.2.0...v0.2.1

- Jupyter Notebook
Published by cmungall almost 3 years ago

ontogpt - v0.2.0

What's Changed

  • If output is YAML, codecs not needed by @hrshdhgd in https://github.com/monarch-initiative/ontogpt/pull/1
  • Readme updates and other doc copyedits by @caufieldjh in https://github.com/monarch-initiative/ontogpt/pull/2
  • owl generation by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/7
  • three cases for 'environmental_sample' by @realmarcin in https://github.com/monarch-initiative/ontogpt/pull/8
  • Env study test cases by @realmarcin in https://github.com/monarch-initiative/ontogpt/pull/10
  • refactor tests by @cmungall in https://github.com/monarch-initiative/ontogpt/pull/12

New Contributors

  • @hrshdhgd made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/1
  • @caufieldjh made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/2
  • @cmungall made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/7
  • @realmarcin made their first contribution in https://github.com/monarch-initiative/ontogpt/pull/8

Full Changelog: https://github.com/monarch-initiative/ontogpt/compare/v0.1.0...v0.2.0

- Jupyter Notebook
Published by cmungall almost 3 years ago

ontogpt - v0.1.1

Full Changelog: https://github.com/monarch-initiative/ontogpt/commits/v0.1.1

- Jupyter Notebook
Published by hrshdhgd about 3 years ago

ontogpt - v0.1.0

Full Changelog: https://github.com/monarch-initiative/ontogpt/commits/v0.1.0

- Jupyter Notebook
Published by cmungall about 3 years ago