monarch-initiative/ontogpt

Issues

• web-ontogpt requires `python-multipart`

  #477 opened 7 days ago by caufieldjh
  0

• web-ontogpt raises KeyError

  #475 opened 7 days ago by caufieldjh
  1

• This error originates from a subprocess

  #474 opened 9 days ago by SaraNiknamHesar
  12

• Using OntoGPT outside BioInformatics

  #471 opened 12 days ago by jamesfebin
  6

• Support including system messages in templates

  #436 opened 3 months ago by caufieldjh
  0

• Don't raise errors when attempting to parse "accessory" text

  #466 opened 25 days ago by caufieldjh
  0

• Add error flag for extracted objects

  #456 opened 2 months ago by caufieldjh
  0

• Do not cache fully empty responses

  #455 opened 2 months ago by caufieldjh
  0

• Better catching of HTTP 401 errors

  #443 opened 3 months ago by caufieldjh
  2

• Add parser for dataframes

  #446 opened 3 months ago by caufieldjh
  0

• Remove Unicode control characters

  #454 opened 2 months ago by caufieldjh
  0

• Test on Python 3.11 to 3.13

  #467 opened 23 days ago by caufieldjh
  0

• `web_extract` is missing target class argument

  #468 opened 14 days ago by ptgolden
  0

• Lots of NewConnectionErrors when grounding with SPIRES

  #457 opened a month ago by justaddcoffee
  2

• Enable including spans of extracted entities

  #462 opened a month ago by caufieldjh
  0

• Remove hardcoded values and references to GPT-3.5-turbo models

  #451 opened 2 months ago by caufieldjh
  0

• TALISMAN: update to work with non-OpenAI models

  #450 opened 2 months ago by caufieldjh
  0

• Logspam from litellm: `Provider List: https://docs.litellm.ai/docs/providers`

  #445 opened 3 months ago by caufieldjh
  1

• Update output options for multilingual analysis

  #438 opened 3 months ago by caufieldjh
  1

• How to customize or configure prompts for languages other than English?

  #440 opened 3 months ago by fishfree
  4

• can't build poetry environment because can't install dependency torch 2.4.0

  #439 opened 3 months ago by turbomam
  1

• Add caching for mapper

  #363 opened 3 months ago by caufieldjh
  0

• Add extraction template for MIRO checklist

  #362 opened 3 months ago by caufieldjh
  0

• HugginFace API + UnboundLocalError: local variable 'results' referenced before assignment

  #404 opened 3 months ago by SimoneAstarita
  4

• Issue parsing PDFs - UnicodeDecodeError: 'charmap' codec can't decode byte 0x8f in position 4422: character maps to <undefined>

  #417 opened 4 months ago by timalamenciak
  5

• Replace `textract` with `PyMuPDF`

  #421 opened 3 months ago by caufieldjh
  0

• Combine the `eliminate_empty` function in the YAML and JSON writers

  #425 opened 3 months ago by caufieldjh
  0

• Pubmed search fails due to `KeyError` when encountering 500 errors

  #427 opened 3 months ago by caufieldjh
  0

• NCIT Mapping error

  #414 opened 4 months ago by pbuendia
  1

• OntoGPT is exporting YAML even with JSON flag

  #420 opened 4 months ago by timalamenciak
  1

• Transient errors with Translator endpoint

  #370 opened 4 months ago by caufieldjh
  2

• Broken links in documentation

  #367 opened 4 months ago by caufieldjh
  0

• Enable omitting or truncating input text in output

  #401 opened 4 months ago by caufieldjh
  0

• Textract plugin fails to install

  #412 opened 4 months ago by timalamenciak
  3

• ModuleNotFoundError: No module named 'ontogpt.templates.fairlyz_study'

  #409 opened 4 months ago by pbuendia
  2

• Make missing API key errors more friendly

  #368 opened 7 months ago by caufieldjh
  0

• Add grounding refiner option for SPIRES

  #361 opened 8 months ago by caufieldjh
  0

• OpenAI base URL

  #371 opened 4 months ago by syaikhipin
  2

• Remove redundant calls to normalize cached objects

  #402 opened 4 months ago by caufieldjh
  1

• ERROR: Could not build wheels for adeft, which is required to install pyproject.toml-based projects

  #387 opened 4 months ago by konashevich
  3

• Fewer results than expected when running ontogpt run_multilingual_analysis

  #407 opened 4 months ago by justaddcoffee
  5

• Failure to parse markdown formatting leads to errors

  #391 opened 5 months ago by caufieldjh
  1

• pubmed-extract no longer works?

  #396 opened 5 months ago by cmungall
  0

• Running web-ontogpt yeilds an "Internal Server Error"

  #374 opened 6 months ago by ddooley
  15

• Make it easier to use custom schemas

  #384 opened 6 months ago by vemonet
  3

• UnboundLocalError: local variable 'normalized_id' referenced before assignment

  #383 opened 6 months ago by caufieldjh
  1

• gpt-4o

  #376 opened 6 months ago by rkboyce
  3

• Update options for embedding models

  #379 opened 6 months ago by caufieldjh
  0

• Update default model for OpenAI

  #364 opened 7 months ago by caufieldjh
  1

• Add template suggestion command

  #358 opened 7 months ago by caufieldjh
  0