Issues

• Feature: ground entity-quality traits to UPHENO by post-composition instead of whole-text match

  enhancement
  monarch-initiative/ontogpt#565 · Filter by author caufieldjh opened on Sep 9, 2026
  1

• Agent Skills: ontology guide lacks UPHENO and the VBO species-suffix rule

  documentation
  monarch-initiative/ontogpt#564 · Filter by author caufieldjh opened on Sep 9, 2026
  1

• Agent Skills: template catalog marks six grounded templates as "ungrounded"

  documentation
  monarch-initiative/ontogpt#563 · Filter by author caufieldjh opened on Sep 9, 2026

• KeyError: 'max_tokens' when running ontogpt list-models

  monarch-initiative/ontogpt#543 · Filter by author jinzhang6688 opened on Nov 17, 2025

• Connect OntoGPT to OpenAI DeepSearch

  monarch-initiative/ontogpt#539 · Filter by author caufieldjh opened on Sep 18, 2025

• How to run in debug mode or how can I get library logs?

  monarch-initiative/ontogpt#531 · Filter by author shivshankarkeshari opened on Aug 6, 2025
  1

• Why I am getting single entity

  monarch-initiative/ontogpt#528 · Filter by author shivshankarkeshari opened on Jul 29, 2025
  1

• Add HPOA extraction template

  template
  monarch-initiative/ontogpt#513 · Filter by author caufieldjh opened on Apr 8, 2025

• Need some guidance on constructing schema

  annotation
  monarch-initiative/ontogpt#512 · Filter by author lzt5269 opened on Apr 2, 2025
  1

• Produce extraction template for Croissant metadata

  monarch-initiative/ontogpt#500 · Filter by author caufieldjh opened on Jan 23, 2025

• Support for a list of urls for web-extract

  monarch-initiative/ontogpt#499 · Filter by author kevinschaper opened on Jan 17, 2025

• odd column values in kgx tsv

  monarch-initiative/ontogpt#498 · Filter by author kevinschaper opened on Jan 17, 2025
  1

• Error using --system-message with LLM (Mistral)

  monarch-initiative/ontogpt#490 · Filter by author mcisneiros opened on Dec 11, 2024
  2

• This error originates from a subprocess

  bug
  monarch-initiative/ontogpt#474 · Filter by author SaraNiknamHesar opened on Nov 10, 2024
  13

• Using OntoGPT outside BioInformatics

  questiontemplate
  monarch-initiative/ontogpt#471 · Filter by author jamesfebin opened on Nov 8, 2024
  6

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

  enhancement
  monarch-initiative/ontogpt#466 · Filter by author caufieldjh opened on Oct 25, 2024

• Add error flag for extracted objects

  enhancement
  monarch-initiative/ontogpt#456 · Filter by author caufieldjh opened on Sep 18, 2024

• Do not cache fully empty responses

  enhancement
  monarch-initiative/ontogpt#455 · Filter by author caufieldjh opened on Sep 18, 2024

• TALISMAN: update to work with non-OpenAI models

  monarch-initiative/ontogpt#450 · Filter by author caufieldjh opened on Sep 6, 2024

• Add parser for dataframes

  enhancement
  monarch-initiative/ontogpt#446 · Filter by author caufieldjh opened on Aug 26, 2024

• Support including system messages in templates

  enhancement
  monarch-initiative/ontogpt#436 · Filter by author caufieldjh opened on Aug 13, 2024

• Make missing API key errors more friendly

  enhancement
  monarch-initiative/ontogpt#368 · Filter by author caufieldjh opened on Apr 29, 2024

• Add grounding refiner option for SPIRES

  enhancement
  monarch-initiative/ontogpt#361 · Filter by author caufieldjh opened on Apr 1, 2024

• Followup on #353 - support including annotations in schemas to model KGX output

  enhancement
  monarch-initiative/ontogpt#356 · Filter by author caufieldjh opened on Mar 26, 2024
  1

• Best way to apply on large quantities of documents?

  monarch-initiative/ontogpt#352 · Filter by author serenalotreck opened on Mar 22, 2024
  19