Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / monarch-initiative/ontogpt issues and pull requests

#502 - `UserWarning` from pydantic about `fields`

Issue - State: open - Opened by caufieldjh 17 days ago

#501 - draft schemas for table extraction

Pull Request - State: closed - Opened by realmarcin 28 days ago

#499 - Support for a list of urls for web-extract

Issue - State: open - Opened by kevinschaper about 1 month ago

#498 - odd column values in kgx tsv

Issue - State: open - Opened by kevinschaper about 1 month ago - 1 comment

#497 - persistent Incorrect API key error

Issue - State: closed - Opened by aschimmenti about 1 month ago - 3 comments

#496 - Prep for v1.0.10

Pull Request - State: closed - Opened by caufieldjh 2 months ago

#495 - Build out MIC extraction template

Pull Request - State: closed - Opened by caufieldjh 2 months ago - 1 comment

#494 - Move codespell into main qc workflow

Pull Request - State: closed - Opened by caufieldjh 2 months ago

#490 - Error using --system-message with LLM (Mistral)

Issue - State: open - Opened by mcisneiros 2 months ago - 2 comments

#489 - Prep for v1.0.9

Pull Request - State: closed - Opened by caufieldjh 2 months ago

#488 - Fix openapi key required for loading ollama models

Pull Request - State: closed - Opened by dnlbauer 3 months ago - 1 comment

#487 - Using ollama/llama3 models fail when no openapi key is set

Issue - State: closed - Opened by dnlbauer 3 months ago - 1 comment

#486 - Explicitly load key for groq when needed

Pull Request - State: closed - Opened by caufieldjh 3 months ago

#485 - Groq model via litellm: 'invalid_api_key' error

Issue - State: closed - Opened by emanuelecavalleri 3 months ago - 4 comments

#484 - Add phenopacket extraction template

Pull Request - State: closed - Opened by caufieldjh 3 months ago - 4 comments

#483 - Cleanup for v1.0.8

Pull Request - State: closed - Opened by caufieldjh 3 months ago

#482 - Add Phenopacket extraction template

Issue - State: closed - Opened by caufieldjh 3 months ago

#481 - Add more error handling by catching specific litellm exceptions

Pull Request - State: closed - Opened by caufieldjh 3 months ago

#480 - Test on Python 3.13

Issue - State: open - Opened by caufieldjh 3 months ago
Labels: bug, documentation

#479 - Expand test matrix to include Python 3.9 to 3.12

Pull Request - State: closed - Opened by caufieldjh 3 months ago - 9 comments

#478 - Update dependency on python-multipart and fastapi

Pull Request - State: closed - Opened by caufieldjh 3 months ago

#477 - web-ontogpt requires `python-multipart`

Issue - State: closed - Opened by caufieldjh 3 months ago

#476 - Fix #475 - Handle templates without descriptions

Pull Request - State: closed - Opened by caufieldjh 3 months ago - 1 comment

#475 - web-ontogpt raises KeyError

Issue - State: closed - Opened by caufieldjh 3 months ago - 1 comment

#474 - This error originates from a subprocess

Issue - State: open - Opened by SaraNiknamHesar 3 months ago - 13 comments
Labels: bug

#473 - Prep for v1.0.7

Pull Request - State: closed - Opened by caufieldjh 3 months ago

#472 - Update pathology extraction template

Pull Request - State: closed - Opened by caufieldjh 3 months ago

#471 - Using OntoGPT outside BioInformatics

Issue - State: open - Opened by jamesfebin 4 months ago - 6 comments
Labels: question, template

#470 - Add --target-class option to web_extract command

Pull Request - State: closed - Opened by ptgolden 4 months ago - 1 comment

#468 - `web_extract` is missing target class argument

Issue - State: closed - Opened by ptgolden 4 months ago

#467 - Test on Python 3.11 to 3.12

Issue - State: closed - Opened by caufieldjh 4 months ago
Labels: enhancement

#466 - Don't raise errors when attempting to parse "accessory" text

Issue - State: open - Opened by caufieldjh 4 months ago
Labels: enhancement

#465 - Do not cache fully empty completion responses or those with empty contents

Pull Request - State: open - Opened by caufieldjh 4 months ago - 2 comments

#464 - Provide spans of named entities

Pull Request - State: closed - Opened by caufieldjh 4 months ago

#463 - Add BioEPIC demo notebook

Pull Request - State: closed - Opened by caufieldjh 4 months ago

#462 - Enable including spans of extracted entities

Issue - State: closed - Opened by caufieldjh 5 months ago

#461 - More updates for pathology report extraction

Pull Request - State: closed - Opened by caufieldjh 5 months ago

#460 - Prep for v1.0.5

Pull Request - State: closed - Opened by caufieldjh 5 months ago

#459 - Removed `pydantic_version` keyword in template_loader.py

Pull Request - State: closed - Opened by gkreder 5 months ago - 1 comment

#458 - Remove hardcoded values and references to gpt-3.5-turbo models

Pull Request - State: closed - Opened by caufieldjh 5 months ago

#457 - Lots of NewConnectionErrors when grounding with SPIRES

Issue - State: closed - Opened by justaddcoffee 5 months ago - 2 comments

#456 - Add error flag for extracted objects

Issue - State: open - Opened by caufieldjh 5 months ago
Labels: enhancement

#455 - Do not cache fully empty responses

Issue - State: open - Opened by caufieldjh 5 months ago
Labels: enhancement

#454 - Remove Unicode control characters

Issue - State: open - Opened by caufieldjh 5 months ago
Labels: enhancement

#453 - Dependency updates and adaptations

Pull Request - State: closed - Opened by caufieldjh 5 months ago

#452 - Improvements for pathology report extractions

Pull Request - State: closed - Opened by caufieldjh 5 months ago

#450 - TALISMAN: update to work with non-OpenAI models

Issue - State: open - Opened by caufieldjh 6 months ago

#449 - Expand option to set token/context limit

Pull Request - State: closed - Opened by caufieldjh 6 months ago

#448 - Suppress litellm debug messages

Pull Request - State: closed - Opened by caufieldjh 6 months ago

#446 - Add parser for dataframes

Issue - State: open - Opened by caufieldjh 6 months ago
Labels: enhancement

#444 - Further development of the pathology extraction template

Pull Request - State: closed - Opened by caufieldjh 6 months ago

#443 - Better catching of HTTP 401 errors

Issue - State: closed - Opened by caufieldjh 6 months ago - 2 comments
Labels: enhancement

#442 - Update output options for multilingual analysis

Pull Request - State: closed - Opened by caufieldjh 6 months ago - 1 comment

#441 - Add new food extraction template

Pull Request - State: closed - Opened by caufieldjh 6 months ago - 1 comment

#440 - How to customize or configure prompts for languages other than English?

Issue - State: closed - Opened by fishfree 6 months ago - 4 comments
Labels: question

#438 - Update output options for multilingual analysis

Issue - State: closed - Opened by caufieldjh 6 months ago - 1 comment
Labels: enhancement

#437 - Add topic classifier

Pull Request - State: closed - Opened by caufieldjh 6 months ago

#436 - Support including system messages in templates

Issue - State: open - Opened by caufieldjh 6 months ago
Labels: enhancement

#435 - Add system-message command

Pull Request - State: closed - Opened by caufieldjh 6 months ago

#434 - Prep for v1.0.3

Pull Request - State: closed - Opened by caufieldjh 6 months ago

#433 - Add caching for mapper

Pull Request - State: closed - Opened by caufieldjh 6 months ago - 1 comment

#432 - Add template for MIRO checklist extraction

Pull Request - State: closed - Opened by caufieldjh 7 months ago

#431 - Prep for V1.0.2

Pull Request - State: closed - Opened by caufieldjh 7 months ago

#430 - Replace `textract` with `pymupdf`

Pull Request - State: closed - Opened by caufieldjh 7 months ago

#429 - Move eliminate_empty function into utils

Pull Request - State: closed - Opened by caufieldjh 7 months ago - 1 comment

#428 - Handle HTTP 500 errors with PubmedClient

Pull Request - State: closed - Opened by caufieldjh 7 months ago - 3 comments

#426 - Added CSV exporter

Pull Request - State: closed - Opened by timalamenciak 7 months ago - 3 comments

#424 - Updates for v1.0.1

Pull Request - State: closed - Opened by caufieldjh 7 months ago

#423 - Add JSON writer

Pull Request - State: closed - Opened by caufieldjh 7 months ago

#422 - Partial fix for #417

Pull Request - State: closed - Opened by caufieldjh 7 months ago

#421 - Replace `textract` with `PyMuPDF`

Issue - State: closed - Opened by caufieldjh 7 months ago
Labels: enhancement

#420 - OntoGPT is exporting YAML even with JSON flag

Issue - State: closed - Opened by timalamenciak 7 months ago - 1 comment

#419 - Add docs section on OpenAI-compatible Proxy Servers

Pull Request - State: closed - Opened by caufieldjh 7 months ago

#418 - Prep for v1.0.0 release

Pull Request - State: closed - Opened by caufieldjh 7 months ago

#416 - Misc changes for 1.0.0rc2

Pull Request - State: closed - Opened by caufieldjh 7 months ago

#415 - eliminate hardcoded gpt4-turbo from multilingual function

Pull Request - State: closed - Opened by leokim-l 7 months ago - 2 comments

#414 - NCIT Mapping error

Issue - State: closed - Opened by pbuendia 7 months ago - 1 comment
Labels: question, template

#413 - Add option to truncate input_text in outputs

Pull Request - State: closed - Opened by caufieldjh 7 months ago

#412 - Textract plugin fails to install

Issue - State: closed - Opened by timalamenciak 7 months ago - 3 comments

#411 - General cleanup: docs, code optimization, and project structure

Pull Request - State: closed - Opened by caufieldjh 7 months ago

#410 - Tests for new LLMClient

Pull Request - State: closed - Opened by caufieldjh 7 months ago

#409 - ModuleNotFoundError: No module named 'ontogpt.templates.fairlyz_study'

Issue - State: closed - Opened by pbuendia 7 months ago - 2 comments
Labels: bug

#408 - Fix issue with early termination of multilanguage analysis runs

Pull Request - State: closed - Opened by caufieldjh 8 months ago

#406 - Additional updates to the Alzheimers extraction template

Pull Request - State: closed - Opened by caufieldjh 8 months ago

#405 - Restructure Alz extraction template; split into two variants

Pull Request - State: closed - Opened by caufieldjh 8 months ago

#403 - Further updates to the ADRD extraction template

Pull Request - State: closed - Opened by caufieldjh 8 months ago