ontogpt

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This extraction process should collect cell types when possible. See https://github.com/monarch-initiative/ontogpt/blob/6ebe777007459390f18ae6d26596974ba65dcf66/src/ontogpt/templates/kidney.yaml

caufieldjh

Add ability to pass in synonymizer rules

1

@realmarcin can direct when running the betacat case it doesn't match "protein kinase" - need to add activity

cmungall

About ERROR:ontogpt.engines.knowledge_engine:Error with GildaImplementation

1

Hello @cmungall, I was able to install ontogpt after adjusting dependencies using poetry. I was trying to run the example your readme, i.e. ``` kih1pal@SYV-C-0001Y:~/ontogpt$ poetry run ontogpt extract -t...

yy20716

I initially set up the HF Hub interface to only work with a pre-established set of models (those defined in `models.yaml`). This was built on the assumption that some models...

caufieldjh

HF models may be accessed through their API, as implemented in #145 , but it's prone to timeouts when using larger models (which is unfortunate, since those are the ones...

caufieldjh

Given a table in a PDF (or text) of a clinical case report, we would like to be able to do the following. 1. Extract variable names, reference ranges (if...

caufieldjh

Add interface for abstract OpenAI-equivalent API

3

From #70: > Currently, I cannot use ontoGPT in my organization as it is due to security concerns around external APIs like OpenAI's. To address this issue, I suggest exploring...

caufieldjh

Template for extraction of knowledge from literature to go into RNA KG (Marco, Emanuele, and friends)

justaddcoffee

See #132

cmungall

mapping a string span in a document to a partially overlapping term label is too risky

1

In the 2023-05-17 EGSB microbial traits hackaton, we found many cases where a text in the input text was mapped to the ENVTHES ontology, based on a partial overlap. Like...

turbomam