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gpt-pheno-cr :: Phenotype concept recognition using GPT models

  • Main annotation and evaluation scripts can be accessed via experiments.py
  • Prerequisites - set the following constants to the appropriate values in Constants.py
    • OPENAI_ORG - OpenAI organization
    • OPENAI_KEY - OpenAI key
    • HPOGS_ANNOT_FOLDER - HPO-GS folder containing the annotations
    • HPOGS_TEXT_FOLDER - HPO-GS folder containing the text of the abstracts
    • BIOCGS_ANNOT_FOLDER- BIOC-GS folder containing the annotations
    • BIOCGS_TEXT_FOLDER - BIOC-GS folder containing the text for the clinical observations
  • Both the annotation and evaluation scripts will also require a local copy of hp.obo
  • Resources (under resources) - the few-shot learning files used for experiments with Prompt 7