├── 0_pipeline.py ├── 1_extract_terms.py ├── 2_extract_more_terms.py ├── 3_extract_entities.py ├── 4_extract_relations.py ├── 5_align_entities.py ├── 5_calibrate_entities.py ├── 6_align_entities.py ├── 6_construct_KG.py ├── 7_construct_KG.py ├── LLM_baseline ├── data │ └── RareDis2023 │ │ ├── 0.txt │ │ ├── test.jsonl │ │ ├── train.jsonl │ │ └── valid.jsonl ├── env.py ├── main.py ├── prompt.py └── utils.py ├── README.md ├── cache_data ├── 0.txt ├── step1_res.jsonl ├── step2_res.jsonl ├── step3_res.jsonl ├── step4_res.jsonl ├── step5_res.jsonl └── step6_res.jsonl ├── data └── RareDis2023 │ └── 0.txt ├── data_preprocessing ├── data │ ├── RareDis-fixed │ │ └── fix_data.py │ ├── RareDis-v1 │ │ └── 0.txt │ └── RareDis2023 │ │ └── 0.txt ├── generate_data.py ├── parse_HOOM.py ├── parse_ORDO.py ├── parse_mondo_obo.py ├── statistic.py └── statistic_2.py ├── env.py ├── finetuning_baseline ├── data │ └── RareDis2023 │ │ └── 0.txt ├── dataloader.py ├── main.py ├── network.py └── utils.py ├── 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