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Issachar Conference Group

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Jacob Taylor
Jacob Taylor

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Data annotationThe 1,073 full rare disease mention annotations (from 312 MIMIC-III discharge summaries) are in full_set_RD_ann_MIMIC_III_disch.csv. The 198 rare disease mention annotations (from 145 MIMIC-III radiology reports) are in test_set_RD_ann_MIMIC_III_rad.csv. Also, they are based on the output of SemEHR, which does not have 100% recall, so the annotations may not cover all rare diseases mentions from the sampled discharge summaries.* In row 323 from the full set or the validation set, the mention nph is not in the document structure (due to error in mention extraction), thus the gold mention-to-UMLS label is -1. in the third sheet, distinct umls-ordo), and for validation - 1000 docs - ori - MIMIC-III-rad (free text removed, with predictions).xlsx (annotations starting from column Z), show the raw annotations




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