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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
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 annotationsI was not able to reproduce this error. check out my old models. CL/CG-Emacs models, better manual annotations, and if you find one, let me know, thanks d2c66b5586