Hello, In comparing the results in file Annotated-table-125230.330453.json, we noticed that the column "Extrnodl_Diss_Involvmnt_Antomic_Sit" was assigned CDE ID 3153874 However, our software assigned it ID 3288482. Is there any specific reason why 3153874 was picked over 3288482? I've copied the contents of the two CDE's below. Thanks! ========3153874========= {'cde_long_name': 'Extranodal Disease Involvement Anatomic Site', 'cde_name': 'Extranodal Disease Involvement Anatomic Site', 'dec_id': 2952457, 'object_class_concepts': 'ncit:C25504|ncit:C25548', 'property_concepts': 'ncit:C13717', 'value_domain_type': 'Enumerated', 'datatype': 'CHARACTER', 'permissible_values': 'Ovary\\Ovary\\ncit:C12404|Intestine\\Small and Large Intestine\\ncit:C12736|Oropharynx\\Oropharynx\\ncit:C12762|Bone\\Bone\\ncit:C12366|Breast\\Breast\\ncit:C12971|Liver\\Liver\\ncit:C12392|Bone Marrow\\Bone Marrow\\ncit:C12431|Lung\\Lung\\ncit:C12468|Central Nervous System\\Central Nervous System\\ncit:C12438|Other\\Other\\ncit:C17649', 'cde_id': 3153874} ===========3288482============== {'cde_long_name': 'Extranodal Disease Involvement Anatomic Site', 'cde_name': 'Extranodal Disease Involvement Anatomic Site', 'dec_id': 3288481, 'object_class_concepts': 'ncit:C39695', 'property_concepts': 'ncit:C25548', 'value_domain_type': 'Enumerated', 'datatype': 'CHARACTER', 'permissible_values': 'Adrenal\\Adrenal Gland\\ncit:C12666|Ascites/Peritoneum\\Ascites Peritoneum\\ncit:C2885 ncit:C12770|Epitrochlear lymph nodes\\Epitrochlear Lymph Node\\ncit:C98182|Femoral lymph nodes\\Femoral Lymph Node\\ncit:C98183|Hilar lymph nodes\\Hilar Lymph Node\\ncit:C98187|Larynx\\Larynx\\ncit:C12420|Nasopharynx\\Nasopharynx\\ncit:C12423|Retroperitoneal lymph nodes\\Retroperitoneal Lymph Node\\ncit:C98189|Small Intestine\\Small Intestine\\ncit:C12386|Stomach\\Stomach\\ncit:C12391|Supraclavicular lymph nodes\\Supraclavicular Lymph Node\\ncit:C12903|Thyroid\\Thyroid Gland\\ncit:C12400|Lung\\Lung\\ncit:C12468|Ovary\\Ovary\\ncit:C12404|Liver\\Liver\\ncit:C12392|Oropharynx\\Oropharynx\\ncit:C12762|Breast\\Breast\\ncit:C12971|Bone Marrow\\Bone Marrow\\ncit:C12431|Bone\\Bone\\ncit:C12366|Submandibular lymph nodes\\Submandibular Lymph Node\\ncit:C77650|Splenic lymph nodes\\Splenic Lymph Node\\ncit:C33600|Soft Tissue (muscle, ligaments, subcutaneous)\\Soft Tissue\\ncit:C12471|Skin\\Skin\\ncit:C12470|Sinus\\Sinus\\ncit:C33556|Salivary Gland\\Salivary Gland\\ncit:C12426|Rectum\\Rectum\\ncit:C12390|Prostate\\Prostate Gland\\ncit:C12410|Popliteal lymph nodes\\Popliteal Lymph Node\\ncit:C53146|Pleura/Pleural Effusion\\Pleura Pleural Effusion\\ncit:C12469 ncit:C3331|Peripheral Blood\\Peripheral Blood\\ncit:C25233 ncit:C12434|Peri-orbital Soft Tissue\\Periorbital Soft Tissue\\ncit:C98190 ncit:C12471|Pericardium\\Pericardium\\ncit:C13005|Parotid lymph nodes\\Parotid Gland Lymph Node\\ncit:C33278|Parotid Gland\\Parotid Gland\\ncit:C12427|Paraaortic lymph nodes\\Paraaortic Lymph Node\\ncit:C77643|Pancreas\\Pancreas\\ncit:C12393|Other Extranodal Site\\Other Extranodal Anatomic Site\\ncit:C17649 ncit:C25504 ncit:C13717|Occipital lymph nodes\\Occipital Lymph Node\\ncit:C98188|Nasal Soft Tissue\\Nasal Soft Tissue\\ncit:C27958 ncit:C12471|Mesenteric lymph nodes\\Mesenteric Lymph Node\\ncit:C77641|Mediastinal Soft Tissue\\Mediastinal Soft Tissue\\ncit:C25310 ncit:C12471|Mediastinal lymph nodes\\Mediastinal Lymph Node\\ncit:C33073|Leptomeninges\\Leptomeninges\\ncit:C32979|Large Intestine\\Large Intestine\\ncit:C12379|Kidney\\Kidney\\ncit:C12415|Intraocular\\Intraocular\\ncit:C96904|Inguinal lymph nodes\\Inguinal Lymph Node\\ncit:C32801|Iliac-external lymph nodes\\External Iliac Lymph Node\\ncit:C88143|Iliac-common lymph nodes\\Iliac Lymph Node\\ncit:C32761|Heart\\Heart\\ncit:C12727|Esophagus\\Esophagus\\ncit:C12389|Epidural\\Epidural\\ncit:C15683|Epididymis\\Epididymis\\ncit:C12328|Cervical lymph nodes\\Cervical Lymph Node\\ncit:C32298|Brain\\Brain\\ncit:C12439|Axillary lymph nodes\\Axillary Lymph Node\\ncit:C12904|Appendix\\Appendix\\ncit:C12380|Uterus\\Uterus\\ncit:C12405|Testes\\Testis\\ncit:C12412|Conjunctiva\\Conjunctiva\\ncit:C12341|Orbit\\Orbit\\ncit:C12347|Gastrointestinal / Abdominal\\Gastrointestinal Abdominal\\ncit:C13359 ncit:C25342|Mediastinal / Intra-thoracic\\Mediastinal Intrathoracal\\ncit:C25310 ncit:C12491|Colon\\Colon\\ncit:C12382|Maxilla\\Maxilla\\ncit:C26470|Mandible\\Mandible\\ncit:C12290|No Known Extranodal Involvement\\No Known Extranodal Involvement\\ncit:C25594 ncit:C80137 ncit:C25504 ncit:C25548|Bladder\\Bladder\\ncit:C12414|Cerebrospinal Fluid\\Cerebrospinal Fluid\\ncit:C12692', 'cde_id': 3288482}

Created by Anand Basu anand.basu
Hello Anand, The caDSR-derived synthetic data in these files (e.g. Annotated-table-125230.330453.json) was not "annotated" with a CDE, but instead our program generated synthetic data side-by-side with the source CDE. The CDE that your software found seems that it would have been a good replacement for the CDE that the synthetic data generator (for lack of a better description) selected to generate that pair of columns. However, the overlap between these two CDEs is partial, and the data values in the table/json file match better the CDE 3153874, e.g. "CENTRAL NERVOUS SYSTEM". A situation like this one with near-dups should not arise in the test datasets used in the leaderboard phase, though. Regards, Gilberto

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