Additional notes- CIVIC
Additional Notes
All the mapping files are available in the scripts repository in the folder: `pipeline/convert_step2/mapping`
The mapping files used for converting CIVIC are:
DOID:
- `tcga_doid_mapping.csv`
CIVIC DOID child terms were mapped to DOID parent terms using the following table (generated from the OncoMX DOID mapping table):
| CIVIC Entity Disease |
|---|
| Acral_Lentiginous_Melanoma_(DOID_6367) |
| Acute_Lymphoblastic_Leukemia_(DOID_9952) |
| Acute_Myelioid_Leukemia_(DOID_9119) |
| Acute_Promyelocytic_Leukemia_(DOID_0060318) |
| Adrenal_Gland_Pheochromocytoma_(DOID_0050892) |
| Angiosarcoma_(DOID_0001816) |
| Basal_Cell_Carcinoma_(DOID_2513) |
| Biliary_Tract_Cancer_(DOID_4607) |
| Bladder_Carcinoma_(DOID_4007) |
| Bladder_Urothelial_Carcinoma_(DOID_4006) |
| Bone_Marrow_Cancer_(DOID_4960) |
| Brain_Glioma_(DOID_0060108) |
| Breast_Cancer_(DOID_1612) |
| Breast_Carcinoma_(DOID_3459) |
| Bronchiolo-alveolar_Adenocarcinoma_(DOID_4926) |
| Cancer_(DOID_162) |
| Cervical_Cancer_(DOID_4362) |
| Cervix_Carcinoma_(DOID_2893) |
| Childhood_Acute_Lymphocytic_Leukemia_(DOID_0080144) |
| Childhood_Low-grade_Glioma_(DOID_0080830) |
| Childhood_Pilocytic_Astrocytoma_(DOID_6812) |
| Cholangiocarcinoma_(DOID_4947) |
| Chromophobe_Renal_Cell_Carcinoma_(DOID_4471) |
| Chronic_Leukemia_(DOID_1036) |
| Chronic_Lymphocytic_Leukemia_(DOID_1040) |
| Chronic_Myeloid_Leukemia_(DOID_8552) |
| Chronic_Neutrophilic_Leukemia_(DOID_0080187) |
| Chuvash_Polycythemia_(DOID_0060474) |
| Clear_Cell_Renal_Cell_Carcinoma_(DOID_4467) |
| Colon_Cancer_(DOID_219) |
| Colon_Mucinous_Adenocarcinoma_(DOID_3029) |
| Colorectal_Adenocarcinoma_(DOID_0050861) |
| Colorectal_Cancer_(DOID_9256) |
| Diffuse_Midline_Glioma_H3_K27M-mutant_(DOID_0080684) |
| Endometrial_Adenocarcinoma_(DOID_2870) |
| Endometrial_Cancer_(DOID_1380) |
| Endometrial_Hyperplasia_(DOID_0080365) |
| Endometrioid_Ovary_Carcinoma_(DOID_5828) |
| Epithelial_Ovarian_Cancer_(DOID_2152) |
| Esophageal_Cancer_(DOID_5041) |
| Esophagus_Squamous_Cell_Carcinoma_(DOID_3748) |
| Estrogen-receptor_Positive_Breast_Cancer_(DOID_0060075) |
| Ewing_Sarcoma_Of_Bone_(DOID_3386) |
| Follicular_Lymphoma_(DOID_0050873) |
| Gastrointestinal_Neuroendocrine_Tumor_(DOID_0050626) |
| Gastrointestinal_Stromal_Tumor_(DOID_9253) |
| Glioblastoma_(DOID_3068) |
| Hairy_Cell_Leukemia_(DOID_285) |
| Head_And_Neck_Cancer_(DOID_11934) |
| Head_And_Neck_Squamous_Cell_Carcinoma_(DOID_5520) |
| Intrahepatic_Cholangiocarcinoma_(DOID_4928) |
| Langerhans_Cell_Sarcoma_(DOID_7146) |
| Laryngeal_Squamous_Cell_Carcinoma_(DOID_2876) |
| Leukemia_(DOID_1240) |
| Li-Fraumeni_Syndrome_(DOID_3012) |
| Lung_Adenocarcinoma_(DOID_3910) |
| Lung_Cancer_(DOID_1324) |
| Lung_Small_Cell_Carcinoma_(DOID_3908) |
| Lung_Small_Cell_Carcinoma_(DOID_5409) |
| Lymphoid_Leukemia_(DOID_1037) |
| Lymphoma_(DOID_0060058) |
| Malignant_Exocrine_Pancreas_Neoplasm_(DOID_1795) |
| Malignant_Mesothelioma_(DOID_1790) |
| Mammary_Analogue_Secretory_Carcinoma_(DOID_0080808) |
| Medulloblastoma_(DOID_0050902) |
| Melanoma_(DOID_1909) |
| Merkel_Cell_Carcinoma_(DOID_3965) |
| Mucosal_Melanoma_(DOID_0050929) |
| Multiple_Myeloma_(DOID_9538) |
| Myelodysplastic_Syndrome_(DOID_0050908) |
| Myeloid_And_Lymphoid_Neoplasms_With_Eosinophilia_And_Abnormalities_Of_PDGFRA_PDGFBR_And_FGFR1_(DOID_0060908) |
| Neuroblastoma_(DOID_769) |
| Oligodendroglioma_(DOID_3181) |
| Osteosarcoma_(DOID_3347) |
| Ovarian_Cancer_(DOID_2394) |
| Ovarian_Clear_Cell_Carcinoma_(DOID_0050934) |
| Ovarian_Granulosa_Cell_Tumor_(DOID_2999) |
| Ovarian_Serous_Carcinoma_(DOID_0050933) |
| Ovarian_Sex-cord_Stromal_Tumor_(DOID_0080369) |
| Ovary_Serous_Adenocarcinoma_(DOID_5744) |
| PTEN_Hamartoma_Tumor_Syndrome_(DOID_0080191) |
| Pancreatic_Adenocarcinoma_(DOID_4074) |
| Pancreatic_Cancer_(DOID_1793) |
| Pancreatic_Carcinoma_(DOID_4905) |
| Polycythemia_Vera_(DOID_8997) |
| Prostate_Cancer_(DOID_10283) |
| Rectum_Cancer_(DOID_1993) |
| Renal_Carcinoma_(DOID_4451) |
| Renal_Cell_Carcinoma_(DOID_4450) |
| Rhabdomyosarcoma_(DOID_3247) |
| Sertoli-Leydig_Cell_Tumor_(DOID_2997) |
| Skin_Melanoma_(DOID_8923) |
| Skin_Squamous_Cell_Carcinoma_(DOID_3151) |
| Solid_Tumor_(DOID_3260) |
| Spindle_Cell_Rhabdomyosarcoma_(DOID_3260) |
| Stomach_Cancer_(DOID_10534) |
| Stomach_Carcinoma_(DOID_5517) |
| Systemic_Mastocytosis_(DOID_349) |
| T-cell_Acute_Lymphoblastic_Leukemia_(DOID_5603) |
| Thymic_Carcinoma_(DOID_3284) |
| Thyroid_Gland_Anaplastic_Carcinoma_(DOID_0080522) |
| Thyroid_Gland_Cancer_(DOID_1781) |
| Thyroid_Gland_Carcinoma_(DOID_3963) |
| Thyroid_Gland_Hurthle_Cell_Carcinoma_(DOID_8161) |
| Thyroid_Gland_Medullary_Carcinoma_(DOID_3973) |
| Thyroid_Gland_Papillary_Carcinoma_(DOID_3969) |
| Transitional_Cell_Carcinoma_(DOID_2671) |
| Tuberous_Sclerosis_(DOID_13515) |
| Villous_Adenoma |
| Von_Hippel-Lindau_Disease_(DOID_14175) |
| Waldenstrom's_Macroglobulinemia_(DOID_0060901) |
Uniprot Accession:
- `human_protein_transcriptlocus.csv`
Transcript ID (starts with ENSP) was mapped to uniprot isoform accession.
Mapping was NOT performed to uniprot canonical accession as this resulted in an issue with the final dataset in which a mutation for the same canonical accession would be listed with different amino acid changes.