View source for Additional Notes - tcga

=== Additional Notes ===
All the mapping files are available in the repository folder:
`pipeline/convert_step2/mapping`

The mapping files used for converting TCGA are:

'''DOID:'''
* `tcga_doid_mapping.csv`

TCGA Projects were mapped to DOID parent terms using the following table (generated from previous Biomuta mapping):


{| class="wikitable"
! DO_slim_id
! DO_slim_name
! TCGA_project
|-
| DOID:5041
| esophageal cancer
| TCGA-ESCA
|-
| DOID:2531
| hematologic cancer
| TCGA-DLBC
|-
| DOID:9256
| colorectal cancer
| TCGA-READ
|-
| DOID:1319
| brain cancer
| TCGA-GBM
|-
| DOID:1319
| brain cancer
| TCGA-LGG
|-
| DOID:1781
| thyroid cancer
| TCGA-THCA
|-
| DOID:11054
| urinary bladder cancer
| TCGA-BLCA
|-
| DOID:363
| uterine cancer
| TCGA-UCEC
|-
| DOID:169
| neuroendocrine tumor
| TCGA-PCPG
|-
| DOID:4362
| cervical cancer
| TCGA-CESC
|-
| DOID:363
| uterine cancer
| TCGA-UCS
|-
| DOID:3277
| thymus cancer
| TCGA-THYM
|-
| DOID:3571
| liver cancer
| TCGA-LIHC
|-
| DOID:11934
| head and neck cancer
| TCGA-HNSC
|-
| DOID:2174
| ocular cancer
| TCGA-UVM
|-
| DOID:4159
| skin cancer
| TCGA-SKCM
|-
| DOID:9256
| colorectal cancer
| TCGA-COAD
|-
| DOID:3953
| adrenal gland cancer
| TCGA-ACC
|-
| DOID:1793
| pancreatic cancer
| TCGA-PAAD
|-
| DOID:2994
| germ cell cancer
| TCGA-TGCT
|-
| DOID:1324
| lung cancer
| TCGA-LUSC
|-
| DOID:1790
| malignant mesothelioma
| TCGA-MESO
|-
| DOID:2394
| ovarian cancer
| TCGA-OV
|-
| DOID:1115
| sarcoma
| TCGA-SARC
|-
| DOID:263
| kidney cancer
| TCGA-KIRP
|-
| DOID:263
| kidney cancer
| TCGA-KICH
|-
| DOID:10534
| stomach cancer
| TCGA-STAD
|-
| DOID:2531
| hematologic cancer
| TCGA-LAML
|-
| DOID:10283
| prostate cancer
| TCGA-PRAD
|-
| DOID:1324
| lung cancer
| TCGA-LUAD
|-
| DOID:1612
| breast cancer
| TCGA-BRCA
|-
| DOID:263
| kidney cancer
| TCGA-KIRC
|-
| DOID:263
| kidney cancer
| TCGA-KICH
|}

'''Uniprot Accession:'''
* `human_protein_transcriptlocus.csv`

Peptide 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.*