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):

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.*