Additional Notes for COSMIC
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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 the COSMIC tsv are:
DOID:
- `cosmic_doid_mapping.csv`
COSMIC tissue site terms were mapped to DOID parent terms using the following table (generated from previous Biomuta mapping):
| Primary Site | Top_Level_Organ_system |
|---|---|
| NS | NA |
| adrenal_gland | DOID:3953 / adrenal gland cancer |
| autonomic_ganglia | NA |
| biliary_tract | DOID:4606 / bile duct cancer |
| bone | DOID:184 / bone cancer |
| breast | DOID:1612 / breast cancer |
| central_nervous_system | DOID:1319 / brain cancer |
| cervix | DOID:4362 / cervical cancer |
| endometrium | DOID:363 / uterine cancer |
| eye | DOID:2174 / ocular cancer |
| fallopian_tube | DOID:1964 / fallopian tube cancer |
| female_genital_tract_(site_indeterminate) | NA |
| female_genitourinary_system | NA |
| gastrointestinal_tract_(site_indeterminate) | DOID:3119 / gastrointestinal system cancer |
| genital_tract | NA |
| haematopoietic_and_lymphoid_tissue | DOID:2531 / hematologic cancer |
| kidney | DOID:263 / kidney cancer |
| large_intestine | DOID:9256 / colorectal cancer |
| liver | DOID:3571 / liver cancer |
| lung | DOID:1324 / lung cancer |
| mediastinum | DOID:3565 / meningioma |
| meninges | DOID:3565 / meningioma |
| oesophagus | DOID:5041 / esophageal cancer |
| ovary | DOID:2394 / ovarian cancer |
| pancreas | DOID:1793 / pancreatic cancer |
| paratesticular_tissues | NA |
| parathyroid | DOID:1540 / parathyroid carcinoma |
| penis | DOID:11615 / penile cancer |
| pericardium | NA |
| perineum | DOID:4045 / muscle cancer |
| peritoneum | DOID:1775 / peritoneum cancer |
| pituitary | DOID:1785 / pituitary cancer |
| placenta | DOID:2021 / placenta cancer |
| pleura | DOID:5158 / pleural cancer |
| prostate | DOID:10283 / prostate cancer |
| retroperitoneum | DOID:5875 / retroperitoneal cancer |
| salivary_gland | DOID:8618 / oral cavity cancer |
| skin | DOID:4159 / skin cancer |
| small_intestine | DOID:9253 / gastrointestinal stromal tumor |
| soft_tissue | NA |
| stomach | DOID:10534 / stomach cancer |
| testis | DOID:2998 / testicular cancer |
| thymus | DOID:3277 / thymus cancer |
| thyroid | DOID:1781 / thyroid gland cancer |
| upper_aerodigestive_tract | DOID:8618 / oral cavity cancer |
| urinary_tract | DOID:11054 / urinary bladder cancer |
| uterine_adnexa | NA |
| vagina | DOID:119 / vaginal cancer |
| vulva | DOID:1245 / vulva cancer |
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.