DO names

[mariacuria]

I looked at unique "do_name" values from data/projects/glygen/downloads/biomuta/v-5.0/biomuta.csv and noticed some inconsistencies:

• From my understanding, thyroid cancer and thyroid gland cancer are the same.
• Gastrointestinal stromal tumor should be under gastrointestinal system cancer.
• Some cancer types, such as sarcoma, mesothelioma, are not "organ" cancer types. They are not present in the documentation either. Is this intentional?

"DOID:10283 / prostate cancer"
"DOID:10534 / stomach cancer"
"DOID:11054 / urinary bladder cancer"
"DOID:1115 / sarcoma"
"DOID:11615 / penile cancer"
"DOID:11934 / head and neck cancer"
"DOID:119 / vaginal cancer"
"DOID:1245 / vulva cancer"
"DOID:1319 / brain cancer"
"DOID:1324 / lung cancer"
"DOID:1540 / parathyroid carcinoma"
"DOID:1612 / breast cancer"
"DOID:169 / neuroendocrine tumor"
"DOID:1725 / peritoneum cancer"
"DOID:1781 / thyroid cancer"
"DOID:1781 / thyroid gland cancer"
"DOID:1785 / pituitary cancer"
"DOID:1790 / malignant mesothelioma"
"DOID:1793 / pancreatic cancer"
"DOID:184 / bone cancer"
"DOID:1964 / fallopian tube cancer"
"DOID:2021 / placenta cancer"
"DOID:2174 / ocular cancer"
"DOID:2394 / ovarian cancer"
"DOID:2531 / hematologic cancer"
"DOID:2596 / larynx cancer"
"DOID:263 / kidney cancer"
"DOID:2994 / germ cell cancer"
"DOID:2998 / testicular cancer"
"DOID:3119 / gastrointestinal system cancer"
"DOID:3277 / thymus cancer"
"DOID:3565 / meningioma"
"DOID:3571 / liver cancer"
"DOID:363 / uterine cancer"
"DOID:3953 / adrenal gland cancer"
"DOID:4045 / muscle cancer"
"DOID:4159 / skin cancer " (sic! extra white space)
"DOID:4159 / skin cancer"
"DOID:4362 / cervical cancer"
"DOID:4606 / bile duct cancer"
"DOID:5041 / esophageal cancer"
"DOID:5158 / pleural cancer"
"DOID:8618 / oral cavity cancer"
"DOID:9253 / gastrointestinal stromal tumor"
"DOID:9256 / colorectal cancer"

Speaking of DO names, I have a couple of cases in cBioPortal where I can't decide which DO name to assign.

• Hepatocellular carcinoma plus intrahepatic cholangiocarcinoma matched on 'DOID:4606 / bile duct cancer' and 'DOID:3571 / liver cancer'. There are some other cancers, such as Esophagogastric Adenocarcinoma, which can be assigned to 2 DOIDs: DOID:5041 / esophageal cancer & DOID:10534 / stomach cancer"
• Soft tissue myoepithelial carcinoma can't be attributed to a specific organ.
• Wilms' tumor is a childhood cancer. We've agreed to get rid of pediatric cancers - is this still in effect?

[mariacuria]

CIViC DOID mapping

• Angiosarcoma is listed as NA, but I found it in the doid-mapping.tsv file which lists DO cancer slim terms under DOID:175 / vascular cancer. Should it remain NA?
• Biliary tract cancer is NA. I found it listed under DOID:3121 / gallbladder cancer and DOID:4606 / bile duct cancer.
• Is there any particular reason why Bronchiolo-alveolar_Adenocarcinoma is NA when it can be easily attributed to DOID:1324 / lung cancer?
• Desmoid Tumor: I often see benign neoplasms listed as part of the DO cancer slim subset, but can't easily find which cancer slim term exactly they belong to. Does that warrant an NA?
  
• Endometrial hyperplasia: again, a benign neoplasm which belongs to the DO cancer slim subset. I would map to DOID:363 / uterine cancer.
• Endometrioid Ovary Carcinoma is NA but I would map it to DOID:2394 / ovarian cancer.
• Extramammary Paget Disease is not a cancer, as far as I know => NA
• Low grade glioma: a cell type benign neoplasm that has_material_basis_in glial cells (astrocytes, oligodendrocytes or ependymocytes) (from Disease Ontology). Is it even a cancer (since it's considered benign), and if it is, which DO cancer slim term should it be?
• Mammary Analogue Secretory Carcinoma is NA but looks like DOID:8618 / oral cavity cancer because it is "a salivary gland carcinoma that has_material_basis_in a chromosomal translocation that results in an ETV6-NTRK3 fusion gene." (from DO)
• Neuroblastoma is NA but found under DOID:1192 / peripheral nervous system neoplasm.
• Parietal Lobe Ependymoma is NA but found under DOID:1319 / brain cancer.
• T-cell Acute Lymphoblastic Leukemia is NA but is clearly a DOID:2531 / hematologic cancer.
• Villous Adenoma is "an adenoma that is located_in the colon and other places in the gastrointestinal tract and sometimes in other parts of the body." (from DO) Should it remain NA or be classified as colorectal cancer?

[mariacuria]

study_id	name	relevant_description	cancer_type_name	proposed_do_names
egc_msk_2017, egc_mskcc_2020, egc_msk_tp53_ccr_2022.json, egc_msk_2023	Esophagogastric Cancer	<...> esophagogastric cancers <...>	Esophagus/Stomach, Esophagogastric Adenocarcinoma	DOID:5041 / esophageal cancer, DOID:10534 / stomach cancer dependent on where in the esophagogastric junction the tumor is centered
stes_tcga_pub	Esophageal Carcinoma	<...> esophageal and gastric carcinoma tumors <...>	Esophagogastric Adenocarcinoma	DOID:5041 / esophageal cancer, DOID:10534 / stomach cancer