Q (sonnet): What kind of cancer are there in the database?

▶ clickhouse_list_tables
{}

◀ result
{"tables":[{"name":"allele_specific_copy_number"},{"name":"alteration_driver_annotation"},{"name":"cancer_study"},{"name":"cancer_study_query_preferences"},{"name":"cancer_study_tags"},{"name":"cbioportal_sequence_state"},{"name":"clinical_attribute_counts"},{"name":"clinical_attribute_meta"},{"name":"clinical_data_derived"},{"name":"clinical_event"},{"name":"clinical_event_data"},{"name":"clinical_event_data_derived"},{"name":"clinical_event_derived"},{"name":"clinical_patient"},{"name":"clinical_sample"},{"name":"cna_event"},{"name":"cna_panel_gene_coverage"},{"name":"cna_wes_coverage"},{"name":"co_altered_genes_in_study"},{"name":"copy_number_seg"},{"name":"copy_number_seg_file"},{"name":"gene"},{"name":"gene_alias"},{"name":"gene_alteration_frequency_by_cancer_type"},{"name":"gene_cna_distribution_in_study"},{"name":"gene_mutation_frequency_by_cancer_type"},{"name":"gene_mutation_frequency_in_studies"},{"name":"gene_mutation_frequency_in_study"},{"name":"gene_mutation_variants_in_study"},{"name":"gene_pair_coexpression"},{"name":"gene_panel"},{"name":"gene_panel_list"},{"name":"gene_panel_to_gene_derived"},{"name":"generic_assay_data_derived"},{"name":"generic_assay_meta_derived"},{"name":"generic_assay_profile_entity_derived"},{"name":"generic_entity_properties"},{"name":"geneset"},{"name":"geneset_gene"},{"name":"geneset_hierarchy_leaf"},{"name":"geneset_hierarchy_node"},{"name":"genetic_alteration"},{"name":"genetic_alteration_derived"},{"name":"genetic_entity"},{"name":"genetic_profile"},{"name":"genetic_profile_link"},{"name":"genetic_profile_samples"},{"name":"genomic_event_derived"},{"name":"gistic"},{"name":"gistic_to_gene"},{"name":"info"},{"name":"mut_sig"},{"name":"mutation"},{"name":"mutation_count_by_keyword"},{"name":"mutation_derived"},{"name":"mutation_event"},{"name":"mutation_panel_gene_coverage"},{"name":"mutation_wes_coverage"},{"name":"patient"},{"name":"reference_genome"},{"name":"reference_genome_gene"},{"name":"resource_definition"},{"name":"resource_patient"},{"name":"resource_sample"},{"name":"resource_study"},{"name":"sample"},{"name":"sample_cna_event"},{"name":"sample_derived"},{"name":"sample_list"},{"name":"sample_list_list"},{"name":"sample_profile"},{"name":"sample_to_gene_panel_derived"},{"name":"structural_variant"},{"name":"sv_panel_gene_coverage"},{"name":"sv_wes_coverage"},{"name":"top_cna_genes_in_study"},{"name":"top_mutated_genes_in_cohort"},{"name":"top_mutated_genes_in_study"},{"name":"top_sv_genes_in_study"},{"name":"treatment_counts_in_study"},{"name":"treatment_regimens_in_study"},{"name":"type_of_cancer"}]}

▶ clickhouse_list_table_columns
{
 "table": "type_of_cancer"
}

◀ result
{"columns":[{"name":"type_of_cancer_id","type":"String"},{"name":"name","type":"String"},{"name":"dedicated_color","type":"String"},{"name":"short_name","type":"Nullable(String)"},{"name":"parent","type":"Nullable(String)"},{"name":"main_type","type":"String","comment":"Broad OncoTree grouping (e.g. Non-Small Cell Lung Cancer, Glioma). Useful for grouping related subtypes."},{"name":"tissue","type":"String","comment":"Tissue of origin (e.g. Lung, CNS/Brain, Breast). Top-level anatomical grouping."},{"name":"level","type":"UInt8","comment":"Depth in OncoTree hierarchy: 1 = tissue, 2-6 = increasingly specific subtypes. Lower = broader."},{"name":"revocations","type":"Array(String)","comment":"Deprecated OncoTree codes that this code replaces (e.g. BLL replaces ALL, GB replaces GBM). Search here when a user code is not found."},{"name":"precursors","type":"Array(String)","comment":"Previous codes merged into this code (e.g. CLLSLL merges CLL and SLL). Similar to revocations but for code merges."}]}

▶ clickhouse_run_select_query
{
 "query": "SELECT DISTINCT tc.tissue, tc.main_type
FROM cancer_study cs
JOIN type_of_cancer tc ON cs.type_of_cancer_id = tc.type_of_cancer_id
ORDER BY tc.tissue, tc.main_type",
 "max_rows": 500
}

◀ result
{"rows":[{"tissue":"Adrenal Gland","main_type":"Adrenocortical Carcinoma"},{"tissue":"Ampulla of Vater","main_type":"Ampullary Cancer"},{"tissue":"Biliary Tract","main_type":"Biliary Tract Cancer"},{"tissue":"Biliary Tract","main_type":"Hepatobiliary Cancer"},{"tissue":"Bladder/Urinary Tract","main_type":"Bladder Cancer"},{"tissue":"Bladder/Urinary Tract","main_type":"Bladder/Urinary Tract Cancer"},{"tissue":"Bone","main_type":"Bone Cancer"},{"tissue":"Bowel","main_type":"Appendiceal Cancer"},{"tissue":"Bowel","main_type":"Bowel Cancer"},{"tissue":"Bowel","main_type":"Colorectal Cancer"},{"tissue":"Breast","main_type":"Breast Cancer"},{"tissue":"Breast","main_type":"Breast Sarcoma"},{"tissue":"CNS/Brain","main_type":"CNS Cancer"},{"tissue":"CNS/Brain","main_type":"CNS/Brain Cancer"},{"tissue":"CNS/Brain","main_type":"Embryonal Tumor"},{"tissue":"CNS/Brain","main_type":"Glioma"},{"tissue":"CNS/Brain","main_type":"Gliomas, Glioneuronal Tumors, and Neuronal Tumors"},{"tissue":"CNS/Brain","main_type":"Miscellaneous Neuroepithelial Tumor"},{"tissue":"CNS/Brain","main_type":"Sellar Tumor"},{"tissue":"Cervix","main_type":"Cervical Cancer"},{"tissue":"Esophagus/Stomach","main_type":"Esophageal/Stomach Cancer"},{"tissue":"Esophagus/Stomach","main_type":"Esophagogastric Cancer"},{"tissue":"Eye","main_type":"Melanoma"},{"tissue":"Eye","main_type":"Retinoblastoma"},{"tissue":"Head and Neck","main_type":"Head and Neck Cancer"},{"tissue":"Head and Neck","main_type":"Salivary Gland Cancer"},{"tissue":"Kidney","main_type":"Renal Cell Carcinoma"},{"tissue":"Kidney","main_type":"Rhabdoid Cancer"},{"tissue":"Kidney","main_type":"Wilms Tumor"},{"tissue":"Liver","main_type":"Hepatobiliary Cancer"},{"tissue":"Lung","main_type":"Lung Cancer"},{"tissue":"Lung","main_type":"Non-Small Cell Lung Cancer"},{"tissue":"Lung","main_type":"Small Cell Lung Cancer"},{"tissue":"Lymphoid","main_type":"B-Lymphoblastic Leukemia/Lymphoma"},{"tissue":"Lymphoid","main_type":"Hodgkin Lymphoma"},{"tissue":"Lymphoid","main_type":"Lymphatic Cancer"},{"tissue":"Lymphoid","main_type":"Mature B-Cell Neoplasms"},{"tissue":"Lymphoid","main_type":"Mature T and NK Neoplasms"},{"tissue":"Lymphoid","main_type":"Non-Hodgkin Lymphoma"},{"tissue":"Myeloid","main_type":"Blood Cancer"},{"tissue":"Myeloid","main_type":"Blood Cancer, NOS"},{"tissue":"Myeloid","main_type":"Histiocytosis"},{"tissue":"Myeloid","main_type":"Leukemia"},{"tissue":"Myeloid","main_type":"Myelodysplastic Syndromes"},{"tissue":"Myeloid","main_type":"Myeloproliferative Neoplasms"},{"tissue":"Other","main_type":"Cancer of Unknown Primary"},{"tissue":"Ovary/Fallopian Tube","main_type":"Ovarian Cancer"},{"tissue":"Ovary/Fallopian Tube","main_type":"Ovarian/Fallopian Tube Cancer"},{"tissue":"Pancreas","main_type":"Pancreatic Cancer"},{"tissue":"Peripheral Nervous System","main_type":"Nerve Sheath Tumor"},{"tissue":"Peripheral Nervous System","main_type":"Peripheral Nervous System"},{"tissue":"Pleura","main_type":"Mesothelioma"},{"tissue": … (730 more chars)

═ answer (success)
The cBioPortal database contains studies spanning cancers from **34 tissue sites**, covering essentially the full spectrum of solid and hematologic malignancies. Grouped by tissue of origin:

| Tissue | Cancer Types |
|---|---|
| **CNS/Brain** | Glioma, Gliomas/Glioneuronal/Neuronal Tumors, CNS Cancer, Embryonal Tumor, Miscellaneous Neuroepithelial Tumor, Sellar Tumor |
| **Breast** | Breast Cancer, Breast Sarcoma |
| **Lung** | Non-Small Cell Lung Cancer, Small Cell Lung Cancer, Lung Cancer |
| **Bowel** | Colorectal Cancer, Appendiceal Cancer, Bowel Cancer |
| **Lymphoid** | Hodgkin Lymphoma, Non-Hodgkin Lymphoma, Mature B-Cell Neoplasms, Mature T and NK Neoplasms, B-Lymphoblastic Leukemia/Lymphoma, Lymphatic Cancer |
| **Myeloid** | Leukemia, Myelodysplastic Syndromes, Myeloproliferative Neoplasms, Histiocytosis, Blood Cancer (NOS) |
| **Skin/Eye** | Melanoma, Skin Cancer (Melanoma & Non-Melanoma), Retinoblastoma |
| **Kidney** | Renal Cell Carcinoma, Wilms Tumor, Rhabdoid Cancer |
| **Prostate** | Prostate Cancer |
| **Pancreas** | Pancreatic Cancer |
| **Bladder/Urinary Tract** | Bladder Cancer |
| **Ovary/Fallopian Tube** | Ovarian Cancer |
| **Uterus** | Endometrial Cancer, Uterine Sarcoma |
| **Cervix / Vulva/Vagina** | Cervical Cancer, Vaginal Cancer |
| **Esophagus/Stomach** | Esophagogastric Cancer |
| **Liver/Biliary Tract** | Hepatobiliary Cancer, Biliary Tract Cancer |
| **Head and Neck** | Head and Neck Cancer, Salivary Gland Cancer |
| **Soft Tissue** | Soft Tissue Sarcoma, Gastrointestinal Stromal Tumor (GIST) |
| **Bone** | Bone Cancer |
| **Thyroid** | Thyroid Cancer |
| **Adrenal Gland** | Adrenocortical Carcinoma |
| **Ampulla of Vater** | Ampullary Cancer |
| **Pleura** | Mesothelioma |
| **Testis** | Germ Cell Tumor, Testicular Cancer |
| **Thymus** | Thymic Tumor |
| **Peripheral Nervous System** | Nerve Sheath Tumor |
| **Other** | Cancer of Unknown Primary |

If you'd like, I can drill into a specific cancer type — e.g., list the individual studies available for lung cancer, or open the cBioPortal StudyView filtered to a particular tissue/type. Just let me know which one interests you.