Q (haiku): 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_run_select_query
{
 "query": "
SELECT DISTINCT 
  cancer_type_id,
  name,
  color,
  short_name
FROM type_of_cancer
ORDER BY name
",
 "max_rows": 200
}

◀ result
{"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 47\n Code: 47. DB::Exception: Unknown expression identifier `cancer_type_id` in scope SELECT DISTINCT cancer_type_id, name, color, short_name FROM type_of_cancer ORDER BY name ASC. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}

▶ 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 
  type_of_cancer_id,
  name,
  short_name,
  main_type,
  tissue,
  level
FROM type_of_cancer
ORDER BY tissue, main_type, name
",
 "max_rows": 500
}

◀ result
Error: result (78,384 characters) exceeds maximum allowed tokens. Output has been saved to /home/ino/.claude-cbioportal-team/projects/-tmp-mcp-qa-claude-491rduy0/f1a7840c-343a-4c99-af11-2277bf74bd58/tool-results/mcp-claude_ai_cBioPortal_MCP-clickhouse_run_select_query-1790298005460.txt.
Format: JSON with schema: {rows: [{...}], truncated: boolean, returned_rows: number, note: string}
- For targeted queries (find a value, filter by field): use jq on the file directly.
- For analysis or summarization that requires reading the full content: first probe the structure (e.g., jq 'type, length, keys?' /home/ino/.claude-cbioportal-team/projects/-tmp-mcp-qa-claude-491rduy0/f1a7840c-343a-4c99-af11-2277bf74bd58/tool-results/mcp-claude_ai_cBioPortal_MCP-clickhouse_run_select_query-1790298005460.txt), then extract slices with jq or python — Read's line-based offset/limit will not chunk this file.
- If the Agent tool is available, do this inside a subagent so the full output stays out of your main context. Give it the instruction above verbatim, and be explicit about what it must return — e.g. "/home/ino/.claude-cbioportal-team/projects/-tmp-mcp-qa-claude-491rduy0/f1a7840c-343a-4c99-af11-2277bf74bd58/tool-results/mcp-claude_ai_cBioPortal_MCP-clickhouse_run_select_query-1790298005460.txt is JSON with schema: {rows: [{...}], truncated: boolean, returned_rows: number, note: string}; probe the structure with jq (type/length/keys), then extract and read the content in full with jq or python, then summarize and quote any key findings verbatim." A vague "summarize this" may lose detail.


▶ clickhouse_run_select_query
{
 "query": "
SELECT COUNT(DISTINCT type_of_cancer_id) as total_cancer_types
FROM type_of_cancer
"
}

◀ result
{"rows":[{"total_cancer_types":897}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT 
  tissue,
  COUNT(DISTINCT type_of_cancer_id) as count,
  COUNT(DISTINCT main_type) as main_types
FROM type_of_cancer
WHERE level <= 3
GROUP BY tissue
ORDER BY count DESC
",
 "max_rows": 100
}

◀ result
{"rows":[{"tissue":"CNS/Brain","count":94,"main_types":14},{"tissue":"Soft Tissue","count":55,"main_types":8},{"tissue":"Ovary/Fallopian Tube","count":36,"main_types":4},{"tissue":"Head and Neck","count":35,"main_types":5},{"tissue":"Skin","count":29,"main_types":3},{"tissue":"Uterus","count":27,"main_types":4},{"tissue":"Breast","count":27,"main_types":2},{"tissue":"Bowel","count":26,"main_types":8},{"tissue":"Bone","count":24,"main_types":1},{"tissue":"Lung","count":23,"main_types":3},{"tissue":"Cervix","count":21,"main_types":1},{"tissue":"Bladder/Urinary Tract","count":18,"main_types":3},{"tissue":"Myeloid","count":17,"main_types":13},{"tissue":"Esophagus/Stomach","count":17,"main_types":5},{"tissue":"Pancreas","count":16,"main_types":1},{"tissue":"Other","count":15,"main_types":5},{"tissue":"Vulva/Vagina","count":14,"main_types":5},{"tissue":"Testis","count":12,"main_types":5},{"tissue":"Liver","count":10,"main_types":4},{"tissue":"Thyroid","count":10,"main_types":1},{"tissue":"Lymphoid","count":9,"main_types":7},{"tissue":"Kidney","count":9,"main_types":6},{"tissue":"Peripheral Nervous System","count":8,"main_types":3},{"tissue":"Eye","count":8,"main_types":4},{"tissue":"Prostate","count":6,"main_types":1},{"tissue":"Ampulla of Vater","count":5,"main_types":2},{"tissue":"Biliary Tract","count":5,"main_types":2},{"tissue":"Pleura","count":5,"main_types":2},{"tissue":"Penis","count":5,"main_types":1},{"tissue":"Thymus","count":5,"main_types":2},{"tissue":"Adrenal Gland","count":4,"main_types":4},{"tissue":"Peritoneum","count":3,"main_types":3}]}

═ answer (success)
## Cancer Types in cBioPortal

The database contains **897 distinct cancer types** organized using the OncoTree classification system. Here's the breakdown by **tissue of origin**:

### Major Cancer Categories (Top 10 by subtype count):

1. **CNS/Brain** – 94 subtypes (14 main types)
2. **Soft Tissue** – 55 subtypes (8 main types)
3. **Ovary/Fallopian Tube** – 36 subtypes (4 main types)
4. **Head and Neck** – 35 subtypes (5 main types)
5. **Skin** – 29 subtypes (3 main types)
6. **Uterus** – 27 subtypes (4 main types)
7. **Breast** – 27 subtypes (2 main types)
8. **Bowel** – 26 subtypes (8 main types)
9. **Bone** – 24 subtypes (1 main type)
10. **Lung** – 23 subtypes (3 main types)

### Other Tissues:
Cervix, Bladder/Urinary Tract, Myeloid, Esophagus/Stomach, Pancreas, Vulva/Vagina, Testis, Liver, Thyroid, Lymphoid, Kidney, Peripheral Nervous System, Eye, Prostate, and others.

The cancer types are hierarchically organized by specificity (level 1 = broad tissue, level 6 = highly specific subtype). You can search for a specific cancer type using **OncoTree codes** (e.g., "LUAD" for lung adenocarcinoma, "GBM" for glioblastoma) to filter studies and samples.

Would you like to search for a specific cancer type or explore studies associated with a particular tissue or cancer subtype?