Q (haiku): Is there a lower grade glioma study with race data? ▶ list_studies { "search": "lower grade glioma", "limit": "20", "verbose": "true" } ✗ error Error: No such tool available: mcp__navigator__list_studies ▶ list_studies { "search": "lower grade glioma", "limit": 20, "verbose": true } ◀ result {"result":[{"cancer_study_identifier":"lgg_tcga","name":"Brain Lower Grade Glioma (TCGA, Firehose Legacy)","description":"TCGA Brain Lower Grade Glioma. Source data from GDAC Firehose. Previously known as TCGA Provisional.","type_of_cancer_id":"difg","sample_count":530,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=lgg_tcga"},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","name":"Brain Lower Grade Glioma (TCGA, PanCancer Atlas)","description":"Brain Lower Grade Glioma TCGA PanCancer data. The original data is here. The publications are here.","type_of_cancer_id":"difg","sample_count":514,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=lgg_tcga_pan_can_atlas_2018"}]} ▶ clickhouse_run_select_query { "query": " SELECT DISTINCT c.cancer_study_id, cs.cancer_study_identifier, cad.display_name, cad.attribute_id FROM clinical_attribute_definition cad JOIN cancer_study cs ON cad.cancer_study_id = cs.cancer_study_id JOIN clinical_data_derived c ON c.cancer_study_id = cs.cancer_study_id AND c.attribute_id = cad.attribute_id WHERE cs.cancer_study_identifier IN ('lgg_tcga', 'lgg_tcga_pan_can_atlas_2018') AND LOWER(cad.attribute_id) LIKE '%race%' ORDER BY cs.cancer_study_identifier, cad.display_name ", "max_rows": 100 } ◀ result {"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 60\n Code: 60. DB::Exception: Unknown table expression identifier 'clinical_attribute_definition' in scope SELECT DISTINCT c.cancer_study_id, cs.cancer_study_identifier, cad.display_name, cad.attribute_id FROM clinical_attribute_definition AS cad INNER JOIN cancer_study AS cs ON cad.cancer_study_id = cs.cancer_study_id INNER JOIN clinical_data_derived AS c ON (c.cancer_study_id = cs.cancer_study_id) AND (c.attribute_id = cad.attribute_id) WHERE (cs.cancer_study_identifier IN ('lgg_tcga', 'lgg_tcga_pan_can_atlas_2018')) AND (LOWER(cad.attribute_id) LIKE '%race%') ORDER BY cs.cancer_study_identifier ASC, cad.display_name ASC. (UNKNOWN_TABLE) (version 26.4.1.2359 (official build))\n"} ▶ 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_study_identifier, attribute_id, display_name FROM clinical_attribute_meta WHERE cancer_study_identifier IN ('lgg_tcga', 'lgg_tcga_pan_can_atlas_2018') AND (LOWER(attribute_id) LIKE '%race%' OR LOWER(display_name) LIKE '%race%') ORDER BY cancer_study_identifier, display_name ", "max_rows": 100 } ◀ 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_study_identifier` in scope SELECT DISTINCT cancer_study_identifier, attribute_id, display_name FROM clinical_attribute_meta WHERE (cancer_study_identifier IN ('lgg_tcga', 'lgg_tcga_pan_can_atlas_2018')) AND ((LOWER(attribute_id) LIKE '%race%') OR (LOWER(display_name) LIKE '%race%')) ORDER BY cancer_study_identifier ASC, display_name ASC. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"} ▶ clickhouse_list_table_columns { "table": "clinical_attribute_meta" } ◀ result {"columns":[{"name":"attr_id","type":"String"},{"name":"display_name","type":"String"},{"name":"description","type":"String"},{"name":"datatype","type":"String"},{"name":"patient_attribute","type":"Int32"},{"name":"priority","type":"String"},{"name":"cancer_study_id","type":"Int64"}]} ▶ clickhouse_run_select_query { "query": " SELECT DISTINCT cs.cancer_study_identifier, cam.attr_id, cam.display_name FROM clinical_attribute_meta cam JOIN cancer_study cs ON cam.cancer_study_id = cs.cancer_study_id WHERE cs.cancer_study_identifier IN ('lgg_tcga', 'lgg_tcga_pan_can_atlas_2018') AND (LOWER(cam.attr_id) LIKE '%race%' OR LOWER(cam.display_name) LIKE '%race%') ORDER BY cs.cancer_study_identifier, cam.display_name ", "max_rows": 100 } ◀ result {"rows":[{"cancer_study_identifier":"lgg_tcga","attr_id":"RACE","display_name":"Race Category"},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","attr_id":"RACE","display_name":"Race Category"}]} ▶ clickhouse_run_select_query { "query": " SELECT cs.cancer_study_identifier, COUNT(DISTINCT cd.patient_id) as patients_with_race_data FROM clinical_data_derived cd JOIN cancer_study cs ON cd.cancer_study_id = cs.cancer_study_id WHERE cs.cancer_study_identifier IN ('lgg_tcga', 'lgg_tcga_pan_can_atlas_2018') AND cd.attribute_id = 'RACE' AND cd.attribute_value != '' GROUP BY cs.cancer_study_identifier ORDER BY cs.cancer_study_identifier ", "max_rows": 100 } ◀ 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: Identifier 'cd.cancer_study_id' cannot be resolved from table with name cd. In scope SELECT cs.cancer_study_identifier, COUNTDistinct(cd.patient_id) AS patients_with_race_data FROM clinical_data_derived AS cd INNER JOIN cancer_study AS cs ON cd.cancer_study_id = cs.cancer_study_id WHERE (cs.cancer_study_identifier IN ('lgg_tcga', 'lgg_tcga_pan_can_atlas_2018')) AND (cd.attribute_id = 'RACE') AND (cd.attribute_value != '') GROUP BY cs.cancer_study_identifier ORDER BY cs.cancer_study_identifier ASC. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"} ▶ clickhouse_list_table_columns { "table": "clinical_data_derived" } ◀ result {"columns":[{"name":"internal_id","type":"Int32"},{"name":"sample_unique_id","type":"String","comment":"Globally unique sample ID: cancer_study_identifier + \"_\" + sample.stable_id. Empty for patient-level attributes. Use this for sample filtering and joins."},{"name":"patient_unique_id","type":"String","comment":"Globally unique patient ID: cancer_study_identifier + \"_\" + patient.stable_id. Present for both sample and patient-level attributes."},{"name":"attribute_name","type":"LowCardinality(String)","comment":"Clinical attribute name (e.g., SAMPLE_TYPE, CANCER_TYPE, AGE, OS_MONTHS). Use with attribute_value for filtering. AGE may be floored or capped for de-identification (e.g. all children recorded as 18, or everyone 89+ recorded as 89 or 90): before age statistics check for a pile-up at the min/max, and if present compute age from DAYS_TO_BIRTH (-days / 365.25)."},{"name":"attribute_value","type":"String","comment":"Value of the clinical attribute (String). For SAMPLE_TYPE: Primary, Metastasis, Local Recurrence, Unknown. Missing values are empty strings, so use toFloat64OrNull(attribute_value) for numeric comparisons — CAST fails on them."},{"name":"cancer_study_identifier","type":"LowCardinality(String)"},{"name":"type","type":"LowCardinality(String)","comment":"Data level: \"sample\" for sample-level attributes (e.g., SAMPLE_TYPE), \"patient\" for patient-level attributes (e.g., AGE, OS_MONTHS)."}]} ▶ clickhouse_run_select_query { "query": " SELECT cancer_study_identifier, COUNT(DISTINCT patient_unique_id) as patients_with_race_data FROM clinical_data_derived WHERE cancer_study_identifier IN ('lgg_tcga', 'lgg_tcga_pan_can_atlas_2018') AND attribute_name = 'RACE' AND attribute_value != '' GROUP BY cancer_study_identifier ORDER BY cancer_study_identifier ", "max_rows": 100 } ◀ result {"rows":[{"cancer_study_identifier":"lgg_tcga","patients_with_race_data":505},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","patients_with_race_data":503}]} ═ answer (success) Yes, there are **two lower grade glioma studies with race data**: 1. **[Brain Lower Grade Glioma (TCGA, Firehose Legacy)](https://www.cbioportal.org/study/summary?id=lgg_tcga)** (`lgg_tcga`) - 530 total samples - **505 patients with race data** 2. **[Brain Lower Grade Glioma (TCGA, PanCancer Atlas)](https://www.cbioportal.org/study/summary?id=lgg_tcga_pan_can_atlas_2018)** (`lgg_tcga_pan_can_atlas_2018`) - 514 total samples - **503 patients with race data** Both studies have comprehensive race category data. The PanCancer Atlas version is the more recent standardized release and is generally preferred for analyses.