Q (sonnet): Is there a lower grade glioma study with race data?

▶ list_studies
{
 "search": "lower grade glioma"
}

◀ result
{"result":[{"cancer_study_identifier":"lgg_tcga","name":"Brain Lower Grade Glioma (TCGA, Firehose Legacy)","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)","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"}]}

▶ read_guide
{
 "uri": "cbioportal://clinical-data-guide"
}

◀ result
# Clinical Data Query Guide

## Overview
Clinical data in cBioPortal is stored at both patient and sample levels. Understanding the distinction is crucial for accurate analysis.

## Data Organization

### Patient-Level vs Sample-Level Data
- **Patient-level**: Demographics, overall survival, disease stage (stored once per patient)
- **Sample-level**: Sample type, sequencing platform, purity (can have multiple per patient)

### Key Tables
- `clinical_patient`: Patient-level clinical attributes
- `clinical_sample`: Sample-level clinical attributes
- `clinical_data_derived`: Pre-joined view combining both levels
- `clinical_attribute_meta`: Metadata about available clinical attributes

## Recommended Approach: Use clinical_data_derived

The `clinical_data_derived` table is pre-joined and optimized for most queries:

```sql
-- Get clinical data for specific attributes
SELECT
    sample_unique_id,
    patient_unique_id,
    attribute_name,
    attribute_value
FROM clinical_data_derived
WHERE
    cancer_study_identifier = 'your_study_id'
    AND attribute_name IN ('CANCER_TYPE', 'SAMPLE_TYPE', 'TMB_NONSYNONYMOUS');
```

## Clinical Attribute Discovery

### Use clinical_attribute_meta for Discovering Available Attributes
**Always start here** to see what clinical attributes are available for a specific study:

```sql
-- Discover available clinical attributes for a study
SELECT
    attr_id,
    description,
    patient_attribute,
    cancer_study_id
FROM clinical_attribute_meta
WHERE
    cancer_study_id = (
        SELECT cancer_study_id
        FROM cancer_study
        WHERE cancer_study_identifier = 'your_study_id'
    )
ORDER BY patient_attribute, attr_id;
```

**Key Fields:**
- **attr_id**: matches attr_id in clinical_sample/clinical_patient tables
- **description**: human-readable description of the attribute
- **patient_attribute**: true = patient attribute, false = sample attribute
- **cancer_study_id**: links to cancer_study table (filter by study)

## Attribute Semantics and Matching

### Case-Insensitive Matching for Attribute Values

Clinical values are free text across studies and may differ only by case. For example, a controlled-looking value such as germline mutation status may appear as `GERMLINE`, `Germline`, or another case variant.

When filtering `clinical_data_derived.attribute_value`, use case-insensitive matching unless you have already profiled the exact values in the target study:

```sql
-- Correct: case-insensitive clinical value filter
SELECT DISTINCT sample_unique_id, patient_unique_id
FROM clinical_data_derived
WHERE cancer_study_identifier = 'your_study_id'
  AND attribute_name = 'MUTATION_STATUS'
  AND upper(attribute_value) = 'GERMLINE';
```

Do not write `attribute_value = 'GERMLINE'` without first checking all distinct values for that attribute in the study.

### Query the Requested Attribute, Not a Proxy

Do not infer one clinical attribute from a related subtype or marker. Query the actual requested attribute when it … (17073 more chars)

▶ clickhouse_run_select_query
{
 "query": "SELECT cancer_study_id, attr_id, description, patient_attribute
FROM clinical_attribute_meta
WHERE cancer_study_id IN (
    SELECT cancer_study_id FROM cancer_study WHERE cancer_study_identifier IN ('lgg_tcga', 'lgg_tcga_pan_can_atlas_2018')
)
AND upper(attr_id) LIKE '%RACE%'"
}

◀ result
{"rows":[{"cancer_study_id":193,"attr_id":"RACE","description":"The text for reporting information about race.","patient_attribute":1},{"cancer_study_id":734,"attr_id":"RACE","description":"The text for reporting information about race.","patient_attribute":1}]}

▶ clickhouse_run_select_query
{
 "query": "SELECT cancer_study_identifier, attribute_value, count(DISTINCT patient_unique_id) AS n_patients
FROM clinical_data_derived
WHERE cancer_study_identifier IN ('lgg_tcga', 'lgg_tcga_pan_can_atlas_2018')
AND attribute_name = 'RACE'
GROUP BY cancer_study_identifier, attribute_value
ORDER BY cancer_study_identifier, n_patients DESC"
}

◀ result
{"rows":[{"cancer_study_identifier":"lgg_tcga","attribute_value":"WHITE","n_patients":475},{"cancer_study_identifier":"lgg_tcga","attribute_value":"BLACK OR AFRICAN AMERICAN","n_patients":21},{"cancer_study_identifier":"lgg_tcga","n_patients":11},{"cancer_study_identifier":"lgg_tcga","attribute_value":"ASIAN","n_patients":8},{"cancer_study_identifier":"lgg_tcga","attribute_value":"AMERICAN INDIAN OR ALASKA NATIVE","n_patients":1},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","attribute_value":"White","n_patients":474},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","attribute_value":"Black or African American","n_patients":21},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","n_patients":11},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","attribute_value":"Asian","n_patients":7},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","attribute_value":"American Indian or Alaska Native","n_patients":1}]}

▶ resolve_and_route
{
 "studyIds": [
  "lgg_tcga_pan_can_atlas_2018"
 ]
}

◀ result
{"success":true,"message":"Found 1 study. Use the metadata to call the appropriate navigation tool(s).","data":{"totalCount":1,"studiesWithMetadata":[{"studyId":"lgg_tcga_pan_can_atlas_2018","name":"Brain Lower Grade Glioma (TCGA, PanCancer Atlas)","sampleCount":514,"studyViewUrl":"https://www.cbioportal.org/study?id=lgg_tcga_pan_can_atlas_2018","metadata":{"clinicalAttributeIds":["AGE","AJCC_PATHOLOGIC_TUMOR_STAGE","AJCC_STAGING_EDITION","ANEUPLOIDY_SCORE","BUFFA_HYPOXIA_SCORE","CANCER_TYPE","CANCER_TYPE_ACRONYM","CANCER_TYPE_DETAILED","DAYS_LAST_FOLLOWUP","DAYS_TO_BIRTH","DAYS_TO_INITIAL_PATHOLOGIC_DIAGNOSIS","DFS_MONTHS","DFS_STATUS","DSS_MONTHS","DSS_STATUS","ETHNICITY","FORM_COMPLETION_DATE","FRACTION_GENOME_ALTERED","GENETIC_ANCESTRY_LABEL","GRADE","HISTORY_NEOADJUVANT_TRTYN","ICD_10","ICD_O_3_HISTOLOGY","ICD_O_3_SITE","INFORMED_CONSENT_VERIFIED","IN_PANCANPATHWAYS_FREEZE","MSI_SCORE_MANTIS","MSI_SENSOR_SCORE","MUTATION_COUNT","NEW_TUMOR_EVENT_AFTER_INITIAL_TREATMENT","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","OTHER_PATIENT_ID","PATH_M_STAGE","PATH_N_STAGE","PATH_T_STAGE","PERSON_NEOPLASM_CANCER_STATUS","PFS_MONTHS","PFS_STATUS","PRIMARY_LYMPH_NODE_PRESENTATION_ASSESSMENT","PRIOR_DX","RACE","RADIATION_THERAPY","RAGNUM_HYPOXIA_SCORE","SAMPLE_COUNT","SAMPLE_TYPE","SEX","SOMATIC_STATUS","SUBTYPE","TBL_SCORE","TISSUE_PROSPECTIVE_COLLECTION_INDICATOR","TISSUE_RETROSPECTIVE_COLLECTION_INDICATOR","TISSUE_SOURCE_SITE","TISSUE_SOURCE_SITE_CODE","TMB_NONSYNONYMOUS","TUMOR_TISSUE_SITE","TUMOR_TYPE","WEIGHT","WINTER_HYPOXIA_SCORE"],"molecularProfileIds":["lgg_tcga_pan_can_atlas_2018_gistic","lgg_tcga_pan_can_atlas_2018_log2CNA","lgg_tcga_pan_can_atlas_2018_mutations","lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna","lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","lgg_tcga_pan_can_atlas_2018_rppa","lgg_tcga_pan_can_atlas_2018_rppa_Zscores","lgg_tcga_pan_can_atlas_2018_structural_variants"],"genericAssayProfiles":["lgg_tcga_pan_can_atlas_2018_armlevel_cna","lgg_tcga_pan_can_atlas_2018_genetic_ancestry","lgg_tcga_pan_can_atlas_2018_methylation_hm27_hm450_merge","lgg_tcga_pan_can_atlas_2018_methylation_hm450"],"heatmapProfileIds":["lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","lgg_tcga_pan_can_atlas_2018_rppa_Zscores"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations","mrna","protein","generic_assay_armlevel_cna","generic_assay_genetic_ancestry","generic_assay_methylation"]}}]}}

▶ navigate_to_study_view
{
 "studyIds": [
  "lgg_tcga_pan_can_atlas_2018"
 ],
 "tab": "clinicalData"
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/study/clinicalData?id=lgg_tcga_pan_can_atlas_2018","url":"https://www.cbioportal.org/study/clinicalData?id=lgg_tcga_pan_can_atlas_2018","data":{"studyIds":["lgg_tcga_pan_can_atlas_2018"],"studies":[{"studyId":"lgg_tcga_pan_can_atlas_2018","name":"Brain Lower Grade Glioma (TCGA, PanCancer Atlas)","sampleCount":514}],"tab":"clinicalData","hasFilters":false,"hasPlotsConfig":false,"pageDescription":"Table of clinical attributes per sample."}}

═ answer (success)
[View Clinical Data — Brain Lower Grade Glioma (TCGA, PanCancer Atlas)](https://www.cbioportal.org/study/clinicalData?id=lgg_tcga_pan_can_atlas_2018)

Table of clinical attributes per sample — the `RACE` column is included and can be used for filtering/charting from the Study View summary page as well.